From 03a4aed2d849bf0b68650e7b5a003a07d276aed4 Mon Sep 17 00:00:00 2001 From: Samuel Rounce Date: Fri, 24 May 2024 01:14:37 +0100 Subject: [PATCH 01/12] feat: Simpler dev shell without Devenv The devshell can now be entered either using Direnv (https://direnv.net) or by manually running `nix develop`. --- .dvc/config | 5 +- .envrc | 3 + .github/workflows/clojure-lint.yaml | 8 +- .github/workflows/clojure-tests.yaml | 10 +- .github/workflows/commit-linter.yaml | 27 +- .github/workflows/python-build-tests.yaml | 22 +- .github/workflows/python-unit-tests.yaml | 12 +- .gitignore | 1 + bin/env-run | 3 + devenv.lock | 298 -- devenv.nix | 56 - devenv.yaml | 15 - devshell.nix | 76 + dvc.lock | 796 ++++ flake.lock | 64 + flake.nix | 18 + package.json | 3 +- pnpm-lock.yaml | 4028 ++++++++++++--------- poetry.lock | 3482 ++++++++++-------- pyproject.toml | 6 +- 20 files changed, 5156 insertions(+), 3777 deletions(-) create mode 100644 .envrc create mode 100755 bin/env-run delete mode 100644 devenv.lock delete mode 100644 devenv.nix delete mode 100644 devenv.yaml create mode 100644 devshell.nix create mode 100644 dvc.lock create mode 100644 flake.lock create mode 100644 flake.nix diff --git a/.dvc/config b/.dvc/config index 65829ee4..965664e2 100644 --- a/.dvc/config +++ b/.dvc/config @@ -1,5 +1,8 @@ [core] analytics = false remote = default-s3-remote + site_cache_dir = ./.dvc/cache +[cache] + dir = cache ['remote "default-s3-remote"'] - url = s3://lpm-research/default \ No newline at end of file + url = s3://lpm-research/default diff --git a/.envrc b/.envrc new file mode 100644 index 00000000..ada66e41 --- /dev/null +++ b/.envrc @@ -0,0 +1,3 @@ +use flake + +watch_file $(find . -name '*.nix') diff --git a/.github/workflows/clojure-lint.yaml b/.github/workflows/clojure-lint.yaml index 28ec485d..cd502058 100644 --- a/.github/workflows/clojure-lint.yaml +++ b/.github/workflows/clojure-lint.yaml @@ -21,12 +21,8 @@ jobs: with: name: devenv - - name: Install devenv - run: nix profile install tarball+https://install.devenv.sh/latest - shell: sh - - name: Build developer environment - run: devenv shell -- echo "devenv built" + run: env-run echo "Devshell built" - name: Lint files - run: devenv shell -- clj-kondo --lint deps.edn src bin test --config '{:output {:pattern "::{{level}} file={{filename}},line={{row}},col={{col}}::{{message}}"}}' + run: env-run clj-kondo --lint deps.edn src bin test --config '{:output {:pattern "::{{level}} file={{filename}},line={{row}},col={{col}}::{{message}}"}}' diff --git a/.github/workflows/clojure-tests.yaml b/.github/workflows/clojure-tests.yaml index e087cba7..9906dde4 100644 --- a/.github/workflows/clojure-tests.yaml +++ b/.github/workflows/clojure-tests.yaml @@ -21,15 +21,11 @@ jobs: with: name: devenv - - name: Install devenv - run: nix profile install tarball+https://install.devenv.sh/latest - shell: sh - - name: Build developer environment - run: devenv shell -- echo "devenv built" + run: env-run echo "Devshell built" - name: Run Clojure tests - run: devenv shell -- clojure -X:test:clj-test + run: env-run clojure -X:test:clj-test - name: Run ClojureScript tests - run: devenv shell -- clojure -M:test:cljs-test + run: env-run clojure -M:test:cljs-test diff --git a/.github/workflows/commit-linter.yaml b/.github/workflows/commit-linter.yaml index 16fca20d..0e45334a 100644 --- a/.github/workflows/commit-linter.yaml +++ b/.github/workflows/commit-linter.yaml @@ -13,30 +13,31 @@ jobs: with: fetch-depth: 0 - - uses: actions/setup-node@v4 - with: - node-version: 20 - case: 'pnpm' + - name: Install Nix + uses: cachix/install-nix-action@v22 + + - uses: DeterminateSystems/magic-nix-cache-action@main - - uses: pnpm/action-setup@v3 + - name: Set up Cachix + uses: cachix/cachix-action@v12 with: - version: 8 + name: devenv - name: Install commitlint run: | - pnpm install --frozen-lockfile + env-run pnpm install --frozen-lockfile - name: Print versions run: | - git --version - node --version - pnpm --version - pnpm exec commitlint --version + env-run 'git --version && + node --version && + pnpm --version && + pnpm exec commitlint --version' - name: Validate current commit (last commit) with commitlint if: github.event_name == 'push' - run: pnpm exec commitlint --last --verbose + run: env-run pnpm exec commitlint --last --verbose - name: Validate PR commits with commitlint if: github.event_name == 'pull_request' - run: pnpm exec commitlint --from ${{ github.event.pull_request.head.sha }}~${{ github.event.pull_request.commits }} --to ${{ github.event.pull_request.head.sha }} --verbose + run: env-run pnpm exec commitlint --from ${{ github.event.pull_request.head.sha }}~${{ github.event.pull_request.commits }} --to ${{ github.event.pull_request.head.sha }} --verbose diff --git a/.github/workflows/python-build-tests.yaml b/.github/workflows/python-build-tests.yaml index eca92673..2eee83c7 100644 --- a/.github/workflows/python-build-tests.yaml +++ b/.github/workflows/python-build-tests.yaml @@ -4,18 +4,16 @@ on: push: paths: - '.github/workflows/python-build-tests.yaml' - - 'devenv.lock' - - 'devenv.nix' - - 'devenv.yaml' + - 'flake.nix' + - 'devshell.nix' - 'pyproject.toml' - 'requirements.txt' pull_request: paths: - '.github/workflows/python-build-tests.yaml' - - 'devenv.lock' - - 'devenv.nix' - - 'devenv.yaml' + - 'flake.nix' + - 'devshell.nix' - 'pyproject.toml' - 'requirements.txt' @@ -44,16 +42,8 @@ jobs: with: name: devenv - - uses: actions/setup-python@v5 - with: - python-version: "3.10.12" - - - name: Install devenv - run: nix profile install tarball+https://install.devenv.sh/latest - shell: sh - - name: Build developer environment - run: devenv shell -- echo "devenv built" + run: env-run echo "Devshell built" - name: Run SPPL tests - run: devenv shell -- python -m pytest --pyargs sppl + run: env-run python -m pytest --pyargs sppl diff --git a/.github/workflows/python-unit-tests.yaml b/.github/workflows/python-unit-tests.yaml index 4cea7060..c6bb6249 100644 --- a/.github/workflows/python-unit-tests.yaml +++ b/.github/workflows/python-unit-tests.yaml @@ -20,16 +20,8 @@ jobs: with: name: devenv - - uses: actions/setup-python@v5 - with: - python-version: "3.10.12" - - - name: Install devenv - run: nix profile install tarball+https://install.devenv.sh/latest - shell: sh - - name: Build developer environment - run: devenv shell -- echo "devenv built" + run: env-run echo "Devshell built" - name: Run Python tests - run: devenv shell -- python -m pytest test/scripts + run: env-run python -m pytest test/scripts diff --git a/.gitignore b/.gitignore index fc8abfc2..fdbf711d 100644 --- a/.gitignore +++ b/.gitignore @@ -30,3 +30,4 @@ sum-product-dsl/ .lsp/.cache/ .lsp/sqlite.*.db +.direnv/ diff --git a/bin/env-run b/bin/env-run new file mode 100755 index 00000000..c602ecfe --- /dev/null +++ b/bin/env-run @@ -0,0 +1,3 @@ +#!/usr/bin/env bash + +nix develop -c bash -c "$@" diff --git a/devenv.lock b/devenv.lock deleted file mode 100644 index aa7356e3..00000000 --- a/devenv.lock +++ /dev/null @@ -1,298 +0,0 @@ -{ - "nodes": { - "devenv": { - "locked": { - "dir": "src/modules", - "lastModified": 1712143604, - "owner": "cachix", - "repo": "devenv", - "rev": "6b274c61bc67e44885920c4c99389ee777bbce71", - "treeHash": "9f62793de434e026d0bc48cd93350cdfc13f2716", - "type": "github" - }, - "original": { - "dir": "src/modules", - "owner": "cachix", - "repo": "devenv", - "type": "github" - } - }, - "flake-compat": { - "flake": false, - "locked": { - "lastModified": 1696426674, - "owner": "edolstra", - "repo": "flake-compat", - "rev": "0f9255e01c2351cc7d116c072cb317785dd33b33", - "treeHash": "2addb7b71a20a25ea74feeaf5c2f6a6b30898ecb", - "type": "github" - }, - "original": { - "owner": "edolstra", - "repo": "flake-compat", - "type": "github" - } - }, - "flake-compat_2": { - "flake": false, - "locked": { - "lastModified": 1696426674, - "owner": "edolstra", - "repo": "flake-compat", - "rev": "0f9255e01c2351cc7d116c072cb317785dd33b33", - "treeHash": "2addb7b71a20a25ea74feeaf5c2f6a6b30898ecb", - "type": "github" - }, - "original": { - "owner": "edolstra", - "repo": "flake-compat", - "type": "github" - } - }, - "flake-utils": { - "inputs": { - "systems": "systems" - }, - "locked": { - "lastModified": 1710146030, - "owner": "numtide", - "repo": "flake-utils", - "rev": "b1d9ab70662946ef0850d488da1c9019f3a9752a", - "treeHash": "bd263f021e345cb4a39d80c126ab650bebc3c10c", - "type": "github" - }, - "original": { - "owner": "numtide", - "repo": "flake-utils", - "type": "github" - } - }, - "flake-utils_2": { - "inputs": { - "systems": "systems_2" - }, - "locked": { - "lastModified": 1710146030, - "owner": "numtide", - "repo": "flake-utils", - "rev": "b1d9ab70662946ef0850d488da1c9019f3a9752a", - "treeHash": "bd263f021e345cb4a39d80c126ab650bebc3c10c", - "type": "github" - }, - "original": { - "id": "flake-utils", - "type": "indirect" - } - }, - "flake-utils_3": { - "inputs": { - "systems": "systems_3" - }, - "locked": { - "lastModified": 1710146030, - "owner": "numtide", - "repo": "flake-utils", - "rev": "b1d9ab70662946ef0850d488da1c9019f3a9752a", - "treeHash": "bd263f021e345cb4a39d80c126ab650bebc3c10c", - "type": "github" - }, - "original": { - "owner": "numtide", - "repo": "flake-utils", - "type": "github" - } - }, - "gitignore": { - "inputs": { - "nixpkgs": [ - "pre-commit-hooks", - "nixpkgs" - ] - }, - "locked": { - "lastModified": 1709087332, - "owner": "hercules-ci", - "repo": "gitignore.nix", - "rev": "637db329424fd7e46cf4185293b9cc8c88c95394", - "treeHash": "ca14199cabdfe1a06a7b1654c76ed49100a689f9", - "type": "github" - }, - "original": { - "owner": "hercules-ci", - "repo": "gitignore.nix", - "type": "github" - } - }, - "mk-shell-bin": { - "locked": { - "lastModified": 1677004959, - "owner": "rrbutani", - "repo": "nix-mk-shell-bin", - "rev": "ff5d8bd4d68a347be5042e2f16caee391cd75887", - "treeHash": "496327dabdc787353a29987f492dd4939151baad", - "type": "github" - }, - "original": { - "owner": "rrbutani", - "repo": "nix-mk-shell-bin", - "type": "github" - } - }, - "nix2container": { - "inputs": { - "flake-utils": "flake-utils", - "nixpkgs": [ - "nixpkgs" - ] - }, - "locked": { - "lastModified": 1711883218, - "owner": "nlewo", - "repo": "nix2container", - "rev": "2154ad0459abfa258edaab038b4716f474656e99", - "treeHash": "d849a384060d067343dc61834cfdb482447d589b", - "type": "github" - }, - "original": { - "owner": "nlewo", - "repo": "nix2container", - "type": "github" - } - }, - "nixpkgs": { - "locked": { - "lastModified": 1712192574, - "owner": "NixOS", - "repo": "nixpkgs", - "rev": "f480f9d09e4b4cf87ee6151eba068197125714de", - "treeHash": "cefb9a3658fbb835a0a97ed92eab5cd82b8e21f6", - "type": "github" - }, - "original": { - "owner": "NixOS", - "ref": "nixpkgs-unstable", - "repo": "nixpkgs", - "type": "github" - } - }, - "nixpkgs-python": { - "inputs": { - "flake-compat": "flake-compat", - "flake-utils": "flake-utils_2", - "nixpkgs": [ - "nixpkgs" - ] - }, - "locked": { - "lastModified": 1712755059, - "owner": "cachix", - "repo": "nixpkgs-python", - "rev": "5f005810800ca2f106b891404326421e6699097a", - "treeHash": "0dc26d5c710abcaf1e8bcd8ce24cfd3588fab14e", - "type": "github" - }, - "original": { - "owner": "cachix", - "repo": "nixpkgs-python", - "type": "github" - } - }, - "nixpkgs-stable": { - "locked": { - "lastModified": 1712168706, - "owner": "NixOS", - "repo": "nixpkgs", - "rev": "1487bdea619e4a7a53a4590c475deabb5a9d1bfb", - "treeHash": "7b1978f9e075f83639f8caed78916f6b025e6519", - "type": "github" - }, - "original": { - "owner": "NixOS", - "ref": "nixos-23.11", - "repo": "nixpkgs", - "type": "github" - } - }, - "pre-commit-hooks": { - "inputs": { - "flake-compat": "flake-compat_2", - "flake-utils": "flake-utils_3", - "gitignore": "gitignore", - "nixpkgs": [ - "nixpkgs" - ], - "nixpkgs-stable": "nixpkgs-stable" - }, - "locked": { - "lastModified": 1712055707, - "owner": "cachix", - "repo": "pre-commit-hooks.nix", - "rev": "e35aed5fda3cc79f88ed7f1795021e559582093a", - "treeHash": "41bee5f5bd9314a987ef3d7cba730fb6aa264a4e", - "type": "github" - }, - "original": { - "owner": "cachix", - "repo": "pre-commit-hooks.nix", - "type": "github" - } - }, - "root": { - "inputs": { - "devenv": "devenv", - "mk-shell-bin": "mk-shell-bin", - "nix2container": "nix2container", - "nixpkgs": "nixpkgs", - "nixpkgs-python": "nixpkgs-python", - "pre-commit-hooks": "pre-commit-hooks" - } - }, - "systems": { - "locked": { - "lastModified": 1681028828, - "owner": "nix-systems", - "repo": "default", - "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e", - "treeHash": "cce81f2a0f0743b2eb61bc2eb6c7adbe2f2c6beb", - "type": "github" - }, - "original": { - "owner": "nix-systems", - "repo": "default", - "type": "github" - } - }, - "systems_2": { - "locked": { - "lastModified": 1681028828, - "owner": "nix-systems", - "repo": "default", - "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e", - "treeHash": "cce81f2a0f0743b2eb61bc2eb6c7adbe2f2c6beb", - "type": "github" - }, - "original": { - "owner": "nix-systems", - "repo": "default", - "type": "github" - } - }, - "systems_3": { - "locked": { - "lastModified": 1681028828, - "owner": "nix-systems", - "repo": "default", - "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e", - "treeHash": "cce81f2a0f0743b2eb61bc2eb6c7adbe2f2c6beb", - "type": "github" - }, - "original": { - "owner": "nix-systems", - "repo": "default", - "type": "github" - } - } - }, - "root": "root", - "version": 7 -} diff --git a/devenv.nix b/devenv.nix deleted file mode 100644 index d5015d9d..00000000 --- a/devenv.nix +++ /dev/null @@ -1,56 +0,0 @@ -{ pkgs, config, ... }: - -{ - # https://devenv.sh/packages/ - packages = let - system-packages = with pkgs; [ - awscli2 - clj-kondo - parallel - xsv - duckdb - giflib - libgcc - ]; - python-packages = with config.languages.python.package.pkgs; [ - setuptools - numpy - pandas - scipy - duckdb - ]; - linux-only-pkgs = if pkgs.stdenv.isLinux then with pkgs; [ - libgcc - ] else []; - darwin-only-pkgs = if pkgs.stdenv.isDarwin then with pkgs; [ - ] else []; - in system-packages ++ python-packages ++ linux-only-pkgs ++ darwin-only-pkgs; - - enterShell = '' - pnpm install - export PYTHONPATH=$PWD/.venv/lib/python3.10/site-packages:$PYTHONPATH - parallel () { - command parallel --will-cite "$@"; - } - ''; - - # https://devenv.sh/languages/ - languages.clojure.enable = true; - - languages.javascript = { - enable = true; - corepack.enable = true; - }; - - languages.python = { - enable = true; - poetry = { - enable = true; - install = { - enable = true; - allExtras = true; - }; - activate.enable = true; - }; - }; -} diff --git a/devenv.yaml b/devenv.yaml deleted file mode 100644 index b94fd55c..00000000 --- a/devenv.yaml +++ /dev/null @@ -1,15 +0,0 @@ -inputs: - nix2container: - url: github:nlewo/nix2container - inputs: - nixpkgs: - follows: nixpkgs - nixpkgs-python: - url: github:cachix/nixpkgs-python - inputs: - nixpkgs: - follows: nixpkgs - nixpkgs: - url: github:NixOS/nixpkgs/nixpkgs-unstable - mk-shell-bin: - url: github:rrbutani/nix-mk-shell-bin diff --git a/devshell.nix b/devshell.nix new file mode 100644 index 00000000..3f6f4c55 --- /dev/null +++ b/devshell.nix @@ -0,0 +1,76 @@ +{ ... }: +{ + perSystem = { config, self', inputs', pkgs, system, ... }: + let + inherit (pkgs) lib; + + python = pkgs.python310; + + nodejs = pkgs.nodejs_20; + pnpm = (pkgs.runCommand "corepack-enable" { } '' + mkdir -p $out/bin + ${nodejs}/bin/corepack enable --install-directory $out/bin + ''); + + parallel = (pkgs.writeScriptBin "parallel" '' + ${lib.getExe pkgs.parallel} --will-cite "$@" + ''); + + system-packages = (with pkgs; [ + awscli2 + parallel + xsv + + clojure + clj-kondo + + nodejs + pnpm + + python + poetry + ]); + + linux-only-pkgs = lib.optionals pkgs.stdenv.isLinux (with pkgs; [ + libgcc + libz + stdenv.cc.cc + ]); + + darwin-only-pkgs = lib.optionals pkgs.stdenv.isDarwin (with pkgs; [ + darwin.apple_sdk.frameworks.CoreText + ]); + + packages = builtins.concatLists [ + system-packages + linux-only-pkgs + darwin-only-pkgs + ]; + + lib-path = pkgs.lib.makeLibraryPath packages; + in + { + devShells.default = pkgs.mkShell { + inherit packages; + + shellHook = '' + export LD_LIBRARY_PATH="${lib-path}:$LD_LIBRARY_PATH" + + pnpm install + + poetry config virtualenvs.path $(pwd)/.venv + poetry env use ${python}/bin/python + + # We need to set PYTHON_KEYRING_BACKEND to use the null backend as + # `poetry install` will hang waiting for the keyring access on some + # distros + PYTHON_KEYRING_BACKEND=keyring.backends.null.Keyring \ + poetry install --no-root + export PATH="$(poetry env info -p)/bin:$PWD/bin:$PATH" + + mkdir -p .dvc/cache + dvc cache dir .dvc/cache + ''; + }; + }; +} diff --git a/dvc.lock b/dvc.lock new file mode 100644 index 00000000..1a889632 --- /dev/null +++ b/dvc.lock @@ -0,0 +1,796 @@ +schema: '2.0' +stages: + subsample: + cmd: "mkdir -p data/test && python scripts/subsample.py --data data/data.csv --test-data-dir + data/test --params params.yaml --output data/subsampled.csv\n" + deps: + - path: data/data.csv + hash: md5 + md5: 2652c974be9aa49bd50061377d39563d + size: 313452 + - path: scripts/subsample.py + hash: md5 + md5: e984c015340dc2e50d926b4e3931b9dd + size: 1821 + params: + params.yaml: + seed: 0 + sub_sample: + N: 1000 + outs: + - path: data/subsampled.csv + hash: md5 + md5: 54da26f21f0fee6db642e1761ebe69b9 + size: 268196 + - path: data/test + hash: md5 + md5: b8d3099ce11e7976c280f51cf51cbb96.dir + size: 45938 + nfiles: 2 + validate-column-names: + cmd: bin/validate.sh + deps: + - path: data/subsampled.csv + hash: md5 + md5: 54da26f21f0fee6db642e1761ebe69b9 + size: 268196 + outs: + - path: data/validated.csv + hash: md5 + md5: 54da26f21f0fee6db642e1761ebe69b9 + size: 268196 + nullify: + cmd: "clojure -X gensql.structure-learning.main/nullify < data/validated.csv > + data/nullified.csv\n" + deps: + - path: data/validated.csv + hash: md5 + md5: 54da26f21f0fee6db642e1761ebe69b9 + size: 268196 + params: + params.yaml: + nullify: + outs: + - path: data/nullified.csv + hash: md5 + md5: 54da26f21f0fee6db642e1761ebe69b9 + size: 268196 + guess-schema: + cmd: "clojure -X gensql.structure-learning.main/guess-schema < data/nullified.csv + > data/schema.edn\n" + deps: + - path: data/nullified.csv + hash: md5 + md5: 54da26f21f0fee6db642e1761ebe69b9 + size: 268196 + params: + params.yaml: + schema: + outs: + - path: data/schema.edn + hash: md5 + md5: 50689cad3539b17cfc255d6dc2545e1c + size: 601 + cgpm-schema: + cmd: "clojure -X gensql.structure-learning.main/cgpm-schema < data/schema.edn + > data/cgpm-schema.edn\n" + deps: + - path: data/schema.edn + hash: md5 + md5: 50689cad3539b17cfc255d6dc2545e1c + size: 601 + outs: + - path: data/cgpm-schema.edn + hash: md5 + md5: 7e6b6810bece6d68677b7f69b0a9bb6b + size: 186 + ignore: + cmd: "clojure -X gensql.structure-learning.main/ignore :schema '\"data/schema.edn\"\ + ' < data/nullified.csv > data/ignored.csv\n" + deps: + - path: data/nullified.csv + hash: md5 + md5: 54da26f21f0fee6db642e1761ebe69b9 + size: 268196 + - path: data/schema.edn + hash: md5 + md5: 50689cad3539b17cfc255d6dc2545e1c + size: 601 + outs: + - path: data/ignored.csv + hash: md5 + md5: 5ffeb41f4182b8f7f062b5f13230557d + size: 77540 + numericalize: + cmd: "clojure -X gensql.structure-learning.main/numericalize :schema '\"data/schema.edn\"\ + ' :table data/mapping-table.edn < data/ignored.csv > data/numericalized.csv\n" + deps: + - path: data/ignored.csv + hash: md5 + md5: 5ffeb41f4182b8f7f062b5f13230557d + size: 77540 + - path: data/schema.edn + hash: md5 + md5: 50689cad3539b17cfc255d6dc2545e1c + size: 601 + outs: + - path: data/mapping-table.edn + hash: md5 + md5: 1d3e7314f20a2b2d50deff70b323f428 + size: 3210 + - path: data/numericalized.csv + hash: md5 + md5: 345eaad4a50da45d1f4d50d326de0f2b + size: 11932 + loom-schema: + cmd: "clojure -X gensql.structure-learning.main/loom-schema < data/schema.edn + > data/loom-schema.json\n" + deps: + - path: data/schema.edn + hash: md5 + md5: 50689cad3539b17cfc255d6dc2545e1c + size: 601 + outs: + - path: data/loom-schema.json + hash: md5 + md5: 68f027a12982e5d4f01f40fe0450b281 + size: 127 + loom-ingest: + cmd: ./bin/loom_task ingest loom data/loom-schema.json data/numericalized.csv + deps: + - path: data/loom-schema.json + hash: md5 + md5: 68f027a12982e5d4f01f40fe0450b281 + size: 127 + - path: data/numericalized.csv + hash: md5 + md5: 345eaad4a50da45d1f4d50d326de0f2b + size: 11932 + outs: + - path: loom/ingest + hash: md5 + md5: 3ff3e980d06fb994c378deaacde35ef5.dir + size: 17782 + nfiles: 7 + - path: loom/query + hash: md5 + md5: 06a58186f51973bdc17aa20755a5ed32.dir + size: 106 + nfiles: 1 + loom-infer-config: + cmd: "clojure -X gensql.structure-learning.main/infer-config < params.yaml > data/infer-config.json\n" + params: + params.yaml: + loom.extra_passes: 1 + seed: 0 + outs: + - path: data/infer-config.json + hash: md5 + md5: 3781d3c543c1a1f8977a7d2ff1c4601c + size: 40 + loom-infer: + cmd: ./bin/loom_task infer loom 3 data/infer-config.json + deps: + - path: data/infer-config.json + hash: md5 + md5: 3781d3c543c1a1f8977a7d2ff1c4601c + size: 40 + - path: loom/ingest + hash: md5 + md5: 3ff3e980d06fb994c378deaacde35ef5.dir + size: 17782 + nfiles: 7 + - path: loom/query + hash: md5 + md5: 06a58186f51973bdc17aa20755a5ed32.dir + size: 106 + nfiles: 1 + params: + params.yaml: + sample_count: 3 + outs: + - path: loom/samples + hash: md5 + md5: 248f9d3a1ea8e7fd842dec7f0ebbd050.dir + size: 52521 + nfiles: 22 + loom-dump-metadata: + cmd: "mkdir -p data/cgpm/raw && find loom/samples -mindepth 1 -maxdepth 1 -type + d | parallel --verbose ./bin/loom python scripts/loom_dump.py {} --output data/cgpm/raw/{/}.json\n" + deps: + - path: loom/samples + hash: md5 + md5: 248f9d3a1ea8e7fd842dec7f0ebbd050.dir + size: 52521 + nfiles: 22 + - path: scripts/loom_dump.py + hash: md5 + md5: c43616fe12258e9314fe1b481a6971e8 + size: 1978 + params: + params.yaml: + parallel.flags: --verbose + outs: + - path: data/cgpm/raw + hash: md5 + md5: e575cb2e33443ba82f8d4c450180a5bc.dir + size: 12284 + nfiles: 3 + cgpm-hydrate-metadata: + cmd: "find data/cgpm/raw -type f | parallel jsonschema --instance {} schemas/cgpm.json + && mkdir -p data/cgpm/hydrated && rm -f data/cgpm/inf.log && find data/cgpm/raw + -type f | sort | parallel --verbose 'python scripts/cgpm_hydrate.py --metadata + {} --output data/cgpm/hydrated/{/} --data data/numericalized.csv --schema data/cgpm-schema.edn + --mapping-table data/mapping-table.edn --seed $((0 + {#} - 1))'\n" + deps: + - path: data/cgpm-schema.edn + hash: md5 + md5: 7e6b6810bece6d68677b7f69b0a9bb6b + size: 186 + - path: data/cgpm/raw + hash: md5 + md5: e575cb2e33443ba82f8d4c450180a5bc.dir + size: 12284 + nfiles: 3 + - path: data/mapping-table.edn + hash: md5 + md5: 1d3e7314f20a2b2d50deff70b323f428 + size: 3210 + - path: data/numericalized.csv + hash: md5 + md5: 345eaad4a50da45d1f4d50d326de0f2b + size: 11932 + - path: schemas/cgpm.json + hash: md5 + md5: 75fb21013e98a73e03fbe1ace14426f2 + size: 4039 + - path: scripts/cgpm_hydrate.py + hash: md5 + md5: 0ad32ff550f8b45a3642bddf279c9664 + size: 2971 + params: + params.yaml: + parallel.flags: --verbose + seed: 0 + outs: + - path: data/cgpm/hydrated + hash: md5 + md5: f0b203a84011a47c6efc7ce8e411898e.dir + size: 125827 + nfiles: 3 + cgpm-infer-hyperparameters: + cmd: "find data/cgpm/hydrated -type f | parallel jsonschema --instance {} schemas/cgpm.json + && mkdir -p data/cgpm/complete && echo 1 >> data/cgpm/inf.log && find data/cgpm/hydrated + -type f | sort | parallel --verbose 'python scripts/cgpm_infer.py {} --kernel + alpha --kernel view_alphas --kernel column_hypers --kernel rows --kernel columns + --output data/cgpm/complete/{/} --data data/numericalized.csv --params params.yaml + --seed $((0 + {#} - 1)) --minutes 1' #--iterations 1\n" + deps: + - path: data/cgpm/hydrated + hash: md5 + md5: f0b203a84011a47c6efc7ce8e411898e.dir + size: 125827 + nfiles: 3 + - path: data/numericalized.csv + hash: md5 + md5: 345eaad4a50da45d1f4d50d326de0f2b + size: 11932 + - path: schemas/cgpm.json + hash: md5 + md5: 75fb21013e98a73e03fbe1ace14426f2 + size: 4039 + - path: scripts/cgpm_infer.py + hash: md5 + md5: 8c953870a8ac391bb77deeb105403131 + size: 4523 + params: + params.yaml: + cgpm: + iterations: 1 + minutes: 1 + parallel.flags: --verbose + seed: 0 + outs: + - path: data/cgpm/complete + hash: md5 + md5: e63d45fe2ed5ab8a01d871b6f7ec05e9.dir + size: 117861 + nfiles: 3 + save-dependencies: + cmd: "find data/cgpm/complete -type f | sort | xargs python scripts/dep_prob.py + --data data/numericalized.csv --output data/dep-prob.json\n" + deps: + - path: data/cgpm/complete + hash: md5 + md5: e63d45fe2ed5ab8a01d871b6f7ec05e9.dir + size: 117861 + nfiles: 3 + outs: + - path: data/dep-prob.json + hash: md5 + md5: 03184adcfc0c6721bd5cdabef8098169 + size: 774 + save-max-number-views: + cmd: "find data/cgpm/complete -type f | xargs python scripts/save_n_views.py >> + data/max-number-views.txt\n" + deps: + - path: data/cgpm/complete + hash: md5 + md5: e63d45fe2ed5ab8a01d871b6f7ec05e9.dir + size: 117861 + nfiles: 3 + outs: + - path: data/max-number-views.txt + hash: md5 + md5: c4ca4238a0b923820dcc509a6f75849b + size: 1 + dep-prob-vl: + cmd: "clojure -X gensql.structure-learning.heatmap/vega-lite :stats-path '\"data/dep-prob.json\"\ + ' :domain '[0.0 1.0]' :default 1.0 :name '\"crosscat\"' :scheme '\"blues\"' + > data/dep-prob.vl.json\n" + deps: + - path: data/dep-prob.json + hash: md5 + md5: 03184adcfc0c6721bd5cdabef8098169 + size: 774 + - path: src/clojure/gensql/structure_learning/heatmap.clj + hash: md5 + md5: 1a9cd1bb8a534431a3836ed066758616 + size: 7364 + outs: + - path: data/dep-prob.vl.json + hash: md5 + md5: e8678ddc010f3b17c3d3d7ede9d09679 + size: 2852 + dep-prob-vg: + cmd: "pnpm vl2vg < data/dep-prob.vl.json > data/dep-prob.vg.json\n" + deps: + - path: data/dep-prob.vl.json + hash: md5 + md5: e8678ddc010f3b17c3d3d7ede9d09679 + size: 2852 + outs: + - path: data/dep-prob.vg.json + hash: md5 + md5: 90b6c1771e1d158da81074ad448005d8 + size: 4675 + dep-prob-svg: + cmd: "pnpm vg2svg < data/dep-prob.vg.json > data/dep-prob.svg\n" + deps: + - path: data/dep-prob.vg.json + hash: md5 + md5: 90b6c1771e1d158da81074ad448005d8 + size: 4675 + outs: + - path: data/dep-prob.svg + hash: md5 + md5: 0718cc6f9322663ea01449cf858ff65b + size: 13898 + save-linear-stats: + cmd: "python scripts/linear_stats.py --data data/ignored.csv --schema data/schema.edn + --output data/linear-stats.json\n" + deps: + - path: data/ignored.csv + hash: md5 + md5: 5ffeb41f4182b8f7f062b5f13230557d + size: 77540 + - path: data/schema.edn + hash: md5 + md5: 50689cad3539b17cfc255d6dc2545e1c + size: 601 + - path: scripts/linear_stats.py + hash: md5 + md5: d5ebd4d1195a949b7c66ea7b77447f11 + size: 4361 + outs: + - path: data/linear-stats.json + hash: md5 + md5: d5e5ecd37ebd8d5cd03c1bbd6a6fe7f6 + size: 2899 + linear-stats-vl: + cmd: "clojure -X gensql.structure-learning.heatmap/vega-lite :stats-path '\"data/linear-stats.json\"\ + ' :sort-path '\"data/dep-prob.json\"' :domain '[1.0 0.0]' :default 0.0 :name + '\"statistics\"' :field '\"p-value\"' :scheme '\"oranges\"' > data/linear-stats.vl.json\n" + deps: + - path: data/dep-prob.json + hash: md5 + md5: 03184adcfc0c6721bd5cdabef8098169 + size: 774 + - path: data/linear-stats.json + hash: md5 + md5: d5e5ecd37ebd8d5cd03c1bbd6a6fe7f6 + size: 2899 + - path: src/clojure/gensql/structure_learning/heatmap.clj + hash: md5 + md5: 1a9cd1bb8a534431a3836ed066758616 + size: 7364 + outs: + - path: data/linear-stats.vl.json + hash: md5 + md5: 1d564d040268106c284b268dd7618abd + size: 3489 + linear-stats-vg: + cmd: "pnpm vl2vg < data/linear-stats.vl.json > data/linear-stats.vg.json\n" + deps: + - path: data/linear-stats.vl.json + hash: md5 + md5: 1d564d040268106c284b268dd7618abd + size: 3489 + outs: + - path: data/linear-stats.vg.json + hash: md5 + md5: a7e6eba1560d847892d815d127e76d8a + size: 5381 + linear-stats-svg: + cmd: "pnpm vg2svg < data/linear-stats.vg.json > data/linear-stats.svg\n" + deps: + - path: data/linear-stats.vg.json + hash: md5 + md5: a7e6eba1560d847892d815d127e76d8a + size: 5381 + outs: + - path: data/linear-stats.svg + hash: md5 + md5: 7eb988a7222ad2519f5819f6ea22da85 + size: 14507 + compare-dep-prob-with-linear: + cmd: "python scripts/compare_deps.py --deps data/dep-prob.json --linear data/linear-stats.json + >> data/qc-statistical-tests.txt\n" + deps: + - path: data/dep-prob.json + hash: md5 + md5: 03184adcfc0c6721bd5cdabef8098169 + size: 774 + - path: data/linear-stats.json + hash: md5 + md5: d5e5ecd37ebd8d5cd03c1bbd6a6fe7f6 + size: 2899 + outs: + - path: data/qc-statistical-tests.txt + hash: md5 + md5: 0d13981f8869abf58feab894ba234aa2 + size: 344 + ast-export: + cmd: + - 'parallel --verbose jsonschema --instance {} schemas/cgpm.json :::: <(find data/cgpm/complete + -type f)' + - mkdir -p data/ast + - "parallel --verbose 'python scripts/ast_export.py --metadata {} --data data/numericalized.csv + --mapping-table data/mapping-table.edn --output data/ast/{/.}.edn' :::: <(find + data/cgpm/complete -type f)" + deps: + - path: data/cgpm/complete + hash: md5 + md5: e63d45fe2ed5ab8a01d871b6f7ec05e9.dir + size: 117861 + nfiles: 3 + - path: data/ignored.csv + hash: md5 + md5: 5ffeb41f4182b8f7f062b5f13230557d + size: 77540 + - path: scripts/ast_export.py + hash: md5 + md5: 301e377deb0aaf75b1a961a6d91153a8 + size: 11045 + params: + params.yaml: + parallel.flags: --verbose + outs: + - path: data/ast + hash: md5 + md5: 6804e574a891197975557eac0a7a8b33.dir + size: 98676 + nfiles: 3 + sppl-import: + cmd: + - mkdir -p data/sppl/unmerged + - "parallel --verbose 'python scripts/sppl_import.py --multi-mix-ast {} --max-number-views + data/max-number-views.txt --output data/sppl/unmerged/{/.}.json' :::: <(find + data/ast -type f)" + deps: + - path: data/ast + hash: md5 + md5: 6804e574a891197975557eac0a7a8b33.dir + size: 98676 + nfiles: 3 + - path: data/max-number-views.txt + hash: md5 + md5: c4ca4238a0b923820dcc509a6f75849b + size: 1 + - path: scripts/sppl_import.py + hash: md5 + md5: 60da181980209f224dd1ed4f8b92c57e + size: 4743 + params: + params.yaml: + parallel.flags: --verbose + outs: + - path: data/sppl/unmerged + hash: md5 + md5: d9c3a37cfb87251994ca43d12c9b7bfc.dir + size: 77928 + nfiles: 3 + sppl-merge: + cmd: "find data/sppl/unmerged -type f | sort | xargs python scripts/sppl_merge.py + --output data/sppl/merged.json\n" + deps: + - path: data/sppl/unmerged + hash: md5 + md5: d9c3a37cfb87251994ca43d12c9b7bfc.dir + size: 77928 + nfiles: 3 + outs: + - path: data/sppl/merged.json + hash: md5 + md5: 9d82bb9f10f513862b1ee3b56899705d + size: 78409 + sppl-sample: + cmd: "python scripts/sppl_sample.py --model data/sppl/merged.json --data data/ignored.csv + > data/synthetic-data-gensql.csv # --sample_count 1000\n" + deps: + - path: data/ignored.csv + hash: md5 + md5: 5ffeb41f4182b8f7f062b5f13230557d + size: 77540 + - path: data/sppl/merged.json + hash: md5 + md5: 9d82bb9f10f513862b1ee3b56899705d + size: 78409 + - path: scripts/sppl_sample.py + hash: md5 + md5: 65c711874e0eda0e7d79b4a4a3eb6076 + size: 1843 + outs: + - path: data/synthetic-data-gensql.csv + hash: md5 + md5: 0de97a209335fac737390e4387012d16 + size: 85251 + qc-tag-samples: + cmd: "clojure -X gensql.structure-learning.qc.samples/tag :data data/ignored.csv + :samples-synthetic data/synthetic-data-gensql.csv > qc/samples/samples.edn\n" + deps: + - path: data/ignored.csv + hash: md5 + md5: 5ffeb41f4182b8f7f062b5f13230557d + size: 77540 + - path: data/synthetic-data-gensql.csv + hash: md5 + md5: 0de97a209335fac737390e4387012d16 + size: 85251 + - path: src/clojure/gensql/structure_learning/qc/samples.clj + hash: md5 + md5: e34e26db3736bb02dd084800c9d6af72 + size: 1090 + outs: + - path: qc/samples/samples.edn + hash: md5 + md5: bcb68c57e40d921a6095485224181ef9 + size: 443141 + xcat-complete-import: + cmd: + - mkdir -p data/xcat/complete/ + - "parallel --verbose 'clojure -X gensql.structure-learning.xcat/import :cgpm-json + {} :data-csv data/ignored.csv :mapping-table data/mapping-table.edn :numericalized-csv + data/numericalized.csv :schema-edn data/schema.edn > data/xcat/complete/{/.}.edn' + :::: <(find data/cgpm/complete -type f)" + deps: + - path: data/cgpm/complete + hash: md5 + md5: e63d45fe2ed5ab8a01d871b6f7ec05e9.dir + size: 117861 + nfiles: 3 + - path: data/ignored.csv + hash: md5 + md5: 5ffeb41f4182b8f7f062b5f13230557d + size: 77540 + - path: data/mapping-table.edn + hash: md5 + md5: 1d3e7314f20a2b2d50deff70b323f428 + size: 3210 + - path: data/numericalized.csv + hash: md5 + md5: 345eaad4a50da45d1f4d50d326de0f2b + size: 11932 + - path: data/schema.edn + hash: md5 + md5: 50689cad3539b17cfc255d6dc2545e1c + size: 601 + - path: src/clojure/gensql/structure_learning/xcat.clj + hash: md5 + md5: 50de15b94242c6c71b6822f11cb58771 + size: 4592 + params: + params.yaml: + parallel.flags: --verbose + outs: + - path: data/xcat/complete/ + hash: md5 + md5: 40c28c7e82357f816a2e4a1199b7c45f.dir + size: 783312 + nfiles: 3 + xcat-merge: + cmd: "clj -X gensql.structure-learning.clojurecat/merge :models data/xcat/complete + :out data/xcat/xcat.merged.edn\n" + deps: + - path: data/xcat/complete + hash: md5 + md5: 40c28c7e82357f816a2e4a1199b7c45f.dir + size: 783312 + nfiles: 3 + outs: + - path: data/xcat/xcat.merged.edn + hash: md5 + md5: 95bb195d42b4b04cbc6743f542ce9c2e + size: 783360 + qc-dashboard-spec: + cmd: "clojure -X gensql.structure-learning.qc.dashboard/spec :samples qc/samples/samples.edn + :schema data/schema.edn :correlation data/linear-stats.json > qc/specs/qc-dashboard.vl.json\n" + deps: + - path: data/linear-stats.json + hash: md5 + md5: d5e5ecd37ebd8d5cd03c1bbd6a6fe7f6 + size: 2899 + - path: data/schema.edn + hash: md5 + md5: 50689cad3539b17cfc255d6dc2545e1c + size: 601 + - path: qc/samples/samples.edn + hash: md5 + md5: bcb68c57e40d921a6095485224181ef9 + size: 443141 + - path: src/clojure/gensql/structure_learning/qc/dashboard.clj + hash: md5 + md5: 11529f94587a9ade1d3fa4cb84ff0445 + size: 28313 + - path: src/clojure/gensql/structure_learning/qc/util.clj + hash: md5 + md5: 57e1815724c43afbd84c9414d32a4aee + size: 4118 + params: + params.yaml: + qc.columns: + outs: + - path: qc/specs/qc-dashboard.vl.json + hash: md5 + md5: 1f6818aca8c5016aa6f7437ebc92b269 + size: 498453 + qc-dashboard-app: + cmd: "clojure -X gensql.structure-learning.qc.app/create :template qc/templates/index.html + :spec qc/specs/qc-dashboard.vl.json :renderer canvas :title '\"QC dashboard\"\ + ' > qc/app/qc-dashboard.html\n" + deps: + - path: qc/specs/qc-dashboard.vl.json + hash: md5 + md5: 1f6818aca8c5016aa6f7437ebc92b269 + size: 498453 + - path: qc/templates/index.html + hash: md5 + md5: ac51efb107febc1caf14b5e2c6d0489d + size: 1685 + - path: src/clojure/gensql/structure_learning/qc/app.clj + hash: md5 + md5: 4a24b05e49591694f1019ed876596ea6 + size: 519 + outs: + - path: qc/app/qc-dashboard.html + hash: md5 + md5: b687400ea5f3351727f73e6a081a145e + size: 500127 + qc-splom-spec: + cmd: "clojure -X gensql.structure-learning.qc.splom/spec :samples qc/samples/samples.edn + :schema data/schema.edn :correlation data/linear-stats.json > qc/specs/qc-splom.vl.json\n" + deps: + - path: data/linear-stats.json + hash: md5 + md5: d5e5ecd37ebd8d5cd03c1bbd6a6fe7f6 + size: 2899 + - path: data/schema.edn + hash: md5 + md5: 50689cad3539b17cfc255d6dc2545e1c + size: 601 + - path: qc/samples/samples.edn + hash: md5 + md5: bcb68c57e40d921a6095485224181ef9 + size: 443141 + - path: src/clojure/gensql/structure_learning/qc/splom.clj + hash: md5 + md5: a753879cef043c55d23dea202b41abe5 + size: 10862 + - path: src/clojure/gensql/structure_learning/qc/util.clj + hash: md5 + md5: 57e1815724c43afbd84c9414d32a4aee + size: 4118 + params: + params.yaml: + qc.columns: + outs: + - path: qc/specs/qc-splom.vl.json + hash: md5 + md5: a773bb0246bff52bb254101ca2c32960 + size: 489264 + qc-splom-app: + cmd: "clojure -X gensql.structure-learning.qc.app/create :template qc/templates/index.html + :spec qc/specs/qc-splom.vl.json :renderer canvas :title '\"QC scatter plot matrix\"\ + ' > qc/app/qc-splom.html\n" + deps: + - path: qc/specs/qc-splom.vl.json + hash: md5 + md5: a773bb0246bff52bb254101ca2c32960 + size: 489264 + - path: qc/templates/index.html + hash: md5 + md5: ac51efb107febc1caf14b5e2c6d0489d + size: 1685 + - path: src/clojure/gensql/structure_learning/qc/app.clj + hash: md5 + md5: 4a24b05e49591694f1019ed876596ea6 + size: 519 + outs: + - path: qc/app/qc-splom.html + hash: md5 + md5: 0f6cfb9dfcec8c01170cf7422433f134 + size: 490948 + predict: + cmd: "python scripts/predict.py --schema data/schema.edn --training data/ignored.csv + --training data/synthetic-data-gensql.csv --test data/test/test.csv --output + data/predictions.csv #--test data/test/test-shifted.csv\n" + deps: + - path: data/ignored.csv + hash: 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data/nullified.csv + hash: md5 + md5: 54da26f21f0fee6db642e1761ebe69b9 + size: 268196 + - path: data/xcat + hash: md5 + md5: 47cc75147058b9a3c9ca48b28ee4fe92.dir + size: 1566672 + nfiles: 4 + params: + params.yaml: + database.model_name: baseline_model + database.model_path: data/xcat/xcat.merged.edn + database.table_name: data + database.table_path: data/nullified.csv + outs: + - path: data/db.edn + hash: md5 + md5: b28c957e4b8c1a3d0b7bfeb0326679bc + size: 1423031 diff --git a/flake.lock b/flake.lock new file mode 100644 index 00000000..6ee48155 --- /dev/null +++ b/flake.lock @@ -0,0 +1,64 @@ +{ + "nodes": { + "flake-parts": { + "inputs": { + "nixpkgs-lib": [ + "nixpkgs" + ] + }, + "locked": { + "lastModified": 1715865404, + "narHash": "sha256-/GJvTdTpuDjNn84j82cU6bXztE0MSkdnTWClUCRub78=", + "owner": "hercules-ci", + "repo": "flake-parts", + "rev": "8dc45382d5206bd292f9c2768b8058a8fd8311d9", + "type": "github" + }, + "original": { + "owner": "hercules-ci", + "repo": "flake-parts", + "type": "github" + } + }, + "nixpkgs": { + "locked": { + "lastModified": 1716509168, + "narHash": "sha256-4zSIhSRRIoEBwjbPm3YiGtbd8HDWzFxJjw5DYSDy1n8=", + "owner": "NixOS", + "repo": "nixpkgs", + "rev": "bfb7a882678e518398ce9a31a881538679f6f092", + "type": "github" + }, + "original": { + "owner": "NixOS", + "ref": "nixos-unstable", + "repo": "nixpkgs", + "type": "github" + } + }, + "root": { + "inputs": { + "flake-parts": "flake-parts", + "nixpkgs": "nixpkgs", + "systems": "systems" + } + }, + "systems": { + "locked": { + "lastModified": 1681028828, + "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=", + "owner": "nix-systems", + "repo": "default", + "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e", + "type": "github" + }, + "original": { + "owner": "nix-systems", + "repo": "default", + "type": "github" + } + } + }, + "root": "root", + "version": 7 +} diff --git a/flake.nix b/flake.nix new file mode 100644 index 00000000..dd385b4c --- /dev/null +++ b/flake.nix @@ -0,0 +1,18 @@ +{ + description = "Description for the project"; + + inputs = { + flake-parts.url = "github:hercules-ci/flake-parts"; + flake-parts.inputs.nixpkgs-lib.follows = "nixpkgs"; + + nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable"; + + systems.url = "github:nix-systems/default"; + }; + + outputs = inputs@{ flake-parts, systems, ... }: + flake-parts.lib.mkFlake { inherit inputs; } { + imports = [ ./devshell.nix ]; + systems = import systems; + }; +} diff --git a/package.json b/package.json index 57233e1c..f7bf125d 100644 --- a/package.json +++ b/package.json @@ -13,5 +13,6 @@ "devDependencies": { "@commitlint/cli": "^19.3.0", "@commitlint/config-conventional": "^19.2.2" - } + }, + "packageManager": "pnpm@9.1.2+sha1.907f57a52517de34399d66401bf220a549e47b57" } diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml index 98648675..4aac752f 100644 --- a/pnpm-lock.yaml +++ b/pnpm-lock.yaml @@ -1,75 +1,1817 @@ -lockfileVersion: '6.0' +lockfileVersion: '9.0' settings: autoInstallPeers: true 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hash = "sha256:928cecb0ef9d5a7946eb6ff58417ad2fe9375762382f1bf5c55e61645f2c43ad"}, + {file = "yarl-1.9.4.tar.gz", hash = "sha256:566db86717cf8080b99b58b083b773a908ae40f06681e87e589a976faf8246bf"}, ] [package.dependencies] @@ -3483,5 +3785,5 @@ test = ["zope.testing"] [metadata] lock-version = "2.0" -python-versions = "3.10.12" -content-hash = "af2029c040dd607934c2baaa3879b450ade400ca6fc35bf7d154e2fb4cc76c71" +python-versions = "~3.10.12" +content-hash = "a07e3c46e52b75a63d2bd9f23083059ed3d53a15902b4302750696f4741f1e0e" diff --git a/pyproject.toml b/pyproject.toml index 8fdb4a41..d789fddb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,10 +7,10 @@ license = "Apache-2.0" readme = "README.md" [tool.poetry.dependencies] -python = "3.10.12" -cgpm = {git = "https://github.com/probcomp/cgpm", branch = "zane/hardcode-version"} +python = "~3.10.12" +cgpm = {git = "https://github.com/probcomp/cgpm.git", branch = "zane/hardcode-version"} dvc = "^3.13.3" -sppl = {git = "https://github.com/probsys/sppl"} +sppl = {git = "https://github.com/probsys/sppl.git"} edn-format = "^0.7.5" jsonschema = "^4.19.0" catboost = "^1.2" From 6c80b42d5dcdcabe9d6b74d6d5245635d319bf8f Mon Sep 17 00:00:00 2001 From: Samuel Rounce Date: Tue, 28 May 2024 11:21:00 +0100 Subject: [PATCH 02/12] fix: Re-enable MacOS GH Actions runners --- .github/workflows/python-build-tests.yaml | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/.github/workflows/python-build-tests.yaml b/.github/workflows/python-build-tests.yaml index 2eee83c7..dc0c2024 100644 --- a/.github/workflows/python-build-tests.yaml +++ b/.github/workflows/python-build-tests.yaml @@ -21,10 +21,7 @@ jobs: run-tests: strategy: matrix: - # n.b. github actions macos runners are currently - # not supporting python 3.10.12. If we upgrade python - # we can resume these tests on mac, if we want to. - os: [ubuntu-latest] + os: [ ubuntu-latest, macos-latest ] runs-on: ${{ matrix.os }} From 648edc23cb9abc727c5d17717398f2aed1637eff Mon Sep 17 00:00:00 2001 From: Samuel Rounce Date: Tue, 28 May 2024 11:29:59 +0100 Subject: [PATCH 03/12] fix: Add pango, cairo deps to deveshell for node-canvas --- devshell.nix | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/devshell.nix b/devshell.nix index 3f6f4c55..82c12c05 100644 --- a/devshell.nix +++ b/devshell.nix @@ -29,6 +29,11 @@ python poetry + + cairo + pango + + pkg-config ]); linux-only-pkgs = lib.optionals pkgs.stdenv.isLinux (with pkgs; [ From 1b2ad2e4be748af105b3e9d6acfa8d86b121d918 Mon Sep 17 00:00:00 2001 From: Samuel Rounce Date: Tue, 4 Jun 2024 17:18:17 +0100 Subject: [PATCH 04/12] fix: Correct env-run paths in CI actions --- .github/workflows/clojure-lint.yaml | 4 ++-- .github/workflows/clojure-tests.yaml | 6 +++--- .github/workflows/commit-linter.yaml | 8 ++++---- .github/workflows/python-build-tests.yaml | 4 ++-- .github/workflows/python-unit-tests.yaml | 4 ++-- bin/env-run | 4 +++- 6 files changed, 16 insertions(+), 14 deletions(-) diff --git a/.github/workflows/clojure-lint.yaml b/.github/workflows/clojure-lint.yaml index cd502058..65aa5785 100644 --- a/.github/workflows/clojure-lint.yaml +++ b/.github/workflows/clojure-lint.yaml @@ -22,7 +22,7 @@ jobs: name: devenv - name: Build developer environment - run: env-run echo "Devshell built" + run: ./bin/env-run echo "Devshell built" - name: Lint files - run: env-run clj-kondo --lint deps.edn src bin test --config '{:output {:pattern "::{{level}} file={{filename}},line={{row}},col={{col}}::{{message}}"}}' + run: ./bin/env-run clj-kondo --lint deps.edn src bin test --config '{:output {:pattern "::{{level}} file={{filename}},line={{row}},col={{col}}::{{message}}"}}' diff --git a/.github/workflows/clojure-tests.yaml b/.github/workflows/clojure-tests.yaml index 9906dde4..45899b9a 100644 --- a/.github/workflows/clojure-tests.yaml +++ b/.github/workflows/clojure-tests.yaml @@ -22,10 +22,10 @@ jobs: name: devenv - name: Build developer environment - run: env-run echo "Devshell built" + run: ./bin/env-run echo "Devshell built" - name: Run Clojure tests - run: env-run clojure -X:test:clj-test + run: ./bin/env-run clojure -X:test:clj-test - name: Run ClojureScript tests - run: env-run clojure -M:test:cljs-test + run: ./bin/env-run clojure -M:test:cljs-test diff --git a/.github/workflows/commit-linter.yaml b/.github/workflows/commit-linter.yaml index 0e45334a..4970178f 100644 --- a/.github/workflows/commit-linter.yaml +++ b/.github/workflows/commit-linter.yaml @@ -25,19 +25,19 @@ jobs: - name: Install commitlint run: | - env-run pnpm install --frozen-lockfile + ./bin/env-run pnpm install --frozen-lockfile - name: Print versions run: | - env-run 'git --version && + ./bin/env-run 'git --version && node --version && pnpm --version && pnpm exec commitlint --version' - name: Validate current commit (last commit) with commitlint if: github.event_name == 'push' - run: env-run pnpm exec commitlint --last --verbose + run: ./bin/env-run pnpm exec commitlint --last --verbose - name: Validate PR commits with commitlint if: github.event_name == 'pull_request' - run: env-run pnpm exec commitlint --from ${{ github.event.pull_request.head.sha }}~${{ github.event.pull_request.commits }} --to ${{ github.event.pull_request.head.sha }} --verbose + run: ./bin/env-run pnpm exec commitlint --from ${{ github.event.pull_request.head.sha }}~${{ github.event.pull_request.commits }} --to ${{ github.event.pull_request.head.sha }} --verbose diff --git a/.github/workflows/python-build-tests.yaml b/.github/workflows/python-build-tests.yaml index dc0c2024..da5b2c56 100644 --- a/.github/workflows/python-build-tests.yaml +++ b/.github/workflows/python-build-tests.yaml @@ -40,7 +40,7 @@ jobs: name: devenv - name: Build developer environment - run: env-run echo "Devshell built" + run: ./bin/env-run echo "Devshell built" - name: Run SPPL tests - run: env-run python -m pytest --pyargs sppl + run: ./bin/env-run python -m pytest --pyargs sppl diff --git a/.github/workflows/python-unit-tests.yaml b/.github/workflows/python-unit-tests.yaml index c6bb6249..fbb1b3c4 100644 --- a/.github/workflows/python-unit-tests.yaml +++ b/.github/workflows/python-unit-tests.yaml @@ -21,7 +21,7 @@ jobs: name: devenv - name: Build developer environment - run: env-run echo "Devshell built" + run: ./bin/env-run echo "Devshell built" - name: Run Python tests - run: env-run python -m pytest test/scripts + run: ./bin/env-run python -m pytest test/scripts diff --git a/bin/env-run b/bin/env-run index c602ecfe..0e59fad5 100755 --- a/bin/env-run +++ b/bin/env-run @@ -1,3 +1,5 @@ #!/usr/bin/env bash -nix develop -c bash -c "$@" +set -euo pipefail + +nix develop -c bash -c "$(printf " %q" "${@}")" From bfb004d3621599e3e26f014e8d345952fe95c7ae Mon Sep 17 00:00:00 2001 From: Samuel Rounce Date: Tue, 4 Jun 2024 18:18:39 +0100 Subject: [PATCH 05/12] fix: Version mismatch of glibc causing lpm-fidelity to crash on invocation --- devshell.nix | 10 +- dvc.lock | 357 +++++++++++++++++++++++++++++++-------------------- dvc.yaml | 5 +- flake.lock | 166 +++++++++++++++++++++++- flake.nix | 5 +- 5 files changed, 394 insertions(+), 149 deletions(-) diff --git a/devshell.nix b/devshell.nix index 82c12c05..694e3117 100644 --- a/devshell.nix +++ b/devshell.nix @@ -17,6 +17,8 @@ ''); system-packages = (with pkgs; [ + nix + awscli2 parallel xsv @@ -34,12 +36,16 @@ pango pkg-config + + inputs'.lpm-fidelity.packages.default + inputs'.lpm-discretize.packages.default ]); linux-only-pkgs = lib.optionals pkgs.stdenv.isLinux (with pkgs; [ - libgcc - libz + gcc.cc.libgcc + zlib stdenv.cc.cc + libcxx ]); darwin-only-pkgs = lib.optionals pkgs.stdenv.isDarwin (with pkgs; [ diff --git a/dvc.lock b/dvc.lock index 1a889632..b25d046c 100644 --- a/dvc.lock +++ b/dvc.lock @@ -1,8 +1,8 @@ schema: '2.0' stages: subsample: - cmd: "mkdir -p data/test && python scripts/subsample.py --data data/data.csv --test-data-dir - data/test --params params.yaml --output data/subsampled.csv\n" + cmd: "mkdir -p data/test && python scripts/subsample.py --data data/data.csv --test-data-dir\ + \ data/test --params params.yaml --output data/subsampled.csv\n" deps: - path: data/data.csv hash: md5 @@ -40,8 +40,8 @@ stages: md5: 54da26f21f0fee6db642e1761ebe69b9 size: 268196 nullify: - cmd: "clojure -X gensql.structure-learning.main/nullify < data/validated.csv > - data/nullified.csv\n" + cmd: "clojure -X gensql.structure-learning.main/nullify < data/validated.csv >\ + \ data/nullified.csv\n" deps: - path: data/validated.csv hash: md5 @@ -56,8 +56,8 @@ stages: md5: 54da26f21f0fee6db642e1761ebe69b9 size: 268196 guess-schema: - cmd: "clojure -X gensql.structure-learning.main/guess-schema < data/nullified.csv - > data/schema.edn\n" + cmd: "clojure -X gensql.structure-learning.main/guess-schema < data/nullified.csv\ + \ > data/schema.edn\n" deps: - path: data/nullified.csv hash: md5 @@ -72,8 +72,8 @@ stages: md5: 50689cad3539b17cfc255d6dc2545e1c size: 601 cgpm-schema: - cmd: "clojure -X gensql.structure-learning.main/cgpm-schema < data/schema.edn - > data/cgpm-schema.edn\n" + cmd: "clojure -X gensql.structure-learning.main/cgpm-schema < data/schema.edn\ + \ > data/cgpm-schema.edn\n" deps: - path: data/schema.edn hash: md5 @@ -123,8 +123,8 @@ stages: md5: 345eaad4a50da45d1f4d50d326de0f2b size: 11932 loom-schema: - cmd: "clojure -X gensql.structure-learning.main/loom-schema < data/schema.edn - > data/loom-schema.json\n" + cmd: "clojure -X gensql.structure-learning.main/loom-schema < data/schema.edn\ + \ > data/loom-schema.json\n" deps: - path: data/schema.edn hash: md5 @@ -149,12 +149,12 @@ stages: outs: - path: loom/ingest hash: md5 - md5: 3ff3e980d06fb994c378deaacde35ef5.dir + md5: 442c82a1ca799f1a0a92ec930bf6fa9b.dir size: 17782 nfiles: 7 - path: loom/query hash: md5 - md5: 06a58186f51973bdc17aa20755a5ed32.dir + md5: 6e16965d6127bf5d755ebfb8b4f558c2.dir size: 106 nfiles: 1 loom-infer-config: @@ -177,12 +177,12 @@ stages: size: 40 - path: loom/ingest hash: md5 - md5: 3ff3e980d06fb994c378deaacde35ef5.dir + md5: 442c82a1ca799f1a0a92ec930bf6fa9b.dir size: 17782 nfiles: 7 - path: loom/query hash: md5 - md5: 06a58186f51973bdc17aa20755a5ed32.dir + md5: 6e16965d6127bf5d755ebfb8b4f558c2.dir size: 106 nfiles: 1 params: @@ -191,17 +191,18 @@ stages: outs: - path: loom/samples hash: md5 - md5: 248f9d3a1ea8e7fd842dec7f0ebbd050.dir - size: 52521 + md5: da9a3174280400cb1fd369db15678dd7.dir + size: 52543 nfiles: 22 loom-dump-metadata: - cmd: "mkdir -p data/cgpm/raw && find loom/samples -mindepth 1 -maxdepth 1 -type - d | parallel --verbose ./bin/loom python scripts/loom_dump.py {} --output data/cgpm/raw/{/}.json\n" + cmd: "mkdir -p data/cgpm/raw && find loom/samples -mindepth 1 -maxdepth 1 -type\ + \ d | parallel --verbose ./bin/loom python scripts/loom_dump.py {} --output\ + \ data/cgpm/raw/{/}.json\n" deps: - path: loom/samples hash: md5 - md5: 248f9d3a1ea8e7fd842dec7f0ebbd050.dir - size: 52521 + md5: da9a3174280400cb1fd369db15678dd7.dir + size: 52543 nfiles: 22 - path: scripts/loom_dump.py hash: md5 @@ -217,11 +218,12 @@ stages: size: 12284 nfiles: 3 cgpm-hydrate-metadata: - cmd: "find data/cgpm/raw -type f | parallel jsonschema --instance {} schemas/cgpm.json - && mkdir -p data/cgpm/hydrated && rm -f data/cgpm/inf.log && find data/cgpm/raw - -type f | sort | parallel --verbose 'python scripts/cgpm_hydrate.py --metadata - {} --output data/cgpm/hydrated/{/} --data data/numericalized.csv --schema data/cgpm-schema.edn - --mapping-table data/mapping-table.edn --seed $((0 + {#} - 1))'\n" + cmd: "find data/cgpm/raw -type f | parallel jsonschema --instance {} schemas/cgpm.json\ + \ && mkdir -p data/cgpm/hydrated && rm -f data/cgpm/inf.log && find data/cgpm/raw\ + \ -type f | sort | parallel --verbose 'python scripts/cgpm_hydrate.py --metadata\ + \ {} --output data/cgpm/hydrated/{/} --data data/numericalized.csv --schema\ + \ data/cgpm-schema.edn --mapping-table data/mapping-table.edn --seed $((0 +\ + \ {#} - 1))'\n" deps: - path: data/cgpm-schema.edn hash: md5 @@ -259,12 +261,12 @@ stages: size: 125827 nfiles: 3 cgpm-infer-hyperparameters: - cmd: "find data/cgpm/hydrated -type f | parallel jsonschema --instance {} schemas/cgpm.json - && mkdir -p data/cgpm/complete && echo 1 >> data/cgpm/inf.log && find data/cgpm/hydrated - -type f | sort | parallel --verbose 'python scripts/cgpm_infer.py {} --kernel - alpha --kernel view_alphas --kernel column_hypers --kernel rows --kernel columns - --output data/cgpm/complete/{/} --data data/numericalized.csv --params params.yaml - --seed $((0 + {#} - 1)) --minutes 1' #--iterations 1\n" + cmd: "find data/cgpm/hydrated -type f | parallel jsonschema --instance {} schemas/cgpm.json\ + \ && mkdir -p data/cgpm/complete && echo 1 >> data/cgpm/inf.log && find data/cgpm/hydrated\ + \ -type f | sort | parallel --verbose 'python scripts/cgpm_infer.py {} --kernel\ + \ alpha --kernel view_alphas --kernel column_hypers --kernel rows --kernel columns\ + \ --output data/cgpm/complete/{/} --data data/numericalized.csv --params params.yaml\ + \ --seed $((0 + {#} - 1)) --minutes 1' #--iterations 1\n" deps: - path: data/cgpm/hydrated hash: md5 @@ -293,17 +295,17 @@ stages: outs: - path: data/cgpm/complete hash: md5 - md5: e63d45fe2ed5ab8a01d871b6f7ec05e9.dir - size: 117861 + md5: b01aaee70e74d3ad3b3dcca27ab61313.dir + size: 117849 nfiles: 3 save-dependencies: - cmd: "find data/cgpm/complete -type f | sort | xargs python scripts/dep_prob.py - --data data/numericalized.csv --output data/dep-prob.json\n" + cmd: "find data/cgpm/complete -type f | sort | xargs python scripts/dep_prob.py\ + \ --data data/numericalized.csv --output data/dep-prob.json\n" deps: - path: data/cgpm/complete hash: md5 - md5: e63d45fe2ed5ab8a01d871b6f7ec05e9.dir - size: 117861 + md5: b01aaee70e74d3ad3b3dcca27ab61313.dir + size: 117849 nfiles: 3 outs: - path: data/dep-prob.json @@ -311,13 +313,13 @@ stages: md5: 03184adcfc0c6721bd5cdabef8098169 size: 774 save-max-number-views: - cmd: "find data/cgpm/complete -type f | xargs python scripts/save_n_views.py >> - data/max-number-views.txt\n" + cmd: "find data/cgpm/complete -type f | xargs python scripts/save_n_views.py >>\ + \ data/max-number-views.txt\n" deps: - path: data/cgpm/complete hash: md5 - md5: e63d45fe2ed5ab8a01d871b6f7ec05e9.dir - size: 117861 + md5: b01aaee70e74d3ad3b3dcca27ab61313.dir + size: 117849 nfiles: 3 outs: - path: data/max-number-views.txt @@ -326,8 +328,8 @@ stages: size: 1 dep-prob-vl: cmd: "clojure -X gensql.structure-learning.heatmap/vega-lite :stats-path '\"data/dep-prob.json\"\ - ' :domain '[0.0 1.0]' :default 1.0 :name '\"crosscat\"' :scheme '\"blues\"' - > data/dep-prob.vl.json\n" + ' :domain '[0.0 1.0]' :default 1.0 :name '\"crosscat\"' :scheme '\"blues\"'\ + \ > data/dep-prob.vl.json\n" deps: - path: data/dep-prob.json hash: md5 @@ -367,8 +369,8 @@ stages: md5: 0718cc6f9322663ea01449cf858ff65b size: 13898 save-linear-stats: - cmd: "python scripts/linear_stats.py --data data/ignored.csv --schema data/schema.edn - --output data/linear-stats.json\n" + cmd: "python scripts/linear_stats.py --data data/ignored.csv --schema data/schema.edn\ + \ --output data/linear-stats.json\n" deps: - path: data/ignored.csv hash: md5 @@ -389,8 +391,8 @@ stages: size: 2899 linear-stats-vl: cmd: "clojure -X gensql.structure-learning.heatmap/vega-lite :stats-path '\"data/linear-stats.json\"\ - ' :sort-path '\"data/dep-prob.json\"' :domain '[1.0 0.0]' :default 0.0 :name - '\"statistics\"' :field '\"p-value\"' :scheme '\"oranges\"' > data/linear-stats.vl.json\n" + ' :sort-path '\"data/dep-prob.json\"' :domain '[1.0 0.0]' :default 0.0 :name\ + \ '\"statistics\"' :field '\"p-value\"' :scheme '\"oranges\"' > data/linear-stats.vl.json\n" deps: - path: data/dep-prob.json hash: md5 @@ -434,8 +436,8 @@ stages: md5: 7eb988a7222ad2519f5819f6ea22da85 size: 14507 compare-dep-prob-with-linear: - cmd: "python scripts/compare_deps.py --deps data/dep-prob.json --linear data/linear-stats.json - >> data/qc-statistical-tests.txt\n" + cmd: "python scripts/compare_deps.py --deps data/dep-prob.json --linear data/linear-stats.json\ + \ >> data/qc-statistical-tests.txt\n" deps: - path: data/dep-prob.json hash: md5 @@ -455,14 +457,14 @@ stages: - 'parallel --verbose jsonschema --instance {} schemas/cgpm.json :::: <(find data/cgpm/complete -type f)' - mkdir -p data/ast - - "parallel --verbose 'python scripts/ast_export.py --metadata {} --data data/numericalized.csv - --mapping-table data/mapping-table.edn --output data/ast/{/.}.edn' :::: <(find - data/cgpm/complete -type f)" + - "parallel --verbose 'python scripts/ast_export.py --metadata {} --data data/numericalized.csv\ + \ --mapping-table data/mapping-table.edn --output data/ast/{/.}.edn' :::: <(find\ + \ data/cgpm/complete -type f)" deps: - path: data/cgpm/complete hash: md5 - md5: e63d45fe2ed5ab8a01d871b6f7ec05e9.dir - size: 117861 + md5: b01aaee70e74d3ad3b3dcca27ab61313.dir + size: 117849 nfiles: 3 - path: data/ignored.csv hash: md5 @@ -478,20 +480,20 @@ stages: outs: - path: data/ast hash: md5 - md5: 6804e574a891197975557eac0a7a8b33.dir - size: 98676 + md5: d723a36d25e183298f79243c03aaa292.dir + size: 98691 nfiles: 3 sppl-import: cmd: - mkdir -p data/sppl/unmerged - - "parallel --verbose 'python scripts/sppl_import.py --multi-mix-ast {} --max-number-views - data/max-number-views.txt --output data/sppl/unmerged/{/.}.json' :::: <(find - data/ast -type f)" + - "parallel --verbose 'python scripts/sppl_import.py --multi-mix-ast {} --max-number-views\ + \ data/max-number-views.txt --output data/sppl/unmerged/{/.}.json' :::: <(find\ + \ data/ast -type f)" deps: - path: data/ast hash: md5 - md5: 6804e574a891197975557eac0a7a8b33.dir - size: 98676 + md5: d723a36d25e183298f79243c03aaa292.dir + size: 98691 nfiles: 3 - path: data/max-number-views.txt hash: md5 @@ -507,26 +509,26 @@ stages: outs: - path: data/sppl/unmerged hash: md5 - md5: d9c3a37cfb87251994ca43d12c9b7bfc.dir - size: 77928 + md5: 857a3be1934d586ff87c54821129a3f2.dir + size: 77713 nfiles: 3 sppl-merge: - cmd: "find data/sppl/unmerged -type f | sort | xargs python scripts/sppl_merge.py - --output data/sppl/merged.json\n" + cmd: "find data/sppl/unmerged -type f | sort | xargs python scripts/sppl_merge.py\ + \ --output data/sppl/merged.json\n" deps: - path: data/sppl/unmerged hash: md5 - md5: d9c3a37cfb87251994ca43d12c9b7bfc.dir - size: 77928 + md5: 857a3be1934d586ff87c54821129a3f2.dir + size: 77713 nfiles: 3 outs: - path: data/sppl/merged.json hash: md5 - md5: 9d82bb9f10f513862b1ee3b56899705d - size: 78409 + md5: ca230a9375be713e0776d2dd1d24ee58 + size: 78194 sppl-sample: - cmd: "python scripts/sppl_sample.py --model data/sppl/merged.json --data data/ignored.csv - > data/synthetic-data-gensql.csv # --sample_count 1000\n" + cmd: "python scripts/sppl_sample.py --model data/sppl/merged.json --data data/ignored.csv\ + \ > data/synthetic-data-gensql.csv # --sample_count 1000\n" deps: - path: data/ignored.csv hash: md5 @@ -534,8 +536,8 @@ stages: size: 77540 - path: data/sppl/merged.json hash: md5 - md5: 9d82bb9f10f513862b1ee3b56899705d - size: 78409 + md5: ca230a9375be713e0776d2dd1d24ee58 + size: 78194 - path: scripts/sppl_sample.py hash: md5 md5: 65c711874e0eda0e7d79b4a4a3eb6076 @@ -543,11 +545,11 @@ stages: outs: - path: data/synthetic-data-gensql.csv hash: md5 - md5: 0de97a209335fac737390e4387012d16 - size: 85251 + md5: a46403f9fa02b0dc465eac9015bd45d0 + size: 84636 qc-tag-samples: - cmd: "clojure -X gensql.structure-learning.qc.samples/tag :data data/ignored.csv - :samples-synthetic data/synthetic-data-gensql.csv > qc/samples/samples.edn\n" + cmd: "clojure -X gensql.structure-learning.qc.samples/tag :data data/ignored.csv\ + \ :samples-synthetic data/synthetic-data-gensql.csv > qc/samples/samples.edn\n" deps: - path: data/ignored.csv hash: md5 @@ -555,8 +557,8 @@ stages: size: 77540 - path: data/synthetic-data-gensql.csv hash: md5 - md5: 0de97a209335fac737390e4387012d16 - size: 85251 + md5: a46403f9fa02b0dc465eac9015bd45d0 + size: 84636 - path: src/clojure/gensql/structure_learning/qc/samples.clj hash: md5 md5: e34e26db3736bb02dd084800c9d6af72 @@ -564,20 +566,20 @@ stages: outs: - path: qc/samples/samples.edn hash: md5 - md5: bcb68c57e40d921a6095485224181ef9 - size: 443141 + md5: 67456841283640cd962e574599a73be9 + size: 442526 xcat-complete-import: cmd: - mkdir -p data/xcat/complete/ - - "parallel --verbose 'clojure -X gensql.structure-learning.xcat/import :cgpm-json - {} :data-csv data/ignored.csv :mapping-table data/mapping-table.edn :numericalized-csv - data/numericalized.csv :schema-edn data/schema.edn > data/xcat/complete/{/.}.edn' - :::: <(find data/cgpm/complete -type f)" + - "parallel --verbose 'clojure -X gensql.structure-learning.xcat/import :cgpm-json\ + \ {} :data-csv data/ignored.csv :mapping-table data/mapping-table.edn :numericalized-csv\ + \ data/numericalized.csv :schema-edn data/schema.edn > data/xcat/complete/{/.}.edn'\ + \ :::: <(find data/cgpm/complete -type f)" deps: - path: data/cgpm/complete hash: md5 - md5: e63d45fe2ed5ab8a01d871b6f7ec05e9.dir - size: 117861 + md5: b01aaee70e74d3ad3b3dcca27ab61313.dir + size: 117849 nfiles: 3 - path: data/ignored.csv hash: md5 @@ -605,26 +607,26 @@ stages: outs: - path: data/xcat/complete/ hash: md5 - md5: 40c28c7e82357f816a2e4a1199b7c45f.dir - size: 783312 + md5: 56cb77fd3801d7cbf5e7504284d45003.dir + size: 783240 nfiles: 3 xcat-merge: - cmd: "clj -X gensql.structure-learning.clojurecat/merge :models data/xcat/complete - :out data/xcat/xcat.merged.edn\n" + cmd: "clj -X gensql.structure-learning.clojurecat/merge :models data/xcat/complete\ + \ :out data/xcat/xcat.merged.edn\n" deps: - path: data/xcat/complete hash: md5 - md5: 40c28c7e82357f816a2e4a1199b7c45f.dir - size: 783312 + md5: 56cb77fd3801d7cbf5e7504284d45003.dir + size: 783240 nfiles: 3 outs: - path: data/xcat/xcat.merged.edn hash: md5 - md5: 95bb195d42b4b04cbc6743f542ce9c2e - size: 783360 + md5: fee4f7c7a25a88fecb6a2de9e75ef5b0 + size: 783288 qc-dashboard-spec: - cmd: "clojure -X gensql.structure-learning.qc.dashboard/spec :samples qc/samples/samples.edn - :schema data/schema.edn :correlation data/linear-stats.json > qc/specs/qc-dashboard.vl.json\n" + cmd: "clojure -X gensql.structure-learning.qc.dashboard/spec :samples qc/samples/samples.edn\ + \ :schema data/schema.edn :correlation data/linear-stats.json > qc/specs/qc-dashboard.vl.json\n" deps: - path: data/linear-stats.json hash: md5 @@ -636,8 +638,8 @@ stages: size: 601 - path: qc/samples/samples.edn hash: md5 - md5: bcb68c57e40d921a6095485224181ef9 - size: 443141 + md5: 67456841283640cd962e574599a73be9 + size: 442526 - path: src/clojure/gensql/structure_learning/qc/dashboard.clj hash: md5 md5: 11529f94587a9ade1d3fa4cb84ff0445 @@ -652,17 +654,17 @@ stages: outs: - path: qc/specs/qc-dashboard.vl.json hash: md5 - md5: 1f6818aca8c5016aa6f7437ebc92b269 - size: 498453 + md5: 47353536a0e2c56390d20c2fc3892a1d + size: 497826 qc-dashboard-app: - cmd: "clojure -X gensql.structure-learning.qc.app/create :template qc/templates/index.html - :spec qc/specs/qc-dashboard.vl.json :renderer canvas :title '\"QC dashboard\"\ + cmd: "clojure -X gensql.structure-learning.qc.app/create :template qc/templates/index.html\ + \ :spec qc/specs/qc-dashboard.vl.json :renderer canvas :title '\"QC dashboard\"\ ' > qc/app/qc-dashboard.html\n" deps: - path: qc/specs/qc-dashboard.vl.json hash: md5 - md5: 1f6818aca8c5016aa6f7437ebc92b269 - size: 498453 + md5: 47353536a0e2c56390d20c2fc3892a1d + size: 497826 - path: qc/templates/index.html hash: md5 md5: ac51efb107febc1caf14b5e2c6d0489d @@ -674,11 +676,11 @@ stages: outs: - path: qc/app/qc-dashboard.html hash: md5 - md5: b687400ea5f3351727f73e6a081a145e - size: 500127 + md5: e3402d22152c64e955cf3388766534f2 + size: 499500 qc-splom-spec: - cmd: "clojure -X gensql.structure-learning.qc.splom/spec :samples qc/samples/samples.edn - :schema data/schema.edn :correlation data/linear-stats.json > qc/specs/qc-splom.vl.json\n" + cmd: "clojure -X gensql.structure-learning.qc.splom/spec :samples qc/samples/samples.edn\ + \ :schema data/schema.edn :correlation data/linear-stats.json > qc/specs/qc-splom.vl.json\n" deps: - path: data/linear-stats.json hash: md5 @@ -690,8 +692,8 @@ stages: size: 601 - path: qc/samples/samples.edn hash: md5 - md5: bcb68c57e40d921a6095485224181ef9 - size: 443141 + md5: 67456841283640cd962e574599a73be9 + size: 442526 - path: src/clojure/gensql/structure_learning/qc/splom.clj hash: md5 md5: a753879cef043c55d23dea202b41abe5 @@ -706,17 +708,17 @@ stages: outs: - path: qc/specs/qc-splom.vl.json hash: md5 - md5: a773bb0246bff52bb254101ca2c32960 - size: 489264 + md5: 171da5a9e3af0f572f79596fff4b5b0b + size: 488635 qc-splom-app: - cmd: "clojure -X gensql.structure-learning.qc.app/create :template qc/templates/index.html - :spec qc/specs/qc-splom.vl.json :renderer canvas :title '\"QC scatter plot matrix\"\ - ' > qc/app/qc-splom.html\n" + cmd: "clojure -X gensql.structure-learning.qc.app/create :template qc/templates/index.html\ + \ :spec qc/specs/qc-splom.vl.json :renderer canvas :title '\"QC scatter plot\ + \ matrix\"' > qc/app/qc-splom.html\n" deps: - path: qc/specs/qc-splom.vl.json hash: md5 - md5: a773bb0246bff52bb254101ca2c32960 - size: 489264 + md5: 171da5a9e3af0f572f79596fff4b5b0b + size: 488635 - path: qc/templates/index.html hash: md5 md5: ac51efb107febc1caf14b5e2c6d0489d @@ -728,12 +730,12 @@ stages: outs: - path: qc/app/qc-splom.html hash: md5 - md5: 0f6cfb9dfcec8c01170cf7422433f134 - size: 490948 + md5: 02b78a8efb352785b73f50856d79f620 + size: 490319 predict: - cmd: "python scripts/predict.py --schema data/schema.edn --training data/ignored.csv - --training data/synthetic-data-gensql.csv --test data/test/test.csv --output - data/predictions.csv #--test data/test/test-shifted.csv\n" + cmd: "python scripts/predict.py --schema data/schema.edn --training data/ignored.csv\ + \ --training data/synthetic-data-gensql.csv --test data/test/test.csv --output\ + \ data/predictions.csv #--test data/test/test-shifted.csv\n" deps: - path: data/ignored.csv hash: md5 @@ -745,8 +747,8 @@ stages: size: 601 - path: data/synthetic-data-gensql.csv hash: md5 - md5: 0de97a209335fac737390e4387012d16 - size: 85251 + md5: a46403f9fa02b0dc465eac9015bd45d0 + size: 84636 - path: data/test/test.csv hash: md5 md5: 6bdd1f24302e6ee6c1836bf15edfada2 @@ -759,20 +761,22 @@ stages: params.yaml: synthetic_data_evaluation: predictor: Random_forest + datasets: + - synthetic-data-gensql.csv outs: - path: data/predictions.csv hash: md5 - md5: 2c3d4c0f67afa1b1786725ac4c773525 - size: 24274 + md5: a4a35684fdfdf5da4e501d7f4833026a + size: 24264 assemble-database: - cmd: "clojure -M:exec gensql.structure-learning.main assemble-database --table-name - data --table-path data/nullified.csv --model-name baseline_model --model-path - data/xcat/xcat.merged.edn > data/db.edn\n" + cmd: "clojure -M:exec gensql.structure-learning.main assemble-database --table-name\ + \ data --table-path data/nullified.csv --model-name baseline_model --model-path\ + \ data/xcat/xcat.merged.edn > data/db.edn\n" deps: - path: data/cgpm hash: md5 - md5: 8e50d90ba4ce4b49e0de4e26c1537dd4.dir - size: 255974 + md5: 166c893fcb41ec48e6955a120eadbd5e.dir + size: 255962 nfiles: 10 - path: data/nullified.csv hash: md5 @@ -780,8 +784,8 @@ stages: size: 268196 - path: data/xcat hash: md5 - md5: 47cc75147058b9a3c9ca48b28ee4fe92.dir - size: 1566672 + md5: 8986883161dcc85bd1cd9b022fd2a29a.dir + size: 1566528 nfiles: 4 params: params.yaml: @@ -792,5 +796,86 @@ stages: outs: - path: data/db.edn hash: md5 - md5: b28c957e4b8c1a3d0b7bfeb0326679bc - size: 1423031 + md5: bfc7ea1d137db6900ceff8775f784707 + size: 1422959 + qc-discretize@synthetic-data-gensql.csv: + cmd: "mkdir -p data/discretized/ && python scripts/discretize.py --real data/ignored.csv\ + \ --synthetic data/synthetic-data-gensql.csv --schema data/loom-schema.json\ + \ --real-disc data/discretized/ignored.csv --synthetic-disc data/discretized/synthetic-data-gensql.csv\n" + deps: + - path: data/ignored.csv + hash: md5 + md5: 5ffeb41f4182b8f7f062b5f13230557d + size: 77540 + - path: data/loom-schema.json + hash: md5 + md5: 68f027a12982e5d4f01f40fe0450b281 + size: 127 + - path: data/synthetic-data-gensql.csv + hash: md5 + md5: a46403f9fa02b0dc465eac9015bd45d0 + size: 84636 + - path: scripts/discretize.py + hash: md5 + md5: 413bc37503837d33c7f2ae72359e994a + size: 2033 + outs: + - path: data/discretized/synthetic-data-gensql.csv + hash: md5 + md5: a46403f9fa02b0dc465eac9015bd45d0 + size: 84636 + qc-fidelity-table@synthetic-data-gensql.csv: + cmd: "mkdir -p data/fidelity/ && (LD_DEBUG=libs assess-distance --data-1 data/discretized/ignored.csv\ + \ --data-2 data/discretized/synthetic-data-gensql.csv --bivariate > data/fidelity/synthetic-data-gensql.csv)\n" + deps: + - path: data/discretized/ignored.csv + hash: md5 + md5: 5ffeb41f4182b8f7f062b5f13230557d + size: 77540 + - path: data/discretized/synthetic-data-gensql.csv + hash: md5 + md5: a46403f9fa02b0dc465eac9015bd45d0 + size: 84636 + outs: + - path: data/fidelity/synthetic-data-gensql.csv + hash: md5 + md5: 4b0979a29feceb30a26e267de1df19f6 + size: 735 + qc-fidelity-json: + cmd: "python scripts/fidelity2json.py --params params.yaml >> data/fidelity.json\n" + deps: + - path: data/fidelity/ + hash: md5 + md5: ee1f5499c3c52f3af72097a8dd5f0051.dir + size: 762 + nfiles: 2 + - path: scripts/fidelity2json.py + hash: md5 + md5: ebe89a5b3530a60999cc3a7c0cfc1493 + size: 860 + params: + params.yaml: + synthetic_data_evaluation.datasets: + - synthetic-data-gensql.csv + outs: + - path: data/fidelity.json + hash: md5 + md5: a53aad464233582b9b8841c3a270df01 + size: 1494 + qc-fidelity-app: + cmd: "sed \"s|{{DATA}}|$(cat data/fidelity.json)|\" qc/templates/fidelity.html\ + \ > qc/app/fidelity.html\n" + deps: + - path: data/fidelity.json + hash: md5 + md5: a53aad464233582b9b8841c3a270df01 + size: 1494 + - path: qc/templates/fidelity.html + hash: md5 + md5: 26cb40e5e0c02c8ca73e3dcdaa21f814 + size: 2037 + outs: + - path: qc/app/fidelity.html + hash: md5 + md5: 5d563d763db76aaf9686fb4a4cd582ca + size: 3522 diff --git a/dvc.yaml b/dvc.yaml index fc083f1a..4632b471 100644 --- a/dvc.yaml +++ b/dvc.yaml @@ -553,7 +553,6 @@ stages: do: cmd: > mkdir -p data/discretized/ && - nix develop github:InferenceQL/lpm.discretize -c python scripts/discretize.py --real data/ignored.csv --synthetic data/${item} @@ -573,9 +572,7 @@ stages: do: cmd: > mkdir -p data/fidelity/ && - # XXX. this is incredibly ugly but if I don't run `nix develop...` first - # then `nix run ...` will not find scipy. - nix develop github:InferenceQL/lpm.fidelity -c nix run github:InferenceQL/lpm.fidelity -- + assess-distance --data-1 data/discretized/ignored.csv --data-2 data/discretized/${item} --bivariate diff --git a/flake.lock b/flake.lock index 6ee48155..beecc617 100644 --- a/flake.lock +++ b/flake.lock @@ -1,5 +1,21 @@ { "nodes": { + "darwin-nixpkgs": { + "locked": { + "lastModified": 1714971268, + "narHash": "sha256-IKwMSwHj9+ec660l+I4tki/1NRoeGpyA2GdtdYpAgEw=", + "owner": "NixOS", + "repo": "nixpkgs", + "rev": "27c13997bf450a01219899f5a83bd6ffbfc70d3c", + "type": "github" + }, + "original": { + "owner": "NixOS", + "ref": "nixos-23.11", + "repo": "nixpkgs", + "type": "github" + } + }, "flake-parts": { "inputs": { "nixpkgs-lib": [ @@ -20,18 +36,124 @@ "type": "github" } }, + "flake-utils": { + "inputs": { + "systems": "systems" + }, + "locked": { + "lastModified": 1710146030, + "narHash": "sha256-SZ5L6eA7HJ/nmkzGG7/ISclqe6oZdOZTNoesiInkXPQ=", + "owner": "numtide", + "repo": "flake-utils", + "rev": "b1d9ab70662946ef0850d488da1c9019f3a9752a", + "type": "github" + }, + "original": { + "owner": "numtide", + "repo": "flake-utils", + "type": "github" + } + }, + "flake-utils_2": { + "inputs": { + "systems": "systems_2" + }, + "locked": { + "lastModified": 1710146030, + "narHash": "sha256-SZ5L6eA7HJ/nmkzGG7/ISclqe6oZdOZTNoesiInkXPQ=", + "owner": "numtide", + "repo": "flake-utils", + "rev": "b1d9ab70662946ef0850d488da1c9019f3a9752a", + "type": "github" + }, + "original": { + "id": "flake-utils", + "type": "indirect" + } + }, + "linux-nixpkgs": { + "locked": { + "lastModified": 1704290814, + "narHash": "sha256-LWvKHp7kGxk/GEtlrGYV68qIvPHkU9iToomNFGagixU=", + "owner": "NixOS", + "repo": "nixpkgs", + "rev": "70bdadeb94ffc8806c0570eb5c2695ad29f0e421", + "type": "github" + }, + "original": { + "owner": "NixOS", + "ref": "nixos-23.05", + "repo": "nixpkgs", + "type": "github" + } + }, + "lpm-discretize": { + "inputs": { + "flake-utils": "flake-utils", + "nixpkgs": "nixpkgs" + }, + "locked": { + "lastModified": 1715161196, + "narHash": "sha256-r5OJiDabEFY9oVUQG7KpOzBgtqU8wlExKR/pKguMgsg=", + "owner": "InferenceQL", + "repo": "lpm.discretize", + "rev": "27593a1b16293e9758b8b979b24882cf0df9ea64", + "type": "github" + }, + "original": { + "owner": "InferenceQL", + "repo": "lpm.discretize", + "type": "github" + } + }, + "lpm-fidelity": { + "inputs": { + "darwin-nixpkgs": "darwin-nixpkgs", + "flake-utils": "flake-utils_2", + "linux-nixpkgs": "linux-nixpkgs" + }, + "locked": { + "lastModified": 1715161174, + "narHash": "sha256-KJSkp/uc0+iIi69n/zJiEkcn1f0+MvrSjaGuVjc7Lew=", + "owner": "InferenceQL", + "repo": "lpm.fidelity", + "rev": "640bd37f1b0ecd5c7d5b19033ec3570c8bb569c2", + "type": "github" + }, + "original": { + "owner": "InferenceQL", + "repo": "lpm.fidelity", + "type": "github" + } + }, "nixpkgs": { "locked": { - "lastModified": 1716509168, - "narHash": "sha256-4zSIhSRRIoEBwjbPm3YiGtbd8HDWzFxJjw5DYSDy1n8=", + "lastModified": 1717159533, + "narHash": "sha256-oamiKNfr2MS6yH64rUn99mIZjc45nGJlj9eGth/3Xuw=", "owner": "NixOS", "repo": "nixpkgs", - "rev": "bfb7a882678e518398ce9a31a881538679f6f092", + "rev": "a62e6edd6d5e1fa0329b8653c801147986f8d446", "type": "github" }, "original": { "owner": "NixOS", - "ref": "nixos-unstable", + "ref": "nixos-23.11", + "repo": "nixpkgs", + "type": "github" + } + }, + "nixpkgs_2": { + "locked": { + "lastModified": 1704290814, + "narHash": "sha256-LWvKHp7kGxk/GEtlrGYV68qIvPHkU9iToomNFGagixU=", + "owner": "NixOS", + "repo": "nixpkgs", + "rev": "70bdadeb94ffc8806c0570eb5c2695ad29f0e421", + "type": "github" + }, + "original": { + "owner": "NixOS", + "ref": "nixos-23.05", "repo": "nixpkgs", "type": "github" } @@ -39,8 +161,10 @@ "root": { "inputs": { "flake-parts": "flake-parts", - "nixpkgs": "nixpkgs", - "systems": "systems" + "lpm-discretize": "lpm-discretize", + "lpm-fidelity": "lpm-fidelity", + "nixpkgs": "nixpkgs_2", + "systems": "systems_3" } }, "systems": { @@ -57,6 +181,36 @@ "repo": "default", "type": "github" } + }, + "systems_2": { + "locked": { + "lastModified": 1681028828, + "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=", + "owner": "nix-systems", + "repo": "default", + "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e", + "type": "github" + }, + "original": { + "owner": "nix-systems", + "repo": "default", + "type": "github" + } + }, + "systems_3": { + "locked": { + "lastModified": 1681028828, + "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=", + "owner": "nix-systems", + "repo": "default", + "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e", + "type": "github" + }, + "original": { + "owner": "nix-systems", + "repo": "default", + "type": "github" + } } }, "root": "root", diff --git a/flake.nix b/flake.nix index dd385b4c..64cf4e5e 100644 --- a/flake.nix +++ b/flake.nix @@ -5,9 +5,12 @@ flake-parts.url = "github:hercules-ci/flake-parts"; flake-parts.inputs.nixpkgs-lib.follows = "nixpkgs"; - nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable"; + nixpkgs.url = "github:NixOS/nixpkgs?ref=nixos-23.05"; systems.url = "github:nix-systems/default"; + + lpm-fidelity.url = "github:InferenceQL/lpm.fidelity"; + lpm-discretize.url = "github:InferenceQL/lpm.discretize"; }; outputs = inputs@{ flake-parts, systems, ... }: From 407514763341511bb38ca171c797e4db604c6f0b Mon Sep 17 00:00:00 2001 From: Samuel Rounce Date: Tue, 4 Jun 2024 22:30:09 +0100 Subject: [PATCH 06/12] fix: Prevent environmental differences across platforms due to venv being too far down PYTHONPATH --- devshell.nix | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/devshell.nix b/devshell.nix index 694e3117..253b64f4 100644 --- a/devshell.nix +++ b/devshell.nix @@ -69,7 +69,9 @@ pnpm install - poetry config virtualenvs.path $(pwd)/.venv + poetry config virtualenvs.path --unset + poetry config virtualenvs.in-project true + poetry env use ${python}/bin/python # We need to set PYTHON_KEYRING_BACKEND to use the null backend as @@ -78,6 +80,9 @@ PYTHON_KEYRING_BACKEND=keyring.backends.null.Keyring \ poetry install --no-root export PATH="$(poetry env info -p)/bin:$PWD/bin:$PATH" + + venvSitePackages="$(python -c 'import sys; print(sys.path.pop())')" + export PYTHONPATH="$venvSitePackages:$PWD/bin:$PYTHONPATH" mkdir -p .dvc/cache dvc cache dir .dvc/cache From ee4f6dbfcbcf8f3cf759daf9724765eef0aebf85 Mon Sep 17 00:00:00 2001 From: Samuel Rounce Date: Tue, 4 Jun 2024 23:59:01 +0100 Subject: [PATCH 07/12] fix: Commit-linter workflow version print step command formatting --- .github/workflows/commit-linter.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/commit-linter.yaml b/.github/workflows/commit-linter.yaml index 4970178f..ee7968bc 100644 --- a/.github/workflows/commit-linter.yaml +++ b/.github/workflows/commit-linter.yaml @@ -29,10 +29,10 @@ jobs: - name: Print versions run: | - ./bin/env-run 'git --version && - node --version && - pnpm --version && - pnpm exec commitlint --version' + ./bin/env-run git --version && + ./bin/env-run node --version && + ./bin/env-run pnpm --version && + ./bin/env-run pnpm exec commitlint --version - name: Validate current commit (last commit) with commitlint if: github.event_name == 'push' From 052468ea391c93935cd2974dc8372173165c04c4 Mon Sep 17 00:00:00 2001 From: Samuel Rounce Date: Wed, 5 Jun 2024 00:10:21 +0100 Subject: [PATCH 08/12] feat: Add E2E test using satellites test data --- .github/workflows/dvc-repro-satellites.yaml | 31 +++++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 .github/workflows/dvc-repro-satellites.yaml diff --git a/.github/workflows/dvc-repro-satellites.yaml b/.github/workflows/dvc-repro-satellites.yaml new file mode 100644 index 00000000..1839ba24 --- /dev/null +++ b/.github/workflows/dvc-repro-satellites.yaml @@ -0,0 +1,31 @@ +name: DVC repro w/ satellites data + +on: + push: + branches: + - main + pull_request: + +jobs: + dvc-satellites: + runs-on: ubuntu-latest + steps: + - name: Check out repository + uses: actions/checkout@v3 + + - name: Install Nix + uses: cachix/install-nix-action@v22 + + - name: Set up Cachix + uses: cachix/cachix-action@v12 + with: + name: devenv + + - name: Build developer environment + run: ./bin/env-run echo "Devshell built" + + - name: Run Clojure tests + run: | + mkdir data || true + cp test/satellites/data.csv data + ./bin/env-run dvc repro From 9c1ba94abba682de11be363b2a7dffc811b82382 Mon Sep 17 00:00:00 2001 From: Samuel Rounce Date: Wed, 5 Jun 2024 00:24:04 +0100 Subject: [PATCH 09/12] Revert "feat: Add E2E test using satellites test data" This reverts commit 052468ea391c93935cd2974dc8372173165c04c4. --- .github/workflows/dvc-repro-satellites.yaml | 31 --------------------- 1 file changed, 31 deletions(-) delete mode 100644 .github/workflows/dvc-repro-satellites.yaml diff --git a/.github/workflows/dvc-repro-satellites.yaml b/.github/workflows/dvc-repro-satellites.yaml deleted file mode 100644 index 1839ba24..00000000 --- a/.github/workflows/dvc-repro-satellites.yaml +++ /dev/null @@ -1,31 +0,0 @@ -name: DVC repro w/ satellites data - -on: - push: - branches: - - main - pull_request: - -jobs: - dvc-satellites: - runs-on: ubuntu-latest - steps: - - name: Check out repository - uses: actions/checkout@v3 - - - name: Install Nix - uses: cachix/install-nix-action@v22 - - - name: Set up Cachix - uses: cachix/cachix-action@v12 - with: - name: devenv - - - name: Build developer environment - run: ./bin/env-run echo "Devshell built" - - - name: Run Clojure tests - run: | - mkdir data || true - cp test/satellites/data.csv data - ./bin/env-run dvc repro From edf2b14490c05c7e5f08e05d63955fcd284adf26 Mon Sep 17 00:00:00 2001 From: Samuel Rounce Date: Wed, 5 Jun 2024 14:57:10 +0100 Subject: [PATCH 10/12] chore: Remove old nix flake attempt --- nix/flake.lock | 60 -------------------------------------------------- nix/flake.nix | 27 ----------------------- 2 files changed, 87 deletions(-) delete mode 100644 nix/flake.lock delete mode 100644 nix/flake.nix diff --git a/nix/flake.lock b/nix/flake.lock deleted file mode 100644 index f2dd4231..00000000 --- a/nix/flake.lock +++ /dev/null @@ -1,60 +0,0 @@ -{ - "nodes": { - "flake-utils": { - "locked": { - "lastModified": 1659877975, - "narHash": "sha256-zllb8aq3YO3h8B/U0/J1WBgAL8EX5yWf5pMj3G0NAmc=", - "owner": "numtide", - "repo": "flake-utils", - "rev": "c0e246b9b83f637f4681389ecabcb2681b4f3af0", - "type": "github" - }, - "original": { - "owner": "numtide", - "repo": "flake-utils", - "type": "github" - } - }, - "nixpkgs-darwin": { - "locked": { - "lastModified": 1659446231, - "narHash": "sha256-hekabNdTdgR/iLsgce5TGWmfIDZ86qjPhxDg/8TlzhE=", - "owner": "NixOS", - "repo": "nixpkgs", - "rev": "eabc38219184cc3e04a974fe31857d8e0eac098d", - "type": "github" - }, - "original": { - "owner": "NixOS", - "ref": "nixpkgs-21.11-darwin", - "repo": "nixpkgs", - "type": "github" - } - }, - "nixpkgs-nixos": { - "locked": { - "lastModified": 1659446231, - "narHash": "sha256-hekabNdTdgR/iLsgce5TGWmfIDZ86qjPhxDg/8TlzhE=", - "owner": "NixOS", - "repo": "nixpkgs", - "rev": "eabc38219184cc3e04a974fe31857d8e0eac098d", - "type": "github" - }, - "original": { - "owner": "NixOS", - "ref": "nixos-21.11", - "repo": "nixpkgs", - "type": "github" - } - }, - "root": { - "inputs": { - "flake-utils": "flake-utils", - "nixpkgs-darwin": "nixpkgs-darwin", - "nixpkgs-nixos": "nixpkgs-nixos" - } - } - }, - "root": "root", - "version": 7 -} diff --git a/nix/flake.nix b/nix/flake.nix deleted file mode 100644 index 6e4aa3f5..00000000 --- a/nix/flake.nix +++ /dev/null @@ -1,27 +0,0 @@ -{ - inputs = { - nixpkgs-nixos.url = "github:NixOS/nixpkgs/nixos-21.11"; - nixpkgs-darwin.url = "github:NixOS/nixpkgs/nixpkgs-21.11-darwin"; - flake-utils.url = "github:numtide/flake-utils"; - }; - - outputs = { self, nixpkgs-nixos, nixpkgs-darwin, flake-utils }: - flake-utils.lib.eachDefaultSystem (system: - let - nixpkgs = if nixpkgs-nixos.legacyPackages.${system}.hostPlatform.isDarwin - then nixpkgs-darwin - else nixpkgs-nixos; - - pkgs = nixpkgs.legacyPackages.${system}; - - pythonPackages = pypkgs: with pypkgs; [sympy]; - python = pkgs.python39.withPackages(pythonPackages); - in { - devShell = pkgs.mkShell { - buildInputs = [ - python - ]; - }; - } - ); -} From 065fb477d5c688c046af1c7de4a8c6f09da83e55 Mon Sep 17 00:00:00 2001 From: Samuel Rounce Date: Wed, 5 Jun 2024 15:01:35 +0100 Subject: [PATCH 11/12] feat: Reload direnv when flake.lock changes --- .envrc | 1 + 1 file changed, 1 insertion(+) diff --git a/.envrc b/.envrc index ada66e41..fbb68b3e 100644 --- a/.envrc +++ b/.envrc @@ -1,3 +1,4 @@ use flake watch_file $(find . -name '*.nix') +watch_file flake.lock From b704c03fab43d7912c2315d796a398deca2b03cd Mon Sep 17 00:00:00 2001 From: Samuel Rounce Date: Wed, 5 Jun 2024 15:20:50 +0100 Subject: [PATCH 12/12] fix: Direnv watch_file uses Bash-native globbing Change .envrc to use Bash file globbing rather than the find sub-shell invocation. --- .envrc | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.envrc b/.envrc index fbb68b3e..5cb2eb08 100644 --- a/.envrc +++ b/.envrc @@ -1,4 +1,6 @@ use flake -watch_file $(find . -name '*.nix') +shopt -s globstar + +watch_file **/*.nix watch_file flake.lock