Merge pull request #5 from molssi-seamm/dev

Updated to new structure; handle symmetry in systems.
molssi-seamm · Nov 5, 2023 · b842109 · b842109
2 parents 17fa7ca + b8cc522
commit b842109
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diff --git a/.github/workflows/BranchCI.yaml b/.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: |
-        flake8 supercell_step tests
-        yapf --diff --recursive supercell_step tests
-    - name: Run tests
-      shell: bash -l {0}
-      run: |
-        pytest -v --cov=supercell_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 : supercell_step
diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml
@@ -8,84 +8,14 @@ on:
     branches:
       - "main"
   schedule:
-    # Run by default Sunday morning at 3:30:
+    # Run on master 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:
-    - name: Echo details
-      env:
-        REF: ${{ github.ref }}
-      run: echo $REF
-    - 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: |
-        flake8 supercell_step tests
-        yapf --diff --recursive supercell_step tests
-
-  test:
-    name: Test ${{ matrix.os }} Py${{ matrix.python-version }}
-    runs-on: ${{ matrix.os }}
-    needs: lint
-    strategy:
-      matrix:
-        os: [macOS-latest, ubuntu-latest, windows-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: ${{ matrix.python-version }}
-        environment-file: devtools/conda-envs/test_env.yaml
-        activate-environment: test
-        auto-update-conda: false
-        auto-activate-base: false
-        show-channel-urls: true
-    - name: Install package
-      shell: bash -l {0}
-      run: |
-        python -m pip install . --no-deps
-        conda list
-    - name: Run tests
-      shell: bash -l {0}
-      run: |
-        pytest -v --cov=supercell_step --cov-report=xml --color=yes tests/
-    - name: CodeCov
-      uses: codecov/codecov-action@v2
-      with:
-        file: ./coverage.xml
-        flags: unittests
-        name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
+  ci:
+    name: CI
+    uses: molssi-seamm/devops/.github/workflows/CI.yaml@main
+    with:
+      src : supercell_step
diff --git a/.github/workflows/CodeQL.yaml b/.github/workflows/CodeQL.yaml
@@ -0,0 +1,13 @@
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ "main" ]
+
+jobs:
+  codeql:
+    name: CodeQL
+    uses: molssi-seamm/devops/.github/workflows/CodeQL.yaml@main
diff --git a/.github/workflows/Docs.yaml b/.github/workflows/Docs.yaml
diff --git a/.github/workflows/Release.yaml b/.github/workflows/Release.yaml
@@ -7,116 +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: |
-        flake8 supercell_step tests
-        yapf --diff --recursive supercell_step tests
-
-  test:
-    name: Test ${{ matrix.os }} Py${{ matrix.python-version }}
-    runs-on: ${{ matrix.os }}
-    needs: lint
-    strategy:
-      matrix:
-        os: [macOS-latest, ubuntu-latest, windows-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: ${{ matrix.python-version }}
-        environment-file: devtools/conda-envs/test_env.yaml
-        activate-environment: test
-        auto-update-conda: false
-        auto-activate-base: false
-        show-channel-urls: true
-    - name: Install package
-      shell: bash -l {0}
-      run: |
-        python -m pip install . --no-deps
-        conda list
-    - name: Run tests
-      shell: bash -l {0}
-      run: |
-        pytest -v --cov=supercell_step --cov-report=xml --color=yes tests/
-    - name: CodeCov
-      uses: codecov/codecov-action@v2
-      with:
-        file: ./coverage.xml
-        flags: unittests
-        name: codecov-${{ 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:
-    - name: Echo details
-      env:
-        REF: ${{ github.ref }}
-        CONTAINS: ${{ contains(github.ref, 'dev') }}
-      run: echo $REF $CONTAINS
-    - 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 : supercell_step
+    secrets: inherit
diff --git a/HISTORY.rst b/HISTORY.rst
@@ -1,36 +1,27 @@
 =======
 History
 =======
-
-2021.2.12 (12 February 2021)
-----------------------------
-
-* Updated the README file to give a better description.
-* Updated the short description in setup.py to work with the new installer.
-* Added keywords for better searchability.
-
-2021.2.4 (4 February 2021)
---------------------------
-
-* Updated for compatibility with the new system classes in MolSystem
-  2021.2.2 release.
-
-2020.12.5 (5 December 2020)
----------------------------
-
-* Added support for non-orthorhombic cells.
-* Updated to be compatible with the new system classes in MolSystem.
-* Internal: switching CI from TravisCI to GitHub Actions, and in the
-  process moving documentation from ReadTheDocs to GitHub Pages where
-  it is consolidated with the main SEAMM documentation.
-
-0.9.1 (20 June 2020)
---------------------
-
-* Bugfix: Was not properly copying charges to the new system.
-
-0.9 (18 June 2020)
--------------------
-
-* First release on PyPI.
-* Working but only for orthorhombic cell.s
+2023.11.5 -- Updated to handle symmetry in systems
+
+2021.2.12 --
+    * Updated the README file to give a better description.
+    * Updated the short description in setup.py to work with the new installer.
+    * Added keywords for better searchability.
+
+2021.2.4 --
+    * Updated for compatibility with the new system classes in MolSystem
+      2021.2.2 release.
+
+2020.12.5 -- 
+    * Added support for non-orthorhombic cells.
+    * Updated to be compatible with the new system classes in MolSystem.
+    * Internal: switching CI from TravisCI to GitHub Actions, and in the
+      process moving documentation from ReadTheDocs to GitHub Pages where
+      it is consolidated with the main SEAMM documentation.
+
+0.9.1 -- 20 June 2020
+    * Bugfix: Was not properly copying charges to the new system.
+
+0.9 -- 18 June 2020
+    * First release on PyPI.
+    * Working but only for orthorhombic cells