From 62f65891d61e3568a42496a9b89cba124213ae23 Mon Sep 17 00:00:00 2001 From: Jerome Dockes Date: Wed, 20 Aug 2025 12:14:40 +0200 Subject: [PATCH 1/6] update packaging & min deps versions --- .github/workflows/testing.yml | 20 +++++------ pyproject.toml | 65 +++++++++++++++++++++++++++++++++-- setup.cfg | 55 ----------------------------- setup.py | 11 ------ tox.ini | 16 ++++----- 5 files changed, 81 insertions(+), 86 deletions(-) delete mode 100644 setup.cfg delete mode 100644 setup.py diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml index 85c5879..b8404db 100644 --- a/.github/workflows/testing.yml +++ b/.github/workflows/testing.yml @@ -30,7 +30,7 @@ jobs: strategy: matrix: os: ["ubuntu-latest", "windows-latest", "macos-latest"] - python-version: ["3.7", "3.10"] + python-version: ["3.10", "3.13"] steps: - uses: actions/checkout@v2 - uses: actions/setup-python@v2 @@ -46,32 +46,32 @@ jobs: name: "upload coverage to CodeCov" run_tests_ubuntu_old_dependencies: - name: "Ubuntu with Python 3.7 min dependencies" + name: "Ubuntu with Python 3.10 min dependencies" runs-on: "ubuntu-latest" steps: - uses: actions/checkout@v2 - uses: actions/setup-python@v2 with: - python-version: "3.7" + python-version: "3.10" name: "setup python" - name: "install tox" run: pip install tox - name: "run tests" - run: tox -e py37-old + run: tox -e py310-old run_tests_with_nimare_installed: - name: "Ubuntu with Python 3.8 and NiMARE" + name: "Ubuntu with Python 3.10 and NiMARE" runs-on: "ubuntu-latest" steps: - uses: actions/checkout@v2 - uses: actions/setup-python@v2 with: - python-version: "3.8" + python-version: "3.10" name: "setup python" - name: "install tox" run: pip install tox - name: "run tests" - run: tox -e py38-nimare + run: tox -e py310-nimare run_test_plugin: name: "Test plugin" @@ -80,7 +80,7 @@ jobs: - uses: actions/checkout@v2 - uses: actions/setup-python@v2 with: - python-version: "3.10" + python-version: "3.12" name: "setup python" - name: "install tox" run: pip install tox @@ -94,7 +94,7 @@ jobs: - uses: actions/checkout@v2 - uses: actions/setup-python@v2 with: - python-version: "3.10" + python-version: "3.11" name: "setup python" - name: "install" run: pip install .[dev] @@ -108,7 +108,7 @@ jobs: - uses: actions/checkout@v2 - uses: actions/setup-python@v2 with: - python-version: "3.10" + python-version: "3.13" - name: "install" run: pip install .[dev] - name: "build" diff --git a/pyproject.toml b/pyproject.toml index f4b49d3..0265d23 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,64 @@ [build-system] -requires = ["setuptools", "wheel"] -build-backend = "setuptools.build_meta" +requires = ["hatchling"] +build-backend = "hatchling.build" + +[project] +name = "pubget" +dynamic = ["version"] +description = "Download neuroimaging articles and extract text and stereotactic coordinates." +readme = "README.md" +requires-python = ">=3.10" +license-files = ["COPYING"] +authors = [ + {name = "Jérôme Dockès", email = "jerome@dockes.org"}, + {name = "Alejandro de la Vega", email = "delavega@utexas.edu"} +] +keywords = ["neuroimaging", "meta-analysis", "text-mining"] +classifiers = [ + "License :: OSI Approved :: MIT License", + "Intended Audience :: Science/Research", + "Operating System :: OS Independent", + "Programming Language :: Python :: 3", + "Topic :: Scientific/Engineering", + "Topic :: Software Development :: Libraries", +] +dependencies = [ + "joblib (>=1.1.1)", + "lxml", + "importlib_metadata (>=3.6)", + "neuroquery", + "numpy (>=1.17.3)", + "pandas (>=1.5.3)", + "requests", + "scikit-learn (>=1.2.1)", + "scipy (>=1.3.2)", +] + +[project.urls] +Documentation = "https://neuroquery.github.io/pubget/" +"Source code" = "https://github.com/neuroquery/pubget" + +[project.optional-dependencies] +dev = [ + "coverage", + "flake8", + "mypy", + "pdoc", + "pylint", + "pytest", + "pytest-cov", + "tox", + "types-requests", + "black", + "isort", +] +nimare = [ + "nimare", +] + +[tool.hatch.version] +path = "src/pubget/_data/VERSION" +pattern = "^(?P.*)$" [tool.mypy] warn_return_any = true @@ -21,3 +79,6 @@ profile = "black" extend_skip = ["data", "_data"] skip_gitignore = true line_length = 79 + +[project.scripts] +pubget = "pubget._commands:pubget_command" \ No newline at end of file diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index 269a253..0000000 --- a/setup.cfg +++ /dev/null @@ -1,55 +0,0 @@ -[metadata] -name = pubget -description = Download neuroimaging articles and extract text and stereotactic coordinates. -long_description = file: README.md, whats_new.md, COPYING -long_description_content_type = text/markdown -keywords = neuroimaging, meta-analysis, text-mining -url = https://neuroquery.github.io/pubget/ -author = Jérôme Dockès -author_email = jerome@dockes.org -maintainer = Jérôme Dockès -maintainer_email = jerome@dockes.org -license = MIT License -classifiers = - License :: OSI Approved :: MIT License - Programming Language :: Python :: 3 - -[options] -zip_safe = False -packages = find: -package_dir = - =src -install_requires = - joblib>=0.17,<=1.1.1 - lxml - importlib_metadata>=3.6 - neuroquery - numpy>=1.16 - pandas>=0.24 - requests - scikit-learn>=0.21 - scipy -python_requires = >=3.7 - -[options.extras_require] -dev = - coverage - flake8 - mypy - pdoc - pylint - pytest - pytest-cov - tox - types-requests - black - isort -nimare = - nimare - -[options.packages.find] -where = src - -[options.entry_points] -console_scripts = - pubget = pubget._commands:pubget_command diff --git a/setup.py b/setup.py deleted file mode 100644 index a92a698..0000000 --- a/setup.py +++ /dev/null @@ -1,11 +0,0 @@ -from pathlib import Path - -from setuptools import setup - -package_dir = Path(__file__).parent.joinpath("src", "pubget") -data_files = [ - str(f.relative_to(package_dir)) - for f in package_dir.joinpath("_data").glob("**/*") -] -version = package_dir.joinpath("_data", "VERSION").read_text("utf-8").strip() -setup(package_data={"pubget": data_files}, version=version) diff --git a/tox.ini b/tox.ini index 66a56ac..0819b4f 100644 --- a/tox.ini +++ b/tox.ini @@ -1,5 +1,5 @@ [tox] -envlist = py{37,310}-latest,py37-old,py38-nimare +envlist = py{310,313}-latest,py310-old,py310-nimare [testenv] deps = @@ -7,19 +7,19 @@ deps = commands = pytest tests -[testenv:py37-old] +[testenv:py310-old] deps = pytest - numpy>=1.16,<1.17 - pandas>=0.24,<0.25 - scikit-learn>=0.21,<0.22 - joblib>=0.17,<0.18 - scipy<=1.1.0 + numpy>=1.17,<1.18 + pandas>=1.5,<1.6 + scikit-learn>=1.2,<1.3 + joblib>=1.1,<1.2 + scipy>=1.3,<1.4 importlib_metadata>=3.6,<3.7 commands = pytest tests -[testenv:py38-nimare] +[testenv:py310-nimare] deps = pytest nimare From b0a2381d95d46d7ae68389405830872c0af49fdf Mon Sep 17 00:00:00 2001 From: Jerome Dockes Date: Wed, 20 Aug 2025 13:17:13 +0200 Subject: [PATCH 2/6] no sparse matrix .A --- src/pubget/_data/_fit_neurosynth/app.py | 2 +- src/pubget/_model_data.py | 2 +- tests/test_fit_neurosynth.py | 2 +- tests/test_vectorization.py | 4 ++-- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/pubget/_data/_fit_neurosynth/app.py b/src/pubget/_data/_fit_neurosynth/app.py index e65887e..43556a8 100755 --- a/src/pubget/_data/_fit_neurosynth/app.py +++ b/src/pubget/_data/_fit_neurosynth/app.py @@ -102,7 +102,7 @@ def _get_image_viewer(term): def _get_similar_docs_table(term): - loadings = tfidf[:, terms_info.loc[term, "pos"]].A.ravel() + loadings = tfidf[:, terms_info.loc[term, "pos"]].toarray().ravel() order = np.argpartition(-loadings, np.arange(min(loadings.shape[0], 20)))[ :20 ] diff --git a/src/pubget/_model_data.py b/src/pubget/_model_data.py index a98ccbd..15cab06 100644 --- a/src/pubget/_model_data.py +++ b/src/pubget/_model_data.py @@ -186,7 +186,7 @@ def _set_pmcids(self) -> None: rindex = pd.Series(np.arange(len(tfidf_pmcids)), index=tfidf_pmcids) self.tfidf = sparse.csr_matrix( - self.tfidf.A[rindex.loc[pmcids].values, :] + self.tfidf.toarray()[rindex.loc[pmcids].values, :] ) self.metadata.set_index("pmcid", inplace=True) diff --git a/tests/test_fit_neurosynth.py b/tests/test_fit_neurosynth.py index 6fa1200..b7fe07a 100644 --- a/tests/test_fit_neurosynth.py +++ b/tests/test_fit_neurosynth.py @@ -19,7 +19,7 @@ def test_chi_square(): z_vals = _fit_neurosynth._chi_square( brain_maps, brain_maps.sum(axis=0), term_vec_sp ) - term_vec = term_vec_sp.A.ravel().astype(bool) + term_vec = term_vec_sp.toarray().ravel().astype(bool) stats_z_vals = [] normal = stats.norm() for voxel in range(n_voxels): diff --git a/tests/test_vectorization.py b/tests/test_vectorization.py index a8d5f05..58d1133 100644 --- a/tests/test_vectorization.py +++ b/tests/test_vectorization.py @@ -54,7 +54,7 @@ def _check_matrices(data_dir): ) assert data.shape == (3, 5) assert data.dtype == int if kind == "counts" else float - body_counts = sparse.load_npz(str(data_dir.joinpath("body_counts.npz"))).A + body_counts = sparse.load_npz(str(data_dir.joinpath("body_counts.npz"))).toarray() assert ( body_counts == [ @@ -110,7 +110,7 @@ def test_voc_mapping_matrix(): voc = ["amygdala", "brain stem", "brainstem", "cortex"] mapping = {"brain stem": "brainstem"} op = _vectorization._voc_mapping_matrix(voc, mapping) - assert np.allclose(op.A, [[1, 0, 0, 0], [0, 1, 1, 0], [0, 0, 0, 1]]) + assert np.allclose(op.toarray(), [[1, 0, 0, 0], [0, 1, 1, 0], [0, 0, 0, 1]]) assert np.allclose(op.dot(np.arange(1, len(voc) + 1)), [1, 5, 4]) From 74737d4c1744cbe5ca71d46bbf4b870f26d234fd Mon Sep 17 00:00:00 2001 From: Jerome Dockes Date: Thu, 21 Aug 2025 02:31:40 +0200 Subject: [PATCH 3/6] _ --- .github/workflows/testing.yml | 94 +- docs/example_plugin/pyproject.toml | 22 +- pixi.lock | 8112 ++++++++++++++++++++++++++++ pyproject.toml | 66 +- src/pubget/_plugins.py | 5 +- tests/test_commands.py | 4 +- tox.ini | 3 +- 7 files changed, 8217 insertions(+), 89 deletions(-) create mode 100644 pixi.lock diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml index b8404db..228ed2a 100644 --- a/.github/workflows/testing.yml +++ b/.github/workflows/testing.yml @@ -13,108 +13,50 @@ jobs: name: checks runs-on: "ubuntu-latest" steps: - - uses: actions/checkout@v2 - - uses: actions/setup-python@v2 + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 with: - python-version: "3.10" + python-version: "3.13" - name: "install" - run: pip install .[dev] + run: pip install ".[dev]" - name: "mypy" run: make test_mypy - name: "flake8" run: make test_flake8 run_tests: - name: ${{ matrix.os }} with Python ${{ matrix.python-version }} + name: ${{ matrix.os }} ${{ matrix.environment }} runs-on: ${{ matrix.os }} strategy: matrix: os: ["ubuntu-latest", "windows-latest", "macos-latest"] - python-version: ["3.10", "3.13"] - steps: - - uses: actions/checkout@v2 - - uses: actions/setup-python@v2 - with: - python-version: ${{ matrix.python-version }} - name: "setup python" - - name: "install" - run: pip install .[dev] - - name: "run tests" - run: make test_coverage - - uses: codecov/codecov-action@v2 - if: success() - name: "upload coverage to CodeCov" - - run_tests_ubuntu_old_dependencies: - name: "Ubuntu with Python 3.10 min dependencies" - runs-on: "ubuntu-latest" - steps: - - uses: actions/checkout@v2 - - uses: actions/setup-python@v2 - with: - python-version: "3.10" - name: "setup python" - - name: "install tox" - run: pip install tox - - name: "run tests" - run: tox -e py310-old - - run_tests_with_nimare_installed: - name: "Ubuntu with Python 3.10 and NiMARE" - runs-on: "ubuntu-latest" - steps: - - uses: actions/checkout@v2 - - uses: actions/setup-python@v2 - with: - python-version: "3.10" - name: "setup python" - - name: "install tox" - run: pip install tox - - name: "run tests" - run: tox -e py310-nimare - - run_test_plugin: - name: "Test plugin" - runs-on: "ubuntu-latest" + environment: ["py310-min-deps", "py313-latest-deps"] steps: - - uses: actions/checkout@v2 - - uses: actions/setup-python@v2 + - uses: actions/checkout@v4 + - uses: prefix-dev/setup-pixi@v0.8.8 with: - python-version: "3.12" - name: "setup python" - - name: "install tox" - run: pip install tox + pixi-version: v0.41.3 + environments: ${{ matrix.environment }} + frozen: true - name: "run tests" - run: make test_plugin - - run_compare_query_vs_pmcid_list: - name: "Compare query vs PMCID list" - runs-on: "ubuntu-latest" - steps: - - uses: actions/checkout@v2 - - uses: actions/setup-python@v2 - with: - python-version: "3.11" - name: "setup python" - - name: "install" - run: pip install .[dev] - - name: "run check" - run: make compare_query_vs_pmcid_list + run: pixi run -e ${{ matrix.environment }} test + - name: "upload coverage to CodeCov" + uses: codecov/codecov-action@v5.4.3 build_doc: name: "build documentation" runs-on: "ubuntu-latest" steps: - - uses: actions/checkout@v2 - - uses: actions/setup-python@v2 + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 with: python-version: "3.13" - name: "install" - run: pip install .[dev] + run: pip install ".[dev]" - name: "build" run: make doc - name: "store doc artifact" - uses: actions/upload-artifact@v2 + uses: actions/upload-artifact@v4 with: name: documentation path: doc_build/pubget.html diff --git a/docs/example_plugin/pyproject.toml b/docs/example_plugin/pyproject.toml index 9787c3b..31f1e35 100644 --- a/docs/example_plugin/pyproject.toml +++ b/docs/example_plugin/pyproject.toml @@ -1,3 +1,21 @@ [build-system] -requires = ["setuptools", "wheel"] -build-backend = "setuptools.build_meta" +requires = ["hatchling"] +build-backend = "hatchling.build" + +[project] +name = "pubget_example_plugin" +version = "0.1.0" +requires-python = ">=3.10" +dependencies = [ + "pandas", + "matplotlib", + "pubget", +] + +[project.optional-dependencies] +dev = [ + "pytest", +] + +[project.entry-points."pubget.plugin_actions"] +get_pubget_actions = "pubget_example_plugin:get_pubget_actions" \ No newline at end of file diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 0000000..288f2cc --- /dev/null +++ b/pixi.lock @@ -0,0 +1,8112 @@ +version: 6 +environments: + default: + channels: + - url: https://conda.anaconda.org/conda-forge/ + indexes: + - https://pypi.org/simple + packages: + linux-64: + - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 + - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2 + - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.1.0-py312h2ec8cdc_3.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2025.8.3-pyhd8ed1ab_0.conda + - conda: 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dependencies = [ "joblib (>=1.1.1)", "lxml", - "importlib_metadata (>=3.6)", "neuroquery", - "numpy (>=1.17.3)", + "numpy (>=1.23.5)", "pandas (>=1.5.3)", "requests", "scikit-learn (>=1.2.1)", - "scipy (>=1.3.2)", + "scipy (>=1.9.3)", ] [project.urls] @@ -47,7 +46,6 @@ dev = [ "pylint", "pytest", "pytest-cov", - "tox", "types-requests", "black", "isort", @@ -81,4 +79,62 @@ skip_gitignore = true line_length = 79 [project.scripts] -pubget = "pubget._commands:pubget_command" \ No newline at end of file +pubget = "pubget._commands:pubget_command" + +[tool.pixi.project] +channels = ["conda-forge"] +platforms = ["linux-64", "osx-arm64", "osx-64", "win-64"] + +[tool.pixi.dependencies] +joblib = ">=1.1.1" +lxml = "*" +numpy = ">=1.23.5" +pandas = ">=1.5.3" +requests = "*" +scikit-learn = ">=1.2.1" +scipy = ">=1.9.3" + +[tool.pixi.pypi-dependencies] +pubget = { path = ".", editable = true } + +[tool.pixi.feature.test.dependencies] +pytest = "*" +pytest-cov = "*" +coverage = "*" + +[tool.pixi.feature.test.tasks] +test = { cmd = "pytest -vsl --cov=pubget tests" } + +[tool.pixi.feature.plugin.pypi-dependencies] +pubget_example_plugin = { path = "docs/example_plugin" } + +[tool.pixi.feature.plugin.tasks] +run_plugin = { cmd = "python docs/example_plugin/tests/run_plugin.py" } + +[tool.pixi.feature.min-dependencies.dependencies] +joblib = "==1.1.1" +lxml = "*" +numpy = "==1.23.5" +pandas = "==1.5.3" +requests = "*" +scikit-learn = "==1.2.1" +scipy = "==1.9.3" + +[tool.pixi.feature.optional-dependencies.pypi-dependencies] +# TODO fix version conflicts +# nimare = "*" + +[tool.pixi.feature.py310.dependencies] +python = "~=3.10.0" + +[tool.pixi.feature.py311.dependencies] +python = "~=3.11.0" + +[tool.pixi.feature.py313.dependencies] +python = "~=3.13.0" + +[tool.pixi.environments] +py310-min-deps = ["py310", "min-dependencies", "test"] +py311-optional-deps = ["py311", "optional-dependencies", "test"] +py313-latest-deps = ["py313", "test"] +plugin = ["py313", "plugin"] \ No newline at end of file diff --git a/src/pubget/_plugins.py b/src/pubget/_plugins.py index 25aa55d..0761d20 100644 --- a/src/pubget/_plugins.py +++ b/src/pubget/_plugins.py @@ -1,8 +1,7 @@ """Utilities for loading pubget plug-in functionality.""" from typing import Any, Dict, List - -import importlib_metadata +import importlib.metadata def get_plugin_actions() -> Dict[str, List[Any]]: @@ -14,7 +13,7 @@ def get_plugin_actions() -> Dict[str, List[Any]]: "pipeline_steps": [], "commands": [], } - for entry_point in importlib_metadata.entry_points().select( + for entry_point in importlib.metadata.entry_points().select( group="pubget.plugin_actions" ): plugin_actions = entry_point.load()() diff --git a/tests/test_commands.py b/tests/test_commands.py index 895ab4a..257373e 100644 --- a/tests/test_commands.py +++ b/tests/test_commands.py @@ -2,8 +2,8 @@ import sys from pathlib import Path from unittest.mock import MagicMock, Mock +import importlib.metadata -import importlib_metadata import numpy as np import pandas as pd import pytest @@ -398,7 +398,7 @@ def _mock_entry_point(): all_ep.select.return_value = [ep] metadata_ep = MagicMock() metadata_ep.return_value = all_ep - monkeypatch.setattr(importlib_metadata, "entry_points", metadata_ep) + monkeypatch.setattr(importlib.metadata, "entry_points", metadata_ep) args = ["run", str(tmp_path), "-q", "fMRI[abstract]"] _commands.pubget_command(args) assert pipeline_plugin.arg_parser_called diff --git a/tox.ini b/tox.ini index 0819b4f..dbd9ad9 100644 --- a/tox.ini +++ b/tox.ini @@ -10,7 +10,8 @@ commands = [testenv:py310-old] deps = pytest - numpy>=1.17,<1.18 + cython==0.29.34 + numpy>=1.23,<1.24 pandas>=1.5,<1.6 scikit-learn>=1.2,<1.3 joblib>=1.1,<1.2 From 14278d69ecea905f30362d0bbed0ea80ee01b6c1 Mon Sep 17 00:00:00 2001 From: Jerome Dockes Date: Thu, 21 Aug 2025 02:34:51 +0200 Subject: [PATCH 4/6] _ --- Makefile | 7 +- docs/example_plugin/tox.ini | 9 - pixi.lock | 2072 +++++++++-------------------------- tox.ini | 36 - 4 files changed, 517 insertions(+), 1607 deletions(-) delete mode 100644 docs/example_plugin/tox.ini delete mode 100644 tox.ini diff --git a/Makefile b/Makefile index 59f4828..dd89165 100644 --- a/Makefile +++ b/Makefile @@ -7,7 +7,7 @@ pubget_version := $(shell cat src/pubget/_data/VERSION) test_all: test_mypy test_flake8 test_coverage_strict test test_plugin test_pylint test: - tox + pytest tests test_coverage_strict: pytest --cov=pubget --cov-report=xml --cov-report=term --cov-fail-under=100 tests @@ -28,8 +28,7 @@ test_pylint: pylint ./src test_plugin: - tox -e run_plugin - tox -c docs/example_plugin/tox.ini + pixi run run_plugin run_full_pipeline: python tests/run_full_pipeline.py -o /tmp/ @@ -58,4 +57,4 @@ clean: rm -rf doc_build build dist htmlcov .coverage .coverage.* clean_all: clean - rm -rf .mypy_cache .pytest_cache .tox + rm -rf .mypy_cache .pytest_cache diff --git a/docs/example_plugin/tox.ini b/docs/example_plugin/tox.ini deleted file mode 100644 index 7e35399..0000000 --- a/docs/example_plugin/tox.ini +++ /dev/null @@ -1,9 +0,0 @@ -[tox] -isolated_build = True -envlist = py - -[testenv] -deps = - pytest -commands = - pytest tests \ No newline at end of file diff --git a/pixi.lock b/pixi.lock index 288f2cc..4f2c7cd 100644 --- a/pixi.lock +++ b/pixi.lock @@ -594,7 +594,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.10.18-hd6af730_0_cpython.conda - conda: https://conda.anaconda.org/conda-forge/noarch/python-dateutil-2.9.0.post0-pyhe01879c_2.conda - conda: https://conda.anaconda.org/conda-forge/noarch/python_abi-3.10-8_cp310.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/pytz-2024.1-pyhd8ed1ab_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/pytz-2025.2-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda - conda: https://conda.anaconda.org/conda-forge/noarch/requests-2.32.5-pyhd8ed1ab_0.conda - conda: 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- pytables >=3.8.0 - - pyarrow >=10.0.1 - - html5lib >=1.1 - - tzdata >=2022.7 - - gcsfs >=2022.11.0 + - numexpr >=2.8.4 + - python-calamine >=0.1.7 license: BSD-3-Clause license_family: BSD purls: - - pkg:pypi/pandas?source=hash-mapping - size: 13924933 - timestamp: 1752082433528 + - pkg:pypi/pandas?source=compressed-mapping + size: 13966284 + timestamp: 1755779637297 - pypi: https://files.pythonhosted.org/packages/01/f4/91d5b3ffa718df2f53b0dc109877993e511f4fd055d7e9508682e8aba092/pillow-11.3.0-cp313-cp313-macosx_10_13_x86_64.whl name: pillow version: 11.3.0 @@ -6645,9 +6636,9 @@ packages: - pkg:pypi/six?source=compressed-mapping size: 18455 timestamp: 1753199211006 -- conda: https://conda.anaconda.org/conda-forge/win-64/tbb-2021.13.0-h18a62a1_2.conda - sha256: f09f3ad838158ce03a07e92acb370d6f547f625319f8defe3bde15dc446a3050 - md5: 6f339f632ba0618d8f42acf80218757b +- conda: https://conda.anaconda.org/conda-forge/win-64/tbb-2021.13.0-h18a62a1_3.conda + sha256: 30e82640a1ad9d9b5bee006da7e847566086f8fdb63d15b918794a7ef2df862c + md5: 72226638648e494aaafde8155d50dab2 depends: - libhwloc >=2.12.1,<2.12.2.0a0 - ucrt >=10.0.20348.0 @@ -6656,8 +6647,8 @@ packages: license: Apache-2.0 license_family: APACHE purls: [] - size: 149955 - timestamp: 1754499612925 + size: 150266 + timestamp: 1755776172092 - conda: https://conda.anaconda.org/conda-forge/win-64/tbb-2021.13.0-h62715c5_1.conda sha256: 03cc5442046485b03dd1120d0f49d35a7e522930a2ab82f275e938e17b07b302 md5: 9190dd0a23d925f7602f9628b3aed511 From ac7b09fe92be33920f5a2ac8acb9ab03036d0f64 Mon Sep 17 00:00:00 2001 From: Jerome Dockes Date: Sat, 23 Aug 2025 16:08:21 +0200 Subject: [PATCH 6/6] _ --- tests/conftest.py | 2 +- tests/test_vectorization.py | 8 ++++++-- 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/tests/conftest.py b/tests/conftest.py index 9dd3ee5..c2ec3d8 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -218,7 +218,7 @@ def extracted_and_tfidf_dir(tmp_path): ).to_csv(extracted_dir.joinpath("coordinate_space.csv"), index=False) voc = [f"term {i}" for i in range(100)] features = voc[:50] - mapping = {f"term {i}": f"term {i //2}" for i in range(50, 100)} + mapping = {f"term {i}": f"term {i // 2}" for i in range(50, 100)} tfidf = rng.poisson(1.0, (len(pmcids), len(features))).astype(float) tfidf /= tfidf.max() tfidf[:, ::3] = 0 diff --git a/tests/test_vectorization.py b/tests/test_vectorization.py index 58d1133..e4b6428 100644 --- a/tests/test_vectorization.py +++ b/tests/test_vectorization.py @@ -54,7 +54,9 @@ def _check_matrices(data_dir): ) assert data.shape == (3, 5) assert data.dtype == int if kind == "counts" else float - body_counts = sparse.load_npz(str(data_dir.joinpath("body_counts.npz"))).toarray() + body_counts = sparse.load_npz( + str(data_dir.joinpath("body_counts.npz")) + ).toarray() assert ( body_counts == [ @@ -110,7 +112,9 @@ def test_voc_mapping_matrix(): voc = ["amygdala", "brain stem", "brainstem", "cortex"] mapping = {"brain stem": "brainstem"} op = _vectorization._voc_mapping_matrix(voc, mapping) - assert np.allclose(op.toarray(), [[1, 0, 0, 0], [0, 1, 1, 0], [0, 0, 0, 1]]) + assert np.allclose( + op.toarray(), [[1, 0, 0, 0], [0, 1, 1, 0], [0, 0, 0, 1]] + ) assert np.allclose(op.dot(np.arange(1, len(voc) + 1)), [1, 5, 4])