Switch instructions & metadata files to use a modern uv workflow (#202)

Author: sampsyo

.github/workflows/build.yml

@@ -24,18 +24,14 @@ jobs:
         with:
           path: ~/.cache/uv
           key: ${{ runner.os }}-python-${{ matrix.python-version }}-uv
-      - name: Create and activate virtualenv with uv
+      - name: uv sync and activate
         run: |
           curl -LsSf https://astral.sh/uv/install.sh | sh
-          uv venv
+          uv sync
           echo "VIRTUAL_ENV=.venv" >> $GITHUB_ENV
           echo "$PWD/.venv/bin" >> $GITHUB_PATH
-      - name: Install Python tools
-        run: uv pip install -r requirements.txt
 
       # Set up for tests.
-      - name: Install Turnt
-        run: uv pip install turnt
       - name: Problem matcher
         run: echo '::add-matcher::.github/tap-matcher.json'
       - name: Fetch test data
@@ -70,14 +66,12 @@ jobs:
         with:
           path: ~/.cache/uv
           key: ${{ runner.os }}-python-${{ matrix.python-version }}-uv
-      - name: Create and activate virtualenv with uv
+      - name: uv sync and activate
         run: |
           curl -LsSf https://astral.sh/uv/install.sh | sh
-          uv venv
+          uv sync
           echo "VIRTUAL_ENV=.venv" >> $GITHUB_ENV
           echo "$PWD/.venv/bin" >> $GITHUB_PATH
-      - name: Install Python tools
-        run: uv pip install -r requirements.txt
 
       # Install odgi
       - name: Pull odgi container

README.md

@@ -34,11 +34,13 @@ Similarly, `slow_odgi` is a set of GFA analyses based on `mygfa`; it's meant to
 
 To set up both of them from this repository, try using [uv][]:
 
-    $ uv venv
-    $ uv pip install -r requirements.txt
-    $ source .venv/bin/activate
+    $ uv run slow_odgi --help
+
+Or, alternatively, you can set up and activate the environment manually:
 
-Now type `slow_odgi --help` to see if everything's working.
+    $ uv sync
+    $ source .venv/bin/activate
+    $ slow_odgi --help
 
 [uv]: https://github.com/astral-sh/uv
 [mygfa-docs]: http://cucapra.github.io/pollen/mygfa/

flatgfa-py/Cargo.lock

@@ -12,32 +12,20 @@ Then, read [the API documentation][flatgfa-py-docs] for details about what it ca
 Development
 -----------
 
-To build this library, first install [Maturin][]:
+The easiest way to get started is with [uv][]:
 
-    $ pipx install maturin
+    $ uv run --package flatgfa python example.py
 
-Next, we'll build and install the Python library in our virtualenv.
-Starting from the repository root:
-
-    $ uv venv  # Unless you already created the virtualenv.
-    $ uv pip install pip  # Maturin depends on pip.
-    $ source .venv/bin/activate
-    $ cd flatgfa-py
-    $ maturin develop
-
-Now the `flatgfa` module is available to Python programs.
-Try our [example][]:
-
-    $ python example.py
+That should build and install the package and then run our `example.py` script.
 
 Or run the tests:
 
-    $ uv pip install pytest
-    $ pytest
+    $ uv run --package flatgfa pytest
 
 [maturin]: https://www.maturin.rs
 [flatgfa-py-docs]: https://cucapra.github.io/pollen/flatgfa/
 [flatgfa]: https://github.com/cucapra/pollen/tree/main/flatgfa
 [gfa]: https://github.com/GFA-spec/GFA-spec/blob/master/GFA1.md
 [flatgfa-pypi]: https://pypi.org/project/flatgfa/
 [example]: https://github.com/cucapra/pollen/blob/main/flatgfa-py/example.py
+[uv]: https://docs.astral.sh/uv/

flatgfa-py/README.md

@@ -15,8 +15,8 @@ classifiers = [
 repository = "https://github.com/cucapra/pollen"
 documentation = "https://cucapra.github.io/pollen/flatgfa/"
 
-[project.optional-dependencies]
-test = ["pytest"]
+[dependency-groups]
+dev = ["pytest>=8.3.0"]
 
 [build-system]
 requires = ["maturin>=1.0,<2.0"]

flatgfa-py/pyproject.toml

@@ -112,8 +112,7 @@ Clone this repository:
 
 And then install the Python tools using [uv][]:
 
-    $ uv venv
-    $ uv pip install -r requirements.txt
+    $ uv sync
     $ source .venv/bin/activate
 
 [calyx]: https://calyxir.org

pollen_py/README.md

@@ -1,15 +1,14 @@
 [build-system]
-requires = ["flit_core >=2,<4"]
+requires = ["flit_core >=3.2,<4"]
 build-backend = "flit_core.buildapi"
 
-[tool.flit.metadata]
-module = "pollen"
-author = "Susan Garry"
-author-email = "shg64@cs.cornell.edu"
-home-page = "https://github.com/cucapra/pollen"
-description-file = "README.md"
-requires-python = ">=3.8"
-requires = []
+[project]
+name = "pollen"
+authors = [
+    { name = "Susan Garry", email = "shg64@cs.cornell.edu" }
+]
+readme = "README.md"
+dynamic = ["version", "description"]
 
-[tool.flit.scripts]
+[project.scripts]
 exine = "pollen.main:main"

pollen_py/pyproject.toml

@@ -0,0 +1,27 @@
+[project]
+name = "pollen_workspace"
+version = "0.0.0"
+requires-python = ">=3.8"
+dependencies = [
+    "mygfa",
+    "slow_odgi",
+    "pollen",
+    "pollen_data_gen",
+    "turnt>=1.11.0",
+]
+
+[tool.uv.sources]
+mygfa = { workspace = true }
+slow_odgi = { workspace = true }
+pollen = { workspace = true }
+pollen_data_gen = { workspace = true }
+flatgfa = { workspace = true }
+
+[tool.uv.workspace]
+members = [
+    "mygfa",
+    "slow_odgi",
+    "pollen_py",
+    "pollen_data_gen",
+    "flatgfa-py",
+]

pyproject.toml

@@ -10,8 +10,7 @@ Think of it as a code-forward spec for `odgi` commands.
 
 One easy way to install everything in the Pollen repo is to use [uv][]:
 
-    $ uv venv
-    $ uv pip install -r requirements.txt
+    $ uv sync
     $ source .venv/bin/activate
 
 [uv]: https://github.com/astral-sh/uv
@@ -30,7 +29,7 @@ To test `slow_odgi`, we treat odgi as an oracle and compare our outputs against
 To run these tests, you will need:
 
 1. [Odgi][]. Our tests were run against a built-from-source copy of odgi (commit `34f006f`).
-2. [Turnt][]. This is installed automatically if you use `requirements.txt` as above.
+2. [Turnt][]. This is installed automatically if you use `uv` as above.
 
 With these in place, run `make test-slow-odgi`. The "oracle" files will be generated first, and this will toss up a large number of warnings which can all be ignored. Then the tests will begin to run, and the `ok`/`not ok` signals there are actually of interest.