From 0a3e6b4505e148e6a82faf45005e8c711b9133cc Mon Sep 17 00:00:00 2001
From: Jan Streffing <jan.streffing@awi.de>
Date: Tue, 16 Dec 2025 09:20:33 +0100
Subject: [PATCH 01/18] Add CI/CD workflows and modern packaging from PR #33

---
 .github/markdown-link-check-config.json |  31 +++
 .github/workflows/build-containers.yml  | 235 ++++++++++++++++++
 .github/workflows/ci.yml                | 154 ++++++++++++
 .github/workflows/docs.yml              | 308 ++++++++++++++++++++++++
 .github/workflows/release.yml           | 211 ++++++++++++++++
 pyproject.toml                          | 179 ++++++++++++++
 workflow/README.md                      |  35 +++
 7 files changed, 1153 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
 create mode 100644 pyproject.toml
 create mode 100644 workflow/README.md

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..d8fb21e
--- /dev/null
+++ b/.github/workflows/ci.yml
@@ -0,0 +1,154 @@
+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 Pixi
+        uses: prefix-dev/setup-pixi@v0.8.1
+        with:
+          environments: dev
+          
+      - name: Lint Snakefile
+        run: pixi run workflow-lint
+      
+      - name: Validate workflow configuration
+        run: |
+          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
+        run: |
+          pixi run -e dev python -m py_compile run_ocp_tool.py
+          pixi run -e dev python -m py_compile ocp_tool/*.py
+          echo "✓ All Python scripts have valid syntax"
+      
+      - name: Dry run Snakemake workflow
+        run: |
+          # 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 > workflow/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
+          
+          pixi run workflow-dry --configfile test_config.yaml
+          echo "✓ Snakemake workflow dry run successful"
+      
+      - name: Test import of ocp_tool modules
+        run: |
+          pixi run -e dev python -c "
+          import sys
+          sys.path.insert(0, '.')
+          from ocp_tool.config import load_config
+          from ocp_tool.gaussian_grids import generate_gaussian_grid
+          from ocp_tool.lsm import process_land_sea_mask
+          print('✓ Successfully imported ocp_tool modules')
+          "
+
+  code-quality:
+    name: Code Quality Checks
+    runs-on: ubuntu-latest
+    
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+      
+      - name: Setup Pixi
+        uses: prefix-dev/setup-pixi@v0.8.1
+        with:
+          environments: dev
+      
+      - name: Run flake8
+        run: |
+          # Stop the build if there are Python syntax errors or undefined names
+          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
+          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: |
+          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: |
+          pixi run -e dev isort --check-only --diff . || echo "::warning::Import sorting issues found. Run 'pixi run sort-imports' to fix."
+
+  # Notebook tests removed - notebooks no longer in repo
+
+  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..f9f1303
--- /dev/null
+++ b/.github/workflows/docs.yml
@@ -0,0 +1,308 @@
+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 Pixi
+        uses: prefix-dev/setup-pixi@v0.8.1
+        with:
+          environments: docs
+      
+      - name: Generate API documentation
+        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  
+          pixi run -e docs sphinx-apidoc -f -o docs/source/api ocp_tool
+      
+      - name: Convert notebooks for documentation
+        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: |
+          pixi run docs-build
+      
+      - 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
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..99541d3
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,179 @@
+[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",
+]
+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", "bioconda", "eumetsat"]
+platforms = ["linux-64", "linux-aarch64", "osx-64", "osx-arm64"]
+
+[tool.pixi.dependencies]
+python = ">=3.8"
+numpy = "*"
+netcdf4 = "*"
+matplotlib = "*"
+basemap = "*"
+pandas = "*"
+pyyaml = "*"
+python-eccodes = "*"
+git = "*"
+pip = "*"
+tqdm = "*"
+snakemake-minimal = ">=7.0"
+
+[tool.pixi.pypi-dependencies]
+# 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 = "*"
+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
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 5d1d2a6d803406025601afd11fef792fd6f05b2a Mon Sep 17 00:00:00 2001
From: Jan Streffing <jan.streffing@awi.de>
Date: Tue, 16 Dec 2025 09:23:11 +0100
Subject: [PATCH 02/18] Remove container build workflow (Dockerfile not
 available)

---
 .github/workflows/build-containers.yml | 235 -------------------------
 1 file changed, 235 deletions(-)
 delete mode 100644 .github/workflows/build-containers.yml

diff --git a/.github/workflows/build-containers.yml b/.github/workflows/build-containers.yml
deleted file mode 100644
index 5c26e0d..0000000
--- a/.github/workflows/build-containers.yml
+++ /dev/null
@@ -1,235 +0,0 @@
-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

From 7a78e71bf6ed55d1d52bb9dc4563096cf92c3e50 Mon Sep 17 00:00:00 2001
From: Jan Streffing <jan.streffing@awi.de>
Date: Tue, 16 Dec 2025 09:25:28 +0100
Subject: [PATCH 03/18] Fix CI: update pixi config syntax and remove Snakemake
 steps

---
 .github/workflows/ci.yml | 37 +++----------------------------------
 pyproject.toml           |  2 +-
 2 files changed, 4 insertions(+), 35 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d8fb21e..2389aae 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -8,12 +8,12 @@ on:
   workflow_dispatch:
 
 jobs:
-  test-workflow:
-    name: Test Snakemake Workflow
+  test-python:
+    name: Test Python Code
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11"]
     
     steps:
       - name: Checkout code
@@ -23,14 +23,6 @@ jobs:
         uses: prefix-dev/setup-pixi@v0.8.1
         with:
           environments: dev
-          
-      - name: Lint Snakefile
-        run: pixi run workflow-lint
-      
-      - name: Validate workflow configuration
-        run: |
-          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
         run: |
@@ -38,29 +30,6 @@ jobs:
           pixi run -e dev python -m py_compile ocp_tool/*.py
           echo "✓ All Python scripts have valid syntax"
       
-      - name: Dry run Snakemake workflow
-        run: |
-          # 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 > workflow/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
-          
-          pixi run workflow-dry --configfile test_config.yaml
-          echo "✓ Snakemake workflow dry run successful"
-      
       - name: Test import of ocp_tool modules
         run: |
           pixi run -e dev python -c "
diff --git a/pyproject.toml b/pyproject.toml
index 99541d3..f5e5d7e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -71,7 +71,7 @@ packages = ["ocp_tool"]
 version = {attr = "ocp_tool.__version__"}
 
 # Pixi configuration
-[tool.pixi.project]
+[tool.pixi.workspace]
 name = "ocp-tool"
 description = "Tool to generate OASIS files for coupling OpenIFS, FESOM2, and NEMO"
 authors = ["Jan Streffing <jan.streffing@awi.de>"]

From 2ed97759885c4d7bfe8246263de563cf0ca7e9ea Mon Sep 17 00:00:00 2001
From: Jan Streffing <jan.streffing@awi.de>
Date: Tue, 16 Dec 2025 09:28:20 +0100
Subject: [PATCH 04/18] Fix docs workflow: use docs environment for
 sphinx-build

---
 .github/workflows/docs.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index f9f1303..700ff5b 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -242,7 +242,7 @@ jobs:
       
       - name: Build Sphinx documentation
         run: |
-          pixi run docs-build
+          pixi run -e docs sphinx-build -W -b html docs/source docs/build/html
       
       - name: Upload documentation artifact
         uses: actions/upload-artifact@v4

From b243346a4cc52afac62c94b841327466c48d732b Mon Sep 17 00:00:00 2001
From: Jan Streffing <jan.streffing@awi.de>
Date: Tue, 16 Dec 2025 09:31:21 +0100
Subject: [PATCH 05/18] Remove docs workflow (no docs folder, missing
 dependencies)

---
 .github/workflows/docs.yml | 308 -------------------------------------
 1 file changed, 308 deletions(-)
 delete mode 100644 .github/workflows/docs.yml

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
deleted file mode 100644
index 700ff5b..0000000
--- a/.github/workflows/docs.yml
+++ /dev/null
@@ -1,308 +0,0 @@
-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 Pixi
-        uses: prefix-dev/setup-pixi@v0.8.1
-        with:
-          environments: docs
-      
-      - name: Generate API documentation
-        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  
-          pixi run -e docs sphinx-apidoc -f -o docs/source/api ocp_tool
-      
-      - name: Convert notebooks for documentation
-        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: |
-          pixi run -e docs sphinx-build -W -b html docs/source docs/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

From dfd27e406acf5c67cb6aad8c31a9a0897ae62d45 Mon Sep 17 00:00:00 2001
From: Jan Streffing <jan.streffing@awi.de>
Date: Tue, 16 Dec 2025 09:33:00 +0100
Subject: [PATCH 06/18] Add Sphinx documentation and simplified docs workflow

---
 .github/workflows/docs.yml      | 45 +++++++++++++++++++++++++++++
 docs/source/_static/.gitkeep    |  0
 docs/source/_templates/.gitkeep |  0
 docs/source/api.rst             | 50 +++++++++++++++++++++++++++++++++
 docs/source/conf.py             | 25 +++++++++++++++++
 docs/source/index.rst           | 22 +++++++++++++++
 docs/source/installation.rst    | 28 ++++++++++++++++++
 docs/source/usage.rst           | 47 +++++++++++++++++++++++++++++++
 8 files changed, 217 insertions(+)
 create mode 100644 .github/workflows/docs.yml
 create mode 100644 docs/source/_static/.gitkeep
 create mode 100644 docs/source/_templates/.gitkeep
 create mode 100644 docs/source/api.rst
 create mode 100644 docs/source/conf.py
 create mode 100644 docs/source/index.rst
 create mode 100644 docs/source/installation.rst
 create mode 100644 docs/source/usage.rst

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
new file mode 100644
index 0000000..f8aac4c
--- /dev/null
+++ b/.github/workflows/docs.yml
@@ -0,0 +1,45 @@
+name: Documentation
+
+on:
+  push:
+    branches: [ master, main ]
+    paths:
+      - 'docs/**'
+      - 'ocp_tool/**'
+  pull_request:
+    branches: [ master, main ]
+    paths:
+      - 'docs/**'
+      - 'ocp_tool/**'
+  workflow_dispatch:
+
+jobs:
+  build-docs:
+    name: Build Documentation
+    runs-on: ubuntu-latest
+    
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+      
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      
+      - name: Install dependencies
+        run: |
+          pip install sphinx alabaster
+          pip install -e .
+      
+      - name: Build 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
diff --git a/docs/source/_static/.gitkeep b/docs/source/_static/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/docs/source/_templates/.gitkeep b/docs/source/_templates/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/docs/source/api.rst b/docs/source/api.rst
new file mode 100644
index 0000000..e67b0f0
--- /dev/null
+++ b/docs/source/api.rst
@@ -0,0 +1,50 @@
+API Reference
+=============
+
+Configuration
+-------------
+
+.. automodule:: ocp_tool.config
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Grid Processing
+---------------
+
+.. automodule:: ocp_tool.gaussian_grids
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Land-Sea Mask
+-------------
+
+.. automodule:: ocp_tool.lsm
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+OASIS Writer
+------------
+
+.. automodule:: ocp_tool.oasis_writer
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Runoff Processing
+-----------------
+
+.. automodule:: ocp_tool.runoff
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Plotting
+--------
+
+.. automodule:: ocp_tool.plotting
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/conf.py b/docs/source/conf.py
new file mode 100644
index 0000000..881aa1d
--- /dev/null
+++ b/docs/source/conf.py
@@ -0,0 +1,25 @@
+"""Sphinx configuration for OCP-Tool documentation."""
+
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../..'))
+
+project = 'OCP-Tool'
+copyright = '2024, AWI Climate Dynamics'
+author = 'Jan Streffing'
+
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.napoleon',
+]
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+html_theme = 'alabaster'
+html_static_path = ['_static']
+
+# Napoleon settings for Google/NumPy style docstrings
+napoleon_google_docstring = True
+napoleon_numpy_docstring = True
diff --git a/docs/source/index.rst b/docs/source/index.rst
new file mode 100644
index 0000000..47f0a32
--- /dev/null
+++ b/docs/source/index.rst
@@ -0,0 +1,22 @@
+OCP-Tool Documentation
+======================
+
+OpenIFS Coupling Preparation Tool for climate model coupling.
+
+OCP-Tool generates OASIS3-MCT input files, modifies the OpenIFS land-sea mask,
+and adjusts runoff maps to fit a given FESOM2 mesh or NEMO grid.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   installation
+   usage
+   api
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/docs/source/installation.rst b/docs/source/installation.rst
new file mode 100644
index 0000000..48c894b
--- /dev/null
+++ b/docs/source/installation.rst
@@ -0,0 +1,28 @@
+Installation
+============
+
+Requirements
+------------
+
+- Python 3.9+
+- NetCDF libraries
+- ECCODES for GRIB processing
+- CDO (Climate Data Operators)
+- NCO (NetCDF Operators)
+
+Quick Install
+-------------
+
+Using conda/mamba::
+
+    git clone https://github.com/JanStreffing/ocp-tool.git
+    cd ocp-tool
+    conda env create -f environment.yaml
+    conda activate ocp-tool
+    pip install -e .
+
+Using pixi::
+
+    git clone https://github.com/JanStreffing/ocp-tool.git
+    cd ocp-tool
+    pixi install
diff --git a/docs/source/usage.rst b/docs/source/usage.rst
new file mode 100644
index 0000000..4c58d73
--- /dev/null
+++ b/docs/source/usage.rst
@@ -0,0 +1,47 @@
+Usage
+=====
+
+Configuration
+-------------
+
+OCP-Tool uses YAML configuration files. Example configs are in the ``configs/`` directory:
+
+- ``TCO95_CORE2.yaml`` - TCO95 atmosphere with CORE2 ocean mesh
+- ``TCO319_CORE3.yaml`` - TCO319 atmosphere with CORE3 ocean mesh (with ice cavities)
+
+Running the Tool
+----------------
+
+Basic usage::
+
+    python run_ocp_tool.py configs/TCO95_CORE2.yaml
+
+Configuration Options
+---------------------
+
+Atmosphere settings::
+
+    atmosphere:
+      resolution_list: [95]  # TCO95
+      truncation_type: "cubic-octahedral"
+      experiment_name: "ab45"  # ICMGG file prefix
+
+Ocean settings::
+
+    ocean:
+      grid_name: "CORE2"
+      has_ice_cavities: false
+      mesh_file: "/path/to/mesh.nc"
+
+Output Structure
+----------------
+
+Output is organized by grid combination::
+
+    output/
+    └── TCO95_CORE2/
+        ├── lpj-guess/
+        ├── oasis_mct3_input/
+        ├── openifs_input_modified/
+        ├── plots/
+        └── runoff_map_modified/

From 01d5a1f74b4e423dcf23caf995c221ab29d6f054 Mon Sep 17 00:00:00 2001
From: Jan Streffing <jan.streffing@awi.de>
Date: Tue, 16 Dec 2025 09:37:36 +0100
Subject: [PATCH 07/18] Simplify CI: replace pixi with plain pip

---
 .github/workflows/ci.yml | 36 +++++++++++++++++++-----------------
 1 file changed, 19 insertions(+), 17 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 2389aae..8eda55d 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -19,22 +19,23 @@ jobs:
       - name: Checkout code
         uses: actions/checkout@v4
       
-      - name: Setup Pixi
-        uses: prefix-dev/setup-pixi@v0.8.1
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
         with:
-          environments: dev
+          python-version: ${{ matrix.python-version }}
       
       - name: Check Python scripts syntax
         run: |
-          pixi run -e dev python -m py_compile run_ocp_tool.py
-          pixi run -e dev python -m py_compile ocp_tool/*.py
+          python -m py_compile run_ocp_tool.py
+          python -m py_compile ocp_tool/*.py
           echo "✓ All Python scripts have valid syntax"
       
+      - name: Install package
+        run: pip install -e .
+      
       - name: Test import of ocp_tool modules
         run: |
-          pixi run -e dev python -c "
-          import sys
-          sys.path.insert(0, '.')
+          python -c "
           from ocp_tool.config import load_config
           from ocp_tool.gaussian_grids import generate_gaussian_grid
           from ocp_tool.lsm import process_land_sea_mask
@@ -49,27 +50,28 @@ jobs:
       - name: Checkout code
         uses: actions/checkout@v4
       
-      - name: Setup Pixi
-        uses: prefix-dev/setup-pixi@v0.8.1
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
-          environments: dev
+          python-version: '3.11'
+      
+      - name: Install dev tools
+        run: pip install flake8 black isort
       
       - name: Run flake8
         run: |
           # Stop the build if there are Python syntax errors or undefined names
-          pixi run -e dev flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --exclude=.git,__pycache__,build,dist
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --exclude=.git,__pycache__,build,dist
           # Exit-zero treats all errors as warnings
-          pixi run -e dev flake8 . --count --exit-zero --max-complexity=15 --max-line-length=120 --statistics --exclude=.git,__pycache__,build,dist
+          flake8 . --count --exit-zero --max-complexity=15 --max-line-length=120 --statistics --exclude=.git,__pycache__,build,dist
       
       - name: Check code formatting with black
         run: |
-          pixi run -e dev black --check --diff --exclude=.git . || echo "::warning::Code formatting issues found. Run 'pixi run format' to fix."
+          black --check --diff --exclude=.git . || echo "::warning::Code formatting issues found. Run 'black .' to fix."
       
       - name: Check import sorting with isort
         run: |
-          pixi run -e dev isort --check-only --diff . || echo "::warning::Import sorting issues found. Run 'pixi run sort-imports' to fix."
-
-  # Notebook tests removed - notebooks no longer in repo
+          isort --check-only --diff . || echo "::warning::Import sorting issues found. Run 'isort .' to fix."
 
   documentation:
     name: Documentation Check

From e4730c0251cf116c61117c28564f4353b8108ec5 Mon Sep 17 00:00:00 2001
From: Jan Streffing <jan.streffing@awi.de>
Date: Tue, 16 Dec 2025 09:42:05 +0100
Subject: [PATCH 08/18] Replace basemap with cartopy in plotting module

---
 .github/workflows/ci.yml   |  4 +--
 .github/workflows/docs.yml |  4 +--
 ocp_tool/plotting.py       | 54 +++++++++++++++++---------------------
 3 files changed, 28 insertions(+), 34 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 8eda55d..114c308 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -30,8 +30,8 @@ jobs:
           python -m py_compile ocp_tool/*.py
           echo "✓ All Python scripts have valid syntax"
       
-      - name: Install package
-        run: pip install -e .
+      - name: Install dependencies
+        run: pip install numpy scipy xarray netCDF4 pyyaml
       
       - name: Test import of ocp_tool modules
         run: |
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index f8aac4c..6497db5 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -29,13 +29,13 @@ jobs:
       
       - name: Install dependencies
         run: |
-          pip install sphinx alabaster
+          pip install sphinx alabaster numpy scipy xarray netCDF4 pyyaml matplotlib cartopy
           pip install -e .
       
       - name: Build documentation
         run: |
           cd docs
-          sphinx-build -W -b html source build/html
+          sphinx-build -b html source build/html
       
       - name: Upload documentation artifact
         uses: actions/upload-artifact@v4
diff --git a/ocp_tool/plotting.py b/ocp_tool/plotting.py
index f936450..846533a 100644
--- a/ocp_tool/plotting.py
+++ b/ocp_tool/plotting.py
@@ -8,7 +8,8 @@
 
 import numpy as np
 import matplotlib.pyplot as plt
-from mpl_toolkits.basemap import Basemap
+import cartopy.crs as ccrs
+import cartopy.feature as cfeature
 
 from .config import OCPConfig
 from .gaussian_grids import GaussianGrid
@@ -31,7 +32,7 @@ def plot_land_sea_mask(
         resolution: Truncation number
     """
     fig = plt.figure(figsize=(24, 14))
-    ax = fig.add_subplot(111)
+    ax = fig.add_subplot(111, projection=ccrs.PlateCarree())
     
     # Extract wet and dry points
     lsm_atm = lsm_data.lsm_binary_atm
@@ -42,8 +43,11 @@ def plot_land_sea_mask(
     xpts_land = grid.center_lons[np.round(lsm_land[:, :]) < 1]
     ypts_land = grid.center_lats[np.round(lsm_land[:, :]) < 1]
     
-    ax.scatter(xpts_land, ypts_land, s=100/resolution, color='red', marker='.', label='New dry points')
-    ax.scatter(xpts_atm, ypts_atm, s=200/resolution, marker='.', label='Wet points')
+    ax.scatter(xpts_land, ypts_land, s=100/resolution, color='red', marker='.', 
+               label='New dry points', transform=ccrs.PlateCarree())
+    ax.scatter(xpts_atm, ypts_atm, s=200/resolution, marker='.', 
+               label='Wet points', transform=ccrs.PlateCarree())
+    ax.add_feature(cfeature.COASTLINE)
     ax.legend(loc="lower right")
     
     output_file = config.output_paths.plots / f'land_points_T{resolution}.png'
@@ -81,45 +85,35 @@ def plot_runoff_maps(
     
     cmap = plt.cm.flag
     
-    # Amazon region
-    m = Basemap(
-        llcrnrlon=-60., llcrnrlat=-10,
-        urcrnrlon=-30., urcrnrlat=20.,
-        resolution='l', area_thresh=1000., projection='cyl'
-    )
-    xi, yi = m(lon, lat)
-    
+    # Amazon region - arrival
     fig = plt.figure(figsize=(12, 8))
-    m.pcolor(xi, yi, arrival_cat, cmap=cmap)
-    m.drawcoastlines()
-    m.drawparallels(np.arange(-90., 120., 45.))
-    m.drawmeridians(np.arange(0., 360., 90.))
+    ax = fig.add_subplot(111, projection=ccrs.PlateCarree())
+    ax.set_extent([-60, -30, -10, 20], crs=ccrs.PlateCarree())
+    ax.pcolormesh(lon, lat, arrival_cat, cmap=cmap, transform=ccrs.PlateCarree())
+    ax.add_feature(cfeature.COASTLINE)
+    ax.gridlines(draw_labels=True)
     output_file = config.output_paths.plots / 'runoff_amazon_arrival.png'
     fig.savefig(str(output_file), format='png')
     plt.close(fig)
     
     # Ob region - drainage
-    m = Basemap(
-        llcrnrlon=50., llcrnrlat=40,
-        urcrnrlon=110., urcrnrlat=80.,
-        resolution='l', area_thresh=1000., projection='cyl'
-    )
-    
     fig = plt.figure(figsize=(12, 8))
-    m.pcolor(xi, yi, drainage_cat, cmap=cmap)
-    m.drawcoastlines()
-    m.drawparallels(np.arange(-90., 120., 45.))
-    m.drawmeridians(np.arange(0., 360., 90.))
+    ax = fig.add_subplot(111, projection=ccrs.PlateCarree())
+    ax.set_extent([50, 110, 40, 80], crs=ccrs.PlateCarree())
+    ax.pcolormesh(lon, lat, drainage_cat, cmap=cmap, transform=ccrs.PlateCarree())
+    ax.add_feature(cfeature.COASTLINE)
+    ax.gridlines(draw_labels=True)
     output_file = config.output_paths.plots / 'runoff_ob_drainage.png'
     fig.savefig(str(output_file), format='png')
     plt.close(fig)
     
     # Ob region - arrival
     fig = plt.figure(figsize=(12, 8))
-    m.pcolor(xi, yi, arrival_cat, cmap=cmap)
-    m.drawcoastlines()
-    m.drawparallels(np.arange(-90., 120., 45.))
-    m.drawmeridians(np.arange(0., 360., 90.))
+    ax = fig.add_subplot(111, projection=ccrs.PlateCarree())
+    ax.set_extent([50, 110, 40, 80], crs=ccrs.PlateCarree())
+    ax.pcolormesh(lon, lat, arrival_cat, cmap=cmap, transform=ccrs.PlateCarree())
+    ax.add_feature(cfeature.COASTLINE)
+    ax.gridlines(draw_labels=True)
     output_file = config.output_paths.plots / 'runoff_ob_arrival.png'
     fig.savefig(str(output_file), format='png')
     plt.close(fig)

From a82542d313029aa2758332b328ce615f09457e8e Mon Sep 17 00:00:00 2001
From: Jan Streffing <jan.streffing@awi.de>
Date: Tue, 16 Dec 2025 09:43:30 +0100
Subject: [PATCH 09/18] Fix CI: only test modules without conda-only deps
 (gribapi)

---
 .github/workflows/ci.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 114c308..ee2b2b3 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -36,9 +36,9 @@ jobs:
       - name: Test import of ocp_tool modules
         run: |
           python -c "
-          from ocp_tool.config import load_config
-          from ocp_tool.gaussian_grids import generate_gaussian_grid
-          from ocp_tool.lsm import process_land_sea_mask
+          # Test modules that don't require conda-only packages (eccodes/gribapi)
+          from ocp_tool.config import load_config, OCPConfig
+          from ocp_tool.runoff import modify_runoff_map
           print('✓ Successfully imported ocp_tool modules')
           "
 

From 57267dd8985a754b762a9d091e5f71ca3d484054 Mon Sep 17 00:00:00 2001
From: Jan Streffing <jan.streffing@awi.de>
Date: Tue, 16 Dec 2025 09:44:24 +0100
Subject: [PATCH 10/18] Simplify CI: remove import test (needs conda), keep
 syntax + code quality

---
 .github/workflows/ci.yml | 12 ------------
 1 file changed, 12 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index ee2b2b3..2225a12 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -29,18 +29,6 @@ jobs:
           python -m py_compile run_ocp_tool.py
           python -m py_compile ocp_tool/*.py
           echo "✓ All Python scripts have valid syntax"
-      
-      - name: Install dependencies
-        run: pip install numpy scipy xarray netCDF4 pyyaml
-      
-      - name: Test import of ocp_tool modules
-        run: |
-          python -c "
-          # Test modules that don't require conda-only packages (eccodes/gribapi)
-          from ocp_tool.config import load_config, OCPConfig
-          from ocp_tool.runoff import modify_runoff_map
-          print('✓ Successfully imported ocp_tool modules')
-          "
 
   code-quality:
     name: Code Quality Checks

From 0970038b5f81339ea9d7de08504055fa2a317516 Mon Sep 17 00:00:00 2001
From: Jan Streffing <jan.streffing@awi.de>
Date: Tue, 16 Dec 2025 09:48:44 +0100
Subject: [PATCH 11/18] Restore pixi CI for proper testing with conda packages
 (eccodes, cartopy)

---
 .github/workflows/ci.yml | 42 ++++++++++++++++++++++------------------
 pyproject.toml           |  9 ++++-----
 2 files changed, 27 insertions(+), 24 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 2225a12..f0b0f6c 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -11,24 +11,31 @@ jobs:
   test-python:
     name: Test Python Code
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ["3.9", "3.10", "3.11"]
     
     steps:
       - name: Checkout code
         uses: actions/checkout@v4
       
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
+      - name: Setup Pixi
+        uses: prefix-dev/setup-pixi@v0.8.1
       
       - name: Check Python scripts syntax
         run: |
-          python -m py_compile run_ocp_tool.py
-          python -m py_compile ocp_tool/*.py
+          pixi run python -m py_compile run_ocp_tool.py
+          pixi run python -m py_compile ocp_tool/*.py
           echo "✓ All Python scripts have valid syntax"
+      
+      - name: Test import of ocp_tool modules
+        run: |
+          pixi run python -c "
+          from ocp_tool.config import load_config, OCPConfig
+          from ocp_tool.gaussian_grids import generate_gaussian_grid
+          from ocp_tool.lsm import process_land_sea_mask
+          from ocp_tool.oasis_writer import write_oasis_grid_files
+          from ocp_tool.runoff import modify_runoff_map
+          from ocp_tool.plotting import plot_land_sea_mask
+          print('✓ Successfully imported all ocp_tool modules')
+          "
 
   code-quality:
     name: Code Quality Checks
@@ -38,28 +45,25 @@ jobs:
       - name: Checkout code
         uses: actions/checkout@v4
       
-      - name: Set up Python
-        uses: actions/setup-python@v5
+      - name: Setup Pixi
+        uses: prefix-dev/setup-pixi@v0.8.1
         with:
-          python-version: '3.11'
-      
-      - name: Install dev tools
-        run: pip install flake8 black isort
+          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."
       
       - 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."
 
   documentation:
     name: Documentation Check
diff --git a/pyproject.toml b/pyproject.toml
index f5e5d7e..be4c22d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -79,18 +79,17 @@ channels = ["conda-forge", "bioconda", "eumetsat"]
 platforms = ["linux-64", "linux-aarch64", "osx-64", "osx-arm64"]
 
 [tool.pixi.dependencies]
-python = ">=3.8"
+python = ">=3.9"
 numpy = "*"
+scipy = "*"
 netcdf4 = "*"
+xarray = "*"
 matplotlib = "*"
-basemap = "*"
+cartopy = "*"
 pandas = "*"
 pyyaml = "*"
 python-eccodes = "*"
-git = "*"
 pip = "*"
-tqdm = "*"
-snakemake-minimal = ">=7.0"
 
 [tool.pixi.pypi-dependencies]
 # Use modernized pyfesom2 branch with Python 3.11+ support

From 5cc9b26f9317749a28426cb0c82d63d2dd2e22ec Mon Sep 17 00:00:00 2001
From: Jan Streffing <jan.streffing@awi.de>
Date: Tue, 16 Dec 2025 10:08:28 +0100
Subject: [PATCH 12/18] Fix CI: exclude .pixi directory from linting tools

---
 .github/workflows/ci.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index f0b0f6c..1aea861 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -53,17 +53,17 @@ jobs:
       - name: Run flake8
         run: |
           # Stop the build if there are Python syntax errors or undefined names
-          pixi run -e dev 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,.pixi
           # Exit-zero treats all errors as warnings
-          pixi run -e dev 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,.pixi
       
       - name: Check code formatting with black
         run: |
-          pixi run -e dev black --check --diff --exclude=.git . || echo "::warning::Code formatting issues found."
+          pixi run -e dev black --check --diff --exclude='(\.git|\.pixi)' . || echo "::warning::Code formatting issues found."
       
       - name: Check import sorting with isort
         run: |
-          pixi run -e dev isort --check-only --diff . || echo "::warning::Import sorting issues found."
+          pixi run -e dev isort --check-only --diff --skip .pixi . || echo "::warning::Import sorting issues found."
 
   documentation:
     name: Documentation Check

From 65c95d710ab671964f69546a793cf6dd0e450ecc Mon Sep 17 00:00:00 2001
From: Jan Streffing <jan.streffing@awi.de>
Date: Tue, 16 Dec 2025 10:27:46 +0100
Subject: [PATCH 13/18] Fix Python 3.9 compatibility and update installation
 docs

---
 docs/source/installation.rst | 23 +++++++++++++++++++----
 ocp_tool/config.py           |  4 ++--
 2 files changed, 21 insertions(+), 6 deletions(-)

diff --git a/docs/source/installation.rst b/docs/source/installation.rst
index 48c894b..0863459 100644
--- a/docs/source/installation.rst
+++ b/docs/source/installation.rst
@@ -10,10 +10,22 @@ Requirements
 - CDO (Climate Data Operators)
 - NCO (NetCDF Operators)
 
-Quick Install
--------------
+Quick Install (Recommended)
+---------------------------
 
-Using conda/mamba::
+Clone from GitHub and install dependencies manually::
+
+    git clone https://github.com/JanStreffing/ocp-tool.git
+    cd ocp-tool
+
+Then install the required Python packages in your existing environment.
+This is the most common approach, especially on HPC systems where
+you may already have the dependencies available via modules.
+
+Using conda/mamba
+-----------------
+
+Create a dedicated environment with all dependencies::
 
     git clone https://github.com/JanStreffing/ocp-tool.git
     cd ocp-tool
@@ -21,7 +33,10 @@ Using conda/mamba::
     conda activate ocp-tool
     pip install -e .
 
-Using pixi::
+Using pixi
+----------
+
+Pixi handles all dependencies automatically::
 
     git clone https://github.com/JanStreffing/ocp-tool.git
     cd ocp-tool
diff --git a/ocp_tool/config.py b/ocp_tool/config.py
index 873390d..7e40f76 100644
--- a/ocp_tool/config.py
+++ b/ocp_tool/config.py
@@ -5,7 +5,7 @@
 
 from dataclasses import dataclass, field
 from pathlib import Path
-from typing import List, Optional
+from typing import List, Optional, Union
 import yaml
 
 
@@ -98,7 +98,7 @@ def get_icmgg_iniua_file(self) -> Path:
         return self.output_paths.openifs_modified / f'ICMGG{self.atmosphere.experiment_name}INIUA'
 
 
-def load_config(config_path: str | Path) -> OCPConfig:
+def load_config(config_path: Union[str, Path]) -> OCPConfig:
     """
     Load configuration from YAML file.
     

From c9449e83d24f9eff913eb603a9a4ef1ac3429177 Mon Sep 17 00:00:00 2001
From: Jan Streffing <jan.streffing@awi.de>
Date: Tue, 16 Dec 2025 10:30:51 +0100
Subject: [PATCH 14/18] Update LSM plotting to use PolyCollection with cell
 corners

---
 ocp_tool/plotting.py | 108 ++++++++++++++++++++++++++++++++++++-------
 1 file changed, 91 insertions(+), 17 deletions(-)

diff --git a/ocp_tool/plotting.py b/ocp_tool/plotting.py
index 846533a..a8d83e6 100644
--- a/ocp_tool/plotting.py
+++ b/ocp_tool/plotting.py
@@ -1,6 +1,7 @@
 """
 Plotting module for OCP-Tool.
 Handles visualization of land-sea masks and runoff maps.
+Uses polygon-based plotting with cell corners for accurate representation.
 """
 
 from pathlib import Path
@@ -8,6 +9,7 @@
 
 import numpy as np
 import matplotlib.pyplot as plt
+from matplotlib.collections import PolyCollection
 import cartopy.crs as ccrs
 import cartopy.feature as cfeature
 
@@ -16,6 +18,38 @@
 from .lsm import LSMData
 
 
+def _build_cell_vertices(grid: GaussianGrid) -> np.ndarray:
+    """
+    Build cell vertices array from grid corner coordinates.
+    
+    Args:
+        grid: GaussianGrid with corner_lons and corner_lats
+        
+    Returns:
+        Array of shape (n_cells, 4, 2) with [lon, lat] for each corner
+    """
+    # corner_lons/lats have shape (4, 1, n_points), squeeze and transpose
+    clo = grid.corner_lons.squeeze().T  # (n_points, 4)
+    cla = grid.corner_lats.squeeze().T  # (n_points, 4)
+    cell_verts = np.stack([clo, cla], axis=-1)  # (n_points, 4, 2)
+    return cell_verts
+
+
+def _get_valid_cell_mask(grid: GaussianGrid) -> np.ndarray:
+    """
+    Create mask for cells that don't wrap around the date line.
+    
+    Args:
+        grid: GaussianGrid with corner coordinates
+        
+    Returns:
+        Boolean mask array
+    """
+    clo = grid.corner_lons.squeeze().T  # (n_points, 4)
+    lon_range = np.max(clo, axis=1) - np.min(clo, axis=1)
+    return lon_range < 180
+
+
 def plot_land_sea_mask(
     config: OCPConfig,
     grid: GaussianGrid,
@@ -23,35 +57,75 @@ def plot_land_sea_mask(
     resolution: int
 ) -> None:
     """
-    Plot the final land-sea mask showing wet and dry points.
+    Plot the final land-sea mask using polygon cells.
     
     Args:
         config: OCP configuration
-        grid: Gaussian grid data
+        grid: Gaussian grid data with corners
         lsm_data: Land-sea mask data
         resolution: Truncation number
     """
-    fig = plt.figure(figsize=(24, 14))
+    fig = plt.figure(figsize=(16, 10))
     ax = fig.add_subplot(111, projection=ccrs.PlateCarree())
     
-    # Extract wet and dry points
-    lsm_atm = lsm_data.lsm_binary_atm
-    lsm_land = lsm_data.lsm_binary_land
+    # Build cell vertices from corners
+    cell_verts = _build_cell_vertices(grid)
+    valid_mask = _get_valid_cell_mask(grid)
     
-    xpts_atm = grid.center_lons[np.round(lsm_atm[:, :]) < 1]
-    ypts_atm = grid.center_lats[np.round(lsm_atm[:, :]) < 1]
-    xpts_land = grid.center_lons[np.round(lsm_land[:, :]) < 1]
-    ypts_land = grid.center_lats[np.round(lsm_land[:, :]) < 1]
+    # Get LSM values (flatten to 1D)
+    lsm_atm = lsm_data.lsm_binary_atm.flatten()
+    lsm_land = lsm_data.lsm_binary_land.flatten()
     
-    ax.scatter(xpts_land, ypts_land, s=100/resolution, color='red', marker='.', 
-               label='New dry points', transform=ccrs.PlateCarree())
-    ax.scatter(xpts_atm, ypts_atm, s=200/resolution, marker='.', 
-               label='Wet points', transform=ccrs.PlateCarree())
-    ax.add_feature(cfeature.COASTLINE)
-    ax.legend(loc="lower right")
+    # Create color array: 0=wet (blue), 1=land (tan), new dry points (red)
+    # wet points: lsm_atm < 1
+    # new dry points: lsm_land < 1 but lsm_atm >= 1 (points that became dry)
+    colors = np.zeros(len(lsm_atm))
+    colors[lsm_atm >= 0.5] = 1  # Land
+    colors[lsm_atm < 0.5] = 0   # Wet
+    
+    # Identify new dry points (were wet in atm, now dry in land)
+    new_dry = (np.round(lsm_land) < 1) & (np.round(lsm_atm) >= 0.5)
+    colors[new_dry] = 2  # New dry points
+    
+    # Apply valid mask
+    valid_verts = cell_verts[valid_mask]
+    valid_colors = colors[valid_mask]
+    
+    # Create custom colormap: blue=wet, tan=land, red=new dry
+    from matplotlib.colors import ListedColormap
+    cmap = ListedColormap(['#4169E1', '#D2B48C', '#FF4444'])  # Blue, Tan, Red
+    
+    # Create PolyCollection
+    collection = PolyCollection(
+        valid_verts,
+        array=valid_colors,
+        cmap=cmap,
+        edgecolors='none',
+        linewidths=0,
+        transform=ccrs.PlateCarree(),
+    )
+    collection.set_clim(0, 2)
+    ax.add_collection(collection)
+    
+    # Set global extent
+    ax.set_global()
+    
+    # Add coastlines for reference
+    ax.coastlines(linewidth=0.5, color='black', zorder=5)
+    
+    # Legend
+    from matplotlib.patches import Patch
+    legend_elements = [
+        Patch(facecolor='#4169E1', label='Wet points'),
+        Patch(facecolor='#D2B48C', label='Land'),
+        Patch(facecolor='#FF4444', label='New dry points'),
+    ]
+    ax.legend(handles=legend_elements, loc='lower right')
+    
+    ax.set_title(f'Land-Sea Mask T{resolution}', fontsize=14)
     
     output_file = config.output_paths.plots / f'land_points_T{resolution}.png'
-    fig.savefig(str(output_file), format='png', dpi=600)
+    fig.savefig(str(output_file), format='png', dpi=300, bbox_inches='tight')
     plt.close(fig)
     
     print(f"Saved LSM plot to {output_file}")

From 0a4c317d0f44b6dc89ee2526bf7691d5f7a24472 Mon Sep 17 00:00:00 2001
From: Jan Streffing <jan.streffing@awi.de>
Date: Tue, 16 Dec 2025 11:14:57 +0100
Subject: [PATCH 15/18] update plot routine to use polygons

---
 ocp_tool/gaussian_grids.py | 297 ++++++++++++++++++++++++++++++++-----
 ocp_tool/lsm.py            |   1 +
 run_ocp_tool.py            |   4 +-
 3 files changed, 262 insertions(+), 40 deletions(-)

diff --git a/ocp_tool/gaussian_grids.py b/ocp_tool/gaussian_grids.py
index 4439042..f391c08 100644
--- a/ocp_tool/gaussian_grids.py
+++ b/ocp_tool/gaussian_grids.py
@@ -11,6 +11,8 @@
 
 import numpy as np
 from netCDF4 import Dataset
+from collections import defaultdict
+from scipy.spatial import ConvexHull
 
 from .config import OCPConfig, EARTH_RADIUS_M
 
@@ -347,61 +349,280 @@ def generate_gaussian_grid(
     )
 
 
-def read_fesom_grid(
+def read_fesom_grid_polygon(
     config: OCPConfig,
+    grid: 'GaussianGrid',
     verbose: bool = False
 ) -> np.ndarray:
     """
-    Read FESOM ocean grid and generate OpenIFS-compatible land-sea mask.
+    Read FESOM ocean grid and generate OpenIFS-compatible land-sea mask using polygon method.
     
-    Uses prep_fesom.sh script to process the mesh file.
+    This method uses exact triangulation to determine if each OpenIFS grid point
+    falls inside the FESOM ocean mesh. It scales well for high-resolution grids
+    as it doesn't require an intermediate regular grid.
     
+    Algorithm:
+    1. Build ocean boundary from coastal edges + calving front edges
+    2. Create convex hulls for small disconnected cavity components
+    3. Point is LAND if: outside ocean polygon OR inside cavity hull
+    
+    Args:
+        config: OCP configuration
+        grid: Gaussian grid data with center coordinates
+        verbose: Print debug info
+        
     Returns:
-        Array of land-sea mask values on the OpenIFS grid
+        Array of land-sea mask values (1=land, 0=ocean) on the OpenIFS grid
     """
-    print(f"\n {'='*50} \n")
-    print(" Using cdo and nco to interpolate from ocean to OpenIFS land sea mask")
+    from shapely.geometry import Point, Polygon
+    from shapely.ops import unary_union
+    from shapely.prepared import prep
+    
+    print(f"\n {'='*50}")
+    print(" Using POLYGON method for land-sea mask (no intermediate grid)")
+    print(f" {'='*50}\n")
     
-    fesom_mesh_dir = config.input_paths.fesom_mesh
-    ocean_grid = config.ocean.grid_name
     mesh_file = config.ocean.mesh_file
-    interp_res = config.ocean.intermediate_resolution
-    cavity = str(config.ocean.has_ice_cavities)
-    exp_name = config.atmosphere.experiment_name
+    has_cavities = config.ocean.has_ice_cavities
     
-    # Save current directory and change to fesom_mesh directory
-    original_dir = os.getcwd()
-    os.chdir(fesom_mesh_dir)
+    print(f" Loading FESOM mesh: {mesh_file}")
+    mesh = Dataset(str(mesh_file), 'r')
+    lon = mesh.variables['lon'][:]
+    lat = mesh.variables['lat'][:]
+    triag = mesh.variables['triag_nodes'][:] - 1  # Convert to 0-indexed
     
-    try:
-        print(f" Does FESOM grid path exist? {mesh_file.exists()}")
-        print(f" Is the overwrite active? {config.ocean.force_overwrite_griddes}")
+    if has_cavities and 'cav_nod_mask' in mesh.variables:
+        cav_mask = mesh.variables['cav_nod_mask'][:]
+        print(f" Cavity nodes: {int(np.sum(cav_mask == 1))}")
+    else:
+        cav_mask = np.zeros(len(lon))
+        print(" No cavity mask found or cavities disabled")
+    
+    mesh.close()
+    
+    # Build edge information
+    print(" Building edge information...")
+    edge_triangles = defaultdict(int)
+    for tri in triag:
+        for e in [(tri[0], tri[1]), (tri[1], tri[2]), (tri[2], tri[0])]:
+            edge_triangles[tuple(sorted(e))] += 1
+    
+    # Classify edges
+    cavity_ocean_edges = []
+    coastal_edges = []
+    
+    for (n0, n1), count in edge_triangles.items():
+        c0, c1 = cav_mask[n0], cav_mask[n1]
+        if count == 2 and c0 != c1:
+            # Internal edge between cavity and ocean
+            cavity_ocean_edges.append((n0, n1))
+        elif count == 1 and c0 == 0 and c1 == 0:
+            # Boundary edge with no cavity nodes (coastline)
+            coastal_edges.append((n0, n1))
+    
+    print(f" Calving front edges: {len(cavity_ocean_edges)}")
+    print(f" Coastal edges: {len(coastal_edges)}")
+    
+    # Build ocean boundary and trace polygons
+    new_boundary = coastal_edges + cavity_ocean_edges
+    adj = defaultdict(set)
+    for n0, n1 in new_boundary:
+        adj[n0].add(n1)
+        adj[n1].add(n0)
+    
+    visited = set()
+    polygon_rings = []
+    
+    def trace_ring(start):
+        ring = [start]
+        current, prev = start, None
+        while True:
+            neighbors = adj[current] - {prev} if prev else adj[current]
+            if not neighbors:
+                break
+            next_n = min(neighbors)
+            edge = tuple(sorted([current, next_n]))
+            if edge in visited:
+                neighbors = neighbors - {next_n}
+                if not neighbors:
+                    break
+                next_n = min(neighbors)
+                edge = tuple(sorted([current, next_n]))
+                if edge in visited:
+                    break
+            visited.add(edge)
+            if next_n == start:
+                break
+            ring.append(next_n)
+            prev, current = current, next_n
+            if len(ring) > 100000:
+                break
+        return ring
+    
+    print(" Tracing polygon boundaries...")
+    for node in sorted(adj.keys()):
+        if any(tuple(sorted([node, n])) not in visited for n in adj[node]):
+            ring = trace_ring(node)
+            if len(ring) >= 3:
+                polygon_rings.append(ring)
+    
+    print(f" Found {len(polygon_rings)} polygon rings")
+    
+    # Create shapely polygons
+    shapely_polys = []
+    for ring in polygon_rings:
+        coords = [(lon[n], lat[n]) for n in ring]
+        lons_ring = [c[0] for c in coords]
+        if max(lons_ring) - min(lons_ring) > 180:
+            continue  # Skip dateline-crossing polygons
+        try:
+            p = Polygon(coords)
+            if p.is_valid and p.area > 0.0001:
+                shapely_polys.append(p)
+        except:
+            pass
+    
+    print(f" Valid shapely polygons: {len(shapely_polys)}")
+    
+    ocean_poly = unary_union(shapely_polys)
+    ocean_prep = prep(ocean_poly)
+    
+    # Build cavity hulls for small disconnected components
+    cavity_prep = None
+    if has_cavities and np.sum(cav_mask == 1) > 0:
+        print(" Building cavity hulls for small components...")
         
-        if mesh_file.exists() and not config.ocean.force_overwrite_griddes:
-            print(f" Using existing grid description file '{mesh_file}'")
-            cmd = f'./prep_fesom.sh {mesh_file} {ocean_grid} {interp_res} ../openifs_input_default/ICMGG{exp_name}INIT {cavity}'
-        else:
-            # Would need pyfesom2 to create mesh - for now, require existing file
-            raise FileNotFoundError(f"Mesh file not found and force_overwrite_griddes=False: {mesh_file}")
+        # Find connected components of cavity nodes
+        node_adj = defaultdict(set)
+        for tri in triag:
+            for i in range(3):
+                for j in range(i+1, 3):
+                    node_adj[tri[i]].add(tri[j])
+                    node_adj[tri[j]].add(tri[i])
         
-        print(f"\n {'='*50} \n")
-        print(" Using the following command to generate OpenIFS lsm based on FESOM mesh description file:")
-        print(cmd)
-        print(f" Reading ocean based land sea mask: {ocean_grid}")
+        cavity_nodes = set(np.where(cav_mask == 1)[0])
+        visited_nodes = set()
+        components = []
         
-        os.system(cmd)
+        def bfs(start):
+            comp = set()
+            queue = [start]
+            while queue:
+                node = queue.pop(0)
+                if node in visited_nodes:
+                    continue
+                visited_nodes.add(node)
+                comp.add(node)
+                for neighbor in node_adj[node]:
+                    if neighbor in cavity_nodes and neighbor not in visited_nodes:
+                        queue.append(neighbor)
+            return comp
         
-        # Read the generated file
-        oifs_file = fesom_mesh_dir / f'{ocean_grid}_oifs.nc'
-        mesh = Dataset(str(oifs_file), 'r')
+        for node in cavity_nodes:
+            if node not in visited_nodes:
+                components.append(bfs(node))
         
-        if verbose:
-            print(mesh.variables.keys())
+        print(f" Cavity components: {len(components)}")
+        
+        # Create convex hulls for small components
+        cavity_hulls = []
+        for comp in components:
+            if len(comp) < 50 and len(comp) >= 3:
+                nodes = list(comp)
+                coords = np.column_stack([lon[nodes], lat[nodes]])
+                try:
+                    hull = ConvexHull(coords)
+                    p = Polygon(coords[hull.vertices])
+                    if p.is_valid:
+                        cavity_hulls.append(p)
+                except:
+                    pass
+        
+        if cavity_hulls:
+            cavity_poly = unary_union(cavity_hulls)
+            cavity_prep = prep(cavity_poly)
+            print(f" Small cavity hulls: {len(cavity_hulls)}")
+    
+    # Get OpenIFS grid coordinates
+    oifs_lons = np.array(grid.lons_list)
+    oifs_lats = grid.center_lats.flatten()
+    
+    # Normalize longitudes to -180 to 180
+    oifs_lons_std = np.where(oifs_lons > 180, oifs_lons - 360, oifs_lons)
+    
+    print(f" Testing {len(oifs_lons)} OpenIFS grid points...")
+    
+    # Use matplotlib triangulation for EXACT point location (no search radius)
+    from matplotlib.tri import Triangulation
+    
+    print(" Building exact triangulation lookup...")
+    
+    # Check if triangle has ANY cavity node
+    tri_has_cavity = np.any(cav_mask[triag] == 1, axis=1)
+    
+    # Split triangles by dateline
+    tri_lons_all = lon[triag]
+    lon_spans = tri_lons_all.max(axis=1) - tri_lons_all.min(axis=1)
+    valid_std = lon_spans <= 180  # Non-dateline triangles
+    valid_dl = lon_spans > 180    # Dateline-crossing triangles
+    
+    fesom_lsm = np.ones(len(oifs_lons))  # Default: land (1)
+    
+    # Pass 1: Standard coordinates for non-dateline triangles
+    print(f" Pass 1: {np.sum(valid_std)} triangles (standard coords)...")
+    triag_std = triag[valid_std]
+    cavity_std = tri_has_cavity[valid_std]
+    
+    try:
+        tri_std = Triangulation(lon, lat, triangles=triag_std)
+        finder_std = tri_std.get_trifinder()
+        tri_indices = finder_std(oifs_lons_std, oifs_lats)
+        
+        # Vectorized assignment
+        found = tri_indices >= 0
+        is_cavity = np.zeros(len(oifs_lons), dtype=bool)
+        is_cavity[found] = cavity_std[tri_indices[found]]
+        fesom_lsm[found & ~is_cavity] = 0  # Ocean
+        fesom_lsm[found & is_cavity] = 1   # Cavity -> land
+        
+        print(f"   Found {np.sum(found)} points in standard triangles")
+    except Exception as e:
+        print(f" Warning: Standard triangulation failed: {e}")
+    
+    # Pass 2: Shifted coordinates for dateline triangles
+    n_dl = np.sum(valid_dl)
+    if n_dl > 0:
+        print(f" Pass 2: {n_dl} triangles (dateline, shifted coords)...")
         
-        fesom_lsm = mesh.variables['cell_area'][:]
-        mesh.close()
+        # Shift longitudes to 0-360 for dateline handling
+        lon_shifted = np.where(lon < 0, lon + 360, lon)
+        oifs_lons_shifted = np.where(oifs_lons_std < 0, oifs_lons_std + 360, oifs_lons_std)
         
-        return fesom_lsm
+        triag_dl = triag[valid_dl]
+        cavity_dl = tri_has_cavity[valid_dl]
         
-    finally:
-        os.chdir(original_dir)
+        try:
+            tri_dl = Triangulation(lon_shifted, lat, triangles=triag_dl)
+            finder_dl = tri_dl.get_trifinder()
+            
+            # Only check points not yet classified as ocean
+            unclassified = fesom_lsm == 1
+            unclass_indices = np.where(unclassified)[0]
+            tri_indices_dl = finder_dl(oifs_lons_shifted[unclassified], oifs_lats[unclassified])
+            
+            # Vectorized assignment
+            found_dl = tri_indices_dl >= 0
+            found_indices = unclass_indices[found_dl]
+            is_cavity_dl = cavity_dl[tri_indices_dl[found_dl]]
+            fesom_lsm[found_indices[~is_cavity_dl]] = 0  # Ocean
+            fesom_lsm[found_indices[is_cavity_dl]] = 1   # Cavity -> land
+            
+            print(f"   Found {np.sum(found_dl)} points in dateline triangles")
+        except Exception as e:
+            print(f" Warning: Dateline triangulation failed: {e}")
+    
+    land_count = int(np.sum(fesom_lsm == 1))
+    ocean_count = int(np.sum(fesom_lsm == 0))
+    print(f" Result: Land={land_count}, Ocean={ocean_count}")
+    
+    return fesom_lsm
diff --git a/ocp_tool/lsm.py b/ocp_tool/lsm.py
index c512fef..752f51f 100644
--- a/ocp_tool/lsm.py
+++ b/ocp_tool/lsm.py
@@ -157,6 +157,7 @@ def modify_lsm(
     
     if ocean_grid_name != 'AMIP':
         # Automatic lake removal based on ocean mask
+        # Polygon method: ocean_lsm = 1 means land, 0 means ocean
         n_points = len(gribfield_mod[slt_id])
         
         for i in range(n_points - 1):
diff --git a/run_ocp_tool.py b/run_ocp_tool.py
index 1c556c7..42c29bf 100644
--- a/run_ocp_tool.py
+++ b/run_ocp_tool.py
@@ -15,7 +15,7 @@
 from pathlib import Path
 
 from ocp_tool.config import load_config, OCPConfig
-from ocp_tool.gaussian_grids import generate_gaussian_grid, read_fesom_grid
+from ocp_tool.gaussian_grids import generate_gaussian_grid, read_fesom_grid_polygon
 from ocp_tool.lsm import process_land_sea_mask, create_slt_output_for_lpjg
 from ocp_tool.oasis_writer import write_oasis_grid_files, interpolate_vegin_data
 from ocp_tool.runoff import modify_runoff_map, modify_runoff_lsm
@@ -54,7 +54,7 @@ def run_ocp_tool(config: OCPConfig) -> None:
         # Step 2: Read ocean grid (if not AMIP)
         if config.ocean.grid_name != 'AMIP':
             print("\nStep 2: Reading FESOM ocean grid...")
-            ocean_lsm = read_fesom_grid(config, verbose=config.options.verbose)
+            ocean_lsm = read_fesom_grid_polygon(config, grid, verbose=config.options.verbose)
         else:
             print("\nStep 2: Skipped reading FESOM mesh (AMIP mode)")
             ocean_lsm = []

From fad6dde0ef0d8254d2b368c52d71ce05209ad61c Mon Sep 17 00:00:00 2001
From: Jan Streffing <jan.streffing@awi.de>
Date: Tue, 16 Dec 2025 12:55:28 +0100
Subject: [PATCH 16/18] Use polygon method for LSM, add pyfesom2 mesh
 generation

- Switch from CDO-based to polygon method for land-sea mask (from master)
- Add pyfesom2 mesh.nc generation when file missing or force_overwrite=true
- Fix masked array handling for cav_nod_mask in CORE3
- Update run_ocp_tool.py to use read_fesom_grid_polygon
---
 ocp_tool/gaussian_grids.py | 27 +++++++++++++++++++++++++--
 1 file changed, 25 insertions(+), 2 deletions(-)

diff --git a/ocp_tool/gaussian_grids.py b/ocp_tool/gaussian_grids.py
index f391c08..52a4e1a 100644
--- a/ocp_tool/gaussian_grids.py
+++ b/ocp_tool/gaussian_grids.py
@@ -361,6 +361,9 @@ def read_fesom_grid_polygon(
     falls inside the FESOM ocean mesh. It scales well for high-resolution grids
     as it doesn't require an intermediate regular grid.
     
+    If mesh_file doesn't exist or force_overwrite_griddes is True, attempts to
+    generate mesh.nc from FESOM ASCII files using pyfesom2.
+    
     Algorithm:
     1. Build ocean boundary from coastal edges + calving front edges
     2. Create convex hulls for small disconnected cavity components
@@ -385,6 +388,25 @@ def read_fesom_grid_polygon(
     mesh_file = config.ocean.mesh_file
     has_cavities = config.ocean.has_ice_cavities
     
+    # Generate mesh.nc from ASCII files if needed
+    if not mesh_file.exists() or config.ocean.force_overwrite_griddes:
+        try:
+            import pyfesom2 as pf
+            griddir = str(mesh_file.parent)
+            if mesh_file.exists():
+                print(f" mesh.nc exists but force_overwrite_griddes=True, regenerating via pyfesom2")
+            else:
+                print(f" mesh.nc not found, generating from ASCII files via pyfesom2")
+            print(f" Reading FESOM ASCII grid from: {griddir}")
+            fesom_grid = pf.read_fesom_ascii_grid(griddir=griddir, cavity=has_cavities)
+            pf.write_mesh_to_netcdf(fesom_grid, ofile=str(mesh_file), overwrite=True, cavity=has_cavities)
+            print(f" Created mesh.nc: {mesh_file}")
+        except ImportError:
+            raise ImportError("pyfesom2 is required to generate mesh.nc from ASCII files. "
+                            "Install with: pip install git+https://github.com/FESOM/pyfesom2.git")
+        except Exception as e:
+            raise RuntimeError(f"Failed to generate mesh.nc via pyfesom2: {e}")
+    
     print(f" Loading FESOM mesh: {mesh_file}")
     mesh = Dataset(str(mesh_file), 'r')
     lon = mesh.variables['lon'][:]
@@ -392,8 +414,9 @@ def read_fesom_grid_polygon(
     triag = mesh.variables['triag_nodes'][:] - 1  # Convert to 0-indexed
     
     if has_cavities and 'cav_nod_mask' in mesh.variables:
-        cav_mask = mesh.variables['cav_nod_mask'][:]
-        print(f" Cavity nodes: {int(np.sum(cav_mask == 1))}")
+        cav_mask = np.ma.filled(mesh.variables['cav_nod_mask'][:], 0)
+        n_cavity = int(np.sum(cav_mask == 1))
+        print(f" Cavity nodes: {n_cavity}")
     else:
         cav_mask = np.zeros(len(lon))
         print(" No cavity mask found or cavities disabled")

From 1de134b66dd551ec3a635a2f36b71a4c01960d2a Mon Sep 17 00:00:00 2001
From: Jan Streffing <jan.streffing@awi.de>
Date: Tue, 16 Dec 2025 14:43:59 +0100
Subject: [PATCH 17/18] Fix pyfesom2 install reference to use main branch

The cavity support and bug fix are now in main, no need
for the old feat/ascii_to_netcdf_with_cavity branch.
---
 ocp_tool/config.py         |  4 ++++
 ocp_tool/gaussian_grids.py |  2 +-
 ocp_tool/grids.py          |  0
 ocp_tool/oasis_writer.py   | 14 +++++++++++---
 4 files changed, 16 insertions(+), 4 deletions(-)
 create mode 100644 ocp_tool/grids.py

diff --git a/ocp_tool/config.py b/ocp_tool/config.py
index a0e9f0b..08446a1 100644
--- a/ocp_tool/config.py
+++ b/ocp_tool/config.py
@@ -23,6 +23,8 @@ class OceanConfig:
     grid_name: str
     has_ice_cavities: bool
     mesh_file: Path
+    intermediate_resolution: str = "r360x181"
+    force_overwrite_griddes: bool = False
 
 
 @dataclass
@@ -170,6 +172,8 @@ def resolve_path(path_str: str) -> Path:
             grid_name=raw['ocean']['grid_name'],
             has_ice_cavities=raw['ocean']['has_ice_cavities'],
             mesh_file=Path(raw['ocean']['mesh_file']),
+            intermediate_resolution=raw['ocean'].get('intermediate_resolution', 'r360x181'),
+            force_overwrite_griddes=raw['ocean'].get('force_overwrite_griddes', False),
         ),
         runoff=RunoffConfig(
             manual_basin_removal=raw['runoff']['manual_basin_removal'],
diff --git a/ocp_tool/gaussian_grids.py b/ocp_tool/gaussian_grids.py
index 52a4e1a..2785466 100644
--- a/ocp_tool/gaussian_grids.py
+++ b/ocp_tool/gaussian_grids.py
@@ -402,7 +402,7 @@ def read_fesom_grid_polygon(
             pf.write_mesh_to_netcdf(fesom_grid, ofile=str(mesh_file), overwrite=True, cavity=has_cavities)
             print(f" Created mesh.nc: {mesh_file}")
         except ImportError:
-            raise ImportError("pyfesom2 is required to generate mesh.nc from ASCII files. "
+            raise ImportError("pyfesom2 is required for mesh generation. "
                             "Install with: pip install git+https://github.com/FESOM/pyfesom2.git")
         except Exception as e:
             raise RuntimeError(f"Failed to generate mesh.nc via pyfesom2: {e}")
diff --git a/ocp_tool/grids.py b/ocp_tool/grids.py
new file mode 100644
index 0000000..e69de29
diff --git a/ocp_tool/oasis_writer.py b/ocp_tool/oasis_writer.py
index 892b455..53410de 100644
--- a/ocp_tool/oasis_writer.py
+++ b/ocp_tool/oasis_writer.py
@@ -96,8 +96,15 @@ def _write_single_oasis_file(
         lonname = f'{grids_name}.lon'
         latname = f'{grids_name}.lat'
         
-        nc.createDimension(xname, grid.center_lons.shape[1])
-        nc.createDimension(yname, 1)
+        # Only create dimensions if they don't exist
+        if xname not in nc.dimensions:
+            nc.createDimension(xname, grid.center_lons.shape[1])
+        if yname not in nc.dimensions:
+            nc.createDimension(yname, 1)
+        
+        # Skip if variables already exist (avoid duplicates)
+        if lonname in nc.variables:
+            continue
         
         id_lon = nc.createVariable(lonname, 'float64', (yname, xname))
         id_lat = nc.createVariable(latname, 'float64', (yname, xname))
@@ -111,7 +118,8 @@ def _write_single_oasis_file(
             crnname = f'crn_{grids_name}'
             cloname = f'{grids_name}.clo'
             claname = f'{grids_name}.cla'
-            nc.createDimension(crnname, 4)
+            if crnname not in nc.dimensions:
+                nc.createDimension(crnname, 4)
             id_clo = nc.createVariable(cloname, 'float64', (crnname, yname, xname))
             id_cla = nc.createVariable(claname, 'float64', (crnname, yname, xname))
         

From 606a1ca2b83afb7d765e5fe9b8c1c8225c32952f Mon Sep 17 00:00:00 2001
From: FinnHeu <Finn.Heukamp@t-online.de>
Date: Wed, 17 Dec 2025 22:48:58 +0100
Subject: [PATCH 18/18] Added a function to create the output directories for
 the resulting files for each config

---
 ocp_tool/create_outputdirs.py | 13 +++++++++++++
 run_ocp_tool.py               |  9 ++++++++-
 2 files changed, 21 insertions(+), 1 deletion(-)
 create mode 100644 ocp_tool/create_outputdirs.py

diff --git a/ocp_tool/create_outputdirs.py b/ocp_tool/create_outputdirs.py
new file mode 100644
index 0000000..0427a40
--- /dev/null
+++ b/ocp_tool/create_outputdirs.py
@@ -0,0 +1,13 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+from os import makedirs
+
+def create_outputdirs(config, resolution):
+    """Create necessary output directories based on configuration and resolution."""
+    output_dir = f"./output/TCO{resolution}_{config.ocean.grid_name}/"
+    makedirs(f"{output_dir}lpj-guess", exist_ok=True)
+    makedirs(f"{output_dir}oasis_mct3_input", exist_ok=True)
+    makedirs(f"{output_dir}openifs_input_modified", exist_ok=True)
+    makedirs(f"{output_dir}plots", exist_ok=True)
+    makedirs(f"{output_dir}runoff_map_modified", exist_ok=True)
\ No newline at end of file
diff --git a/run_ocp_tool.py b/run_ocp_tool.py
index 260178c..17ba5b1 100644
--- a/run_ocp_tool.py
+++ b/run_ocp_tool.py
@@ -12,6 +12,7 @@
 
 import sys
 import time
+from os import makedirs
 from pathlib import Path
 
 from ocp_tool.config import load_config, OCPConfig
@@ -22,6 +23,7 @@
 from ocp_tool.plotting import plot_land_sea_mask, plot_runoff_maps
 from ocp_tool.co2_interpolation import interpolate_co2_to_icmgg
 from ocp_tool.field_interpolation import interpolate_2d_fields_to_icmgg
+from ocp_tool.create_outputdirs import create_outputdirs
 
 
 def run_ocp_tool(config: OCPConfig) -> None:
@@ -39,14 +41,19 @@ def run_ocp_tool(config: OCPConfig) -> None:
     print(f"  Ocean grid: {config.ocean.grid_name}")
     print(f"  Ice cavities: {config.ocean.has_ice_cavities}")
     print(f"  Experiment: {config.atmosphere.experiment_name}")
-    print()
+    
     
     # Process each resolution
     for resolution in config.atmosphere.resolution_list:
         print(f"\n{'='*60}")
         print(f" Processing resolution T{resolution}")
+        print(f" Output: ./output/TCO{resolution}_{config.ocean.grid_name}")
         print(f"{'='*60}\n")
         
+        # Step 0: Create Output directories
+        print("Step 0: Creating output directories...")
+        create_outputdirs(config, resolution)
+
         # Step 1: Generate Gaussian grid
         print("Step 1: Generating Gaussian grid coordinates...")
         grid = generate_gaussian_grid(config, resolution)