Merge pull request #10 from JoKra1/main

v0.1.3

Author: JoKra1

.github/workflows/python-package.yml

@@ -45,7 +45,38 @@ jobs:
 
     - uses: actions/upload-artifact@v3
       with:
+        name: wheels
         path: ./wheelhouse/*.whl
+  
+  test-coverage:
+    # Runs tests for one build for which coverage is computed as well
+    needs: build
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python for Coverage
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install .
+      - name: Test with pytest
+        run: |
+          pip install pytest pytest-cov
+          pytest ./tests --cov=mssm --cov-report=xml --cov-report=html
+      - name: Upload coverage reports to Codecov with GitHub Action
+        uses: codecov/codecov-action@v3
+        
+      # Also store coverage as artifact
+      - uses: actions/upload-artifact@v3
+        with:
+          name: coverage
+          path: |
+            coverage.xml
+            ./htmlcov/index.html
         
   release:
     # https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
@@ -70,6 +101,7 @@ jobs:
       - name: Download Artifacts
         uses: actions/download-artifact@v3
         with:
+          name: wheels
           path: ./wheelhouse/
 
       - name: Create GitHub Release
@@ -86,15 +118,14 @@ jobs:
           GITHUB_TOKEN: ${{ github.token }}
         run: >-
           gh release upload
-          '${{ github.ref_name }}' ./wheelhouse/artifact/**
+          '${{ github.ref_name }}' ./wheelhouse/**
           --repo '${{ github.repository }}'
 
   publish-test:
     # https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
-    # test pypi now gets all un-tagged pushes
-    if: ${{ !startsWith(github.ref, 'refs/tags/') }}
+    # Publish to test-pypi - only if release is triggered.
     needs:
-      - build
+      - release
     runs-on: ubuntu-latest
 
     environment:
@@ -108,12 +139,16 @@ jobs:
       - name: Download Artifacts
         uses: actions/download-artifact@v3
         with:
+          name: wheels
           path: ./wheelhouse/
+      
+      - name: Print wheel content
+        run: ls ./wheelhouse
 
       - name: Publish wheels to test-pypi
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
-          packages-dir: ./wheelhouse/artifact
+          packages-dir: ./wheelhouse/
           repository-url: https://test.pypi.org/legacy/
 
   publish-release:
@@ -134,9 +169,10 @@ jobs:
       - name: Download Artifacts
         uses: actions/download-artifact@v3
         with:
+          name: wheels
           path: ./wheelhouse/
 
       - name: Publish wheels to test-pypi
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
-          packages-dir: ./wheelhouse/artifact
+          packages-dir: ./wheelhouse/

README.md

@@ -20,11 +20,7 @@ pip install mssm
 pip install matplotlib # Only needed for tutorials
 ```
 
-The fourth line, installing ``matplotlib`` is only necessary if you want to run the tutorials. Note: pypi will only reflect releases (Basically, the state of the stable branch). Pushes to main continue to be distributed to test.pypi, so if you need the latest changes you can get them from [test.pypi](https://test.pypi.org/project/mssm/#description). In that case, you need to replace the third line in the code above with:
-
-```
-pip install -i https://test.pypi.org/simple/ mssm
-```
+The fourth line, installing ``matplotlib`` is only necessary if you want to run the tutorials. Note: pypi will only reflect releases (Basically, the state of the stable branch). If you urgently need a feature currently only available on the main branch, consider building from source.
 
 ### Building from source
 
@@ -43,4 +39,4 @@ pip install .
 
 ## Contributing
 
-Contributions are welcome! Feel free to open issues or make pull-requests to main.
+Contributions are welcome! Feel free to open issues or make pull-requests to main. Some problems that could use work are listed below.

pyproject.toml

@@ -7,10 +7,17 @@ requires = [
 ]
 build-backend = "setuptools.build_meta"
 
+[tool.cibuildwheel]
+before-test = "ls"
+test-skip = "*-win32 pp* *i686"
+test-requires = ["pytest", "pytest-cov"]
+test-command = "pytest {project}/tests --cov={project}"
+
 [project]
 dependencies=["numpy >= 1.24.1",
               "pandas >= 1.5.3",
-              "scipy >= 1.10.0"]
+              "scipy >= 1.10.0",
+              "tqdm >= 4.66.1"]
 name = "mssm"
 authors = [
   { name="Joshua Krause", email="jokra001@proton.me" }
@@ -27,4 +34,4 @@ dynamic = ["version"]
 
 [tool.setuptools_scm]
 # https://github.com/pypa/setuptools_scm/issues/342
-local_scheme = "no-local-version" 
+local_scheme = "no-local-version"