From b11f8292e06dd9a3ee99e56cd26d0efe427710a3 Mon Sep 17 00:00:00 2001
From: Yannick DAYER <yannick.dayer@idiap.ch>
Date: Thu, 18 Jul 2024 14:48:33 +0200
Subject: [PATCH 1/5] ci: follow the same workflow structure as clapper.

Adds a packaging step in tests, publish binaries to gitlab on a release,
changed the file name to be uniform with other projects.
---
 .github/workflows/coverage.yml                |  2 +-
 .../{publish-pypi.yml => deploy.yml}          | 20 ++++++++++++
 ...ocumentation-links.yml => doc-preview.yml} |  0
 .github/workflows/{pre-commit.yml => qa.yml}  |  0
 .github/workflows/{build.yml => tests.yml}    | 31 +++++++++++++++++--
 README.md                                     |  2 +-
 6 files changed, 51 insertions(+), 4 deletions(-)
 rename .github/workflows/{publish-pypi.yml => deploy.yml} (68%)
 rename .github/workflows/{documentation-links.yml => doc-preview.yml} (100%)
 rename .github/workflows/{pre-commit.yml => qa.yml} (100%)
 rename .github/workflows/{build.yml => tests.yml} (74%)

diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
index 0b1d0e9..3ce1af9 100644
--- a/.github/workflows/coverage.yml
+++ b/.github/workflows/coverage.yml
@@ -7,7 +7,7 @@ name: Post coverage comment
 
 on:
   workflow_run:
-    workflows: ["build"]
+    workflows: ["tests"]
     types:
       - completed
 
diff --git a/.github/workflows/publish-pypi.yml b/.github/workflows/deploy.yml
similarity index 68%
rename from .github/workflows/publish-pypi.yml
rename to .github/workflows/deploy.yml
index 8bbd6a8..b3e7725 100644
--- a/.github/workflows/publish-pypi.yml
+++ b/.github/workflows/deploy.yml
@@ -35,6 +35,7 @@ jobs:
         with:
           name: release-dists
           path: dist/
+          if-no-files-found: error
 
   pypi-publish:
     runs-on: ubuntu-22.04
@@ -61,3 +62,22 @@ jobs:
 
       - name: Publish release distributions to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-publish:
+    name: Upload the release package to GitHub Release
+    needs:
+      - release-build
+    runs-on: ubuntu-22.04
+    permissions:
+      contents: write  # IMPORTANT: mandatory for making GitHub Releases
+    steps:
+      - name: Retrieve the package from GitHub actions artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: release-dist
+          path: dist/
+      - name: Upload the release package to GitHub Release
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        # Upload to GitHub Release using the `gh` CLI.
+        run: gh release upload '${{ github.ref_name }}' dist/** --repo '${{ github.repository }}'
diff --git a/.github/workflows/documentation-links.yml b/.github/workflows/doc-preview.yml
similarity index 100%
rename from .github/workflows/documentation-links.yml
rename to .github/workflows/doc-preview.yml
diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/qa.yml
similarity index 100%
rename from .github/workflows/pre-commit.yml
rename to .github/workflows/qa.yml
diff --git a/.github/workflows/build.yml b/.github/workflows/tests.yml
similarity index 74%
rename from .github/workflows/build.yml
rename to .github/workflows/tests.yml
index 9f234a4..cfabecb 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/tests.yml
@@ -3,7 +3,7 @@
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
 
-name: build
+name: tests
 
 on:
   push:
@@ -57,7 +57,7 @@ jobs:
           pixi-version: v0.25.0
           environments: test
       - name: Run Tests
-        run: pixi run test-ci
+        run: pixi run -e test test-ci
       - name: Coverage comment
         id: coverage_comment
         uses: py-cov-action/python-coverage-comment-action@v3
@@ -89,3 +89,30 @@ jobs:
         run: pixi run doc
       - name: Run doctests
         run: pixi run doctest
+
+  test-packaging:
+    name: Package the project into a distributable file
+    runs-on: ubuntu-22.04
+    steps:
+      - name: Checkout project
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Install python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.9"
+      - name: Install build dependencies
+        run: |
+          pip install --upgrade pip
+          pip install build
+      - name: Package the project to the dist dir
+        run: python -m build
+      - name: Try installing from the new dists
+        run: pip install dist/*.whl
+      - name: Produce a GitHub actions artifact (the distributable package)
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+          if-no-files-found: error
diff --git a/README.md b/README.md
index 8856502..23bed7f 100644
--- a/README.md
+++ b/README.md
@@ -6,7 +6,7 @@ SPDX-License-Identifier: GPL-3.0-or-later
 -->
 
 [![docs](https://img.shields.io/badge/docs-stable-orange.svg)](https://gridtk.readthedocs.io/en/stable/)
-[![build](https://github.com/idiap/gridtk/actions/workflows/build.yml/badge.svg)](https://github.com/idiap/gridtk/actions/workflows/build.yml)
+[![tests](https://github.com/idiap/gridtk/actions/workflows/tests.yml/badge.svg)](https://github.com/idiap/gridtk/actions/workflows/tests.yml)
 [![coverage](https://raw.githubusercontent.com/idiap/gridtk/python-coverage-comment-action-data/badge.svg)](https://htmlpreview.github.io/?https://github.com/idiap/gridtk/blob/python-coverage-comment-action-data/htmlcov/index.html)
 [![repository](https://img.shields.io/badge/github-project-0000c0.svg)](https://github.com/idiap/gridtk)
 

From f8cc0a8307e04868e98b8d7df383cd6a139ee497 Mon Sep 17 00:00:00 2001
From: Yannick DAYER <yannick.dayer@idiap.ch>
Date: Thu, 18 Jul 2024 14:50:03 +0200
Subject: [PATCH 2/5] ci(coverage): remove the junit and xml cov reports

junit was used by GitLab to parse the output. The coverage reports are
now generated by a GitHub action from "raw" .coverage files.
---
 pixi.lock      | 4 ++--
 pyproject.toml | 4 +---
 2 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/pixi.lock b/pixi.lock
index 814bb62..b0367cb 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -375,9 +375,9 @@ packages:
   requires_python: '>=3.7'
 - kind: pypi
   name: gridtk
-  version: 3.0.1.dev4+ge1d63ef
+  version: 3.0.1.dev6+ge9198f6.d20240718
   path: .
-  sha256: 098b931aa522fe8a839ee2b94a621e244b55c28f03fc0d230afa1ed2f6ae175d
+  sha256: 068b1e5ec9a01cbf94250179856352dbc58e5eaea1629f4122977f22dcf8b84a
   requires_dist:
   - click~=8.1
   - sqlalchemy~=2.0
diff --git a/pyproject.toml b/pyproject.toml
index 1dd157f..f15fc2b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -63,7 +63,7 @@ doctest = "sphinx-build -aEb doctest doc html/doctest"
 
 [tool.pixi.feature.test.tasks]
 test = "pytest -sv tests/"
-test-ci = "pytest -sv --cov-branch --cov-report xml --ignore '.profile' tests/"
+test-ci = "pytest -sv --cov-branch tests/"
 
 [tool.pixi.environments]
 default = { features = ["doc", "test"], solve-group = "default" }
@@ -161,8 +161,6 @@ convention = "numpy"
 
 [tool.pytest.ini_options]
 addopts = ["--cov=gridtk", "--cov-report=term-missing", "--import-mode=append"]
-junit_logging = "all"
-junit_log_passing_tests = false
 
 [tool.coverage.run]
 relative_files = true

From 0266c256a7e506c87af9957e6741124cda14e80f Mon Sep 17 00:00:00 2001
From: Yannick DAYER <yannick.dayer@idiap.ch>
Date: Thu, 18 Jul 2024 15:06:14 +0200
Subject: [PATCH 3/5] ci: remove the CodeQL workflow.

---
 .github/workflows/codeql.yml | 98 ------------------------------------
 1 file changed, 98 deletions(-)
 delete mode 100644 .github/workflows/codeql.yml

diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
deleted file mode 100644
index be7bc94..0000000
--- a/.github/workflows/codeql.yml
+++ /dev/null
@@ -1,98 +0,0 @@
-# SPDX-FileCopyrightText: 2024 Idiap Research Institute <contact@idiap.ch>
-# SPDX-FileContributor: Amir Mohammadi  <amir.mohammadi@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-# 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.
-#
-# ******** NOTE ********
-# We have attempted to detect the languages in your repository. Please check
-# the `language` matrix defined below to confirm you have the correct set of
-# supported CodeQL languages.
-#
-name: "CodeQL"
-
-on:
-  push:
-    branches: [ "main" ]
-  pull_request:
-    branches: [ "main" ]
-  schedule:
-    - cron: '36 22 * * 0'
-
-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-22.04' }}
-    timeout-minutes: ${{ (matrix.language == 'swift' && 120) || 360 }}
-    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: Checkout repository
-      uses: actions/checkout@v4
-
-    # Initializes the CodeQL tools for scanning.
-    - name: Initialize CodeQL
-      uses: github/codeql-action/init@v3
-      with:
-        languages: ${{ matrix.language }}
-        build-mode: ${{ matrix.build-mode }}
-        # If you wish to specify custom queries, you can do so here or in a config file.
-        # By default, queries listed here will override any specified in a config file.
-        # Prefix the list here with "+" to use these queries and those in the config file.
-
-        # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
-        # queries: security-extended,security-and-quality
-
-    # If the analyze step fails for one of the languages you are analyzing with
-    # "We were unable to automatically build your code", modify the matrix above
-    # to set the build mode to "manual" for that language. Then modify this step
-    # to build your code.
-    # ℹ️ Command-line programs to run using the OS shell.
-    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
-    - if: matrix.build-mode == 'manual'
-      shell: bash
-      run: |
-        echo 'If you are using a "manual" build mode for one or more of the' \
-          'languages you are analyzing, replace this with the commands to build' \
-          'your code, for example:'
-        echo '  make bootstrap'
-        echo '  make release'
-        exit 1
-
-    - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v3
-      with:
-        category: "/language:${{matrix.language}}"

From 22372c271101d1ef091952620b5902c6d7e286a4 Mon Sep 17 00:00:00 2001
From: Yannick DAYER <yannick.dayer@idiap.ch>
Date: Thu, 18 Jul 2024 17:00:45 +0200
Subject: [PATCH 4/5] ci: add environments for different python versions

Test the project against each minor python version in GitHub Actions.
---
 .github/workflows/tests.yml |  53 ++-
 pixi.lock                   | 723 +++++++++++++++++++++++++++++++-----
 pyproject.toml              |  28 +-
 3 files changed, 685 insertions(+), 119 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index cfabecb..ae860db 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -25,9 +25,9 @@ jobs:
         uses: prefix-dev/setup-pixi@v0.8.1
         with:
           pixi-version: v0.25.0
-          environments: self
+          environments: default
       - name: Run Simple Tests
-        shell: pixi run -e self bash -e {0}
+        shell: pixi run -e default bash -e {0}
         run: |
           gridtk --help
           gridtk submit --help
@@ -38,38 +38,61 @@ jobs:
           gridtk delete --help
 
   tests:
+    strategy:
+      matrix:
+        pixi_environment: [test, test-py311, test-py310, test-py39]
     runs-on: ubuntu-22.04
-    permissions:
-      # Gives the action the necessary permissions for publishing new
-      # comments in pull requests.
-      pull-requests: write
-      # Gives the action the necessary permissions for pushing data to the
-      # python-coverage-comment-action branch, and for editing existing
-      # comments (to avoid publishing multiple comments in the same PR)
-      contents: write
     steps:
-      - uses: actions/checkout@v4
+      - name: Checkout repository
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - name: Setup Pixi
         uses: prefix-dev/setup-pixi@v0.8.1
         with:
           pixi-version: v0.25.0
-          environments: test
+          environments: ${{ matrix.pixi_environment }}
       - name: Run Tests
-        run: pixi run -e test test-ci
+        run: pixi run -e ${{ matrix.pixi_environment }} test-ci
+        env:
+          COVERAGE_FILE: ".coverage.${{ matrix.pixi_environment }}"
+      - name: Store coverage report
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-${{ matrix.pixi_environment }}
+          path: .coverage.${{ matrix.pixi_environment }}
+
+  merge-coverage:
+    name: Merge the coverage reports from multiple coverages
+    needs: tests
+    runs-on: ubuntu-22.04
+    permissions:
+      # Gives the action the necessary permissions for publishing new
+      # comments in pull requests.
+      pull-requests: write
+      # Gives the action the necessary permissions for editing existing
+      # comments (to avoid publishing multiple comments in the same PR)
+      contents: write
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Retrieve coverage artifacts
+        uses: actions/download-artifact@v4
+        id: download
+        with:
+          pattern: coverage-*
+          merge-multiple: true
       - name: Coverage comment
         id: coverage_comment
         uses: py-cov-action/python-coverage-comment-action@v3
         with:
           GITHUB_TOKEN: ${{ github.token }}
+          MERGE_COVERAGE_FILES: true
       - name: Store Pull Request comment to be posted
         uses: actions/upload-artifact@v4
         if: steps.coverage_comment.outputs.COMMENT_FILE_WRITTEN == 'true'
         with:
-          # If you use a different name, update COMMENT_ARTIFACT_NAME accordingly
           name: python-coverage-comment-action
-          # If you use a different name, update COMMENT_FILENAME accordingly
           path: python-coverage-comment-action.txt
 
   doc:
diff --git a/pixi.lock b/pixi.lock
index b0367cb..6337b09 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -12,6 +12,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.2-h59595ed_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h77fa898_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_0.conda
@@ -22,7 +23,41 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-h4ab18f5_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4ab18f5_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.9.19-h0755675_0_cpython.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.12.4-h194c7f8_0_cpython.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2
+      - pypi: https://files.pythonhosted.org/packages/00/2e/d53fa4befbf2cfa713304affc7ca780ce4fc1fd8710527771b58311a3229/click-8.1.7-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/bd/37/56b0da468a85e7704f3b2bc045015301bdf4be2184a44868c71f6dca6fe2/greenlet-3.0.3-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
+      - pypi: https://files.pythonhosted.org/packages/60/f8/7794f3055d50e96cee04c19c7faeedacb323c7762f334660ba03bed95485/SQLAlchemy-2.0.31-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
+      - pypi: https://files.pythonhosted.org/packages/40/44/4a5f08c96eb108af5cb50b41f76142f0afa346dfa99d5296fe7202a11854/tabulate-0.9.0-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/26/9f/ad63fc0248c5379346306f8668cda6e2e2e9c95e01216d2b8ffd9ff037d0/typing_extensions-4.12.2-py3-none-any.whl
+      - pypi: .
+  dev:
+    channels:
+    - url: https://conda.anaconda.org/conda-forge/
+    indexes:
+    - https://pypi.org/simple
+    packages:
+      linux-64:
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.2-h59595ed_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h77fa898_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.46.0-hde9e2c9_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-h4ab18f5_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4ab18f5_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.12.4-h194c7f8_0_cpython.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda
@@ -31,30 +66,36 @@ environments:
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+  - pytest-cov>=4.1 ; extra == 'test'
+  - pytest-mock>=3.12 ; extra == 'test'
+  - pytest>=7.4.3 ; extra == 'test'
+  - mypy>=1.8 ; extra == 'type'
+  requires_python: '>=3.8'
 - kind: pypi
   name: pluggy
   version: 1.5.0
@@ -736,6 +1034,18 @@ packages:
   - pytest ; extra == 'testing'
   - pytest-benchmark ; extra == 'testing'
   requires_python: '>=3.8'
+- kind: pypi
+  name: pre-commit
+  version: 3.7.1
+  url: https://files.pythonhosted.org/packages/b9/0f/d6d0b4e2f5b2933a557087fc0560371aa545a18232d4d3427eb3bb3af12e/pre_commit-3.7.1-py2.py3-none-any.whl
+  sha256: fae36fd1d7ad7d6a5a1c0b0d5adb2ed1a3bda5a21bf6c3e5372073d7a11cd4c5
+  requires_dist:
+  - cfgv>=2.0.0
+  - identify>=1.0.0
+  - nodeenv>=0.11.1
+  - pyyaml>=5.1
+  - virtualenv>=20.10.0
+  requires_python: '>=3.9'
 - kind: pypi
   name: pygments
   version: 2.18.0
@@ -809,11 +1119,103 @@ packages:
   purls: []
   size: 23800555
   timestamp: 1710940120866
+- kind: conda
+  name: python
+  version: 3.10.14
+  build: hd12c33a_0_cpython
+  subdir: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/python-3.10.14-hd12c33a_0_cpython.conda
+  sha256: 76a5d12e73542678b70a94570f7b0f7763f9a938f77f0e75d9ea615ef22aa84c
+  md5: 2b4ba962994e8bd4be9ff5b64b75aff2
+  depends:
+  - bzip2 >=1.0.8,<2.0a0
+  - ld_impl_linux-64 >=2.36.1
+  - libffi >=3.4,<4.0a0
+  - libgcc-ng >=12
+  - libnsl >=2.0.1,<2.1.0a0
+  - libsqlite >=3.45.2,<4.0a0
+  - libuuid >=2.38.1,<3.0a0
+  - libxcrypt >=4.4.36
+  - libzlib >=1.2.13,<2.0.0a0
+  - ncurses >=6.4.20240210,<7.0a0
+  - openssl >=3.2.1,<4.0a0
+  - readline >=8.2,<9.0a0
+  - tk >=8.6.13,<8.7.0a0
+  - tzdata
+  - xz >=5.2.6,<6.0a0
+  constrains:
+  - python_abi 3.10.* *_cp310
+  license: Python-2.0
+  purls: []
+  size: 25517742
+  timestamp: 1710939725109
+- kind: conda
+  name: python
+  version: 3.11.9
+  build: hb806964_0_cpython
+  subdir: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/python-3.11.9-hb806964_0_cpython.conda
+  sha256: 177f33a1fb8d3476b38f73c37b42f01c0b014fa0e039a701fd9f83d83aae6d40
+  md5: ac68acfa8b558ed406c75e98d3428d7b
+  depends:
+  - bzip2 >=1.0.8,<2.0a0
+  - ld_impl_linux-64 >=2.36.1
+  - libexpat >=2.6.2,<3.0a0
+  - libffi >=3.4,<4.0a0
+  - libgcc-ng >=12
+  - libnsl >=2.0.1,<2.1.0a0
+  - libsqlite >=3.45.3,<4.0a0
+  - libuuid >=2.38.1,<3.0a0
+  - libxcrypt >=4.4.36
+  - libzlib >=1.2.13,<2.0.0a0
+  - ncurses >=6.4.20240210,<7.0a0
+  - openssl >=3.2.1,<4.0a0
+  - readline >=8.2,<9.0a0
+  - tk >=8.6.13,<8.7.0a0
+  - tzdata
+  - xz >=5.2.6,<6.0a0
+  constrains:
+  - python_abi 3.11.* *_cp311
+  license: Python-2.0
+  purls: []
+  size: 30884494
+  timestamp: 1713553104915
+- kind: conda
+  name: python
+  version: 3.12.4
+  build: h194c7f8_0_cpython
+  subdir: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/python-3.12.4-h194c7f8_0_cpython.conda
+  sha256: 97a78631e6c928bf7ad78d52f7f070fcf3bd37619fa48dc4394c21cf3058cdee
+  md5: d73490214f536cccb5819e9873048c92
+  depends:
+  - bzip2 >=1.0.8,<2.0a0
+  - ld_impl_linux-64 >=2.36.1
+  - libexpat >=2.6.2,<3.0a0
+  - libffi >=3.4,<4.0a0
+  - libgcc-ng >=12
+  - libnsl >=2.0.1,<2.1.0a0
+  - libsqlite >=3.46.0,<4.0a0
+  - libuuid >=2.38.1,<3.0a0
+  - libxcrypt >=4.4.36
+  - libzlib >=1.3.1,<2.0a0
+  - ncurses >=6.5,<7.0a0
+  - openssl >=3.3.1,<4.0a0
+  - readline >=8.2,<9.0a0
+  - tk >=8.6.13,<8.7.0a0
+  - tzdata
+  - xz >=5.2.6,<6.0a0
+  constrains:
+  - python_abi 3.12.* *_cp312
+  license: Python-2.0
+  purls: []
+  size: 32073625
+  timestamp: 1718621771849
 - kind: pypi
   name: pyyaml
   version: 6.0.1
-  url: https://files.pythonhosted.org/packages/7d/39/472f2554a0f1e825bd7c5afc11c817cd7a2f3657460f7159f691fbb37c51/PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
-  sha256: bc1bf2925a1ecd43da378f4db9e4f799775d6367bdb94671027b73b393a7c42c
+  url: https://files.pythonhosted.org/packages/b4/33/720548182ffa8344418126017aa1d4ab4aeec9a2275f04ce3f3573d8ace8/PyYAML-6.0.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
+  sha256: 6c22bec3fbe2524cde73d7ada88f6566758a8f7227bfbf93a408a9d86bcc12a0
   requires_python: '>=3.6'
 - kind: conda
   name: readline
@@ -845,6 +1247,12 @@ packages:
   - pysocks!=1.5.7,>=1.5.6 ; extra == 'socks'
   - chardet<6,>=3.0.2 ; extra == 'use-chardet-on-py3'
   requires_python: '>=3.8'
+- kind: pypi
+  name: ruff
+  version: 0.5.2
+  url: https://files.pythonhosted.org/packages/ec/60/e2a9ae058b34128caa5f863f268e1c9bd083793264f4bf7e8e469be651f9/ruff-0.5.2-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
+  sha256: 1ed02fb52e3741f0738db5f93e10ae0fb5c71eb33a4f2ba87c9a2fa97462a649
+  requires_python: '>=3.7'
 - kind: pypi
   name: snowballstemmer
   version: 2.2.0
@@ -1024,6 +1432,123 @@ packages:
   - sphinx>=5 ; extra == 'standalone'
   - pytest ; extra == 'test'
   requires_python: '>=3.9'
+- kind: pypi
+  name: sqlalchemy
+  version: 2.0.31
+  url: https://files.pythonhosted.org/packages/60/f8/7794f3055d50e96cee04c19c7faeedacb323c7762f334660ba03bed95485/SQLAlchemy-2.0.31-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
+  sha256: 74afabeeff415e35525bf7a4ecdab015f00e06456166a2eba7590e49f8db940e
+  requires_dist:
+  - typing-extensions>=4.6.0
+  - greenlet!=0.4.17 ; python_version < '3.13' and (platform_machine == 'aarch64' or (platform_machine == 'ppc64le' or (platform_machine == 'x86_64' or (platform_machine == 'amd64' or (platform_machine == 'AMD64' or (platform_machine == 'win32' or platform_machine == 'WIN32'))))))
+  - importlib-metadata ; python_version < '3.8'
+  - greenlet!=0.4.17 ; extra == 'aiomysql'
+  - aiomysql>=0.2.0 ; extra == 'aiomysql'
+  - greenlet!=0.4.17 ; extra == 'aioodbc'
+  - aioodbc ; extra == 'aioodbc'
+  - greenlet!=0.4.17 ; extra == 'aiosqlite'
+  - aiosqlite ; extra == 'aiosqlite'
+  - typing-extensions!=3.10.0.1 ; extra == 'aiosqlite'
+  - greenlet!=0.4.17 ; extra == 'asyncio'
+  - greenlet!=0.4.17 ; extra == 'asyncmy'
+  - asyncmy!=0.2.4,!=0.2.6,>=0.2.3 ; extra == 'asyncmy'
+  - mariadb!=1.1.2,!=1.1.5,>=1.0.1 ; extra == 'mariadb-connector'
+  - pyodbc ; extra == 'mssql'
+  - pymssql ; extra == 'mssql-pymssql'
+  - pyodbc ; extra == 'mssql-pyodbc'
+  - mypy>=0.910 ; extra == 'mypy'
+  - mysqlclient>=1.4.0 ; extra == 'mysql'
+  - mysql-connector-python ; extra == 'mysql-connector'
+  - cx-oracle>=8 ; extra == 'oracle'
+  - oracledb>=1.0.1 ; extra == 'oracle-oracledb'
+  - psycopg2>=2.7 ; extra == 'postgresql'
+  - greenlet!=0.4.17 ; extra == 'postgresql-asyncpg'
+  - asyncpg ; extra == 'postgresql-asyncpg'
+  - pg8000>=1.29.1 ; extra == 'postgresql-pg8000'
+  - psycopg>=3.0.7 ; extra == 'postgresql-psycopg'
+  - psycopg2-binary ; extra == 'postgresql-psycopg2binary'
+  - psycopg2cffi ; extra == 'postgresql-psycopg2cffi'
+  - psycopg[binary]>=3.0.7 ; extra == 'postgresql-psycopgbinary'
+  - pymysql ; extra == 'pymysql'
+  - sqlcipher3-binary ; extra == 'sqlcipher'
+  requires_python: '>=3.7'
+- kind: pypi
+  name: sqlalchemy
+  version: 2.0.31
+  url: https://files.pythonhosted.org/packages/bb/be/4045425132a2fde3422e0d2062e6a3b874e385b98b0442c1d7d29ac152bc/SQLAlchemy-2.0.31-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
+  sha256: 2196208432deebdfe3b22185d46b08f00ac9d7b01284e168c212919891289396
+  requires_dist:
+  - typing-extensions>=4.6.0
+  - greenlet!=0.4.17 ; python_version < '3.13' and (platform_machine == 'aarch64' or (platform_machine == 'ppc64le' or (platform_machine == 'x86_64' or (platform_machine == 'amd64' or (platform_machine == 'AMD64' or (platform_machine == 'win32' or platform_machine == 'WIN32'))))))
+  - importlib-metadata ; python_version < '3.8'
+  - greenlet!=0.4.17 ; extra == 'aiomysql'
+  - aiomysql>=0.2.0 ; extra == 'aiomysql'
+  - greenlet!=0.4.17 ; extra == 'aioodbc'
+  - aioodbc ; extra == 'aioodbc'
+  - greenlet!=0.4.17 ; extra == 'aiosqlite'
+  - aiosqlite ; extra == 'aiosqlite'
+  - typing-extensions!=3.10.0.1 ; extra == 'aiosqlite'
+  - greenlet!=0.4.17 ; extra == 'asyncio'
+  - greenlet!=0.4.17 ; extra == 'asyncmy'
+  - asyncmy!=0.2.4,!=0.2.6,>=0.2.3 ; extra == 'asyncmy'
+  - mariadb!=1.1.2,!=1.1.5,>=1.0.1 ; extra == 'mariadb-connector'
+  - pyodbc ; extra == 'mssql'
+  - pymssql ; extra == 'mssql-pymssql'
+  - pyodbc ; extra == 'mssql-pyodbc'
+  - mypy>=0.910 ; extra == 'mypy'
+  - mysqlclient>=1.4.0 ; extra == 'mysql'
+  - mysql-connector-python ; extra == 'mysql-connector'
+  - cx-oracle>=8 ; extra == 'oracle'
+  - oracledb>=1.0.1 ; extra == 'oracle-oracledb'
+  - psycopg2>=2.7 ; extra == 'postgresql'
+  - greenlet!=0.4.17 ; extra == 'postgresql-asyncpg'
+  - asyncpg ; extra == 'postgresql-asyncpg'
+  - pg8000>=1.29.1 ; extra == 'postgresql-pg8000'
+  - psycopg>=3.0.7 ; extra == 'postgresql-psycopg'
+  - psycopg2-binary ; extra == 'postgresql-psycopg2binary'
+  - psycopg2cffi ; extra == 'postgresql-psycopg2cffi'
+  - psycopg[binary]>=3.0.7 ; extra == 'postgresql-psycopgbinary'
+  - pymysql ; extra == 'pymysql'
+  - sqlcipher3-binary ; extra == 'sqlcipher'
+  requires_python: '>=3.7'
+- kind: pypi
+  name: sqlalchemy
+  version: 2.0.31
+  url: https://files.pythonhosted.org/packages/bf/90/0ce8c76cd2ef8a5e0838d61d6648a1193859e1990bc1d65c8b0fd1f77ca8/SQLAlchemy-2.0.31-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
+  sha256: 9f2bee229715b6366f86a95d497c347c22ddffa2c7c96143b59a2aa5cc9eebbc
+  requires_dist:
+  - typing-extensions>=4.6.0
+  - greenlet!=0.4.17 ; python_version < '3.13' and (platform_machine == 'aarch64' or (platform_machine == 'ppc64le' or (platform_machine == 'x86_64' or (platform_machine == 'amd64' or (platform_machine == 'AMD64' or (platform_machine == 'win32' or platform_machine == 'WIN32'))))))
+  - importlib-metadata ; python_version < '3.8'
+  - greenlet!=0.4.17 ; extra == 'aiomysql'
+  - aiomysql>=0.2.0 ; extra == 'aiomysql'
+  - greenlet!=0.4.17 ; extra == 'aioodbc'
+  - aioodbc ; extra == 'aioodbc'
+  - greenlet!=0.4.17 ; extra == 'aiosqlite'
+  - aiosqlite ; extra == 'aiosqlite'
+  - typing-extensions!=3.10.0.1 ; extra == 'aiosqlite'
+  - greenlet!=0.4.17 ; extra == 'asyncio'
+  - greenlet!=0.4.17 ; extra == 'asyncmy'
+  - asyncmy!=0.2.4,!=0.2.6,>=0.2.3 ; extra == 'asyncmy'
+  - mariadb!=1.1.2,!=1.1.5,>=1.0.1 ; extra == 'mariadb-connector'
+  - pyodbc ; extra == 'mssql'
+  - pymssql ; extra == 'mssql-pymssql'
+  - pyodbc ; extra == 'mssql-pyodbc'
+  - mypy>=0.910 ; extra == 'mypy'
+  - mysqlclient>=1.4.0 ; extra == 'mysql'
+  - mysql-connector-python ; extra == 'mysql-connector'
+  - cx-oracle>=8 ; extra == 'oracle'
+  - oracledb>=1.0.1 ; extra == 'oracle-oracledb'
+  - psycopg2>=2.7 ; extra == 'postgresql'
+  - greenlet!=0.4.17 ; extra == 'postgresql-asyncpg'
+  - asyncpg ; extra == 'postgresql-asyncpg'
+  - pg8000>=1.29.1 ; extra == 'postgresql-pg8000'
+  - psycopg>=3.0.7 ; extra == 'postgresql-psycopg'
+  - psycopg2-binary ; extra == 'postgresql-psycopg2binary'
+  - psycopg2cffi ; extra == 'postgresql-psycopg2cffi'
+  - psycopg[binary]>=3.0.7 ; extra == 'postgresql-psycopgbinary'
+  - pymysql ; extra == 'pymysql'
+  - sqlcipher3-binary ; extra == 'sqlcipher'
+  requires_python: '>=3.7'
 - kind: pypi
   name: sqlalchemy
   version: 2.0.31
@@ -1125,6 +1650,36 @@ packages:
   - pysocks!=1.5.7,<2.0,>=1.5.6 ; extra == 'socks'
   - zstandard>=0.18.0 ; extra == 'zstd'
   requires_python: '>=3.8'
+- kind: pypi
+  name: virtualenv
+  version: 20.26.3
+  url: https://files.pythonhosted.org/packages/07/4d/410156100224c5e2f0011d435e477b57aed9576fc7fe137abcf14ec16e11/virtualenv-20.26.3-py3-none-any.whl
+  sha256: 8cc4a31139e796e9a7de2cd5cf2489de1217193116a8fd42328f1bd65f434589
+  requires_dist:
+  - distlib<1,>=0.3.7
+  - filelock<4,>=3.12.2
+  - importlib-metadata>=6.6 ; python_version < '3.8'
+  - platformdirs<5,>=3.9.1
+  - furo>=2023.7.26 ; extra == 'docs'
+  - proselint>=0.13 ; extra == 'docs'
+  - sphinx!=7.3,>=7.1.2 ; extra == 'docs'
+  - sphinx-argparse>=0.4 ; extra == 'docs'
+  - sphinxcontrib-towncrier>=0.2.1a0 ; extra == 'docs'
+  - towncrier>=23.6 ; extra == 'docs'
+  - covdefaults>=2.3 ; extra == 'test'
+  - coverage-enable-subprocess>=1 ; extra == 'test'
+  - coverage>=7.2.7 ; extra == 'test'
+  - flaky>=3.7 ; extra == 'test'
+  - packaging>=23.1 ; extra == 'test'
+  - pytest-env>=0.8.2 ; extra == 'test'
+  - pytest-freezer>=0.4.8 ; (platform_python_implementation == 'PyPy' or (platform_python_implementation == 'CPython' and sys_platform == 'win32' and python_version >= '3.13')) and extra == 'test'
+  - pytest-mock>=3.11.1 ; extra == 'test'
+  - pytest-randomly>=3.12 ; extra == 'test'
+  - pytest-timeout>=2.1 ; extra == 'test'
+  - pytest>=7.4 ; extra == 'test'
+  - setuptools>=68 ; extra == 'test'
+  - time-machine>=2.10 ; platform_python_implementation == 'CPython' and extra == 'test'
+  requires_python: '>=3.7'
 - kind: conda
   name: xz
   version: 5.2.6
@@ -1139,29 +1694,3 @@ packages:
   purls: []
   size: 418368
   timestamp: 1660346797927
-- kind: pypi
-  name: zipp
-  version: 3.19.2
-  url: https://files.pythonhosted.org/packages/20/38/f5c473fe9b90c8debdd29ea68d5add0289f1936d6f923b6b9cc0b931194c/zipp-3.19.2-py3-none-any.whl
-  sha256: f091755f667055f2d02b32c53771a7a6c8b47e1fdbc4b72a8b9072b3eef8015c
-  requires_dist:
-  - sphinx>=3.5 ; extra == 'doc'
-  - jaraco-packaging>=9.3 ; extra == 'doc'
-  - rst-linker>=1.9 ; extra == 'doc'
-  - furo ; extra == 'doc'
-  - sphinx-lint ; extra == 'doc'
-  - jaraco-tidelift>=1.4 ; extra == 'doc'
-  - pytest!=8.1.*,>=6 ; extra == 'test'
-  - pytest-checkdocs>=2.4 ; extra == 'test'
-  - pytest-cov ; extra == 'test'
-  - pytest-mypy ; extra == 'test'
-  - pytest-enabler>=2.2 ; extra == 'test'
-  - pytest-ruff>=0.2.1 ; extra == 'test'
-  - jaraco-itertools ; extra == 'test'
-  - jaraco-functools ; extra == 'test'
-  - more-itertools ; extra == 'test'
-  - big-o ; extra == 'test'
-  - pytest-ignore-flaky ; extra == 'test'
-  - jaraco-test ; extra == 'test'
-  - importlib-resources ; python_version < '3.9' and extra == 'test'
-  requires_python: '>=3.8'
diff --git a/pyproject.toml b/pyproject.toml
index f15fc2b..d85c9d7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -45,6 +45,7 @@ doc = [
   "myst-parser",
 ]
 test = ["pytest", "pytest-cov", "coverage"]
+dev = ["gridtk[doc,test]", "pre-commit", "ruff"]
 
 [project.scripts]
 gridtk = "gridtk.cli:cli"
@@ -56,6 +57,18 @@ platforms = ["linux-64"]
 [tool.pixi.pypi-dependencies]
 gridtk = { path = ".", editable = true }
 
+[tool.pixi.feature.py312.dependencies]
+python = "~=3.12.0"
+
+[tool.pixi.feature.py311.dependencies]
+python = "~=3.11.0"
+
+[tool.pixi.feature.py310.dependencies]
+python = "~=3.10.0"
+
+[tool.pixi.feature.py39.dependencies]
+python = "~=3.9.0"
+
 [tool.pixi.feature.doc.tasks]
 doc-clean = "rm -rf doc/api && rm -rf html"
 doc = "sphinx-build -aEW doc html"
@@ -66,13 +79,14 @@ test = "pytest -sv tests/"
 test-ci = "pytest -sv --cov-branch tests/"
 
 [tool.pixi.environments]
-default = { features = ["doc", "test"], solve-group = "default" }
-self = { solve-group = "default" }
-test = { features = ["test"], solve-group = "default" }
-doc = { features = ["doc"], solve-group = "default" }
-
-[tool.pixi.dependencies]
-python = "3.9.*"
+default = { features = ["py312"], solve-group = "latest-python" }
+test = { features = ["test", "py312"], solve-group = "latest-python" }
+doc = { features = ["doc", "py312"], solve-group = "latest-python" }
+dev = { features = ["dev", "doc", "test", "py312"], solve-group = "latest-python" }
+
+test-py311 = { features = ["test", "py311"], solve-group = "python311" }
+test-py310 = { features = ["test", "py310"], solve-group = "python310" }
+test-py39 = { features = ["test", "py39"], solve-group = "python39" }
 
 [tool.hatch.version]
 source = "versioningit"

From 355de48f54ea36025954acd5fa436d68155b66d5 Mon Sep 17 00:00:00 2001
From: Yannick DAYER <yannick.dayer@idiap.ch>
Date: Thu, 18 Jul 2024 17:11:13 +0200
Subject: [PATCH 5/5] ci: specify pixi environments to use for doc jobs.

---
 .github/workflows/tests.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index ae860db..c72e142 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -107,11 +107,11 @@ jobs:
           pixi-version: v0.25.0
           environments: doc
       - name: Clean previous docs
-        run: pixi run doc-clean
+        run: pixi run -e doc doc-clean
       - name: Build docs
-        run: pixi run doc
+        run: pixi run -e doc doc
       - name: Run doctests
-        run: pixi run doctest
+        run: pixi run -e doc doctest
 
   test-packaging:
     name: Package the project into a distributable file