Merge pull request #5 from MolSSI/improved_text

Improved text output in support of SEAMM

.github/workflows/CI.yaml

@@ -0,0 +1,89 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - "master"
+      - "main"
+  pull_request:
+    branches:
+      - "master"
+      - "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 Py3.8
+    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: 3.8
+        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 reference_handler
+        yapf --diff --recursive reference_handler
+      
+  test:
+    name: Test ${{ matrix.os }} Py${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    needs: lint
+    strategy:
+      matrix:
+        os: [macOS-latest, ubuntu-latest]
+        python-version: [3.7, 3.8]
+    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: ${{ matrix.python-version }}
+        environment-file: devtools/conda-envs/test_env.yaml
+        activate-environment: test
+        auto-update-conda: false
+        auto-activate-base: false
+        show-channel-urls: true
+    - name: Install package
+      shell: bash -l {0}
+      run: |
+        python -m pip install . --no-deps
+        conda list
+    - name: Run tests
+      shell: bash -l {0}
+      run: |
+        pytest -v --cov=reference_handler --cov-report=xml --color=yes reference_handler/tests/
+    - name: CodeCov
+      uses: codecov/codecov-action@v1
+      with:
+        file: ./coverage.xml
+        flags: unittests
+        name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}

.github/workflows/Release.yaml

@@ -0,0 +1,162 @@
+name: Release
+
+on:
+  # GitHub has started calling new repo's first branch "main" https://github.com/github/renaming
+  # Existing codes likely still have "master" as the primary branch
+  # Both are tracked here to keep legacy and new codes working
+  release:
+    types: [published]
+    branches:
+      - "master"
+      - "main"
+
+jobs:
+  lint:
+    name: Lint ${{ matrix.os }} Py${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: [3.8]
+
+    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: ${{ matrix.python-version }}
+        environment-file: devtools/conda-envs/test_env.yaml
+
+        # channels: conda-forge,defaults
+
+        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
+
+      # conda setup requires this special shell
+      shell: bash -l {0}
+
+      run: |
+        flake8 reference_handler reference_handler/tests
+        yapf --diff --recursive reference_handler
+      
+  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: [3.7, 3.8]
+
+    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: ${{ matrix.python-version }}
+        environment-file: devtools/conda-envs/test_env.yaml
+        activate-environment: test
+        auto-update-conda: false
+        auto-activate-base: false
+        show-channel-urls: true
+
+    - name: Install package
+
+      # conda setup requires this special shell
+      shell: bash -l {0}
+      run: |
+        python -m pip install . --no-deps
+        conda list
+
+
+    - name: Run tests
+
+      # conda setup requires this special shell
+      shell: bash -l {0}
+
+      run: |
+        pytest -v --cov=reference_handler --cov-report=xml --color=yes reference_handler/tests/
+
+    - name: CodeCov
+      uses: codecov/codecov-action@v1
+      with:
+        file: ./coverage.xml
+        flags: unittests
+        name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
+
+  deploy:
+    name: PyPi ${{ matrix.os }} Py${{ matrix.python-version }}
+    # Run only for tagged releases.
+    if: github.event_name == 'release' && startsWith(github.ref, 'refs/tags')
+    runs-on: ${{ matrix.os }}
+    needs: [lint, test]
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: [3.8]
+
+    steps:
+    - uses: actions/checkout@v1
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install package
+
+      # conda setup requires this special shell
+      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
+      uses: pypa/gh-action-pypi-publish@master
+      with:
+        password: ${{ secrets.pypi_password }}

MANIFEST.in

@@ -1,6 +1,7 @@
 include LICENSE
 include MANIFEST.in
 include versioneer.py
+include requirements*.txt
 
 graft reference_handler
 global-exclude *.py[cod] __pycache__ *.so

devtools/conda-envs/test_env.yaml

@@ -15,6 +15,8 @@ dependencies:
 
     # Pip-only installs
   - pip:
+    - bibtexparser
+
       # Testing
     - yapf
 

reference_handler/__init__.py

@@ -10,6 +10,7 @@
 
 # Handle versioneer
 from ._version import get_versions
+
 versions = get_versions()
 __version__ = versions['version']
 __git_revision__ = versions['full-revisionid']