From fd0407a4a788c37518acc574f10028384b9c3bda Mon Sep 17 00:00:00 2001
From: Paul Gierz <pgierz@awi.de>
Date: Thu, 4 Sep 2025 15:48:46 +0200
Subject: [PATCH 01/10] Add comprehensive CI/CD pipeline with GitHub Actions

- Add continuous integration workflow for testing Snakemake workflows
- Add container build pipeline for Docker and Singularity images
- Add documentation build and deployment workflow
- Add automated release workflow with container publishing
- Add markdown link checking configuration
- Support testing across multiple Python versions (3.8, 3.9, 3.10)
- Include code quality checks with flake8, black, and isort
- Add security scanning with Trivy
- Support multi-architecture container builds (linux/amd64, linux/arm64)
---
 .github/markdown-link-check-config.json |  31 +++
 .github/workflows/build-containers.yml  | 235 +++++++++++++++++
 .github/workflows/ci.yml                | 228 +++++++++++++++++
 .github/workflows/docs.yml              | 325 ++++++++++++++++++++++++
 .github/workflows/release.yml           | 211 +++++++++++++++
 5 files changed, 1030 insertions(+)
 create mode 100644 .github/markdown-link-check-config.json
 create mode 100644 .github/workflows/build-containers.yml
 create mode 100644 .github/workflows/ci.yml
 create mode 100644 .github/workflows/docs.yml
 create mode 100644 .github/workflows/release.yml

diff --git a/.github/markdown-link-check-config.json b/.github/markdown-link-check-config.json
new file mode 100644
index 0000000..40b883e
--- /dev/null
+++ b/.github/markdown-link-check-config.json
@@ -0,0 +1,31 @@
+{
+  "ignorePatterns": [
+    {
+      "pattern": "^http://localhost"
+    },
+    {
+      "pattern": "^https://127.0.0.1"
+    },
+    {
+      "pattern": "^file://"
+    }
+  ],
+  "replacementPatterns": [
+    {
+      "pattern": "^/",
+      "replacement": "{{BASEURL}}/"
+    }
+  ],
+  "httpHeaders": [
+    {
+      "urls": ["https://github.com"],
+      "headers": {
+        "Accept": "text/html"
+      }
+    }
+  ],
+  "timeout": "20s",
+  "retryOn429": true,
+  "retryCount": 3,
+  "fallbackHttpStatus": [400, 401, 403, 404, 405, 500, 502, 503, 504]
+}
\ No newline at end of file
diff --git a/.github/workflows/build-containers.yml b/.github/workflows/build-containers.yml
new file mode 100644
index 0000000..5c26e0d
--- /dev/null
+++ b/.github/workflows/build-containers.yml
@@ -0,0 +1,235 @@
+name: Build and Push Containers
+
+on:
+  push:
+    branches: [ master, main ]
+    tags: [ 'v*' ]
+  pull_request:
+    branches: [ master, main ]
+  workflow_dispatch:
+    inputs:
+      push_images:
+        description: 'Push images to registry'
+        required: false
+        default: false
+        type: boolean
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  build-docker:
+    name: Build Docker Images
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+    
+    strategy:
+      matrix:
+        target: [production, development]
+    
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+      
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+      
+      - name: Log in to Container Registry
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      
+      - name: Extract metadata
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          flavor: |
+            suffix=-${{ matrix.target }}
+          tags: |
+            type=ref,event=branch
+            type=ref,event=pr
+            type=semver,pattern={{version}}
+            type=semver,pattern={{major}}.{{minor}}
+            type=semver,pattern={{major}}
+            type=raw,value=latest,enable={{is_default_branch}}
+      
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: workflow/containers/Dockerfile
+          target: ${{ matrix.target }}
+          push: ${{ github.event_name != 'pull_request' && (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags/v') || github.event.inputs.push_images == 'true') }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+          platforms: linux/amd64,linux/arm64
+
+  test-containers:
+    name: Test Container Images  
+    runs-on: ubuntu-latest
+    needs: build-docker
+    if: github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch'
+    
+    strategy:
+      matrix:
+        target: [production, development]
+    
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+      
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+      
+      - name: Build test image
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: workflow/containers/Dockerfile
+          target: ${{ matrix.target }}
+          load: true
+          tags: ocp-tool:test-${{ matrix.target }}
+          cache-from: type=gha
+      
+      - name: Test production container
+        if: matrix.target == 'production'
+        run: |
+          # Test basic functionality
+          docker run --rm ocp-tool:test-production python --version
+          docker run --rm ocp-tool:test-production snakemake --version
+          
+          # Test OCP-tool imports
+          docker run --rm ocp-tool:test-production python -c "import ocp_tool; print('✓ OCP-tool import successful')"
+          
+          # Test conda environment
+          docker run --rm ocp-tool:test-production conda list | grep -E "(numpy|matplotlib|netcdf4)"
+      
+      - name: Test development container
+        if: matrix.target == 'development'
+        run: |
+          # Test Jupyter installation
+          docker run --rm ocp-tool:test-development jupyter --version
+          docker run --rm ocp-tool:test-development jupyter kernelspec list
+      
+      - name: Test container security
+        uses: aquasecurity/trivy-action@master
+        with:
+          image-ref: 'ocp-tool:test-${{ matrix.target }}'
+          format: 'table'
+          severity: 'CRITICAL,HIGH'
+        continue-on-error: true
+
+  build-singularity:
+    name: Build Singularity Image
+    runs-on: ubuntu-latest
+    if: github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags/v')
+    
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+      
+      - name: Setup Singularity
+        uses: eWaterCycle/setup-singularity@v7
+        with:
+          singularity-version: 3.11.4
+      
+      - name: Build Singularity container
+        run: |
+          sudo singularity build ocp-tool.sif workflow/containers/singularity.def
+      
+      - name: Test Singularity container
+        run: |
+          # Test basic functionality
+          singularity exec ocp-tool.sif python --version
+          singularity exec ocp-tool.sif snakemake --version
+          
+          # Test OCP-tool imports  
+          singularity exec ocp-tool.sif python -c "import ocp_tool; print('✓ OCP-tool import successful')"
+      
+      - name: Upload Singularity image as artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: singularity-image
+          path: ocp-tool.sif
+          retention-days: 30
+
+  container-scan:
+    name: Container Security Scan
+    runs-on: ubuntu-latest
+    needs: build-docker
+    if: github.event_name != 'pull_request'
+    
+    steps:
+      - name: Run Trivy vulnerability scanner
+        uses: aquasecurity/trivy-action@master
+        with:
+          image-ref: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:latest-production
+          format: 'sarif'
+          output: 'trivy-results.sarif'
+      
+      - name: Upload Trivy results to GitHub Security
+        uses: github/codeql-action/upload-sarif@v2
+        with:
+          sarif_file: 'trivy-results.sarif'
+
+  integration-test:
+    name: Integration Test with Containers
+    runs-on: ubuntu-latest
+    needs: build-docker
+    if: github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch'
+    
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+      
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+      
+      - name: Build test image
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: workflow/containers/Dockerfile
+          target: production
+          load: true
+          tags: ocp-tool:integration-test
+          cache-from: type=gha
+      
+      - name: Create test data structure
+        run: |
+          mkdir -p test_data/{input,output}
+          mkdir -p test_data/input/{gaussian_grids_full,gaussian_grids_linear_reduced,openifs_input_default,runoff_map_default,fesom_mesh}
+          mkdir -p test_data/output/{openifs_input_modified,oasis_mct3_input,runoff_map_modified,plots}
+          
+          # Create minimal test config
+          cat > test_data/test_config.yaml << EOF
+          res_num: 159
+          truncation_type: "linear"
+          exp_name_oifs: "test"
+          num_fields: 50
+          grid_name_oce: "TEST"
+          cavity: false
+          interp_res: "r360x181"
+          fesom_grid_file_path: "/app/data/input/test_mesh.nc"
+          do_paleo: false
+          manual_basin_removal: []
+          EOF
+      
+      - name: Run integration test
+        run: |
+          docker run --rm \
+            -v $(pwd)/test_data:/app/data \
+            -w /app \
+            ocp-tool:integration-test \
+            snakemake --dry-run --configfile /app/data/test_config.yaml
+          
+          echo "✓ Integration test completed successfully"
\ No newline at end of file
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
new file mode 100644
index 0000000..3b88ebd
--- /dev/null
+++ b/.github/workflows/ci.yml
@@ -0,0 +1,228 @@
+name: CI
+
+on:
+  push:
+    branches: [ master, main, develop ]
+  pull_request:
+    branches: [ master, main ]
+  workflow_dispatch:
+
+jobs:
+  test-workflow:
+    name: Test Snakemake Workflow
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10"]
+    
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+      
+      - name: Setup Micromamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: environment.yaml
+          environment-name: ocp-tool
+          cache-environment: true
+          cache-downloads: true
+          generate-run-shell: true
+      
+      - name: Install Snakemake
+        shell: micromamba-shell {0}
+        run: |
+          micromamba install -y -c conda-forge -c bioconda snakemake>=7.0
+          
+      - name: Lint Snakefile
+        shell: micromamba-shell {0}
+        run: |
+          cd workflow
+          snakemake --lint
+      
+      - name: Validate workflow configuration
+        shell: micromamba-shell {0}
+        run: |
+          cd workflow
+          python -c "import yaml; yaml.safe_load(open('config/config.yaml'))"
+          echo "✓ Configuration file is valid YAML"
+      
+      - name: Check Python scripts syntax
+        shell: micromamba-shell {0}
+        run: |
+          python -m py_compile ocp-tool.py
+          python -m py_compile ocp_tool/*.py
+          find workflow/scripts -name "*.py" -exec python -m py_compile {} +
+          echo "✓ All Python scripts have valid syntax"
+      
+      - name: Dry run Snakemake workflow
+        shell: micromamba-shell {0}
+        run: |
+          cd workflow
+          # Create minimal test data structure
+          mkdir -p ../input/{gaussian_grids_full,gaussian_grids_linear_reduced,openifs_input_default,runoff_map_default,fesom_mesh}
+          mkdir -p ../output/{openifs_input_modified,oasis_mct3_input,runoff_map_modified,plots}
+          
+          # Test dry run with modified config for CI
+          cat > test_config.yaml << EOF
+          res_num: 159
+          truncation_type: "linear"
+          exp_name_oifs: "test"
+          num_fields: 50
+          grid_name_oce: "TEST"
+          cavity: false
+          interp_res: "r360x181"
+          fesom_grid_file_path: "/tmp/test_mesh.nc"
+          do_paleo: false
+          manual_basin_removal: []
+          EOF
+          
+          snakemake --dry-run --configfile test_config.yaml
+          echo "✓ Snakemake workflow dry run successful"
+      
+      - name: Test import of ocp_tool modules
+        shell: micromamba-shell {0}
+        run: |
+          python -c "
+          import sys
+          sys.path.insert(0, '.')
+          from ocp_tool import ocp_tool
+          print('✓ Successfully imported ocp_tool module')
+          "
+
+  code-quality:
+    name: Code Quality Checks
+    runs-on: ubuntu-latest
+    
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+      
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.9"
+      
+      - name: Install linting tools
+        run: |
+          pip install --upgrade pip
+          pip install flake8 black isort mypy
+      
+      - name: Run flake8
+        run: |
+          # Stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --exclude=.git,__pycache__,build,dist
+          # Exit-zero treats all errors as warnings
+          flake8 . --count --exit-zero --max-complexity=15 --max-line-length=120 --statistics --exclude=.git,__pycache__,build,dist
+      
+      - name: Check code formatting with black
+        run: |
+          black --check --diff --exclude=.git . || echo "::warning::Code formatting issues found. Run 'black .' to fix."
+      
+      - name: Check import sorting with isort
+        run: |
+          isort --check-only --diff . || echo "::warning::Import sorting issues found. Run 'isort .' to fix."
+
+  notebook-tests:
+    name: Test Jupyter Notebooks
+    runs-on: ubuntu-latest
+    
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+      
+      - name: Setup Micromamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: environment.yaml
+          environment-name: ocp-tool
+          cache-environment: true
+          generate-run-shell: true
+      
+      - name: Validate notebook structure
+        shell: micromamba-shell {0}
+        run: |
+          pip install nbformat
+          python -c "
+          import nbformat
+          import json
+          
+          nb = nbformat.read('ocp_tool.ipynb', as_version=4)
+          print(f'✓ Notebook has {len(nb.cells)} cells')
+          print(f'✓ Notebook format version: {nb.nbformat}.{nb.nbformat_minor}')
+          
+          # Check for basic structure
+          code_cells = [c for c in nb.cells if c.cell_type == 'code']
+          print(f'✓ Found {len(code_cells)} code cells')
+          "
+      
+      - name: Check notebook for output clearing
+        shell: micromamba-shell {0}
+        run: |
+          python -c "
+          import nbformat
+          import sys
+          
+          nb = nbformat.read('ocp_tool.ipynb', as_version=4)
+          has_outputs = False
+          
+          for cell in nb.cells:
+              if cell.cell_type == 'code' and cell.outputs:
+                  has_outputs = True
+                  break
+          
+          if has_outputs:
+              print('::warning::Notebook contains outputs. Consider clearing before commit.')
+          else:
+              print('✓ Notebook outputs are cleared')
+          "
+
+  documentation:
+    name: Documentation Check
+    runs-on: ubuntu-latest
+    
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+      
+      - name: Check README files
+        run: |
+          for readme in README.md workflow/README.md; do
+            if [ -f "$readme" ]; then
+              echo "✓ Found $readme"
+            else
+              echo "::error::Missing $readme"
+              exit 1
+            fi
+          done
+      
+      - name: Check for broken links in documentation
+        uses: gaurav-nelson/github-action-markdown-link-check@v1
+        with:
+          use-quiet-mode: 'yes'
+          config-file: '.github/markdown-link-check-config.json'
+        continue-on-error: true
+
+  security-scan:
+    name: Security Scanning
+    runs-on: ubuntu-latest
+    
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+      
+      - name: Run Trivy security scanner
+        uses: aquasecurity/trivy-action@master
+        with:
+          scan-type: 'fs'
+          scan-ref: '.'
+          format: 'sarif'
+          output: 'trivy-results.sarif'
+          severity: 'CRITICAL,HIGH'
+        continue-on-error: true
+      
+      - name: Upload Trivy results to GitHub Security
+        uses: github/codeql-action/upload-sarif@v2
+        if: always()
+        with:
+          sarif_file: 'trivy-results.sarif'
+        continue-on-error: true
\ No newline at end of file
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
new file mode 100644
index 0000000..4cd76c0
--- /dev/null
+++ b/.github/workflows/docs.yml
@@ -0,0 +1,325 @@
+name: Documentation
+
+on:
+  push:
+    branches: [ master, main ]
+    paths:
+      - 'docs/**'
+      - '**.md'
+      - '**.py' 
+      - 'workflow/**'
+  pull_request:
+    branches: [ master, main ]
+    paths:
+      - 'docs/**'
+      - '**.md'
+      - '**.py'
+      - 'workflow/**'
+  workflow_dispatch:
+
+jobs:
+  build-docs:
+    name: Build Documentation
+    runs-on: ubuntu-latest
+    
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # Full history for proper versioning
+      
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.9"
+      
+      - name: Install documentation dependencies
+        run: |
+          pip install --upgrade pip
+          pip install sphinx sphinx-rtd-theme nbsphinx pandoc
+          pip install myst-parser sphinx-autoapi
+      
+      - name: Setup Micromamba for environment
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: environment.yaml
+          environment-name: ocp-tool
+          cache-environment: true
+          generate-run-shell: true
+      
+      - name: Generate API documentation
+        shell: micromamba-shell {0}
+        run: |
+          # Create docs directory structure if it doesn't exist
+          mkdir -p docs/{source,build}
+          
+          # Generate Sphinx configuration if it doesn't exist
+          if [ ! -f docs/source/conf.py ]; then
+            cat > docs/source/conf.py << 'EOF'
+          import os
+          import sys
+          sys.path.insert(0, os.path.abspath('../..'))
+          
+          project = 'OCP-tool'
+          copyright = '2024, OCP-tool developers'
+          author = 'OCP-tool developers'
+          
+          extensions = [
+              'sphinx.ext.autodoc',
+              'sphinx.ext.viewcode',
+              'sphinx.ext.napoleon',
+              'sphinx.ext.intersphinx',
+              'nbsphinx',
+              'myst_parser',
+          ]
+          
+          templates_path = ['_templates']
+          exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+          
+          html_theme = 'sphinx_rtd_theme'
+          html_static_path = ['_static']
+          
+          # Notebook execution settings
+          nbsphinx_execute = 'never'
+          nbsphinx_allow_errors = True
+          
+          # Intersphinx mapping
+          intersphinx_mapping = {
+              'python': ('https://docs.python.org/3/', None),
+              'numpy': ('https://numpy.org/doc/stable/', None),
+              'matplotlib': ('https://matplotlib.org/stable/', None),
+          }
+          
+          # MyST settings
+          myst_enable_extensions = [
+              "colon_fence",
+              "deflist", 
+              "html_image",
+              "linkify",
+              "replacements",
+              "smartquotes",
+              "tasklist",
+          ]
+          EOF
+          fi
+          
+          # Generate main index if it doesn't exist
+          if [ ! -f docs/source/index.rst ]; then
+            cat > docs/source/index.rst << 'EOF'
+          OCP-tool Documentation
+          ======================
+          
+          OpenIFS Coupling Preparation Tool for climate modeling.
+          
+          .. toctree::
+             :maxdepth: 2
+             :caption: Contents:
+          
+             installation
+             workflow
+             api
+             notebooks
+             examples
+          
+          Indices and tables
+          ==================
+          
+          * :ref:`genindex`
+          * :ref:`modindex`
+          * :ref:`search`
+          EOF
+          fi
+          
+          # Build API docs with autoapi  
+          sphinx-apidoc -f -o docs/source/api ocp_tool
+      
+      - name: Convert notebooks for documentation
+        shell: micromamba-shell {0}
+        run: |
+          mkdir -p docs/source/notebooks
+          
+          # Copy main notebook
+          if [ -f ocp_tool.ipynb ]; then
+            cp ocp_tool.ipynb docs/source/notebooks/
+          fi
+          
+          # Create notebook index
+          cat > docs/source/notebooks.rst << 'EOF'
+          Jupyter Notebooks
+          =================
+          
+          Example notebooks demonstrating OCP-tool usage.
+          
+          .. toctree::
+             :maxdepth: 2
+          
+             notebooks/ocp_tool
+          EOF
+      
+      - name: Create additional documentation pages
+        run: |
+          # Installation guide
+          cat > docs/source/installation.md << 'EOF'
+          # Installation
+          
+          ## Requirements
+          
+          - Python 3.8+
+          - Conda/Mamba package manager
+          - NetCDF libraries
+          - ECCODES for GRIB processing
+          
+          ## Quick Install
+          
+          ```bash
+          git clone https://github.com/pgierz/ocp-tool.git
+          cd ocp-tool
+          conda env create -f environment.yaml
+          conda activate ocp-tool
+          pip install -e .
+          ```
+          
+          ## Container Installation
+          
+          ### Docker
+          ```bash
+          docker pull ghcr.io/pgierz/ocp-tool:latest-production
+          ```
+          
+          ### Singularity
+          ```bash
+          singularity pull ocp-tool.sif oras://ghcr.io/pgierz/ocp-tool:latest-singularity
+          ```
+          EOF
+          
+          # Workflow documentation
+          cat > docs/source/workflow.md << 'EOF'
+          # Snakemake Workflow
+          
+          The OCP-tool provides a complete Snakemake workflow for automated processing.
+          
+          ## Configuration
+          
+          Edit `workflow/config/config.yaml`:
+          
+          ```yaml
+          res_num: 159
+          truncation_type: "linear"
+          exp_name_oifs: "abda"
+          grid_name_oce: "CORE2"
+          ```
+          
+          ## Execution
+          
+          ```bash
+          # Local execution
+          snakemake --cores 4 --use-conda
+          
+          # HPC cluster
+          snakemake --profile workflow/profiles/slurm
+          
+          # Container execution
+          docker run --rm -v $(pwd):/app/data ocp-tool:latest snakemake --cores 4
+          ```
+          
+          ## Workflow Rules
+          
+          - `prepare_gaussian_grids`: Process OpenIFS grid files
+          - `process_fesom_grid`: Handle ocean model grids  
+          - `modify_land_sea_mask`: Core LSM modification
+          - `generate_oasis_files`: Create OASIS3-MCT files
+          - `modify_runoff_maps`: Adjust runoff routing
+          - `generate_plots`: Create visualizations
+          EOF
+          
+          # Examples page
+          cat > docs/source/examples.md << 'EOF'
+          # Examples
+          
+          ## Basic Usage
+          
+          ```python
+          from ocp_tool import ocp_tool
+          
+          # Generate coordinate and area fields
+          center_lats, center_lons, crn_lats, crn_lons, gridcell_area, lons_list, NN = \
+              ocp_tool.generate_coord_area(
+                  res_num=159,
+                  input_path_reduced_grid="input/gaussian_grids_linear_reduced/",
+                  input_path_full_grid="input/gaussian_grids_full/",
+                  truncation_type="linear"
+              )
+          ```
+          
+          ## Workflow Examples
+          
+          See the `workflow/` directory for complete Snakemake workflow examples.
+          EOF
+      
+      - name: Build Sphinx documentation
+        run: |
+          cd docs
+          sphinx-build -W -b html source build/html
+      
+      - name: Upload documentation artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: documentation
+          path: docs/build/html/
+          retention-days: 30
+
+  deploy-docs:
+    name: Deploy Documentation
+    runs-on: ubuntu-latest
+    needs: build-docs
+    if: github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main'
+    
+    permissions:
+      contents: read
+      pages: write
+      id-token: write
+    
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    
+    steps:
+      - name: Download documentation artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: documentation
+          path: ./docs
+      
+      - name: Setup Pages
+        uses: actions/configure-pages@v4
+      
+      - name: Upload to GitHub Pages
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: ./docs
+      
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4
+
+  link-check:
+    name: Check Documentation Links
+    runs-on: ubuntu-latest
+    needs: build-docs
+    
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+      
+      - name: Download documentation artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: documentation
+          path: ./docs
+      
+      - name: Check HTML links
+        uses: lycheeverse/lychee-action@v1
+        with:
+          args: --verbose --no-progress --exclude-all-private docs/**/*.html
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
\ No newline at end of file
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
new file mode 100644
index 0000000..c0d24a6
--- /dev/null
+++ b/.github/workflows/release.yml
@@ -0,0 +1,211 @@
+name: Release
+
+on:
+  push:
+    tags:
+      - 'v*'
+  workflow_dispatch:
+    inputs:
+      tag:
+        description: 'Release tag'
+        required: true
+        type: string
+
+jobs:
+  create-release:
+    name: Create Release
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      packages: write
+    
+    outputs:
+      upload_url: ${{ steps.create_release.outputs.upload_url }}
+      version: ${{ steps.get_version.outputs.version }}
+    
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      
+      - name: Get version
+        id: get_version
+        run: |
+          if [ "${{ github.event_name }}" = "workflow_dispatch" ]; then
+            VERSION="${{ github.event.inputs.tag }}"
+          else
+            VERSION=${GITHUB_REF#refs/tags/}
+          fi
+          echo "version=${VERSION}" >> $GITHUB_OUTPUT
+      
+      - name: Generate changelog
+        id: changelog
+        run: |
+          # Generate changelog from git commits since last tag
+          LAST_TAG=$(git describe --tags --abbrev=0 HEAD^ 2>/dev/null || echo "")
+          if [ -z "$LAST_TAG" ]; then
+            CHANGES=$(git log --pretty=format:"- %s (%h)" --no-merges)
+          else
+            CHANGES=$(git log ${LAST_TAG}..HEAD --pretty=format:"- %s (%h)" --no-merges)
+          fi
+          
+          cat > CHANGELOG.md << EOF
+          # Changes in ${{ steps.get_version.outputs.version }}
+          
+          ${CHANGES}
+          
+          ## Full Changelog
+          
+          See [commits](https://github.com/${{ github.repository }}/compare/${LAST_TAG}...${{ steps.get_version.outputs.version }}) for full details.
+          EOF
+      
+      - name: Create Release
+        id: create_release
+        uses: actions/create-release@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          tag_name: ${{ steps.get_version.outputs.version }}
+          release_name: Release ${{ steps.get_version.outputs.version }}
+          body_path: CHANGELOG.md
+          draft: false
+          prerelease: ${{ contains(steps.get_version.outputs.version, '-') }}
+
+  build-release-containers:
+    name: Build Release Containers
+    needs: create-release
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+    
+    strategy:
+      matrix:
+        target: [production, development]
+    
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+      
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+      
+      - name: Log in to Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      
+      - name: Extract metadata
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ghcr.io/${{ github.repository }}
+          flavor: |
+            suffix=-${{ matrix.target }}
+          tags: |
+            type=semver,pattern={{version}}
+            type=semver,pattern={{major}}.{{minor}}
+            type=semver,pattern={{major}}
+      
+      - name: Build and push release image
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: workflow/containers/Dockerfile
+          target: ${{ matrix.target }}
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+          platforms: linux/amd64,linux/arm64
+
+  build-singularity-release:
+    name: Build Singularity Release
+    needs: create-release
+    runs-on: ubuntu-latest
+    
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+      
+      - name: Setup Singularity
+        uses: eWaterCycle/setup-singularity@v7
+        with:
+          singularity-version: 3.11.4
+      
+      - name: Build Singularity container
+        run: |
+          sudo singularity build ocp-tool-${{ needs.create-release.outputs.version }}.sif workflow/containers/singularity.def
+      
+      - name: Upload Singularity image to release
+        uses: actions/upload-release-asset@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          upload_url: ${{ needs.create-release.outputs.upload_url }}
+          asset_path: ./ocp-tool-${{ needs.create-release.outputs.version }}.sif
+          asset_name: ocp-tool-${{ needs.create-release.outputs.version }}.sif
+          asset_content_type: application/octet-stream
+
+  upload-workflow-assets:
+    name: Upload Workflow Assets
+    needs: create-release
+    runs-on: ubuntu-latest
+    
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+      
+      - name: Create workflow archive
+        run: |
+          tar -czf ocp-tool-workflow-${{ needs.create-release.outputs.version }}.tar.gz \
+            workflow/ \
+            environment.yaml \
+            README.md \
+            --exclude='workflow/logs' \
+            --exclude='workflow/temp'
+      
+      - name: Upload workflow archive to release
+        uses: actions/upload-release-asset@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          upload_url: ${{ needs.create-release.outputs.upload_url }}
+          asset_path: ./ocp-tool-workflow-${{ needs.create-release.outputs.version }}.tar.gz
+          asset_name: ocp-tool-workflow-${{ needs.create-release.outputs.version }}.tar.gz
+          asset_content_type: application/gzip
+
+  notify-release:
+    name: Notify Release
+    needs: [create-release, build-release-containers, build-singularity-release]
+    runs-on: ubuntu-latest
+    if: always()
+    
+    steps:
+      - name: Create release summary
+        run: |
+          cat > $GITHUB_STEP_SUMMARY << EOF
+          # 🚀 Release ${{ needs.create-release.outputs.version }} Complete
+          
+          ## 📦 Available Assets
+          
+          - **Docker Images**: \`ghcr.io/${{ github.repository }}:${{ needs.create-release.outputs.version }}-production\`
+          - **Development Image**: \`ghcr.io/${{ github.repository }}:${{ needs.create-release.outputs.version }}-development\`  
+          - **Singularity Container**: \`ocp-tool-${{ needs.create-release.outputs.version }}.sif\`
+          - **Workflow Archive**: \`ocp-tool-workflow-${{ needs.create-release.outputs.version }}.tar.gz\`
+          
+          ## 🐳 Quick Start with Docker
+          
+          \`\`\`bash
+          docker pull ghcr.io/${{ github.repository }}:${{ needs.create-release.outputs.version }}-production
+          docker run --rm -v \$(pwd):/app/data ghcr.io/${{ github.repository }}:${{ needs.create-release.outputs.version }}-production snakemake --cores 4
+          \`\`\`
+          
+          ## 📖 Documentation
+          
+          Visit the [documentation](https://${{ github.repository_owner }}.github.io/ocp-tool/) for usage guides and API reference.
+          EOF
\ No newline at end of file

From ef15bbac8bd15a545902bde8f4b7c2cdf9432a54 Mon Sep 17 00:00:00 2001
From: Paul Gierz <pgierz@awi.de>
Date: Thu, 4 Sep 2025 16:02:45 +0200
Subject: [PATCH 02/10] Add temporary push triggers to register workflows

---
 .github/workflows/build-containers.yml | 2 +-
 .github/workflows/ci.yml               | 2 +-
 .github/workflows/docs.yml             | 2 +-
 .github/workflows/release.yml          | 2 ++
 4 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/build-containers.yml b/.github/workflows/build-containers.yml
index 5c26e0d..4f4fa8c 100644
--- a/.github/workflows/build-containers.yml
+++ b/.github/workflows/build-containers.yml
@@ -2,7 +2,7 @@ name: Build and Push Containers
 
 on:
   push:
-    branches: [ master, main ]
+    branches: [ master, main, awi-hpc/pgierz/feat/ci ]
     tags: [ 'v*' ]
   pull_request:
     branches: [ master, main ]
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 3b88ebd..b138663 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -2,7 +2,7 @@ name: CI
 
 on:
   push:
-    branches: [ master, main, develop ]
+    branches: [ master, main, develop, awi-hpc/pgierz/feat/ci ]
   pull_request:
     branches: [ master, main ]
   workflow_dispatch:
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 4cd76c0..5414d7b 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -2,7 +2,7 @@ name: Documentation
 
 on:
   push:
-    branches: [ master, main ]
+    branches: [ master, main, awi-hpc/pgierz/feat/ci ]
     paths:
       - 'docs/**'
       - '**.md'
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index c0d24a6..453b2d3 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -4,6 +4,8 @@ on:
   push:
     tags:
       - 'v*'
+    branches:
+      - awi-hpc/pgierz/feat/ci
   workflow_dispatch:
     inputs:
       tag:

From 664ad7e3ccbad9a3387623d712f0415fdeafd65e Mon Sep 17 00:00:00 2001
From: Paul Gierz <pgierz@awi.de>
Date: Thu, 4 Sep 2025 16:03:33 +0200
Subject: [PATCH 03/10] Remove temporary push triggers after workflow
 registration

---
 .github/workflows/build-containers.yml | 2 +-
 .github/workflows/ci.yml               | 2 +-
 .github/workflows/docs.yml             | 2 +-
 .github/workflows/release.yml          | 2 --
 4 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/build-containers.yml b/.github/workflows/build-containers.yml
index 4f4fa8c..5c26e0d 100644
--- a/.github/workflows/build-containers.yml
+++ b/.github/workflows/build-containers.yml
@@ -2,7 +2,7 @@ name: Build and Push Containers
 
 on:
   push:
-    branches: [ master, main, awi-hpc/pgierz/feat/ci ]
+    branches: [ master, main ]
     tags: [ 'v*' ]
   pull_request:
     branches: [ master, main ]
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index b138663..3b88ebd 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -2,7 +2,7 @@ name: CI
 
 on:
   push:
-    branches: [ master, main, develop, awi-hpc/pgierz/feat/ci ]
+    branches: [ master, main, develop ]
   pull_request:
     branches: [ master, main ]
   workflow_dispatch:
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 5414d7b..4cd76c0 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -2,7 +2,7 @@ name: Documentation
 
 on:
   push:
-    branches: [ master, main, awi-hpc/pgierz/feat/ci ]
+    branches: [ master, main ]
     paths:
       - 'docs/**'
       - '**.md'
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 453b2d3..c0d24a6 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -4,8 +4,6 @@ on:
   push:
     tags:
       - 'v*'
-    branches:
-      - awi-hpc/pgierz/feat/ci
   workflow_dispatch:
     inputs:
       tag:

From ed599e68f021cc175ebf1511b490c59b13daae34 Mon Sep 17 00:00:00 2001
From: Paul Gierz <pgierz@awi.de>
Date: Thu, 4 Sep 2025 16:35:58 +0200
Subject: [PATCH 04/10] Convert to modern pyproject.toml with pixi support

- Replace setup.py with comprehensive pyproject.toml
- Add pixi configuration with multiple environments (dev, jupyter, docs)
- Update CI workflows to use pixi instead of micromamba
- Add version info to ocp_tool package
- Include useful pixi tasks for development workflow
---
 .github/workflows/ci.yml   |  80 ++++++-----------
 .github/workflows/docs.yml |  27 ++----
 ocp_tool/__init__.py       |   3 +
 pyproject.toml             | 180 +++++++++++++++++++++++++++++++++++++
 4 files changed, 214 insertions(+), 76 deletions(-)
 create mode 100644 pyproject.toml

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 3b88ebd..38fdb87 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -19,51 +19,34 @@ jobs:
       - name: Checkout code
         uses: actions/checkout@v4
       
-      - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1
+      - name: Setup Pixi
+        uses: prefix-dev/setup-pixi@v0.8.1
         with:
-          environment-file: environment.yaml
-          environment-name: ocp-tool
-          cache-environment: true
-          cache-downloads: true
-          generate-run-shell: true
-      
-      - name: Install Snakemake
-        shell: micromamba-shell {0}
-        run: |
-          micromamba install -y -c conda-forge -c bioconda snakemake>=7.0
+          environments: dev
           
       - name: Lint Snakefile
-        shell: micromamba-shell {0}
-        run: |
-          cd workflow
-          snakemake --lint
+        run: pixi run workflow-lint
       
       - name: Validate workflow configuration
-        shell: micromamba-shell {0}
         run: |
-          cd workflow
-          python -c "import yaml; yaml.safe_load(open('config/config.yaml'))"
+          pixi run -e dev python -c "import yaml; yaml.safe_load(open('workflow/config/config.yaml'))"
           echo "✓ Configuration file is valid YAML"
       
       - name: Check Python scripts syntax
-        shell: micromamba-shell {0}
         run: |
-          python -m py_compile ocp-tool.py
-          python -m py_compile ocp_tool/*.py
-          find workflow/scripts -name "*.py" -exec python -m py_compile {} +
+          pixi run -e dev python -m py_compile ocp-tool.py
+          pixi run -e dev python -m py_compile ocp_tool/*.py
+          find workflow/scripts -name "*.py" -exec pixi run -e dev python -m py_compile {} +
           echo "✓ All Python scripts have valid syntax"
       
       - name: Dry run Snakemake workflow
-        shell: micromamba-shell {0}
         run: |
-          cd workflow
           # Create minimal test data structure
-          mkdir -p ../input/{gaussian_grids_full,gaussian_grids_linear_reduced,openifs_input_default,runoff_map_default,fesom_mesh}
-          mkdir -p ../output/{openifs_input_modified,oasis_mct3_input,runoff_map_modified,plots}
+          mkdir -p input/{gaussian_grids_full,gaussian_grids_linear_reduced,openifs_input_default,runoff_map_default,fesom_mesh}
+          mkdir -p output/{openifs_input_modified,oasis_mct3_input,runoff_map_modified,plots}
           
           # Test dry run with modified config for CI
-          cat > test_config.yaml << EOF
+          cat > workflow/test_config.yaml << EOF
           res_num: 159
           truncation_type: "linear"
           exp_name_oifs: "test"
@@ -76,13 +59,12 @@ jobs:
           manual_basin_removal: []
           EOF
           
-          snakemake --dry-run --configfile test_config.yaml
+          pixi run workflow-dry --configfile test_config.yaml
           echo "✓ Snakemake workflow dry run successful"
       
       - name: Test import of ocp_tool modules
-        shell: micromamba-shell {0}
         run: |
-          python -c "
+          pixi run -e dev python -c "
           import sys
           sys.path.insert(0, '.')
           from ocp_tool import ocp_tool
@@ -97,30 +79,25 @@ jobs:
       - name: Checkout code
         uses: actions/checkout@v4
       
-      - name: Setup Python
-        uses: actions/setup-python@v4
+      - name: Setup Pixi
+        uses: prefix-dev/setup-pixi@v0.8.1
         with:
-          python-version: "3.9"
-      
-      - name: Install linting tools
-        run: |
-          pip install --upgrade pip
-          pip install flake8 black isort mypy
+          environments: dev
       
       - name: Run flake8
         run: |
           # Stop the build if there are Python syntax errors or undefined names
-          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --exclude=.git,__pycache__,build,dist
+          pixi run -e dev flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --exclude=.git,__pycache__,build,dist
           # Exit-zero treats all errors as warnings
-          flake8 . --count --exit-zero --max-complexity=15 --max-line-length=120 --statistics --exclude=.git,__pycache__,build,dist
+          pixi run -e dev flake8 . --count --exit-zero --max-complexity=15 --max-line-length=120 --statistics --exclude=.git,__pycache__,build,dist
       
       - name: Check code formatting with black
         run: |
-          black --check --diff --exclude=.git . || echo "::warning::Code formatting issues found. Run 'black .' to fix."
+          pixi run -e dev black --check --diff --exclude=.git . || echo "::warning::Code formatting issues found. Run 'pixi run format' to fix."
       
       - name: Check import sorting with isort
         run: |
-          isort --check-only --diff . || echo "::warning::Import sorting issues found. Run 'isort .' to fix."
+          pixi run -e dev isort --check-only --diff . || echo "::warning::Import sorting issues found. Run 'pixi run sort-imports' to fix."
 
   notebook-tests:
     name: Test Jupyter Notebooks
@@ -130,19 +107,15 @@ jobs:
       - name: Checkout code
         uses: actions/checkout@v4
       
-      - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1
+      - name: Setup Pixi
+        uses: prefix-dev/setup-pixi@v0.8.1
         with:
-          environment-file: environment.yaml
-          environment-name: ocp-tool
-          cache-environment: true
-          generate-run-shell: true
+          environments: jupyter
       
       - name: Validate notebook structure
-        shell: micromamba-shell {0}
         run: |
-          pip install nbformat
-          python -c "
+          pixi run -e jupyter pip install nbformat
+          pixi run -e jupyter python -c "
           import nbformat
           import json
           
@@ -156,9 +129,8 @@ jobs:
           "
       
       - name: Check notebook for output clearing
-        shell: micromamba-shell {0}
         run: |
-          python -c "
+          pixi run -e jupyter python -c "
           import nbformat
           import sys
           
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 4cd76c0..f9f1303 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -28,27 +28,12 @@ jobs:
         with:
           fetch-depth: 0  # Full history for proper versioning
       
-      - name: Setup Python
-        uses: actions/setup-python@v4
+      - name: Setup Pixi
+        uses: prefix-dev/setup-pixi@v0.8.1
         with:
-          python-version: "3.9"
-      
-      - name: Install documentation dependencies
-        run: |
-          pip install --upgrade pip
-          pip install sphinx sphinx-rtd-theme nbsphinx pandoc
-          pip install myst-parser sphinx-autoapi
-      
-      - name: Setup Micromamba for environment
-        uses: mamba-org/setup-micromamba@v1
-        with:
-          environment-file: environment.yaml
-          environment-name: ocp-tool
-          cache-environment: true
-          generate-run-shell: true
+          environments: docs
       
       - name: Generate API documentation
-        shell: micromamba-shell {0}
         run: |
           # Create docs directory structure if it doesn't exist
           mkdir -p docs/{source,build}
@@ -131,10 +116,9 @@ jobs:
           fi
           
           # Build API docs with autoapi  
-          sphinx-apidoc -f -o docs/source/api ocp_tool
+          pixi run -e docs sphinx-apidoc -f -o docs/source/api ocp_tool
       
       - name: Convert notebooks for documentation
-        shell: micromamba-shell {0}
         run: |
           mkdir -p docs/source/notebooks
           
@@ -258,8 +242,7 @@ jobs:
       
       - name: Build Sphinx documentation
         run: |
-          cd docs
-          sphinx-build -W -b html source build/html
+          pixi run docs-build
       
       - name: Upload documentation artifact
         uses: actions/upload-artifact@v4
diff --git a/ocp_tool/__init__.py b/ocp_tool/__init__.py
index e69de29..ffb0900 100644
--- a/ocp_tool/__init__.py
+++ b/ocp_tool/__init__.py
@@ -0,0 +1,3 @@
+"""OCP-tool: OpenIFS Coupling Preparation Tool."""
+
+__version__ = "0.1.0"
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..d527d5f
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,180 @@
+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "ocp-tool"
+description = "Tool to generate OASIS files for coupling OpenIFS, FESOM2, and NEMO"
+authors = [
+    {name = "Jan Streffing", email = "jan.streffing@awi.de"}
+]
+readme = "README.md"
+license = {file = "licence"}
+requires-python = ">=3.8"
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Topic :: Scientific/Engineering :: Atmospheric Science",
+]
+dependencies = [
+    "numpy",
+    "netcdf4",
+    "eccodes",
+    "matplotlib",
+    "pandas",
+    "pyyaml",
+    "tqdm",
+    "pyfesom2 @ git+https://github.com/FESOM/pyfesom2.git",
+]
+dynamic = ["version"]
+
+[project.urls]
+Homepage = "https://github.com/pgierz/ocp-tool"
+Repository = "https://github.com/pgierz/ocp-tool"
+Issues = "https://github.com/pgierz/ocp-tool/issues"
+
+[project.entry-points."scriptengine.tasks"]
+"ocpt.main" = "ocp_tool.scriptengine_task:OCPTool"
+
+[project.optional-dependencies]
+dev = [
+    "pytest",
+    "pytest-cov",
+    "black",
+    "isort",
+    "flake8",
+    "mypy",
+]
+jupyter = [
+    "jupyterlab",
+    "notebook",
+    "ipykernel",
+]
+docs = [
+    "sphinx",
+    "sphinx-rtd-theme",
+    "nbsphinx",
+    "myst-parser",
+    "sphinx-autoapi",
+]
+
+[tool.setuptools]
+packages = ["ocp_tool"]
+
+[tool.setuptools.dynamic]
+version = {attr = "ocp_tool.__version__"}
+
+# Pixi configuration
+[tool.pixi.project]
+name = "ocp-tool"
+description = "Tool to generate OASIS files for coupling OpenIFS, FESOM2, and NEMO"
+authors = ["Jan Streffing <jan.streffing@awi.de>"]
+channels = ["conda-forge", "eumetsat"]
+platforms = ["linux-64", "osx-64", "osx-arm64"]
+
+[tool.pixi.dependencies]
+python = ">=3.8,<3.12"
+numpy = "*"
+netcdf4 = "*"
+matplotlib = "*"
+basemap = "*"
+pandas = "*"
+pyyaml = "*"
+python-eccodes = "*"
+git = "*"
+pip = "*"
+tqdm = "*"
+snakemake = ">=7.0"
+
+[tool.pixi.pypi-dependencies]
+pyfesom2 = { git = "https://github.com/FESOM/pyfesom2.git" }
+ocp-tool = { path = ".", editable = true }
+
+[tool.pixi.feature.jupyter.dependencies]
+jupyterlab = "*"
+notebook = "*"
+ipykernel = "*"
+
+[tool.pixi.feature.dev.dependencies]
+pytest = "*"
+pytest-cov = "*"
+black = "*"
+isort = "*"
+flake8 = "*"
+mypy = "*"
+
+[tool.pixi.feature.docs.dependencies]
+sphinx = "*"
+sphinx-rtd-theme = "*"
+nbsphinx = "*"
+myst-parser = "*"
+sphinx-autoapi = "*"
+
+[tool.pixi.environments]
+default = { solve-group = "default" }
+jupyter = { features = ["jupyter"], solve-group = "default" }
+dev = { features = ["dev"], solve-group = "default" }
+docs = { features = ["docs"], solve-group = "default" }
+full = { features = ["jupyter", "dev", "docs"], solve-group = "default" }
+
+[tool.pixi.tasks]
+lint = "flake8 ocp_tool"
+format = "black ocp_tool"
+sort-imports = "isort ocp_tool"
+type-check = "mypy ocp_tool"
+test = "pytest"
+clean-format = { depends_on = ["format", "sort-imports"] }
+jupyter = "jupyter lab"
+notebook = "jupyter notebook"
+docs-build = "sphinx-build -W -b html docs/source docs/build/html"
+docs-clean = "rm -rf docs/build"
+docs-serve = "python -m http.server 8000 --directory docs/build/html"
+workflow-dry = { cmd = "snakemake --dry-run", cwd = "workflow" }
+workflow-lint = { cmd = "snakemake --lint", cwd = "workflow" }
+workflow-run = { cmd = "snakemake --cores 4 --use-conda", cwd = "workflow" }
+build = "python -m build"
+install-dev = "pip install -e ."
+
+[tool.black]
+line-length = 88
+target-version = ['py38']
+include = '\.pyi?$'
+extend-exclude = '''
+/(
+  # directories
+  \.eggs
+  | \.git
+  | \.hg
+  | \.mypy_cache
+  | \.tox
+  | \.venv
+  | build
+  | dist
+)/
+'''
+
+[tool.isort]
+profile = "black"
+multi_line_output = 3
+line_length = 88
+known_first_party = ["ocp_tool"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+python_files = ["test_*.py", "*_test.py"]
+python_classes = ["Test*"]
+python_functions = ["test_*"]
+addopts = [
+    "--strict-markers",
+    "--strict-config",
+    "--cov=ocp_tool",
+    "--cov-report=term-missing",
+    "--cov-report=html",
+]
\ No newline at end of file

From 48c832e489c05c043a5a065810e65591463dabbf Mon Sep 17 00:00:00 2001
From: Paul Gierz <pgierz@awi.de>
Date: Thu, 4 Sep 2025 16:38:25 +0200
Subject: [PATCH 05/10] Fix duplicate pyfesom2 dependency in pyproject.toml

Remove pyfesom2 from main dependencies to avoid conflict with pixi-dependencies section
---
 pyproject.toml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index d527d5f..0fdc5f8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -31,7 +31,6 @@ dependencies = [
     "pandas",
     "pyyaml",
     "tqdm",
-    "pyfesom2 @ git+https://github.com/FESOM/pyfesom2.git",
 ]
 dynamic = ["version"]
 

From eab32b468a3a95182ee689ecb1193a9f77ca366f Mon Sep 17 00:00:00 2001
From: Paul Gierz <pgierz@awi.de>
Date: Thu, 4 Sep 2025 16:54:59 +0200
Subject: [PATCH 06/10] Fix pixi configuration issues and add workflow README

- Replace snakemake with snakemake-minimal for better compatibility
- Add bioconda channel for snakemake-minimal
- Fix deprecated depends_on to depends-on syntax
- Add missing workflow/README.md for documentation check
---
 pyproject.toml     |  6 +++---
 workflow/README.md | 35 +++++++++++++++++++++++++++++++++++
 2 files changed, 38 insertions(+), 3 deletions(-)
 create mode 100644 workflow/README.md

diff --git a/pyproject.toml b/pyproject.toml
index 0fdc5f8..13275e1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -75,7 +75,7 @@ version = {attr = "ocp_tool.__version__"}
 name = "ocp-tool"
 description = "Tool to generate OASIS files for coupling OpenIFS, FESOM2, and NEMO"
 authors = ["Jan Streffing <jan.streffing@awi.de>"]
-channels = ["conda-forge", "eumetsat"]
+channels = ["conda-forge", "bioconda", "eumetsat"]
 platforms = ["linux-64", "osx-64", "osx-arm64"]
 
 [tool.pixi.dependencies]
@@ -90,7 +90,7 @@ python-eccodes = "*"
 git = "*"
 pip = "*"
 tqdm = "*"
-snakemake = ">=7.0"
+snakemake-minimal = ">=7.0"
 
 [tool.pixi.pypi-dependencies]
 pyfesom2 = { git = "https://github.com/FESOM/pyfesom2.git" }
@@ -129,7 +129,7 @@ format = "black ocp_tool"
 sort-imports = "isort ocp_tool"
 type-check = "mypy ocp_tool"
 test = "pytest"
-clean-format = { depends_on = ["format", "sort-imports"] }
+clean-format = { depends-on = ["format", "sort-imports"] }
 jupyter = "jupyter lab"
 notebook = "jupyter notebook"
 docs-build = "sphinx-build -W -b html docs/source docs/build/html"
diff --git a/workflow/README.md b/workflow/README.md
new file mode 100644
index 0000000..988ceb7
--- /dev/null
+++ b/workflow/README.md
@@ -0,0 +1,35 @@
+# OCP-tool Snakemake Workflow
+
+This directory contains the Snakemake workflow for automated climate model preparation.
+
+## Usage
+
+Configure your settings in `config/config.yaml`, then run:
+
+```bash
+# Local execution  
+snakemake --cores 4
+
+# With pixi
+pixi run workflow-run
+
+# Dry run to check workflow
+pixi run workflow-dry
+```
+
+## Configuration
+
+Edit `config/config.yaml` to specify:
+- Grid resolution (`res_num`)  
+- Experiment name (`exp_name_oifs`)
+- Ocean grid name (`grid_name_oce`)
+- Input/output paths
+
+## Rules
+
+- `prepare_gaussian_grids`: Process OpenIFS grid files
+- `process_fesom_grid`: Handle ocean model grids
+- `modify_land_sea_mask`: Core LSM modification  
+- `generate_oasis_files`: Create OASIS3-MCT files
+- `modify_runoff_maps`: Adjust runoff routing
+- `generate_plots`: Create visualizations
\ No newline at end of file

From 178e9707f4d9963091fda5f98fba608ff99df383 Mon Sep 17 00:00:00 2001
From: Paul Gierz <pgierz@awi.de>
Date: Thu, 4 Sep 2025 16:57:15 +0200
Subject: [PATCH 07/10] Fix Python version compatibility issues

- Remove obsolete setup.py that was causing version conflicts
- Update Python version constraint to >=3.8,<3.12 in pyproject.toml
- This resolves pixi installation failures in CI due to Python 3.11 incompatibility
---
 .claude/settings.local.json | 24 ++++++++++++++++++++++++
 pyproject.toml              |  2 +-
 setup.py                    | 23 -----------------------
 3 files changed, 25 insertions(+), 24 deletions(-)
 create mode 100644 .claude/settings.local.json
 delete mode 100644 setup.py

diff --git a/.claude/settings.local.json b/.claude/settings.local.json
new file mode 100644
index 0000000..88eb830
--- /dev/null
+++ b/.claude/settings.local.json
@@ -0,0 +1,24 @@
+{
+  "permissions": {
+    "allow": [
+      "Bash(grep:*)",
+      "Bash(chmod:*)",
+      "Bash(mkdir:*)",
+      "Bash(git checkout:*)",
+      "Bash(git config:*)",
+      "Bash(git show:*)",
+      "Bash(git push:*)",
+      "Bash(gh workflow run:*)",
+      "Bash(gh run list:*)",
+      "Bash(git add:*)",
+      "Bash(git commit:*)",
+      "Bash(gh run view:*)",
+      "Bash(gh api:*)"
+    ],
+    "deny": [],
+    "ask": [],
+    "additionalDirectories": [
+      "/Users/pgierz/.local/sbin"
+    ]
+  }
+}
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 13275e1..5871d28 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -10,7 +10,7 @@ authors = [
 ]
 readme = "README.md"
 license = {file = "licence"}
-requires-python = ">=3.8"
+requires-python = ">=3.8,<3.12"
 classifiers = [
     "Development Status :: 4 - Beta",
     "Intended Audience :: Science/Research",
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 7fd3247..0000000
--- a/setup.py
+++ /dev/null
@@ -1,23 +0,0 @@
-import setuptools
-
-
-setuptools.setup(
-    name='ocp-tool',
-    author='Jan Streffing',
-    author_email='jan.streffing@awi.de',
-    description='Tool to generate OASIS files for coupling OpenIFS, FESOM2, and NEMO',
-    url='https://github.com/JanStreffing/ocp-tool',
-    packages=setuptools.find_packages(),
-    python_requires='>=3.6',
-    install_requires=[
-        'numpy',
-        'netcdf4',
-        'eccodes',
-        'pyfesom2',
-    ],
-    entry_points={
-        'scriptengine.tasks': [
-            'ocpt.main = ocp_tool.scriptengine_task:OCPTool',
-        ],
-    },
-)

From 20bd340c9461a19d0e261ec355cb1e2db46f8f11 Mon Sep 17 00:00:00 2001
From: Paul Gierz <pgierz@awi.de>
Date: Thu, 4 Sep 2025 17:06:10 +0200
Subject: [PATCH 08/10] Fix Python compatibility and platform support

- Remove pyfesom2 from pypi-dependencies due to its Python <3.10 restriction
- Remove self-referential ocp-tool installation from pypi-dependencies
- Support all Python versions >=3.8 (no upper limit)
- Add linux-aarch64 platform support for ARM servers
- This should resolve all pixi installation issues in CI
---
 pyproject.toml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 5871d28..0b67d1f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -10,7 +10,7 @@ authors = [
 ]
 readme = "README.md"
 license = {file = "licence"}
-requires-python = ">=3.8,<3.12"
+requires-python = ">=3.8"
 classifiers = [
     "Development Status :: 4 - Beta",
     "Intended Audience :: Science/Research",
@@ -76,10 +76,10 @@ name = "ocp-tool"
 description = "Tool to generate OASIS files for coupling OpenIFS, FESOM2, and NEMO"
 authors = ["Jan Streffing <jan.streffing@awi.de>"]
 channels = ["conda-forge", "bioconda", "eumetsat"]
-platforms = ["linux-64", "osx-64", "osx-arm64"]
+platforms = ["linux-64", "linux-aarch64", "osx-64", "osx-arm64"]
 
 [tool.pixi.dependencies]
-python = ">=3.8,<3.12"
+python = ">=3.8"
 numpy = "*"
 netcdf4 = "*"
 matplotlib = "*"
@@ -93,8 +93,8 @@ tqdm = "*"
 snakemake-minimal = ">=7.0"
 
 [tool.pixi.pypi-dependencies]
-pyfesom2 = { git = "https://github.com/FESOM/pyfesom2.git" }
-ocp-tool = { path = ".", editable = true }
+# pyfesom2 has Python <3.10 restriction, skip for now
+# pyfesom2 = { git = "https://github.com/FESOM/pyfesom2.git" }
 
 [tool.pixi.feature.jupyter.dependencies]
 jupyterlab = "*"

From 0e41c4225aa5d80ab67af16020f025fce67ee6b2 Mon Sep 17 00:00:00 2001
From: Paul Gierz <pgierz@awi.de>
Date: Thu, 4 Sep 2025 23:57:15 +0200
Subject: [PATCH 09/10] Enable pyfesom2 dependency with modernized packaging
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

- Re-enabled pyfesom2 dependency using modernize-packaging branch
- Verified local pixi configuration validates successfully
- Tested CI workflows locally using act tool
- All environments (dev, docs, jupyter, full) properly configured

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>
---
 .claude/settings.local.json | 22 +++++-----------------
 pyproject.toml              |  4 ++--
 2 files changed, 7 insertions(+), 19 deletions(-)

diff --git a/.claude/settings.local.json b/.claude/settings.local.json
index 88eb830..bacae49 100644
--- a/.claude/settings.local.json
+++ b/.claude/settings.local.json
@@ -1,24 +1,12 @@
 {
   "permissions": {
     "allow": [
-      "Bash(grep:*)",
-      "Bash(chmod:*)",
-      "Bash(mkdir:*)",
-      "Bash(git checkout:*)",
-      "Bash(git config:*)",
-      "Bash(git show:*)",
-      "Bash(git push:*)",
-      "Bash(gh workflow run:*)",
-      "Bash(gh run list:*)",
-      "Bash(git add:*)",
-      "Bash(git commit:*)",
-      "Bash(gh run view:*)",
-      "Bash(gh api:*)"
+      "Bash(git cherry-pick:*)",
+      "Bash(gh:*)",
+      "Bash(act:*)",
+      "Bash(pixi install:*)"
     ],
     "deny": [],
-    "ask": [],
-    "additionalDirectories": [
-      "/Users/pgierz/.local/sbin"
-    ]
+    "ask": []
   }
 }
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 0b67d1f..99541d3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -93,8 +93,8 @@ tqdm = "*"
 snakemake-minimal = ">=7.0"
 
 [tool.pixi.pypi-dependencies]
-# pyfesom2 has Python <3.10 restriction, skip for now
-# pyfesom2 = { git = "https://github.com/FESOM/pyfesom2.git" }
+# Use modernized pyfesom2 branch with Python 3.11+ support
+pyfesom2 = { git = "https://github.com/FESOM/pyfesom2.git", branch = "modernize-packaging" }
 
 [tool.pixi.feature.jupyter.dependencies]
 jupyterlab = "*"

From e9381c0a800aba0ed3e0eb701d477ff9b71d18d1 Mon Sep 17 00:00:00 2001
From: Paul Gierz <pgierz@awi.de>
Date: Fri, 5 Sep 2025 07:39:46 +0200
Subject: [PATCH 10/10] Update Claude Code permissions for git operations

---
 .claude/settings.local.json | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.claude/settings.local.json b/.claude/settings.local.json
index bacae49..82d6d15 100644
--- a/.claude/settings.local.json
+++ b/.claude/settings.local.json
@@ -4,7 +4,8 @@
       "Bash(git cherry-pick:*)",
       "Bash(gh:*)",
       "Bash(act:*)",
-      "Bash(pixi install:*)"
+      "Bash(pixi install:*)",
+      "Bash(git for-each-ref:*)"
     ],
     "deny": [],
     "ask": []