From e3fb3073fa143fa0bcea59e44ccee37de1e25990 Mon Sep 17 00:00:00 2001 From: Jessica Mauvais Date: Tue, 7 Apr 2026 14:04:48 -0700 Subject: [PATCH 01/37] uv check-in for cpu --- .gitignore | 2 + Makefile | 28 +- atomsci/ddm/__init__.py | 2 - atomsci/ddm/pipeline/model_wrapper.py | 6 +- atomsci/ddm/pipeline/parameter_parser.py | 5 +- pyproject.toml | 88 + sync_env.sh | 34 + update_lock.sh | 42 + uv.lock.cpu | 3525 ++++++++++++++++++++++ 9 files changed, 3723 insertions(+), 9 deletions(-) create mode 100644 pyproject.toml create mode 100755 sync_env.sh create mode 100755 update_lock.sh create mode 100644 uv.lock.cpu diff --git a/.gitignore b/.gitignore index 976e80b8..e70d13d7 100644 --- a/.gitignore +++ b/.gitignore @@ -123,6 +123,8 @@ celerybeat.pid # Environments .env .venv +.venv-* +uv.lock env/ venv/ ENV/ diff --git a/Makefile b/Makefile index f910f734..7284f020 100644 --- a/Makefile +++ b/Makefile @@ -46,7 +46,8 @@ VENV ?= atomsci-env # Work Directory WORK_DIR ?= work -.PHONY: build-docker install install-dev install-system install-venv jupyter-notebook jupyter-lab \ +.PHONY: sync-cpu sync-cuda sync-rocm sync-mps test-cpu test-gpu test-rocm test-mps \ + build-docker install install-dev install-system install-venv jupyter-notebook jupyter-lab \ pytest ruff ruff-fix setup uninstall uninstall-dev uninstall-system uninstall-venv # Load Docker image @@ -157,6 +158,31 @@ setup: uninstall: uninstall-system +# for uv env +sync-cpu: + UV_PROJECT_ENVIRONMENT=.venv-cpu uv sync --extra cpu + +sync-cuda: + UV_PROJECT_ENVIRONMENT=.venv-cuda uv sync --extra cuda + +sync-rocm: + UV_PROJECT_ENVIRONMENT=.venv-rocm uv sync --extra rocm + +sync-mps: + UV_PROJECT_ENVIRONMENT=.venv-mps uv sync --extra mps + +test-cpu: + UV_PROJECT_ENVIRONMENT=.venv-cpu uv run pytest + +test-gpu: + UV_PROJECT_ENVIRONMENT=.venv-cuda uv run pytest + +test-rocm: + UV_PROJECT_ENVIRONMENT=.venv-rocm uv run pytest + +test-mps: + UV_PROJECT_ENVIRONMENT=.venv-mps uv run pytest + # Uninstall atomsci-ampl from user space uninstall-dev: @echo "Uninstalling atomsci-ampl for user" diff --git a/atomsci/ddm/__init__.py b/atomsci/ddm/__init__.py index e14d682c..1509b651 100644 --- a/atomsci/ddm/__init__.py +++ b/atomsci/ddm/__init__.py @@ -4,10 +4,8 @@ #except TypeError: # pass try: - # Python 3.8+ from importlib.metadata import version, PackageNotFoundError except ImportError: - # For very old Pythons, use backport if available try: from importlib_metadata import version, PackageNotFoundError except ImportError: diff --git a/atomsci/ddm/pipeline/model_wrapper.py b/atomsci/ddm/pipeline/model_wrapper.py index 5f16c4b3..5d8af885 100644 --- a/atomsci/ddm/pipeline/model_wrapper.py +++ b/atomsci/ddm/pipeline/model_wrapper.py @@ -2616,10 +2616,8 @@ def make_pred(dset): pipeline.metric_type, test_perf)) layer1_weights = self.model.model.layers[0].weight - feature_weights = np.zeros(nfeatures, dtype=float) - for node_weights in layer1_weights: - node_feat_weights = torch.abs(node_weights).detach().numpy() - feature_weights += node_feat_weights + feature_weights = layer1_weights.detach().abs().mean(dim=0).cpu().numpy() + for fnum, fname in enumerate(feature_names): self.feature_weights[fname].append(feature_weights[fnum]) diff --git a/atomsci/ddm/pipeline/parameter_parser.py b/atomsci/ddm/pipeline/parameter_parser.py index 02778fee..6f67dc5d 100644 --- a/atomsci/ddm/pipeline/parameter_parser.py +++ b/atomsci/ddm/pipeline/parameter_parser.py @@ -7,6 +7,7 @@ import deepchem.models as dcm import deepchem.models.torch_models as dcmt +from deepchem.models import GraphConvModel import deepchem.feat as dcf import inspect @@ -34,8 +35,8 @@ model_wl = {'AttentiveFPModel':dcm.AttentiveFPModel, 'GCNModel':dcm.GCNModel, - 'MPNNModel':dcm.MPNNModel, - 'GraphConvModel':dcm.GraphConvModel, + 'MPNNModel':dcmt.MPNNModel, + 'GraphConvModel': GraphConvModel, 'PytorchMPNNModel':dcmt.MPNNModel}#, dcm.GCNModel, dcm.GATModel] # featurizer white list diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 00000000..337140ad --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,88 @@ +[project] +name = "atomsci-ampl" +dynamic = ["version"] +description = "atomsci AMPL python package" +readme = "README.md" +requires-python = ">=3.10,<3.11" +dependencies = [ + "lightning==2.2.5", + "pydantic>=1.10,<2", + "numpy<2", + "scipy>=1.10", + "scikit-learn==1.2.2", + "hyperopt", + "xgboost", + "lightgbm", + "umap-learn", + "bokeh", + "matplotlib", + "matplotlib-venn", + "seaborn>=0.13.0", + "pyarrow", + "pyyaml>=6.0", + "bravado", + "imbalanced-learn", + "maestrowf", + "deepchem==2.8", + "rdkit==2024.3.5", + "mordred", + "dgllife==0.3.2", + "setuptools", +] + +[dependency-groups] +dev = [ + "ipykernel", + "jupyter", + "jupyterlab", + "pytest", + "pytest-cov", + "pytest-mock", + "pytest-xdist", + "matplotcheck", + "ruff", +] + +[project.optional-dependencies] +cpu = [ + "torchdata==0.7.1", + "tensorflow-cpu~=2.14.0; platform_system == 'Linux'", + "tensorflow~=2.14.0; platform_system == 'Darwin'", + "dgl==2.1.0", + "torch_geometric==2.7.0", +] + +cuda = [ + "torchdata==0.7.1", + "dgl==2.1.0", + "torch_geometric==2.7.0", +] + +rocm = [ + "torchdata==0.7.1", + "dgl==2.1.0", + "torch_geometric==2.7.0", +] + +mchip = [ + "torch==2.1.2", + "torchdata", + "tensorflow~=2.14.0", + "torch_geometric==2.7.0", +] + +[build-system] +requires = ["hatchling>=1.24.0"] +build-backend = "hatchling.build" + +[tool.hatch.version] +path = "VERSION" +pattern = "(?P\\d+\\.\\d+\\.\\d+.*)" + +[tool.hatch.build.targets.wheel] +packages = ["atomsci"] + +[tool.pytest.ini_options] +testpaths = ["atomsci/ddm/test"] +addopts = "-ra" + diff --git a/sync_env.sh b/sync_env.sh new file mode 100755 index 00000000..fd1f0222 --- /dev/null +++ b/sync_env.sh @@ -0,0 +1,34 @@ +#!/usr/bin/env bash +set -euo pipefail + +platform="${1:?usage: $0 }" + +case "$platform" in + cpu) + venv_dir=".venv-cpu" + uv venv --python 3.10 "$venv_dir" + uv pip install --python "$venv_dir/bin/python" --index-url https://download.pytorch.org/whl/cpu torch==2.1.2 + VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra cpu --group dev + ;; + cuda) + venv_dir=".venv-cuda" + uv venv --python 3.10 "$venv_dir" + uv pip install --python "$venv_dir/bin/python" --index-url https://download.pytorch.org/whl/cu121 torch==2.1.2 + VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra cuda --group dev + ;; + rocm) + venv_dir=".venv-rocm" + uv venv --python 3.10 "$venv_dir" + uv pip install --python "$venv_dir/bin/python" --index-url https://download.pytorch.org/whl/rocm5.6 torch==2.1.2 + VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra rocm --group dev + ;; + mchip) + venv_dir=".venv-mchip" + uv venv --python 3.10 "$venv_dir" + VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra mchip --group dev + ;; + *) + echo "Invalid platform: $platform" + exit 1 + ;; +esac diff --git a/update_lock.sh b/update_lock.sh new file mode 100755 index 00000000..5dbf1ef7 --- /dev/null +++ b/update_lock.sh @@ -0,0 +1,42 @@ +#!/usr/bin/env bash +set -euo pipefail + +platform="${1:?usage: $0 }" + +rm -f uv.lock + +case "$platform" in + cpu) + venv_dir=".venv-cpu" + rm -rf "$venv_dir" + uv venv --python 3.10 "$venv_dir" + uv pip install --python "$venv_dir/bin/python" --index-url https://download.pytorch.org/whl/cpu torch==2.1.2 + VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra cpu --group dev + ;; + cuda) + venv_dir=".venv-cuda" + rm -rf "$venv_dir" + uv venv --python 3.10 "$venv_dir" + uv pip install --python "$venv_dir/bin/python" --index-url https://download.pytorch.org/whl/cu121 torch==2.1.2 + VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra cuda --group dev + ;; + rocm) + venv_dir=".venv-rocm" + rm -rf "$venv_dir" + uv venv --python 3.10 "$venv_dir" + uv pip install --python "$venv_dir/bin/python" --index-url 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b/.github/actions/python-uv-setup/action.yml index 03c3f004..6ac9145d 100644 --- a/.github/actions/python-uv-setup/action.yml +++ b/.github/actions/python-uv-setup/action.yml @@ -1,5 +1,6 @@ name: "python-uv-setup" description: "Common Python + uv setup, deps install, and optional debug" + inputs: python-version: description: "Python version" @@ -8,6 +9,18 @@ inputs: description: "Enable debug output" required: false default: "false" + lockfile: + description: "Lockfile to use" + required: false + default: "uv.lock.cpu" + extras: + description: "Extra dependency set to install" + required: false + default: "cpu" + dependency-groups: + description: "Dependency group to install" + required: false + default: "dev" runs: using: "composite" @@ -40,34 +53,22 @@ runs: uses: actions/cache@v4 with: path: ~/.cache/uv - key: ${{ runner.os }}-uv-${{ hashFiles('pip/*.txt') }} + key: ${{ runner.os }}-py${{ inputs.python-version }}-uv-${{ hashFiles('pyproject.toml', 'uv.lock.cpu') }} restore-keys: | - ${{ runner.os }}-uv- - - - name: Create virtual environment - shell: bash - run: | - uv venv --seed .venv + ${{ runner.os }}-py${{ inputs.python-version }}-uv- - name: Install dependencies shell: bash run: | set -euxo pipefail + cp "${{ inputs.lockfile }}" uv.lock + uv venv .venv . .venv/bin/activate - - which python - python -V - - uv pip install -e . - if [ -f pip/cpu_requirements.txt ]; then uv pip install -r pip/cpu_requirements.txt; fi - if [ -f pip/dev_requirements.txt ]; then uv pip install -r pip/dev_requirements.txt; fi + uv sync --extra "${{ inputs.extras }}" --group "${{ inputs.dependency-groups }}" --locked - name: Debug - what is installed if: ${{ inputs.debug == 'true' }} shell: bash run: | . .venv/bin/activate - python -m pip --version - python -V - uv --version - uv pip list \ No newline at end of file + uv pip list diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index 98087924..e372a67d 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -20,14 +20,24 @@ jobs: - uses: ./.github/actions/python-uv-setup with: python-version: ${{ matrix.python-version }} + lockfile: uv.lock.cpu + extras: cpu + dependency-groups: dev debug: "false" - - name: pytest + - name: Run modac unit tests shell: bash + working-directory: atomsci/modac/test/unit run: | - . .venv/bin/activate - cd atomsci/modac/test/unit && python -m pytest --capture=sys --capture=fd --cov=atomsci/ -vv - cd "${{ github.workspace }}/atomsci/ddm/test/unit" && python -m pytest -m "not moe_required" -n 2 --capture=fd --cov=atomsci -vv --durations=4 --durations-min=0.05 + . "${{ github.workspace }}/.venv/bin/activate" + python -m pytest --capture=sys --capture=fd --cov=atomsci/ -vv + + - name: Run ddm unit tests + shell: bash + working-directory: atomsci/ddm/test/unit + run: | + . "${{ github.workspace }}/.venv/bin/activate" + python -m pytest -m "not moe_required" -n 2 --capture=fd --cov=atomsci -vv --durations=4 --durations-min=0.05 - name: Save coverage uses: actions/upload-artifact@v4 @@ -56,13 +66,16 @@ jobs: - uses: ./.github/actions/python-uv-setup with: python-version: ${{ matrix.python-version }} + lockfile: uv.lock.cpu + extras: cpu + dependency-groups: dev debug: "false" - name: Debug - dgl + torchdata + shadowing shell: bash if: ${{ env.DEBUG_DGL == 'true' }} run: | - . .venv/bin/activate + . "${{ github.workspace }}/.venv/bin/activate" set -x which python @@ -76,11 +89,11 @@ jobs: python -m pip show torch torchdata dgl dgllife || true python -m pip freeze | grep -E '^(torch|torchdata|dgl|dgllife|numpy)=' || true - - name: pytest + - name: Run integrative tests shell: bash + working-directory: atomsci/ddm/test/integrative run: | - . .venv/bin/activate - cd atomsci/ddm/test/integrative + . "${{ github.workspace }}/.venv/bin/activate" ./integrative_batch_chunk_tests ${{ matrix.chunk }} - name: Save coverage From a4403127b9fd634cf58fcd372523efbd93646dac Mon Sep 17 00:00:00 2001 From: Jessica Mauvais Date: Tue, 7 Apr 2026 16:32:55 -0700 Subject: [PATCH 03/37] fixed ci. added doc --- atomsci/ddm/pipeline/model_wrapper.py | 1 - sync_env.sh | 35 +++++++++++++++++++++------ update_lock.sh | 25 ++++++++++++------- uv.lock.cpu | 10 +++++--- 4 files changed, 49 insertions(+), 22 deletions(-) diff --git a/atomsci/ddm/pipeline/model_wrapper.py b/atomsci/ddm/pipeline/model_wrapper.py index 5d8af885..5e65f294 100644 --- a/atomsci/ddm/pipeline/model_wrapper.py +++ b/atomsci/ddm/pipeline/model_wrapper.py @@ -2588,7 +2588,6 @@ def train_with_early_stopping(self, pipeline): """ self.data = pipeline.data feature_names = self.data.featurization.get_feature_columns() - nfeatures = len(feature_names) self.feature_weights = dict(zip(feature_names, [[] for f in feature_names])) em = perf.EpochManager(self, diff --git a/sync_env.sh b/sync_env.sh index fd1f0222..46be0bf1 100755 --- a/sync_env.sh +++ b/sync_env.sh @@ -1,34 +1,53 @@ #!/usr/bin/env bash +# Purpose: +# syncs the environment, does not save a platform lockfile +# +# Use when: +# want to create/update a local env from existing lock/deps. build an env to run. +# +# Usage: +# ./sync_env.sh + set -euo pipefail platform="${1:?usage: $0 }" +lockfile="uv.lock.${platform}" +venv_dir=".venv-${platform}" + +if [[ ! -f "$lockfile" ]]; then + echo "Missing lockfile: $lockfile" + echo "Run ./update_lock.sh $platform first" + exit 1 +fi + +cp "$lockfile" uv.lock +rm -rf "$venv_dir" + case "$platform" in cpu) - venv_dir=".venv-cpu" uv venv --python 3.10 "$venv_dir" uv pip install --python "$venv_dir/bin/python" --index-url https://download.pytorch.org/whl/cpu torch==2.1.2 - VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra cpu --group dev + VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra cpu --group dev --locked ;; cuda) - venv_dir=".venv-cuda" uv venv --python 3.10 "$venv_dir" uv pip install --python "$venv_dir/bin/python" --index-url https://download.pytorch.org/whl/cu121 torch==2.1.2 - VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra cuda --group dev + VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra cuda --group dev --locked ;; rocm) - venv_dir=".venv-rocm" uv venv --python 3.10 "$venv_dir" uv pip install --python "$venv_dir/bin/python" --index-url https://download.pytorch.org/whl/rocm5.6 torch==2.1.2 - VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra rocm --group dev + VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra rocm --group dev --locked ;; mchip) - venv_dir=".venv-mchip" uv venv --python 3.10 "$venv_dir" - VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra mchip --group dev + VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra mchip --group dev --locked ;; *) echo "Invalid platform: $platform" exit 1 ;; esac + +echo "Synced $venv_dir from $lockfile" diff --git a/update_lock.sh b/update_lock.sh index 5dbf1ef7..2162d42f 100755 --- a/update_lock.sh +++ b/update_lock.sh @@ -1,35 +1,41 @@ #!/usr/bin/env bash +# +# Purpose: +# regenerates uv.lock. +# +# Use when: +# dependencies changed, pyproject.toml changed, or lockfile mismatch happens. refresh the commited lockfile. +# +# Usage: +# ./update_lock.sh + set -euo pipefail platform="${1:?usage: $0 }" +lockfile="uv.lock.${platform}" +venv_dir=".venv-${platform}" + rm -f uv.lock +rm -rf "$venv_dir" case "$platform" in cpu) - venv_dir=".venv-cpu" - rm -rf "$venv_dir" uv venv --python 3.10 "$venv_dir" uv pip install --python "$venv_dir/bin/python" --index-url https://download.pytorch.org/whl/cpu torch==2.1.2 VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra cpu --group dev ;; cuda) - venv_dir=".venv-cuda" - rm -rf "$venv_dir" uv venv --python 3.10 "$venv_dir" uv pip install --python "$venv_dir/bin/python" --index-url https://download.pytorch.org/whl/cu121 torch==2.1.2 VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra cuda --group dev ;; rocm) - venv_dir=".venv-rocm" - rm -rf "$venv_dir" uv venv --python 3.10 "$venv_dir" uv pip install --python "$venv_dir/bin/python" --index-url https://download.pytorch.org/whl/rocm5.6 torch==2.1.2 VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra rocm --group dev ;; mchip) - venv_dir=".venv-mchip" - rm -rf "$venv_dir" uv venv --python 3.10 "$venv_dir" VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra mchip --group dev ;; @@ -39,4 +45,5 @@ case "$platform" in ;; esac -cp uv.lock "uv.lock.${platform}" +cp uv.lock "$lockfile" +echo "Updated $lockfile" diff --git a/uv.lock.cpu b/uv.lock.cpu index 057abcf6..e2de648e 100644 --- a/uv.lock.cpu +++ b/uv.lock.cpu @@ -218,6 +218,7 @@ dependencies = [ { name = "scikit-learn" }, { name = "scipy" }, { name = "seaborn" }, + { name = "setuptools" }, { name = "umap-learn" }, { name = "xgboost" }, ] @@ -225,7 +226,8 @@ dependencies = [ [package.optional-dependencies] cpu = [ { name = "dgl" }, - { name = "tensorflow-cpu" }, + { name = "tensorflow", marker = "sys_platform == 'darwin'" }, + { name = "tensorflow-cpu", marker = "sys_platform == 'linux'" }, { name = "torch-geometric" }, { name = "torchdata" }, ] @@ -284,8 +286,10 @@ requires-dist = [ { name = "scikit-learn", specifier = "==1.2.2" }, { name = "scipy", specifier = ">=1.10" }, { name = "seaborn", specifier = ">=0.13.0" }, + { name = "setuptools" }, + { name = "tensorflow", marker = "sys_platform == 'darwin' and extra == 'cpu'", specifier = "~=2.14.0" }, { name = "tensorflow", marker = "extra == 'mchip'", specifier = "~=2.14.0" }, - { name = "tensorflow-cpu", marker = "extra == 'cpu'", specifier = "~=2.14.0" }, + { name = "tensorflow-cpu", marker = "sys_platform == 'linux' and extra == 'cpu'", specifier = "~=2.14.0" }, { name = "torch", marker = "extra == 'mchip'", specifier = "==2.1.2" }, { name = "torch-geometric", marker = "extra == 'cpu'", specifier = "==2.7.0" }, { name = "torch-geometric", marker = "extra == 'cuda'", specifier = "==2.7.0" }, @@ -3094,9 +3098,7 @@ dependencies = [ { name = "wrapt" }, ] wheels = [ - { url = "https://files.pythonhosted.org/packages/61/83/5c17a657faf96262400e9b3127485dd1c67708a6e554e44892758279a8ce/tensorflow_cpu-2.14.1-cp310-cp310-macosx_10_15_x86_64.whl", hash = "sha256:d57057ba570c1a6b73a300759dd09057d721d2d04dc9e82fb1b8b4fe4c2ca380", size = 229650285, upload-time = "2023-11-14T18:57:56.447Z" }, { url = "https://files.pythonhosted.org/packages/4f/ea/acd6d4c6a23de999e7fbb20d68eefa65d395df7ae16249294a02dd1772d5/tensorflow_cpu-2.14.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:97f63588962997f2816031578450f747468f9441b17f5bbf352fc93adecc2051", size = 198216087, upload-time = "2023-11-14T19:00:57.579Z" }, - { url = "https://files.pythonhosted.org/packages/d6/c8/a4f108e13b8cb8f6d7fa08cc61242b2881a175c6472ce0405e5a84d518d8/tensorflow_cpu-2.14.1-cp310-cp310-win_amd64.whl", hash = "sha256:2aced2fd217d95d53f3968372bc741b9967b266ae59c45622a5af1aff12eda68", size = 2131, upload-time = "2023-11-14T19:01:51.168Z" }, ] [[package]] From deb7692823ce4110b2ed83b6ad10895e7f32d893 Mon Sep 17 00:00:00 2001 From: Jessica Mauvais Date: Thu, 9 Apr 2026 12:12:55 -0700 Subject: [PATCH 04/37] added cuda env build --- pyproject.toml | 16 +- sync_env.sh => sync_uv_env.sh | 3 +- update_lock.sh => update_uv_lock.sh | 2 +- uv.lock.cpu | 152 +- uv.lock.cuda | 3559 +++++++++++++++++++++++++++ 5 files changed, 3667 insertions(+), 65 deletions(-) rename sync_env.sh => sync_uv_env.sh (92%) rename update_lock.sh => update_uv_lock.sh (96%) create mode 100644 uv.lock.cuda diff --git a/pyproject.toml b/pyproject.toml index 337140ad..5489987e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -22,11 +22,11 @@ dependencies = [ "pyyaml>=6.0", "bravado", "imbalanced-learn", + "imblearn", "maestrowf", "deepchem==2.8", "rdkit==2024.3.5", "mordred", - "dgllife==0.3.2", "setuptools", ] @@ -45,29 +45,39 @@ dev = [ [project.optional-dependencies] cpu = [ + "torch==2.1.2", "torchdata==0.7.1", "tensorflow-cpu~=2.14.0; platform_system == 'Linux'", "tensorflow~=2.14.0; platform_system == 'Darwin'", "dgl==2.1.0", + "dgllife==0.3.2", "torch_geometric==2.7.0", ] cuda = [ + "torch==2.1.2", "torchdata==0.7.1", + "tensorflow~=2.14.0", "dgl==2.1.0", - "torch_geometric==2.7.0", + "dgllife==0.3.2", + "torch-geometric==2.7.0", ] rocm = [ + "torch==2.1.2", "torchdata==0.7.1", + "tensorflow~=2.14.0", "dgl==2.1.0", - "torch_geometric==2.7.0", + "dgllife==0.3.2", + "torch-geometric==2.7.0", ] mchip = [ "torch==2.1.2", "torchdata", "tensorflow~=2.14.0", + "dgl==2.1.0", + "dgllife==0.3.2", "torch_geometric==2.7.0", ] diff --git a/sync_env.sh b/sync_uv_env.sh similarity index 92% rename from sync_env.sh rename to sync_uv_env.sh index 46be0bf1..a823dfc6 100755 --- a/sync_env.sh +++ b/sync_uv_env.sh @@ -6,7 +6,7 @@ # want to create/update a local env from existing lock/deps. build an env to run. # # Usage: -# ./sync_env.sh +# ./sync_uv_env.sh set -euo pipefail @@ -31,6 +31,7 @@ case "$platform" in VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra cpu --group dev --locked ;; cuda) + # to force the right torch wheel into the env before syncing, especially for GPU variants uv venv --python 3.10 "$venv_dir" uv pip install --python "$venv_dir/bin/python" --index-url https://download.pytorch.org/whl/cu121 torch==2.1.2 VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra cuda --group dev --locked diff --git a/update_lock.sh b/update_uv_lock.sh similarity index 96% rename from update_lock.sh rename to update_uv_lock.sh index 2162d42f..0ce1c3e5 100755 --- a/update_lock.sh +++ b/update_uv_lock.sh @@ -7,7 +7,7 @@ # dependencies changed, pyproject.toml changed, or lockfile mismatch happens. refresh the commited lockfile. # # Usage: -# ./update_lock.sh +# ./update_uv_lock.sh set -euo pipefail diff --git a/uv.lock.cpu b/uv.lock.cpu index e2de648e..a8948104 100644 --- a/uv.lock.cpu +++ b/uv.lock.cpu @@ -201,9 +201,9 @@ dependencies = [ { name = "bokeh" }, { name = "bravado" }, { name = "deepchem" }, - { name = "dgllife" }, { name = "hyperopt" }, { name = "imbalanced-learn" }, + { name = "imblearn" }, { name = "lightgbm" }, { name = "lightning" }, { name = "maestrowf" }, @@ -226,17 +226,24 @@ dependencies = [ [package.optional-dependencies] cpu = [ { name = "dgl" }, + { name = "dgllife" }, { name = "tensorflow", marker = "sys_platform == 'darwin'" }, { name = "tensorflow-cpu", marker = "sys_platform == 'linux'" }, + { name = "torch" }, { name = "torch-geometric" }, { name = "torchdata" }, ] cuda = [ { name = "dgl" }, + { name = "dgllife" }, + { name = "tensorflow" }, + { name = "torch" }, { name = "torch-geometric" }, { name = "torchdata" }, ] mchip = [ + { name = "dgl" }, + { name = "dgllife" }, { name = "tensorflow" }, { name = "torch" }, { name = "torch-geometric" }, @@ -244,6 +251,9 @@ mchip = [ ] rocm = [ { name = "dgl" }, + { name = "dgllife" }, + { name = "tensorflow" }, + { name = "torch" }, { name = "torch-geometric" }, { name = "torchdata" }, ] @@ -268,10 +278,15 @@ requires-dist = [ { name = "deepchem", specifier = "==2.8" }, { name = "dgl", marker = "extra == 'cpu'", specifier = "==2.1.0" }, { name = "dgl", marker = "extra == 'cuda'", specifier = "==2.1.0" }, + { name = "dgl", marker = "extra == 'mchip'", specifier = "==2.1.0" }, { name = "dgl", marker = "extra == 'rocm'", specifier = "==2.1.0" }, - { name = "dgllife", specifier = "==0.3.2" }, + { name = "dgllife", marker = "extra == 'cpu'", specifier = "==0.3.2" }, + { name = "dgllife", marker = "extra == 'cuda'", specifier = "==0.3.2" }, + { name = "dgllife", marker = "extra == 'mchip'", specifier = "==0.3.2" }, + { name = "dgllife", marker = "extra == 'rocm'", specifier = "==0.3.2" }, { name = "hyperopt" }, { name = "imbalanced-learn" }, + { name = "imblearn" }, { name = "lightgbm" }, { name = "lightning", specifier = "==2.2.5" }, { name = "maestrowf" }, @@ -288,9 +303,14 @@ requires-dist = [ { name = "seaborn", specifier = ">=0.13.0" }, { name = "setuptools" }, { name = "tensorflow", marker = "sys_platform == 'darwin' and extra == 'cpu'", specifier = "~=2.14.0" }, + { name = "tensorflow", marker = "extra == 'cuda'", specifier = "~=2.14.0" }, { name = "tensorflow", marker = "extra == 'mchip'", specifier = "~=2.14.0" }, + { name = "tensorflow", marker = "extra == 'rocm'", specifier = "~=2.14.0" }, { name = "tensorflow-cpu", marker = "sys_platform == 'linux' and extra == 'cpu'", specifier = "~=2.14.0" }, + { name = "torch", marker = "extra == 'cpu'", specifier = "==2.1.2" }, + { name = "torch", marker = "extra == 'cuda'", specifier = "==2.1.2" }, { name = "torch", marker = "extra == 'mchip'", specifier = "==2.1.2" }, + { name = "torch", marker 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16:03:35 -0700 Subject: [PATCH 05/37] updated pyproject.toml --- pyproject.toml | 7 +- sync_uv_env.sh | 38 +- update_uv_lock.sh | 36 +- uv.lock.cpu | 28 +- uv.lock.cuda | 76 +- uv.lock.rocm | 3545 +++++++++++++++++++++++++++++++++++++++++++++ 6 files changed, 3654 insertions(+), 76 deletions(-) create mode 100644 uv.lock.rocm diff --git a/pyproject.toml b/pyproject.toml index 5489987e..b3edb9cb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -22,7 +22,6 @@ dependencies = [ "pyyaml>=6.0", "bravado", "imbalanced-learn", - "imblearn", "maestrowf", "deepchem==2.8", "rdkit==2024.3.5", @@ -51,7 +50,7 @@ cpu = [ "tensorflow~=2.14.0; platform_system == 'Darwin'", "dgl==2.1.0", "dgllife==0.3.2", - "torch_geometric==2.7.0", + "torch-geometric==2.7.0", ] cuda = [ @@ -74,11 +73,11 @@ rocm = [ mchip = [ "torch==2.1.2", - "torchdata", + "torchdata==0.7.1", "tensorflow~=2.14.0", "dgl==2.1.0", "dgllife==0.3.2", - "torch_geometric==2.7.0", + "torch-geometric==2.7.0", ] [build-system] diff --git a/sync_uv_env.sh b/sync_uv_env.sh index a823dfc6..ce03720c 100755 --- a/sync_uv_env.sh +++ b/sync_uv_env.sh @@ -10,39 +10,57 @@ set -euo pipefail -platform="${1:?usage: $0 }" +platform="${1:-}" + +case "$platform" in + cpu|cuda|rocm|mchip) + ;; + "") + echo "Usage: $0 " + exit 1 + ;; + *) + echo "Invalid platform: $platform" + echo "Supported platforms: cpu cuda rocm mchip" + echo "Usage: $0 " + exit 1 + ;; +esac lockfile="uv.lock.${platform}" venv_dir=".venv-${platform}" if [[ ! -f "$lockfile" ]]; then echo "Missing lockfile: $lockfile" - echo "Run ./update_lock.sh $platform first" + echo "Run ./update_uv_lock.sh $platform first" exit 1 fi cp "$lockfile" uv.lock rm -rf "$venv_dir" +uv venv --python 3.10 "$venv_dir" + case "$platform" in cpu) - uv venv --python 3.10 "$venv_dir" - uv pip install --python "$venv_dir/bin/python" --index-url https://download.pytorch.org/whl/cpu torch==2.1.2 + uv pip install --python "$venv_dir/bin/python" \ + --index-url https://download.pytorch.org/whl/cpu \ + torch==2.1.2 torchdata==0.7.1 VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra cpu --group dev --locked ;; cuda) - # to force the right torch wheel into the env before syncing, especially for GPU variants - uv venv --python 3.10 "$venv_dir" - uv pip install --python "$venv_dir/bin/python" --index-url https://download.pytorch.org/whl/cu121 torch==2.1.2 + uv pip install --python "$venv_dir/bin/python" \ + --index-url https://download.pytorch.org/whl/cu121 \ + torch==2.1.2 torchdata==0.7.1 VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra cuda --group dev --locked ;; rocm) - uv venv --python 3.10 "$venv_dir" - uv pip install --python "$venv_dir/bin/python" --index-url https://download.pytorch.org/whl/rocm5.6 torch==2.1.2 + uv pip install --python "$venv_dir/bin/python" \ + --index-url https://download.pytorch.org/whl/rocm5.6 \ + torch==2.1.2 torchdata==0.7.1 VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra rocm --group dev --locked ;; mchip) - uv venv --python 3.10 "$venv_dir" VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra mchip --group dev --locked ;; *) diff --git a/update_uv_lock.sh b/update_uv_lock.sh index 0ce1c3e5..71a63832 100755 --- a/update_uv_lock.sh +++ b/update_uv_lock.sh @@ -2,6 +2,7 @@ # # Purpose: # regenerates uv.lock. +# generates the righ lockfile for the specified platform # # Use when: # dependencies changed, pyproject.toml changed, or lockfile mismatch happens. refresh the commited lockfile. @@ -11,7 +12,22 @@ set -euo pipefail -platform="${1:?usage: $0 }" +platform="${1:-}" + +case "$platform" in + cpu|cuda|rocm|mchip) + ;; + "") + echo "Usage: $0 " + exit 1 + ;; + *) + echo "Invalid platform: $platform" + echo "Supported platforms: cpu cuda rocm mchip" + echo "Usage: $0 " + exit 1 + ;; +esac lockfile="uv.lock.${platform}" venv_dir=".venv-${platform}" @@ -19,24 +35,28 @@ venv_dir=".venv-${platform}" rm -f uv.lock rm -rf "$venv_dir" +uv venv --python 3.10 "$venv_dir" + case "$platform" in cpu) - uv venv --python 3.10 "$venv_dir" - uv pip install --python "$venv_dir/bin/python" --index-url https://download.pytorch.org/whl/cpu torch==2.1.2 + uv pip install --python "$venv_dir/bin/python" \ + --index-url https://download.pytorch.org/whl/cpu \ + torch==2.1.2 torchdata==0.7.1 VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra cpu --group dev ;; cuda) - uv venv --python 3.10 "$venv_dir" - uv pip install --python "$venv_dir/bin/python" --index-url https://download.pytorch.org/whl/cu121 torch==2.1.2 + uv pip install --python "$venv_dir/bin/python" \ + --index-url https://download.pytorch.org/whl/cu121 \ + torch==2.1.2 torchdata==0.7.1 VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra cuda --group dev ;; rocm) - uv venv --python 3.10 "$venv_dir" - uv pip install --python "$venv_dir/bin/python" --index-url https://download.pytorch.org/whl/rocm5.6 torch==2.1.2 + uv pip install --python "$venv_dir/bin/python" \ + --index-url https://download.pytorch.org/whl/rocm5.6 \ + torch==2.1.2 torchdata==0.7.1 VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra rocm --group dev ;; mchip) - uv venv --python 3.10 "$venv_dir" VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra mchip --group dev ;; *) diff --git a/uv.lock.cpu b/uv.lock.cpu index a8948104..db79ec97 100644 --- a/uv.lock.cpu +++ b/uv.lock.cpu @@ -252,7 +252,6 @@ mchip = [ rocm = [ { name = "dgl" }, { name = "dgllife" }, - { name = "tensorflow" }, { name = "torch" }, { name = "torch-geometric" }, { name = "torchdata" }, @@ -305,7 +304,6 @@ requires-dist = [ { name = "tensorflow", marker = "sys_platform == 'darwin' and extra == 'cpu'", specifier = "~=2.14.0" }, { name = "tensorflow", marker = "extra == 'cuda'", specifier = "~=2.14.0" }, { name = "tensorflow", marker = "extra == 'mchip'", specifier = "~=2.14.0" }, - { name = "tensorflow", marker 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11:55:29 -0700 Subject: [PATCH 06/37] updated for cpu, cuda, rocm. first draft of the readme --- README.md | 219 ++++++++++++++++++++++++++++++++++------------------ uv.lock.cpu | 16 +--- 2 files changed, 146 insertions(+), 89 deletions(-) diff --git a/README.md b/README.md index ecb459c2..3889f177 100644 --- a/README.md +++ b/README.md @@ -25,11 +25,20 @@ In addition to our written tutorials, we now provide a series of video tutorials --- ## Table of contents -- [Install](#install) - - [Quick Install](#installation-quick-summary) - - [Jupyter kernel](#create-jupyter-notebook-kernel-optional) - - [Docker](#install-with-docker) - - [Uninstall](#uninstall) +- [Installation](#installation) + - [What is `uv`?](#what-is-uv) + - [Requirements](#requirements) + - [Install `uv`](#install-uv) + - [Clone the repository](#clone-the-repository) +- [Create and activate an environment](#create-and-activate-an-environment) +- [Platform-specific setup](#platform-specific-setup) +- [Update lockfiles](#update-lockfiles) +- [Troubleshooting](#troubleshooting) + - [`uv` not found](#uv-not-found) + - [Missing lockfile](#missing-lockfile) + - [Wrong Python/Pytest](#wrong-python-pytest) + - [Library not found after activation](#library-not-found-after-activation) + - [Package import fails](#package-import-fails) - [AMPL Features](#ampl-features) - [Running AMPL](#running-ampl) - [Tests](#tests) @@ -44,85 +53,171 @@ In addition to our written tutorials, we now provide a series of video tutorials - [Pipeline parameters (options)](atomsci/ddm/docs/PARAMETERS.md) - [Library documentation](https://ampl.readthedocs.io/en/latest/index.html) --- -## Install -AMPL 1.8 supports Python 3.10 CPU or CUDA-enabled machines using CUDA 11.8 on Linux. All other systems are experimental. For a quick install summary, see [here](#install-summary). We do not support other CUDA versions because there are multiple ML package dependency conflicts that can occur. For more information you can look at [DeepChem](https://deepchem.readthedocs.io/en/latest/get_started/installation.html), [TensorFlow](https://www.tensorflow.org/install/pip), [PyTorch](https://pytorch.org/get-started/locally/), [DGL](https://www.dgl.ai/pages/start.html). + +## Installation +AMPL 1.8 supports Python 3.10 CPU or CUDA-enabled machines using CUDA 11.8 on Linux. All other systems are experimental. For a quick install summary, see [here](#install-summary). For more information you can look at [DeepChem](https://deepchem.readthedocs.io/en/latest/get_started/installation.html), [TensorFlow](https://www.tensorflow.org/install/pip), [PyTorch](https://pytorch.org/get-started/locally/), [DGL](https://www.dgl.ai/pages/start.html). For installation on Apple Silicon M Chips, please see the Docker container instructions. -### Create pip environment +AMPL uses [`uv`](https://docs.astral.sh/uv/) for Python environment and dependency management. + +## Installation + +AMPL uses [`uv`](https://docs.astral.sh/uv/) for Python environment and dependency management. + +### What is `uv`? + +`uv` is a fast Python tool used in this project to: + +| Use | Command | +|---|---| +| Create virtual environments | `uv venv` | +| Sync dependencies from `pyproject.toml` | `uv sync` | +| Install packages into the environment | `uv pip install` | -#### 1. Create a virtual env with Python 3.10 -Make sure to create your virtual env in a convenient directory that has at least 12Gb space. +AMPL environments are created from: -Go to the directory where the new environment directory be installed in. Define an environment variable - "ENVROOT". +- `pyproject.toml` +- platform-specific lockfiles: + - `uv.lock.cpu` + - `uv.lock.cuda` + - `uv.lock.rocm` + - `uv.lock.mchip` +### Requirements + +| Item | Requirement | +|---|---| +| Python | 3.10 | +| Supported range | `>=3.10,<3.11` | +| Platforms | `cpu`, `cuda`, `rocm`, `mchip` | + +### Install `uv` + +Install `uv` using one of the following methods: ```bash -export ENVROOT=~/workspace # for LLNL LC users, use your workspace +curl -LsSf https://astral.sh/uv/install.sh | sh +``` or -export ENVROOT=~ # or the directory as your environment root +```bash +pip install uv +``` +Verify installation: +```bash +uv --version +``` +### Clone the repository +```bash +git clone https://github.com/ATOMScience-org/AMPL.git +cd AMPL ``` +## Create and activate an environment + +Use the provided sync script for your target platform. -> *We use "workspace" and "atomsci-env" as an example here.* +| Platform | Sync command | Environment | Activate command | +|---|---|---|---| +| CPU | `./sync_uv_env.sh cpu` | `.venv-cpu` | `source .venv-cpu/bin/activate` | +| CUDA | `./sync_uv_env.sh cuda` | `.venv-cuda` | `source .venv-cuda/bin/activate` | +| ROCm | `./sync_uv_env.sh rocm` | `.venv-rocm` | `source .venv-rocm/bin/activate` | +| Apple Silicon / M chip | `./sync_uv_env.sh mchip` | `.venv-mchip` | `source .venv-mchip/bin/activate` | +After activating the environment, install AMPL in editable mode: ```bash -# LLNL only: -# module load python/3.10.8 -cd $ENVROOT -python3.10 -m venv atomsci-env +uv pip install -e . ``` +## Platform-specific setup + +The following settings may be useful depending on your platform and runtime environment. + +| Platform | Optional setup | Useful environment variables | +|---|---|---| +| CPU | none | `export OPENBLAS_NUM_THREADS=1` | +| CUDA | load site CUDA module if required | `export CUDA_HOME=/usr/local/cuda`
`export PATH="$CUDA_HOME/bin:$PATH"`
`export LD_LIBRARY_PATH="$CUDA_HOME/lib64:$LD_LIBRARY_PATH"`| +| ROCm | site-specific ROCm setup if required | `module load rocm`
`export ROCM_HOME="$(dirname "$(dirname "$(readlink -f "$(which hipcc)")")")"`
`export PATH="$ROCM_HOME/bin:$PATH"`| +| Apple Silicon / M chip | none | usually none required | + +## Update lockfiles + +If `pyproject.toml` dependencies are updated, regenerate the lockfile for the appropriate target platform. + +| Platform | Command | Lockfile | +|---|---|---| +| CPU | `./update_uv_lock.sh cpu` | `uv.lock.cpu` | +| CUDA | `./update_uv_lock.sh cuda` | `uv.lock.cuda` | +| ROCm | `./update_uv_lock.sh rocm` | `uv.lock.rocm` | +| Apple Silicon / M chip | `./update_uv_lock.sh mchip` | `uv.lock.mchip` | + +**Note:** This is for administrative, internal support. Please don't run this if `pyproject.toml` hasn't been changed. Ideally we want to retest on all supported platforms when `pyproject.toml` configuration changes. After the quick tests, push `uv.lock.` to AMPL's git repo. + +## Troubleshooting -#### 2. Activate the environment +### `uv` not found + +Install `uv`, then verify: ```bash -source $ENVROOT/atomsci-env/bin/activate +uv --version ``` +If needed, start a new shell session or update your `PATH`. + +### Missing lockfile -#### 3. Update pip +If you see: +```bash +Missing lockfile: uv.lock. +``` +run: ```bash -pip install pip --upgrade +./update_uv_lock.sh ``` +### Wrong Python, Pytest -#### 4. Clone AMPL repository +Check that Python 3.10 is being used: ```bash -git clone https://github.com/ATOMScience-org/AMPL.git +which python +python --version +which pytest ``` -#### 5. Install pip requirements -Depending on system performance, creating the environment can take some time. -> ***Note:*** *Based on which environment (CPU or CUDA) to run on, only run one of the following:* +They should come from the virtual env, like '.venv-cpu/bin/python', '.venv-cpu/bin/pytest' + +If fails, refer to [Package import fails](#package-import-fails), use `uv sync ...` command shown there to get your VM sync up. -- CPU-only installation: +### Library not found after activation + +Confirm the correct environment is active: +```bash +which python +echo $VIRTUAL_ENV +``` +If needed, set: ```bash -cd AMPL/pip -pip install -r cpu_requirements.txt +export LD_LIBRARY_PATH=$VIRTUAL_ENV/lib:$LD_LIBRARY_PATH ``` -- CUDA installation: +If fails, refer to [Package import fails](#package-import-fails), use `uv sync ...` command shown there to get your VM sync up. -First load the CUDA module. Then run cuda specific package install. +### Package import fails +Try: ```bash -cd AMPL/pip -# LLNL only: -# module load cuda/11.8 -pip install -r cuda_requirements.txt +python -c "import torch; print(torch.__version__)" +python -c "import tensorflow as tf; print(tf.__version__)" +python -c "import rdkit; print('rdkit ok')" ``` -If you get `out of memory` errors, try setting these environment variables: -``` -export LD_LIBRARY_PATH=/lib:$LD_LIBRARY_PATH -export PYTHONUSERBASE= -export OPENBLAS_NUM_THREADS=1 -export OMP_NUM_THREADS=48 -export PYTORCH_HIP_ALLOC_CONF=gargage_collection_threshold:0.9,max_split_size_mb:128 -export TF_FORCE_GPU_ALLOW_GROWTH=true +If imports fail, rerun: + +```bash +./sync_uv_env.sh ``` -- Install pytest, plotting packages for development, test use. +If still not finding the packages, from your current .venv-, then run this: -```bash -cd AMPL/pip -pip install -r dev_requirements.txt ``` -#### 6. *(Optional) LLNL LC only*: if you use [model_tracker](https://ampl.readthedocs.io/en/latest/pipeline.html#module-pipeline.model_tracker), install atomsci.clients +uv sync --active --group dev --extra +``` + +#### *(Optional) LLNL LC only*: if you use [model_tracker](https://ampl.readthedocs.io/en/latest/pipeline.html#module-pipeline.model_tracker), install atomsci.clients ```bash # LLNL only: required for ATOM model_tracker pip install -r clients_requirements.txt @@ -133,32 +228,6 @@ Run the following to build the "atomsci" modules. This is required. ```bash # return to AMPL parent directory -cd .. -./build.sh -pip install -e . -``` ---- -## Installation Quick Summary -```bash -export ENVROOT=~/workspace # set ENVROOT example -# LLNL only: -# module load python/3.10.8 - -python3.10 -m venv atomsci-env # create environment with Python 3.10 -source $ENVROOT/atomsci-env/bin/activate -pip install pip --upgrade - -git clone https://github.com/ATOMScience-org/AMPL.git # clone AMPL -cd AMPL/pip -# LLNL only: -# If use CUDA: -# module load cuda/11.8 -pip install -r cpu_requirements.txt # install cpu_requirements.txt OR cuda_requirements.txt -pip install -r dev_requirements.txt # install pytest, plotting packages. - -# LLNL only: required for ATOM model_tracker -# pip install -r clients_requirements.txt - cd .. ./build.sh pip install -e . diff --git a/uv.lock.cpu b/uv.lock.cpu index db79ec97..f996ed8c 100644 --- a/uv.lock.cpu +++ b/uv.lock.cpu @@ -203,7 +203,6 @@ dependencies = [ { name = "deepchem" }, { name = "hyperopt" }, { name = "imbalanced-learn" }, - { name = "imblearn" }, { name = "lightgbm" }, { name = "lightning" }, { name = "maestrowf" }, @@ -252,6 +251,7 @@ mchip = [ rocm = [ { name = "dgl" }, { name = "dgllife" }, + { name = "tensorflow" }, { name = "torch" }, { name = "torch-geometric" }, { name = "torchdata" }, @@ -285,7 +285,6 @@ requires-dist = [ { name = "dgllife", marker = "extra == 'rocm'", specifier = "==0.3.2" }, { name = "hyperopt" }, { name = "imbalanced-learn" }, - { name = "imblearn" }, { name = "lightgbm" }, { name = "lightning", specifier = "==2.2.5" }, { name = "maestrowf" }, @@ -304,6 +303,7 @@ requires-dist = [ { name = "tensorflow", marker = "sys_platform == 'darwin' and extra == 'cpu'", specifier = "~=2.14.0" }, { name = "tensorflow", marker = "extra == 'cuda'", specifier = "~=2.14.0" }, { name = "tensorflow", marker = "extra == 'mchip'", specifier = "~=2.14.0" }, + { name = "tensorflow", marker = "extra == 'rocm'", specifier = "~=2.14.0" }, { name = "tensorflow-cpu", marker = "sys_platform == 'linux' and extra == 'cpu'", specifier = "~=2.14.0" }, { name = "torch", marker = "extra == 'cpu'", specifier = "==2.1.2" }, { name = "torch", marker = "extra == 'cuda'", specifier = "==2.1.2" }, @@ -1123,18 +1123,6 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/d8/0d/c3bfccc5d460eec8ff56889802aa88f5d07280d5282b307a74558e6edc44/imbalanced_learn-0.12.4-py3-none-any.whl", hash = "sha256:d47fc599160d3ea882e712a3a6b02bdd353c1a6436d8d68d41b1922e6ee4a703", size = 258324, upload-time = "2024-10-04T17:00:52.715Z" }, ] -[[package]] -name = "imblearn" -version = "0.0" -source = { registry = "https://pypi.org/simple" } -dependencies = [ - { name = "imbalanced-learn" }, -] -sdist = { url = "https://files.pythonhosted.org/packages/32/0a/f83099534a77757abf27427d339590c83cc68c3386690d4741d6454e185f/imblearn-0.0.tar.gz", hash = "sha256:d8fbb662919c1b16f438ad91a8256220e53bcf6815c9ad5502c518b798de34f2", size = 945, upload-time = "2017-01-19T11:52:35.89Z" } -wheels = [ - { url = "https://files.pythonhosted.org/packages/81/a7/4179e6ebfd654bd0eac0b9c06125b8b4c96a9d0a8ff9e9507eb2a26d2d7e/imblearn-0.0-py2.py3-none-any.whl", hash = "sha256:d42c2d709d22c00d2b9a91e638d57240a8b79b4014122d92181fcd2549a2f79a", size = 1874, upload-time = "2017-01-19T11:52:37.416Z" }, -] - [[package]] name = "importlib-resources" version = "7.1.0" From 23141925e486d410e08da64af35e4e779049c780 Mon Sep 17 00:00:00 2001 From: Jessica Mauvais Date: Tue, 14 Apr 2026 13:27:49 -0700 Subject: [PATCH 07/37] update docs --- README.md | 45 +++++++++++++++++++++------------ atomsci/ddm/docs/source/conf.py | 2 +- 2 files changed, 30 insertions(+), 17 deletions(-) diff --git a/README.md b/README.md index 3889f177..8c600040 100644 --- a/README.md +++ b/README.md @@ -27,6 +27,7 @@ In addition to our written tutorials, we now provide a series of video tutorials ## Table of contents - [Installation](#installation) - [What is `uv`?](#what-is-uv) + - [Repository helper scripts](#repository-helper-scripts) - [Requirements](#requirements) - [Install `uv`](#install-uv) - [Clone the repository](#clone-the-repository) @@ -61,10 +62,6 @@ For installation on Apple Silicon M Chips, please see the Docker container instr AMPL uses [`uv`](https://docs.astral.sh/uv/) for Python environment and dependency management. -## Installation - -AMPL uses [`uv`](https://docs.astral.sh/uv/) for Python environment and dependency management. - ### What is `uv`? `uv` is a fast Python tool used in this project to: @@ -75,14 +72,32 @@ AMPL uses [`uv`](https://docs.astral.sh/uv/) for Python environment and dependen | Sync dependencies from `pyproject.toml` | `uv sync` | | Install packages into the environment | `uv pip install` | -AMPL environments are created from: +### Repository helper scripts + +This repository includes two helper scripts that wrap the `uv` workflow for each supported platform. + +| Script | Purpose | What it does | +|---|---|---| +| `update_uv_lock.sh` | Regenerate a platform lockfile | Creates a fresh `uv` virtual environment, installs platform-specific packages, runs `uv sync`, then saves the result as `uv.lock.` | +| `sync_uv_env.sh` | Recreate a platform environment from a lockfile | Copies `uv.lock.` to `uv.lock`, creates a fresh `uv` virtual environment, installs platform-specific packages, then runs `uv sync --locked` | + +These scripts tie directly to the `uv` virtual environment workflow: + +| Platform | Virtual environment | Lockfile | +|---|---|---| +| CPU | `.venv-cpu` | `uv.lock.cpu` | +| CUDA | `.venv-cuda` | `uv.lock.cuda` | +| ROCm | `.venv-rocm` | `uv.lock.rocm` | +| Apple Silicon / M chip | `.venv-mchip` | `uv.lock.mchip` | + +In practice: + +- run `./update_uv_lock.sh ` when dependencies change and a lockfile needs to be refreshed +- run `./sync_uv_env.sh ` when you want to create a local environment from the saved lockfile +- activate the created environment with `source .venv-/bin/activate` + +-**Note:** `./update_uv_lock.sh` is for internal admin/support use only. Do not run it unless `pyproject.toml` has changed. When it does change, update and quick-test on all supported platforms, then push uv.lock. to the AMPL git repo.` -- `pyproject.toml` -- platform-specific lockfiles: - - `uv.lock.cpu` - - `uv.lock.cuda` - - `uv.lock.rocm` - - `uv.lock.mchip` ### Requirements @@ -133,7 +148,7 @@ The following settings may be useful depending on your platform and runtime envi | Platform | Optional setup | Useful environment variables | |---|---|---| | CPU | none | `export OPENBLAS_NUM_THREADS=1` | -| CUDA | load site CUDA module if required | `export CUDA_HOME=/usr/local/cuda`
`export PATH="$CUDA_HOME/bin:$PATH"`
`export LD_LIBRARY_PATH="$CUDA_HOME/lib64:$LD_LIBRARY_PATH"`| +| CUDA | load site CUDA module if required | `module load cuda`
`export CUDA_HOME=/usr/local/cuda`
`export PATH="$CUDA_HOME/bin:$PATH"`
`export LD_LIBRARY_PATH="$CUDA_HOME/lib64:$LD_LIBRARY_PATH"`| | ROCm | site-specific ROCm setup if required | `module load rocm`
`export ROCM_HOME="$(dirname "$(dirname "$(readlink -f "$(which hipcc)")")")"`
`export PATH="$ROCM_HOME/bin:$PATH"`| | Apple Silicon / M chip | none | usually none required | @@ -148,8 +163,6 @@ If `pyproject.toml` dependencies are updated, regenerate the lockfile for the ap | ROCm | `./update_uv_lock.sh rocm` | `uv.lock.rocm` | | Apple Silicon / M chip | `./update_uv_lock.sh mchip` | `uv.lock.mchip` | -**Note:** This is for administrative, internal support. Please don't run this if `pyproject.toml` hasn't been changed. Ideally we want to retest on all supported platforms when `pyproject.toml` configuration changes. After the quick tests, push `uv.lock.` to AMPL's git repo. - ## Troubleshooting ### `uv` not found @@ -181,7 +194,7 @@ which pytest They should come from the virtual env, like '.venv-cpu/bin/python', '.venv-cpu/bin/pytest' -If fails, refer to [Package import fails](#package-import-fails), use `uv sync ...` command shown there to get your VM sync up. +If fails, refer to [Package import fails](#package-import-fails), use `uv sync --active --group dev --extra ` command shown there to get your VM sync up. ### Library not found after activation @@ -195,7 +208,7 @@ If needed, set: export LD_LIBRARY_PATH=$VIRTUAL_ENV/lib:$LD_LIBRARY_PATH ``` -If fails, refer to [Package import fails](#package-import-fails), use `uv sync ...` command shown there to get your VM sync up. +If fails, refer to [Package import fails](#package-import-fails), use `uv sync --active --group dev --extra ` command shown there to get your VM sync up. ### Package import fails diff --git a/atomsci/ddm/docs/source/conf.py b/atomsci/ddm/docs/source/conf.py index 7cafdd40..a0790e66 100644 --- a/atomsci/ddm/docs/source/conf.py +++ b/atomsci/ddm/docs/source/conf.py @@ -28,7 +28,7 @@ # import atomsci.ddm #version = atomsci.ddm.__version__ # The short X.Y version -version = '1.7.0' +version = '1.8.0' copyright = f'{datetime.datetime.now().year}, {author}' # The full version, including alpha/beta/rc tags From e5b249b53ec0e69ee2e48d92762f3b8c848b5dab Mon Sep 17 00:00:00 2001 From: Jessica Mauvais Date: Tue, 14 Apr 2026 14:44:39 -0700 Subject: [PATCH 08/37] updated docker, readthedocs related build. need to test --- .readthedocs.yml | 17 +++++++---- Dockerfile.arm | 52 +++++++------------------------- Dockerfile.cpu | 52 +++++--------------------------- Dockerfile.gpu | 53 +++++---------------------------- atomsci/ddm/docs/source/conf.py | 15 ++++++++-- pyproject.toml | 16 ++++++++++ 6 files changed, 67 insertions(+), 138 deletions(-) diff --git a/.readthedocs.yml b/.readthedocs.yml index 6c7fb338..73139e0f 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -1,14 +1,21 @@ # .readthedocs.yml # Read the Docs configuration file # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details +# -# Required -version: 1 +version: 2 + +build: + os: ubuntu-22.04 + tools: + python: "3.10" -# Build documentation in the docs/ directory with Sphinx sphinx: configuration: docs/source/conf.py -# Optionally set the version of Python and requirements required to build your docs python: - version: 3.7 + install: + - method: pip + path: . + extra_requirements: + - docs diff --git a/Dockerfile.arm b/Dockerfile.arm index 7078fd3f..65476b23 100644 --- a/Dockerfile.arm +++ b/Dockerfile.arm @@ -1,50 +1,20 @@ -FROM python:3.10 +FROM --platform=linux/arm64 python:3.10-slim -# Prevent interactive dialogs from halting the build -ENV DEBIAN_FRONTEND=noninteractive - -RUN apt-get update -y && apt-get install -y \ +RUN apt-get update && apt-get install -y \ build-essential \ - libcairo2-dev \ - libhdf5-dev \ - pkg-config \ - && apt-get clean \ + git \ + curl \ + ca-certificates \ && rm -rf /var/lib/apt/lists/* -# Install uv -# Option A (recommended): official installer -RUN curl -LsSf https://astral.sh/uv/install.sh | sh -ENV PATH="/root/.local/bin:${PATH}" - -COPY ./pip/mchip_requirements.txt ./pip/mchip_requirements.txt -RUN uv pip install --system -v --no-cache-dir \ - --trusted-host pypi.python.org \ - --trusted-host files.pythonhosted.org \ - --trusted-host pypi.org \ - --trusted-host data.dgl.ai \ - --trusted-host download.pytorch.org \ - -r ./pip/mchip_requirements.txt +RUN pip install --no-cache-dir uv -COPY ./pip/mchip_dev_requirements.txt ./pip/mchip_dev_requirements.txt -RUN uv pip install --system -v --no-cache-dir \ - --trusted-host pypi.python.org \ - --trusted-host files.pythonhosted.org \ - --trusted-host pypi.org \ - --trusted-host data.dgl.ai \ - --trusted-host download.pytorch.org \ - -r ./pip/mchip_dev_requirements.txt +WORKDIR /app -COPY setup.py . +COPY pyproject.toml . COPY VERSION . -COPY build.sh . -COPY ./atomsci atomsci/ +COPY atomsci ./atomsci -# Install atomsci-ampl -RUN ./build.sh -RUN uv pip install -e . +RUN uv sync --extra mchip --group docker --no-dev -# Clean up -RUN apt-get purge -y build-essential && \ - apt-get autoremove -y && \ - rm -rf /var/lib/apt/lists/* -RUN rm -rf /root/.cache/pip +CMD ["uv", "run", "python", "-c", "import atomsci; print('arm64/mchip-style ok')"] diff --git a/Dockerfile.cpu b/Dockerfile.cpu index 0c372b24..100ee8e3 100644 --- a/Dockerfile.cpu +++ b/Dockerfile.cpu @@ -1,50 +1,12 @@ -FROM python:3.10 +FROM python:3.10-slim -# Prevent interactive dialogs from halting the build -ENV DEBIAN_FRONTEND=noninteractive +RUN pip install uv +WORKDIR /app -RUN apt-get update -y && apt-get install -y \ - build-essential \ - libcairo2-dev \ - libhdf5-dev \ - pkg-config \ - && apt-get clean \ - && rm -rf /var/lib/apt/lists/* - -# Install uv -# Option A (recommended): official installer -RUN curl -LsSf https://astral.sh/uv/install.sh | sh -ENV PATH="/root/.local/bin:${PATH}" - -COPY ./pip/cpu_requirements.txt ./pip/cpu_requirements.txt -RUN uv pip install --system -v --no-cache-dir \ - --trusted-host pypi.python.org \ - --trusted-host files.pythonhosted.org \ - --trusted-host pypi.org \ - --trusted-host data.dgl.ai \ - --trusted-host download.pytorch.org \ - -r ./pip/cpu_requirements.txt - -COPY ./pip/dev_requirements.txt ./pip/dev_requirements.txt -RUN uv pip install --system -v --no-cache-dir \ - --trusted-host pypi.python.org \ - --trusted-host files.pythonhosted.org \ - --trusted-host pypi.org \ - --trusted-host data.dgl.ai \ - --trusted-host download.pytorch.org \ - -r ./pip/dev_requirements.txt - -COPY setup.py . +COPY pyproject.toml . +COPY atomsci ./atomsci COPY VERSION . -COPY build.sh . -COPY ./atomsci atomsci/ -# Install atomsci-ampl -RUN ./build.sh -RUN pip install -e . +RUN uv sync --extra cpu -# Clean up -RUN apt-get purge -y build-essential && \ - apt-get autoremove -y && \ - rm -rf /var/lib/apt/lists/* -RUN rm -rf /root/.cache/pip +CMD ["uv", "run", "python", "-c", "import atomsci; print('cpu ok')"] diff --git a/Dockerfile.gpu b/Dockerfile.gpu index 6a0c497a..88ed0553 100644 --- a/Dockerfile.gpu +++ b/Dockerfile.gpu @@ -1,50 +1,13 @@ -FROM python:3.10 +FROM nvidia/cuda:12.1.1-cudnn8-runtime-ubuntu22.04 -# Prevent interactive dialogs from halting the build -ENV DEBIAN_FRONTEND=noninteractive +RUN apt-get update && apt-get install -y python3.10 python3-pip +RUN python3.10 -m pip install uv -RUN apt-get update -y && apt-get install -y \ - build-essential \ - libcairo2-dev \ - libhdf5-dev \ - pkg-config \ - && apt-get clean \ - && rm -rf /var/lib/apt/lists/* - -# Install uv -# Option A (recommended): official installer -RUN curl -LsSf https://astral.sh/uv/install.sh | sh -ENV PATH="/root/.local/bin:${PATH}" - -COPY ./pip/cuda_requirements.txt ./pip/cuda_requirements.txt -RUN uv pip install --system -v --no-cache-dir \ - --trusted-host pypi.python.org \ - --trusted-host files.pythonhosted.org \ - --trusted-host pypi.org \ - --trusted-host data.dgl.ai \ - --trusted-host download.pytorch.org \ - -r ./pip/cuda_requirements.txt - -COPY ./pip/dev_requirements.txt ./pip/dev_requirements.txt -RUN uv pip install --system -v --no-cache-dir \ - --trusted-host pypi.python.org \ - --trusted-host files.pythonhosted.org \ - --trusted-host pypi.org \ - --trusted-host data.dgl.ai \ - --trusted-host download.pytorch.org \ - -r ./pip/dev_requirements.txt - -COPY setup.py . +WORKDIR /app +COPY pyproject.toml . +COPY atomsci ./atomsci COPY VERSION . -COPY build.sh . -COPY ./atomsci atomsci/ -# Install atomsci-ampl -RUN ./build.sh -RUN pip install -e . +RUN uv sync --extra cuda -# Clean up -RUN apt-get purge -y build-essential && \ - apt-get autoremove -y && \ - rm -rf /var/lib/apt/lists/* -RUN rm -rf /root/.cache/pip +CMD ["uv", "run", "python3.10", "-c", "import atomsci; print('cuda ok')"] diff --git a/atomsci/ddm/docs/source/conf.py b/atomsci/ddm/docs/source/conf.py index a0790e66..701ad34e 100644 --- a/atomsci/ddm/docs/source/conf.py +++ b/atomsci/ddm/docs/source/conf.py @@ -195,5 +195,16 @@ # -- Extension configuration ------------------------------------------------- -autodoc_mock_imports = ["rdkit", "tensorflow.contrib", "atomsci", "yaml", "sklearn.preprocessing.Imputer"] - +autodoc_mock_imports = [ + "torch", + "torchdata", + "tensorflow", + "dgl", + "dgllife", + "torch_geometric", + "deepchem", + "rdkit", + "tensorflow.contrib", + "yaml", + "sklearn.preprocessing.Imputer", +] diff --git a/pyproject.toml b/pyproject.toml index b3edb9cb..98c63415 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -29,6 +29,7 @@ dependencies = [ "setuptools", ] +# local developer tools [dependency-groups] dev = [ "ipykernel", @@ -42,7 +43,22 @@ dev = [ "ruff", ] +docker = [ + "networkx==2.8.8", +] + [project.optional-dependencies] +# RTD-installable docs deps +docs = [ + "ipython", + "joblib", + "pandas", + "pygments", + "sphinx", + "sphinx_rtd_theme", +] + +# hardware/runtime variants cpu = [ "torch==2.1.2", "torchdata==0.7.1", From f9484911145ee8247c21c2ebc015399fe9587189 Mon Sep 17 00:00:00 2001 From: Jessica Mauvais Date: Tue, 14 Apr 2026 16:51:28 -0700 Subject: [PATCH 09/37] updated lock files after pyproject.toml change --- uv.lock.cpu | 170 ++++++++++++++++++++++++++++++++++++++++++++-- uv.lock.cuda | 186 ++++++++++++++++++++++++++++++++++++++++++++++----- uv.lock.rocm | 170 ++++++++++++++++++++++++++++++++++++++++++++-- 3 files changed, 500 insertions(+), 26 deletions(-) diff --git a/uv.lock.cpu b/uv.lock.cpu index f996ed8c..4d0301f7 100644 --- a/uv.lock.cpu +++ b/uv.lock.cpu @@ -77,6 +77,15 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/fb/76/641ae371508676492379f16e2fa48f4e2c11741bd63c48be4b12a6b09cba/aiosignal-1.4.0-py3-none-any.whl", hash = "sha256:053243f8b92b990551949e63930a839ff0cf0b0ebbe0597b0f3fb19e1a0fe82e", size = 7490, upload-time = "2025-07-03T22:54:42.156Z" }, ] 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mchip = [ { name = "dgl" }, { name = "dgllife" }, @@ -269,6 +286,9 @@ dev = [ { name = "pytest-xdist" }, { name = "ruff" }, ] +docker = [ + { name = "networkx" }, +] [package.metadata] requires-dist = [ @@ -285,6 +305,8 @@ requires-dist = [ { name = "dgllife", marker = "extra == 'rocm'", specifier = "==0.3.2" }, { name = "hyperopt" }, { name = "imbalanced-learn" }, + { name = "ipython", marker = "extra == 'docs'" }, + { name = "joblib", marker = "extra == 'docs'" }, { name = "lightgbm" }, { name = "lightning", specifier = "==2.2.5" }, { name = "maestrowf" }, @@ -292,14 +314,18 @@ requires-dist = [ { name = "matplotlib-venn" }, { name = "mordred" }, { name = "numpy", specifier = "<2" }, + { name = "pandas", marker = "extra == 'docs'" }, { name = "pyarrow" }, { name = "pydantic", specifier = ">=1.10,<2" }, + { name = "pygments", marker = "extra == 'docs'" }, { name = "pyyaml", specifier = ">=6.0" }, { name = "rdkit", specifier = "==2024.3.5" }, { name = "scikit-learn", specifier = 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size = 92072, upload-time = "2024-07-29T01:10:08.203Z" }, +] + [[package]] name = "stack-data" version = "0.6.3" From b6c341220ecb447b4fe8df1a5c8cfbc6c38baca9 Mon Sep 17 00:00:00 2001 From: Jessica Mauvais Date: Wed, 15 Apr 2026 10:25:48 -0700 Subject: [PATCH 10/37] updated makefile --- Makefile | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/Makefile b/Makefile index 7284f020..b097eef8 100644 --- a/Makefile +++ b/Makefile @@ -46,7 +46,7 @@ VENV ?= atomsci-env # Work Directory WORK_DIR ?= work -.PHONY: sync-cpu sync-cuda sync-rocm sync-mps test-cpu test-gpu test-rocm test-mps \ +.PHONY: sync-cpu sync-cuda sync-rocm sync-mchip test-cpu test-gpu test-rocm test-mchip \ build-docker install install-dev install-system install-venv jupyter-notebook jupyter-lab \ pytest ruff ruff-fix setup uninstall uninstall-dev uninstall-system uninstall-venv @@ -160,16 +160,16 @@ uninstall: uninstall-system # for uv env sync-cpu: - UV_PROJECT_ENVIRONMENT=.venv-cpu uv sync --extra cpu + UV_PROJECT_ENVIRONMENT=.venv-cpu uv sync --group dev --extra cpu sync-cuda: - UV_PROJECT_ENVIRONMENT=.venv-cuda uv sync --extra cuda + UV_PROJECT_ENVIRONMENT=.venv-cuda uv sync --group dev --extra cuda sync-rocm: - UV_PROJECT_ENVIRONMENT=.venv-rocm uv sync --extra rocm + UV_PROJECT_ENVIRONMENT=.venv-rocm uv sync --group dev --extra rocm -sync-mps: - UV_PROJECT_ENVIRONMENT=.venv-mps uv sync --extra mps +sync-mchip: + UV_PROJECT_ENVIRONMENT=.venv-mchip uv sync --group dev --extra mchip test-cpu: UV_PROJECT_ENVIRONMENT=.venv-cpu uv run pytest @@ -180,8 +180,8 @@ test-gpu: test-rocm: UV_PROJECT_ENVIRONMENT=.venv-rocm uv run pytest -test-mps: - UV_PROJECT_ENVIRONMENT=.venv-mps uv run pytest +test-mchip: + UV_PROJECT_ENVIRONMENT=.venv-mchip uv run pytest # Uninstall atomsci-ampl from user space uninstall-dev: From de9e11298c826eeaac2d343f5aae9cfa537c728d Mon Sep 17 00:00:00 2001 From: Jessica Mauvais Date: Wed, 15 Apr 2026 10:57:19 -0700 Subject: [PATCH 11/37] added Dockerfile.rocm. will test later --- Dockerfile.rocm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 Dockerfile.rocm diff --git a/Dockerfile.rocm b/Dockerfile.rocm new file mode 100644 index 00000000..c75e3f71 --- /dev/null +++ b/Dockerfile.rocm @@ -0,0 +1,22 @@ +FROM rocm/dev-ubuntu-22.04:6.1 + +RUN apt-get update && apt-get install -y \ + python3.10 \ + python3-pip \ + python3.10-venv \ + build-essential \ + git \ + curl \ + ca-certificates + +RUN python3.10 -m pip install --no-cache-dir uv + +WORKDIR /app + +COPY pyproject.toml . +COPY VERSION . +COPY atomsci ./atomsci + +RUN uv sync --extra rocm --group docker --no-dev + +CMD ["uv", "run", "python3.10", "-c", "import atomsci; print('rocm ok')"] From e32d88747affff3c04212ee64eb51b9a22b1d624 Mon Sep 17 00:00:00 2001 From: Jessica Mauvais Date: Wed, 15 Apr 2026 15:21:18 -0700 Subject: [PATCH 12/37] Update README --- README.md | 110 +++++++++++++++++++++--------------------------------- 1 file changed, 42 insertions(+), 68 deletions(-) diff --git a/README.md b/README.md index 8c600040..6b983548 100644 --- a/README.md +++ b/README.md @@ -33,13 +33,12 @@ In addition to our written tutorials, we now provide a series of video tutorials - [Clone the repository](#clone-the-repository) - [Create and activate an environment](#create-and-activate-an-environment) - [Platform-specific setup](#platform-specific-setup) -- [Update lockfiles](#update-lockfiles) - [Troubleshooting](#troubleshooting) - [`uv` not found](#uv-not-found) - [Missing lockfile](#missing-lockfile) - - [Wrong Python/Pytest](#wrong-python-pytest) + - [Wrong Python/Pytest](#wrong-pythonpytest) - [Library not found after activation](#library-not-found-after-activation) - - [Package import fails](#package-import-fails) + - [Package import fails or environment out of sync](#package-import-fails-or-environment-out-of-sync) - [AMPL Features](#ampl-features) - [Running AMPL](#running-ampl) - [Tests](#tests) @@ -53,12 +52,14 @@ In addition to our written tutorials, we now provide a series of video tutorials ## Useful links - [Pipeline parameters (options)](atomsci/ddm/docs/PARAMETERS.md) - [Library documentation](https://ampl.readthedocs.io/en/latest/index.html) + --- ## Installation -AMPL 1.8 supports Python 3.10 CPU or CUDA-enabled machines using CUDA 11.8 on Linux. All other systems are experimental. For a quick install summary, see [here](#install-summary). For more information you can look at [DeepChem](https://deepchem.readthedocs.io/en/latest/get_started/installation.html), [TensorFlow](https://www.tensorflow.org/install/pip), [PyTorch](https://pytorch.org/get-started/locally/), [DGL](https://www.dgl.ai/pages/start.html). -For installation on Apple Silicon M Chips, please see the Docker container instructions. +AMPL 1.8 supports Python 3.10 on CPU systems and CUDA-enabled Linux systems using CUDA 11.8. All other systems are experimental. For a quick install summary, see [here](#install-summary). For more information, see [DeepChem](https://deepchem.readthedocs.io/en/latest/get_started/installation.html), [TensorFlow](https://www.tensorflow.org/install/pip), [PyTorch](https://pytorch.org/get-started/locally/), and [DGL](https://www.dgl.ai/pages/start.html). + +For installation on Apple Silicon M chips, see the Docker container instructions. AMPL uses [`uv`](https://docs.astral.sh/uv/) for Python environment and dependency management. @@ -74,14 +75,15 @@ AMPL uses [`uv`](https://docs.astral.sh/uv/) for Python environment and dependen ### Repository helper scripts -This repository includes two helper scripts that wrap the `uv` workflow for each supported platform. +This repository includes helper commands for managing platform-specific `uv` environments and lockfiles. -| Script | Purpose | What it does | +| Command | Purpose | What it does | |---|---|---| -| `update_uv_lock.sh` | Regenerate a platform lockfile | Creates a fresh `uv` virtual environment, installs platform-specific packages, runs `uv sync`, then saves the result as `uv.lock.` | -| `sync_uv_env.sh` | Recreate a platform environment from a lockfile | Copies `uv.lock.` to `uv.lock`, creates a fresh `uv` virtual environment, installs platform-specific packages, then runs `uv sync --locked` | +| `make sync-` | Preferred way to create or refresh a local environment | Uses the checked-in platform lockfile to create or update `.venv-` | +| `sync_uv_env.sh` | Internal helper used by the Makefile sync targets | Applies `uv.lock.` and runs `uv sync --locked` for the selected platform | +| `update_uv_lock.sh` | Regenerate a platform-specific lockfile | Creates a fresh `uv` environment, resolves platform-specific dependencies, and writes the result to `uv.lock.` | -These scripts tie directly to the `uv` virtual environment workflow: +These commands map to the platform-specific environments and lockfiles below: | Platform | Virtual environment | Lockfile | |---|---|---| @@ -92,12 +94,11 @@ These scripts tie directly to the `uv` virtual environment workflow: In practice: -- run `./update_uv_lock.sh ` when dependencies change and a lockfile needs to be refreshed -- run `./sync_uv_env.sh ` when you want to create a local environment from the saved lockfile -- activate the created environment with `source .venv-/bin/activate` - --**Note:** `./update_uv_lock.sh` is for internal admin/support use only. Do not run it unless `pyproject.toml` has changed. When it does change, update and quick-test on all supported platforms, then push uv.lock. to the AMPL git repo.` +- Run `make sync-` to create or refresh your local environment. +- Activate the environment with `source .venv-/bin/activate`. +- Only run `./update_uv_lock.sh ` when `pyproject.toml` dependencies change and the corresponding lockfile must be regenerated. +> **Note:** `update_uv_lock.sh` is intended for internal system support use. Most users should use `make sync-` and should not need to run `sync_uv_env.sh` directly. ### Requirements @@ -128,18 +129,19 @@ cd AMPL ``` ## Create and activate an environment -Use the provided sync script for your target platform. +Use the Makefile to create or sync the environment for your target platform. -| Platform | Sync command | Environment | Activate command | +| Platform | Environment | Sync command | Activate command | |---|---|---|---| -| CPU | `./sync_uv_env.sh cpu` | `.venv-cpu` | `source .venv-cpu/bin/activate` | -| CUDA | `./sync_uv_env.sh cuda` | `.venv-cuda` | `source .venv-cuda/bin/activate` | -| ROCm | `./sync_uv_env.sh rocm` | `.venv-rocm` | `source .venv-rocm/bin/activate` | -| Apple Silicon / M chip | `./sync_uv_env.sh mchip` | `.venv-mchip` | `source .venv-mchip/bin/activate` | +| CPU | `.venv-cpu` | `make sync-cpu` | `source .venv-cpu/bin/activate` | +| CUDA | `.venv-cuda` | `make sync-cuda` | `source .venv-cuda/bin/activate` | +| ROCm | `.venv-rocm` | `make sync-rocm` | `source .venv-rocm/bin/activate` | +| Apple Silicon / M chip | `.venv-mchip` | `make sync-mchip` | `source .venv-mchip/bin/activate` | -After activating the environment, install AMPL in editable mode: +Example: ```bash -uv pip install -e . +make sync-cpu +source .venv-cpu/bin/activate ``` ## Platform-specific setup @@ -148,21 +150,10 @@ The following settings may be useful depending on your platform and runtime envi | Platform | Optional setup | Useful environment variables | |---|---|---| | CPU | none | `export OPENBLAS_NUM_THREADS=1` | -| CUDA | load site CUDA module if required | `module load cuda`
`export CUDA_HOME=/usr/local/cuda`
`export PATH="$CUDA_HOME/bin:$PATH"`
`export LD_LIBRARY_PATH="$CUDA_HOME/lib64:$LD_LIBRARY_PATH"`| -| ROCm | site-specific ROCm setup if required | `module load rocm`
`export ROCM_HOME="$(dirname "$(dirname "$(readlink -f "$(which hipcc)")")")"`
`export PATH="$ROCM_HOME/bin:$PATH"`| +| CUDA | load site CUDA module if required | `module load cuda`,
`export CUDA_HOME=/usr/local/cuda`,
`export PATH="$CUDA_HOME/bin:$PATH"`,
`export LD_LIBRARY_PATH="$CUDA_HOME/lib64:$LD_LIBRARY_PATH"` | +| ROCm | site-specific ROCm setup if required | `module load rocm`,
`export ROCM_HOME="$(dirname "$(dirname "$(readlink -f "$(which hipcc)")")")"`,
`export PATH="$ROCM_HOME/bin:$PATH"` | | Apple Silicon / M chip | none | usually none required | -## Update lockfiles - -If `pyproject.toml` dependencies are updated, regenerate the lockfile for the appropriate target platform. - -| Platform | Command | Lockfile | -|---|---|---| -| CPU | `./update_uv_lock.sh cpu` | `uv.lock.cpu` | -| CUDA | `./update_uv_lock.sh cuda` | `uv.lock.cuda` | -| ROCm | `./update_uv_lock.sh rocm` | `uv.lock.rocm` | -| Apple Silicon / M chip | `./update_uv_lock.sh mchip` | `uv.lock.mchip` | - ## Troubleshooting ### `uv` not found @@ -175,15 +166,15 @@ If needed, start a new shell session or update your `PATH`. ### Missing lockfile -If you see: +After `make sync-`, if you see: ```bash Missing lockfile: uv.lock. ``` -run: -```bash -./update_uv_lock.sh -``` -### Wrong Python, Pytest +the platform lockfile is not present in your checkout. Confirm that you are on the correct branch and that the lockfile has been committed. + +If the lockfile is genuinely missing, contact the maintainers or regenerate it only if you are updating dependencies. + +### Wrong Python/Pytest Check that Python 3.10 is being used: ```bash @@ -191,10 +182,11 @@ which python python --version which pytest ``` - -They should come from the virtual env, like '.venv-cpu/bin/python', '.venv-cpu/bin/pytest' - -If fails, refer to [Package import fails](#package-import-fails), use `uv sync --active --group dev --extra ` command shown there to get your VM sync up. +They should come from the virtual environment, for example: +```bash +.venv-cpu/bin/python +.venv-cpu/bin/pytest +``` ### Library not found after activation @@ -207,10 +199,7 @@ If needed, set: ```bash export LD_LIBRARY_PATH=$VIRTUAL_ENV/lib:$LD_LIBRARY_PATH ``` - -If fails, refer to [Package import fails](#package-import-fails), use `uv sync --active --group dev --extra ` command shown there to get your VM sync up. - -### Package import fails +### Package import fails or environment out of sync Try: ```bash @@ -218,16 +207,11 @@ python -c "import torch; print(torch.__version__)" python -c "import tensorflow as tf; print(tf.__version__)" python -c "import rdkit; print('rdkit ok')" ``` -If imports fail, rerun: +If imports fail, resync the environment: ```bash -./sync_uv_env.sh -``` - -If still not finding the packages, from your current .venv-, then run this: - -``` -uv sync --active --group dev --extra +make sync- +source .venv-/bin/activate ``` #### *(Optional) LLNL LC only*: if you use [model_tracker](https://ampl.readthedocs.io/en/latest/pipeline.html#module-pipeline.model_tracker), install atomsci.clients @@ -236,15 +220,6 @@ uv sync --active --group dev --extra pip install -r clients_requirements.txt ``` -### Install AMPL -Run the following to build the "atomsci" modules. This is required. - -```bash -# return to AMPL parent directory -cd .. -./build.sh -pip install -e . -``` --- ## Create jupyter notebook kernel (optional) To run AMPL from Jupyter Notebook. To setup a new kernel, first activate your environment and then run the following command: @@ -321,7 +296,6 @@ pip cache purge - Test set selection - Cross-validation - Uncertainty quantification -- Hyperparameter optimization ### 4. Supported models - scikit-learn random forest models From 1ce23dc9ce886744dd488f34c0e4f283c073c07d Mon Sep 17 00:00:00 2001 From: Amanda Paulson Date: Tue, 14 Apr 2026 14:02:35 -0700 Subject: [PATCH 13/37] update mchip specific tensorflow import --- pyproject.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 98c63415..30aa8c98 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -63,7 +63,7 @@ cpu = [ "torch==2.1.2", "torchdata==0.7.1", "tensorflow-cpu~=2.14.0; platform_system == 'Linux'", - "tensorflow~=2.14.0; platform_system == 'Darwin'", + "tensorflow-macos~=2.14.0; platform_system == 'Darwin'", "dgl==2.1.0", "dgllife==0.3.2", "torch-geometric==2.7.0", @@ -90,7 +90,7 @@ rocm = [ mchip = [ "torch==2.1.2", "torchdata==0.7.1", - "tensorflow~=2.14.0", + "tensorflow-macos~=2.14.0", "dgl==2.1.0", "dgllife==0.3.2", "torch-geometric==2.7.0", From bd01eac2df4152b5566c8713f49f5ddec94b0ddd Mon Sep 17 00:00:00 2001 From: Amanda Paulson Date: Tue, 14 Apr 2026 14:03:42 -0700 Subject: [PATCH 14/37] change VIRTUAL_ENV to UV_PROJECT_ENV to install packages in the right folder --- sync_uv_env.sh | 13 ++++++++----- update_uv_lock.sh | 8 ++++---- 2 files changed, 12 insertions(+), 9 deletions(-) diff --git a/sync_uv_env.sh b/sync_uv_env.sh index ce03720c..6564ff58 100755 --- a/sync_uv_env.sh +++ b/sync_uv_env.sh @@ -46,22 +46,22 @@ case "$platform" in uv pip install --python "$venv_dir/bin/python" \ --index-url https://download.pytorch.org/whl/cpu \ torch==2.1.2 torchdata==0.7.1 - VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra cpu --group dev --locked + UV_PROJECT_ENVIRONMENT="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra cpu --group dev --locked ;; cuda) uv pip install --python "$venv_dir/bin/python" \ --index-url https://download.pytorch.org/whl/cu121 \ torch==2.1.2 torchdata==0.7.1 - VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra cuda --group dev --locked + UV_PROJECT_ENVIRONMENT="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra cuda --group dev --locked ;; rocm) uv pip install --python "$venv_dir/bin/python" \ --index-url https://download.pytorch.org/whl/rocm5.6 \ torch==2.1.2 torchdata==0.7.1 - VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra rocm --group dev --locked + UV_PROJECT_ENVIRONMENT="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra rocm --group dev --locked ;; mchip) - VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra mchip --group dev --locked + UV_PROJECT_ENVIRONMENT="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra mchip --group dev --locked ;; *) echo "Invalid platform: $platform" @@ -69,4 +69,7 @@ case "$platform" in ;; esac -echo "Synced $venv_dir from $lockfile" +# Install AMPL in editable mode without re-resolving dependencies. +uv pip install --python "$venv_dir/bin/python" -e . --no-deps + +echo "Synced $venv_dir from $lockfile and installed AMPL editable (--no-deps)" diff --git a/update_uv_lock.sh b/update_uv_lock.sh index 71a63832..a435380d 100755 --- a/update_uv_lock.sh +++ b/update_uv_lock.sh @@ -42,22 +42,22 @@ case "$platform" in uv pip install --python "$venv_dir/bin/python" \ --index-url https://download.pytorch.org/whl/cpu \ torch==2.1.2 torchdata==0.7.1 - VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra cpu --group dev + UV_PROJECT_ENVIRONMENT="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra cpu --group dev ;; cuda) uv pip install --python "$venv_dir/bin/python" \ --index-url https://download.pytorch.org/whl/cu121 \ torch==2.1.2 torchdata==0.7.1 - VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra cuda --group dev + UV_PROJECT_ENVIRONMENT="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra cuda --group dev ;; rocm) uv pip install --python "$venv_dir/bin/python" \ --index-url https://download.pytorch.org/whl/rocm5.6 \ torch==2.1.2 torchdata==0.7.1 - VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra rocm --group dev + UV_PROJECT_ENVIRONMENT="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra rocm --group dev ;; mchip) - VIRTUAL_ENV="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra mchip --group dev + UV_PROJECT_ENVIRONMENT="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra mchip --group dev ;; *) echo "Invalid platform: $platform" From e8465c95ce047b5f5646b633340946e17440fe48 Mon Sep 17 00:00:00 2001 From: Amanda Paulson Date: Tue, 14 Apr 2026 14:04:03 -0700 Subject: [PATCH 15/37] lockfile for mchip --- uv.lock.mchip | 3577 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 3577 insertions(+) create mode 100644 uv.lock.mchip diff --git a/uv.lock.mchip b/uv.lock.mchip new file mode 100644 index 00000000..de66c2b1 --- /dev/null +++ b/uv.lock.mchip @@ -0,0 +1,3577 @@ +version = 1 +revision = 3 +requires-python = "==3.10.*" + +[[package]] +name = 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size = 1424879, upload-time = "2023-09-29T23:36:23.591Z" }, +] + [[package]] name = "termcolor" version = "3.3.0" diff --git a/uv.lock.cuda b/uv.lock.cuda index 4d0301f7..97415bc9 100644 --- a/uv.lock.cuda +++ b/uv.lock.cuda @@ -235,8 +235,8 @@ dependencies = [ cpu = [ { name = "dgl" }, { name = "dgllife" }, - { name = "tensorflow", marker = "sys_platform == 'darwin'" }, { name = "tensorflow-cpu", marker = "sys_platform == 'linux'" }, + { name = "tensorflow-macos", marker = "sys_platform == 'darwin'" }, { name = "torch" }, { name = "torch-geometric" }, { name = "torchdata" }, @@ -260,7 +260,7 @@ docs = [ mchip = [ { name = "dgl" }, { name = "dgllife" }, - { name = "tensorflow" }, + { name = "tensorflow-macos" }, { name = "torch" }, { name = "torch-geometric" }, { name = "torchdata" }, @@ -326,11 +326,11 @@ requires-dist = [ { name = "setuptools" }, { name = "sphinx", marker = "extra == 'docs'" }, { name = "sphinx-rtd-theme", marker = "extra == 'docs'" }, - { name = "tensorflow", marker 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"torch-geometric" }, { name = "torchdata" }, @@ -269,6 +288,9 @@ dev = [ { name = "pytest-xdist" }, { name = "ruff" }, ] +docker = [ + { name = "networkx" }, +] [package.metadata] requires-dist = [ @@ -285,6 +307,9 @@ requires-dist = [ { name = "dgllife", marker = "extra == 'rocm'", specifier = "==0.3.2" }, { name = "hyperopt" }, { name = "imbalanced-learn" }, + { name = "imblearn" }, + { name = "ipython", marker = "extra == 'docs'" }, + { name = "joblib", marker = "extra == 'docs'" }, { name = "lightgbm" }, { name = "lightning", specifier = "==2.2.5" }, { name = "maestrowf" }, @@ -292,19 +317,24 @@ requires-dist = [ { name = "matplotlib-venn" }, { name = "mordred" }, { name = "numpy", specifier = "<2" }, + { name = "pandas", marker = "extra == 'docs'" }, { name = "pyarrow" }, { name = "pydantic", specifier = ">=1.10,<2" }, + { name = "pygments", marker = "extra == 'docs'" }, { name = "pyyaml", specifier = ">=6.0" }, { name = "rdkit", specifier = "==2024.3.5" }, { name = 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+| Command | Purpose | When to use it | |---|---|---| -| `make sync-` | Preferred way to create or refresh a local environment | Uses the checked-in platform lockfile to create or update `.venv-` | -| `sync_uv_env.sh` | Internal helper used by the Makefile sync targets | Applies `uv.lock.` and runs `uv sync --locked` for the selected platform | -| `update_uv_lock.sh` | Regenerate a platform-specific lockfile | Creates a fresh `uv` environment, resolves platform-specific dependencies, and writes the result to `uv.lock.` | +| `./update_uv_lock.sh ` | Regenerate a platform-specific lockfile | Run when dependencies change, for example after editing `pyproject.toml` | +| `./sync_uv_env.sh ` | Create or rebuild a local platform environment from an existing platform lockfile | Run the first time you set up `.venv-`, or anytime you want a clean rebuild | +| `make sync-` | Sync an existing local environment | Run when `.venv-` already exists and you want to refresh it for local work | +| `source .venv-/bin/activate` | Activate the virtual environment in your shell | Run after the environment has been created or synced | These commands map to the platform-specific environments and lockfiles below: @@ -94,11 +95,12 @@ These commands map to the platform-specific environments and lockfiles below: In practice: -- Run `make sync-` to create or refresh your local environment. -- Activate the environment with `source .venv-/bin/activate`. -- Only run `./update_uv_lock.sh ` when `pyproject.toml` dependencies change and the corresponding lockfile must be regenerated. +- Run `./update_uv_lock.sh ` only when dependency definitions change and the platform lockfile must be regenerated. +- Run `./sync_uv_env.sh ` when creating a platform environment for the first time, or when rebuilding it from scratch. +- Run `make sync-` only for routine syncing of an existing local environment. +- Run `source .venv-/bin/activate` to use the environment in your shell. -> **Note:** `update_uv_lock.sh` is intended for internal system support use. Most users should use `make sync-` and should not need to run `sync_uv_env.sh` directly. +> **Note:** Most users should start with `./sync_uv_env.sh `. `update_uv_lock.sh` is mainly for maintainers updating lockfiles. ### Requirements @@ -129,16 +131,32 @@ cd AMPL ``` ## Create and activate an environment -Use the Makefile to create or sync the environment for your target platform. +Use `sync_uv_env.sh` to create or rebuild the environment for your target platform from the committed platform lockfile. -| Platform | Environment | Sync command | Activate command | +| Platform | Environment | Create or rebuild | Activate command | |---|---|---|---| -| CPU | `.venv-cpu` | `make sync-cpu` | `source .venv-cpu/bin/activate` | -| CUDA | `.venv-cuda` | `make sync-cuda` | `source .venv-cuda/bin/activate` | -| ROCm | `.venv-rocm` | `make sync-rocm` | `source .venv-rocm/bin/activate` | -| Apple Silicon / M chip | `.venv-mchip` | `make sync-mchip` | `source .venv-mchip/bin/activate` | +| CPU | `.venv-cpu` | `./sync_uv_env.sh cpu` | `source .venv-cpu/bin/activate` | +| CUDA | `.venv-cuda` | `./sync_uv_env.sh cuda` | `source .venv-cuda/bin/activate` | +| ROCm | `.venv-rocm` | `./sync_uv_env.sh rocm` | `source .venv-rocm/bin/activate` | +| Apple Silicon / M chip | `.venv-mchip` | `./sync_uv_env.sh mchip` | `source .venv-mchip/bin/activate` | -Example: +If you already have the environment and only want to refresh it, you may use: + +| Platform | Environment | Refresh command | +|---|---|---| +| CPU | `.venv-cpu` | `make sync-cpu` | +| CUDA | `.venv-cuda` | `make sync-cuda` | +| ROCm | `.venv-rocm` | `make sync-rocm` | +| Apple Silicon / M chip | `.venv-mchip` | `make sync-mchip` | + +Example, first-time setup: + +```bash +./sync_uv_env.sh cpu +source .venv-cpu/bin/activate +``` + +If `.venv-cpu` already exists and you only want to refresh it: ```bash make sync-cpu source .venv-cpu/bin/activate @@ -151,7 +169,7 @@ The following settings may be useful depending on your platform and runtime envi |---|---|---| | CPU | none | `export OPENBLAS_NUM_THREADS=1` | | CUDA | load site CUDA module if required | `module load cuda`,
`export CUDA_HOME=/usr/local/cuda`,
`export PATH="$CUDA_HOME/bin:$PATH"`,
`export LD_LIBRARY_PATH="$CUDA_HOME/lib64:$LD_LIBRARY_PATH"` | -| ROCm | site-specific ROCm setup if required | `module load rocm`,
`export ROCM_HOME="$(dirname "$(dirname "$(readlink -f "$(which hipcc)")")")"`,
`export PATH="$ROCM_HOME/bin:$PATH"` | +| ROCm | site-specific ROCm setup if required | `module load rocm`,
`export ROCM_HOME="$(dirname "$(dirname "$(readlink -f "$(which hipcc)")")")"`,
`export PATH="$ROCM_HOME/bin:$PATH"` | | Apple Silicon / M chip | none | usually none required | ## Troubleshooting @@ -166,7 +184,8 @@ If needed, start a new shell session or update your `PATH`. ### Missing lockfile -After `make sync-`, if you see: +After `uv sync`, if you see: + ```bash Missing lockfile: uv.lock. ``` @@ -187,7 +206,6 @@ They should come from the virtual environment, for example: .venv-cpu/bin/python .venv-cpu/bin/pytest ``` - ### Library not found after activation Confirm the correct environment is active: @@ -207,13 +225,26 @@ python -c "import torch; print(torch.__version__)" python -c "import tensorflow as tf; print(tf.__version__)" python -c "import rdkit; print('rdkit ok')" ``` - If imports fail, resync the environment: ```bash make sync- source .venv-/bin/activate ``` +--- +#### *(Optional) LLNL LC only*: if you use [model_tracker](https://ampl.readthedocs.io/en/latest/pipeline.html#module-pipeline.model_tracker), install `atomsci.clients` +```bash +# LLNL only: required for ATOM model_tracker +pip install -r clients_requirements.txt +``` +--- +## Create jupyter notebook kernel (optional) + +To run AMPL from Jupyter Notebook, first activate your environment and then run: +```bash +python -m ipykernel install --user --name atomsci-env +``` +--- #### *(Optional) LLNL LC only*: if you use [model_tracker](https://ampl.readthedocs.io/en/latest/pipeline.html#module-pipeline.model_tracker), install atomsci.clients ```bash # LLNL only: required for ATOM model_tracker From b301f12a50ef37bd29503d5fbb55f205c2a5ed7a Mon Sep 17 00:00:00 2001 From: Jessica Mauvais Date: Fri, 17 Apr 2026 09:20:31 -0700 Subject: [PATCH 19/37] deleted unused scripts since switched to uv --- build.sh | 16 ---------------- install.sh | 21 --------------------- install_dev.sh | 7 ------- setup.py | 29 ----------------------------- 4 files changed, 73 deletions(-) delete mode 100755 build.sh delete mode 100755 install.sh delete mode 100755 install_dev.sh delete mode 100644 setup.py diff --git a/build.sh b/build.sh deleted file mode 100755 index 97b990c0..00000000 --- a/build.sh +++ /dev/null @@ -1,16 +0,0 @@ -#!/bin/bash - -APP=ampl - -DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" -cd $DIR - -TOPDIR=`readlink -f .` - -BUILD_DIR=${TOPDIR}.build/$APP -DIST_DIR=${TOPDIR}.dist - -mkdir -p $DIST_DIR -mkdir -p $BUILD_DIR - -python3 setup.py build -b $BUILD_DIR egg_info --egg-base $BUILD_DIR bdist_wheel --dist-dir $DIST_DIR || exit 1 diff --git a/install.sh b/install.sh deleted file mode 100755 index 22d13b29..00000000 --- a/install.sh +++ /dev/null @@ -1,21 +0,0 @@ -#!/bin/bash - -PACKAGE=atomsci -APP=ampl - -INSTALL=--user -if [ "$1" = "system" ]; then - INSTALL= -fi - -DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" -echo "DIR: $DIR" -cd $DIR - -TOPDIR=`readlink -f .` - -DIST_DIR=${TOPDIR}.dist - -mkdir -p $DIST_DIR - -python3 -m pip install --pre --upgrade --no-index --find-links=$DIST_DIR --no-deps ${PACKAGE}_${APP} $INSTALL --force-reinstall -I -v || exit 1 diff --git a/install_dev.sh b/install_dev.sh deleted file mode 100755 index 3a0b8c32..00000000 --- a/install_dev.sh +++ /dev/null @@ -1,7 +0,0 @@ -#!/bin/bash - -DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" -cd $DIR - -pip install -e . --user - diff --git a/setup.py b/setup.py deleted file mode 100644 index efb6e9c9..00000000 --- a/setup.py +++ /dev/null @@ -1,29 +0,0 @@ -# -# setup.py -# - -from setuptools import setup, find_namespace_packages -import os -import glob - -PACKAGE = 'atomsci' - -here = os.path.abspath(os.path.dirname(__file__)) -parent_dir = os.path.abspath(os.path.join(here, os.pardir)) -script_files = glob.glob("scripts/*") - -setup( - name='{}-ampl'.format(PACKAGE), - # install_requires=['distribute'], - include_package_data=True, - version=open('VERSION').read().strip(), - description='{} AMPL Python Package'.format(PACKAGE), - zip_safe=False, - data_files=[], - packages=find_namespace_packages(include=['atomsci.*']), - scripts=script_files, - install_requires=[ - ], - entry_points={ - }, -) \ No newline at end of file From 0a715ee42bf0e4476c035717f17da2071e30c8b6 Mon Sep 17 00:00:00 2001 From: Jessica Mauvais Date: Fri, 17 Apr 2026 11:55:28 -0700 Subject: [PATCH 20/37] updated to include 'optuna' changes --- README.md | 6 +- pyproject.toml | 2 +- sync_uv_env.sh | 83 ++++++++++--------- update_uv_lock.sh | 80 +++++++++--------- uv.lock.cpu | 138 +++++++++++++++++++++++++------ uv.lock.cuda | 170 ++++++++++++++++++++++++++++++++------ uv.lock.rocm | 202 ++++++++++++++++++++++++++++++++++++++++------ 7 files changed, 527 insertions(+), 154 deletions(-) diff --git a/README.md b/README.md index 45246f90..2616a278 100644 --- a/README.md +++ b/README.md @@ -168,8 +168,8 @@ The following settings may be useful depending on your platform and runtime envi | Platform | Optional setup | Useful environment variables | |---|---|---| | CPU | none | `export OPENBLAS_NUM_THREADS=1` | -| CUDA | load site CUDA module if required | `module load cuda`,
`export CUDA_HOME=/usr/local/cuda`,
`export PATH="$CUDA_HOME/bin:$PATH"`,
`export LD_LIBRARY_PATH="$CUDA_HOME/lib64:$LD_LIBRARY_PATH"` | -| ROCm | site-specific ROCm setup if required | `module load rocm`,
`export ROCM_HOME="$(dirname "$(dirname "$(readlink -f "$(which hipcc)")")")"`,
`export PATH="$ROCM_HOME/bin:$PATH"` | +| CUDA | load site CUDA module if required | `module load cuda`
`export CUDA_HOME=/usr/local/cuda`
`export PATH="$CUDA_HOME/bin:$PATH"`
`export LD_LIBRARY_PATH="$CUDA_HOME/lib64:$LD_LIBRARY_PATH"` | +| ROCm | site-specific ROCm setup if required | `module load rocm`
`export ROCM_HOME="$(dirname "$(dirname "$(readlink -f "$(which hipcc)")")")"`
`export PATH="$ROCM_HOME/bin:$PATH"` | | Apple Silicon / M chip | none | usually none required | ## Troubleshooting @@ -337,7 +337,7 @@ pip cache purge ### 5. Visualization and analysis - Visualization and analysis tools -Details of running specific features are within the [parameter (options) documentation](#Pipeline-parameters). More detailed documentation is in the [library documentation](#Library-documentation). +Details of running specific features are within the [parameter (options) documentation](#pipeline-parameters). More detailed documentation is in the [library documentation](#library-documentation). --- ## Running AMPL diff --git a/pyproject.toml b/pyproject.toml index 561b3046..6f44b1c2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -10,7 +10,7 @@ dependencies = [ "numpy<2", "scipy>=1.10", "scikit-learn==1.2.2", - "hyperopt", + "optuna", "xgboost", "lightgbm", "umap-learn", diff --git a/sync_uv_env.sh b/sync_uv_env.sh index 6564ff58..7d4311bc 100755 --- a/sync_uv_env.sh +++ b/sync_uv_env.sh @@ -8,68 +8,71 @@ # Usage: # ./sync_uv_env.sh -set -euo pipefail +usage() { + echo "Usage: $0 " +} platform="${1:-}" +[[ -n "$platform" ]] || { usage; exit 1; } case "$platform" in - cpu|cuda|rocm|mchip) + cpu) + extra="cpu" + torch_index="https://download.pytorch.org/whl/cpu" + bootstrap_torch=true ;; - "") - echo "Usage: $0 " - exit 1 + cuda) + extra="cuda" + torch_index="https://download.pytorch.org/whl/cu121" + bootstrap_torch=true + ;; + rocm) + extra="rocm" + torch_index="https://download.pytorch.org/whl/rocm5.6" + bootstrap_torch=true + ;; + mchip) + extra="mchip" + torch_index="" + bootstrap_torch=false ;; *) echo "Invalid platform: $platform" - echo "Supported platforms: cpu cuda rocm mchip" - echo "Usage: $0 " + usage exit 1 ;; esac -lockfile="uv.lock.${platform}" venv_dir=".venv-${platform}" +lockfile="uv.lock.${platform}" +temp_lock="uv.lock" -if [[ ! -f "$lockfile" ]]; then +[[ -f "$lockfile" ]] || { echo "Missing lockfile: $lockfile" echo "Run ./update_uv_lock.sh $platform first" exit 1 -fi +} + +cleanup() { + rm -f "$temp_lock" +} +trap cleanup EXIT -cp "$lockfile" uv.lock +cp "$lockfile" "$temp_lock" rm -rf "$venv_dir" uv venv --python 3.10 "$venv_dir" -case "$platform" in - cpu) - uv pip install --python "$venv_dir/bin/python" \ - --index-url https://download.pytorch.org/whl/cpu \ - torch==2.1.2 torchdata==0.7.1 - UV_PROJECT_ENVIRONMENT="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra cpu --group dev --locked - ;; - cuda) - uv pip install --python "$venv_dir/bin/python" \ - --index-url https://download.pytorch.org/whl/cu121 \ - torch==2.1.2 torchdata==0.7.1 - UV_PROJECT_ENVIRONMENT="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra cuda --group dev --locked - ;; - rocm) - uv pip install --python "$venv_dir/bin/python" \ - --index-url https://download.pytorch.org/whl/rocm5.6 \ - torch==2.1.2 torchdata==0.7.1 - UV_PROJECT_ENVIRONMENT="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra rocm --group dev --locked - ;; - mchip) - UV_PROJECT_ENVIRONMENT="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra mchip --group dev --locked - ;; - *) - echo "Invalid platform: $platform" - exit 1 - ;; -esac +if [[ "$bootstrap_torch" == true ]]; then + uv pip install --python "$venv_dir/bin/python" \ + --index-url "$torch_index" \ + torch==2.1.2 torchdata==0.7.1 +fi + +UV_PROJECT_ENVIRONMENT="$venv_dir" \ + uv sync --python "$venv_dir/bin/python" --group dev --extra "$extra" --locked -# Install AMPL in editable mode without re-resolving dependencies. uv pip install --python "$venv_dir/bin/python" -e . --no-deps -echo "Synced $venv_dir from $lockfile and installed AMPL editable (--no-deps)" +echo "Refreshed $venv_dir from $lockfile" +echo "Activate with: source $venv_dir/bin/activate" \ No newline at end of file diff --git a/update_uv_lock.sh b/update_uv_lock.sh index a435380d..64ad9aa2 100755 --- a/update_uv_lock.sh +++ b/update_uv_lock.sh @@ -4,7 +4,7 @@ # regenerates uv.lock. # generates the righ lockfile for the specified platform # -# Use when: +# Use when: # dependencies changed, pyproject.toml changed, or lockfile mismatch happens. refresh the commited lockfile. # # Usage: @@ -13,57 +13,63 @@ set -euo pipefail platform="${1:-}" - -case "$platform" in - cpu|cuda|rocm|mchip) - ;; - "") - echo "Usage: $0 " - exit 1 - ;; - *) - echo "Invalid platform: $platform" - echo "Supported platforms: cpu cuda rocm mchip" - echo "Usage: $0 " - exit 1 - ;; -esac - -lockfile="uv.lock.${platform}" venv_dir=".venv-${platform}" +temp_lock="uv.lock" -rm -f uv.lock -rm -rf "$venv_dir" - -uv venv --python 3.10 "$venv_dir" +usage() { + echo "Usage: $0 " +} case "$platform" in cpu) - uv pip install --python "$venv_dir/bin/python" \ - --index-url https://download.pytorch.org/whl/cpu \ - torch==2.1.2 torchdata==0.7.1 - UV_PROJECT_ENVIRONMENT="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra cpu --group dev + extra="cpu" + torch_index="https://download.pytorch.org/whl/cpu" + bootstrap_torch="yes" ;; cuda) - uv pip install --python "$venv_dir/bin/python" \ - --index-url https://download.pytorch.org/whl/cu121 \ - torch==2.1.2 torchdata==0.7.1 - UV_PROJECT_ENVIRONMENT="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra cuda --group dev + extra="cuda" + torch_index="https://download.pytorch.org/whl/cu121" + bootstrap_torch="yes" ;; rocm) - uv pip install --python "$venv_dir/bin/python" \ - --index-url https://download.pytorch.org/whl/rocm5.6 \ - torch==2.1.2 torchdata==0.7.1 - UV_PROJECT_ENVIRONMENT="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra rocm --group dev + extra="rocm" + torch_index="https://download.pytorch.org/whl/rocm5.6" + bootstrap_torch="yes" ;; mchip) - UV_PROJECT_ENVIRONMENT="$venv_dir" uv sync --python "$venv_dir/bin/python" --extra mchip --group dev + extra="mchip" + torch_index="" + bootstrap_torch="no" + ;; + "") + usage + exit 1 ;; *) echo "Invalid platform: $platform" + usage exit 1 ;; esac -cp uv.lock "$lockfile" -echo "Updated $lockfile" +lockfile="uv.lock.${platform}" + +cleanup() { + rm -f "$temp_lock" +} +trap cleanup EXIT + +rm -rf "$venv_dir" +uv venv --python 3.10 "$venv_dir" + +if [[ "$bootstrap_torch" == "yes" ]]; then + uv pip install --python "$venv_dir/bin/python" \ + --index-url "$torch_index" \ + torch==2.1.2 torchdata==0.7.1 +fi + +UV_PROJECT_ENVIRONMENT="$venv_dir" \ + uv sync --python "$venv_dir/bin/python" --extra "$extra" --group dev + +cp "$temp_lock" "$lockfile" +echo 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a/Makefile +++ b/Makefile @@ -48,7 +48,7 @@ WORK_DIR ?= work .PHONY: sync-cpu sync-cuda sync-rocm sync-mchip test-cpu test-gpu test-rocm test-mchip \ build-docker install install-dev install-system install-venv jupyter-notebook jupyter-lab \ - pytest ruff ruff-fix setup uninstall uninstall-dev uninstall-system uninstall-venv + pytest ruff ruff-fix setup # Load Docker image load-docker: @@ -156,8 +156,6 @@ setup: $(VENV)/bin/pip install -r pip/dev_requirements.txt $(MAKE) install-venv -uninstall: uninstall-system - # for uv env sync-cpu: UV_PROJECT_ENVIRONMENT=.venv-cpu uv sync --group dev --extra cpu @@ -182,18 +180,3 @@ test-rocm: test-mchip: UV_PROJECT_ENVIRONMENT=.venv-mchip uv run pytest - -# Uninstall atomsci-ampl from user space -uninstall-dev: - @echo "Uninstalling atomsci-ampl for user" - $(PYTHON_BIN) -m pip uninstall atomsci-ampl --user --yes - -# Uninstall atomsci-ampl system-wide -uninstall-system: - @echo "Uninstalling atomsci-ampl from $(PYTHON_BIN)" - $(PYTHON_BIN) -m pip uninstall atomsci-ampl --yes - -# Uninstall atomsci-ampl from virtual environment -uninstall-venv: - @echo "Uninstalling atomsci-ampl from $(VENV)/" - $(VENV)/bin/python -m pip uninstall atomsci-ampl --yes diff --git a/Makefile.md b/Makefile.md index 73965288..6050d4cf 100644 --- a/Makefile.md +++ b/Makefile.md @@ -39,13 +39,6 @@ This Makefile is designed to manage Jupyter environments, Docker images, and the - `make save-docker`: Save the Docker image to a tarball (`ampl-$(PLATFORM)-$(ENV).tar.gz`). - `make build-docker`: Build the Docker image for the specified platform and environment. -- **Installation:** - - - `make install`: Install `atomsci-ampl` system-wide. - - `make install-dev`: Install `atomsci-ampl` in user space. - - `make install-system`: Install `atomsci-ampl` system-wide. - - `make install-venv`: Install `atomsci-ampl` in a virtual environment. - - **Jupyter Notebook and Lab:** - `make jupyter-notebook`: Start a Jupyter Notebook server. @@ -63,13 +56,6 @@ This Makefile is designed to manage Jupyter environments, Docker images, and the - `make shell`: Go inside the container's shell. -- **Setup and Uninstallation:** - - `make setup`: Set up a virtual environment and install dependencies. - - `make uninstall`: Uninstall `atomsci-ampl` system-wide. - - `make uninstall-dev`: Uninstall `atomsci-ampl` from user space. - - `make uninstall-system`: Uninstall `atomsci-ampl` system-wide. - - `make uninstall-venv`: Uninstall `atomsci-ampl` from the virtual environment. - ### **Usage Examples** #### **Managing Docker Images** @@ -108,10 +94,10 @@ make jupyter-lab #### **Setting Up the Development Environment** -To set up a virtual environment with the appropriate dependencies: +To set up a virtual environment with a specified platform: ```bash -make setup +make sync- ``` This Makefile provides a comprehensive approach to managing Docker images, running Jupyter servers, and handling the installation and setup of your development environment. It streamlines workflows, making it easier to maintain and develop the `atomsci-ampl` project. diff --git a/README.md b/README.md index 2616a278..d7ed0ca2 100644 --- a/README.md +++ b/README.md @@ -26,11 +26,13 @@ In addition to our written tutorials, we now provide a series of video tutorials --- ## Table of contents - [Installation](#installation) - - [What is `uv`?](#what-is-uv) - - [Repository helper scripts](#repository-helper-scripts) - - [Requirements](#requirements) - - [Install `uv`](#install-uv) - - [Clone the repository](#clone-the-repository) + - [Set up uv](#setup-uv) + - [What is `uv`?](#what-is-uv) + - [Repository helper scripts](#repository-helper-scripts) + - [Requirements](#requirements) + - [Install `uv`](#install-uv) + - [Install AMPL](#install-ampl) + - [Clone the repository](#clone-the-repository) - [Create and activate an environment](#create-and-activate-an-environment) - [Platform-specific setup](#platform-specific-setup) - [Troubleshooting](#troubleshooting) @@ -63,7 +65,9 @@ For installation on Apple Silicon M chips, see the Docker container instructions AMPL uses [`uv`](https://docs.astral.sh/uv/) for Python environment and dependency management. -### What is `uv`? +### Set up `uv` + +#### What is `uv`? `uv` is a fast Python tool used in this project to: @@ -73,7 +77,7 @@ AMPL uses [`uv`](https://docs.astral.sh/uv/) for Python environment and dependen | Sync dependencies from `pyproject.toml` | `uv sync` | | Install packages into the environment | `uv pip install` | -### Repository helper scripts +#### Repository helper scripts This repository includes helper commands for managing platform-specific `uv` environments and lockfiles. @@ -102,7 +106,7 @@ In practice: > **Note:** Most users should start with `./sync_uv_env.sh `. `update_uv_lock.sh` is mainly for maintainers updating lockfiles. -### Requirements +#### Requirements | Item | Requirement | |---|---| @@ -110,7 +114,7 @@ In practice: | Supported range | `>=3.10,<3.11` | | Platforms | `cpu`, `cuda`, `rocm`, `mchip` | -### Install `uv` +#### Install `uv` Install `uv` using one of the following methods: ```bash @@ -124,7 +128,24 @@ Verify installation: ```bash uv --version ``` -### Clone the repository + +### Install AMPL + +Since `1.8.0`, AMPL is publised to PyPI so users can install it directly without building it locally, improving accessibility, and supporting broader adoption through a trusted distribution channel. + +To install: + +```bash + python -m pip install atomsci-ampl +``` + +or + +```bash +python -m pip install --index-url https://pypi.org/simple atomsci-ampl +``` + +#### Clone the repository ```bash git clone https://github.com/ATOMScience-org/AMPL.git cd AMPL @@ -292,22 +313,11 @@ For additional options related to building, running, and other Docker developmen --- -## Uninstall -To remove AMPL from a pip environment use: -```bash -pip uninstall atomsci-ampl -``` - To remove an entire virtual environment named "atomsci-env": ```bash rm -rf $ENVROOT/atomsci-env ``` -To remove cached packages and clear space: -```bash -pip cache purge -``` - --- ## AMPL Features
AMPL enables tasks for modeling and prediction from data ingestion to data analysis and can be broken down into the following stages: diff --git a/atomsci/ddm/docs/source/advanced/advanced_installation.rst b/atomsci/ddm/docs/source/advanced/advanced_installation.rst index c802365a..aadab39c 100644 --- a/atomsci/ddm/docs/source/advanced/advanced_installation.rst +++ b/atomsci/ddm/docs/source/advanced/advanced_installation.rst @@ -9,15 +9,7 @@ Deployment * Red Hat Enterprise Linux 7 with SLURM * Ubuntu 16.04 - -Uninstallation --------------- -To remove AMPL from a pip environment use: -:: - deactivate - pip uninstall atomsci-ampl - To remove the atomsci pip environment entirely from a system use: :: diff --git a/atomsci/ddm/docs/source/get_started/install.rst b/atomsci/ddm/docs/source/get_started/install.rst index 0ab87c93..f372a1a6 100644 --- a/atomsci/ddm/docs/source/get_started/install.rst +++ b/atomsci/ddm/docs/source/get_started/install.rst @@ -10,32 +10,17 @@ Clone git repository:: git clone https://github.com/ATOMScience-org/AMPL.git -Please refer to this `install link `_, for details. -Create pip environment:: +Create a virtual environment:: - module load python/3.10.8 # use python 3.10.8 - python3 -m venv atomsci-env # create a new pip env - source atomsci-env/bin/activate # activate the environemt + module load python/3.10.8 # use python 3.10.8 + make sync- # for example sync-cpu + source .venv-/bin/activate # to activate your environment - python3 -m pip install pip --upgrade - cd $AMPL_HOME/pip # cd to AMPL repo's pip directory +To install AMPL python package:: - pip3 install --force-reinstall -r requirements.txt + python -m pip install --index-url https://pypi.org/simple atomsci-ampl .. note:: - Depending on system performance, creating the environment can take some time. - -Build and Install AMPL ----------------------- -Go to the AMPL root directory and install the `AMPL `_ package:: - - source atomsci-env/bin/activate # activate the environemt - cd .. - ./build.sh - pip3 install -e . - -* The `install.sh` system command installs AMPL directly in the pip environment. If `install.sh` alone is used, then AMPL is installed in the `$HOME/.local` directory. - -* After this process, you will have an `atomsci-env` pip environment with all dependencies installed. The name of the AMPL package is `atomsci-ampl` and is installed in the `install.sh` script to the environment with pip. + Depending on system performance, creating the environment can take some time. \ No newline at end of file diff --git a/atomsci/ddm/docs/source/get_started/introduction.rst b/atomsci/ddm/docs/source/get_started/introduction.rst index d9fc08a8..e47f0258 100644 --- a/atomsci/ddm/docs/source/get_started/introduction.rst +++ b/atomsci/ddm/docs/source/get_started/introduction.rst @@ -5,8 +5,20 @@ Introduction The ATOM Modeling PipeLine `AMPL `_ is a Python 3 package that has been developed and run in a specific pip environment. -There are two alternative paths for installing `AMPL `_: +There are two alternative paths for installing `AMPL `_: -1. Cloning the git repo, setting up the pip environment and running the AMPL install command. Please refer to `Installation `_. +1. Cloning the git repo, download from PyPI. Either -2. `Install With Docker `_. +.. code-block:: bash + + python -m pip install atomsci-ampl + + or + + .. code-block:: bash + + python -m pip install --index-url https://pypi.org/simple atomsci-ampl + + Please refer to `Installation `_. + +2. `Install With Docker `_. diff --git a/pyproject.toml b/pyproject.toml index 6f44b1c2..6fa603ba 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -108,8 +108,15 @@ pattern = "(?P\\d+\\.\\d+\\.\\d+.*)" [tool.hatch.build.targets.wheel] packages = ["atomsci"] +exclude = [ + "atomsci/ddm/examples/archive/**", # old tutorials +] + +[tool.hatch.build.targets.sdist] +exclude = [ + "atomsci/ddm/examples/archive/**", # old tutorials +] [tool.pytest.ini_options] testpaths = ["atomsci/ddm/test"] addopts = "-ra" - From 2f9405587734d89b3ee36a3f5447299c4c41a671 Mon Sep 17 00:00:00 2001 From: Jessica Mauvais Date: Wed, 22 Apr 2026 09:13:16 -0700 Subject: [PATCH 23/37] merged with 1.8.0. add more info in pyproject.toml --- pyproject.toml | 25 +++++++++++++++++++++++-- 1 file changed, 23 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 6fa603ba..8ec0505f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,9 +1,18 @@ [project] name = "atomsci-ampl" dynamic = ["version"] -description = "atomsci AMPL python package" +description = "ATOMSCI AMPL is an open-source Python package for molecular property prediction in drug discovery." +requires-python = ">=3.10" readme = "README.md" -requires-python = ">=3.10,<3.11" +license = "MIT" +license-files = ["LICENSE"] + +[project.urls] +Homepage = "https://atomscience.org/" +Documentation = "https://ampl.readthedocs.io/en/latest/" +Repository = "https://github.com/ATOMScience-org/AMPL" +Source = "https://github.com/ATOMScience-org/AMPL" + dependencies = [ "lightning==2.2.5", "pydantic>=1.10,<2", @@ -110,12 +119,24 @@ pattern = "(?P\\d+\\.\\d+\\.\\d+.*)" packages = ["atomsci"] exclude = [ "atomsci/ddm/examples/archive/**", # old tutorials + "**/*.tar.gz", + "**/*.ipynb", + "**/*.rst", ] +force-include = { + "atomsci/modac/examples/tutorials/01_modac_client_run_model.ipynb" = "atomsci/modac/examples/tutorials/01_modac_client_run_model.ipynb" +} [tool.hatch.build.targets.sdist] exclude = [ "atomsci/ddm/examples/archive/**", # old tutorials + "**/*.tar.gz", + "**/*.ipynb", + "**/*.rst", ] +force-include = { + "atomsci/modac/examples/tutorials/01_modac_client_run_model.ipynb" = "atomsci/modac/examples/tutorials/01_modac_client_run_model.ipynb" +} [tool.pytest.ini_options] testpaths = ["atomsci/ddm/test"] From 99896ae4fd6dce187dbb28199e25afbd3f941b11 Mon Sep 17 00:00:00 2001 From: Jessica Mauvais Date: Wed, 22 Apr 2026 09:19:37 -0700 Subject: [PATCH 24/37] fixed pyproject.tooml --- pyproject.toml | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 8ec0505f..d59912dd 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,13 +6,6 @@ requires-python = ">=3.10" readme = "README.md" license = "MIT" license-files = ["LICENSE"] - -[project.urls] -Homepage = "https://atomscience.org/" -Documentation = "https://ampl.readthedocs.io/en/latest/" -Repository = "https://github.com/ATOMScience-org/AMPL" -Source = "https://github.com/ATOMScience-org/AMPL" - dependencies = [ "lightning==2.2.5", "pydantic>=1.10,<2", @@ -39,6 +32,12 @@ dependencies = [ "setuptools", ] +[project.urls] +Homepage = "https://atomscience.org/" +Documentation = "https://ampl.readthedocs.io/en/latest/" +Repository = "https://github.com/ATOMScience-org/AMPL" +Source = "https://github.com/ATOMScience-org/AMPL" + # local developer tools [dependency-groups] dev = [ From 23ae055caedd4fce97f78708794f106a2d4269fc Mon Sep 17 00:00:00 2001 From: Jessica Mauvais Date: Wed, 22 Apr 2026 09:31:20 -0700 Subject: [PATCH 25/37] put '>=3.10,<3.11' back to avoid rebuild of all lock files --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index d59912dd..767b810c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -2,7 +2,7 @@ name = "atomsci-ampl" dynamic = ["version"] description = "ATOMSCI AMPL is an open-source Python package for molecular property prediction in drug discovery." -requires-python = ">=3.10" +requires-python = ">=3.10,<3.11" readme = "README.md" license = "MIT" license-files = ["LICENSE"] From 76a53187a05bcfdd0b9fd1cb9b8549eadc25f7da Mon Sep 17 00:00:00 2001 From: Jessica Mauvais Date: Wed, 22 Apr 2026 10:30:42 -0700 Subject: [PATCH 26/37] include new params in the test --- .../ddm/test/unit/test_parameter_parser_invalid_pred.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/atomsci/ddm/test/unit/test_parameter_parser_invalid_pred.py b/atomsci/ddm/test/unit/test_parameter_parser_invalid_pred.py index 9ea672c5..6f2c621a 100644 --- a/atomsci/ddm/test/unit/test_parameter_parser_invalid_pred.py +++ b/atomsci/ddm/test/unit/test_parameter_parser_invalid_pred.py @@ -47,6 +47,13 @@ def __contains__(self, item): id_col='compound_id', smiles_col='smiles', response_cols=['y'], + robustscaler_with_centering='none', + robustscaler_with_scaling='none', + robustscaler_quartile_range='none', + robustscaler_unit_variance='none', + powertransformer_standardize='none', + powertransformer_method='none', + imputer_strategy='none', feature_transform_type='none', response_transform_type='none', weight_transform_type='none', From 168e341e417af61b37fab6b1e0dc5019078da8ed Mon Sep 17 00:00:00 2001 From: Jessica Mauvais Date: Wed, 22 Apr 2026 11:06:18 -0700 Subject: [PATCH 27/37] moved the atom logo file and reformatted to work for pypi --- README.md | 5 +++-- assets/ATOM_cymatics_black_wordmark.jpg | Bin 0 -> 185636 bytes 2 files changed, 3 insertions(+), 2 deletions(-) create mode 100755 assets/ATOM_cymatics_black_wordmark.jpg diff --git a/README.md b/README.md index d7ed0ca2..759a5cce 100644 --- a/README.md +++ b/README.md @@ -10,8 +10,9 @@ An open-source, end-to-end software pipeline for data curation, model building, *Created by the [Accelerating Therapeutics for Opportunities in Medicine (ATOM) Consortium](https://atomscience.org)* - - +

+ AMPL logo +

The ATOM Modeling PipeLine (AMPL) extends the functionality of DeepChem and supports an array of machine learning and molecular featurization tools to predict key potency, safety and pharmacokinetic-relevant parameters. AMPL has been benchmarked on a large collection of pharmaceutical datasets covering a wide range of parameters. This is a living software project with active development. Check back for continued updates. Feedback is welcomed and appreciated, and the project is open to contributions! An [article describing the AMPL project](https://pubs.acs.org/doi/abs/10.1021/acs.jcim.9b01053) was published in JCIM. 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zGe>Pf@CJ3}LoT|KjTYvZ;|~ye;XJ7s3%+rz_fcvS?HK!Y1H+8K=b^ZpR%10I&5ZJesVxvWshNAZEcf9{^UoSN=iEH>~ecJR=~e4X`PHz{|h3zxv_V82Ei-;JX8bBFY9Cn|SEd z!h*wCgAZ4H2*!Jh6v`T`v?&AygbjKQ`t>TF6O#8OaFRBk##+-Lhr1yf1uQpqvz@Xh zouj5x7wO+T-cVmmNiM`u_DmkEjAEF0ZV1{|s1KAnd>$u47h!jv$-kT5>MFtDJZC9$ z@{#(5$n!dNX2R5q>1@UG;FX2z4VHj3oy23&&oQlFC^WJaF^SNSPg<3))@othv_mbS zaqr9F^Sxcjbiii{JQ#AOE8*)J*i56X`jlYfJ)Wf*gHV*dFLN&1|16?){vXF_#QR;0 zkB(LUHM#tnTz^(L@89;kngalFb%OdnyasK-7YOAP6%Ec&XP;}FL#VJ|Id#Fh1%S$Gepm`hh&xij&5f$^_-l#- zmvffW+y>sxgJXe3F zh6#$lmmT`A+WiN^{^wBOJKK)RNPvSNopxn;>=5FN_~-!XpQ#o2b?$$yMDJhs>+iZ> ze^5{=8YqGwwkW{*37v6 Date: Wed, 22 Apr 2026 14:47:04 -0700 Subject: [PATCH 28/37] updated readme, pyproject.toml --- README.md | 73 ++++++++++++++++++++++++-------------------------- pyproject.toml | 10 +++---- 2 files changed, 38 insertions(+), 45 deletions(-) diff --git a/README.md b/README.md index 759a5cce..583a9a4d 100644 --- a/README.md +++ b/README.md @@ -32,16 +32,16 @@ In addition to our written tutorials, we now provide a series of video tutorials - [Repository helper scripts](#repository-helper-scripts) - [Requirements](#requirements) - [Install `uv`](#install-uv) + - [Create and activate an environment](#create-and-activate-an-environment) + - [Platform-specific setup](#platform-specific-setup) + - [Troubleshooting](#troubleshooting) + - [`uv` not found](#uv-not-found) + - [Missing lockfile](#missing-lockfile) + - [Wrong Python/Pytest](#wrong-pythonpytest) + - [Library not found after activation](#library-not-found-after-activation) + - [Package import fails or environment out of sync](#package-import-fails-or-environment-out-of-sync) - [Install AMPL](#install-ampl) - [Clone the repository](#clone-the-repository) -- [Create and activate an environment](#create-and-activate-an-environment) -- [Platform-specific setup](#platform-specific-setup) -- [Troubleshooting](#troubleshooting) - - [`uv` not found](#uv-not-found) - - [Missing lockfile](#missing-lockfile) - - [Wrong Python/Pytest](#wrong-pythonpytest) - - [Library not found after activation](#library-not-found-after-activation) - - [Package import fails or environment out of sync](#package-import-fails-or-environment-out-of-sync) - [AMPL Features](#ampl-features) - [Running AMPL](#running-ampl) - [Tests](#tests) @@ -60,7 +60,7 @@ In addition to our written tutorials, we now provide a series of video tutorials ## Installation -AMPL 1.8 supports Python 3.10 on CPU systems and CUDA-enabled Linux systems using CUDA 11.8. All other systems are experimental. For a quick install summary, see [here](#install-summary). For more information, see [DeepChem](https://deepchem.readthedocs.io/en/latest/get_started/installation.html), [TensorFlow](https://www.tensorflow.org/install/pip), [PyTorch](https://pytorch.org/get-started/locally/), and [DGL](https://www.dgl.ai/pages/start.html). +AMPL 1.8 supports `Python 3.10` on CPU systems and CUDA-enabled Linux systems using CUDA 11.8. All other systems are experimental. For a quick install summary, see [here](#install-summary). For more information, see [DeepChem](https://deepchem.readthedocs.io/en/latest/get_started/installation.html), [TensorFlow](https://www.tensorflow.org/install/pip), [PyTorch](https://pytorch.org/get-started/locally/), and [DGL](https://www.dgl.ai/pages/start.html). For installation on Apple Silicon M chips, see the Docker container instructions. @@ -130,28 +130,7 @@ Verify installation: uv --version ``` -### Install AMPL - -Since `1.8.0`, AMPL is publised to PyPI so users can install it directly without building it locally, improving accessibility, and supporting broader adoption through a trusted distribution channel. - -To install: - -```bash - python -m pip install atomsci-ampl -``` - -or - -```bash -python -m pip install --index-url https://pypi.org/simple atomsci-ampl -``` - -#### Clone the repository -```bash -git clone https://github.com/ATOMScience-org/AMPL.git -cd AMPL -``` -## Create and activate an environment +#### Create and activate an environment Use `sync_uv_env.sh` to create or rebuild the environment for your target platform from the committed platform lockfile. @@ -183,7 +162,7 @@ If `.venv-cpu` already exists and you only want to refresh it: make sync-cpu source .venv-cpu/bin/activate ``` -## Platform-specific setup +#### Platform-specific setup The following settings may be useful depending on your platform and runtime environment. @@ -194,9 +173,9 @@ The following settings may be useful depending on your platform and runtime envi | ROCm | site-specific ROCm setup if required | `module load rocm`
`export ROCM_HOME="$(dirname "$(dirname "$(readlink -f "$(which hipcc)")")")"`
`export PATH="$ROCM_HOME/bin:$PATH"` | | Apple Silicon / M chip | none | usually none required | -## Troubleshooting +#### Troubleshooting -### `uv` not found +##### `uv` not found Install `uv`, then verify: ```bash @@ -204,7 +183,7 @@ uv --version ``` If needed, start a new shell session or update your `PATH`. -### Missing lockfile +##### Missing lockfile After `uv sync`, if you see: @@ -215,7 +194,7 @@ the platform lockfile is not present in your checkout. Confirm that you are on t If the lockfile is genuinely missing, contact the maintainers or regenerate it only if you are updating dependencies. -### Wrong Python/Pytest +##### Wrong Python/Pytest Check that Python 3.10 is being used: ```bash @@ -228,7 +207,7 @@ They should come from the virtual environment, for example: .venv-cpu/bin/python .venv-cpu/bin/pytest ``` -### Library not found after activation +##### Library not found after activation Confirm the correct environment is active: ```bash @@ -239,7 +218,7 @@ If needed, set: ```bash export LD_LIBRARY_PATH=$VIRTUAL_ENV/lib:$LD_LIBRARY_PATH ``` -### Package import fails or environment out of sync +##### Package import fails or environment out of sync Try: ```bash @@ -253,6 +232,24 @@ make sync- source .venv-/bin/activate ``` --- +### Install AMPL + +Since `1.8.0`, AMPL is publised to PyPI so users can install it directly without building it locally, improving accessibility, and supporting broader adoption through a trusted distribution channel. + +> **Note:** Please ensure `Python 3.10` is used or loaded for the package to run. For LLNL users on LC, run `module load python/3.10.8` to load the right version of python. + +To install: + +```bash + python -m pip install atomsci-ampl +``` + +#### Clone the repository +```bash +git clone https://github.com/ATOMScience-org/AMPL.git +cd AMPL +``` +--- #### *(Optional) LLNL LC only*: if you use [model_tracker](https://ampl.readthedocs.io/en/latest/pipeline.html#module-pipeline.model_tracker), install `atomsci.clients` ```bash # LLNL only: required for ATOM model_tracker diff --git a/pyproject.toml b/pyproject.toml index 767b810c..fdf570bf 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -33,7 +33,7 @@ dependencies = [ ] [project.urls] -Homepage = "https://atomscience.org/" +Homepage = "https://github.com/ATOMScience-org/AMPL" Documentation = "https://ampl.readthedocs.io/en/latest/" Repository = "https://github.com/ATOMScience-org/AMPL" Source = "https://github.com/ATOMScience-org/AMPL" @@ -118,24 +118,20 @@ pattern = "(?P\\d+\\.\\d+\\.\\d+.*)" packages = ["atomsci"] exclude = [ "atomsci/ddm/examples/archive/**", # old tutorials + "atomsci/ddm/test/test_datasets/**", # test datasets "**/*.tar.gz", "**/*.ipynb", "**/*.rst", ] -force-include = { - "atomsci/modac/examples/tutorials/01_modac_client_run_model.ipynb" = "atomsci/modac/examples/tutorials/01_modac_client_run_model.ipynb" -} [tool.hatch.build.targets.sdist] exclude = [ "atomsci/ddm/examples/archive/**", # old tutorials + "atomsci/ddm/test/test_datasets/**", # test datasets "**/*.tar.gz", "**/*.ipynb", "**/*.rst", ] -force-include = { - "atomsci/modac/examples/tutorials/01_modac_client_run_model.ipynb" = "atomsci/modac/examples/tutorials/01_modac_client_run_model.ipynb" -} [tool.pytest.ini_options] testpaths = ["atomsci/ddm/test"] From c542f883336923f1d1b12f53039f2d2e78774fa7 Mon Sep 17 00:00:00 2001 From: Jessica Mauvais Date: Wed, 22 Apr 2026 15:12:59 -0700 Subject: [PATCH 29/37] use relative path for the icon file for now. after push to master, change it to raw path for pypi to work. --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 583a9a4d..4433a8cb 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ An open-source, end-to-end software pipeline for data curation, model building, *Created by the [Accelerating Therapeutics for Opportunities in Medicine (ATOM) Consortium](https://atomscience.org)*

- AMPL logo + AMPL logo

The ATOM Modeling PipeLine (AMPL) extends the functionality of DeepChem and supports an array of machine learning and molecular featurization tools to predict key potency, safety and pharmacokinetic-relevant parameters. AMPL has been benchmarked on a large collection of pharmaceutical datasets covering a wide range of parameters. This is a living software project with active development. Check back for continued updates. Feedback is welcomed and appreciated, and the project is open to contributions! An [article describing the AMPL project](https://pubs.acs.org/doi/abs/10.1021/acs.jcim.9b01053) was published in JCIM. The AMPL pipeline documentation is available [here](https://ampl.readthedocs.io/en/latest/pipeline.html). From 338133e3de36adbc584ff71f684dbbd7852f08b6 Mon Sep 17 00:00:00 2001 From: Jessica Mauvais Date: Thu, 23 Apr 2026 09:41:55 -0700 Subject: [PATCH 30/37] brought files from prep-1.8.0. restored the build.sh, install*.sh and updated related docs on building locally --- .github/workflows/publish.yml | 108 ++++++++++++++++++ CONTRIBUTING.md | 14 ++- README.md | 39 +++++-- .../ddm/docs/source/get_started/install.rst | 59 ++++++++-- .../docs/source/get_started/introduction.rst | 21 ++-- build.sh | 16 +++ install.sh | 21 ++++ install_dev.sh | 7 ++ 8 files changed, 255 insertions(+), 30 deletions(-) create mode 100644 .github/workflows/publish.yml create mode 100755 build.sh create mode 100755 install.sh create mode 100755 install_dev.sh diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml new file mode 100644 index 00000000..1a2aef63 --- /dev/null +++ b/.github/workflows/publish.yml @@ -0,0 +1,108 @@ +name: Publish Python Package + +# publish atomsci-ampl to pypi +# +# Owner → ATOMScience-org +# Repository name → AMPL +# Project → atomsci-ampl +# +# The workflow: +# +# * build +# +# * For testing: +# +# manual run → TestPyPI only +# +# Note: For version name, once it's used, it can't be reused. For test version, try +# these naming convesions: +# +# dev release 1.2.3.dev1 +# +# * Tag push → TestPyPI then PyPI +# +# to trigger the tag push: +# +# git tag v1.0.0 +# git push origin v1.0.0 +# +on: + push: + tags: + - "v*" + workflow_dispatch: + +permissions: + contents: read + +jobs: + # Job 1: Build the distribution package + build: + name: Build package + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v4 + + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: "3.x" + + - name: Install uv + uses: astral-sh/setup-uv@v4 + + - name: Build sdist and wheel + run: uv build + + - name: Upload dist as artifact + uses: actions/upload-artifact@v4 + with: + name: dist + path: dist/ + retention-days: 7 + + # Job 2: Publish to TestPyPI first + publish-test: + name: Publish to TestPyPI + runs-on: ubuntu-latest + needs: build + if: (github.event_name == 'workflow_dispatch' && github.ref == 'refs/heads/main') || startsWith(github.ref, 'refs/tags/v') + environment: testpypi + + steps: + - name: Download dist artifact + uses: actions/download-artifact@v4 + with: + name: dist + path: dist/ + + - name: Publish to TestPyPI + uses: pypa/gh-action-pypi-publish@release/v1 + with: + repository-url: https://test.pypi.org/legacy/ + user: __token__ + password: ${{ secrets.TEST_PYPI_API_TOKEN }} # defined in environment `testpypi` + + # Job 3: Publish to real PyPI + # - requires manual approval if you set up + # a "pypi" environment with protection rules + publish-pypi: + name: Publish to PyPI + runs-on: ubuntu-latest + needs: publish-test + if: startsWith(github.ref, 'refs/tags/v') + environment: pypi + + steps: + - name: Download dist artifact + uses: actions/download-artifact@v4 + with: + name: dist + path: dist/ + + - name: Publish to PyPI + uses: pypa/gh-action-pypi-publish@release/v1 + with: + user: __token__ + password: ${{ secrets.PYPI_API_TOKEN }} # defined in environment `pypi` diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index e608b538..da95a870 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -50,7 +50,19 @@ git fetch upstream git rebase upstream/master ``` -2. Set up a new environment for AMPL by following these [instructions](https://github.com/ATOMScience-org/AMPL#install). +2. Set up a new environment for AMPL by following these [instructions](https://github.com/ATOMScience-org/AMPL#installation). + +This project uses [`uv`](https://docs.astral.sh/uv/) (a fast Python package and project manager) together with `pyproject.toml` and `uv.lock` for dependency management. + +### Prerequisites +- Install **uv** (recommended way): + ```bash + # On macOS / Linux + curl -LsSf https://astral.sh/uv/install.sh | sh + + # On Windows (PowerShell) + powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex" + ``` Keep in mind, every contribution must pass the unit tests. diff --git a/README.md b/README.md index 4433a8cb..4ef08303 100644 --- a/README.md +++ b/README.md @@ -41,7 +41,9 @@ In addition to our written tutorials, we now provide a series of video tutorials - [Library not found after activation](#library-not-found-after-activation) - [Package import fails or environment out of sync](#package-import-fails-or-environment-out-of-sync) - [Install AMPL](#install-ampl) - - [Clone the repository](#clone-the-repository) + - [Install from PyPI](#install-from-pypi) + - [Install from a local clone for development](#install-from-a-local-clone-for-development) + - [Build and install from a local clone](#build-and-install-from-a-local-clone) - [AMPL Features](#ampl-features) - [Running AMPL](#running-ampl) - [Tests](#tests) @@ -234,22 +236,41 @@ source .venv-/bin/activate --- ### Install AMPL -Since `1.8.0`, AMPL is publised to PyPI so users can install it directly without building it locally, improving accessibility, and supporting broader adoption through a trusted distribution channel. +Since `1.8.0`, AMPL is published to PyPI. Users can install it directly, without building it locally. -> **Note:** Please ensure `Python 3.10` is used or loaded for the package to run. For LLNL users on LC, run `module load python/3.10.8` to load the right version of python. +> **Note:** Please ensure `Python 3.10` is used or loaded for the package to run. For LLNL users on LC, run `module load python/3.10.8`. -To install: +#### Install from PyPI -```bash - python -m pip install atomsci-ampl +Install the published package directly from PyPI: + +``` +uv pip install atomsci-ampl ``` -#### Clone the repository -```bash +#### Install from a local clone for development + +If you want to develop AMPL locally, clone the repository and install it in editable mode: + +``` git clone https://github.com/ATOMScience-org/AMPL.git cd AMPL +./install-dev.sh ``` ---- + +This installs the package from the local source tree, so changes to the code are available without reinstalling. + +#### Build and install from a local clone + +If you want to build the package locally and then install the built artifact: + +``` +git clone https://github.com/ATOMScience-org/AMPL.git +cd AMPL +./build.sh +./install.sh +``` + #### *(Optional) LLNL LC only*: if you use [model_tracker](https://ampl.readthedocs.io/en/latest/pipeline.html#module-pipeline.model_tracker), install `atomsci.clients` ```bash # LLNL only: required for ATOM model_tracker diff --git a/atomsci/ddm/docs/source/get_started/install.rst b/atomsci/ddm/docs/source/get_started/install.rst index f372a1a6..f92c9e31 100644 --- a/atomsci/ddm/docs/source/get_started/install.rst +++ b/atomsci/ddm/docs/source/get_started/install.rst @@ -3,24 +3,61 @@ Installation ============ -Setup Repo, Pip Environment ---------------------------- +Python Environment +------------------ -Clone git repository:: +AMPL requires Python 3.10. + +For LLNL users on LC:: + + module load python/3.10.8 + +Create and activate a virtual environment:: + + make sync- # for example: make sync-cpu + source .venv-/bin/activate + +.. note:: + + Depending on system performance, creating the environment can take some time. + +Install AMPL from PyPI +---------------------- + +AMPL is published to PyPI, so most users can install it directly without cloning the repository or building it locally:: + + uv pip install atomsci-ampl + +This installs the released AMPL package into your active virtual environment. + +Install AMPL from a Local Clone +------------------------------- + +If you want to work from the source code, first clone the repository:: git clone https://github.com/ATOMScience-org/AMPL.git + cd AMPL +Then choose one of the following workflows. -Create a virtual environment:: +Development Install +~~~~~~~~~~~~~~~~~~~ - module load python/3.10.8 # use python 3.10.8 - make sync- # for example sync-cpu - source .venv-/bin/activate # to activate your environment +For local development, install AMPL from the source tree in editable mode:: -To install AMPL python package:: + ./install-dev.sh - python -m pip install --index-url https://pypi.org/simple atomsci-ampl +This is the recommended workflow for development. Changes to the local source code are picked up without reinstalling the package. -.. note:: +Build and Install Locally +~~~~~~~~~~~~~~~~~~~~~~~~~ + +If you want to build the package locally and install the built artifact:: + + ./build.sh + ./install.sh + +In this workflow: - Depending on system performance, creating the environment can take some time. \ No newline at end of file +* ``build.sh`` builds the package artifacts locally. +* ``install.sh`` installs the locally built package into the active environment. \ No newline at end of file diff --git a/atomsci/ddm/docs/source/get_started/introduction.rst b/atomsci/ddm/docs/source/get_started/introduction.rst index e47f0258..be3e06b4 100644 --- a/atomsci/ddm/docs/source/get_started/introduction.rst +++ b/atomsci/ddm/docs/source/get_started/introduction.rst @@ -3,22 +3,25 @@ Introduction ************ -The ATOM Modeling PipeLine `AMPL `_ is a Python 3 package that has been developed and run in a specific pip environment. +The ATOM Modeling PipeLine, `AMPL `_, is a Python 3 package. -There are two alternative paths for installing `AMPL `_: +There are two main ways to use `AMPL `_: -1. Cloning the git repo, download from PyPI. Either +1. Install the AMPL Python package from PyPI, or clone the Git repository for local development. -.. code-block:: bash + To install the released package from PyPI: - python -m pip install atomsci-ampl + .. code-block:: bash + + uv pip install atomsci-ampl - or + To work from a local source checkout instead: .. code-block:: bash - python -m pip install --index-url https://pypi.org/simple atomsci-ampl + git clone https://github.com/ATOMScience-org/AMPL.git + cd AMPL - Please refer to `Installation `_. + Please refer to `Installation `_. -2. `Install With Docker `_. +2. `Install With Docker `_. \ No newline at end of file diff --git a/build.sh b/build.sh new file mode 100755 index 00000000..3b55d23f --- /dev/null +++ b/build.sh @@ -0,0 +1,16 @@ +#!/bin/bash + +APP=ampl + +DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" +cd $DIR + +TOPDIR=`readlink -f .` + +BUILD_DIR=${TOPDIR}.build/$APP +DIST_DIR=${TOPDIR}.dist + +mkdir -p $DIST_DIR +mkdir -p $BUILD_DIR + +uv build --wheel --out-dir "$DIST_DIR" || exit 1 \ No newline at end of file diff --git a/install.sh b/install.sh new file mode 100755 index 00000000..b492cc4c --- /dev/null +++ b/install.sh @@ -0,0 +1,21 @@ +#!/bin/bash + +PACKAGE=atomsci +APP=ampl + +INSTALL=--user +if [ "$1" = "system" ]; then + INSTALL= +fi + +DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" +echo "DIR: $DIR" +cd $DIR + +TOPDIR=`readlink -f .` + +DIST_DIR=${TOPDIR}.dist + +mkdir -p $DIST_DIR + +uv pip install --pre --upgrade --no-index --find-links="$DIST_DIR" --no-deps ${PACKAGE}_${APP} --reinstall -v || exit 1 \ No newline at end of file diff --git a/install_dev.sh b/install_dev.sh new file mode 100755 index 00000000..51ffcf53 --- /dev/null +++ b/install_dev.sh @@ -0,0 +1,7 @@ +#!/bin/bash + +DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" +cd $DIR + +uv pip install -e . + From da8e0780009643980c950ff8fd1f55b3509ce6a8 Mon Sep 17 00:00:00 2001 From: Jessica Mauvais Date: Thu, 23 Apr 2026 16:43:57 -0700 Subject: [PATCH 31/37] updated README.md and makefile --- Makefile | 37 ++++---- README.md | 253 +++++++++++++++++++++++++----------------------------- 2 files changed, 138 insertions(+), 152 deletions(-) diff --git a/Makefile b/Makefile index e42157ce..cffca96a 100644 --- a/Makefile +++ b/Makefile @@ -46,7 +46,7 @@ VENV ?= atomsci-env # Work Directory WORK_DIR ?= work -.PHONY: sync-cpu sync-cuda sync-rocm sync-mchip test-cpu test-gpu test-rocm test-mchip \ +.PHONY: update-lock-cpu update-lock-cuda update-lock-rocm update-lock-mchip sync-cpu sync-cuda sync-rocm sync-mchip \ build-docker install install-dev install-system install-venv jupyter-notebook jupyter-lab \ pytest ruff ruff-fix setup @@ -157,26 +157,29 @@ setup: $(MAKE) install-venv # for uv env -sync-cpu: - UV_PROJECT_ENVIRONMENT=.venv-cpu uv sync --group dev --extra cpu -sync-cuda: - UV_PROJECT_ENVIRONMENT=.venv-cuda uv sync --group dev --extra cuda +# use these to create/update a lock env. for maintainers only +update-lock-cpu: + ./update_uv_lock.sh cpu -sync-rocm: - UV_PROJECT_ENVIRONMENT=.venv-rocm uv sync --group dev --extra rocm +update-lock-cuda: + ./update_uv_lock.sh cuda -sync-mchip: - UV_PROJECT_ENVIRONMENT=.venv-mchip uv sync --group dev --extra mchip +update-lock-rocm: + ./update_uv_lock.sh rocm -test-cpu: - UV_PROJECT_ENVIRONMENT=.venv-cpu uv run pytest +update-lock-mchip: + ./update_uv_lock.sh mchip -test-gpu: - UV_PROJECT_ENVIRONMENT=.venv-cuda uv run pytest +# use the matching lockfile to create or refresh .venv-. for general users +sync-cpu: + ./sync_uv_env.sh cpu -test-rocm: - UV_PROJECT_ENVIRONMENT=.venv-rocm uv run pytest +sync-cuda: + ./sync_uv_env.sh cuda + +sync-rocm: + ./sync_uv_env.sh rocm -test-mchip: - UV_PROJECT_ENVIRONMENT=.venv-mchip uv run pytest +sync-mchip: + ./sync_uv_env.sh mchip \ No newline at end of file diff --git a/README.md b/README.md index 4ef08303..430c5298 100644 --- a/README.md +++ b/README.md @@ -27,23 +27,23 @@ In addition to our written tutorials, we now provide a series of video tutorials --- ## Table of contents - [Installation](#installation) - - [Set up uv](#setup-uv) + - [Set up a local `uv` environment](#set-up-a-local-uv-environment) - [What is `uv`?](#what-is-uv) - - [Repository helper scripts](#repository-helper-scripts) - [Requirements](#requirements) - [Install `uv`](#install-uv) - - [Create and activate an environment](#create-and-activate-an-environment) - - [Platform-specific setup](#platform-specific-setup) + - [Choose your platform](#choose-your-platform) + - [Create or refresh your environment](#create-or-refresh-your-environment) + - [Daily use](#daily-use) + - [Platform lockfiles](#platform-lockfiles) + - [For maintainers only](#for-maintainers-only) - [Troubleshooting](#troubleshooting) - [`uv` not found](#uv-not-found) - - [Missing lockfile](#missing-lockfile) - - [Wrong Python/Pytest](#wrong-pythonpytest) - - [Library not found after activation](#library-not-found-after-activation) - - [Package import fails or environment out of sync](#package-import-fails-or-environment-out-of-sync) - - [Install AMPL](#install-ampl) - - [Install from PyPI](#install-from-pypi) - - [Install from a local clone for development](#install-from-a-local-clone-for-development) - - [Build and install from a local clone](#build-and-install-from-a-local-clone) + - [Wrong Python or missing `pytest`](#wrong-python-or-missing-pytest) + - [Import or package problems](#import-or-package-problems) + - [Install the published package from PyPI](#install-the-published-package-from-pypi) + - [Install from a local clone for development](#install-from-a-local-clone-for-development) + - [Build and install from a local clone](#build-and-install-from-a-local-clone) + - [Optional, LLNL LC only](#optional-llnl-lc-only) - [AMPL Features](#ampl-features) - [Running AMPL](#running-ampl) - [Tests](#tests) @@ -62,56 +62,27 @@ In addition to our written tutorials, we now provide a series of video tutorials ## Installation -AMPL 1.8 supports `Python 3.10` on CPU systems and CUDA-enabled Linux systems using CUDA 11.8. All other systems are experimental. For a quick install summary, see [here](#install-summary). For more information, see [DeepChem](https://deepchem.readthedocs.io/en/latest/get_started/installation.html), [TensorFlow](https://www.tensorflow.org/install/pip), [PyTorch](https://pytorch.org/get-started/locally/), and [DGL](https://www.dgl.ai/pages/start.html). +AMPL supports Python 3.10 and provides platform-specific environments for `cpu`, `cuda`, `rocm`, and `mchip`. -For installation on Apple Silicon M chips, see the Docker container instructions. +For dependency-specific installation details, see: +- [DeepChem](https://deepchem.readthedocs.io/en/latest/get_started/installation.html) +- [TensorFlow](https://www.tensorflow.org/install/pip) +- [PyTorch](https://pytorch.org/get-started/locally/) +- [DGL](https://www.dgl.ai/pages/start.html) AMPL uses [`uv`](https://docs.astral.sh/uv/) for Python environment and dependency management. -### Set up `uv` +### Set up a local `uv` environment -#### What is `uv`? - -`uv` is a fast Python tool used in this project to: - -| Use | Command | -|---|---| -| Create virtual environments | `uv venv` | -| Sync dependencies from `pyproject.toml` | `uv sync` | -| Install packages into the environment | `uv pip install` | - -#### Repository helper scripts - -This repository includes helper commands for managing platform-specific `uv` environments and lockfiles. - -| Command | Purpose | When to use it | -|---|---|---| -| `./update_uv_lock.sh ` | Regenerate a platform-specific lockfile | Run when dependencies change, for example after editing `pyproject.toml` | -| `./sync_uv_env.sh ` | Create or rebuild a local platform environment from an existing platform lockfile | Run the first time you set up `.venv-`, or anytime you want a clean rebuild | -| `make sync-` | Sync an existing local environment | Run when `.venv-` already exists and you want to refresh it for local work | -| `source .venv-/bin/activate` | Activate the virtual environment in your shell | Run after the environment has been created or synced | - -These commands map to the platform-specific environments and lockfiles below: +Use this workflow if you want to run or develop AMPL from a local clone of this repository. -| Platform | Virtual environment | Lockfile | -|---|---|---| -| CPU | `.venv-cpu` | `uv.lock.cpu` | -| CUDA | `.venv-cuda` | `uv.lock.cuda` | -| ROCm | `.venv-rocm` | `uv.lock.rocm` | -| Apple Silicon / M chip | `.venv-mchip` | `uv.lock.mchip` | - -In practice: - -- Run `./update_uv_lock.sh ` only when dependency definitions change and the platform lockfile must be regenerated. -- Run `./sync_uv_env.sh ` when creating a platform environment for the first time, or when rebuilding it from scratch. -- Run `make sync-` only for routine syncing of an existing local environment. -- Run `source .venv-/bin/activate` to use the environment in your shell. +#### What is `uv`? -> **Note:** Most users should start with `./sync_uv_env.sh `. `update_uv_lock.sh` is mainly for maintainers updating lockfiles. +`uv` is the Python environment and dependency tool used by this project. It creates virtual environments and installs the packages defined in `pyproject.toml`. #### Requirements -| Item | Requirement | +| Item | Value | |---|---| | Python | 3.10 | | Supported range | `>=3.10,<3.11` | @@ -119,7 +90,7 @@ In practice: #### Install `uv` -Install `uv` using one of the following methods: +Install `uv` with one of the following: ```bash curl -LsSf https://astral.sh/uv/install.sh | sh ``` @@ -127,155 +98,167 @@ or ```bash pip install uv ``` -Verify installation: +Verify the installation: ```bash uv --version ``` +#### Choose your platform -#### Create and activate an environment - -Use `sync_uv_env.sh` to create or rebuild the environment for your target platform from the committed platform lockfile. - -| Platform | Environment | Create or rebuild | Activate command | -|---|---|---|---| -| CPU | `.venv-cpu` | `./sync_uv_env.sh cpu` | `source .venv-cpu/bin/activate` | -| CUDA | `.venv-cuda` | `./sync_uv_env.sh cuda` | `source .venv-cuda/bin/activate` | -| ROCm | `.venv-rocm` | `./sync_uv_env.sh rocm` | `source .venv-rocm/bin/activate` | -| Apple Silicon / M chip | `.venv-mchip` | `./sync_uv_env.sh mchip` | `source .venv-mchip/bin/activate` | - -If you already have the environment and only want to refresh it, you may use: - -| Platform | Environment | Refresh command | +| Platform | Use this if... | Environment | |---|---|---| -| CPU | `.venv-cpu` | `make sync-cpu` | -| CUDA | `.venv-cuda` | `make sync-cuda` | -| ROCm | `.venv-rocm` | `make sync-rocm` | -| Apple Silicon / M chip | `.venv-mchip` | `make sync-mchip` | +| `cpu` | you want a CPU-only environment | `.venv-cpu` | +| `cuda` | you are using NVIDIA GPUs on Linux | `.venv-cuda` | +| `rocm` | you are using AMD GPUs | `.venv-rocm` | +| `mchip` | you are on Apple Silicon | `.venv-mchip` | -Example, first-time setup: +#### Create or refresh your environment +For most users, use the `make sync-` commands: +```bash +make sync-cpu +``` +Other options: +```bash +make sync-cuda +make sync-rocm +make sync-mchip +``` +Then activate the environment: ```bash -./sync_uv_env.sh cpu source .venv-cpu/bin/activate ``` +Replace `cpu` with your platform as needed. -If `.venv-cpu` already exists and you only want to refresh it: +Example: ```bash make sync-cpu source .venv-cpu/bin/activate ``` -#### Platform-specific setup +#### Daily use -The following settings may be useful depending on your platform and runtime environment. +If the environment is already working, you can usually just activate it: +```bash +source .venv-cpu/bin/activate +``` +If commands like `pytest` are missing, or imports fail, refresh the environment: +```bash +make sync-cpu +source .venv-cpu/bin/activate +``` +#### Platform lockfiles + +This project keeps one lockfile per platform: -| Platform | Optional setup | Useful environment variables | +| Platform | Lockfile | Environment | |---|---|---| -| CPU | none | `export OPENBLAS_NUM_THREADS=1` | -| CUDA | load site CUDA module if required | `module load cuda`
`export CUDA_HOME=/usr/local/cuda`
`export PATH="$CUDA_HOME/bin:$PATH"`
`export LD_LIBRARY_PATH="$CUDA_HOME/lib64:$LD_LIBRARY_PATH"` | -| ROCm | site-specific ROCm setup if required | `module load rocm`
`export ROCM_HOME="$(dirname "$(dirname "$(readlink -f "$(which hipcc)")")")"`
`export PATH="$ROCM_HOME/bin:$PATH"` | -| Apple Silicon / M chip | none | usually none required | +| `cpu` | `uv.lock.cpu` | `.venv-cpu` | +| `cuda` | `uv.lock.cuda` | `.venv-cuda` | +| `rocm` | `uv.lock.rocm` | `.venv-rocm` | +| `mchip` | `uv.lock.mchip` | `.venv-mchip` | -#### Troubleshooting +The `make sync-` commands use the matching lockfile to create or refresh `.venv-`. -##### `uv` not found +#### For maintainers only -Install `uv`, then verify: +If dependencies change, regenerate the platform lockfile with: ```bash -uv --version +make update-lock-cpu ``` -If needed, start a new shell session or update your `PATH`. +Other options: +```bash +make update-lock-cuda +make update-lock-rocm +make update-lock-mchip +``` +These commands create the lockfile if it does not exist yet, or update it if it already exists. + +Then commit: +- `pyproject.toml` +- updated `uv.lock.` files -##### Missing lockfile +Most users do not need to run `make update-lock-`. -After `uv sync`, if you see: +#### Troubleshooting +##### `uv` not found ```bash -Missing lockfile: uv.lock. +uv --version ``` -the platform lockfile is not present in your checkout. Confirm that you are on the correct branch and that the lockfile has been committed. +If this fails, install `uv` and start a new shell. -If the lockfile is genuinely missing, contact the maintainers or regenerate it only if you are updating dependencies. +##### Wrong Python or missing `pytest` -##### Wrong Python/Pytest - -Check that Python 3.10 is being used: +Check: ```bash which python python --version which pytest ``` -They should come from the virtual environment, for example: +They should point into the active environment, for example: ```bash .venv-cpu/bin/python .venv-cpu/bin/pytest ``` -##### Library not found after activation - -Confirm the correct environment is active: +If not, refresh the environment: ```bash -which python -echo $VIRTUAL_ENV -``` -If needed, set: -```bash -export LD_LIBRARY_PATH=$VIRTUAL_ENV/lib:$LD_LIBRARY_PATH +make sync-cpu +source .venv-cpu/bin/activate ``` -##### Package import fails or environment out of sync +##### Import or package problems -Try: -```bash -python -c "import torch; print(torch.__version__)" -python -c "import tensorflow as tf; print(tf.__version__)" -python -c "import rdkit; print('rdkit ok')" -``` -If imports fail, resync the environment: +Refresh the environment: ```bash -make sync- -source .venv-/bin/activate +make sync-cpu +source .venv-cpu/bin/activate ``` ---- -### Install AMPL +### Install the published package from PyPI -Since `1.8.0`, AMPL is published to PyPI. Users can install it directly, without building it locally. +Use this option if you want to install the released `atomsci-ampl` package without cloning this repository. -> **Note:** Please ensure `Python 3.10` is used or loaded for the package to run. For LLNL users on LC, run `module load python/3.10.8`. +If you are working from a local checkout of this repo, use the local `uv` environment workflow above instead. -#### Install from PyPI - -Install the published package directly from PyPI: +> **Note:** AMPL requires Python 3.10. For LLNL users on LC, run `module load python/3.10.8`. +Create or activate a Python 3.10 environment, then install: +```bash +uv pip install atomsci-ampl +``` +You can also use standard `pip`: +```bash +pip install atomsci-ampl ``` +Example: +```bash +uv venv --python 3.10 .venv +source .venv/bin/activate uv pip install atomsci-ampl ``` +### Install from a local clone for development -#### Install from a local clone for development - -If you want to develop AMPL locally, clone the repository and install it in editable mode: - -``` +If you want to develop AMPL locally from a repository checkout: +```bash git clone https://github.com/ATOMScience-org/AMPL.git cd AMPL ./install-dev.sh ``` +This installs the package from the local source tree, so code changes are available without reinstalling. -This installs the package from the local source tree, so changes to the code are available without reinstalling. - -#### Build and install from a local clone +### Build and install from a local clone If you want to build the package locally and then install the built artifact: - -``` +```bash git clone https://github.com/ATOMScience-org/AMPL.git cd AMPL ./build.sh ./install.sh ``` +### Optional, LLNL LC only -#### *(Optional) LLNL LC only*: if you use [model_tracker](https://ampl.readthedocs.io/en/latest/pipeline.html#module-pipeline.model_tracker), install `atomsci.clients` +If you use [model_tracker](https://ampl.readthedocs.io/en/latest/pipeline.html#module-pipeline.model_tracker), install `atomsci.clients`: ```bash -# LLNL only: required for ATOM model_tracker pip install -r clients_requirements.txt ``` + --- ## Create jupyter notebook kernel (optional) @@ -366,7 +349,7 @@ rm -rf $ENVROOT/atomsci-env ### 5. Visualization and analysis - Visualization and analysis tools
-Details of running specific features are within the [parameter (options) documentation](#pipeline-parameters). More detailed documentation is in the [library documentation](#library-documentation). +Details of running specific features are within the [parameter (options) documentation](atomsci/ddm/docs/PARAMETERS.md). More detailed documentation is in the [library documentation](https://ampl.readthedocs.io/en/latest/). --- ## Running AMPL From 5424a483518ffd4b673b68b781a905e740380115 Mon Sep 17 00:00:00 2001 From: Jessica Mauvais Date: Fri, 24 Apr 2026 12:33:54 -0700 Subject: [PATCH 32/37] updated publish.yml to manaul only --- .github/workflows/publish.yml | 85 ++++++++++++++++++++++------------- 1 file changed, 54 insertions(+), 31 deletions(-) diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index 1a2aef63..a4f90e24 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -1,48 +1,71 @@ name: Publish Python Package -# publish atomsci-ampl to pypi +# Publish atomsci-ampl to TestPyPI and PyPI # -# Owner → ATOMScience-org -# Repository name → AMPL -# Project → atomsci-ampl +# Owner -> ATOMScience-org +# Repository name -> AMPL +# Project -> atomsci-ampl # -# The workflow: +# This workflow is manual only. # -# * build -# -# * For testing: -# -# manual run → TestPyPI only +# Workflow behavior: # -# Note: For version name, once it's used, it can't be reused. For test version, try -# these naming convesions: +# 1. Build the package distribution +# 2. Optionally publish to TestPyPI +# 3. Optionally publish to PyPI # -# dev release 1.2.3.dev1 +# How to use: # -# * Tag push → TestPyPI then PyPI +# - Run this workflow manually from the GitHub Actions tab +# - Choose whether to publish to TestPyPI +# - Choose whether to publish to PyPI # -# to trigger the tag push: +# Notes: # -# git tag v1.0.0 -# git push origin v1.0.0 +# - Package versions cannot be reused once published +# - For TestPyPI testing, use development version names such as: # +# 1.2.3.dev1 +# +# - If you want PyPI publication to require approval, configure +# protection rules on the "pypi" environment +# +# Recommended usage: +# +# - TestPyPI only: +# publish_testpypi = true +# publish_pypi = false +# +# - TestPyPI and PyPI: +# publish_testpypi = true +# publish_pypi = true + on: - push: - tags: - - "v*" workflow_dispatch: + inputs: + publish_testpypi: + description: "Publish to TestPyPI" + required: true + type: boolean + default: true + publish_pypi: + description: "Publish to PyPI" + required: true + type: boolean + default: false permissions: contents: read jobs: - # Job 1: Build the distribution package + # Job 1: Build the source distribution and wheel build: name: Build package runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 + - name: Check out repository + uses: actions/checkout@v4 - name: Set up Python uses: actions/setup-python@v5 @@ -55,19 +78,19 @@ jobs: - name: Build sdist and wheel run: uv build - - name: Upload dist as artifact + - name: Upload dist artifact uses: actions/upload-artifact@v4 with: name: dist path: dist/ retention-days: 7 - # Job 2: Publish to TestPyPI first + # Job 2: Optionally publish to TestPyPI publish-test: name: Publish to TestPyPI runs-on: ubuntu-latest needs: build - if: (github.event_name == 'workflow_dispatch' && github.ref == 'refs/heads/main') || startsWith(github.ref, 'refs/tags/v') + if: ${{ inputs.publish_testpypi }} environment: testpypi steps: @@ -82,16 +105,16 @@ jobs: with: repository-url: https://test.pypi.org/legacy/ user: __token__ - password: ${{ secrets.TEST_PYPI_API_TOKEN }} # defined in environment `testpypi` + password: ${{ secrets.TEST_PYPI_API_TOKEN }} - # Job 3: Publish to real PyPI - # - requires manual approval if you set up - # a "pypi" environment with protection rules + # Job 3: Optionally publish to PyPI + # This runs only if PyPI publishing was selected. + # It also depends on the TestPyPI job, so TestPyPI must be selected too. publish-pypi: name: Publish to PyPI runs-on: ubuntu-latest needs: publish-test - if: startsWith(github.ref, 'refs/tags/v') + if: ${{ inputs.publish_testpypi && inputs.publish_pypi }} environment: pypi steps: @@ -105,4 +128,4 @@ jobs: uses: pypa/gh-action-pypi-publish@release/v1 with: user: __token__ - password: ${{ secrets.PYPI_API_TOKEN }} # defined in environment `pypi` + password: ${{ secrets.PYPI_API_TOKEN }} From a4a7111041c6c85eda44ae4f20d78e6584c5a5de Mon Sep 17 00:00:00 2001 From: stewarthe6 <40305524+stewarthe6@users.noreply.github.com> Date: Mon, 27 Apr 2026 09:24:23 -0700 Subject: [PATCH 33/37] Add installation instructions for atomsci-ampl Added instructions to install the latest release version from PyPI. --- README.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/README.md b/README.md index 430c5298..dfb538df 100644 --- a/README.md +++ b/README.md @@ -72,6 +72,11 @@ For dependency-specific installation details, see: AMPL uses [`uv`](https://docs.astral.sh/uv/) for Python environment and dependency management. +### Get the latest release version from PyPI +```bash +pip install atomsci-ampl +``` + ### Set up a local `uv` environment Use this workflow if you want to run or develop AMPL from a local clone of this repository. From 95b32999ae96b7b1e082e61be5ae08cfc8fb4cb7 Mon Sep 17 00:00:00 2001 From: Jessica Mauvais Date: Mon, 27 Apr 2026 13:23:45 -0700 Subject: [PATCH 34/37] 1) updated readme. rearranged the toc 2) added generate_transformers to docs --- README.md | 62 +++++++++++++++---------------- atomsci/ddm/docs/source/conf.py | 14 ++----- atomsci/ddm/docs/source/utils.rst | 8 ++++ 3 files changed, 43 insertions(+), 41 deletions(-) diff --git a/README.md b/README.md index dfb538df..b756a6a0 100644 --- a/README.md +++ b/README.md @@ -27,7 +27,9 @@ In addition to our written tutorials, we now provide a series of video tutorials --- ## Table of contents - [Installation](#installation) - - [Set up a local `uv` environment](#set-up-a-local-uv-environment) + - [Install the published package from PyPI](#install-the-published-package-from-pypi) + - [Get the latest release version from PyPI](#get-the-latest-release-version-from-pypi) + - [Set up an `uv` environment for development](#set-up-an-uv-environment-for-development) - [What is `uv`?](#what-is-uv) - [Requirements](#requirements) - [Install `uv`](#install-uv) @@ -40,10 +42,9 @@ In addition to our written tutorials, we now provide a series of video tutorials - [`uv` not found](#uv-not-found) - [Wrong Python or missing `pytest`](#wrong-python-or-missing-pytest) - [Import or package problems](#import-or-package-problems) - - [Install the published package from PyPI](#install-the-published-package-from-pypi) - - [Install from a local clone for development](#install-from-a-local-clone-for-development) - - [Build and install from a local clone](#build-and-install-from-a-local-clone) - - [Optional, LLNL LC only](#optional-llnl-lc-only) + - [Building AMPL for Local Development](#building-ampl-for-local-development) + - [Build and install from a local clone](#build-and-install-from-a-local-clone) + - [Optional, for LLNL LC only](#optional-for-llnl-lc-only) - [AMPL Features](#ampl-features) - [Running AMPL](#running-ampl) - [Tests](#tests) @@ -72,12 +73,33 @@ For dependency-specific installation details, see: AMPL uses [`uv`](https://docs.astral.sh/uv/) for Python environment and dependency management. +### Install the published package from PyPI + +Use this option if you want to install the released `atomsci-ampl` package without cloning this repository. + +If you are working from a local checkout of this repo, use the local `uv` environment workflow above instead. + +> **Note:** AMPL requires Python 3.10. For LLNL users on LC, run `module load python/3.10.8`. + ### Get the latest release version from PyPI + +Create or activate a Python 3.10 environment, then install: ```bash pip install atomsci-ampl ``` -### Set up a local `uv` environment +Or use `uv` install: + +Example: +```bash +uv venv --python 3.10 <_.venv_name> +source <_.venv_name>/bin/activate +uv pip install atomsci-ampl +``` + +--- + +### Set up an `uv` environment for local development Use this workflow if you want to run or develop AMPL from a local clone of this repository. @@ -216,29 +238,7 @@ Refresh the environment: make sync-cpu source .venv-cpu/bin/activate ``` -### Install the published package from PyPI - -Use this option if you want to install the released `atomsci-ampl` package without cloning this repository. - -If you are working from a local checkout of this repo, use the local `uv` environment workflow above instead. - -> **Note:** AMPL requires Python 3.10. For LLNL users on LC, run `module load python/3.10.8`. - -Create or activate a Python 3.10 environment, then install: -```bash -uv pip install atomsci-ampl -``` -You can also use standard `pip`: -```bash -pip install atomsci-ampl -``` -Example: -```bash -uv venv --python 3.10 .venv -source .venv/bin/activate -uv pip install atomsci-ampl -``` -### Install from a local clone for development +### Building AMPL for Local Development If you want to develop AMPL locally from a repository checkout: ```bash @@ -248,7 +248,7 @@ cd AMPL ``` This installs the package from the local source tree, so code changes are available without reinstalling. -### Build and install from a local clone +#### Build and install from a local clone If you want to build the package locally and then install the built artifact: ```bash @@ -257,7 +257,7 @@ cd AMPL ./build.sh ./install.sh ``` -### Optional, LLNL LC only +#### Optional, for LLNL LC only If you use [model_tracker](https://ampl.readthedocs.io/en/latest/pipeline.html#module-pipeline.model_tracker), install `atomsci.clients`: ```bash diff --git a/atomsci/ddm/docs/source/conf.py b/atomsci/ddm/docs/source/conf.py index 701ad34e..0045ed0b 100644 --- a/atomsci/ddm/docs/source/conf.py +++ b/atomsci/ddm/docs/source/conf.py @@ -23,7 +23,7 @@ project = 'ATOM Data-Driven Modeling Pipeline' author = 'ATOM DDM Team' - + #note: wait on this # import atomsci.ddm #version = atomsci.ddm.__version__ @@ -196,15 +196,9 @@ # -- Extension configuration ------------------------------------------------- autodoc_mock_imports = [ - "torch", - "torchdata", - "tensorflow", - "dgl", - "dgllife", - "torch_geometric", - "deepchem", - "rdkit", + "rdkit", "tensorflow.contrib", + "atomsci", "yaml", - "sklearn.preprocessing.Imputer", + "sklearn.preprocessing.Imputer" ] diff --git a/atomsci/ddm/docs/source/utils.rst b/atomsci/ddm/docs/source/utils.rst index 6ad9db91..d5d01353 100644 --- a/atomsci/ddm/docs/source/utils.rst +++ b/atomsci/ddm/docs/source/utils.rst @@ -36,6 +36,14 @@ utils.datastore\_functions module :undoc-members: :show-inheritance: +utils.generate\_transformers module +----------------------------------- + +.. automodule:: utils.generate_transformers + :members: + :undoc-members: + :show-inheritance: + utils.hyperparam\_search\_wrapper module ---------------------------------------- From 5e46ed528d7c27d3ecc2a1d3de8a0c88f528d26e Mon Sep 17 00:00:00 2001 From: Jessica Mauvais Date: Mon, 27 Apr 2026 14:27:18 -0700 Subject: [PATCH 35/37] changed the docker build to manual, added comments --- .github/workflows/build.yml | 45 ++++++++++++++++++++++++++++++++++--- Makefile | 2 +- 2 files changed, 43 insertions(+), 4 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 7987f0f9..f740d5f5 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -1,8 +1,34 @@ +# How to run manually: +# 1. Go to the GitHub repository. +# 2. Click the "Actions" tab. +# 3. Select this workflow, "docker publish". +# 4. Click "Run workflow". +# 5. Choose the desired inputs, then click "Run workflow". + name: docker publish on: - release: - types: [published] + workflow_dispatch: + inputs: + env: + description: "Deployment environment" + required: true + default: "prod" + type: choice + options: + - prod + - staging + target: + description: "Which image(s) to build" + required: true + default: "all" + type: choice + options: + - all + - gpu + - rocm + - cpu-amd64 + - cpu-arm64 jobs: build-and-push: @@ -11,14 +37,27 @@ jobs: fail-fast: false matrix: include: + # Uses Dockerfile.gpu - name: gpu platform: gpu + arch: "" + # Uses Dockerfile.rocm + - name: rocm + platform: rocm + arch: "" + # Uses Dockerfile.cpu - name: cpu-amd64 platform: cpu + arch: "" + # Uses Dockerfile.arm - name: cpu-arm64 platform: arm arch: linux/arm64 + if: | + github.event.inputs.target == 'all' || + github.event.inputs.target == matrix.name + steps: - name: Set up QEMU if: ${{ matrix.arch == 'linux/arm64' }} @@ -34,7 +73,7 @@ jobs: password: ${{ secrets.DOCKER_PASSWORD }} - name: Checkout code - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: fetch-depth: 1 diff --git a/Makefile b/Makefile index cffca96a..71be804a 100644 --- a/Makefile +++ b/Makefile @@ -68,7 +68,7 @@ save-docker: # Build Docker image build-docker: - @echo "Building Docker image for $(PLATFORM)" + @echo "Building Docker image for $(PLATFORM) " docker buildx build -t $(IMAGE_REPO):$(TAG) --build-arg ENV=$(ENV) $(PLATFORM_ARG) --load -f Dockerfile.$(PLATFORM) . install: install-system From 46a06fda6bb91dc2107c5a2ab05d4e75c1e08dd9 Mon Sep 17 00:00:00 2001 From: Jessica Mauvais Date: Mon, 27 Apr 2026 14:31:57 -0700 Subject: [PATCH 36/37] fixed syntax --- .github/workflows/build.yml | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index f740d5f5..ff978b62 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -54,10 +54,6 @@ jobs: platform: arm arch: linux/arm64 - if: | - github.event.inputs.target == 'all' || - github.event.inputs.target == matrix.name - steps: - name: Set up QEMU if: ${{ matrix.arch == 'linux/arm64' }} @@ -78,9 +74,9 @@ jobs: fetch-depth: 1 - name: Build and push Docker image - run: | - make push-docker + if: ${{ github.event.inputs.target == 'all' || github.event.inputs.target == matrix.name }} + run: make push-docker env: - ENV: prod + ENV: ${{ github.event.inputs.env }} PLATFORM: ${{ matrix.platform }} ARCH: ${{ matrix.arch }} From 0ee43341aa882a3544a9718591bc76beac61ea7f Mon Sep 17 00:00:00 2001 From: Jessica Mauvais Date: Mon, 27 Apr 2026 15:14:09 -0700 Subject: [PATCH 37/37] cleaned up readme --- README.md | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index b756a6a0..248928de 100644 --- a/README.md +++ b/README.md @@ -92,8 +92,8 @@ Or use `uv` install: Example: ```bash -uv venv --python 3.10 <_.venv_name> -source <_.venv_name>/bin/activate +uv venv --python 3.10 <.venv_name> +source <.venv_name>/bin/activate uv pip install atomsci-ampl ``` @@ -187,21 +187,22 @@ The `make sync-` commands use the matching lockfile to create or refre #### For maintainers only -If dependencies change, regenerate the platform lockfile with: +If dependencies change in `pyproject.toml`, you **must** regenerate the platform lockfile: + ```bash make update-lock-cpu ``` -Other options: + +Other supported targets: ```bash make update-lock-cuda make update-lock-rocm make update-lock-mchip ``` -These commands create the lockfile if it does not exist yet, or update it if it already exists. -Then commit: -- `pyproject.toml` -- updated `uv.lock.` files +These commands create the lockfile if it does not already exist, or update it if it does. + +**Any changes to `pyproject.toml` or `uv.lock.` must be committed and pushed to the AMPL GitHub repository. Do not leave regenerated lockfiles uncommitted.** Most users do not need to run `make update-lock-`.