Merge pull request #42 from molssi-seamm/dev

Updating to the standard SEAMM workflows for GitHub actions

.github/workflows/BranchCI.yaml

@@ -4,47 +4,11 @@ on:
   push:
     branches-ignore:
       - 'main'
+      - 'master'
 
 jobs:
-  light-ci:
-    name: Lint ubuntu-latest Py3.9
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v1
-    - name: Additional info about the build
-      shell: bash
-      run: |
-        uname -a
-        df -h
-        ulimit -a
-    # More info on options: https://github.com/conda-incubator/setup-miniconda
-    - uses: conda-incubator/setup-miniconda@v2
-      with:
-        python-version: 3.9
-        environment-file: devtools/conda-envs/test_env.yaml
-        activate-environment: test
-        auto-update-conda: false
-        auto-activate-base: false
-        show-channel-urls: true
-    - name: Install package
-      # conda setup requires this special shell
-      shell: bash -l {0}
-      run: |
-        python -m pip install . --no-deps
-        conda list
-    - name: Run linters
-      shell: bash -l {0}
-      run: |
-        black --extend-exclude '_version.py' --check --diff read_structure_step tests
-        flake8 read_structure_step tests
-    - name: Run tests
-      shell: bash -l {0}
-      run: |
-        pytest -v --cov=read_structure_step --cov-report=xml --color=yes tests/
-    - name: CodeCov
-      uses: codecov/codecov-action@v2
-      with:
-        file: ./coverage.xml
-        flags: unittests
-        name: codecov-ubuntu-latest-py3.9
-
+  branch-ci:
+    name: Branch CI
+    uses: molssi-seamm/devops/.github/workflows/BranchCI.yaml@main
+    with:
+      src : read_structure_step

.github/workflows/CI.yaml

@@ -7,81 +7,10 @@ on:
   pull_request:
     branches:
       - "main"
-  schedule:
-    # Run by default Sunday morning at 3:30:
-    #   Scheduled workflows run on the latest commit on the default or base branch.
-    #   (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
-    - cron: "30 3 * * 0"
 
 jobs:
-  lint:
-    name: Lint ubuntu-latest Py3.9
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v1
-    - name: Additional info about the build
-      shell: bash
-      run: |
-        uname -a
-        df -h
-        ulimit -a
-    # More info on options: https://github.com/conda-incubator/setup-miniconda
-    - uses: conda-incubator/setup-miniconda@v2
-      with:
-        python-version: 3.9
-        environment-file: devtools/conda-envs/test_env.yaml
-        activate-environment: test
-        auto-update-conda: false
-        auto-activate-base: false
-        show-channel-urls: true
-    - name: Install package
-      # conda setup requires this special shell
-      shell: bash -l {0}
-      run: |
-        python -m pip install . --no-deps
-        conda list
-    - name: Run linters
-      shell: bash -l {0}
-      run: |
-        black --extend-exclude '_version.py' --check --diff read_structure_step tests
-        flake8 read_structure_step tests
-
-  test:
-    name: Test ${{ matrix.os }} Py${{ matrix.python-version }}
-    runs-on: ${{ matrix.os }}
-    needs: lint
-    strategy:
-      matrix:
-        os: [macOS-latest, ubuntu-latest]
-        python-version: [3.8, 3.9]
-    steps:
-    - uses: actions/checkout@v1
-    - name: Additional info about the build
-      shell: bash
-      run: |
-        uname -a
-        df -h
-        ulimit -a
-    - uses: conda-incubator/setup-miniconda@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-        environment-file: devtools/conda-envs/test_env.yaml
-        activate-environment: test
-        auto-update-conda: false
-        auto-activate-base: false
-        show-channel-urls: true
-    - name: Install package
-      shell: bash -l {0}
-      run: |
-        python -m pip install . --no-deps
-        conda list
-    - name: Run tests
-      shell: bash -l {0}
-      run: |
-        pytest -v --cov=read_structure_step --cov-report=xml --color=yes tests/
-    - name: CodeCov
-      uses: codecov/codecov-action@v2
-      with:
-        file: ./coverage.xml
-        flags: unittests
-        name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
+  ci:
+    name: CI
+    uses: molssi-seamm/devops/.github/workflows/CI.yaml@main
+    with:
+      src : read_structure_step

.github/workflows/Release.yaml

@@ -7,111 +7,9 @@ on:
       - "main"
 
 jobs:
-  lint:
-    name: Lint ubuntu-latest Py3.9
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v1
-    - name: Additional info about the build
-      shell: bash
-      run: |
-        uname -a
-        df -h
-        ulimit -a
-    # More info on options: https://github.com/conda-incubator/setup-miniconda
-    - uses: conda-incubator/setup-miniconda@v2
-      with:
-        python-version: 3.9
-        environment-file: devtools/conda-envs/test_env.yaml
-        activate-environment: test
-        auto-update-conda: false
-        auto-activate-base: false
-        show-channel-urls: true
-    - name: Install package
-      # conda setup requires this special shell
-      shell: bash -l {0}
-      run: |
-        python -m pip install . --no-deps
-        conda list
-    - name: Run linters
-      shell: bash -l {0}
-      run: |
-        black --extend-exclude '_version.py' --check --diff read_structure_step tests
-        flake8 read_structure_step tests
-
-  test:
-    name: Test ${{ matrix.os }} Py${{ matrix.python-version }}
-    runs-on: ${{ matrix.os }}
-    needs: lint
-    strategy:
-      matrix:
-        os: [macOS-latest, ubuntu-latest]
-        python-version: [3.8, 3.9]
-    steps:
-    - uses: actions/checkout@v1
-    - name: Additional info about the build
-      shell: bash
-      run: |
-        uname -a
-        df -h
-        ulimit -a
-    - uses: conda-incubator/setup-miniconda@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-        environment-file: devtools/conda-envs/test_env.yaml
-        activate-environment: test
-        auto-update-conda: false
-        auto-activate-base: false
-        show-channel-urls: true
-    - name: Install package
-      shell: bash -l {0}
-      run: |
-        python -m pip install . --no-deps
-        conda list
-    - name: Run tests
-      shell: bash -l {0}
-      run: |
-        pytest -v --cov=read_structure_step --cov-report=xml --color=yes tests/
-    - name: CodeCov
-      uses: codecov/codecov-action@v2
-      with:
-        file: ./coverage.xml
-        flags: unittests
-        name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
-
-  deploy:
-    name: PyPi ubuntu-latest Py3.9
-    # Run only for tagged releases publishing development or release candidates
-    # only to test.pypi, otherwise to both it and the main pypi.
-    if: github.event_name == 'release' && startsWith(github.ref, 'refs/tags')
-    runs-on: ubuntu-latest
-    needs: [lint, test]
-    steps:
-    - uses: actions/checkout@v1
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v1
-      with:
-        python-version: 3.9
-    - name: Install package
-      shell: bash -l {0}
-      run: |
-        python -m pip install . --no-deps
-        conda list
-    - name: Install pypa/build
-      run: |
-        python -m pip install build --user
-    - name: Build a binary wheel and a source tarball
-      run: |
-        python -m build --sdist --wheel --outdir dist/
-        ls -l dist/
-    - name: Publish distribution 📦 to Test PyPI
-      uses: pypa/gh-action-pypi-publish@master
-      with:
-        password: ${{ secrets.test_pypi_password }}
-        repository_url: https://test.pypi.org/legacy/
-        skip_existing: true
-    - name: Publish distribution 📦 to PyPI
-      if: contains(github.ref, 'dev') == false && contains(github.ref, 'rc') == false
-      uses: pypa/gh-action-pypi-publish@master
-      with:
-        password: ${{ secrets.pypi_password }}
+  release:
+    name: Release
+    uses: molssi-seamm/devops/.github/workflows/Release.yaml@main
+    with:
+      src : read_structure_step
+    secrets: inherit

docs/_static/README.md

@@ -0,0 +1,16 @@
+# Static Doc Directory
+
+Add any paths that contain custom static files (such as style sheets) here,
+relative to the `conf.py` file's directory. 
+They are copied after the builtin static files,
+so a file named "default.css" will overwrite the builtin "default.css".
+
+The path to this folder is set in the Sphinx `conf.py` file in the line: 
+```python
+templates_path = ['_static']
+```
+
+## Examples of file to add to this directory
+* Custom Cascading Style Sheets
+* Custom JavaScript code
+* Static logo images

docs/_templates/README.md

@@ -0,0 +1,14 @@
+# Templates Doc Directory
+
+Add any paths that contain templates here, relative to  
+the `conf.py` file's directory.
+They are copied after the builtin template files,
+so a file named "page.html" will overwrite the builtin "page.html".
+
+The path to this folder is set in the Sphinx `conf.py` file in the line: 
+```python
+html_static_path = ['_templates']
+```
+
+## Examples of file to add to this directory
+* HTML extensions of stock pages like `page.html` or `layout.html`

docs/_templates/molssi_footer.html

@@ -0,0 +1,44 @@
+{% if not theme_logo.get("link") %}
+  {% set href = pathto(root_doc) %}
+{% elif hasdoc(theme_logo.get("link")) %}
+  {% set href = pathto(theme_logo.get("link")) %} {# internal page #}
+{% else %}
+  {% set href = theme_logo.get("link") %} {# external url #}
+{% endif %}
+
+{# get all the brand information from html_theme_option #}
+  {% set is_logo = logo or theme_logo.get("image_light") or theme_logo.get("image_dark") %}
+  {% set image_light = theme_logo.get("molssi_light") or logo %}
+  {% set image_dark = theme_logo.get("molssi_dark") or logo %}
+  {% set image_light = image_light if image_light.startswith("http") else pathto('_static/' + image_light, 1) %}
+  {% set image_dark = image_dark if image_dark.startswith("http") else pathto('_static/' + image_dark, 1) %}
+  {% set alt = theme_logo.get("alt_text", "Logo image") %}
+  {% set nsf_logo = pathto('_static/' + 'nsf.png', 1)  %}
+
+
+<div class="row h-10">
+    <div class="col-2">
+        <a href="https://molssi.org/" target="_blank" title="Go to MolSSI in a new tab">
+            <img src="{{ image_light }}" class="logo__image only-light footer_logo" alt="{{ alt }}">
+            <img src="{{ image_dark }}" class="logo__image only-dark footer_logo" alt="{{ alt }}">
+        </a>
+    </div>
+    <div class="col-8">
+        <p> &copy; Copyright 2019-2023 <a href="https://molssi.org/">The Molecular Sciences Software Institute</a></p>
+        <p>Funded by the National Science Foundation 
+          <a href="https://nsf.gov/awardsearch/showAward?AWD_ID=1547580">OAC-1547580</a> and 
+          <a href="https://www.nsf.gov/awardsearch/showAward?AWD_ID=2136142">CHE-2136142.</a></p>
+
+        {% if show_sphinx %}
+        <p class="sphinx-version">
+        {% trans sphinx_version=sphinx_version|e %}Created using <a href="http://sphinx-doc.org/">Sphinx</a> {{ sphinx_version }}.{% endtrans %}<br>
+        </p>
+        {% endif %}
+
+    </div>
+    <div class="col-2">
+        <a href="https://nsf.gov/" target="_blank" title="Go to the NSF in a new tab">
+            <img src="{{ nsf_logo }}" class="footer_logo" alt="The NSF">
+          </a>
+    </div>
+</div>