Update main.py

.github/workflows/python-package.yml

@@ -27,17 +27,64 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install . -U
-        python -m pip install flake8 pytest
+        python -m pip install -e .
+        python -m pip install flake8 pytest pytest-cov
+        python -m pip uninstall -y cobra
+        python -m pip install 'cobra @ git+https://github.com/opencobra/cobrapy@devel'
         pip install -r requirements.txt
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-    - name: Set up gurobi license
+    - name: Update semantic version
+      uses: paulhatch/[email protected]
+      with:
+        # The prefix to use to identify tags
+        tag_prefix: "v"
+        # A string which, if present in a git commit, indicates that a change represents a
+        # major (breaking) change, supports regular expressions wrapped with '/'
+        major_pattern: "(MAJOR)"
+        # A string which indicates the flags used by the `major_pattern` regular expression. Supported flags: idgs
+        major_regexp_flags: ""
+        # Same as above except indicating a minor change, supports regular expressions wrapped with '/'
+        minor_pattern: "(MINOR)"
+        # A string which indicates the flags used by the `minor_pattern` regular expression. Supported flags: idgs
+        minor_regexp_flags: ""
+        # A string to determine the format of the version output
+        version_format: "${major}.${minor}.${patch}-prerelease${increment}"
+        # Optional path to check for changes. If any changes are detected in the path the
+        # 'changed' output will true. Enter multiple paths separated by spaces.
+        change_path: "pymgpipe/"
+        # Named version, will be used as suffix for name version tag
+        namespace: pymgpipe
+        # If this is set to true, *every* commit will be treated as a new version.
+        bump_each_commit: true
+        # If true, the body of commits will also be searched for major/minor patterns to determine the version type.
+        search_commit_body: false
+        # The output method used to generate list of users, 'csv' or 'json'.
+        user_format_type: "csv"
+        # Prevents pre-v1.0.0 version from automatically incrementing the major version.
+        # If enabled, when the major version is 0, major releases will be treated as minor and minor as patch. Note that the version_type output is unchanged.
+        enable_prerelease_mode: true
+    - name: Build coverage file
       run: |
-        conda install -c gurobi gurobi
-        export GRB_LICENSE_FILE=tests/gurobi.lic
-    - name: Test with pytest
+        echo '[run]\nomit =\n\tpymgpipe/tests/*\n\tpymgpipe/__init__.py' > .coveragerc
+        pytest --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=pymgpipe pymgpipe/tests/ | tee pytest-coverage.txt
+    - name: Pytest coverage comment
+      if: ${{ github.ref == 'refs/heads/main' }}
+      id: coverageComment
+      uses: MishaKav/pytest-coverage-comment@main
+      with:
+        pytest-coverage-path: ./pytest-coverage.txt
+        junitxml-path: ./pytest.xml
+    - name: Update Readme with Coverage Html
+      if: ${{ github.ref == 'refs/heads/main' }}
       run: |
-        pytest
+        sed -i '/<!-- Pytest Coverage Comment:Begin -->/,/<!-- Pytest Coverage Comment:End -->/c\<!-- Pytest Coverage Comment:Begin -->\n\${{ steps.coverageComment.outputs.coverageHtml }}\n<!-- Pytest Coverage Comment:End -->' ./README.md
+    - name: Commit & Push changes to Readme
+      if: ${{ github.ref == 'refs/heads/main' }}
+      uses: actions-js/push@master
+      with:
+        message: Update coverage on Readme
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        force: true

.github/workflows/tests.yml

@@ -0,0 +1,41 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Tests
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10"]
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install -e .
+        python -m pip install flake8 pytest pytest-cov
+        python -m pip uninstall -y cobra
+        python -m pip install 'cobra @ git+https://github.com/opencobra/cobrapy@devel'
+        pip install -r requirements.txt
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+    - name: Test with pytest
+      run: |
+        pytest
+

.gitignore

@@ -130,6 +130,9 @@ dmypy.json
 
 #tests
 test/
+pytest-coverage.txt
+pytest.xml 
+*.coverage*
 
 # examples
 examples/out/*