Update CI & use pre-commit for linting

.gitattributes

@@ -0,0 +1,2 @@
+# GitHub syntax highlighting
+pixi.lock linguist-language=YAML

.github/dependabot.yml

@@ -0,0 +1,8 @@
+version: 2
+# there is no conda support for dependabot so this is the closest analog
+# since the conda deps are also built from pyproject.toml it should work well enough
+updates:
+  - package-ecosystem: "pip"
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

.github/workflows/docs.yml

@@ -1,61 +1,70 @@
-name: Build Docs
+name: Build Documentation
 
-# We don't want pushes (or PRs) to gh-pages to kick anything off
 on:
+  workflow_dispatch:
   push:
-    branches: [ main ]
+    branches: [main]
+    paths:
+      - tests/*
+      - hydromt/*
+      - docs/*
+      - examples/*
+      - pyproject.toml
   pull_request:
-    branches: [ main ]
+    branches: [main]
+    paths:
+      - tests/*
+      - hydromt/*
+      - docs/*
+      - examples/*
+      - pyproject.toml
 
 jobs:
   # Build docs on Linux
-  Docs:
-    name: linux docs
-    runs-on: ubuntu-latest
+  test-docs:
     env:
       DOC_VERSION: dev
-    defaults:
-      run:
-        shell: bash -l {0}
+      PYDEVD_DISABLE_FILE_VALIDATION: 1
+    timeout-minutes: 30
+    runs-on: ubuntu-latest
     steps:
-      - name: Checkout source
-        uses: actions/checkout@v2
-
-      # - name: Get tags
-      #   run: git fetch --depth=1 origin +refs/tags/*:refs/tags/*
+      - name: checkout code
+        uses: actions/checkout@v3
 
-      - name: Setup environment
+      - name: Setup Mambaforge
         uses: conda-incubator/setup-miniconda@v2
         with:
-          python-version: "3.10"
-          mamba-version: "*"
-          channels: conda-forge,defaults
-          channel-priority: true
-          environment-file: envs/hydromt-sfincs-dev.yml
-          activate-environment: hydromt-sfincs-dev
+            python-version: '3.11'
+            miniforge-variant: Mambaforge
+            miniforge-version: latest
+            use-mamba: true
 
-      - name: Install hydromt-sfincs
-        run: flit install
+      - name: Setup env
+        run: |
+          python make_env.py full -p 3.11 -n hydromt-sfincs -o environment-doc.yml
+          mamba env create -f environment-doc.yml
+          mamba run -n hydromt-sfincs pip install -e .
 
-      # Move examples folder before make html for nbsphinx
-      - name: Build docs
+      # if we're not publishing we don't have to write them, so we might as well
+      # save ourself a bunch of IO time
+      - name: Build dummy docs
+        if: ${{ github.event_name == 'pull_request' }}
         run: |
-          pushd docs
-          make html
-          popd
+          mamba run -n hydromt-sfincs sphinx-build ./docs ./docs/_build -b dummy -W
 
-      # This overrides the version "dev" with the proper version if we're building off a
-      # branch that's not master (which is confined to n.nn.x above) or on a tag.
-      - name: Set doc version
-        run: echo "DOC_VERSION=$(python -c 'from hydromt_sfincs import __version__ as v; print("dev" if "dev" in v else "v"+v)')" >> $GITHUB_ENV
+      - name: Build html docs
+        if: ${{ github.event_name != 'pull_request' }}
+        run: |
+          mamba run -n hydromt-sfincs sphinx-build -M html ./docs ./docs/_build -W
+          echo "DOC_VERSION=$(mamba run -n hydromt-sfincs python -c 'from hydromt_sfincs import __version__ as v; print("dev" if "dev" in v else "v"+v)')" >> $GITHUB_ENV
 
       - name: Upload to GitHub Pages
         if: ${{ github.event_name != 'pull_request'}}
         uses: peaceiris/[email protected]
         with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
+          github_token: ${{ secrets.GITHUB_TOKEN }}path
           publish_dir: ./docs/_build/html
           exclude_assets: '.buildinfo,_sources/*,_examples/*.ipynb'
           destination_dir: ./${{ env.DOC_VERSION }}
           keep_files: false
-          full_commit_message: Deploy ${{ env.DOC_VERSION }} to GitHub Pages
+          full_commit_message: Deploy ${{ env.DOC_VERSION }} to GitHub Pages

.github/workflows/linting.yml

@@ -0,0 +1,16 @@
+name: Linting
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+      - uses: pre-commit/[email protected]

.github/workflows/publish.yml

@@ -16,11 +16,11 @@ jobs:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
- 
-      - uses: actions/setup-python@v4
+
+      - uses: actions/setup-python@v5
         name: Install Python
         with:
-          python-version: 3.8
+          python-version: 3.11
 
       - name: Install dependencies
         run: |
@@ -113,4 +113,4 @@ jobs:
         with:
           user: __token__
           password: ${{ secrets.PYPI_TOKEN }}
-          verbose: true
+          verbose: true

.github/workflows/tests.yml

@@ -1,47 +1,61 @@
-name: Tests stable
+name: Tests
 
 on:
   push:
-    branches: [ main ]
+    branches: [main]
+    paths:
+      - tests/*
+      - hydromt_sfincs/*
+      - pyproject.toml
   pull_request:
-    branches: [ main ]
+    branches: [main]
+    paths:
+      - tests/*
+      - hydromt_sfincs/*
+      - pyproject.toml
+
 
 jobs:
-  Test:
-    name: ${{ matrix.os }} - py${{ matrix.python-version }}
-    runs-on: ${{ matrix.os }}
+  build:
     defaults:
       run:
         shell: bash -l {0}
     strategy:
       fail-fast: false
       matrix:
-        os: ["ubuntu-latest"] #, "macos-latest", "windows-latest"]
-        python-version: ["3.10", "3.11"] # TODO: add 3.9 back
-
+        os: [ubuntu-latest]
+        python-version: ['3.10','3.11'] # '3.9'
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    concurrency:
+      group: ${{ github.workflow }}-${{ matrix.python-version }}-${{ github.ref }}
+      cancel-in-progress: true
     steps:
-      - uses: actions/checkout@v2
-      - uses: conda-incubator/setup-miniconda@v2
+
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-python@v5
+        id: py
         with:
-          python-version: ${{ matrix.python-version }}
-          mamba-version: "*"
-          channels: conda-forge,defaults
-          channel-priority: true
-          environment-file: envs/hydromt-sfincs-dev.yml
-          activate-environment: hydromt-sfincs-dev
-
-      - name: Conda info
-        run: |
-         conda info
-         conda list
+          # caching, see https://github.com/actions/setup-python/blob/main/docs/advanced-usage.md#caching-packages
+          cache: 'pip'
+          cache-dependency-path: pyproject.toml
 
-      - name: Intall hydromt_sfincs
-        run: pip install .
+      # true if cache-hit occurred on the primary key
+      - name: Cache hit
+        run: echo '${{ steps.py.outputs.cache-hit }}'
 
-      - name: Test
-        run: python -m pytest --verbose --cov=hydromt_sfincs --cov-report xml
+      # build environment with pip
+      - name: Install hydromt-sfincs
+        run: |
+          pip install --upgrade pip
+          pip install .[test,examples]
 
-      - name: Check style
-        run: black --check .
+      # run test
+      - name: Test
+        run: |
+          export NUMBA_DISABLE_JIT=1
+          python -m pytest --verbose --cov=hydromt_sfincs --cov-report xml
 
+      # upload coverage
       - uses: codecov/codecov-action@v3

.github/workflows/tests_dev.yml

@@ -1,47 +1,60 @@
-name: Tests dev
+name: Tests with HydroMT dev
 
 on:
+  # trigger weekly on monday at 00:00 UTC
+  schedule:
+    - cron: '0 0 * * 1'
   push:
-    branches: [ main ]
+    branches: [main]
+    paths:
+      - tests/*
+      - hydromt_sfincs/*
+      - pyproject.toml
   pull_request:
-    branches: [ main ]
+    branches: [main]
+    paths:
+      - tests/*
+      - hydromt_sfincs/*
+      - pyproject.toml
+
 
 jobs:
-  Test:
-    name: ubuntu-latest - py3.9
-    runs-on: "ubuntu-latest"
+  build:
     defaults:
       run:
         shell: bash -l {0}
     strategy:
       fail-fast: false
-
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    concurrency:
+      group: ${{ github.workflow }}-${{ matrix.python-version }}-${{ github.ref }}
+      cancel-in-progress: true
     steps:
-      - uses: actions/checkout@v2
-      - uses: conda-incubator/setup-miniconda@v2
-        with:
-          python-version: "3.9"
-          mamba-version: "*"
-          channels: conda-forge,defaults
-          channel-priority: true
-          environment-file: envs/hydromt-sfincs-dev.yml
-          activate-environment: hydromt-sfincs-dev
-
-      - name: Conda info
-        run: |
-         conda info
-         conda list
 
-      - name: Intall hydromt core dev version
-        run: pip install git+https://github.com/Deltares/hydromt.git
+      - uses: actions/checkout@v3
 
-      - name: Intall hydromt_sfincs
-        run: pip install .
+      - uses: actions/setup-python@v5
+        id: py311
+        with:
+          python-version: 3.11
+          # caching, see https://github.com/actions/setup-python/blob/main/docs/advanced-usage.md#caching-packages
+          cache: 'pip'
+          cache-dependency-path: pyproject.toml
 
-      - name: Test
-        run: python -m pytest --verbose --cov=hydromt_sfincs --cov-report xml
+      # true if cache-hit occurred on the primary key
+      - name: Cache hit
+        run: echo '${{ steps.py311.outputs.cache-hit }}'
 
-      - name: Check style
-        run: black --check .
+      # build environment with pip
+      - name: Install hydromt-sfincs
+        run: |
+          pip install --upgrade pip
+          pip install .[test,examples]
+          pip install git+https://github.com/Deltares/hydromt.git
 
-      - uses: codecov/codecov-action@v3
+      # run test
+      - name: Test
+        run: |
+          export NUMBA_DISABLE_JIT=1
+          python -m pytest --verbose

.gitignore

@@ -118,3 +118,11 @@ venv.bak/
 
 # dask
 dask-worker-space/
+
+#ruff linting
+.ruff_cache
+.envrc
+pyrightconfig.json
+
+pixi.lock
+.pixi

.pre-commit-config.yaml

@@ -0,0 +1,34 @@
+---
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+      - id: check-ast
+      - id: check-json
+      - id: debug-statements
+      - id: mixed-line-ending
+  # make sure notebooks are stripped of output before committing
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.6.1
+    hooks:
+      - id: nbstripout
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 23.12.0
+    hooks:
+      - id: black-jupyter
+        description: Black, with Jupyter Notebook support
+  # - repo: https://github.com/astral-sh/ruff-pre-commit
+  #   rev: v0.1.2
+  #   hooks:
+  #     - id: ruff
+  #       args: [--fix, --exit-non-zero-on-fix]
+  #     - id: ruff-format
+  # - repo: https://github.com/python-jsonschema/check-jsonschema
+  #   rev: 0.24.0
+  #   hooks:
+  #     - id: check-github-workflows
+  #     - id: check-github-actions

.zenodo.json

@@ -36,4 +36,4 @@
     ],
     "access_right": "open",
     "license": "GPL-3.0"
-}
+}

LICENSE

@@ -671,4 +671,4 @@ into proprietary programs.  If your program is a subroutine library, you
 may consider it more useful to permit linking proprietary applications with
 the library.  If this is what you want to do, use the GNU Lesser General
 Public License instead of this License.  But first, please read
-<https://www.gnu.org/licenses/why-not-lgpl.html>.
+<https://www.gnu.org/licenses/why-not-lgpl.html>.