Update workflows (#503)

Summary of changes:

 1.   updated all the used action versions to the latest vesion, as some were really quite out of date, and made any changes necessary to fix whatever broke
  2.  removed black in favour of ruff formatting as ruff formatting implements the same formatting rules as black but runs at least an order of magnitude faster
  3.  did the same two things for the pre-commit config
   4.  ran pre-commit on all files
    5. removed the manual linting steps in favor of just using the pre-commit action which is both faster (does better caching) and ensures both local and ci checks are consistent

.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'
 
@@ -45,7 +45,7 @@ jobs:
         # 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'

.github/workflows/docs.yml

@@ -3,9 +3,9 @@ on:
   push:
     branches: [main]
   pull_request:
-    branches: [main] 
+    branches: [main]
   workflow_dispatch:
-  
+
 permissions:
   contents: write
 
@@ -30,10 +30,10 @@ jobs:
 
     steps:
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup Miniforge3
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           python-version: ${{ matrix.python-version }}
           miniforge-variant: Miniforge3
@@ -59,12 +59,12 @@ jobs:
       - name: Generate docs
         run: |
           export PATH=/usr/share/miniconda3/bin:$PATH
-          source /usr/share/miniconda3/etc/profile.d/conda.sh
+          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

.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; }
-

_extensions/quarto-ext/fontawesome/fontawesome.lua

@@ -44,7 +44,7 @@ return {
       group = icon
       icon = pandoc.utils.stringify(args[2])
     end
-    
+
     local title = pandoc.utils.stringify(kwargs["title"])
     if not isEmpty(title) then
       title = " title=\"" .. title  .. "\""
@@ -58,7 +58,7 @@ return {
     end
 
     local size = pandoc.utils.stringify(kwargs["size"])
-    
+
     -- detect html (excluding epub which won't handle fa)
     if quarto.doc.is_format("html:js") then
       ensureHtmlDeps()

docs/.gitignore

@@ -6,4 +6,3 @@
 !api/.gitkeep
 *.jupyter_cache/
 objects.json
-