Conda to uv

Author: keller-mark

.envrc

@@ -16,28 +16,22 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
+      - uses: astral-sh/setup-uv@v3
+        with:
+          version: "latest"
       - name: Install system dependencies
         run: |
           sudo apt-get update
           sudo apt-get install -y pandoc
-      - uses: actions/setup-python@v2
-        with:
-          python-version: '3.9'
       - name: Install vitessce
-        run: pip install -e .[dev,docs,all]
+        run: uv sync --extra dev --extra docs --extra all
       - name: Run tests
-        run: pytest
+        run: uv run pytest
       - name: Build a binary wheel and a source tarball
-        run: >-
-          python -m
-          build
-          --sdist
-          --wheel
-          --outdir dist/
-          .
+        run: uv build --sdist --wheel
       - name: Build docs
         run: |
-          make html
+          uv run make html
           touch docs-dist/html/.nojekyll
       - uses: actions/upload-pages-artifact@v1
         with:

.github/workflows/deploy.yml

@@ -7,12 +7,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
+      - uses: astral-sh/setup-uv@v3
+        with:
+          version: "latest"
       - name: Install system dependencies
         run: |
           sudo apt-get update
           sudo apt-get install -y pandoc
-      - uses: actions/setup-python@v2
-        with:
-          python-version: '3.9'
-      - run: pip install -e .[docs,all]
-      - run: make html
+      - run: uv sync --extra docs --extra all
+      - run: uv run make html

.github/workflows/docs.yml

@@ -7,9 +7,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: astral-sh/setup-uv@v3
         with:
-          python-version: '3.9'
-          architecture: 'x64'
-      - run: pip install .[dev]
+          version: "latest"
+      - run: uv sync --extra dev
       - run: flake8

.github/workflows/lint.yml

@@ -7,19 +7,21 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        version: ['3.9', '3.12']
+        version: ['3.10', '3.12']
     steps:
       - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: astral-sh/setup-uv@v3
         with:
-          python-version: ${{ matrix.version }}
+          version: "latest"
+        env:
+          UV_PYTHON: ${{ matrix.version }}
       - name: Install vitessce
-        run: pip install -e .[dev,all]
+        run: uv sync --extra dev --extra all
       - name: Run tests and report coverage with omits
         run: |
-          coverage run --rcfile .coveragerc_omit --module pytest && \
-          coverage report --show-missing --fail-under 100
+          uv run coverage run --rcfile .coveragerc_omit --module pytest && \
+          uv run coverage report --show-missing --fail-under 100
       - name: Run tests and report coverage without omits
         run: |
-          coverage run --rcfile .coveragerc_real --module pytest && \
-          coverage report --show-missing
+          uv run coverage run --rcfile .coveragerc_real --module pytest && \
+          uv run coverage report --show-missing

.github/workflows/test.yml

@@ -7,15 +7,11 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: astral-sh/setup-uv@v3
         with:
-          python-version: '3.9'
-      - run: |
-          pip install "pulp==2.7.0"
-          pip install snakemake
-          pip install pyyaml
+          version: "latest"
       - name: Install vitessce
-        run: pip install -e .[dev,all]
+        run: uv sync --extra dev --extra all --extra demos
       - name: Run tests
         working-directory: ./demos
-        run: snakemake -j 1 --dry-run
+        run: uv run snakemake -j 1 --dry-run

.github/workflows/test_demos.yml

@@ -0,0 +1 @@
+3.10

.python-version

@@ -28,9 +28,7 @@ For a development installation (requires NodeJS and NPM),
 
     $ git clone https://github.com/vitessce/vitessce-python.git
     $ cd vitessce-python
-    $ conda env create -f environment.yml
-    $ conda activate vitessce-python-dev
-    $ pip install -e ".[dev,docs,all]"
+    $ uv sync --extra dev --extra docs --extra all
 
 ### Conda environments
 
@@ -43,29 +41,29 @@ In this repository, there are multiple conda environments for different purposes
 ## Linting and testing
 
 ```sh
-flake8
-pytest
+uv run flake8
+uv run pytest
 ```
 
 ### Formatting
 
 One file:
 
 ```sh
-autopep8 --in-place --aggressive ./path/to/file.py
+uv run autopep8 --in-place --aggressive ./path/to/file.py
 ```
 
 All `.py` files:
 
 ```sh
-find . -name '*.py' -exec autopep8 --in-place --aggressive '{}' \;
+find . -name '*.py' -exec uv run autopep8 --in-place --aggressive '{}' \;
 ```
 
 
 ## Documentation
 
 ```sh
-make html
+uv run make html
 ```
 
 

README.md

@@ -8,15 +8,13 @@ Some of the example notebooks rely on external single-cell data analysis package
 
 ```sh
 cd docs/notebooks
-conda env create -f environment.yml
-conda activate vitessce-python-notebooks
-pip install -e "../..[dev]"
+uv sync --extra dev --extra docs --extra all
 ```
 
 ## Run
 
 ```sh
-jupyter lab
+uv run jupyter lab
 ```
 
 ## Troubleshooting