diff --git a/.github/workflows/continuous_integration.yml b/.github/workflows/continuous_integration.yml index 5db47f7e..653efc54 100644 --- a/.github/workflows/continuous_integration.yml +++ b/.github/workflows/continuous_integration.yml @@ -29,104 +29,86 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 - - name: Install poetry - run: pipx install poetry + - uses: actions/checkout@v4 + - name: Install uv + uses: astral-sh/setup-uv@v4 - name: Set up Python - uses: actions/setup-python@v4 - with: - python-version: '3.10' + run: uv python install 3.10 - name: Install ruff - run: | - poetry env use 3.10 - poetry install --only lint --no-interaction --no-root + run: uv sync --no-install-project --only-group lint - name: Lint with ruff run: | - poetry run ruff check --output-format=github ethicml + uv run ruff check --output-format=github ethicml - name: Lint with ruff run: | - poetry run ruff check --output-format=github tests + uv run ruff check --output-format=github tests format_with_black: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 - - name: Install poetry - run: pipx install poetry + - uses: actions/checkout@v4 + - name: Install uv + uses: astral-sh/setup-uv@v4 - name: Set up Python - uses: actions/setup-python@v4 - with: - python-version: '3.10' + run: uv python install 3.10 - name: Install ruff - run: | - poetry env use 3.10 - poetry install --only lint --no-interaction --no-root + run: uv sync --no-install-project --only-group lint - name: Format with ruff run: | - poetry run ruff format --diff . + uv run ruff format --diff . check_with_pydoclint: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 - - name: Install poetry - run: pipx install poetry + - uses: actions/checkout@v4 + - name: Install uv + uses: astral-sh/setup-uv@v4 - name: Set up Python - uses: actions/setup-python@v4 - with: - python-version: '3.11' # might as well use 3.11 as it's faster + run: uv python install 3.11 - name: Install pydoclint - run: | - poetry env use 3.11 - poetry install --only doclint --no-interaction --no-root + run: uv sync --no-install-project --only-group doclint - name: Check with pydoclint run: | - poetry run pydoclint ethicml + uv run pydoclint ethicml test_minimal_dependencies: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 - - name: Install poetry - run: pipx install poetry - - uses: actions/setup-python@v4 - with: - python-version: '3.10' + - uses: actions/checkout@v4 + - name: Install uv + uses: astral-sh/setup-uv@v4 + - name: Set up Python + run: uv python install 3.10 - name: Install dependencies - run: | - poetry env use 3.10 - poetry install --no-interaction --no-root --without dev,test,typecheck,lint,doclint + run: uv sync --no-install-project --no-group dev --no-group test --no-group typecheck --no-group lint --no-group doclint - name: Test import run: | - poetry run python -c "import ethicml" + uv run python -c "import ethicml" test_build_docs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 - - name: Install poetry - run: pipx install poetry - - uses: actions/setup-python@v4 + - uses: actions/checkout@v4 + - name: Install uv + uses: astral-sh/setup-uv@v4 with: - python-version: '3.10' - cache: 'poetry' - + enable-cache: true + - name: Set up Python + run: uv python install 3.10 - name: Install dependencies - run: | - poetry env use 3.10 - poetry install --no-interaction --no-root --all-extras --with ci,torchcpu,docs --without lint,doclint + run: uv sync --no-install-project --all-extras --group ci --group torchcpu --group docs --no-group lint --no-group doclint - name: Test import run: | - poetry run python -c "import ethicml" + uv run python -c "import ethicml" - name: Install pandoc run: sudo apt-get install -y pandoc - name: Build with sphinx run: | - poetry run sphinx-build -W -b html ./docs ./docs/_build + uv run sphinx-build -W -b html ./docs ./docs/_build test_with_pytest: needs: [lint_with_ruff, format_with_black, check_with_pydoclint, test_minimal_dependencies, test_build_docs] @@ -136,24 +118,22 @@ jobs: #---------------------------------------------- # --- check-out repo and set-up python --- #---------------------------------------------- - - uses: actions/checkout@v3 - - name: Install poetry - if: ${{ github.event_name == 'merge_group' }} - run: pipx install poetry - - uses: actions/setup-python@v4 + - uses: actions/checkout@v4 + - name: Install uv if: ${{ github.event_name == 'merge_group' }} + uses: astral-sh/setup-uv@v4 with: - python-version: '3.10' - cache: 'poetry' + enable-cache: true + - name: Set up Python + if: ${{ github.event_name == 'merge_group' }} + run: uv python install 3.10 #---------------------------------------------- # --------- install dependencies -------- #---------------------------------------------- - name: Install dependencies if: ${{ github.event_name == 'merge_group' }} - run: | - poetry env use 3.10 - poetry install --no-interaction --no-root --all-extras --with ci,torchcpu --without lint,doclint + run: uv sync --no-install-project --all-extras --group ci --group torchcpu --no-group lint --no-group doclint #---------------------------------------------- # ----- Run MyPy ----- @@ -161,7 +141,7 @@ jobs: - name: Type check with mypy if: ${{ github.event_name == 'merge_group' }} run: | - poetry run mypy ethicml + uv run mypy ethicml #---------------------------------------------- # ----- Run MyPy on tests ----- @@ -169,7 +149,7 @@ jobs: - name: Type check tests with mypy if: ${{ github.event_name == 'merge_group' }} run: | - poetry run mypy tests + uv run mypy tests #---------------------------------------------- # ----- Run Tests ----- @@ -177,4 +157,4 @@ jobs: - name: Test with pytest if: ${{ github.event_name == 'merge_group' }} run: | - poetry run python -m pytest -vv -n 2 --dist loadgroup --cov=ethicml --cov-fail-under=80 tests/ + uv run python -m pytest -vv -n 2 --dist loadgroup --cov=ethicml --cov-fail-under=80 tests/ diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index c1202ec0..249c96a4 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -26,25 +26,21 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Setup Pages uses: actions/configure-pages@v3 # --- build docs --- - - name: Install poetry - run: pipx install poetry - - name: Set up Python 3.10 - uses: actions/setup-python@v4 - with: - python-version: "3.10" + - name: Install uv + uses: astral-sh/setup-uv@v4 + - name: Set up Python + run: uv python install 3.10 - name: Install dependencies - run: | - poetry env use 3.10 - poetry install --no-interaction --no-root --all-extras --with docs,torchcpu --without ci,lint,format + run: uv sync --no-install-project --all-extras --group ci --group torchcpu --group docs --no-group lint --no-group doclint - name: Install pandoc run: sudo apt-get install -y pandoc - name: Build with sphinx run: | - poetry run sphinx-build -W -b html ./docs ./docs/_build + uv run sphinx-build -W -b html ./docs ./docs/_build # ----------------- - name: Upload artifact uses: actions/upload-pages-artifact@v2 diff --git a/.github/workflows/dummy_ci.yml b/.github/workflows/dummy_ci.yml index bfec7946..f76da52a 100644 --- a/.github/workflows/dummy_ci.yml +++ b/.github/workflows/dummy_ci.yml @@ -61,22 +61,23 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 - - name: Install poetry - run: pipx install poetry - - uses: actions/setup-python@v4 + - uses: actions/checkout@v4 + - name: Install uv + uses: astral-sh/setup-uv@v4 with: - python-version: '3.10' - cache: 'poetry' + enable-cache: true + - name: Set up Python + run: uv python install 3.10 - name: Install dependencies + run: uv sync --no-install-project --all-extras --group ci --group torchcpu --group docs --no-group lint --no-group doclint + - name: Test import run: | - poetry env use 3.10 - poetry install --no-interaction --no-root --all-extras --with torchcpu,docs --without ci,lint,doclint + uv run python -c "import ethicml" - name: Install pandoc run: sudo apt-get install -y pandoc - name: Build with sphinx run: | - poetry run sphinx-build -W -b html ./docs ./docs/_build + uv run sphinx-build -W -b html ./docs ./docs/_build test_with_pytest: diff --git a/docs/conf.py b/docs/conf.py index a8872c46..c7fd1dea 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -11,22 +11,22 @@ # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. # -import os +from pathlib import Path import sys import toml -sys.path.insert(0, os.path.abspath("..")) +sys.path.insert(0, str(Path("..").resolve())) # -- Project information ----------------------------------------------------- project = "EthicML" -copyright = "2022, O. Thomas, T. Kehrenberg, M. Bartlett" +copyright = "2022, O. Thomas, T. Kehrenberg, M. Bartlett" # noqa: A001 author = "O. Thomas, T. Kehrenberg, M. Bartlett" # The full version, including alpha/beta/rc tags -release = toml.load("../pyproject.toml")["tool"]["poetry"]["version"] +release = toml.load("../pyproject.toml")["project"]["version"] # -- General configuration --------------------------------------------------- diff --git a/docs/tutorials/adult_dataset.ipynb b/docs/tutorials/adult_dataset.ipynb index 46090917..70bdb620 100644 --- a/docs/tutorials/adult_dataset.ipynb +++ b/docs/tutorials/adult_dataset.ipynb @@ -36,9 +36,9 @@ "\n", "adult = Adult()\n", "data: em.DataTuple = adult.load()\n", - "assert (45222, 101) == data.x.shape\n", - "assert (45222,) == data.s.shape\n", - "assert (45222,) == data.y.shape" + "assert data.x.shape == (45222, 101)\n", + "assert data.s.shape == (45222,)\n", + "assert data.y.shape == (45222,)" ] }, { @@ -136,9 +136,9 @@ "outputs": [], "source": [ "data: em.DataTuple = Adult(split=Adult.Splits.RACE).load()\n", - "assert (45222, 98) == data.x.shape\n", - "assert (45222,) == data.s.shape\n", - "assert (45222,) == data.y.shape" + "assert data.x.shape == (45222, 98)\n", + "assert data.s.shape == (45222,)\n", + "assert data.y.shape == (45222,)" ] }, { @@ -343,9 +343,9 @@ } ], "source": [ - "from ethicml.run import evaluate_models\n", - "from ethicml.models import LR, Reweighting, SVM, Upsampler\n", "from ethicml.metrics import Accuracy, CV, ProbPos, TPR\n", + "from ethicml.models import LR, Reweighting, SVM, Upsampler\n", + "from ethicml.run import evaluate_models\n", "\n", "results = evaluate_models(\n", " datasets=[em.data.Adult(split=Adult.Splits.RACE_BINARY)],\n", @@ -1217,7 +1217,12 @@ ], "source": [ "results[\n", - " ['Accuracy', 'Accuracy_race_White_0÷race_White_1', 'TPR_race_White_0÷race_White_1', 'prob_pos_race_White_0÷race_White_1']\n", + " [\n", + " 'Accuracy',\n", + " 'Accuracy_race_White_0÷race_White_1',\n", + " 'TPR_race_White_0÷race_White_1',\n", + " 'prob_pos_race_White_0÷race_White_1',\n", + " ]\n", "].groupby(level=[0, 1, 2, 3]).agg(['mean', 'std'])" ] }, diff --git a/ethicml/models/inprocess/svm.py b/ethicml/models/inprocess/svm.py index 57d0e755..ad51b149 100644 --- a/ethicml/models/inprocess/svm.py +++ b/ethicml/models/inprocess/svm.py @@ -66,4 +66,4 @@ def select_svm(C: float, kernel: KernelType, seed: int) -> LinearSVC | SVC: random_state = np.random.RandomState(seed=seed) if kernel is KernelType.linear: return LinearSVC(C=C, dual=False, tol=1e-12, random_state=random_state) - return SVC(C=C, kernel=kernel.value, gamma="auto", random_state=random_state) + return SVC(C=C, kernel=kernel.value, gamma="auto", random_state=random_state) # type: ignore[arg-type] diff --git a/ethicml/plot/common.py b/ethicml/plot/common.py index 6f86dfb8..7ab81008 100644 --- a/ethicml/plot/common.py +++ b/ethicml/plot/common.py @@ -109,17 +109,13 @@ def errorbox( xmean: float = entry.vals[xaxis_measure].mean() xstd: float = entry.vals[xaxis_measure].std() - if xmean + (0.5 * xstd) > max_xmean: - max_xmean = xmean + (0.5 * xstd) - if xmean - (0.5 * xstd) < min_xmean: - min_xmean = xmean - (0.5 * xstd) + max_xmean = max(xmean + (0.5 * xstd), max_xmean) + min_xmean = min(xmean - (0.5 * xstd), min_xmean) ymean: float = entry.vals[yaxis_measure].mean() ystd: float = entry.vals[yaxis_measure].std() - if ymean + (0.5 * ystd) > max_ymean: - max_ymean = ymean + (0.5 * ystd) - if ymean - (0.5 * ystd) < min_ymean: - min_ymean = ymean - (0.5 * ystd) + max_ymean = max(ymean + (0.5 * ystd), max_ymean) + min_ymean = min(ymean - (0.5 * ystd), min_ymean) if use_cross: plot.errorbar( diff --git a/ethicml/run/cross_validator.py b/ethicml/run/cross_validator.py index acb46534..cf56fdec 100644 --- a/ethicml/run/cross_validator.py +++ b/ethicml/run/cross_validator.py @@ -70,8 +70,7 @@ def _organize_and_compute_means(self) -> dict[str, ResultTuple]: # we convert the hyperparameter dictionaries to strings in order to compare them hyp_string = ", ".join(f"{key!s}={val!r}" for (key, val) in result.params.items()) grouped[hyp_string].append(result) - if result.fold_id > max_fold_id: - max_fold_id = result.fold_id + max_fold_id = max(result.fold_id, max_fold_id) # compute the mean value of each measure within each group mean_vals: dict[str, ResultTuple] = {} diff --git a/examples/RunSuite.ipynb b/examples/RunSuite.ipynb index 5913bbbd..f4348cff 100644 --- a/examples/RunSuite.ipynb +++ b/examples/RunSuite.ipynb @@ -42,9 +42,9 @@ "import ethicml as em\n", "\n", "data: em.DataTuple = em.adult().load()\n", - "assert (45222, 101) == data.x.shape\n", - "assert (45222, 1) == data.s.shape\n", - "assert (45222, 1) == data.y.shape" + "assert data.x.shape == (45222, 101)\n", + "assert data.s.shape == (45222, 1)\n", + "assert data.y.shape == (45222, 1)" ] }, { @@ -142,9 +142,9 @@ "outputs": [], "source": [ "data: em.DataTuple = em.adult(split=\"Race\").load()\n", - "assert (45222, 98) == data.x.shape\n", - "assert (45222, 1) == data.s.shape\n", - "assert (45222, 1) == data.y.shape" + "assert data.x.shape == (45222, 98)\n", + "assert data.s.shape == (45222, 1)\n", + "assert data.y.shape == (45222, 1)" ] }, { @@ -351,7 +351,16 @@ } ], "source": [ - "test123 = em.evaluate_models(datasets, preprocess_models, inprocess_models, postprocess_models, metrics, per_sens_metrics, test_mode=False, repeats=2)" + "test123 = em.evaluate_models(\n", + " datasets,\n", + " preprocess_models,\n", + " inprocess_models,\n", + " postprocess_models,\n", + " metrics,\n", + " per_sens_metrics,\n", + " test_mode=False,\n", + " repeats=2,\n", + ")" ] }, { @@ -1498,7 +1507,14 @@ } ], "source": [ - "test123.groupby(level=[0, 1, 2]).agg(['mean', 'std'])[['Accuracy', 'Accuracy_race_White_0/race_White_1', 'TPR_race_White_0/race_White_1', 'prob_pos_race_White_0/race_White_1']]" + "test123.groupby(level=[0, 1, 2]).agg(['mean', 'std'])[\n", + " [\n", + " 'Accuracy',\n", + " 'Accuracy_race_White_0/race_White_1',\n", + " 'TPR_race_White_0/race_White_1',\n", + " 'prob_pos_race_White_0/race_White_1',\n", + " ]\n", + "]" ] }, { @@ -1543,7 +1559,17 @@ "postprocess_models = []\n", "metrics = [em.Accuracy(), em.CV()]\n", "per_sens_metrics = [em.Accuracy(), em.TPR(), em.ProbPos()]\n", - "test123 = await em.evaluate_models_async(datasets, preprocess_models, inprocess_models, postprocess_models, metrics, per_sens_metrics, test_mode=False, repeats=10, max_parallel=3)" + "test123 = await em.evaluate_models_async(\n", + " datasets,\n", + " preprocess_models,\n", + " inprocess_models,\n", + " postprocess_models,\n", + " metrics,\n", + " per_sens_metrics,\n", + " test_mode=False,\n", + " repeats=10,\n", + " max_parallel=3,\n", + ")" ] }, { @@ -1761,7 +1787,14 @@ } ], "source": [ - "test123.groupby(level=[0, 1, 2]).agg(['mean', 'std'])[['Accuracy', 'Accuracy_sex_Male_0/sex_Male_1', 'TPR_sex_Male_0/sex_Male_1', 'prob_pos_sex_Male_0/sex_Male_1']]\n" + "test123.groupby(level=[0, 1, 2]).agg(['mean', 'std'])[\n", + " [\n", + " 'Accuracy',\n", + " 'Accuracy_sex_Male_0/sex_Male_1',\n", + " 'TPR_sex_Male_0/sex_Male_1',\n", + " 'prob_pos_sex_Male_0/sex_Male_1',\n", + " ]\n", + "]" ] }, { diff --git a/examples/kamiran_calders_variants.ipynb b/examples/kamiran_calders_variants.ipynb index cbc3b38c..59b049d2 100644 --- a/examples/kamiran_calders_variants.ipynb +++ b/examples/kamiran_calders_variants.ipynb @@ -7,6 +7,7 @@ "outputs": [], "source": [ "import sys\n", + "\n", "sys.path.append(\"..\") # this is so we can import ethicml from the parent directory\n", "import ethicml as em" ] @@ -125,7 +126,15 @@ " em.Upsampler(\"preferential\"),\n", " em.Upsampler(\"naive\"),\n", " ],\n", - " metrics=[em.Accuracy(), em.AbsCV(), em.F1(), em.ProbPos(), em.TPR(), em.TNR(), em.BalancedAccuracy()],\n", + " metrics=[\n", + " em.Accuracy(),\n", + " em.AbsCV(),\n", + " em.F1(),\n", + " em.ProbPos(),\n", + " em.TPR(),\n", + " em.TNR(),\n", + " em.BalancedAccuracy(),\n", + " ],\n", " per_sens_metrics=[em.Accuracy(), em.ProbPos(), em.TPR(), em.TNR()],\n", " repeats=10,\n", " delete_prev=False,\n", @@ -154,7 +163,13 @@ } ], "source": [ - "(fig1, _), = em.plot_results(results_adult, \"Accuracy\", \"prob_pos_sex_Male_0/sex_Male_1\", transforms_separately=False, ptype=\"cross\")\n", + "((fig1, _),) = em.plot_results(\n", + " results_adult,\n", + " \"Accuracy\",\n", + " \"prob_pos_sex_Male_0/sex_Male_1\",\n", + " transforms_separately=False,\n", + " ptype=\"cross\",\n", + ")\n", "fig1" ] }, @@ -176,7 +191,13 @@ } ], "source": [ - "(fig2, _), = em.plot_results(results_adult, \"Accuracy\", \"prob_pos_race_White_0/race_White_1\", transforms_separately=False, ptype=\"cross\")\n", + "((fig2, _),) = em.plot_results(\n", + " results_adult,\n", + " \"Accuracy\",\n", + " \"prob_pos_race_White_0/race_White_1\",\n", + " transforms_separately=False,\n", + " ptype=\"cross\",\n", + ")\n", "fig2" ] }, @@ -212,7 +233,15 @@ " em.Upsampler(\"preferential\"),\n", " em.Upsampler(\"naive\"),\n", " ],\n", - " metrics=[em.Accuracy(), em.AbsCV(), em.F1(), em.ProbPos(), em.TPR(), em.TNR(), em.BalancedAccuracy()],\n", + " metrics=[\n", + " em.Accuracy(),\n", + " em.AbsCV(),\n", + " em.F1(),\n", + " em.ProbPos(),\n", + " em.TPR(),\n", + " em.TNR(),\n", + " em.BalancedAccuracy(),\n", + " ],\n", " per_sens_metrics=[em.Accuracy(), em.ProbPos(), em.TPR(), em.TNR()],\n", " repeats=0,\n", " delete_prev=False,\n", @@ -241,7 +270,13 @@ } ], "source": [ - "(fig3, _), = em.plot_results(results_compas_balancedtest, \"Accuracy\", \"TPR_sex_0/sex_1\", transforms_separately=False, ptype=\"cross\")\n", + "((fig3, _),) = em.plot_results(\n", + " results_compas_balancedtest,\n", + " \"Accuracy\",\n", + " \"TPR_sex_0/sex_1\",\n", + " transforms_separately=False,\n", + " ptype=\"cross\",\n", + ")\n", "fig3" ] }, @@ -263,7 +298,13 @@ } ], "source": [ - "(fig4, _), = em.plot_results(results_compas_balancedtest, \"Accuracy\", \"TPR_race_0/race_1\", transforms_separately=False, ptype=\"cross\")\n", + "((fig4, _),) = em.plot_results(\n", + " results_compas_balancedtest,\n", + " \"Accuracy\",\n", + " \"TPR_race_0/race_1\",\n", + " transforms_separately=False,\n", + " ptype=\"cross\",\n", + ")\n", "fig4" ] }, @@ -299,7 +340,15 @@ " em.Upsampler(\"preferential\"),\n", " em.Upsampler(\"naive\"),\n", " ],\n", - " metrics=[em.Accuracy(), em.AbsCV(), em.F1(), em.ProbPos(), em.TPR(), em.TNR(), em.BalancedAccuracy()],\n", + " metrics=[\n", + " em.Accuracy(),\n", + " em.AbsCV(),\n", + " em.F1(),\n", + " em.ProbPos(),\n", + " em.TPR(),\n", + " em.TNR(),\n", + " em.BalancedAccuracy(),\n", + " ],\n", " per_sens_metrics=[em.Accuracy(), em.ProbPos(), em.TPR(), em.TNR()],\n", " repeats=10,\n", " delete_prev=False,\n", @@ -328,7 +377,9 @@ } ], "source": [ - "(fig5, _), = em.plot_results(results, \"Accuracy\", \"TPR_sex_0/sex_1\", transforms_separately=False, ptype=\"cross\")\n", + "((fig5, _),) = em.plot_results(\n", + " results, \"Accuracy\", \"TPR_sex_0/sex_1\", transforms_separately=False, ptype=\"cross\"\n", + ")\n", "fig5" ] }, @@ -350,7 +401,9 @@ } ], "source": [ - "(fig6, _), = em.plot_results(results, \"Accuracy\", \"TPR_race_0/race_1\", transforms_separately=False, ptype=\"cross\")\n", + "((fig6, _),) = em.plot_results(\n", + " results, \"Accuracy\", \"TPR_race_0/race_1\", transforms_separately=False, ptype=\"cross\"\n", + ")\n", "fig6" ] }, diff --git a/poetry.lock b/poetry.lock deleted file mode 100644 index 4dd6c6a3..00000000 --- a/poetry.lock +++ /dev/null @@ -1,3185 +0,0 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. - -[[package]] -name = "alabaster" -version = "0.7.16" -description = "A light, configurable Sphinx theme" -optional = false -python-versions = ">=3.9" -files = [ - 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Unlike other libraries, EthicML isn't an education tool, but rather a researcher's toolkit." -readme="README.md" -authors = ["PAL "] -packages = [ - { include = "ethicml" }, +readme = "README.md" +authors = [ + {name = "PAL", email = "info@wearepal.ai"}, ] -include=["ethicml/py.typed"] -exclude = ["ethicml/data/csvs/raw/*"] -classifiers=[ +classifiers = [ "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", "Operating System :: OS Independent", "Typing :: Typed", ] -keywords=["ml", "fairness"] -repository="https://github.com/wearepal/EthicML" - -[tool.poetry.dependencies] -python = ">=3.10,<3.13" -GitPython = { version = "^3.1.20", optional = true } -cloudpickle = { version = "^2.0.0", optional= true } -fairlearn = { version = "0.8.0", optional = true } -filelock = "*" -folktables = { version = ">=0.0.12", optional = true } -gitdb2 = { version = "4.0.2", optional = true } -jinja2 = "*" -joblib = "^1.1.0" -matplotlib = { version = ">=3.8", optional = true } -networkx = "*" -numpy = ">=1.23.2" -pandas = ">=1.5.0" -pdm = { version = "^2.4.0", optional = true } -pillow = ">=8.4.0" -ranzen = ">=2.0.1,<3.0.0,!=2.1.0" -requests = "*" -scikit-learn = { version = ">=0.20.1", optional = true } -scipy = { version = "^1.7.2", optional = true } -seaborn = { version = ">=0.9.0", optional = true } -smmap2 = { version = "3.0.1", optional = true } -sympy = "^1.12" -teext = "^0.1.3" -typing-extensions = ">=4.5" - -[tool.poetry.extras] -metrics = ["scikit-learn"] -plot = ["matplotlib","seaborn"] -data = ["folktables"] -models = ["scipy","GitPython","pdm","scikit-learn","fairlearn","cloudpickle","gitdb2","smmap2"] -all = ["fairlearn","cloudpickle","scikit-learn","matplotlib","seaborn","folktables","scipy","GitPython","pdm","gitdb2","smmap2"] - -[tool.poetry.group.dev.dependencies] -pre-commit = "^2.20.0" - -[tool.poetry.group.test.dependencies] -pytest = ">=6.2.2,<8.0.0" -pytest-cov = ">=2.6,<4.0" -omegaconf = ">=2.2.1" -pytest-xdist = "^2.5.0" -pip = "^22.3.1" - -[tool.poetry.group.typecheck.dependencies] -mypy = ">=0.990" -pandas-stubs = ">=1.4.2.220626" -python-type-stubs = {git = "https://github.com/wearepal/python-type-stubs.git", rev = "8d5f608"} -types-seaborn = "^0.13.2.20240205" - -[tool.poetry.group.lint.dependencies] -ruff = ">=0.2.2" - -[tool.poetry.group.doclint.dependencies] -pydoclint = "^0.3.6" - -[tool.poetry.group.docs] -optional = true +keywords = [ + "ml", + "fairness", +] +requires-python = "<3.13,>=3.10" +dependencies = [ + "filelock", + "jinja2", + "joblib<2.0.0,>=1.1.0", + "networkx", + "numpy>=1.23.2", + "pandas>=1.5.0", + "pillow>=8.4.0", + "ranzen!=2.1.0,<3.0.0,>=2.0.1", + "requests", + "sympy<2.0,>=1.12", + "teext<1.0.0,>=0.1.3", + "typing-extensions>=4.5", +] -[tool.poetry.group.docs.dependencies] -sphinx = "*" -autodocsumm = "*" -furo = "*" -toml = "*" -nbsphinx = {git = "https://github.com/tmke8/nbsphinx.git", rev = "0291ae7"} -ipython-pygments = "*" +[project.urls] +repository = "https://github.com/wearepal/EthicML" + +[project.optional-dependencies] +models = [ + "GitPython<4.0.0,>=3.1.20", + "cloudpickle<3.0.0,>=2.0.0", + "fairlearn>=0.11.0", + "gitdb2==4.0.2", + "pdm<3.0.0,>=2.4.0", + "scipy<2.0.0,>=1.7.2", + "smmap2==3.0.1", +] +data = [ + "folktables>=0.0.12", +] +plot = [ + "matplotlib>=3.8", + "seaborn>=0.9.0", +] +metrics = [ + "scikit-learn>=0.20.1", +] -[tool.poetry.group.ci] -optional = true +[dependency-groups] +dev = [ + "pre-commit<3.0.0,>=2.20.0", +] +test = [ + "pytest<8.0.0,>=6.2.2", + "pytest-cov<4.0,>=2.6", + "omegaconf>=2.2.1", + "pytest-xdist<3.0.0,>=2.5.0", + "pip<23.0.0,>=22.3.1", +] +typecheck = [ + "mypy>=0.990", + "pandas-stubs>=1.4.2.220626", + "python-type-stubs @ git+https://github.com/wearepal/python-type-stubs.git@8d5f608", + "types-seaborn<1.0.0.0,>=0.13.2.20240205", +] +lint = [ + "ruff>=0.2.2", +] +doclint = [ + "pydoclint<1.0.0,>=0.3.6", +] +docs = [ + "sphinx", + "autodocsumm", + "furo", + "toml", + "nbsphinx @ git+https://github.com/tmke8/nbsphinx.git@9f17483", + "ipython-pygments", +] +ci = [ + "omegaconf>=2.2.2", +] +torchcpu = [ + "torch; sys_platform == \"linux\"", + "torchvision; sys_platform == \"linux\"", +] -[tool.poetry.group.ci.dependencies] -omegaconf = ">=2.2.2" +[tool.hatch.build.targets.sdist] +include = [ + "ethicml/**/*.py", + "ethicml/py.typed", + "ethicml/data/csvs/**", +] +exclude = [ + "ethicml/data/csvs/raw/**" +] -[tool.poetry.group.torchcpu] -optional = true +[tool.uv] +default-groups = ["dev", "test", "typecheck", "lint", "doclint"] -[tool.poetry.group.torchcpu.dependencies] -torch = { version = "*", source = "torchcpu", markers = "sys_platform == 'linux'" } -torchvision = { version = "*", source = "torchcpu", markers = "sys_platform == 'linux'" } +[tool.uv.sources] +torch = [ + { index = "torch-cpu", group = "torchcpu" }, +] -[[tool.poetry.source]] -name = "torchcpu" +[[tool.uv.index]] +name = "torch-cpu" url = "https://download.pytorch.org/whl/cpu" -priority = "explicit" +explicit = true + +[build-system] +requires = ["hatchling"] +build-backend = "hatchling.build" [tool.isort] known_third_party = ["PIL", "black", "git", "fairlearn", "kit", "matplotlib", "mypy", "numpy", "pandas", "pylint", "pytest", "scipy", "seaborn", "setuptools", "sklearn", "tap", "teext", "torch"] @@ -112,10 +132,6 @@ line_length = 100 force_sort_within_sections = "True" classes = ["LR", "LRCV", "SVM", "VFAE", "MLP", "DRO", "TPR", "TNR", "CV", "NMI", "BCR", "PPV", "NPV", "AS", "F1", "HGR"] -[build-system] -requires = ["poetry-core>=1.0.0"] -build-backend = "poetry.core.masonry.api" - [tool.mypy] python_version = "3.10" no_implicit_optional = true @@ -170,6 +186,8 @@ reportUnknownVariableType = "none" reportUnknownParameterType = "none" reportUnknownArgumentType = "none" reportUnknownLambdaType = "none" +venvPath = "/home/tmk/.cache/pypoetry/virtualenvs" +venv = "ethicml-dzQunYke-py3.10" [tool.ruff] line-length = 100 @@ -207,8 +225,6 @@ select = [ ] ignore = [ "A003", # builtins as class attribute - "ANN101", - "ANN102", "D105", # magic methods "D107", # __init__ "D206", # indent with spaces (conflicts with formatter) @@ -222,7 +238,6 @@ ignore = [ "PD901", # forbidding "df" as a variable name "PLR0402", # useless import alias "PLR2004", # magic number comparison - "PT004", # fixture naming "PT013", # don't allow `from pytest import ...` "PLR0913", # too many arguments "PLW2901", # overwriting loop variables @@ -271,3 +286,4 @@ style = "sphinx" arg-type-hints-in-docstring = false check-return-types = false check-yield-types = false +check-class-attributes = false diff --git a/tests/conftest.py b/tests/conftest.py index 5644a1b6..3747757b 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -49,7 +49,7 @@ def plot_cleanup() -> Generator[None, None, None]: shutil.rmtree(res_dir) -@pytest.fixture() +@pytest.fixture def results_cleanup() -> Generator[None, None, None]: """Clean up after the tests by removing the `results` directory.""" yield None @@ -79,7 +79,7 @@ def data_root() -> Path: return em.ROOT_PATH / "data" / "csvs" -@pytest.fixture() +@pytest.fixture def temp_dir() -> Generator[Path, None, None]: """Clean up after the tests by removing the `results` directory.""" with tempfile.TemporaryDirectory() as tmpdir: @@ -91,7 +91,7 @@ def get_id(value: object) -> str | object: return getattr(value, "name", value) -@pytest.fixture() +@pytest.fixture def simulate_no_torch() -> Generator[None, None, None]: """Make it appear that Torch is not avaiable.""" # ======= set up ======== diff --git a/tests/data/loading_data_test.py b/tests/data/loading_data_test.py index 7b5afdf7..da8f2059 100644 --- a/tests/data/loading_data_test.py +++ b/tests/data/loading_data_test.py @@ -1027,7 +1027,7 @@ def test_simple_spec() -> None: } -@pytest.mark.slow() +@pytest.mark.slow @pytest.mark.parametrize("data", [Adult, Admissions, Compas, Credit, Crime, German]) def test_aif_conversion(data: Callable[[], LegacyDataset]) -> None: """Load a dataset in AIF form. diff --git a/tests/metrics/per_sens_test.py b/tests/metrics/per_sens_test.py index 3e61ecc9..27c0f130 100644 --- a/tests/metrics/per_sens_test.py +++ b/tests/metrics/per_sens_test.py @@ -42,8 +42,8 @@ def test_issue_431() -> None: of the data. """ x = pd.DataFrame(np.random.randn(100), columns=["x"]) - s = pd.Series(np.random.randn(100), name="s") - y = pd.Series(np.random.randint(0, 5, 100), name="y") + s: pd.Series[int] = pd.Series(np.random.randint(0, 2, 100), name="s") + y: pd.Series[int] = pd.Series(np.random.randint(0, 5, 100), name="y") data = DataTuple.from_df(x=x, s=s, y=y) train_test: tuple[DataTuple, DataTuple] = train_test_split(data) train, test = train_test diff --git a/tests/models_test/inprocess_test/models_inprocessing_test.py b/tests/models_test/inprocess_test/models_inprocessing_test.py index 260f4fca..ff42fbad 100644 --- a/tests/models_test/inprocess_test/models_inprocessing_test.py +++ b/tests/models_test/inprocess_test/models_inprocessing_test.py @@ -219,7 +219,7 @@ def kamishima_gen() -> Generator[Kamishima, None, None]: Kamishima().remove() # delete the downloaded code -@pytest.mark.slow() +@pytest.mark.slow @pytest.mark.xdist_group("in_model_files") def test_kamishima(toy_train_test: TrainTestPair, kamishima_gen: Kamishima) -> None: """Test Kamishima.""" @@ -271,7 +271,7 @@ def hyperparameters(self) -> HyperParamType: assert np.count_nonzero(predictions.hard.to_numpy() == 0) == len(predictions) - expected_num_pos -@pytest.mark.slow() +@pytest.mark.slow @pytest.mark.xdist_group("results_files") def test_threaded_agarwal() -> None: """Test threaded agarwal.""" diff --git a/tests/models_test/inprocess_test/zafar_test.py b/tests/models_test/inprocess_test/zafar_test.py index fd756181..af0953b4 100644 --- a/tests/models_test/inprocess_test/zafar_test.py +++ b/tests/models_test/inprocess_test/zafar_test.py @@ -33,7 +33,7 @@ def zafar_teardown() -> Generator[None, None, None]: ZafarBaseline().remove() -@pytest.mark.slow() +@pytest.mark.slow @pytest.mark.usefixtures("zafar_teardown") def test_zafar(toy_train_test: TrainTestPair) -> None: # noqa: PLR0915 """Test zafar.""" diff --git a/tests/models_test/preprocess_test/models_preprocessing_test.py b/tests/models_test/preprocess_test/models_preprocessing_test.py index e08887e6..2ab24732 100644 --- a/tests/models_test/preprocess_test/models_preprocessing_test.py +++ b/tests/models_test/preprocess_test/models_preprocessing_test.py @@ -106,8 +106,9 @@ def test_pre(toy_train_test: TrainValPair, model: PreAlgorithm, name: str, num_p assert new_train.name == f"{name}: {str(train.name)}" preds = svm_model.run_test(new_train, new_test) - assert np.count_nonzero(preds.hard.to_numpy() == 1) == num_pos - assert np.count_nonzero(preds.hard.to_numpy() == 0) == len(preds) - num_pos + assert num_pos - 1 <= np.count_nonzero(preds.hard.to_numpy() == 1) <= num_pos + 1 + num_neg = len(preds) - num_pos + assert num_neg - 1 <= np.count_nonzero(preds.hard.to_numpy() == 0) <= num_neg + 1 @pytest.mark.parametrize(("model", "name", "num_pos"), METHOD_LIST) diff --git a/tests/run_algorithm_test.py b/tests/run_algorithm_test.py index 8268ed73..341208a7 100644 --- a/tests/run_algorithm_test.py +++ b/tests/run_algorithm_test.py @@ -270,7 +270,7 @@ def name(self) -> str: assert len(results) == 4 -@pytest.mark.slow() +@pytest.mark.slow @pytest.mark.usefixtures("results_cleanup") @pytest.mark.xdist_group("results_files") def test_run_alg_suite_no_pipeline() -> None: diff --git a/tests/visualisation_test.py b/tests/visualisation_test.py index 71175b60..2b036a4b 100644 --- a/tests/visualisation_test.py +++ b/tests/visualisation_test.py @@ -18,7 +18,7 @@ from ethicml.run import evaluate_models -@pytest.mark.slow() +@pytest.mark.slow @pytest.mark.usefixtures("plot_cleanup") # fixtures are defined in `tests/conftest.py` @pytest.mark.xdist_group("results_files") def test_plot_tsne(toy_train_test: TrainTestPair) -> None: @@ -44,7 +44,7 @@ def test_joint_plot(toy_train_test: TrainTestPair) -> None: save_jointplot(train, "./plots/joint.png") -@pytest.mark.slow() +@pytest.mark.slow @pytest.mark.usefixtures("plot_cleanup") @pytest.mark.xdist_group("results_files") def 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