Merge pull request #25 from molssi-seamm/dev

Updating CI to newer version

.github/workflows/BranchCI.yaml

@@ -4,46 +4,11 @@ on:
   push:
     branches-ignore:
       - 'main'
+  workflow_dispatch:
 
 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 --check --diff from_smiles_step tests
-        flake8 from_smiles_step tests
-    - name: Run tests
-      shell: bash -l {0}
-      run: |
-        pytest -v --cov=from_smiles_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 : from_smiles_step

.github/workflows/CI.yaml

@@ -7,81 +7,11 @@ 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"
+  workflow_dispatch:
 
 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 --check --diff from_smiles_step tests
-        flake8 from_smiles_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: ${{ matrix.python-version }}
-        environment-file: devtools/conda-envs/test_env.yaml
-        activate-environment: test
-        auto-update-conda: false
-        auto-activate-base: false
-        show-channel-urls: true
-    - name: Install package
-      shell: bash -l {0}
-      run: |
-        python -m pip install . --no-deps
-        conda list
-    - name: Run tests
-      shell: bash -l {0}
-      run: |
-        pytest -v --cov=from_smiles_step --cov-report=xml --color=yes tests/
-    - name: CodeCov
-      uses: codecov/codecov-action@v2
-      with:
-        file: ./coverage.xml
-        flags: unittests
-        name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
+  ci:
+    name: CI
+    uses: molssi-seamm/devops/.github/workflows/CI.yaml@main
+    with:
+      src : from_smiles_step

.github/workflows/CodeQL.yaml

@@ -0,0 +1,14 @@
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ "main" ]
+  workflow_dispatch:
+
+jobs:
+  codeql:
+    name: CodeQL
+    uses: molssi-seamm/devops/.github/workflows/CodeQL.yaml@main

.github/workflows/Release.yaml

@@ -5,113 +5,13 @@ on:
     types: [published]
     branches:
       - "main"
+  workflow_dispatch:
 
 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 --check --diff from_smiles_step tests
-        flake8 from_smiles_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: ${{ matrix.python-version }}
-        environment-file: devtools/conda-envs/test_env.yaml
-        activate-environment: test
-        auto-update-conda: false
-        auto-activate-base: false
-        show-channel-urls: true
-    - name: Install package
-      shell: bash -l {0}
-      run: |
-        python -m pip install . --no-deps
-        conda list
-    - name: Run tests
-      shell: bash -l {0}
-      run: |
-        pytest -v --cov=from_smiles_step --cov-report=xml --color=yes tests/
-    - name: CodeCov
-      uses: codecov/codecov-action@v2
-      with:
-        file: ./coverage.xml
-        flags: unittests
-        name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
+  release:
+    name: Release
+    uses: molssi-seamm/devops/.github/workflows/Release.yaml@main
+    with:
+      src : from_smiles_step
+    secrets: inherit
 
-  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 }}

versioneer.py

@@ -339,9 +339,9 @@ def get_config_from_root(root):
     # configparser.NoOptionError (if it lacks "VCS="). See the docstring at
     # the top of versioneer.py for instructions on writing your setup.cfg .
     setup_cfg = os.path.join(root, "setup.cfg")
-    parser = configparser.SafeConfigParser()
+    parser = configparser.ConfigParser()
     with open(setup_cfg, "r") as f:
-        parser.readfp(f)
+        parser.read_file(f)
     VCS = parser.get("versioneer", "VCS")  # mandatory
 
     def get(parser, name):