feat: ⭐ Introducing UV as package manager (#1785)

* feat: ✨ Introduce UV instead of poetry

* feat: 🔧 bump version to 1.2.0 and update tests

* chore: ✨ update project configuration and improve build process

* feat: ✨ migrate CI workflow from Poetry to UV for dependency management

* fix: ✅ clean up file handling and remove unnecessary type ignore in tests

* fix: ✅ update pre-commit configuration to exclude uv.lock instead of poetry.lock

* fix: 🚨 standardize YAML formatting in GitHub workflows and labeler configuration

* fix: ✅ remove quotes from cache-dependency-glob in CI workflow

* ci: 👷 update trunk.yaml to latest plugin versions and CLI version

* fix: ✏️ correct command syntax in CI workflow for running tests

* fix: 📝 add uv.lock to labeler configuration for dependency tracking

* ci: 👷 enhance CI workflow for uv installation and project setup

* fix: 🐛 add stacklevel argument to DeprecationWarning for clearer warning context

* fix: ✏️ update CI workflow to install any wheel file and run spectrafit with verbose output

* fix: 🚨 adjust stacklevel argument in DeprecationWarning for clearer warning context

* ci: 👷 add uv build step to CI workflow for project installation

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* fix: 🐛 add type ignore comment for AutoPeakDetection instantiation in tests

* fix: 🐛 remove type ignore comment for AutoPeakDetection instantiation in tests

* fix: 🐛 add type ignore comment for AutoPeakDetection instantiation in tests

* ci: 👷 update CI workflow to rename project installation step and add wheel installation

* feat: 🎨 update devcontainer configuration to use latest features and install uv for environment setup

* feat: 🎨 update devcontainer configuration to use latest versions of GitHub CLI and remove unused features

* fix: 🐛 update devcontainer configuration to include Docker-in-Docker and Git features, and adjust GitHub CLI installation

* docs: 📝 update installation instructions to replace Poetry with UV as the package manager for SpectraFit

* feat: 🎨 update GitHub Actions workflow to replace Poetry with uv for dependency management

* ci: ✅ update GitHub Actions workflow to replace Poetry with uv for dependency management

* docs: 📝 clean up reference links in documentation files

* chore: 📝 clean up formatting in CONTRIBUTING.md, codecov.yml, and renovate.json

* fix: 🐛 add stacklevel parameter to warning messages for better traceability

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: Anselmoo

.devcontainer/devcontainer.json

@@ -5,13 +5,13 @@
   // Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
   "image": "mcr.microsoft.com/devcontainers/python:dev-3.10",
   "features": {
-    "ghcr.io/devcontainers/features/git:1": {},
-    "ghcr.io/devcontainers-contrib/features/poetry:2": {},
     "ghcr.io/devcontainers-contrib/features/pre-commit:2": {},
     "ghcr.io/devcontainers-contrib/features/prettier:1": {},
-    "ghcr.io/devcontainers/features/github-cli:1": {},
     "ghcr.io/devcontainers-contrib/features/bash-command:1": {},
-    "ghcr.io/devcontainers/features/docker-in-docker:2": {}
+    "ghcr.io/devcontainers/features/docker-in-docker:2": {},
+    "ghcr.io/devcontainers/features/git:1": {},
+    "ghcr.io/devcontainers/features/github-cli:1": {},
+    "ghcr.io/jsburckhardt/devcontainer-features/uv:1": {}
   },
 
   // Features to add to the dev container. More info: https://containers.dev/features.
@@ -29,7 +29,8 @@
         "njpwerner.autodocstring",
         "ms-python.isort",
         "ms-python.vscode-pylance",
-        "ms-python.python"
+        "ms-python.python",
+        "charliermarsh.ruff"
       ]
     }
   }

.devcontainer/setup.sh

@@ -1,4 +1,4 @@
 python -m pip install --upgrade pip
-python -m pip install poetry
-poetry config virtualenvs.in-project true
-python -m poetry install --with dev,docs --all-extras
+python -m pip install uv
+uv venv --python 3.10
+uv sync --all-extras --all-groups

.github/labeler.yml

@@ -1,82 +1,83 @@
 root:
-- changed-files:
-  - any-glob-to-any-file: '*'
+  - changed-files:
+      - any-glob-to-any-file: "*"
 codeowners:
-- changed-files:
-  - any-glob-to-any-file: .github/CODEOWNERS
+  - changed-files:
+      - any-glob-to-any-file: .github/CODEOWNERS
 codespaces:
-- changed-files:
-  - any-glob-to-any-file:  .devcontainer/**
+  - changed-files:
+      - any-glob-to-any-file: .devcontainer/**
 dependencies:
-- changed-files:
-  - any-glob-to-any-file:
-    - poetry.lock
-    - github/dependabot.yml
+  - changed-files:
+      - any-glob-to-any-file:
+          - uv.lock
+          - poetry.lock
+          - github/dependabot.yml
 documentation:
-- changed-files:
-  - any-glob-to-any-file:
-    - docs/**
-    - Examples/**
-    - mkdocs.yml
-    - README.md
-    - INSTALLATION.md
+  - changed-files:
+      - any-glob-to-any-file:
+          - docs/**
+          - Examples/**
+          - mkdocs.yml
+          - README.md
+          - INSTALLATION.md
 forms:
-- changed-files:
-  - any-glob-to-any-file:
-    - .github/ISSUE_TEMPLATE/**
-    - .github/pull_request_template.md
+  - changed-files:
+      - any-glob-to-any-file:
+          - .github/ISSUE_TEMPLATE/**
+          - .github/pull_request_template.md
 github-actions:
-- changed-files:
-  - any-glob-to-any-file: .github/workflows/**
+  - changed-files:
+      - any-glob-to-any-file: .github/workflows/**
 pre-commit:
-- changed-files:
-  - any-glob-to-any-file:
-    - .pre-commit-config.yaml
-    - .pre-commit-hooks.yaml
+  - changed-files:
+      - any-glob-to-any-file:
+          - .pre-commit-config.yaml
+          - .pre-commit-hooks.yaml
 python:
-- changed-files:
-  - any-glob-to-any-file: "spectrafit/**/*.py"
+  - changed-files:
+      - any-glob-to-any-file: "spectrafit/**/*.py"
 testing:
-- changed-files:
-  - any-glob-to-any-file: "spectrafit/**/test_*.py"
+  - changed-files:
+      - any-glob-to-any-file: "spectrafit/**/test_*.py"
 docker:
-- changed-files:
-  - any-glob-to-any-file:
-    - Dockerfile
-    - .dockerignore
-    - .devcontainer/Dockerfile
+  - changed-files:
+      - any-glob-to-any-file:
+          - Dockerfile
+          - .dockerignore
+          - .devcontainer/Dockerfile
 release:
-- changed-files:
-    - any-glob-to-any-file: spectrafit/__init__.py
+  - changed-files:
+      - any-glob-to-any-file: spectrafit/__init__.py
 vendor:
-- changed-files:
-  - any-glob-to-any-file: vendor/**
+  - changed-files:
+      - any-glob-to-any-file: vendor/**
 maintenance:
-- changed-files:
-  - any-glob-to-any-file:
-    - .gitignore
-    - .github/dependabot.yml
-    - .github/release-drafter.yml
-    - .github/labeler.yml
-    - .github/workflows/label.yml
-    - .sonarcloud.properties
-    - .pre-commit-config.yaml
-    - .prettierignore
-    - .pylintrc
-    - .sonarcloud.properties
-    - .sourcery.yaml
-    - "pyproject.toml"
+  - changed-files:
+      - any-glob-to-any-file:
+          - .gitignore
+          - .github/dependabot.yml
+          - .github/release-drafter.yml
+          - .github/labeler.yml
+          - .github/workflows/label.yml
+          - .sonarcloud.properties
+          - .pre-commit-config.yaml
+          - .prettierignore
+          - .pylintrc
+          - .sonarcloud.properties
+          - .sourcery.yaml
+          - "pyproject.toml"
 license:
-- changed-files:
-  - any-glob-to-any-file:
-    - LICENSE
-    - THIRD_PARTY_LICENSES
+  - changed-files:
+      - any-glob-to-any-file:
+          - LICENSE
+          - THIRD_PARTY_LICENSES
 security:
-- changed-files:
-  - any-glob-to-any-file: SECURITY.md
+  - changed-files:
+      - any-glob-to-any-file: SECURITY.md
 code-of-conduct:
-- changed-files:
-  - any-glob-to-any-file: CODE_OF_CONDUCT.md
+  - changed-files:
+      - any-glob-to-any-file: CODE_OF_CONDUCT.md
 changelog:
-- changed-files:
-  - any-glob-to-any-file: CHANGELOG.md
+  - changed-files:
+      - any-glob-to-any-file: CHANGELOG.md

.github/workflows/codeql.yml

@@ -22,7 +22,6 @@ on:
   repository_dispatch:
     types: [create-pull-request]
 
-
 jobs:
   analyze:
     name: Analyze

.github/workflows/conda_check.yml

@@ -15,18 +15,18 @@ jobs:
       max-parallel: 5
 
     steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v5
-      with:
-        python-version: '3.10'
-    - name: Add conda to system path
-      run: |
-        # $CONDA is an environment variable pointing to the root of the miniconda directory
-        echo $CONDA/bin >> $GITHUB_PATH
-    # - name: Install dependencies
-    #   run: |
-    #     conda env update --file environment.yml --name base
-    - name: Install spectrafit package
-      run: |
-        conda install -c conda-forge ${{ matrix.package }}
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+      - name: Add conda to system path
+        run: |
+          # $CONDA is an environment variable pointing to the root of the miniconda directory
+          echo $CONDA/bin >> $GITHUB_PATH
+      # - name: Install dependencies
+      #   run: |
+      #     conda env update --file environment.yml --name base
+      - name: Install spectrafit package
+        run: |
+          conda install -c conda-forge ${{ matrix.package }}

.github/workflows/docker-ci.yml

@@ -7,7 +7,6 @@ on:
   repository_dispatch:
     types: [create-pull-request]
 
-
 jobs:
   docker:
     # Only if Dockerfile is changed

.github/workflows/python-ci.yml

@@ -48,26 +48,15 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Check out repository
-        uses: actions/checkout@v4
-      - name: Set up python ${{ matrix.python-version }}
-        id: setup-python
-        uses: actions/setup-python@v5
+        uses: astral-sh/setup-uv@v5
         with:
+          enable-cache: true
+          cache-dependency-glob: uv.lock
           python-version: ${{ matrix.python-version }}
-      - name: Install Poetry and dependencies with dev-dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install poetry
-          poetry config virtualenvs.create true
-          poetry config virtualenvs.in-project true
-          poetry config virtualenvs.path .venv
-          poetry install --no-interaction --with dev -E all
+      - name: Install the project
+        run: uv sync --all-extras --dev
       - name: Test SpectraFit
-        run: poetry run pytest
+        run: uv run --group dev --all-extras pytest spectrafit/
       - name: Codecov
         uses: codecov/[email protected]
         with:
@@ -83,17 +72,36 @@ jobs:
     needs: build
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
         with:
+          enable-cache: true
+          cache-dependency-glob: uv.lock
           python-version: "3.10"
-      - name: Install Poetry and dependencies without dev-dependencies
+      - name: Install the project
         run: |
-          python -m pip install --upgrade pip
-          pip install poetry
-          poetry config virtualenvs.create true
-          poetry config virtualenvs.in-project true
-          poetry config virtualenvs.path .venv
-          poetry install --no-interaction --only main
+          uv sync --all-extras
+          uv run pip install -e .
+  install-build:
+    name: Install SpectraFit from wheel
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+          cache-dependency-glob: uv.lock
+          python-version: "3.10"
+      - name: Setup the project
+        run: |
+          uv sync --all-extras
+          uv build
+      - name: Install the wheel
+        run: |
+          uv pip install dist/*.whl
+          uv run spectrafit -v
   documentation:
     name: Build Documentation
     runs-on: ubuntu-latest
@@ -102,27 +110,24 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v5
+      - name: Install uv and dependencies with doc-dependencies
+        uses: astral-sh/setup-uv@v5
         with:
+          enable-cache: true
+          cache-dependency-glob: uv.lock
           python-version: "3.10"
-      - name: Install Poetry and dependencies with doc-dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install poetry
-          poetry config virtualenvs.create true
-          poetry config virtualenvs.in-project true
-          poetry config virtualenvs.path .venv
-          poetry install --no-interaction --with docs --all-extras
+      - name: Install the project
+        run: uv sync --all-extras --group docs
       - name: Set git config
         run: |
           git config --local user.email "[email protected]"
           git config --local user.name "GitHub Action"
       - name: Build documentation
         if: ${{ !contains(github.ref, 'refs/heads/main')}}
-        run: poetry run mkdocs build --clean
+        run: uv run --group docs --all-extras mkdocs build --clean
       - name: Deploy documentation develops
         if: contains(github.ref, 'refs/heads/main')
-        run: poetry run mike deploy --push --update-aliases develop
+        run: uv run --group docs --all-extras mike deploy --push --update-aliases develop
   devcontainer:
     name: Devcontainer
     needs: build

.github/workflows/update-changelog.yaml

@@ -78,16 +78,15 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: "3.10"
-      - name: Install Poetry and dependencies with doc-dependencies
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+          cache-dependency-glob: uv.lock
+          python-version: "3.10"
+      - name: Install the project
         run: |
-          python -m pip install --upgrade pip
-          pip install poetry
-          poetry config virtualenvs.create true
-          poetry config virtualenvs.in-project true
-          poetry config virtualenvs.path .venv
-          poetry install --no-interaction --with docs --all-extras
-      - name: Install library
-        run: poetry install --no-interaction --with docs --all-extras
+          uv sync --all-extras --all-groups
       - name: Set git config
         run: |
           git config --local user.email "[email protected]"
@@ -108,9 +107,9 @@ jobs:
           previous_version=$(echo $previous_tag | cut -d '.' -f 1,2)
           current_version=$(echo $current_tag | cut -d '.' -f 1,2)
           if [[ "$previous_version" == "$current_version" ]]; then
-            poetry run mike delete ${{ steps.previous_release.outputs.previous_tag }} --push
+            uv run mike delete ${{ steps.previous_release.outputs.previous_tag }} --push
           fi
       - name: Deploy documentation develops
         run: |
-          poetry run mike deploy --push --update-aliases ${{ github.event.release.tag_name }} latest --message "Release ${{ github.event.release.tag_name }}"
-          poetry run mike set-default --push latest
+          uv run mike deploy --push --update-aliases ${{ github.event.release.tag_name }} latest --message "Release ${{ github.event.release.tag_name }}"
+          uv run mike set-default --push latest