Merge branch 'main' into edit_req

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,33 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ""
+labels: ""
+assignees: ""
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+
+- OS: [e.g. iOS]
+- Browser [e.g. chrome, safari]
+- Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,19 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ""
+labels: ""
+assignees: ""
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/additional_files/environment.yml

@@ -108,4 +108,4 @@ dependencies:
       - zarr==2.18.2
       - zict==3.0.0
       - zipp==3.19.0
-      - xarray==2024.5.0
+      - xarray==2024.5.0

.github/workflows/generate_documentation.yml

@@ -1,43 +1,81 @@
 # This is a basic workflow to help you get started with Actions
 
-name: Build Documentation
+name: Build and Deploy Documentation
 
-on: [push]
+on:
+  # Runs on pushes targeting the default branch
+  push:
+    branches: ["main"]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
 
 jobs:
-  build-linux:
+  build:
     runs-on: ubuntu-latest
     strategy:
       max-parallel: 5
 
     steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v2
-      with:
-        python-version: '3.10'
-    - name: set up Pandoc    
-      uses: r-lib/actions/setup-pandoc@v2
-      with:
-        pandoc-version: '3.1.11' # The pandoc version to download (if necessary) and use.
-    - name: Add conda to system path
-      run: |
-        # $CONDA is an environment variable pointing to the root of the miniconda directory
-        echo $CONDA/bin >> $GITHUB_PATH
-    - name: Install dependencies
-      run: |
-        conda install -y python=3.10
-        conda env update --file .github/additional_files/environment.yml --name base
-    - name:  Install package
-      run: |
-        pip install ./
-    - name: Install Sphinx and additional dependences
-      run: |
-        sudo apt install pandoc
-        pip install sphinx sphinx-rtd-theme==2.0.0 sphinx-autodoc-typehints sphinx-argparse nbsphinx renku-sphinx-theme 
-    - name: Generate Documentation
-      run: |
-        cd docs_source
-        make clean
-        make html
-      
+      - uses: actions/checkout@v4
+      - name: Setup pip cache
+        uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.10"
+      - name: set up Pandoc
+        uses: r-lib/actions/setup-pandoc@v2
+        with:
+          pandoc-version: "3.1.11" # The pandoc version to download (if necessary) and use.
+      - name: Add conda to system path
+        run: |
+          # $CONDA is an environment variable pointing to the root of the miniconda directory
+          echo $CONDA/bin >> $GITHUB_PATH
+      - name: Install dependencies
+        run: |
+          conda install -y python=3.10
+          sudo apt install pandoc
+          pip install ."[dev]"/
+          #conda env update --file .github/additional_files/environment.yml --name base
+      - uses: Mushus/checkout-submodule@v1
+        with:
+          basePath: .
+          submodulePath: ./examples/notebooks
+      - name: Generate Documentation
+        run: |
+          cd docs
+          make clean
+          make html
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          name: github-pages
+          path: docs/_build/html/
+
+  # Deployment job
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.github/workflows/unit_test.yml

@@ -9,23 +9,32 @@ jobs:
       max-parallel: 5
 
     steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v2
-      with:
-        python-version: '3.10'
-    - name: Add conda to system path
-      run: |
-        # $CONDA is an environment variable pointing to the root of the miniconda directory
-        echo $CONDA/bin >> $GITHUB_PATH
-    - name: Install dependencies
-      run: |
-        conda install -y python=3.10
-        conda env update --file .github/additional_files/environment.yml --name base
-    - name:  Install package
-      run: |
-        pip install ./    
-    - name: Test with pytest
-      run: |
-        pip install pytest
-        pytest
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+      - name: Add conda to system path
+        run: |
+          echo $CONDA/bin >> $GITHUB_PATH
+      - name: Install dependencies
+        run: |
+          conda install -y python=3.10
+          conda env update --file .github/additional_files/environment.yml --name base
+      - name: Install package
+        run: |
+          pip install uv
+          uv pip install --system .
+
+      - name: Install pre-commit
+        run: |
+          uv pip install --system pre-commit
+      - name: Run pre-commit checks
+        run: |
+          pre-commit install
+          pre-commit run --all-files
+
+      - name: Test with pytest
+        run: |
+          uv pip install --system pytest
+          pytest

.gitignore

@@ -6,6 +6,12 @@ development/
 development.ipynb
 config_test.yml
 segmentation_workflows/
+scportrait_data/
+
+
+#do not track output generated by sphinx-gallery
+sg_execution_times.rst
+docs/auto_examples/
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
@@ -21,6 +27,7 @@ __pycache__/
 # Distribution / packaging
 .Python
 build/
+_build/
 develop-eggs/
 dist/
 downloads/

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "examples/notebooks"]
+	path = examples/notebooks
+	url = https://github.com/MannLabs/scPortrait-notebooks.git

.pre-commit-config.yaml

@@ -0,0 +1,50 @@
+fail_fast: false
+default_language_version:
+  python: python3
+default_stages:
+  - commit
+  - push
+minimum_pre_commit_version: 2.16.0
+repos:
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v4.0.0-alpha.8
+    hooks:
+      - id: prettier
+        exclude: |
+          (?x)(
+              docs/|
+              docs_source/|
+              example_data/
+          )
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.7.2
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
+      - id: ruff-format
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: detect-private-key
+      - id: check-ast
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args: [--fix=lf]
+      - id: trailing-whitespace
+      - id: check-case-conflict
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.13.0
+    hooks:
+      - id: mypy
+        args: [--no-strict-optional, --ignore-missing-imports]
+        additional_dependencies:
+          ["types-requests", "types-attrs", "types-PyYAML"]
+  - repo: local
+    hooks:
+      - id: forbid-to-commit
+        name: Don't commit rej files
+        entry: |
+          Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
+          Fix the merge conflicts manually and remove the .rej files.
+        language: fail
+        files: '.*\.rej$'

CODE_OF_CONDUCT.md

@@ -17,23 +17,23 @@ diverse, inclusive, and healthy community.
 Examples of behavior that contributes to a positive environment for our
 community include:
 
-* Demonstrating empathy and kindness toward other people
-* Being respectful of differing opinions, viewpoints, and experiences
-* Giving and gracefully accepting constructive feedback
-* Accepting responsibility and apologizing to those affected by our mistakes,
+- Demonstrating empathy and kindness toward other people
+- Being respectful of differing opinions, viewpoints, and experiences
+- Giving and gracefully accepting constructive feedback
+- Accepting responsibility and apologizing to those affected by our mistakes,
   and learning from the experience
-* Focusing on what is best not just for us as individuals, but for the
+- Focusing on what is best not just for us as individuals, but for the
   overall community
 
 Examples of unacceptable behavior include:
 
-* The use of sexualized language or imagery, and sexual attention or
+- The use of sexualized language or imagery, and sexual attention or
   advances of any kind
-* Trolling, insulting or derogatory comments, and personal or political attacks
-* Public or private harassment
-* Publishing others' private information, such as a physical or email
+- Trolling, insulting or derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information, such as a physical or email
   address, without their explicit permission
-* Other conduct which could reasonably be considered inappropriate in a
+- Other conduct which could reasonably be considered inappropriate in a
   professional setting
 
 ## Enforcement Responsibilities
@@ -106,7 +106,7 @@ Violating these terms may lead to a permanent ban.
 ### 4. Permanent Ban
 
 **Community Impact**: Demonstrating a pattern of violation of community
-standards, including sustained inappropriate behavior,  harassment of an
+standards, including sustained inappropriate behavior, harassment of an
 individual, or aggression toward or disparagement of classes of individuals.
 
 **Consequence**: A permanent ban from any sort of public interaction within

MANIFEST.in

@@ -1 +1 @@
-include src/pretrained_models
+include src/pretrained_models