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rhowardstonerhowardstone
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Merge branch 'develop' into optimize-rdf-histogram-cython
2 parents d0b1267 + 5c7c480 commit 9fd2803

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‎.github/actions/setup-deps/action.yaml‎

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@@ -64,6 +64,8 @@ inputs:
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default: 'h5py>=2.10'
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hole2:
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default: 'hole2'
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imdclient:
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default: 'imdclient>=0.2.2'
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joblib:
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default: 'joblib>=0.12'
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netcdf4:
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${{ inputs.gsd }}
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${{ inputs.h5py }}
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${{ inputs.hole2 }}
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${{ inputs.imdclient }}
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${{ inputs.joblib }}
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${{ inputs.netcdf4 }}
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${{ inputs.networkx }}

‎.github/workflows/deploy.yaml‎

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@@ -41,7 +41,7 @@ jobs:
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- [macos-13, macosx_*, x86_64]
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- [windows-2022, win_amd64, AMD64]
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- [macos-14, macosx_*, arm64]
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python: ["cp310", "cp311", "cp312", "cp313"]
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python: ["cp311", "cp312", "cp313", "cp314"]
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defaults:
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run:
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working-directory: ./package
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fetch-depth: 0
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- name: Build wheels
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uses: pypa/cibuildwheel@v2.23.0
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uses: pypa/cibuildwheel@v3.2.0
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with:
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package-dir: package
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env:
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mv dist/mdanalysistests-* testsuite/dist
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- name: upload_source_and_wheels
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uses: pypa/gh-action-pypi-publish@v1.12.4
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uses: pypa/gh-action-pypi-publish@v1.13.0
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with:
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skip_existing: true
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repository_url: https://test.pypi.org/legacy/
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mv dist/mdanalysistests-* testsuite/dist
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- name: upload_tests
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uses: pypa/gh-action-pypi-publish@v1.12.4
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uses: pypa/gh-action-pypi-publish@v1.13.0
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with:
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packages_dir: testsuite/dist
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skip_existing: true
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mv dist/mdanalysistests-* testsuite/dist
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- name: upload_source_and_wheels
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uses: pypa/gh-action-pypi-publish@v1.12.4
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uses: pypa/gh-action-pypi-publish@v1.13.0
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upload_pypi_mdanalysistests:
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if: |
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mv dist/mdanalysistests-* testsuite/dist
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- name: upload_tests
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uses: pypa/gh-action-pypi-publish@v1.12.4
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uses: pypa/gh-action-pypi-publish@v1.13.0
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with:
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packages_dir: testsuite/dist
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@@ -246,14 +246,13 @@ jobs:
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fail-fast: false
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matrix:
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os: [ubuntu-latest, macos-latest, windows-latest]
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python-version: ["3.10", "3.11", "3.12", "3.13"]
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python-version: ["3.11", "3.12", "3.13", "3.14"]
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type: ["FULL", "MIN"]
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exclude:
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# Multiple deps don't like windows
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- os: windows-latest
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type: "FULL"
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# Chemfiles won't install over py3.13
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- python-version: "3.13"
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- python-version: "3.14"
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type: "FULL"
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env:
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MPLBACKEND: agg

‎.github/workflows/gh-ci-cron.yaml‎

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@@ -6,8 +6,8 @@ on:
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workflow_dispatch:
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# Uncomment when you need to test on a PR
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# pull_request:
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# branches:
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# - develop
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# branches:
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# - develop
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concurrency:
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pip
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condarc: |
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channels:
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- jaimergp/label/unsupported-cudatoolkit-shim
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- conda-forge
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- bioconda
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-20.04, macos-13]
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os: [ubuntu-22.04, macos-13]
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steps:
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- uses: actions/checkout@v4
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with:
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environment-name: mda
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create-args: >-
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python=3.10
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python=3.11
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pip
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condarc: |
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channels:
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- jaimergp/label/unsupported-cudatoolkit-shim
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- conda-forge
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- bioconda
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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.10", "3.11", "3.12", "3.13"]
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python-version: ["3.11", "3.12", "3.13", "3.14"]
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steps:
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- uses: actions/checkout@v4
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matrix:
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# Stick to macos-13 because some of our
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# optional deps don't support arm64 (i.e. macos-14)
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#
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# add "3.13" once conda-forge packages are available (see #4805)
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os: [ubuntu-latest, macos-13]
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python-version: ["3.10", "3.11", "3.12"]
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python-version: ["3.10", "3.11", "3.12", "3.13"]
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steps:
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- uses: actions/checkout@v4
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create-args: >-
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python=${{ matrix.python-version }}
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pip
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# using jaime's shim to avoid pulling down the cudatoolkit
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condarc: |
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channels:
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- jaimergp/label/unsupported-cudatoolkit-shim
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- conda-forge
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- bioconda
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with:
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python-version: ${{ matrix.python-version }}
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- name: install_deps
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shell: bash
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run: |
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pip install pytest-xdist pytest-timeout "numpy<2.3" "cython<3.1" wheel "setuptools>=40.9.0" packaging
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- name: install_mdanalysis
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shell: bash
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run: |
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# If wheels is False we build directly from source so we use the --no-binary flag
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# to avoid pulling down wheels for MDAnalysis (which are already precompiled)
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# Also need to add `--no-build-isolation` until next release, see Issue #5125
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if [ "${{ matrix.wheels }}" == "false" ]; then
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INSTALL_FLAGS="-vvv --no-binary"
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INSTALL_FLAGS="--no-build-isolation --no-binary"
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fi
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pip install ${INSTALL_FLAGS} mdanalysis mdanalysistests pytest-xdist pytest-timeout
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pip install ${INSTALL_FLAGS} mdanalysis mdanalysistests
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- name: run_tests
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shell: bash

‎.github/workflows/gh-ci.yaml‎

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@@ -28,29 +28,43 @@ jobs:
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fail-fast: false
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matrix:
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os: [ubuntu-latest, ]
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python-version: ["3.10", "3.11", "3.12"]
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python-version: ["3.11", "3.12", "3.13"]
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full-deps: [true, ]
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codecov: [true, ]
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cython: ["cython<3.1", ]
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include:
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- name: python_313
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# Including 3.14 and 3.11 without coverage
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# and cython >=3.1 to deal temporarily with
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# keeping on testing Cython whilst issue #5057
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# is not fixed
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- name: python_314_nocov
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os: ubuntu-latest
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python-version: "3.13"
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python-version: "3.14"
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full-deps: false
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codecov: true
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- name: macOS_14_arm64_py312
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codecov: false
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cython: "cython>=3.1"
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- name: python_311_nocov
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os: ubuntu-latest
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python-version: "3.11"
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full-deps: false
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codecov: false
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cython: "cython>=3.1"
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- name: macOS_14_arm64_py313
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os: macOS-14
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python-version: "3.12"
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python-version: "3.13"
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full-deps: false
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codecov: true
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cython: "cython<3.1"
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- name: numpy_min
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os: ubuntu-latest
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python-version: "3.10"
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python-version: "3.11"
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full-deps: false
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codecov: true
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numpy: numpy=1.23.2
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numpy: numpy=1.26.0
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cython: "cython<3.1"
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- name: asv_check
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os: ubuntu-latest
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python-version: "3.10"
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python-version: "3.11"
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full-deps: true
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codecov: false
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extra-pip-deps: asv
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# disable GSD because it occasionally introduce hanging in testing #4209
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gsd: ''
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# pin cython
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cython: 'cython<3.1'
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cython: ${{ matrix.cython }}
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# in most cases will just default to empty, i.e. pick up max version from other deps
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numpy: ${{ matrix.numpy }}
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extra-pip-deps: ${{ matrix.extra-pip-deps }}
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with:
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environment-name: mda
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create-args: >-
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python=3.10
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python=3.11
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pip
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# using jaime's shim to avoid pulling down the cudatoolkit
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condarc: |
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channels:
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- jaimergp/label/unsupported-cudatoolkit-shim
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- conda-forge
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- bioconda
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‎.github/workflows/linters.yaml‎

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- uses: actions/setup-python@v5
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with:
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python-version: "3.10"
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python-version: "3.11"
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- uses: psf/black@stable
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with:
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- uses: actions/setup-python@v5
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with:
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python-version: "3.10"
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python-version: "3.11"
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- name: install
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run: |
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with:
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environment-name: mda
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create-args: >-
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python=3.10
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python=3.11
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pip
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# using jaime's shim to avoid pulling down the cudatoolkit
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condarc: |
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channels:
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- jaimergp/label/unsupported-cudatoolkit-shim
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- conda-forge
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- bioconda
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with:
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micromamba: true
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full-deps: true
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numpy: numpy=1.23.2
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numpy: numpy=1.26.0
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rdkit: rdkit=2023.09.3
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- name: install

‎azure-pipelines.yml‎

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MPLBACKEND: agg
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strategy:
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matrix:
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Win-Python310-64bit-full:
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PYTHON_VERSION: '3.10'
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Win-Python311-64bit-full:
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PYTHON_VERSION: '3.11'
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PYTHON_ARCH: 'x64'
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BUILD_TYPE: 'normal'
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imageName: 'windows-2019'
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Win-Python312-64bit-full:
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PYTHON_VERSION: '3.12'
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Win-Python313-64bit-full:
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PYTHON_VERSION: '3.13'
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PYTHON_ARCH: 'x64'
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BUILD_TYPE: 'normal'
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imageName: 'windows-2019'
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Win-Python312-64bit-full-wheel:
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PYTHON_VERSION: '3.12'
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Win-Python313-64bit-full-wheel:
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PYTHON_VERSION: '3.13'
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PYTHON_ARCH: 'x64'
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BUILD_TYPE: 'wheel'
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NUMPY_MIN: '1.26.0'
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NUMPY_MIN: '2.1.0'
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imageName: 'windows-2019'
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Win-Python310-64bit-full-wheel:
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PYTHON_VERSION: '3.10'
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Win-Python311-64bit-full-wheel:
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PYTHON_VERSION: '3.11'
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PYTHON_ARCH: 'x64'
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BUILD_TYPE: 'wheel'
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NUMPY_MIN: '1.23.2'
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NUMPY_MIN: '1.26.0'
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imageName: 'windows-2019'
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Linux-Python312-64bit-full-wheel:
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PYTHON_VERSION: '3.12'
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Linux-Python313-64bit-full-wheel:
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PYTHON_VERSION: '3.13'
4848
PYTHON_ARCH: 'x64'
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BUILD_TYPE: 'wheel'
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NUMPY_MIN: '2.1.0'
5151
imageName: 'ubuntu-latest'
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Linux-Python310-64bit-full-wheel:
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PYTHON_VERSION: '3.10'
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Linux-Python311-64bit-full-wheel:
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PYTHON_VERSION: '3.11'
5454
PYTHON_ARCH: 'x64'
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BUILD_TYPE: 'wheel'
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NUMPY_MIN: '1.23.2'
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NUMPY_MIN: '1.26.0'
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imageName: 'ubuntu-latest'
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pool:
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vmImage: $(imageName)
@@ -103,16 +103,18 @@ jobs:
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- script: >-
104104
python -m pip install -vvv
105105
biopython
106-
"chemfiles>=0.10,<0.10.4"
106+
chemfiles>=0.10
107107
duecredit
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joblib
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GridDataFormats
110110
mmtf-python
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networkx
112112
parmed
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pytng>=0.2.3
114113
rdkit>=2024.03.4
115114
tidynamics>=1.0.0
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imdclient>=0.2.2
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pytng>=0.3.4
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116118
# remove from azure to avoid test hanging #4707
117119
# "gsd>3.0.0"
118120
displayName: 'Install additional dependencies for 64-bit tests'

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