Conda to uv (#390)

* Conda to uv

* Update flake8 command

* Update

.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

.github/workflows/deploy.yml

@@ -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/docs.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/lint.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/test.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_demos.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

.python-version

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

README.md

@@ -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
 ```
 
 

docs/notebooks/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

pyproject.toml

@@ -1,6 +1,6 @@
 [build-system]
-requires = ["setuptools>=67.0", "wheel>=0.38.4"]
-build-backend = "setuptools.build_meta"
+requires = ["hatchling"]
+build-backend = "hatchling.build"
 
 [project]
 name = "vitessce"
@@ -11,7 +11,7 @@ authors = [
 description = "Jupyter widget facilitating interactive visualization of spatial single-cell data with Vitessce"
 readme = "README.md"
 license = {file = "LICENSE"}
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 keywords = ["ipython", "jupyter", "widgets"]
 classifiers = [
   'Development Status :: 4 - Beta',
@@ -31,24 +31,19 @@ dependencies = [
   'negspy>=0.2.24',
   'pandas>=1.1.2',
   'black>=21.11b1',
-  'numpy>=1.21.2,<2.0',
-  'anndata>=0.7.8,<0.11',
-  'scanpy>=1.9.3',
+  'numpy>=1.21.2',
+  'anndata>=0.7.8',
+  # scanpy < 1.10.3 does not support numpy >= 2.0.0 and does not 
+  # Reference: https://github.com/scverse/scanpy/pull/3115/files
+  'scanpy>=1.10.2',
   'ome-zarr>=0.8.3',
   'tifffile>=2020.10.1',
   'jsonschema>=3.2',
   'tqdm>=4.1.0'
 ]
 
 [project.optional-dependencies]
-dev = [
-  'build==0.1.0',
-  'pytest>=6.2.4',
-  'loompy>=3.0.6',
-  'coverage>=6.3.2',
-  'flake8==3.8.4',
-  'spatialdata>=0.2.2',
-]
+dev = []
 docs = [
   'sphinx==4.2.0',
   'sphinx-rtd-theme==1.0.0',
@@ -79,7 +74,7 @@ all = [
   'uvicorn>=0.17.0',
   'ujson>=4.0.1',
   'starlette==0.14.0',
-  'generate-tiff-offsets>=0.1.7',
+  'generate-tiff-offsets>=0.1.8',
   'kerchunk>=0.2.6',
   'fsspec',
 
@@ -93,9 +88,46 @@ building = []
 testing = []
 linting = []
 notebook = []
+demos = [
+  "pulp==2.7.0",
+  "snakemake",
+  "pyyaml",
+]
+
+[dependency-groups]
+dev = [
+  'build==0.1.0',
+  'pytest>=6.2.4',
+  'loompy>=3.0.6',
+  'coverage>=6.3.2',
+  'flake8==3.8.4',
+  #'spatialdata>=0.2.2',
+  'jupyterlab',
+  'numba>=0.53.0',
+  'jupyterlab>=3',
+  'boto3>=1.16.30',
+  'scikit-misc>=0.1.3',
+]
+
+[tool.uv]
+default-groups = ["dev"]
+override-dependencies = [
+  'starlette==0.14.0'
+]
+
+[tool.hatch.build]
+exclude = [".github", "docs", "demos", "binder"]
 
 [project.urls]
 repository = "https://github.com/vitessce/vitessce-python"
 
 [tool.setuptools]
 packages = ["vitessce", "vitessce.data_utils", "vitessce.widget_plugins"]
+package-dir = {"" = "src"}
+
+# Reference: https://stackoverflow.com/a/50156706
+[tool.pytest.ini_options]
+pythonpath = ["src"]
+testpaths = ["tests"]
+addopts = ["--doctest-modules", "--verbose", "--ignore=docs", "--ignore=demos"]
+

setup.cfg

@@ -4,9 +4,9 @@ universal=1
 [flake8]
 per-file-ignores =
   # Special case: names are reimported from __init__.py, so unused imports are expected.
-  vitessce/__init__.py: F401
-  vitessce/data_utils/__init__.py: F401
-  vitessce/widget_plugins/__init__.py: F401
+  src/vitessce/__init__.py: F401
+  src/vitessce/data_utils/__init__.py: F401
+  src/vitessce/widget_plugins/__init__.py: F401
 ignore =
   # Ignore line too long
   E501,
@@ -20,6 +20,10 @@ ignore =
   E128
 exclude =
   ./js/node_modules/,
+  ./docs/,
+  ./demos/,
+  ./binder/,
+  ./.venv/,
   ./docs/notebooks/.ipynb_checkpoints/,
   ./build/,
   ./.ipynb_checkpoints/