Merge branch 'develop' into simple-atomic-distance-analysis

.cirrus.star

@@ -0,0 +1,18 @@
+# See https://cirrus-ci.org/guide/programming-tasks/ for more information on
+# starlark CirrusCI files
+# Inspired by scipy's .cirrus.star script https://github.com/scipy/scipy/blob/main/.cirrus.star
+# In the spirit of ensuring this can also be freely used in derviative works by
+# the community, we release the contents of this file under the MIT license.
+
+
+load("cirrus", "env", "fs")
+
+
+def main(ctx):
+    # Default case: don't do anything if not in the core repo
+    # or if you're not targetting the develop branch
+    if ((env.get("CIRRUS_REPO_FULL_NAME") != "MDAnalysis/mdanalysis")
+        or (env.get("CIRRUS_BASE_BRANCH") != "develop")):
+        return []
+
+    return fs.read("maintainer/ci/cirrus-ci.yml")

.github/actions/build-src/action.yaml

@@ -1,10 +1,6 @@
 name: 'build-src'
 description: 'make source builds for CI'
 inputs:
-  build-hole:
-    description: 'build HOLE2'
-    required: true
-    default: true
   build-tests:
     description: 'build MDA tests'
     required: true
@@ -21,7 +17,6 @@ runs:
     - name: echo_inputs
       shell: bash -l {0}
       run: |
-        echo ${{ inputs.build-hole }}
         echo ${{ inputs.build-tests }}
         echo ${{ inputs.build-docs }}
 
@@ -36,19 +31,6 @@ runs:
         conda info
         conda list
 
-    - name: build_hole
-      if: ${{ inputs.build-hole == 'true' }}
-      shell: bash -l {0}
-      run: |
-        # We manually build hole2 to avoid OS incompatibilities
-        git clone https://github.com/MDAnalysis/hole2.git
-        cd hole2/src
-        source ../source.apache
-        (make FC=${FC}) && (make PREFIX=${HOME}/hole2 FC=${FC} install)
-        source ../source.unset
-        echo "HOLE_BINDIR=${HOME}/hole2/bin" >> $GITHUB_ENV
-        echo "${HOME}/hole2/bin" >> $GITHUB_PATH
-
     - name: build_mda_main
       shell: bash -l {0}
       run: |

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

@@ -13,6 +13,9 @@ inputs:
   mamba:
     description: 'use mamba instead of conda'
     default: false
+  micromamba:
+    description: 'use micromamba instead of conda'
+    default: false
   # conda-installed min dependencies
   biopython:
     default: 'biopython>=1.80'
@@ -57,6 +60,8 @@ inputs:
     default: 'distopia>=0.2.0'
   h5py:
     default: 'h5py>=2.10'
+  hole2:
+    default: 'hole2'
   joblib:
     default: 'joblib>=0.12'
   netcdf4:
@@ -119,6 +124,7 @@ runs:
           ${{ inputs.clustalw }}
           ${{ inputs.distopia }}
           ${{ inputs.h5py }}
+          ${{ inputs.hole2 }}
           ${{ inputs.joblib }}
           ${{ inputs.netcdf4 }}
           ${{ inputs.openmm }}
@@ -139,6 +145,8 @@ runs:
         # do the install
         if [ ${{ inputs.mamba }} = "true" ]; then
           mamba install ${CONDA_DEPS}
+        elif [ ${{ inputs.micromamba }} == "true" ]; then
+          micromamba install ${CONDA_DEPS}
         else
           conda install ${CONDA_DEPS}
         fi

.github/workflows/deploy.yaml

@@ -12,6 +12,9 @@ on:
   release:
     types:
       - published
+  schedule:
+    # 3 am Tuesdays and Fridays
+    - cron: "0 3 * * 2,5"
 
 
 concurrency:
@@ -36,7 +39,7 @@ jobs:
           - [ubuntu-20.04, manylinux_x86_64]
           - [macos-11, macosx_*]
           - [windows-2019, win_amd64]
-        python: ["cp38", "cp39", "cp310", "cp311"]
+        python: ["cp39", "cp310", "cp311"]
     defaults:
       run:
         working-directory: ./package
@@ -212,22 +215,21 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
-      - name: setup_miniconda
-        uses: conda-incubator/setup-miniconda@v2
+      - name: setup_micromamba
+        uses: mamba-org/provision-with-micromamba@main
         with:
-          python-version: ${{ matrix.python-version }}
-          auto-update-conda: true
-          channel-priority: flexible
-          channels: conda-forge, bioconda
-          add-pip-as-python-dependency: true
-          mamba-version: "*"
-          architecture: x64
+          environment-file: False
+          environment-name: mda
+          extra-specs: |
+            python==${{ matrix.python-version }}
+            pip
+          channels: jaimergp/label/unsupported-cudatoolkit-shim, conda-forge, bioconda
 
       - name: install_full_deps
         uses: ./.github/actions/setup-deps
         if: "matrix.type == 'FULL'"
         with:
-          mamba: true
+          micromamba: true
           full-deps: true
 
       - name: install_min_deps

.github/workflows/gh-ci-cron.yaml

@@ -32,21 +32,20 @@ jobs:
       with:
         os-type: "ubuntu"
 
-    - name: setup_miniconda
-      uses: conda-incubator/setup-miniconda@v2
+    - name: setup_micromamba
+      uses: mamba-org/provision-with-micromamba@main
       with:
-        python-version: "3.11"
-        miniforge-variant: Mambaforge
-        miniforge-version: latest
-        channel-priority: strict
-        channels: conda-forge, bioconda
-        add-pip-as-python-dependency: true
-        architecture: x64
+        environment-file: False
+        environment-name: mda
+        extra-specs: |
+          python=="3.11"
+          pip
+        channels: jaimergp/label/unsupported-cudatoolkit-shim, conda-forge, bioconda
 
     - name: install_deps
       uses: ./.github/actions/setup-deps
       with:
-        mamba: true
+        micromamba: true
         full-deps: true
 
       # overwrite installs by picking up nightly wheels
@@ -56,14 +55,13 @@ jobs:
 
     - name: list_deps
       run: |
-        mamba list
+        micromamba list
         pip list
 
       # Intentionally going with setup.py builds so we can build with latest
     - name: build_srcs
       uses: ./.github/actions/build-src
       with:
-        build-hole: true
         build-tests: true
         build-docs: false
 
@@ -85,30 +83,72 @@ jobs:
       with:
         os-type: "ubuntu"
 
-    - name: setup_miniconda
-      uses: conda-incubator/setup-miniconda@v2
+    - name: setup_micromamba
+      uses: mamba-org/provision-with-micromamba@main
       with:
-        python-version: 3.11
-        auto-update-conda: true
-        channel-priority: flexible
-        channels: conda-forge, bioconda
-        use-mamba: true
-        miniforge-variant: Mambaforge
-        add-pip-as-python-dependency: true
-        architecture: x64
+        environment-file: False
+        environment-name: mda
+        extra-specs: |
+          python=="3.11"
+          pip
+        channels: jaimergp/label/unsupported-cudatoolkit-shim, conda-forge, bioconda
 
     - name: install_deps
       uses: ./.github/actions/setup-deps
+      with:
+        micromamba: true
+        full-deps: true
 
     - name: set_extra_flags
       run: |
         sed -i "s/#extra_cflags =/extra_cflags = -march=native -mtune=native/g" package/setup.cfg
         cat package/setup.cfg
+    - name: build_srcs
+      uses: ./.github/actions/build-src
+      with:
+        build-tests: true
+        build-docs: false
+
+    - name: run_tests
+      run: |
+        pytest -n $numprocs testsuite/MDAnalysisTests --disable-pytest-warnings --durations=50
+
+
+  old_ubuntu_macos:
+    if: "github.repository == 'MDAnalysis/mdanalysis'"
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-20.04, macos-11]
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: setup_os
+      uses: ./.github/actions/setup-os
+      with:
+        os-type: ${{ matrix.os }}
+
+    - name: setup_micromamba
+      uses: mamba-org/provision-with-micromamba@main
+      with:
+        environment-file: False
+        environment-name: mda
+        extra-specs: |
+          python=="3.9"
+          pip
+        channels: jaimergp/label/unsupported-cudatoolkit-shim, conda-forge, bioconda
+
+    - name: install_deps
+      uses: ./.github/actions/setup-deps
+      with:
+        micromamba: true
+        full-deps: true
 
     - name: build_srcs
       uses: ./.github/actions/build-src
       with:
-        build-hole: true
         build-tests: true
         build-docs: false