Merge branch 'MDAnalysis:develop' into develop

MDAnalysis · Jul 29, 2023 · e358dcb · e358dcb
2 parents 921616b + 439435e
commit e358dcb
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diff --git a/.github/actions/setup-deps/action.yaml b/.github/actions/setup-deps/action.yaml
@@ -28,7 +28,7 @@ inputs:
   griddataformats:
     default: 'griddataformats'
   gsd:
-    default: 'gsd'
+    default: 'gsd>3.0.0'
   hypothesis:
     default: 'hypothesis'
   matplotlib:
@@ -107,7 +107,6 @@ runs:
           ${{ inputs.cython }}
           ${{ inputs.fasteners }}
           ${{ inputs.griddataformats }}
-          ${{ inputs.gsd }}
           ${{ inputs.hypothesis }}
           ${{ inputs.matplotlib }}
           ${{ inputs.mmtf-python }}
@@ -123,6 +122,7 @@ runs:
           ${{ inputs.chemfiles-python }}
           ${{ inputs.clustalw }}
           ${{ inputs.distopia }}
+          ${{ inputs.gsd }}
           ${{ inputs.h5py }}
           ${{ inputs.hole2 }}
           ${{ inputs.joblib }}

diff --git a/.github/workflows/darkerbot.yaml b/.github/workflows/darkerbot.yaml
@@ -19,6 +19,7 @@ jobs:
   darker_bot:
     if: "github.repository == 'MDAnalysis/mdanalysis'"
     runs-on: ubuntu-latest
+    timeout-minutes: 5
     steps:
       - uses: actions/checkout@v3
 

diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml
@@ -32,6 +32,7 @@ jobs:
     if: "github.repository == 'MDAnalysis/mdanalysis'"
     name: Build wheels
     runs-on: ${{ matrix.buildplat[0] }}
+    timeout-minutes: 15
     strategy:
       fail-fast: false
       matrix:
@@ -69,6 +70,7 @@ jobs:
     if: "github.repository == 'MDAnalysis/mdanalysis'"
     name: build package source distribution
     runs-on: ubuntu-latest
+    timeout-minutes: 10
     defaults:
       run:
         working-directory: ./package
@@ -93,6 +95,7 @@ jobs:
     if: "github.repository == 'MDAnalysis/mdanalysis'"
     name: build test source distribution
     runs-on: ubuntu-latest
+    timeout-minutes: 10
     defaults:
       run:
         working-directory: ./testsuite
@@ -187,6 +190,7 @@ jobs:
       (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/package'))
     name: testpypi check
     runs-on: ${{ matrix.os }}
+    timeout-minutes: 60
     needs: upload_testpypi
     strategy:
       fail-fast: false

diff --git a/.github/workflows/gh-ci-cron.yaml b/.github/workflows/gh-ci-cron.yaml
@@ -23,6 +23,7 @@ jobs:
   numpy_and_scipy_dev:
     if: "github.repository == 'MDAnalysis/mdanalysis'"
     runs-on: ubuntu-latest
+    timeout-minutes: 60
 
     steps:
     - uses: actions/checkout@v3
@@ -51,7 +52,7 @@ jobs:
       # overwrite installs by picking up nightly wheels
     - name: nightly_wheels
       run: |
-        pip install --pre -U -i https://pypi.anaconda.org/scipy-wheels-nightly/simple scipy numpy h5py matplotlib
+        pip install --pre -U -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple scipy numpy networkx matplotlib
 
     - name: list_deps
       run: |
@@ -74,6 +75,7 @@ jobs:
   native_march:
     if: "github.repository == 'MDAnalysis/mdanalysis'"
     runs-on: ubuntu-latest
+    timeout-minutes: 60
 
     steps:
     - uses: actions/checkout@v3
@@ -117,6 +119,7 @@ jobs:
   old_ubuntu_macos:
     if: "github.repository == 'MDAnalysis/mdanalysis'"
     runs-on: ${{ matrix.os }}
+    timeout-minutes: 60
     strategy:
       fail-fast: false
       matrix:
@@ -158,9 +161,10 @@ jobs:
 
 
   # Issue 1727
-  pip-only:
+  pip-only-develop:
     if: "github.repository == 'MDAnalysis/mdanalysis'"
     runs-on: ubuntu-latest
+    timeout-minutes: 60
     strategy:
         fail-fast: false
         matrix:
@@ -192,3 +196,71 @@ jobs:
     - name: run_tests
       run: |
         pytest -n $numprocs testsuite/MDAnalysisTests --disable-pytest-warnings --durations=50
+        
+  # Issue 4208
+  conda-latest-release:
+    # A set of runner to check that the latest conda release works as expected
+    if: "github.repository == 'MDAnalysis/mdanalysis'"
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 60
+    strategy:
+        fail-fast: false
+        matrix:
+          os: [ubuntu-latest, macos-latest]
+          python-version: ["3.9", "3.10", "3.11"]
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: setup_micromamba
+      uses: mamba-org/setup-micromamba@v1
+      with:
+        environment-name: mda
+        create-args: >-
+          python=${{ matrix.python-version }}
+          pip
+        # using jaime's shim to avoid pulling down the cudatoolkit
+        condarc: |
+          channels:
+            - jaimergp/label/unsupported-cudatoolkit-shim
+            - conda-forge
+            - bioconda
+
+    - name: install_deps
+      uses: ./.github/actions/setup-deps
+      with:
+        micromamba: true
+        full-deps: true
+        gsd: "gsd<3.0"
+
+    - name: install_mdanalysis
+      run: |
+          micromamba install mdanalysis mdanalysistests
+
+    - name: run_tests
+      run: |
+          pytest -n auto --pyargs MDAnalysisTests
+          
+  pypi-latest-release:
+    # A set of runner to check that the latest conda release works as expected
+    if: "github.repository == 'MDAnalysis/mdanalysis'"
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 60
+    strategy:
+        fail-fast: false
+        matrix:
+          os: [ubuntu-latest, macos-latest, windows-latest]
+          python-version: ["3.9", "3.10", "3.11"]
+    steps:
+    - uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: install_mdanalysis
+      shell: bash
+      run: |
+          pip install mdanalysis mdanalysistests pytest-xdist "gsd<3.0"
+
+    - name: run_tests
+      shell: bash
+      run: |
+          pytest -n auto --pyargs MDAnalysisTests
diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml
@@ -22,6 +22,7 @@ jobs:
   main_tests:
     if: "github.repository == 'MDAnalysis/mdanalysis'"
     runs-on: ${{ matrix.os }}
+    timeout-minutes: 60
     strategy:
         fail-fast: false
         matrix:
@@ -40,7 +41,7 @@ jobs:
               python-version: 3.9
               full-deps: false
               codecov: true
-              numpy: numpy=1.21.0
+              numpy: numpy=1.22.3
             - name: asv_check
               os: ubuntu-latest
               python-version: 3.9
@@ -113,6 +114,7 @@ jobs:
   build_docs:
     if: "github.repository == 'MDAnalysis/mdanalysis'"
     runs-on: ubuntu-latest
+    timeout-minutes: 15
     env:
       CYTHON_TRACE_NOGIL: 1
       MPLBACKEND: agg
@@ -135,7 +137,7 @@ jobs:
       with:
         micromamba: true
         full-deps: true
-        extra-pip-deps: "sphinx sphinx-sitemap sphinx_rtd_theme msmb_theme==1.2.0 sphinxcontrib-bibtex pybtex pybtex-docutils"
+        extra-pip-deps: "docutils<0.18 sphinx<7.0 sphinx-sitemap sphinx_rtd_theme msmb_theme==1.2.0 sphinxcontrib-bibtex pybtex pybtex-docutils"
 
     - name: build_srcs
       uses: ./.github/actions/build-src
@@ -207,6 +209,7 @@ jobs:
   sdist_check_and_build:
     if: "github.repository == 'MDAnalysis/mdanalysis'"
     runs-on: ubuntu-latest
+    timeout-minutes: 30
 
     steps:
     - uses: actions/checkout@v3

diff --git a/.github/workflows/greetings.yaml b/.github/workflows/greetings.yaml
@@ -10,6 +10,7 @@ jobs:
   greeting:
     if: "github.repository == 'MDAnalysis/mdanalysis'"
     runs-on: ubuntu-latest
+    timeout-minutes: 10
     permissions:
       pull-requests: write
     steps:

diff --git a/.github/workflows/labels.yaml b/.github/workflows/labels.yaml
@@ -8,6 +8,7 @@ on:
 jobs:
   triage-on-file-paths:
     runs-on: ubuntu-latest
+    timeout-minutes: 10
     steps:
     - uses: actions/labeler@v3
       with:

diff --git a/.github/workflows/linters.yaml b/.github/workflows/linters.yaml
@@ -19,6 +19,7 @@ jobs:
   darker_lint:
     if: "github.repository == 'MDAnalysis/mdanalysis'"
     runs-on: ubuntu-latest
+    timeout-minutes: 10
     permissions:
       pull-requests: write
     defaults:
@@ -99,6 +100,7 @@ jobs:
   pylint_check:
     if: "github.repository == 'MDAnalysis/mdanalysis'"
     runs-on: ubuntu-latest
+    timeout-minutes: 10
     steps:
     - uses: actions/checkout@v3
 
@@ -120,6 +122,7 @@ jobs:
   mypy :
     if: "github.repository == 'MDAnalysis/mdanalysis'"
     runs-on: ubuntu-latest
+    timeout-minutes: 10
     steps:
       - uses: actions/checkout@v3
 
@@ -138,7 +141,7 @@ jobs:
         with:
           micromamba: true
           full-deps: true
-          numpy: numpy=1.21.0
+          numpy: numpy=1.22.3
 
       - name: install
         run: |

diff --git a/.github/workflows/rtd.yaml b/.github/workflows/rtd.yaml
@@ -10,6 +10,7 @@ jobs:
   rtdpreview:
     if: "github.repository == 'MDAnalysis/mdanalysis'"
     runs-on: ubuntu-latest
+    timeout-minutes: 5
     permissions:
       pull-requests: write
     steps:

diff --git a/README.rst b/README.rst
@@ -25,7 +25,7 @@ This project is bound by a `Code of Conduct`_.
 
 |powered_by_MDA|
 
-If you use MDAnalysis_ in your project consider lettting your users and the world know about it by displaying the MDAnalysis_ badge! `Embedding code`_ is available for different markups.
+If you use MDAnalysis_ in your project consider letting your users and the world know about it by displaying the MDAnalysis_ badge! `Embedding code`_ is available for different markups.
 
 Example analysis script
 =======================

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -21,12 +21,6 @@ jobs:
     MPLBACKEND: agg
   strategy:
     matrix:
-        Win-Python39-32bit-full:
-          PYTHON_VERSION: '3.9'
-          PYTHON_ARCH: 'x86'
-          BUILD_TYPE: 'normal'
-          NUMPY_MIN: '1.21.0'
-          imageName: 'windows-2019'
         Win-Python39-64bit-full:
           PYTHON_VERSION: '3.9'
           PYTHON_ARCH: 'x64'
@@ -47,7 +41,7 @@ jobs:
           PYTHON_VERSION: '3.9'
           PYTHON_ARCH: 'x64'
           BUILD_TYPE: 'wheel'
-          NUMPY_MIN: '1.21.0'
+          NUMPY_MIN: '1.22.3'
           imageName: 'windows-2019'
         Linux-Python311-64bit-full-wheel:
           PYTHON_VERSION: '3.11'
@@ -59,7 +53,7 @@ jobs:
           PYTHON_VERSION: '3.9'
           PYTHON_ARCH: 'x64'
           BUILD_TYPE: 'wheel'
-          NUMPY_MIN: '1.21.0'
+          NUMPY_MIN: '1.22.3'
           imageName: 'ubuntu-latest'
   pool:
     vmImage: $(imageName)
@@ -82,9 +76,10 @@ jobs:
   - script: python -m pip install --upgrade pip setuptools wheel
     displayName: 'Install tools'
   - script: >-
-      python -m pip install --only-binary=scipy
+      python -m pip install --only-binary=scipy,h5py
       cython
       hypothesis
+      h5py>=2.10
       matplotlib
       numpy
       packaging
@@ -96,27 +91,20 @@ jobs:
       threadpoolctl
       fasteners
     displayName: 'Install dependencies'
-  # H5PY wheels are problematic on 32bit py3.9, so we don't install
-  # it in that specific case. Note: prefer binary because building
-  # h5py is difficult on azure.
-  - script: >-
-      pip install --prefer-binary h5py>=2.10
-    displayName: 'Install non 32bit dependencies'
-    condition: and(succeeded(), ne(variables['PYTHON_ARCH'], 'x86'))
   # for wheel install testing, we pin to an
   # older NumPy, the oldest version we support and that
   # supports the Python version in use
   # to check the ABI compatibility of our wheels
   - script: >-
       python -m pip install numpy==$(NUMPY_MIN)
-    displayName: 'pin to older NumPy (wheel test and 32bit)'
+    displayName: 'pin to older NumPy (wheel test)'
     condition: and(succeeded(), ne(variables['NUMPY_MIN'], ''))
   - script: >-
       python -m pip install
       biopython
       "chemfiles>=0.10,<0.10.4"
       duecredit
-      gsd
+      "gsd>3.0.0"
       joblib
       GridDataFormats
       mmtf-python

diff --git a/maintainer/conda/environment.yml b/maintainer/conda/environment.yml
@@ -6,6 +6,7 @@ dependencies:
   - chemfiles>=0.10
   - codecov
   - cython
+  - docutils <0.18
   - fasteners
   - griddataformats
   - gsd
@@ -16,14 +17,14 @@ dependencies:
   - mmtf-python
   - mock
   - networkx
-  - numpy>=1.21
+  - numpy>=1.22.3
   - pytest
   - python==3.9
   - pytng>=0.2.3
   - scikit-learn
   - scipy
   - pip
-  - sphinx
+  - sphinx <7.0
   - tidynamics>=1.0.0
   - tqdm>=4.43.0
   - sphinxcontrib-bibtex

diff --git a/package/AUTHORS b/package/AUTHORS
@@ -217,6 +217,8 @@ Chronological list of authors
   - Egor Marin
   - Shaivi Malik
   - Daniel J. Evans
+  - Mohit Kumar
+  - Shubham Kumar
 
 External code
 -------------