Refactor ECCC functionality and create Preprocess module

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/Ouranosinc/cookiecutter-pypackage",
-  "commit": "1d9ee5f08d3e8e4f78a4aabb75e2ce4eff8750bf",
+  "commit": "63f44fcbfe2e16118a4fa6b09fe847aa44e0715a",
   "checkout": null,
   "context": {
     "cookiecutter": {

.github/workflows/bump-version.yml

@@ -56,7 +56,7 @@ jobs:
             github.com:443
             pypi.org:443
       - name: Checkout Repository (no persist-credentials)
-        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
         with:
           persist-credentials: false
           fetch-depth: 0
@@ -68,23 +68,20 @@ jobs:
         run: |
           git config --local user.email "bumpversion[bot]@ouranos.ca"
           git config --local user.name "bumpversion[bot]"
-      - name: Current Version
-        run: |
-          CURRENT_VERSION="$(grep -E '__version__' src/miranda/__init__.py | cut -d ' ' -f3)"
-          echo "CURRENT_VERSION=${CURRENT_VERSION}" >> $GITHUB_ENV
       - name: Install CI libraries
         run: |
           python -m pip install --require-hashes -r CI/requirements_ci.txt
       - name: Conditional Bump Version
         run: |
-          if [[ ${{ env.CURRENT_VERSION }} =~ -dev(\.\d+)? ]]; then
+          CURRENT_VERSION=$(bump-my-version show current_version)
+          if [[ ${CURRENT_VERSION} =~ -dev(\.\d+)? ]]; then
             echo "Development version (ends in 'dev(\.\d+)?'), bumping 'build' version"
             bump-my-version bump build
           else
             echo "Version is stable, bumping 'patch' version"
             bump-my-version bump patch
           fi
-          bump-my-version show-bump
+          echo "new_version=$(bump-my-version show current_version)"
       - name: Push Changes
         uses: ad-m/github-push-action@d91a481090679876dfc4178fef17f286781251df # v0.8.0
         with:

.github/workflows/cache-cleaner.yml

@@ -26,7 +26,9 @@ jobs:
             objects.githubusercontent.com:443
 
       - name: Checkout Repository
-        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        with:
+          persist-credentials: false
 
       - name: Cleanup
         run: |

.github/workflows/codeql-analysis.yml

@@ -13,7 +13,8 @@ name: "CodeQL"
 
 on:
   push:
-    branches: [ "main" ]
+    branches:
+      - main
     paths-ignore:
       - ../../CHANGELOG.rst
       - pyproject.toml
@@ -43,6 +44,8 @@ jobs:
     steps:
     - name: Checkout repository
       uses: actions/checkout@v4
+      with:
+        persist-credentials: false
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL

.github/workflows/dependency-review.yml

@@ -28,7 +28,9 @@ jobs:
             github.com:443
 
       - name: Checkout Repository
-        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        with:
+          persist-credentials: false
 
       - name: Dependency Review
         uses: actions/dependency-review-action@3b139cfc5fae8b618d3eae3675e383bb1769c019 # v4.5.0

.github/workflows/main.yml

@@ -38,7 +38,9 @@ jobs:
         with:
           egress-policy: audit
       - name: Checkout Repository
-        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        with:
+          persist-credentials: false
       - name: Set up Python${{ matrix.python-version }}
         uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5.3.0
         with:
@@ -60,14 +62,21 @@ jobs:
     strategy:
       matrix:
         os: [ 'ubuntu-latest' ]
-        python-version: [ "3.9", "3.10", "3.11", "3.12" ] # "3.13"
+        python-version:
+          - "3.9"
+          - "3.10"
+          - "3.11"
+          - "3.12"
+          # - "3.13"
     steps:
       - name: Harden Runner
         uses: step-security/harden-runner@0080882f6c36860b6ba35c610c98ce87d4e2f26f # v2.10.2
         with:
           egress-policy: audit
       - name: Checkout Repository
-        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        with:
+          persist-credentials: false
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5.3.0
         with:
@@ -102,7 +111,12 @@ jobs:
     strategy:
       matrix:
         os: [ 'ubuntu-latest' ]
-        python-version: [ "3.9", "3.10", "3.11", "3.12" ]
+        python-version:
+          - "3.9"
+          - "3.10"
+          - "3.11"
+          - "3.12"
+          # - "3.13"
     defaults:
       run:
         shell: bash -l {0}
@@ -112,15 +126,16 @@ jobs:
         with:
           egress-policy: audit
       - name: Checkout Repository
-        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        with:
+          persist-credentials: false
       - name: Setup Conda (Micromamba) with Python${{ matrix.python-version }}
         uses: mamba-org/setup-micromamba@068f1ab4b37ed9b3d9f73da7db90a0cda0a48d29 # v2.0.3
         with:
           cache-downloads: true
           environment-file: environment-dev.yml
           create-args: >-
             python=${{ matrix.python-version }}
-          micromamba-version: 1.5.10-0 # Pin micromamba version because of following issue: https://github.com/mamba-org/setup-micromamba/issues/225
       - name: Install miranda
         run: |
           python -m pip install --no-deps .

.github/workflows/publish-pypi.yml

@@ -28,7 +28,9 @@ jobs:
             pypi.org:443
             upload.pypi.org:443
       - name: Checkout Repository
-        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        with:
+          persist-credentials: false
       - name: Set up Python3
         uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5.3.0
         with:

.github/workflows/scorecard.yml

@@ -16,7 +16,9 @@ on:
       - main
 
 # Declare default permissions as read only.
-permissions: read-all
+# Read-all permission is not technically needed for this workflow.
+permissions:
+  contents: read
 
 jobs:
   analysis:
@@ -47,7 +49,7 @@ jobs:
             www.bestpractices.dev:443
 
       - name: Checkout Repository
-        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
         with:
           persist-credentials: false
 

.github/workflows/tag-testpypi.yml

@@ -21,7 +21,9 @@ jobs:
         with:
           egress-policy: audit
       - name: Checkout Repository
-        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        with:
+          persist-credentials: false
       - name: Create Release
         uses: softprops/action-gh-release@7b4da11513bf3f43f9999e90eabced41ab8bb048 # 2.2.0
         env:
@@ -52,7 +54,9 @@ jobs:
             pypi.org:443
             test.pypi.org:443
       - name: Checkout Repository
-        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        with:
+          persist-credentials: false
       - name: Set up Python3
         uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5.3.0
         with:

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ repos:
     rev: v3.19.0
     hooks:
       - id: pyupgrade
-        args: [ '--py38-plus' ]
+        args: [ '--py39-plus' ]
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
     hooks:
@@ -41,7 +41,7 @@ repos:
     hooks:
       - id: isort
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.1
+    rev: v0.8.2
     hooks:
       - id: ruff
         args: [ '--fix' ]
@@ -78,6 +78,11 @@ repos:
     hooks:
       - id: check-github-workflows
       - id: check-readthedocs
+  - repo: https://github.com/woodruffw/zizmor-pre-commit
+    rev: v0.8.0
+    hooks:
+      - id: zizmor
+        args: [ '--config=.zizmor.yml' ]
   - repo: meta
     hooks:
       - id: check-hooks-apply

.zizmor.yml

@@ -0,0 +1,6 @@
+rules:
+  dangerous-triggers:
+    ignore:
+      - label.yml:9
+      - first-pull-request.yml:3
+      - workflow-warning.yml:3

CI/requirements_ci.in

@@ -1,6 +1,6 @@
-bump-my-version==0.27.0
+bump-my-version==0.28.0
 coveralls==4.0.1
 pip==24.3.1
 flit==3.9.0
 tox==4.23.2
-tox-gh==1.3.2
+tox-gh==1.4.4

CI/requirements_ci.txt

@@ -1,5 +1,5 @@
 #
-# This file is autogenerated by pip-compile with Python 3.8
+# This file is autogenerated by pip-compile with Python 3.9
 # by the following command:
 #
 #    pip-compile --generate-hashes --output-file=CI/requirements_ci.txt CI/requirements_ci.in
@@ -12,9 +12,9 @@ bracex==2.4 \
     --hash=sha256:a27eaf1df42cf561fed58b7a8f3fdf129d1ea16a81e1fadd1d17989bc6384beb \
     --hash=sha256:efdc71eff95eaff5e0f8cfebe7d01adf2c8637c8c92edaf63ef348c241a82418
     # via wcmatch
-bump-my-version==0.27.0 \
-    --hash=sha256:483c517af91559644d45036648e5d99f4f8c85f8d01394097d3d3e42c9e6acad \
-    --hash=sha256:911bfaf7d847d4348844c8fd16f7a11322233fb8dc90123f638069a369003642
+bump-my-version==0.28.0 \
+    --hash=sha256:cc84ace477022a4cc8c401ef5c035f2f752df45488be90ccb764a47f7de0e395 \
+    --hash=sha256:ff3cb51bb15509ae8ebb8e8efa3eaa7c02209677f45457c8b007ef2f5bef7179
     # via -r CI/requirements_ci.in
 cachetools==5.5.0 \
     --hash=sha256:02134e8439cdc2ffb62023ce1debca2944c3f289d66bb17ead3ab3dede74b292 \
@@ -399,27 +399,25 @@ tox==4.23.2 \
     # via
     #   -r CI/requirements_ci.in
     #   tox-gh
-tox-gh==1.3.2 \
-    --hash=sha256:beb8d277d5d7c1a1f09c107e4ef80bd7dd2f8f5d020edfaf4c1e3ae8fd45bf6f \
-    --hash=sha256:c2d6e977f66712e7cd5e5d1b655a1bd4c91ebaf3be104befdb53c81587292d7e
+tox-gh==1.4.4 \
+    --hash=sha256:4ea585f66585b90f5826b1677cfc9453747792a0f9ff83d468603bc17556e07b \
+    --hash=sha256:b962e0f8c4619e98d11c2a135939876691e148b843b7dac4cff7de1dc4f7c215
     # via -r CI/requirements_ci.in
 typing-extensions==4.12.2 \
     --hash=sha256:04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d \
     --hash=sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8
     # via
-    #   annotated-types
     #   pydantic
     #   pydantic-core
-    #   rich
     #   rich-click
     #   tox
 urllib3==2.2.2 \
     --hash=sha256:a448b2f64d686155468037e1ace9f2d2199776e17f0a46610480d311f73e3472 \
     --hash=sha256:dd505485549a7a552833da5e6063639d0d177c04f23bc3864e41e5dc5f612168
     # via requests
-virtualenv==20.26.6 \
-    --hash=sha256:280aede09a2a5c317e409a00102e7077c6432c5a38f0ef938e643805a7ad2c48 \
-    --hash=sha256:7345cc5b25405607a624d8418154577459c3e0277f5466dd79c49d5e492995f2
+virtualenv==20.27.1 \
+    --hash=sha256:142c6be10212543b32c6c45d3d3893dff89112cc588b7d0879ae5a1ec03a47ba \
+    --hash=sha256:f11f1b8a29525562925f745563bfd48b189450f61fb34c4f9cc79dd5aa32a1f4
     # via tox
 wcmatch==8.5.2 \
     --hash=sha256:17d3ad3758f9d0b5b4dedc770b65420d4dac62e680229c287bf24c9db856a478 \

environment-dev.yml

@@ -33,20 +33,20 @@ dependencies:
   - xesmf
   - zarr
   # Dev tools and testing
-  - pip >=24.2.0
-  - bump-my-version >=0.25.1
-  - watchdog >=4.0.0
+  - pip >=24.3.1
+  - black ==24.10.0
+  - blackdoc ==0.3.9
+  - bump-my-version >=0.28.0
+  - coverage >=7.5.0
+  - coveralls >=4.0.1
   - flake8 >=7.1.1
   - flake8-rst-docstrings >=0.3.0
   - flit >=3.9.0,<4.0
-  - tox >=4.17.1
-  - coverage >=7.5.0
-  - coveralls >=4.0.1
-  - pytest >=8.3.2
-  - pytest-cov >=5.0.0
-  - black ==24.8.0
-  - blackdoc ==0.3.9
   - isort ==5.13.2
   - numpydoc >=1.8.0
   - pre-commit >=3.5.0
-  - ruff >=0.5.7
+  - pytest >=8.3.2
+  - pytest-cov >=5.0.0
+  - ruff >=0.8.2
+  - tox >=4.23.2
+  - watchdog >=4.0.0

environment-docs.yml

@@ -3,16 +3,16 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - python >=3.12,<3.13
-  - sphinx >=7.0.0
-  - pandoc
-  - furo >=2023.07.26
-  - ipython
+  - python >=3.9,<3.13
   - ipykernel
+  - ipython
   - nbsphinx
+  # Docs
+  - furo >=2023.07.26
+  - pandoc
+  - sphinx >=7.1.0
   - sphinx-autoapi
   - sphinx-codeautolink
   - sphinx-copybutton
   - sphinx-intl
   - sphinx-mdinclude
-  - sphinxcontrib-napoleon