Tipping points

.github/ISSUE_TEMPLATE/bug_report.yaml

@@ -1,6 +1,6 @@
 ---
 name: Bug Report
-description: Report incorrect behavior 
+description: Report incorrect behavior
 labels: [bug, needs refinement]
 
 body:
@@ -18,8 +18,8 @@ body:
     attributes:
       description: >
         Please provide a minimal, copy-pastable example or a link to a public repository that reproduces the behavior. If providing a copy pastable example,
-        you may assume your in a clean up to date version of FloodAdapt with a python enviroment active. In the case of a repository, ensure the repository
-        has a README.md which includes intructions to reproduce the behaviour.
+        you may assume your in a clean up to date version of FloodAdapt with a python environment active. In the case of a repository, ensure the repository
+        has a README.md which includes instructions to reproduce the behaviour.
       label: Reproducible Example
     validations:
       required: true
@@ -43,7 +43,7 @@ body:
     id: task-list
     attributes:
       description: >
-        Please provide a list of tasks that need to be completed before this issue can be closed. 
+        Please provide a list of tasks that need to be completed before this issue can be closed.
       label: Task list
     validations:
       required: true

.github/ISSUE_TEMPLATE/feature_request.yaml

@@ -25,7 +25,7 @@ body:
     id: task-list
     attributes:
       description: >
-        Please provide a list of tasks that need to be completed before this issue can be closed. 
+        Please provide a list of tasks that need to be completed before this issue can be closed.
       label: Task list
     validations:
       required: true

.github/workflows/auto_code_doc.yml

@@ -11,10 +11,10 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
 
@@ -24,13 +24,29 @@ jobs:
         pip install sphinx sphinx_rtd_theme
 
     - name: Build docs
-      run: make -C flood_adapt/api html
+      run: |
+        # Change to the directory where the Makefile is located
+        cd flood_adapt/api
+
+        # Build the documentation
+        make html
+
+        # Verify the build output
+        ls -la build/html
 
     - name: Publish to Wiki
       run: |
-        git clone https://github.com/${{ github.repository }}.wiki.git
-        cp -r _build/html/* .wiki
-        cd .wiki
+        # Clone the Wiki repository into a directory named '.wiki'
+        git clone https://github.com/${{ github.repository }}.wiki.git .wiki
+
+        # Copy the built documentation to the Wiki repo
+        cp -r flood_adapt/api/build/html/* .wiki/
+
+        # Set up Git to use the GitHub Actions token for authentication
+        git config user.name 'github-actions[bot]'
+        git config user.email 'github-actions[bot]@users.noreply.github.com'
+
+        # Commit and push the changes
         git add .
         git -c user.name='github-actions[bot]' -c user.email='github-actions[bot]@users.noreply.github.com' commit -m 'Update Wiki'
-        git push
+        git push

.github/workflows/docs.yml

@@ -1,10 +1,10 @@
----
 name: Build Documentation
 on:
   push:
     branches: [main]
   pull_request:
     branches: [main]
+  workflow_dispatch:
 
 permissions:
   contents: write
@@ -18,7 +18,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: ["ubuntu-latest" ]
+        os: ["ubuntu-latest"]
         python-version: ["3.11"]
         include:
           - os: ubuntu-latest
@@ -29,53 +29,45 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     steps:
-      - name: checkout code
-        uses: actions/checkout@v3
+      - name: Checkout code
+        uses: actions/checkout@v4
 
       - name: Setup Miniforge3
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
-            python-version: ${{ matrix.python-version }}
-            miniforge-variant: Miniforge3
-            miniforge-version: latest
-            use-mamba: true
+          python-version: ${{ matrix.python-version }}
+          miniforge-variant: Miniforge3
+          miniforge-version: latest
+          use-mamba: true
 
       - name: Setup env
         run: |
-          pip install tomli
-          mamba env create --file=docs/environment_docs.yml
+                pip install tomli
+                mamba env create --file=docs/environment_docs.yml
+                mamba run -n floodadapt_docs pip install . --no-deps
+                VERSION=$(mamba run -n floodadapt_docs python -c "from flood_adapt import __version__; print(__version__)")
+                echo "DOC_VERSION=${VERSION}" >> $GITHUB_ENV
 
-      - name: Setup quarto
+      - name: Setup Quarto
         run: |
-          sudo apt install -y curl
-          sudo apt install -y gdebi-core
-          mkdir tmp
+          sudo apt update
+          sudo apt install -y curl gdebi-core
+          mkdir -p tmp
           curl -L https://github.com/quarto-dev/quarto-cli/releases/download/v1.3.450/quarto-1.3.450-linux-amd64.deb --output tmp/quarto.deb
-          chmod +x tmp/quarto.deb
           sudo gdebi -n tmp/quarto.deb
 
-#      - name: Setup api -double check
-#        run: |
-#          export PATH=/usr/share/miniconda3/bin:$PATH
-#          mamba run -n floodadapt_docs python -m pip install tomli-w
-#          cd docs
-#          mamba run -n floodadapt_docs python api.py
-#          mamba run -n floodadapt_docs python -m quartodoc interlinks
-
       - name: Generate docs
         run: |
           export PATH=/usr/share/miniconda3/bin:$PATH
-          source /usr/share/miniconda3/etc/profile.d/conda.sh
-          conda activate floodadapt_docs
-          quarto render docs/ --execute
-          echo "DOC_VERSION=$(mamba run -n floodadapt_docs python -c 'from floodadapt import __version__ as v; print("dev" if "dev" in v else "v"+v.replace(".dev",""))')" >> $GITHUB_ENV
+          source /usr/share/miniconda/etc/profile.d/conda.sh
+          mamba run -n floodadapt_docs quarto render docs/ --execute
 
       - name: Upload to GitHub Pages
         if: ${{ github.event_name != 'pull_request' && !github.event.act }}
-        uses: peaceiris/actions-gh-pages@v3.9.3
+        uses: peaceiris/actions-gh-pages@v4
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: ./docs/_site
-          destination_dir: ./${{ env.DOC_VERSION }}
+          #destination_dir: ./${{ env.DOC_VERSION }}
           keep_files: false
           full_commit_message: Deploy ${{ env.DOC_VERSION }} to GitHub Pages

.github/workflows/lint.yml

@@ -1,41 +1,14 @@
-name: CI
-on: push
-jobs:
-  ruff:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-      - name: Install Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.10"
-      - name: Install dependencies
-        run: |
-          pip install ruff==0.4.8 # Make sure these are the same as the versions in pyproject.toml
-      # Include `--format=github` to enable automatic inline annotations.
-      - name: Run Ruff
-        run: ruff check . --fix
-  black:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-      - name: Install Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.10"
-      - name: Install dependencies
-        run: |
-          pip install black==24.1.1 # Make sure these are the same as the versions in pyproject.toml
-      - name: Check black version
-        run: black --version
-      - name: Run black
-        run: black --check .
+name: pre-commit
+
+on:
+  pull_request:
+  push:
+    branches: [main]
 
-  typos:
-    name: Spell Check with Typos
+jobs:
+  pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - name: Checkout Actions Repository
-        uses: actions/checkout@v3
-      - name: Check spelling
-        uses: crate-ci/typos@master
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+    - uses: pre-commit/[email protected]

.github/workflows/publish-to-test-pypi.yml

@@ -10,11 +10,11 @@ jobs:
   build-artifacts:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         name: Install Python
         with:
           python-version: '3.11'
@@ -26,7 +26,7 @@ jobs:
       - name: Build artifacts
         run: make pypi
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: releases
           path: dist
@@ -38,9 +38,9 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           name: releases
           path: dist
@@ -49,7 +49,7 @@ jobs:
           ls -ltrh
           ls -ltrh dist
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.10'
 
@@ -62,12 +62,12 @@ jobs:
     needs: test-built-dist
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           name: releases
           path: dist
       - name: Publish package to PyPI
-        uses: pypa/gh-action-pypi-publish@v1.5.1
+        uses: pypa/gh-action-pypi-publish@v1.9.0
         with:
           user: __token__
           password: ${{ secrets.PYPI_TOKEN }}

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.3.0
+    rev: v4.6.0
     hooks:
     -   id: check-yaml
     -   id: end-of-file-fixer
@@ -12,16 +12,15 @@ repos:
         exclude: '^environment/'
     -   id: check-merge-conflict
     -   id: trailing-whitespace
--   repo: https://github.com/psf/black
-    rev: 24.1.1
-    hooks:
-    -   id: black
--   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.8
-    hooks:
-    -   id: ruff
-        args: [--fix, --exit-non-zero-on-fix]
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.5.5
+  hooks:
+    # Run the linter.
+    - id: ruff
+    # Run the formatter.
+    - id: ruff-format
 -   repo: https://github.com/crate-ci/typos
-    rev: v1.22.7
+    rev: v1.23.6
     hooks:
     -   id: typos

.teamcity/FloodAdapt/buildTypes/FloodAdapt_TestbenchFloodAdaptWindows.xml

@@ -93,4 +93,3 @@ call pytest tests --junitxml="report.xml"]]></param>
     <cleanup />
   </settings>
 </build-type>
-

.teamcity/FloodAdapt/project-config.xml

@@ -15,4 +15,3 @@
   </project-extensions>
   <cleanup />
 </project>
-

.teamcity/FloodAdapt/vcsRoots/FloodAdapt_FloodAdapt.xml

@@ -15,4 +15,3 @@
   <param name="username" value="teamcity-deltares" />
   <param name="usernameStyle" value="USERID" />
 </vcs-root>
-

.teamcity/FloodAdapt/vcsRoots/FloodAdapt_SfincTestData.xml

@@ -11,4 +11,3 @@
   <param name="user" value="%svn_buildserver_username%" />
   <param name="working-copy-format" value="1.8" />
 </vcs-root>
-

.teamcity/FloodAdapt/vcsRoots/FloodAdapt_SfincsTestData.xml

@@ -11,4 +11,3 @@
   <param name="user" value="peiter" />
   <param name="working-copy-format" value="1.8" />
 </vcs-root>
-

_extensions/quarto-ext/fontawesome/assets/css/all.css

@@ -16,7 +16,7 @@
 .fa-regular,
 .fab,
 .fa-brands,
-.fal, 
+.fal,
 .fa-light,
 .fat,
 .fa-thin,
@@ -7968,4 +7968,3 @@ readers do not read off random characters that represent icons */
   font-display: block;
   src: url("../webfonts/FontAwesome6Free-Regular-400.woff2") format("woff2"), url("../../webfonts/FontAwesome6Free-Regular-400.ttf") format("truetype");
   unicode-range: U+F003,U+F006,U+F014,U+F016-F017,U+F01A-F01B,U+F01D,U+F022,U+F03E,U+F044,U+F046,U+F05C-F05D,U+F06E,U+F070,U+F087-F088,U+F08A,U+F094,U+F096-F097,U+F09D,U+F0A0,U+F0A2,U+F0A4-F0A7,U+F0C5,U+F0C7,U+F0E5-F0E6,U+F0EB,U+F0F6-F0F8,U+F10C,U+F114-F115,U+F118-F11A,U+F11C-F11D,U+F133,U+F147,U+F14E,U+F150-F152,U+F185-F186,U+F18E,U+F190-F192,U+F196,U+F1C1-F1C9,U+F1D9,U+F1DB,U+F1E3,U+F1EA,U+F1F7,U+F1F9,U+F20A,U+F247-F248,U+F24A,U+F24D,U+F255-F25B,U+F25D,U+F271-F274,U+F278,U+F27B,U+F28C,U+F28E,U+F29C,U+F2B5,U+F2B7,U+F2BA,U+F2BC,U+F2BE,U+F2C0-F2C1,U+F2C3,U+F2D0,U+F2D2,U+F2D4,U+F2DC; }
-