Cookiecutter update

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/Ouranosinc/cookiecutter-pypackage",
-  "commit": "1d9ee5f08d3e8e4f78a4aabb75e2ce4eff8750bf",
+  "commit": "2b31b0f76a180ad93e5a49fe5744306fefb48c9c",
   "checkout": null,
   "context": {
     "cookiecutter": {
@@ -23,7 +23,8 @@
       "open_source_license": "Apache Software License 2.0",
       "generated_with_cruft": "y",
       "__gh_slug": "https://github.com/hydrologie/xhydro-lstm",
-      "_template": "https://github.com/Ouranosinc/cookiecutter-pypackage"
+      "_template": "https://github.com/Ouranosinc/cookiecutter-pypackage",
+      "_commit": "2b31b0f76a180ad93e5a49fe5744306fefb48c9c"
     }
   },
   "directory": null

.github/workflows/bump-version.yml

@@ -44,7 +44,7 @@ jobs:
       actions: read
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@0080882f6c36860b6ba35c610c98ce87d4e2f26f # v2.10.2
+        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
         with:
           disable-sudo: true
           egress-policy: block
@@ -62,9 +62,10 @@ jobs:
       - name: Checkout Repository
         uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
         with:
+          persist-credentials: false
           token: ${{ steps.token_generator.outputs.token }}
       - name: Set up Python3
-        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5.3.0
+        uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5.4.0
         with:
           python-version: "3.x"
       - name: Import GPG Key
@@ -75,28 +76,23 @@ jobs:
           git_user_signingkey: true
           git_commit_gpgsign: true
           trust_level: 5
-      - name: Current Version
-        run: |
-          CURRENT_VERSION="$(grep -E '__version__' src/xhydro_lstm/__init__.py | cut -d ' ' -f3)"
-          echo "current_version=${CURRENT_VERSION}"
-          echo "CURRENT_VERSION=${CURRENT_VERSION}" >> $GITHUB_ENV
       - name: Install CI libraries
         run: |
           python -m pip install --require-hashes -r CI/requirements_ci.txt
       - name: Conditional Bump
         run: |
-          if [[ ${{ env.CURRENT_VERSION }} =~ -dev(\.\d+)? ]]; then
+          CURRENT_VERSION=$(bump-my-version show current_version)
+          if [[ ${CURRENT_VERSION} =~ -dev(\.\d+)? ]]; then
             echo "Development version (ends in 'dev(\.\d+)?'), bumping 'build' version"
             bump-my-version bump build
           else
             echo "Version is stable, bumping 'patch' version"
             bump-my-version bump patch
           fi
-          NEW_VERSION="$(grep -E '__version__' src/xhydro_lstm/__init__.py | cut -d ' ' -f3)"
-          echo "new_version=${NEW_VERSION}"
-          echo "NEW_VERSION=${NEW_VERSION}" >> $GITHUB_ENV
+          echo "new_version=$(bump-my-version show current_version)"
       - name: Push Changes
         uses: ad-m/github-push-action@d91a481090679876dfc4178fef17f286781251df # v0.8.0
         with:
-          force: false
           branch: ${{ github.ref }}
+          force: false
+          github_token: ${{ steps.token_generator.outputs.token }}

.github/workflows/cache-cleaner.yml

@@ -5,7 +5,7 @@ on:
     types:
       - closed
 
-permissions:  # added using https://github.com/step-security/secure-repo
+permissions:
   contents: read
 
 jobs:
@@ -16,7 +16,7 @@ jobs:
       actions: write
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@0080882f6c36860b6ba35c610c98ce87d4e2f26f # v2.10.2
+        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
         with:
           disable-sudo: true
           egress-policy: block
@@ -27,6 +27,8 @@ jobs:
 
       - name: Checkout Repository
         uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        with:
+          persist-credentials: false
 
       - name: Cleanup
         run: |

.github/workflows/codeql.yml

@@ -0,0 +1,99 @@
+# For most projects, this workflow file will not need changing; you simply need to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+name: "CodeQL Advanced"
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  schedule:
+    - cron: '36 9 * * 1'
+
+permissions:
+  contents: read
+
+jobs:
+  analyze:
+    name: Analyze (${{ matrix.language }})
+    # Runner size impacts CodeQL analysis time. To learn more, please see:
+    #   - https://gh.io/recommended-hardware-resources-for-running-codeql
+    #   - https://gh.io/supported-runners-and-hardware-resources
+    #   - https://gh.io/using-larger-runners (GitHub.com only)
+    # Consider using larger runners or machines with greater resources for possible analysis time improvements.
+    runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
+    permissions:
+      # required for all workflows
+      security-events: write
+
+      # required to fetch internal or private CodeQL packs
+      packages: read
+
+      # only required for workflows in private repositories
+      actions: read
+      contents: read
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+        - language: python
+          build-mode: none
+        # CodeQL supports the following values keywords for 'language': 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'swift'
+        # Use `c-cpp` to analyze code written in C, C++ or both
+        # Use 'java-kotlin' to analyze code written in Java, Kotlin or both
+        # Use 'javascript-typescript' to analyze code written in JavaScript, TypeScript or both
+        # To learn more about changing the languages that are analyzed or customizing the build mode for your analysis,
+        # see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/customizing-your-advanced-setup-for-code-scanning.
+        # If you are analyzing a compiled language, you can modify the 'build-mode' for that language to customize how
+        # your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages
+    steps:
+      - name: Harden Runner
+        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
+        with:
+          disable-sudo: true
+          egress-policy: audit
+
+      - name: Checkout Repository
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        with:
+          persist-credentials: false
+
+      # Initializes the CodeQL tools for scanning.
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@48ab28a6f5dbc2a99bf1e0131198dd8f1df78169 # v3.28.0
+        with:
+          languages: ${{ matrix.language }}
+          build-mode: ${{ matrix.build-mode }}
+          # If you wish to specify custom queries, you can do so here or in a config file.
+          # By default, queries listed here will override any specified in a config file.
+          # Prefix the list here with "+" to use these queries and those in the config file.
+
+          # For more details on CodeQL's query packs, refer to:
+          # https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+          # queries: security-extended,security-and-quality
+
+      # If the analyze step fails for one of the languages you are analyzing with
+      # "We were unable to automatically build your code", modify the matrix above
+      # to set the build mode to "manual" for that language. Then modify this step
+      # to build your code.
+      # ℹ️ Command-line programs to run using the OS shell.
+      # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+      - if: matrix.build-mode == 'manual'
+        shell: bash
+        run: |
+          echo 'If you are using a "manual" build mode for one or more of the' \
+            'languages you are analyzing, replace this with the commands to build' \
+            'your code, for example:'
+          echo '  make bootstrap'
+          echo '  make release'
+          exit 1
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@48ab28a6f5dbc2a99bf1e0131198dd8f1df78169 # v3.28.0
+        with:
+          category: "/language:${{matrix.language}}"

.github/workflows/dependency-review.yml

@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@0080882f6c36860b6ba35c610c98ce87d4e2f26f # v2.10.2
+        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
         with:
           disable-sudo: true
           egress-policy: block
@@ -28,6 +28,8 @@ jobs:
 
       - name: Checkout Repository
         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/first-pull-request.yml

@@ -16,7 +16,7 @@ jobs:
       pull-requests: write
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@0080882f6c36860b6ba35c610c98ce87d4e2f26f # v2.10.2
+        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
         with:
           disable-sudo: true
           egress-policy: block

.github/workflows/label.yml

@@ -23,7 +23,7 @@ jobs:
       pull-requests: write
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@0080882f6c36860b6ba35c610c98ce87d4e2f26f # v2.10.2
+        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
         with:
           disable-sudo: true
           egress-policy: block

.github/workflows/main.yml

@@ -31,19 +31,27 @@ jobs:
           - "3.x"
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@0080882f6c36860b6ba35c610c98ce87d4e2f26f # v2.10.2
+        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
         with:
           egress-policy: audit
       - name: Checkout Repository
         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
+        uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5.4.0
         with:
           python-version: ${{ matrix.python-version }}
           cache: "pip"
       - name: Install CI libraries
         run: |
           python -m pip install --require-hashes -r CI/requirements_ci.txt
+      - name: Environment Caching
+        uses: actions/cache@1bd1e32a3bdc45362d1e726936510720a7c30a57 # v4.2.0
+        with:
+          path: |
+            .tox
+          key: ${{ hashFiles('pyproject.toml', 'tox.ini') }}-lint
       - name: Run linting suite
         run: |
           python -m tox -e lint
@@ -63,13 +71,15 @@ jobs:
           # - "3.13
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@0080882f6c36860b6ba35c610c98ce87d4e2f26f # v2.10.2
+        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
         with:
           egress-policy: audit
       - name: Checkout Repository
         uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        with:
+          persist-credentials: false
       - name: Set up Python${{ matrix.python-version }}
-        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5.3.0
+        uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5.4.0
         with:
           python-version: ${{ matrix.python-version }}
           cache: "pip"
@@ -97,34 +107,32 @@ jobs:
     strategy:
       matrix:
         os: [ 'ubuntu-latest' ]
-        python-version: [ "3.9", "3.10", "3.11", "3.12" ]
+        python-version: [ "3.10", "3.11", "3.12" ]
     defaults:
       run:
         shell: bash -l {0}
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@0080882f6c36860b6ba35c610c98ce87d4e2f26f # v2.10.2
+        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
         with:
           egress-policy: audit
       - name: Checkout Repository
         uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        with:
+          persist-credentials: false
       - name: Setup Conda (Micromamba) with Python${{ matrix.python-version }}
-        uses: mamba-org/setup-micromamba@068f1ab4b37ed9b3d9f73da7db90a0cda0a48d29 # v2.0.3
+        uses: mamba-org/setup-micromamba@0dea6379afdaffa5d528b3d1dabc45da37f443fc # v2.0.4
         with:
           cache-downloads: true
           environment-file: environment-dev.yml
           create-args: >-
             python=${{ matrix.python-version }}
-          micromamba-version: "1.5.10-0"  # pinned to avoid the breaking changes with mamba and micromamba (2.0.0).
-      - name: Conda and Mamba versions
-        run: |
-          echo "micromamba $(micromamba --version)"
       - name: Install xhydro-lstm
         run: |
           python -m pip install --no-deps .
       - name: Check versions
         run: |
-          conda list
+          micromamba list
           python -m pip check || true
       - name: Test with pytest
         run: |
@@ -145,7 +153,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@0080882f6c36860b6ba35c610c98ce87d4e2f26f # v2.10.2
+        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
         with:
           disable-sudo: true
           egress-policy: audit

.github/workflows/publish-pypi.yml

@@ -18,19 +18,22 @@ jobs:
       id-token: write
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@0080882f6c36860b6ba35c610c98ce87d4e2f26f # v2.10.2
+        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
         with:
           disable-sudo: true
           egress-policy: block
           allowed-endpoints: >
             files.pythonhosted.org:443
             github.com:443
             pypi.org:443
+            ruf-repo-cdn.sigstore.dev:443
             upload.pypi.org:443
       - name: Checkout Repository
         uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        with:
+          persist-credentials: false
       - name: Set up Python3
-        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5.3.0
+        uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5.4.0
         with:
           python-version: "3.x"
       - name: Install CI libraries
@@ -40,4 +43,4 @@ jobs:
         run: |
           python -m flit build
       - name: Publish distribution 📦 to PyPI
-        uses: pypa/gh-action-pypi-publish@67339c736fd9354cd4f8cb0b744f2b82a74b5c70 # v1.12.3
+        uses: pypa/gh-action-pypi-publish@76f52bc884231f62b9a034ebfe128415bbaabdfc # v1.12.4

.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:
@@ -29,7 +31,7 @@ jobs:
       id-token: write
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@0080882f6c36860b6ba35c610c98ce87d4e2f26f # v2.10.2
+        uses: step-security/harden-runner@cb605e52c26070c328afc4562f0b4ada7618a84e # v2.10.4
         with:
           disable-sudo: true
           egress-policy: block