From 69f4accf6470fda2b4e92f0164aae75e5959a10f Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 16:19:42 -0400 Subject: [PATCH 01/62] Add CI for windows and macos --- .github/workflows/CI.yaml | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml index 44b0824e..3f89a93e 100644 --- a/.github/workflows/CI.yaml +++ b/.github/workflows/CI.yaml @@ -15,6 +15,15 @@ jobs: matrix: python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"] runs-on: ["ubuntu-latest"] + include: + - os: "macos-latest" + python: "3.13" + - os: "windows-latest" + python: "3.13" + - os: "windows-latest" + python: "3.9" + - os: "macos-latest" + python: "3.9" # Pull in the test script from run_tests and distribute python from matrix versions uses: ./.github/workflows/run_tests.yaml with: @@ -28,7 +37,7 @@ jobs: fail-fast: false # Legacy versions are much less stable - run tests independently matrix: # Code works on py3.6, but type annotations are broken python-version: ["3.7", "3.8"] - runs-on: ["ubuntu-20.04"] + runs-on: ["ubuntu-20.04", "windows-latest", "macos-14"] uses: ./.github/workflows/run_tests.yaml with: python-version: ${{ matrix.python-version }} From 40f0b90c33998159e373698d4468eb0d60729597 Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 16:21:53 -0400 Subject: [PATCH 02/62] Fix variable names --- .github/workflows/CI.yaml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml index 3f89a93e..d5c2897d 100644 --- a/.github/workflows/CI.yaml +++ b/.github/workflows/CI.yaml @@ -16,14 +16,14 @@ jobs: python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"] runs-on: ["ubuntu-latest"] include: - - os: "macos-latest" - python: "3.13" - - os: "windows-latest" - python: "3.13" - - os: "windows-latest" - python: "3.9" - - os: "macos-latest" - python: "3.9" + - runs-on: "macos-latest" + python-version: "3.13" + - runs-on: "windows-latest" + python-version: "3.13" + - runs-on: "windows-latest" + python-version: "3.9" + - runs-on: "macos-latest" + python-version: "3.9" # Pull in the test script from run_tests and distribute python from matrix versions uses: ./.github/workflows/run_tests.yaml with: From 3b8d43a2b029492c23335d039d12f8b6e726e45d Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 16:30:17 -0400 Subject: [PATCH 03/62] Fix conflicting versions --- .github/workflows/CI.yaml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml index d5c2897d..9db37c8e 100644 --- a/.github/workflows/CI.yaml +++ b/.github/workflows/CI.yaml @@ -37,7 +37,10 @@ jobs: fail-fast: false # Legacy versions are much less stable - run tests independently matrix: # Code works on py3.6, but type annotations are broken python-version: ["3.7", "3.8"] - runs-on: ["ubuntu-20.04", "windows-latest", "macos-14"] + runs-on: ["ubuntu-20.04", "windows-latest"] + include: + - runs-on: "macos-14" + python-version: "3.8" uses: ./.github/workflows/run_tests.yaml with: python-version: ${{ matrix.python-version }} From cdade82884d6bd0d0caea85e69744c494e434109 Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 16:30:23 -0400 Subject: [PATCH 04/62] Update script to work on windows --- .github/workflows/run_tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 5db51c45..c9a0f9a2 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -25,7 +25,7 @@ jobs: version: "0.5.11" - name: Set up environment with dependencies run: | - uv venv && . .venv/bin/activate + uv venv && (source .venv/bin/activate || .venv\Scripts\activate.bat) echo PATH=$PATH >> $GITHUB_ENV - name: Install package run: | From 2c3f857c2b1a61835baba16222fa0584dc32884c Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 16:32:42 -0400 Subject: [PATCH 05/62] Fix activation script --- .github/workflows/run_tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index c9a0f9a2..da8feca8 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -25,7 +25,7 @@ jobs: version: "0.5.11" - name: Set up environment with dependencies run: | - uv venv && (source .venv/bin/activate || .venv\Scripts\activate.bat) + uv venv && . .venv/bin/activate 2> /dev/null || .venv\Scripts\activate echo PATH=$PATH >> $GITHUB_ENV - name: Install package run: | From f85e4060828c5b5f728901b8e0788f02a77fa188 Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 16:53:07 -0400 Subject: [PATCH 06/62] Test uv run --- .github/workflows/run_tests.yaml | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index da8feca8..b6231767 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -22,16 +22,15 @@ jobs: uses: astral-sh/setup-uv@v4 with: python-version: ${{ inputs.python-version }} - version: "0.5.11" - - name: Set up environment with dependencies - run: | - uv venv && . .venv/bin/activate 2> /dev/null || .venv\Scripts\activate - echo PATH=$PATH >> $GITHUB_ENV + version: "0.6.6" + - name: Install parsnip + run: uv sync --all-extras --dev + # - name: Set up environment with dependencies + # run: | + # uv venv && . .venv/bin/activate 2> /dev/null || .venv\Scripts\activate + # echo PATH=$PATH >> $GITHUB_ENV - name: Install package run: | - python --version uv pip install . -r ${{ inputs.requirements-file }} -v - python -c "import parsnip; print('parsnip', parsnip.__version__)" - name: Test with pytest - run: | - python -m pytest -v + run: uv run --verbose --no-sync pytest From 27fec1824b480244e5504ff9da26354984123a00 Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 16:54:26 -0400 Subject: [PATCH 07/62] Remove uv sync --- .github/workflows/run_tests.yaml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index b6231767..8fd11cdf 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -23,13 +23,11 @@ jobs: with: python-version: ${{ inputs.python-version }} version: "0.6.6" - - name: Install parsnip - run: uv sync --all-extras --dev # - name: Set up environment with dependencies # run: | # uv venv && . .venv/bin/activate 2> /dev/null || .venv\Scripts\activate # echo PATH=$PATH >> $GITHUB_ENV - - name: Install package + - name: Install parsnip run: | uv pip install . -r ${{ inputs.requirements-file }} -v - name: Test with pytest From 1b500cb382f59e61f50d0a14a447718d1ef4013a Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 17:06:31 -0400 Subject: [PATCH 08/62] Use pure uv run --- .github/workflows/run_tests.yaml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 8fd11cdf..1e64321b 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -27,8 +27,6 @@ jobs: # run: | # uv venv && . .venv/bin/activate 2> /dev/null || .venv\Scripts\activate # echo PATH=$PATH >> $GITHUB_ENV - - name: Install parsnip - run: | - uv pip install . -r ${{ inputs.requirements-file }} -v - name: Test with pytest - run: uv run --verbose --no-sync pytest + run: | + uv run -v --frozen --with-requirements ${{ inputs.requirements-file }} pytest From fd12a9b592aa603a03ac67987376c2ebecbf756b Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 19:54:17 -0400 Subject: [PATCH 09/62] Restore venv --- .github/workflows/run_tests.yaml | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 1e64321b..80822cfa 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -23,10 +23,15 @@ jobs: with: python-version: ${{ inputs.python-version }} version: "0.6.6" - # - name: Set up environment with dependencies - # run: | - # uv venv && . .venv/bin/activate 2> /dev/null || .venv\Scripts\activate - # echo PATH=$PATH >> $GITHUB_ENV + - name: Set up environment with dependencies + run: | + uv venv && . .venv/bin/activate 2> /dev/null || .venv\Scripts\activate + echo PATH=$PATH >> $GITHUB_ENV + - name: Install package + run: | + python --version + uv pip install . -r ${{ inputs.requirements-file }} -v + python -c "import parsnip; print('parsnip', parsnip.__version__)" - name: Test with pytest - run: | - uv run -v --frozen --with-requirements ${{ inputs.requirements-file }} pytest + run: | + python -m pytest -v From 6d30e60ee7f91620fd75f9cb5e7e5dc909da0aab Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 19:56:35 -0400 Subject: [PATCH 10/62] Swap order of conditions --- .github/workflows/run_tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 80822cfa..43a0ed4e 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -25,7 +25,7 @@ jobs: version: "0.6.6" - name: Set up environment with dependencies run: | - uv venv && . .venv/bin/activate 2> /dev/null || .venv\Scripts\activate + uv venv && . (.venv\Scripts\Activate || .venv/bin/activate) echo PATH=$PATH >> $GITHUB_ENV - name: Install package run: | From 55d5cb1eedd9ee6d3eea7172d596b717ec7a68be Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 19:57:40 -0400 Subject: [PATCH 11/62] Strip failed outputs --- .github/workflows/run_tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 43a0ed4e..49dcbcd4 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -25,7 +25,7 @@ jobs: version: "0.6.6" - name: Set up environment with dependencies run: | - uv venv && . (.venv\Scripts\Activate || .venv/bin/activate) + uv venv && . (.venv\Scripts\Activate 2> /dev/null || .venv/bin/activate) echo PATH=$PATH >> $GITHUB_ENV - name: Install package run: | From 9613791f4b81e105843ba609e9b925fe3d5b8478 Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 19:59:54 -0400 Subject: [PATCH 12/62] Test wildcard --- .github/workflows/run_tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 49dcbcd4..ab47e387 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -25,7 +25,7 @@ jobs: version: "0.6.6" - name: Set up environment with dependencies run: | - uv venv && . (.venv\Scripts\Activate 2> /dev/null || .venv/bin/activate) + uv venv && . .venv/*/activate echo PATH=$PATH >> $GITHUB_ENV - name: Install package run: | From 27683d722d58faa35ec1c8c59933dc42382d40a6 Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 20:03:44 -0400 Subject: [PATCH 13/62] Fix path seperator --- .github/workflows/run_tests.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index ab47e387..a2b12bdb 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -23,10 +23,10 @@ jobs: with: python-version: ${{ inputs.python-version }} version: "0.6.6" - - name: Set up environment with dependencies + - name: Set up uv venv run: | uv venv && . .venv/*/activate - echo PATH=$PATH >> $GITHUB_ENV + echo "PATH=$PATH" >> $GITHUB_ENV - name: Install package run: | python --version From 683ddcc3e68874e574afdfd45548e3d52f0e2ea5 Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 20:07:06 -0400 Subject: [PATCH 14/62] Swap to pip sync --- .github/workflows/run_tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index a2b12bdb..38facf3a 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -30,7 +30,7 @@ jobs: - name: Install package run: | python --version - uv pip install . -r ${{ inputs.requirements-file }} -v + uv pip sync ${{ inputs.requirements-file }} --only-binary=:all: --reinstall python -c "import parsnip; print('parsnip', parsnip.__version__)" - name: Test with pytest run: | From 2d2bd8a0df5284f12cd14168525fd374584833f6 Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 20:08:36 -0400 Subject: [PATCH 15/62] Remove only-binary --- .github/workflows/run_tests.yaml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 38facf3a..5031dd97 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -30,8 +30,7 @@ jobs: - name: Install package run: | python --version - uv pip sync ${{ inputs.requirements-file }} --only-binary=:all: --reinstall + uv pip sync ${{ inputs.requirements-file }} --only-binary=:none: --reinstall python -c "import parsnip; print('parsnip', parsnip.__version__)" - name: Test with pytest - run: | - python -m pytest -v + run: python -m pytest -v From 13c4d4cdec2eaae6fe838e44da7fc1a3c74a5da1 Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 20:15:36 -0400 Subject: [PATCH 16/62] Test print numpy --- .github/workflows/run_tests.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 5031dd97..05397aaa 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -32,5 +32,6 @@ jobs: python --version uv pip sync ${{ inputs.requirements-file }} --only-binary=:none: --reinstall python -c "import parsnip; print('parsnip', parsnip.__version__)" + python -c "import numpy; print('numpy', numpy.__version__)" - name: Test with pytest run: python -m pytest -v From 741e9b36899a6026f21f9563508478ae53ba4649 Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 20:17:59 -0400 Subject: [PATCH 17/62] Remove path modification --- .github/workflows/run_tests.yaml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 05397aaa..48224755 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -24,9 +24,7 @@ jobs: python-version: ${{ inputs.python-version }} version: "0.6.6" - name: Set up uv venv - run: | - uv venv && . .venv/*/activate - echo "PATH=$PATH" >> $GITHUB_ENV + run: uv venv && . .venv/*/activate - name: Install package run: | python --version From bacc15be38f523f5c06db53bd6267d79c3caad6e Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 20:19:07 -0400 Subject: [PATCH 18/62] Confirm path is issue --- .github/workflows/run_tests.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 48224755..05397aaa 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -24,7 +24,9 @@ jobs: python-version: ${{ inputs.python-version }} version: "0.6.6" - name: Set up uv venv - run: uv venv && . .venv/*/activate + run: | + uv venv && . .venv/*/activate + echo "PATH=$PATH" >> $GITHUB_ENV - name: Install package run: | python --version From 43865a24251e589d5755e29b327864805df0d1cd Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 20:28:07 -0400 Subject: [PATCH 19/62] Swap to explicit ternary --- .github/workflows/run_tests.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 05397aaa..d749b1b3 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -26,6 +26,7 @@ jobs: - name: Set up uv venv run: | uv venv && . .venv/*/activate + [ $RUNNER_OS == 'Windows' ] && .\\venv\\Scripts\\activate || . .venv/bin/activate echo "PATH=$PATH" >> $GITHUB_ENV - name: Install package run: | From 336d5f149cdd84b103cab9662d493caf7bf1e1b6 Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 20:30:21 -0400 Subject: [PATCH 20/62] Use explicit if-else --- .github/workflows/run_tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index d749b1b3..5a8521e7 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -26,7 +26,7 @@ jobs: - name: Set up uv venv run: | uv venv && . .venv/*/activate - [ $RUNNER_OS == 'Windows' ] && .\\venv\\Scripts\\activate || . .venv/bin/activate + if [ $RUNNER_OS != 'Windows' ]; then source venv/bin/activate; else .\\venv\\Scripts\\activate; fi echo "PATH=$PATH" >> $GITHUB_ENV - name: Install package run: | From 6f3cc0668dfb1a16a0b901b698ee883fb82bd34e Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 20:31:08 -0400 Subject: [PATCH 21/62] Fix typo --- .github/workflows/run_tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 5a8521e7..4eef481b 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -26,7 +26,7 @@ jobs: - name: Set up uv venv run: | uv venv && . .venv/*/activate - if [ $RUNNER_OS != 'Windows' ]; then source venv/bin/activate; else .\\venv\\Scripts\\activate; fi + if [ $RUNNER_OS != 'Windows' ]; then . .venv/bin/activate; else .\\venv\\Scripts\\activate; fi echo "PATH=$PATH" >> $GITHUB_ENV - name: Install package run: | From 7b322bbe58f65621c0f9a1e8f878955d22a1a66b Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 20:32:49 -0400 Subject: [PATCH 22/62] Use bash on windows --- .github/workflows/run_tests.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 4eef481b..8494c5af 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -28,6 +28,7 @@ jobs: uv venv && . .venv/*/activate if [ $RUNNER_OS != 'Windows' ]; then . .venv/bin/activate; else .\\venv\\Scripts\\activate; fi echo "PATH=$PATH" >> $GITHUB_ENV + shell: bash - name: Install package run: | python --version From 1698a10fc8767d9dbd0566d2d609ae47be8690f5 Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 20:34:02 -0400 Subject: [PATCH 23/62] Remove duplicate --- .github/workflows/run_tests.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 8494c5af..dbefc1bd 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -25,8 +25,8 @@ jobs: version: "0.6.6" - name: Set up uv venv run: | - uv venv && . .venv/*/activate - if [ $RUNNER_OS != 'Windows' ]; then . .venv/bin/activate; else .\\venv\\Scripts\\activate; fi + uv venv && . .venv/bin/activate + # if [ $RUNNER_OS != 'Windows' ]; then . .venv/bin/activate; else .\\venv\\Scripts\\activate; fi echo "PATH=$PATH" >> $GITHUB_ENV shell: bash - name: Install package From cb957145e5a3f5b981563fbfc66c01a3fd6f5bd6 Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 20:36:54 -0400 Subject: [PATCH 24/62] Alternate if --- .github/workflows/run_tests.yaml | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index dbefc1bd..f5f8acd1 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -25,8 +25,12 @@ jobs: version: "0.6.6" - name: Set up uv venv run: | - uv venv && . .venv/bin/activate - # if [ $RUNNER_OS != 'Windows' ]; then . .venv/bin/activate; else .\\venv\\Scripts\\activate; fi + uv venv + if [ ${{ runner.os }} == 'Windows' ]; then + .\venv\Scripts\activate + else + . .venv/bin/activate + fi echo "PATH=$PATH" >> $GITHUB_ENV shell: bash - name: Install package From 3d6f830f000bfca8a42ddeb29d2189afdfce1137 Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 20:37:53 -0400 Subject: [PATCH 25/62] Disable ubuntu --- .github/workflows/CI.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml index 9db37c8e..f50dc676 100644 --- a/.github/workflows/CI.yaml +++ b/.github/workflows/CI.yaml @@ -13,8 +13,8 @@ jobs: strategy: fail-fast: true matrix: - python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"] - runs-on: ["ubuntu-latest"] + # python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"] + # runs-on: ["ubuntu-latest"] include: - runs-on: "macos-latest" python-version: "3.13" From 3ae64cfe267d1f76180b6f996d53a55e2a6d279c Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 20:37:57 -0400 Subject: [PATCH 26/62] remove bash shell on windows --- .github/workflows/run_tests.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index f5f8acd1..bf847d3b 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -32,7 +32,6 @@ jobs: . .venv/bin/activate fi echo "PATH=$PATH" >> $GITHUB_ENV - shell: bash - name: Install package run: | python --version From cc4f1e92919a21d40af3e36b011b9777f1a95f7d Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 20:41:24 -0400 Subject: [PATCH 27/62] Fix condition --- .github/workflows/run_tests.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index bf847d3b..2bbfa031 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -26,10 +26,10 @@ jobs: - name: Set up uv venv run: | uv venv - if [ ${{ runner.os }} == 'Windows' ]; then - .\venv\Scripts\activate + if [ "$RUNNER_OS" == "Windows" ]; then + .\venv\Scripts\activate else - . .venv/bin/activate + . .venv/bin/activate fi echo "PATH=$PATH" >> $GITHUB_ENV - name: Install package From 665b331fe8f6d3fd307fd43e7c9c462256014df6 Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 21:07:04 -0400 Subject: [PATCH 28/62] Use seperate steps for windows --- .github/workflows/run_tests.yaml | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 2bbfa031..6fe0dcdd 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -24,14 +24,13 @@ jobs: python-version: ${{ inputs.python-version }} version: "0.6.6" - name: Set up uv venv - run: | - uv venv - if [ "$RUNNER_OS" == "Windows" ]; then - .\venv\Scripts\activate - else - . .venv/bin/activate - fi - echo "PATH=$PATH" >> $GITHUB_ENV + run: uv venv + - name: Activate environment (Windows) + if: $RUNNER_OS == "Windows" + run: .\venv\Scripts\activate && echo "PATH=$PATH" >> $GITHUB_ENV + - name: Activate environment (Unix) + if: $RUNNER_OS != "Windows" + run: . .venv/bin/activate && echo "PATH=$PATH" >> $GITHUB_ENV - name: Install package run: | python --version From faa3aa75ede65007e0400745298477760693549f Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 21:12:29 -0400 Subject: [PATCH 29/62] Fix syntax --- .github/workflows/run_tests.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 6fe0dcdd..04656a0c 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -26,10 +26,10 @@ jobs: - name: Set up uv venv run: uv venv - name: Activate environment (Windows) - if: $RUNNER_OS == "Windows" + if: runner.os == "Windows" run: .\venv\Scripts\activate && echo "PATH=$PATH" >> $GITHUB_ENV - name: Activate environment (Unix) - if: $RUNNER_OS != "Windows" + if: runner.os != "Windows" run: . .venv/bin/activate && echo "PATH=$PATH" >> $GITHUB_ENV - name: Install package run: | From 64f0aa3731390e4f8ae1210344f4466c93f91e17 Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 21:13:36 -0400 Subject: [PATCH 30/62] Swap to single quotes --- .github/workflows/run_tests.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 04656a0c..1069d1be 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -26,10 +26,10 @@ jobs: - name: Set up uv venv run: uv venv - name: Activate environment (Windows) - if: runner.os == "Windows" + if: runner.os == 'Windows' run: .\venv\Scripts\activate && echo "PATH=$PATH" >> $GITHUB_ENV - name: Activate environment (Unix) - if: runner.os != "Windows" + if: runner.os != 'Windows' run: . .venv/bin/activate && echo "PATH=$PATH" >> $GITHUB_ENV - name: Install package run: | From 07b32286db0a0fe68a46a186a685a58532c5425e Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 21:15:25 -0400 Subject: [PATCH 31/62] Fix typo --- .github/workflows/run_tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 1069d1be..eb3b4221 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -27,7 +27,7 @@ jobs: run: uv venv - name: Activate environment (Windows) if: runner.os == 'Windows' - run: .\venv\Scripts\activate && echo "PATH=$PATH" >> $GITHUB_ENV + run: .venv\Scripts\activate && echo "PATH=$PATH" >> $GITHUB_ENV - name: Activate environment (Unix) if: runner.os != 'Windows' run: . .venv/bin/activate && echo "PATH=$PATH" >> $GITHUB_ENV From 0aa303ddd1e5e0bc317ac05f44833fad6365f83e Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 21:21:19 -0400 Subject: [PATCH 32/62] Swap sync -> install --- .github/workflows/run_tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index eb3b4221..57edbecd 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -34,7 +34,7 @@ jobs: - name: Install package run: | python --version - uv pip sync ${{ inputs.requirements-file }} --only-binary=:none: --reinstall + uv pip install ${{ inputs.requirements-file }} --system --reinstall python -c "import parsnip; print('parsnip', parsnip.__version__)" python -c "import numpy; print('numpy', numpy.__version__)" - name: Test with pytest From 59ecc7927385a869545e1be9e99ec14afc828182 Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 21:22:01 -0400 Subject: [PATCH 33/62] Add -r --- .github/workflows/run_tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 57edbecd..5202265b 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -34,7 +34,7 @@ jobs: - name: Install package run: | python --version - uv pip install ${{ inputs.requirements-file }} --system --reinstall + uv pip install -r ${{ inputs.requirements-file }} --system --reinstall python -c "import parsnip; print('parsnip', parsnip.__version__)" python -c "import numpy; print('numpy', numpy.__version__)" - name: Test with pytest From 1008cd092ad93a54f00f0e44bc3e7b20c9b34e2d Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 21:23:19 -0400 Subject: [PATCH 34/62] Remove --system --- .github/workflows/run_tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git 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b26be5d4..aac4246f 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -31,11 +31,5 @@ jobs: - name: Activate environment (Unix) if: runner.os != 'Windows' run: . .venv/bin/activate && echo "PATH=$PATH" >> $GITHUB_ENV - - name: Install package - run: | - python --version - uv pip install -r ${{ inputs.requirements-file }} --reinstall - python -c "import parsnip; print('parsnip', parsnip.__version__)" - python -c "import numpy; print('numpy', numpy.__version__)" - name: Test with pytest - run: python -m pytest -v + run: uv run --no-sync --with-requirements ${{ inputs.requirements-file }} pytest diff --git a/pyproject.toml b/pyproject.toml index 1fb899b6..8ab6c157 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -25,7 +25,7 @@ keywords = [ "Topic :: Scientific/Engineering :: Physics", "Topic :: Scientific/Engineering :: Chemistry", ] -dynamic = ["optional-dependencies"] +# dynamic = ["optional-dependencies"] [project.urls] Source = 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b/.github/workflows/run_tests.yaml @@ -31,5 +31,11 @@ jobs: - name: Activate environment (Unix) if: runner.os != 'Windows' run: . .venv/bin/activate && echo "PATH=$PATH" >> $GITHUB_ENV + - name: Install package + run: | + python --version + uv pip install -v . + python -c "import parsnip; print('parsnip', parsnip.__version__)" + python -c "import numpy; print('numpy', numpy.__version__)" - name: Test with pytest run: uv run --no-sync --with-requirements ${{ inputs.requirements-file }} pytest From 33027c6bca4717c8a4954394005b411c7100e15c Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 21:41:22 -0400 Subject: [PATCH 37/62] Optional dependencies --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 8ab6c157..bbc5c626 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -100,7 +100,7 @@ omit = [ "parsnip/coverage.py", ] -[dependency-groups] +[optional-dependencies] dev = [ "ase", "gemmi", From 62a37fbcb89025111ebce43c14fedfed1ab957de Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 21:42:51 -0400 Subject: [PATCH 38/62] Revert deps --- pyproject.toml | 24 +++--------------------- 1 file changed, 3 insertions(+), 21 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index bbc5c626..1fb899b6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -25,7 +25,7 @@ keywords = [ "Topic :: Scientific/Engineering :: Physics", "Topic :: Scientific/Engineering :: Chemistry", ] -# dynamic = ["optional-dependencies"] +dynamic = ["optional-dependencies"] [project.urls] Source = "https://github.com/glotzerlab/parsnip" @@ -34,8 +34,8 @@ Issues = "https://github.com/glotzerlab/parsnip/issues" [tool.setuptools] packages=["parsnip"] -# [tool.setuptools.dynamic] -# optional-dependencies = {tests = { file = ["tests/requirements.in"] }, doc = { file = ["doc/requirements.txt"] }} +[tool.setuptools.dynamic] +optional-dependencies = {tests = { file = ["tests/requirements.in"] }, doc = { file = ["doc/requirements.txt"] }} [tool.pytest.ini_options] testpaths = ["tests", "parsnip", "doc"] @@ -99,21 +99,3 @@ indent-style = "space" omit = [ "parsnip/coverage.py", ] - -[optional-dependencies] -dev = [ - "ase", - "gemmi", - "pycifrw", - "pytest", - "pytest-doctestplus", -] -doc = [ - "autodocsumm>=0.2.14", - "furo>=2023.3.27", - "numpy>=1.21.6", - "pytest-doctestplus>=1.0.0", - "sphinx>=5.3.0", - "sphinx-copybutton>=0.5.2", - "sphinx-notfound-page>=0.8.3", -] From e07e8e56896fdff2ae2a053d35761201eb392f32 Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 21:50:44 -0400 Subject: [PATCH 39/62] Revert --- .github/workflows/run_tests.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 38192813..b0b48bbc 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -34,8 +34,9 @@ jobs: - name: Install package run: | python --version - uv pip install -v . + which python + uv pip install . -r ${{ inputs.requirements-file }} -v --reinstall python -c "import parsnip; print('parsnip', parsnip.__version__)" python -c "import numpy; print('numpy', numpy.__version__)" - name: Test with pytest - run: uv run --no-sync --with-requirements ${{ inputs.requirements-file }} pytest + run: python -m pytest -v From d447aff6b748c62ca971463ff58764617dff44d7 Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 21:58:24 -0400 Subject: [PATCH 40/62] Debug --- .github/workflows/CI.yaml | 8 ++++---- .github/workflows/run_tests.yaml | 1 + 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml index f50dc676..9648729c 100644 --- a/.github/workflows/CI.yaml +++ b/.github/workflows/CI.yaml @@ -16,14 +16,14 @@ jobs: # python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"] # runs-on: ["ubuntu-latest"] include: - - runs-on: "macos-latest" - python-version: "3.13" + # - runs-on: "macos-latest" + # python-version: "3.13" - runs-on: "windows-latest" python-version: "3.13" - runs-on: "windows-latest" python-version: "3.9" - - runs-on: "macos-latest" - python-version: "3.9" + # - runs-on: "macos-latest" + # python-version: "3.9" # Pull in the test script from run_tests and distribute python from matrix versions uses: ./.github/workflows/run_tests.yaml with: diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index b0b48bbc..19884d84 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -35,6 +35,7 @@ jobs: run: | python --version which python + ls .venv uv pip install . -r ${{ inputs.requirements-file }} -v --reinstall python -c "import parsnip; print('parsnip', parsnip.__version__)" python -c "import numpy; print('numpy', numpy.__version__)" From 87ce6775cabf0c069b89735dce108a608c110cc1 Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 21:59:31 -0400 Subject: [PATCH 41/62] More debug --- .github/workflows/run_tests.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 19884d84..fe12b928 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -36,6 +36,8 @@ jobs: python --version which python ls .venv + ls .venv\Lib + ls .venv\Scripts uv pip install . -r ${{ inputs.requirements-file }} -v --reinstall python -c "import parsnip; print('parsnip', parsnip.__version__)" python -c "import numpy; print('numpy', numpy.__version__)" From f49ad39f876a2d5170541b3003f1e88b3918e217 Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 22:01:58 -0400 Subject: [PATCH 42/62] --python --- .github/workflows/run_tests.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index fe12b928..5becbaf4 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -37,9 +37,10 @@ jobs: which python ls .venv ls .venv\Lib + ls .venv\Lib\site-packages ls .venv\Scripts - uv pip install . -r ${{ inputs.requirements-file }} -v --reinstall + uv pip install . -r ${{ inputs.requirements-file }} -v --reinstall --python .venv\Scripts\python.exe python -c "import parsnip; print('parsnip', parsnip.__version__)" python -c "import numpy; print('numpy', numpy.__version__)" - name: Test with pytest - run: python -m pytest -v + run: .venv\Scripts\python -m pytest -v From df682e15753db0c2dec7f28654cf0496dda8c739 Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 22:07:03 -0400 Subject: [PATCH 43/62] Disable windows tests --- .github/workflows/CI.yaml | 18 +++++++++--------- .github/workflows/run_tests.yaml | 20 +++++++++----------- 2 files changed, 18 insertions(+), 20 deletions(-) diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml index 9648729c..92a3d90f 100644 --- a/.github/workflows/CI.yaml +++ b/.github/workflows/CI.yaml @@ -13,17 +13,17 @@ jobs: strategy: fail-fast: true matrix: - # python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"] - # runs-on: ["ubuntu-latest"] + python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"] + runs-on: ["ubuntu-latest"] include: - # - runs-on: "macos-latest" - # python-version: "3.13" - - runs-on: "windows-latest" + - runs-on: "macos-latest" python-version: "3.13" - - runs-on: "windows-latest" - python-version: "3.9" - # - runs-on: "macos-latest" + # - runs-on: "windows-latest" + # python-version: "3.13" + # - runs-on: "windows-latest" # python-version: "3.9" + - runs-on: "macos-latest" + python-version: "3.9" # Pull in the test script from run_tests and distribute python from matrix versions uses: ./.github/workflows/run_tests.yaml with: @@ -37,7 +37,7 @@ jobs: fail-fast: false # Legacy versions are much less stable - run tests independently matrix: # Code works on py3.6, but type annotations are broken python-version: ["3.7", "3.8"] - runs-on: ["ubuntu-20.04", "windows-latest"] + runs-on: ["ubuntu-20.04"] include: - runs-on: "macos-14" python-version: "3.8" diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 5becbaf4..75fcc8a8 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -23,24 +23,22 @@ jobs: with: python-version: ${{ inputs.python-version }} version: "0.6.6" + - name: Set up uv venv run: uv venv - - name: Activate environment (Windows) - if: runner.os == 'Windows' - run: .venv\Scripts\activate && echo "PATH=$PATH" >> $GITHUB_ENV - name: Activate environment (Unix) if: runner.os != 'Windows' run: . .venv/bin/activate && echo "PATH=$PATH" >> $GITHUB_ENV + - name: Activate environment (Windows) + if: runner.os == 'Windows' + run: .venv\Scripts\activate && echo "PATH=$PATH" >> $GITHUB_ENV + - name: Install package run: | - python --version which python - ls .venv - ls .venv\Lib - ls .venv\Lib\site-packages - ls .venv\Scripts - uv pip install 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"https://pypi.org/simple" } -resolution-markers = [ - "python_full_version == '3.9.*'", -] -sdist = { url = "https://files.pythonhosted.org/packages/3f/50/bad581df71744867e9468ebd0bcd6505de3b275e06f202c2cb016e3ff56f/zipp-3.21.0.tar.gz", hash = "sha256:2c9958f6430a2040341a52eb608ed6dd93ef4392e02ffe219417c1b28b5dd1f4", size = 24545 } -wheels = [ - { url = "https://files.pythonhosted.org/packages/b7/1a/7e4798e9339adc931158c9d69ecc34f5e6791489d469f5e50ec15e35f458/zipp-3.21.0-py3-none-any.whl", hash = "sha256:ac1bbe05fd2991f160ebce24ffbac5f6d11d83dc90891255885223d42b3cd931", size = 9630 }, -] From aca5b3b4f76360cc75c11da19324f59cc00f1f8f Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 22:10:23 -0400 Subject: [PATCH 45/62] Attemp --system --- .github/workflows/run_tests.yaml | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 75fcc8a8..7bbbf11d 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -24,20 +24,20 @@ jobs: python-version: ${{ inputs.python-version }} version: "0.6.6" - - name: Set up uv venv - run: uv venv - - name: Activate environment (Unix) - if: runner.os != 'Windows' - run: . .venv/bin/activate && echo "PATH=$PATH" >> $GITHUB_ENV - - name: Activate environment (Windows) - if: runner.os == 'Windows' - run: .venv\Scripts\activate && echo "PATH=$PATH" >> $GITHUB_ENV + # - name: Set up uv venv + # run: uv venv + # - name: Activate environment (Unix) + # if: runner.os != 'Windows' + # run: . .venv/bin/activate && echo "PATH=$PATH" >> $GITHUB_ENV + # - name: Activate environment (Windows) + # if: runner.os == 'Windows' + # run: .venv\Scripts\activate && echo "PATH=$PATH" >> $GITHUB_ENV - name: Install package run: | which python python --version - uv pip install . -r ${{ inputs.requirements-file }} -v --reinstall + uv pip install . -r ${{ inputs.requirements-file }} -v --reinstall --system python -c "import parsnip; print('parsnip', parsnip.__version__)" - name: Test with pytest From 0a01eadc347e66f9f3de964227b8a9a91c127be7 Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 22:12:54 -0400 Subject: [PATCH 46/62] uv python install --- .github/workflows/run_tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 7bbbf11d..c4ce1c88 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -21,7 +21,6 @@ jobs: - name: Install uv uses: astral-sh/setup-uv@v4 with: - python-version: ${{ inputs.python-version }} version: "0.6.6" # - name: Set up uv venv @@ -35,6 +34,7 @@ jobs: - name: Install package run: | + uv python install ${{ inputs.python-version }} which python python --version uv pip install . -r ${{ inputs.requirements-file }} -v --reinstall --system From 346848e3d8005f0d74d689e0588effa6c4727441 Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 22:14:58 -0400 Subject: [PATCH 47/62] use setup-python --- .github/workflows/run_tests.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index c4ce1c88..64f7ac9e 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -18,6 +18,9 @@ jobs: runs-on: ${{ inputs.runs-on }} steps: - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 + with: + python-version: ${{ inputs.python-version }} - name: Install uv uses: astral-sh/setup-uv@v4 with: @@ -34,7 +37,6 @@ jobs: - name: Install package run: | - uv python install ${{ inputs.python-version }} which python python --version uv pip install . -r ${{ inputs.requirements-file }} -v --reinstall --system From ae71de82467f64fea683f7eca9fded20c637db85 Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 22:16:00 -0400 Subject: [PATCH 48/62] Test on windows-latest py3.13 --- .github/workflows/CI.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml index 92a3d90f..dc2d8db6 100644 --- a/.github/workflows/CI.yaml +++ b/.github/workflows/CI.yaml @@ -18,8 +18,8 @@ jobs: include: - runs-on: "macos-latest" python-version: "3.13" - # - runs-on: "windows-latest" - # python-version: "3.13" + - runs-on: "windows-latest" + python-version: "3.13" # - runs-on: "windows-latest" # python-version: "3.9" - runs-on: "macos-latest" From e0931e7809816a792c72d4881ac36368e0c61f8a Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 22:24:41 -0400 Subject: [PATCH 49/62] Disable doctests on windows --- .github/workflows/run_tests.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 64f7ac9e..8d4a1fce 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -42,5 +42,5 @@ jobs: uv pip install . -r ${{ inputs.requirements-file }} -v --reinstall --system python -c "import parsnip; print('parsnip', parsnip.__version__)" - - name: Test with pytest - run: python -m pytest -v + - name: Test with pytest # Skip doctests on Windows + run: ${{ runner.os != 'Windows' && 'pytest' || 'pytest tests' }} From d55f84f46db37d1b3647ad85b3f9ef2e071ae1ca Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 22:25:53 -0400 Subject: [PATCH 50/62] Run pytest as module --- .github/workflows/run_tests.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 8d4a1fce..0b1d46d7 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -42,5 +42,5 @@ jobs: uv pip install . -r ${{ inputs.requirements-file }} -v --reinstall --system python -c "import parsnip; print('parsnip', parsnip.__version__)" - - name: Test with pytest # Skip doctests on Windows - run: ${{ runner.os != 'Windows' && 'pytest' || 'pytest tests' }} + - name: Test with pytest + run: python -m ${{ runner.os != 'Windows' && 'pytest' || 'pytest tests' }} -v From 557f4ce7eaf05f7893a752ac4ccdeecfa16c2c30 Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 22:30:12 -0400 Subject: [PATCH 51/62] Test repr --- .github/workflows/CI.yaml | 2 +- tests/test_patterns.py | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml index dc2d8db6..ef9f7550 100644 --- a/.github/workflows/CI.yaml +++ b/.github/workflows/CI.yaml @@ -37,7 +37,7 @@ jobs: fail-fast: false # Legacy versions are much less stable - run tests independently matrix: # Code works on py3.6, but type annotations are broken python-version: ["3.7", "3.8"] - runs-on: ["ubuntu-20.04"] + runs-on: ["ubuntu-20.04", "windows-latest"] include: - runs-on: "macos-14" python-version: "3.8" diff --git a/tests/test_patterns.py b/tests/test_patterns.py index 4fd6c99c..0b55ad53 100644 --- a/tests/test_patterns.py +++ b/tests/test_patterns.py @@ -202,10 +202,11 @@ def test_try_cast_to_numeric(s): assert isinstance(result, int) +# @pytest.mark.skipif(os.getenv("RUNNER_OS") == "Windows", reason="String formatting") @cif_files_mark def test_repr(cif_data): import re - + print(cif_data.file.__repr__()) repr = re.sub(r"[a-z\s]*", "", cif_data.file.__repr__().split(":")[1]).split(",") n_pairs, n_tabs = [int(i) for i in repr] assert n_pairs == len(cif_data.file.pairs) From bc31b7eff26b6c451383597619eab2faabc7ea9e Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 22:37:05 -0400 Subject: [PATCH 52/62] Fix tests on windows --- tests/test_patterns.py | 5 ++--- tests/test_table_reader.py | 3 +++ 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/tests/test_patterns.py b/tests/test_patterns.py index 0b55ad53..93e4f469 100644 --- a/tests/test_patterns.py +++ b/tests/test_patterns.py @@ -202,12 +202,11 @@ def test_try_cast_to_numeric(s): assert isinstance(result, int) -# @pytest.mark.skipif(os.getenv("RUNNER_OS") == "Windows", reason="String formatting") @cif_files_mark def test_repr(cif_data): import re - print(cif_data.file.__repr__()) - repr = re.sub(r"[a-z\s]*", "", cif_data.file.__repr__().split(":")[1]).split(",") + + repr = re.sub(r"[a-z\s]*", "", cif_data.file.__repr__().split(" : ")[1]).split(",") n_pairs, n_tabs = [int(i) for i in repr] assert n_pairs == len(cif_data.file.pairs) assert n_tabs == len(cif_data.file.loops) diff --git a/tests/test_table_reader.py b/tests/test_table_reader.py index 35df9ef7..6aefd265 100644 --- a/tests/test_table_reader.py +++ b/tests/test_table_reader.py @@ -30,10 +30,13 @@ def test_reads_all_keys(cif_data): for key in all_keys: assert key in found_labels, f"Missing label: {found_labels}" + for loop in pycif.loops.values(): loop = [pycif.true_case[key] for key in loop] parsnip_data = cif_data.file.get_from_loops(loop) gemmi_data = _gemmi_read_table(cif_data.filename, loop) + print(parsnip_data[parsnip_data!=gemmi_data]) + print(gemmi_data[parsnip_data!=gemmi_data]) np.testing.assert_array_equal(parsnip_data, gemmi_data) From f003dbe7c918e2efbee0ce6fde17483636e8f96d Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 22:41:19 -0400 Subject: [PATCH 53/62] Strip carriage returns --- .github/workflows/run_tests.yaml | 9 --------- tests/test_table_reader.py | 7 +++---- 2 files changed, 3 insertions(+), 13 deletions(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 0b1d46d7..419bdefd 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -26,15 +26,6 @@ jobs: with: version: "0.6.6" - # - name: Set up uv venv - # run: uv venv - # - name: Activate environment (Unix) - # if: runner.os != 'Windows' - # run: . .venv/bin/activate && echo "PATH=$PATH" >> $GITHUB_ENV - # - name: Activate environment (Windows) - # if: runner.os == 'Windows' - # run: .venv\Scripts\activate && echo "PATH=$PATH" >> $GITHUB_ENV - - name: Install package run: | which python diff --git a/tests/test_table_reader.py b/tests/test_table_reader.py index 6aefd265..8e06fe8a 100644 --- a/tests/test_table_reader.py +++ b/tests/test_table_reader.py @@ -30,14 +30,13 @@ def test_reads_all_keys(cif_data): for key in all_keys: assert key in found_labels, f"Missing label: {found_labels}" - for loop in pycif.loops.values(): loop = [pycif.true_case[key] for key in loop] parsnip_data = cif_data.file.get_from_loops(loop) gemmi_data = _gemmi_read_table(cif_data.filename, loop) - print(parsnip_data[parsnip_data!=gemmi_data]) - print(gemmi_data[parsnip_data!=gemmi_data]) - np.testing.assert_array_equal(parsnip_data, gemmi_data) + np.testing.assert_array_equal( + parsnip_data, [s.replace(r"\r", "") for s in gemmi_data] + ) @cif_files_mark From 05415aba8c72cc9a91bc1c1af68bcc348879dcc2 Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 22:43:40 -0400 Subject: [PATCH 54/62] Centralize _arrstriip --- tests/conftest.py | 5 +++++ tests/test_table_reader.py | 6 ++---- tests/test_unitcells.py | 7 +------ 3 files changed, 8 insertions(+), 10 deletions(-) diff --git a/tests/conftest.py b/tests/conftest.py index b22e7a8e..9ef1bd7f 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -2,6 +2,7 @@ from __future__ import annotations import os +import re from dataclasses import dataclass import numpy as np @@ -14,6 +15,10 @@ data_file_path = os.path.dirname(__file__) + "/sample_data/" +def _arrstrip(arr: np.ndarray, pattern: str): + return np.vectorize(lambda x: re.sub(pattern, "", x))(arr) + + @dataclass class CifData: filename: str diff --git a/tests/test_table_reader.py b/tests/test_table_reader.py index 8e06fe8a..d12cea9e 100644 --- a/tests/test_table_reader.py +++ b/tests/test_table_reader.py @@ -4,7 +4,7 @@ import pytest from ase.io import cif as asecif from CifFile import CifFile as pycifRW -from conftest import bad_cif, cif_files_mark +from conftest import _arrstrip, bad_cif, cif_files_mark from gemmi import cif from more_itertools import flatten @@ -34,9 +34,7 @@ def test_reads_all_keys(cif_data): loop = [pycif.true_case[key] for key in loop] parsnip_data = cif_data.file.get_from_loops(loop) gemmi_data = _gemmi_read_table(cif_data.filename, loop) - np.testing.assert_array_equal( - parsnip_data, [s.replace(r"\r", "") for s in gemmi_data] - ) + np.testing.assert_array_equal(parsnip_data, _arrstrip(gemmi_data, r"\r")) @cif_files_mark diff --git a/tests/test_unitcells.py b/tests/test_unitcells.py index 17c03bb8..1088c84c 100644 --- a/tests/test_unitcells.py +++ b/tests/test_unitcells.py @@ -1,4 +1,3 @@ -import re import warnings from contextlib import nullcontext @@ -6,7 +5,7 @@ import pytest from ase import io from ase.build import supercells -from conftest import box_keys, cif_files_mark +from conftest import _arrstrip, box_keys, cif_files_mark from gemmi import cif from more_itertools import flatten @@ -22,10 +21,6 @@ def _gemmi_read_keys(filename, keys, as_number=True): return np.array([file_block.find_value(key) for key in keys]) -def _arrstrip(arr: np.ndarray, pattern: str): - return np.vectorize(lambda x: re.sub(pattern, "", x))(arr) - - @cif_files_mark # TODO: test with conversions to numeric as well def test_read_wyckoff_positions(cif_data): if "PDB_4INS_head.cif" in cif_data.filename: From 5213ec1d6beb0870e52fa67ef56895e6ca8bcc63 Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 22:47:30 -0400 Subject: [PATCH 55/62] Enable windows-3.9 --- .github/workflows/CI.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml index ef9f7550..1b4131f3 100644 --- a/.github/workflows/CI.yaml +++ b/.github/workflows/CI.yaml @@ -16,12 +16,12 @@ jobs: python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"] runs-on: ["ubuntu-latest"] include: - - runs-on: "macos-latest" + - runs-on: "windows-latest" python-version: "3.13" - runs-on: "windows-latest" + python-version: "3.9" + - runs-on: "macos-latest" python-version: "3.13" - # - runs-on: "windows-latest" - # python-version: "3.9" - runs-on: "macos-latest" python-version: "3.9" # Pull in the test script from run_tests and distribute python from matrix versions From 0c761fd659845a072902ea2aa22504507a86e15e Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 22:54:25 -0400 Subject: [PATCH 56/62] Add update-uv-lockfiles.sh --- .github/workflows/update-uv-lockfiles.sh | 3 +++ 1 file changed, 3 insertions(+) create mode 100755 .github/workflows/update-uv-lockfiles.sh diff --git a/.github/workflows/update-uv-lockfiles.sh b/.github/workflows/update-uv-lockfiles.sh new file mode 100755 index 00000000..5c34281a --- /dev/null +++ b/.github/workflows/update-uv-lockfiles.sh @@ -0,0 +1,3 @@ +for version in 3.{9..13}; do + uv pip compile --python-version="$version" pyproject.toml tests/requirements.in > ".github/requirements-$version.txt" +done From 049f13b937e9a48e1866e15168f5599afbeec56c Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 22:54:31 -0400 Subject: [PATCH 57/62] Update requirements files --- .github/requirements-3.10.txt | 23 ++++++++++++----------- .github/requirements-3.11.txt | 23 ++++++++++++----------- .github/requirements-3.12.txt | 23 ++++++++++++----------- .github/requirements-3.13.txt | 23 ++++++++++++----------- .github/requirements-3.9.txt | 17 +++++++++-------- 5 files changed, 57 insertions(+), 52 deletions(-) diff --git a/.github/requirements-3.10.txt b/.github/requirements-3.10.txt index 986ca9e2..1f191187 100644 --- a/.github/requirements-3.10.txt +++ b/.github/requirements-3.10.txt @@ -8,7 +8,7 @@ cycler==0.12.1 # via matplotlib exceptiongroup==1.2.2 # via pytest -fonttools==4.55.3 +fonttools==4.56.0 # via matplotlib gemmi==0.7.0 # via -r tests/requirements.in @@ -16,17 +16,16 @@ iniconfig==2.0.0 # via pytest kiwisolver==1.4.8 # via matplotlib -matplotlib==3.10.0 +matplotlib==3.10.1 # via ase more-itertools==10.6.0 - # via parsnip (pyproject.toml) -numpy==2.2.1 + # via parsnip-cif (pyproject.toml) +numpy==2.2.3 # via - # parsnip (pyproject.toml) + # parsnip-cif (pyproject.toml) # ase # contourpy # matplotlib - # pycifrw # scipy packaging==24.2 # via @@ -37,23 +36,25 @@ pillow==11.1.0 # via matplotlib pluggy==1.5.0 # via pytest -ply==3.11 +prettytable==3.15.1 # via pycifrw -pycifrw==4.4.6 +pycifrw==5.0.0 # via -r tests/requirements.in pyparsing==3.2.1 # via matplotlib -pytest==8.3.4 +pytest==8.3.5 # via # -r tests/requirements.in # pytest-doctestplus -pytest-doctestplus==1.3.0 +pytest-doctestplus==1.4.0 # via -r tests/requirements.in python-dateutil==2.9.0.post0 # via matplotlib -scipy==1.15.1 +scipy==1.15.2 # via ase six==1.17.0 # via python-dateutil tomli==2.2.1 # via pytest +wcwidth==0.2.13 + # via prettytable diff --git a/.github/requirements-3.11.txt b/.github/requirements-3.11.txt index 4d1b928d..a134748c 100644 --- a/.github/requirements-3.11.txt +++ b/.github/requirements-3.11.txt @@ -6,7 +6,7 @@ contourpy==1.3.1 # via matplotlib cycler==0.12.1 # via matplotlib -fonttools==4.55.3 +fonttools==4.56.0 # via matplotlib gemmi==0.7.0 # via -r tests/requirements.in @@ -14,17 +14,16 @@ iniconfig==2.0.0 # via pytest kiwisolver==1.4.8 # via matplotlib -matplotlib==3.10.0 +matplotlib==3.10.1 # via ase more-itertools==10.6.0 - # via parsnip (pyproject.toml) -numpy==2.2.1 + # via parsnip-cif (pyproject.toml) +numpy==2.2.3 # via - # parsnip (pyproject.toml) + # parsnip-cif (pyproject.toml) # ase # contourpy # matplotlib - # pycifrw # scipy packaging==24.2 # via @@ -35,21 +34,23 @@ pillow==11.1.0 # via matplotlib pluggy==1.5.0 # via pytest -ply==3.11 +prettytable==3.15.1 # via pycifrw -pycifrw==4.4.6 +pycifrw==5.0.0 # via -r tests/requirements.in pyparsing==3.2.1 # via matplotlib -pytest==8.3.4 +pytest==8.3.5 # via # -r tests/requirements.in # pytest-doctestplus -pytest-doctestplus==1.3.0 +pytest-doctestplus==1.4.0 # via -r tests/requirements.in python-dateutil==2.9.0.post0 # via matplotlib -scipy==1.15.1 +scipy==1.15.2 # via ase six==1.17.0 # via python-dateutil +wcwidth==0.2.13 + # via prettytable diff --git a/.github/requirements-3.12.txt b/.github/requirements-3.12.txt index 1fa3c123..f73eb8bc 100644 --- a/.github/requirements-3.12.txt +++ b/.github/requirements-3.12.txt @@ -6,7 +6,7 @@ contourpy==1.3.1 # via matplotlib cycler==0.12.1 # via matplotlib -fonttools==4.55.3 +fonttools==4.56.0 # via matplotlib gemmi==0.7.0 # via -r tests/requirements.in @@ -14,17 +14,16 @@ iniconfig==2.0.0 # via pytest kiwisolver==1.4.8 # via matplotlib -matplotlib==3.10.0 +matplotlib==3.10.1 # via ase more-itertools==10.6.0 - # via parsnip (pyproject.toml) -numpy==2.2.1 + # via parsnip-cif (pyproject.toml) +numpy==2.2.3 # via - # parsnip (pyproject.toml) + # parsnip-cif (pyproject.toml) # ase # contourpy # matplotlib - # pycifrw # scipy packaging==24.2 # via @@ -35,21 +34,23 @@ pillow==11.1.0 # via matplotlib pluggy==1.5.0 # via pytest -ply==3.11 +prettytable==3.15.1 # via pycifrw -pycifrw==4.4.6 +pycifrw==5.0.0 # via -r tests/requirements.in pyparsing==3.2.1 # via matplotlib -pytest==8.3.4 +pytest==8.3.5 # via # -r tests/requirements.in # pytest-doctestplus -pytest-doctestplus==1.3.0 +pytest-doctestplus==1.4.0 # via -r tests/requirements.in python-dateutil==2.9.0.post0 # via matplotlib -scipy==1.15.1 +scipy==1.15.2 # via ase six==1.17.0 # via python-dateutil +wcwidth==0.2.13 + # via prettytable diff --git a/.github/requirements-3.13.txt b/.github/requirements-3.13.txt index aaab9daf..d8811aaf 100644 --- a/.github/requirements-3.13.txt +++ b/.github/requirements-3.13.txt @@ -6,7 +6,7 @@ contourpy==1.3.1 # via matplotlib cycler==0.12.1 # via matplotlib -fonttools==4.55.3 +fonttools==4.56.0 # via matplotlib gemmi==0.7.0 # via -r tests/requirements.in @@ -14,17 +14,16 @@ iniconfig==2.0.0 # via pytest kiwisolver==1.4.8 # via matplotlib -matplotlib==3.10.0 +matplotlib==3.10.1 # via ase more-itertools==10.6.0 - # via parsnip (pyproject.toml) -numpy==2.2.1 + # via parsnip-cif (pyproject.toml) +numpy==2.2.3 # via - # parsnip (pyproject.toml) + # parsnip-cif (pyproject.toml) # ase # contourpy # matplotlib - # pycifrw # scipy packaging==24.2 # via @@ -35,21 +34,23 @@ pillow==11.1.0 # via matplotlib pluggy==1.5.0 # via pytest -ply==3.11 +prettytable==3.15.1 # via pycifrw -pycifrw==4.4.6 +pycifrw==5.0.0 # via -r tests/requirements.in pyparsing==3.2.1 # via matplotlib -pytest==8.3.4 +pytest==8.3.5 # via # -r tests/requirements.in # pytest-doctestplus -pytest-doctestplus==1.3.0 +pytest-doctestplus==1.4.0 # via -r tests/requirements.in python-dateutil==2.9.0.post0 # via matplotlib -scipy==1.15.1 +scipy==1.15.2 # via ase six==1.17.0 # via python-dateutil +wcwidth==0.2.13 + # via prettytable diff --git a/.github/requirements-3.9.txt b/.github/requirements-3.9.txt index 8ee932f7..fe77e8e9 100644 --- a/.github/requirements-3.9.txt +++ b/.github/requirements-3.9.txt @@ -8,7 +8,7 @@ cycler==0.12.1 # via matplotlib exceptiongroup==1.2.2 # via pytest -fonttools==4.55.3 +fonttools==4.56.0 # via matplotlib gemmi==0.7.0 # via -r tests/requirements.in @@ -21,14 +21,13 @@ kiwisolver==1.4.7 matplotlib==3.9.4 # via ase more-itertools==10.6.0 - # via parsnip (pyproject.toml) + # via parsnip-cif (pyproject.toml) numpy==2.0.2 # via - # parsnip (pyproject.toml) + # parsnip-cif (pyproject.toml) # ase # contourpy # matplotlib - # pycifrw # scipy packaging==24.2 # via @@ -39,17 +38,17 @@ pillow==11.1.0 # via matplotlib pluggy==1.5.0 # via pytest -ply==3.11 +prettytable==3.15.1 # via pycifrw -pycifrw==4.4.6 +pycifrw==5.0.0 # via -r tests/requirements.in pyparsing==3.2.1 # via matplotlib -pytest==8.3.4 +pytest==8.3.5 # via # -r tests/requirements.in # pytest-doctestplus -pytest-doctestplus==1.3.0 +pytest-doctestplus==1.4.0 # via -r tests/requirements.in python-dateutil==2.9.0.post0 # via matplotlib @@ -59,5 +58,7 @@ six==1.17.0 # via python-dateutil tomli==2.2.1 # via pytest +wcwidth==0.2.13 + # via prettytable zipp==3.21.0 # via importlib-resources From 9f282d45ea8dbd2a0cf4ab67fd169af216841318 Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 23:04:47 -0400 Subject: [PATCH 58/62] Ban pycifrw>=5.0.0 --- .github/requirements-3.10.txt | 7 +++---- .github/requirements-3.11.txt | 7 +++---- .github/requirements-3.12.txt | 7 +++---- .github/requirements-3.13.txt | 7 +++---- .github/requirements-3.9.txt | 7 +++---- tests/requirements.in | 2 +- 6 files changed, 16 insertions(+), 21 deletions(-) diff --git a/.github/requirements-3.10.txt b/.github/requirements-3.10.txt index 1f191187..33faa80b 100644 --- a/.github/requirements-3.10.txt +++ b/.github/requirements-3.10.txt @@ -26,6 +26,7 @@ numpy==2.2.3 # ase # contourpy # matplotlib + # pycifrw # scipy packaging==24.2 # via @@ -36,9 +37,9 @@ pillow==11.1.0 # via matplotlib pluggy==1.5.0 # via pytest -prettytable==3.15.1 +ply==3.11 # via pycifrw -pycifrw==5.0.0 +pycifrw==4.4.6 # via -r tests/requirements.in pyparsing==3.2.1 # via matplotlib @@ -56,5 +57,3 @@ six==1.17.0 # via python-dateutil tomli==2.2.1 # via pytest -wcwidth==0.2.13 - # via prettytable diff --git a/.github/requirements-3.11.txt b/.github/requirements-3.11.txt index a134748c..e2c19975 100644 --- a/.github/requirements-3.11.txt +++ b/.github/requirements-3.11.txt @@ -24,6 +24,7 @@ numpy==2.2.3 # ase # contourpy # matplotlib + # pycifrw # scipy packaging==24.2 # via @@ -34,9 +35,9 @@ pillow==11.1.0 # via matplotlib pluggy==1.5.0 # via pytest -prettytable==3.15.1 +ply==3.11 # via pycifrw -pycifrw==5.0.0 +pycifrw==4.4.6 # via -r tests/requirements.in pyparsing==3.2.1 # via matplotlib @@ -52,5 +53,3 @@ scipy==1.15.2 # via ase six==1.17.0 # via python-dateutil -wcwidth==0.2.13 - # via prettytable diff --git a/.github/requirements-3.12.txt b/.github/requirements-3.12.txt index f73eb8bc..1ce14145 100644 --- a/.github/requirements-3.12.txt +++ b/.github/requirements-3.12.txt @@ -24,6 +24,7 @@ numpy==2.2.3 # ase # contourpy # matplotlib + # pycifrw # scipy packaging==24.2 # via @@ -34,9 +35,9 @@ pillow==11.1.0 # via matplotlib pluggy==1.5.0 # via pytest -prettytable==3.15.1 +ply==3.11 # via pycifrw -pycifrw==5.0.0 +pycifrw==4.4.6 # via -r tests/requirements.in pyparsing==3.2.1 # via matplotlib @@ -52,5 +53,3 @@ scipy==1.15.2 # via ase six==1.17.0 # via python-dateutil -wcwidth==0.2.13 - # via prettytable diff --git a/.github/requirements-3.13.txt b/.github/requirements-3.13.txt index d8811aaf..edb13ea2 100644 --- a/.github/requirements-3.13.txt +++ b/.github/requirements-3.13.txt @@ -24,6 +24,7 @@ numpy==2.2.3 # ase # contourpy # matplotlib + # pycifrw # scipy packaging==24.2 # via @@ -34,9 +35,9 @@ pillow==11.1.0 # via matplotlib pluggy==1.5.0 # via pytest -prettytable==3.15.1 +ply==3.11 # via pycifrw -pycifrw==5.0.0 +pycifrw==4.4.6 # via -r tests/requirements.in pyparsing==3.2.1 # via matplotlib @@ -52,5 +53,3 @@ scipy==1.15.2 # via ase six==1.17.0 # via python-dateutil -wcwidth==0.2.13 - # via prettytable diff --git a/.github/requirements-3.9.txt b/.github/requirements-3.9.txt index fe77e8e9..6a81d63e 100644 --- a/.github/requirements-3.9.txt +++ b/.github/requirements-3.9.txt @@ -28,6 +28,7 @@ numpy==2.0.2 # ase # contourpy # matplotlib + # pycifrw # scipy packaging==24.2 # via @@ -38,9 +39,9 @@ pillow==11.1.0 # via matplotlib pluggy==1.5.0 # via pytest -prettytable==3.15.1 +ply==3.11 # via pycifrw -pycifrw==5.0.0 +pycifrw==4.4.6 # via -r tests/requirements.in pyparsing==3.2.1 # via matplotlib @@ -58,7 +59,5 @@ six==1.17.0 # via python-dateutil tomli==2.2.1 # via pytest -wcwidth==0.2.13 - # via prettytable zipp==3.21.0 # via importlib-resources diff --git a/tests/requirements.in b/tests/requirements.in index 1902320f..ad3103c9 100644 --- a/tests/requirements.in +++ b/tests/requirements.in @@ -1,5 +1,5 @@ ase gemmi -pycifrw +pycifrw<5.0.0 pytest pytest-doctestplus From ef96db4a894543565ef57fc977aff3533d383e9b Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 23:08:31 -0400 Subject: [PATCH 59/62] Add missing shebang --- .github/workflows/update-uv-lockfiles.sh | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/update-uv-lockfiles.sh b/.github/workflows/update-uv-lockfiles.sh index 5c34281a..e52abe2e 100755 --- a/.github/workflows/update-uv-lockfiles.sh +++ b/.github/workflows/update-uv-lockfiles.sh @@ -1,3 +1,5 @@ +#!/bin/bash + for version in 3.{9..13}; do uv pip compile --python-version="$version" pyproject.toml tests/requirements.in > ".github/requirements-$version.txt" done From b97ec9c1cb132b94912abac1bc96c87d92e5838f Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 23:09:30 -0400 Subject: [PATCH 60/62] Separate windows CI into action --- .github/workflows/CI.yaml | 19 ++++++++++++++----- 1 file changed, 14 insertions(+), 5 deletions(-) diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml index 1b4131f3..59ee0fb1 100644 --- a/.github/workflows/CI.yaml +++ b/.github/workflows/CI.yaml @@ -16,10 +16,6 @@ jobs: python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"] runs-on: ["ubuntu-latest"] include: - - runs-on: "windows-latest" - python-version: "3.13" - - runs-on: "windows-latest" - python-version: "3.9" - runs-on: "macos-latest" python-version: "3.13" - runs-on: "macos-latest" @@ -37,7 +33,7 @@ jobs: fail-fast: false # Legacy versions are much less stable - run tests independently matrix: # Code works on py3.6, but type annotations are broken python-version: ["3.7", "3.8"] - runs-on: ["ubuntu-20.04", "windows-latest"] + runs-on: ["ubuntu-20.04"] include: - runs-on: "macos-14" python-version: "3.8" @@ -46,3 +42,16 @@ jobs: python-version: ${{ matrix.python-version }} runs-on: ${{ matrix.runs-on }} requirements-file: ".github/requirements-${{ matrix.python-version }}.txt" + + run-tests-windows: + needs: run-tests-modern-python + strategy: + fail-fast: false + matrix: + python-version: ["3.7", "3.9", "3.13"] + runs-on: [windows-latest"] + uses: ./.github/workflows/run_tests.yaml + with: + python-version: ${{ matrix.python-version }} + runs-on: ${{ matrix.runs-on }} + requirements-file: ".github/requirements-${{ matrix.python-version }}.txt" From 22d536df59e9a9746638f692bb07aa6757103c83 Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 23:11:28 -0400 Subject: [PATCH 61/62] Fix typo --- .github/workflows/CI.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml index 59ee0fb1..c8a991b1 100644 --- a/.github/workflows/CI.yaml +++ b/.github/workflows/CI.yaml @@ -49,7 +49,7 @@ jobs: fail-fast: false matrix: python-version: ["3.7", "3.9", "3.13"] - runs-on: [windows-latest"] + runs-on: ["windows-latest"] uses: ./.github/workflows/run_tests.yaml with: python-version: ${{ matrix.python-version }} From d14165ee4f2e5d715c63a6fb4baf2bf75e5b0382 Mon Sep 17 00:00:00 2001 From: janbridley Date: Wed, 12 Mar 2025 23:16:36 -0400 Subject: [PATCH 62/62] Update changelog --- changelog.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/changelog.rst b/changelog.rst index 41e1c295..1c5474ab 100644 --- a/changelog.rst +++ b/changelog.rst @@ -12,6 +12,7 @@ Added - New ``additional_columns`` parameter for ``build_unit_cell`` that allows the return of atom site labels and similar data alongside unit cell positions. - Ensured consistent ordering of lattice positions returned from ``build_unit_cell``. +- CI testing on Windows and macOS Fixed ~~~~~