merge develop into main

.github/workflows/count_locs

@@ -0,0 +1,37 @@
+name: Count LOC in Python Files
+
+on:
+  push:
+    branches: [ develop ]
+  pull_request:
+    branches: [ main, develop ]
+
+jobs:
+  count-loc:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Count Total Lines of Code in Python Files
+        id: loc  # Give this step an ID to reference later
+        run: |
+          echo "Counting total lines of Python code..."
+          LOC_COUNT=$(git ls-files '*.py' | xargs wc -l | tail -n 1)
+          echo "LOC_COUNT=${LOC_COUNT}" >> $GITHUB_ENV
+          echo "Python Lines of Code (LOC): $LOC_COUNT"
+
+      - name: Post LOC Count as PR Comment (Only for Main Branch)
+        if: github.event_name == 'pull_request' && github.base_ref == 'main'
+        uses: peter-evans/create-or-update-comment@v3
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          issue-number: ${{ github.event.pull_request.number }}
+          body: |
+            ### Python Lines of Code (LOC) Summary
+            Total lines of Python code in this repository:
+            ```
+            ${{ env.LOC_COUNT }}
+            ```
+

.github/workflows/python_ci.yml

@@ -11,7 +11,7 @@ jobs:
       runs-on: ubuntu-latest
       strategy:
         matrix:
-          python-version: ['3.8', '3.9', '3.10', '3.11']
+          python-version: ['3.10', '3.11', '3.12']
 
       steps:
         - uses: actions/checkout@v4
@@ -24,4 +24,4 @@ jobs:
             python3 -m pip install --editable .[test,docs]
         - name: Run pytest tests
           run: |
-            pytest
+            pytest --cov=template_for_python_projects

.gitignore

@@ -161,3 +161,4 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 .idea/
+.vscode/

README.md

@@ -51,6 +51,33 @@ If you want to run sphinx locally:
 - `make.bat` html
 - Open `docs/_build/html/index.html` in your browser
 
+### Submodules
+Sometimes it is necessary to have other repositories as submodules. To initiate this you can follow this tutorial by Git itself on [Submodules](https://git-scm.com/book/en/v2/Git-Tools-Submodules). But in essence you need this command:
+
+`git submodule add https://github.com/frehburg/TemplateForPythonProjects`
+
+If you then want to import the submodule as a python package in your code, the ci will not be able to resolve it. To fix this, add the following lines to `python_ci.yml`:
+
+```
+- name: Checkout code
+        uses: actions/checkout@v3
+        with:  # this
+          submodules: true   # this to ensure submodules are checked out
+```
+
+and further down
+
+```
+ run: |
+          python3 -m pip install --upgrade pip
+          python3 -m pip install --editable .[test,docs]
+          python3 -m pip install --editable ./submodules/TemplateForPythonProjects  # this to install the submodule package
+```
+
+### Add custom badges to your README
+Please check the tutorial in [custom_badges.md](https://github.com/frehburg/TemplateForPythonProjects/blob/develop/custom_badges.md) for information on creating custom badges for your github repo.
+
+
 
 
 You can also add a badge like this one to your README.md file:
@@ -110,4 +137,4 @@ Guidelines for contributing to your project. Include information about how other
 
 Specify the license under which your project is distributed.
 
-## Acknowledgements
+## Acknowledgements

custom_badges.md

@@ -0,0 +1,66 @@
+## Custom Badges
+You can create custom badges such as [![LOCs](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/frehburg/25d4f4d4d222fcb5f266a280b1dd60d4/raw/phenopacket_mapper_locs.JSON)](https://github.com/bih-cei/phenopacket_mapper/actions/workflows/locs.yml).
+
+This relies on a GitHub workflow such as:
+
+```
+name: Count LOC in Python Files
+
+on:
+  push:
+    branches: [ develop ]
+  pull_request:
+    branches: [ main, develop ]
+
+jobs:
+  count-loc:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Count Total Lines of Code in Python Files
+        id: loc  # Give this step an ID to reference later
+        run: |
+          echo "Counting total lines of Python code..."
+          LOC_COUNT=$(git ls-files '*.py' | xargs wc -l | tail -n 1)
+          echo "LOC_COUNT=${LOC_COUNT}" >> $GITHUB_ENV
+          echo "Python Lines of Code (LOC): $LOC_COUNT"
+
+      - name: Post LOC Count as PR Comment (Only for Main Branch)
+        if: github.event_name == 'pull_request' && github.base_ref == 'main'
+        uses: peter-evans/create-or-update-comment@v3
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          issue-number: ${{ github.event.pull_request.number }}
+          body: |
+            ### Python Lines of Code (LOC) Summary
+            Total lines of Python code in this repository:
+            ```
+            ${{ env.LOC_COUNT }}
+            ```
+
+      - name: Create Awesome Badge
+        uses: schneegans/dynamic-badges-action@v1.7.0
+        with:
+          auth: ${{ secrets.GIST_SECRET }}
+          gistID: 25d4f4d4d222fcb5f266a280b1dd60d4
+          filename: phenopacket_mapper_locs.JSON # Use test.svg if you want to use the SVG mode.
+          label: Lines of Code
+          message: ${{ env.LOC_COUNT }}
+          color: blue
+```
+
+You can see the last section on creating a badge. In order for this to work, you need to follow the steps in this tutorial: [Dynamic Badges Action](https://github.com/marketplace/actions/dynamic-badges)
+
+TLDR:
+
+1. Create a gist file (e.g., `test.json`) at https://gist.github.com/.
+2. Create a GitHub Access token with the Gist access.
+3. Create a secret in your repository and call it `GIST_SECRET`
+4. Configure the workflow to write to the gist as seen above
+5. Add the badge to your README like this:
+```
+![badge](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/<user>/<gist-ID>/raw/test.json)
+```

pyproject.toml

@@ -9,7 +9,7 @@ authors = [
      ]
 description = "TODO"
 readme = "README.md"
-requires-python = ">=3.8"
+requires-python = ">=3.10"
 keywords = [
     "Test",
     "TODO",
@@ -20,10 +20,9 @@ classifiers = [
     "License :: OSI Approved :: MIT License",
     "Operating System :: OS Independent",
     "Development Status :: 3 - Alpha",
-    "Programming Language :: Python :: 3.8",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "Intended Audience :: Science/Research",
     "Topic :: Scientific/Engineering :: Machine Learning"
 ]
@@ -33,7 +32,7 @@ dependencies = [
 dynamic = ["version"]
 
 [project.optional-dependencies]
-test = ["pytest>=7.0.0,<8.0.0"]
+test = ["pytest>=7.0.0,<8.0.0", "pytest-cov"]
 docs = ["sphinx>=7.0.0", "sphinx-rtd-theme>=1.3.0", "sphinx-copybutton>=0.5.0"]
 
 [project.urls]

pytest.ini

@@ -6,3 +6,6 @@ python_files = _test*.py test*.py
 
 ; Also test the documentation tests and the tutorial scripts.
 addopts = --doctest-modules --doctest-glob *.rst
+
+# Exclude certain directories from recursion when discovering tests.
+norecursedirs = docs submodules