Merge

Author: keller-mark

.coveragerc_omit

@@ -1,16 +1,16 @@
 [run]
 omit =
-    vitessce/config.py
-    vitessce/export.py
-    vitessce/file_def_utils.py
-    vitessce/routes.py
-    vitessce/widget.py
-    vitessce/wrappers.py
-    vitessce/repr.py
-    vitessce/utils.py
-    vitessce/data_utils/anndata.py
-    vitessce/data_utils/ome.py
-    vitessce/data_utils/entities.py
-    vitessce/data_utils/multivec.py
-    vitessce/widget_plugins/demo_plugin.py
-    vitessce/widget_plugins/spatial_query.py
+    src/vitessce/config.py
+    src/vitessce/export.py
+    src/vitessce/file_def_utils.py
+    src/vitessce/routes.py
+    src/vitessce/widget.py
+    src/vitessce/wrappers.py
+    src/vitessce/repr.py
+    src/vitessce/utils.py
+    src/vitessce/data_utils/anndata.py
+    src/vitessce/data_utils/ome.py
+    src/vitessce/data_utils/entities.py
+    src/vitessce/data_utils/multivec.py
+    src/vitessce/widget_plugins/demo_plugin.py
+    src/vitessce/widget_plugins/spatial_query.py

.envrc

@@ -15,31 +15,25 @@ jobs:
   pre_deploy:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
+      - 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
+      - uses: actions/upload-pages-artifact@v3
         with:
           path: ./docs-dist/html
       - name: Deploy package to PyPI
@@ -57,4 +51,4 @@ jobs:
     steps:
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v1
+        uses: actions/deploy-pages@v4

.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]
-      - run: flake8
+          version: "latest"
+      - run: uv sync --extra dev
+      - run: uv 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

@@ -28,44 +28,35 @@ 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
-
-In this repository, there are multiple conda environments for different purposes:
-
-- `vitessce-python-dev` (defined in [environment.yml](./environment.yml)) is used for the development of the `vitessce` package itself
-- `vitessce-python-notebooks` (defined in [docs/notebooks/environment.yml](./docs/notebooks/environment.yml)) is used for running the example notebooks in the `docs/notebooks/` directory (see [`docs/notebooks/README.md`](./docs/notebooks#readme) for more information)
-- `vitessce-python-binder` (defined in [binder/environment.yml](./binder/environment.yml)) is the environment used by Binder upon opening notebooks from this repository
 
 ## 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
 ```
 
 
@@ -121,6 +112,8 @@ or
 vc.display(proxy=True, host_name="http://localhost:8888")
 ```
 
+For more information see the [data location options documentation](https://python-docs.vitessce.io/data_options.html).
+
 ### Ensure that Vitessce and Jupyter are installed in the same environment
 
 With the environment activated, run `pip list` on the command line: