Add doctest step to docs build (#3997)

* move linters to separate CI file
* don't run darker on merge
* add doctest to docs building step
* CI actions invoke use-mamba not uses-mamba

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

@@ -93,7 +93,7 @@ jobs:
         auto-update-conda: true
         channel-priority: flexible
         channels: conda-forge, bioconda
-        uses-mamba: true
+        use-mamba: true
         miniforge-variant: Mambaforge
         add-pip-as-python-dependency: true
         architecture: x64

.github/workflows/gh-ci.yaml

@@ -89,7 +89,7 @@ jobs:
         channel-priority: flexible
         channels: conda-forge, bioconda
         add-pip-as-python-dependency: true
-        uses-mamba: true
+        use-mamba: true
         miniforge-variant: Mambaforge
         architecture: x64
 
@@ -154,7 +154,7 @@ jobs:
         channels: conda-forge, bioconda
         add-pip-as-python-dependency: true
         architecture: x64
-        uses-mamba: true
+        use-mamba: true
         miniforge-variant: Mambaforge
 
     - name: install_deps
@@ -171,6 +171,12 @@ jobs:
         build-tests: false
         build-docs: true
 
+    - name: doctests
+      if: github.event_name == 'pull_request'
+      continue-on-error: true
+      run: |
+        cd package && sphinx-build -b doctest --keep-going ./doc/sphinx/source ./doc/html
+
     - name: deploy_docs
       if: github.event_name != 'pull_request'
       env:
@@ -226,64 +232,6 @@ jobs:
         git push -q upstream HEAD:gh-pages
 
 
-  pylint_check:
-    if: "github.repository == 'MDAnalysis/mdanalysis'"
-    runs-on: ubuntu-latest
-
-    steps:
-    - uses: actions/checkout@v3
-
-    - uses: actions/setup-python@v4
-      with:
-        python-version: 3.8
-
-    - name: install
-      run: |
-        python -m pip install pylint
-
-    - name: pylint
-      env:
-        PYLINTRC: package/.pylintrc
-      run: |
-        pylint package/MDAnalysis && pylint testsuite/MDAnalysisTests
-
-
-  darker_lint:
-    if: "github.repository == 'MDAnalysis/mdanalysis'"
-    runs-on: ubuntu-latest
-    defaults:
-      run:
-        shell: bash
-
-    steps:
-    - uses: actions/checkout@v3
-      with:
-        fetch-depth: 0
-
-    - uses: actions/setup-python@v4
-      with:
-        python-version: 3.8
-
-    - name: darker main code
-      uses: akaihola/[email protected]
-      with:
-        version: "@master"
-        options: "--check --diff --color"
-        src: "./package/MDAnalysis"
-        revision: "HEAD^"
-        lint: "flake8"
-
-    - name: darker test code
-      uses: akaihola/[email protected]
-      if: success() || failure()
-      with:
-        version: "@master"
-        options: "--check --diff --color"
-        src: "./testsuite/MDAnalysisTests"
-        revision: "HEAD^"
-        lint: "flake8"
-
-
   pypi_check:
     if: "github.repository == 'MDAnalysis/mdanalysis'"
     runs-on: ubuntu-latest

.github/workflows/linters.yaml

@@ -0,0 +1,113 @@
+name: "linters"
+on:
+  push:
+    branches:
+      - develop
+  pull_request:
+    branches:
+      - develop
+
+concurrency:
+  # Probably overly cautious group naming.
+  # Commits to develop/master will cancel each other, but PRs will only cancel
+  # commits within the same PR
+  group: "${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}"
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+  darker_lint:
+    if: |
+      github.repository == 'MDAnalysis/mdanalysis' &&
+      github.event_name == 'pull_request'
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash
+
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
+
+    - uses: actions/setup-python@v4
+      with:
+        python-version: 3.8
+
+    - name: darker main code
+      uses: akaihola/[email protected]
+      with:
+        version: "@master"
+        options: "--check --diff --color"
+        src: "./package/MDAnalysis"
+        revision: "HEAD^"
+        lint: "flake8"
+
+    - name: darker test code
+      uses: akaihola/[email protected]
+      if: success() || failure()
+      with:
+        version: "@master"
+        options: "--check --diff --color"
+        src: "./testsuite/MDAnalysisTests"
+        revision: "HEAD^"
+        lint: "flake8"
+
+
+  pylint_check:
+    if: "github.repository == 'MDAnalysis/mdanalysis'"
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - uses: actions/setup-python@v4
+      with:
+        python-version: 3.8
+
+    - name: install
+      run: |
+        python -m pip install pylint
+
+    - name: pylint
+      env:
+        PYLINTRC: package/.pylintrc
+      run: |
+        pylint package/MDAnalysis && pylint testsuite/MDAnalysisTests
+
+
+  mypy :
+    if: "github.repository == 'MDAnalysis/mdanalysis'"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: setup_miniconda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          python-version: 3.8
+          auto-update-conda: true
+          channel-priority: flexible
+          channels: conda-forge, bioconda
+          add-pip-as-python-dependency: true
+          use-mamba: true
+          miniforge-variant: Mambaforge
+          architecture: x64
+
+      - name: install_deps
+        uses: ./.github/actions/setup-deps
+        with:
+          mamba: true
+          full-deps: true
+          numpy: numpy=1.20.0
+
+      - name: install
+        run: |
+          python -m pip install mypy
+
+      - name: "Run mypy"
+        run: |
+          mypy package/MDAnalysis/

README.rst

@@ -2,7 +2,7 @@
   MDAnalysis Repository README
 ================================
 
-|numfocus| |build| |cron| |travis| |cov|
+|numfocus| |build| |cron| |travis| |linters| |cov|
 
 |docs| |devdocs| |usergroup| |developergroup| |anaconda| |mybinder| |asv|
 
@@ -176,6 +176,10 @@ For citations of included algorithms and sub-modules please see the references_.
    :alt: Travis CI Build Status
    :target: https://travis-ci.com/MDAnalysis/mdanalysis
 
+.. |linters| image:: https://github.com/MDAnalysis/mdanalysis/actions/workflows/linters.yaml/badge.svg
+   :alt: Github Actions Linters Status
+   :target: https://github.com/MDAnalysis/mdanalysis/actions/workflows/linters.yaml
+
 .. |cov|   image:: https://codecov.io/gh/MDAnalysis/mdanalysis/branch/develop/graph/badge.svg
    :alt: Coverage Status
    :target: https://codecov.io/gh/MDAnalysis/mdanalysis