From f0bfaa1a5f868e686c1bdc7bd934995e6b92bc9d Mon Sep 17 00:00:00 2001
From: Adrian Sampson <adrian@radbox.org>
Date: Mon, 30 Dec 2024 17:23:15 -0500
Subject: [PATCH 1/6] Try setting up a uv workspace

---
 pollen_py/pyproject.toml | 19 +++++++++----------
 pyproject.toml           | 24 ++++++++++++++++++++++++
 2 files changed, 33 insertions(+), 10 deletions(-)
 create mode 100644 pyproject.toml

diff --git a/pollen_py/pyproject.toml b/pollen_py/pyproject.toml
index f38ca7f6..65ec14b9 100644
--- a/pollen_py/pyproject.toml
+++ b/pollen_py/pyproject.toml
@@ -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"
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 00000000..4f540f23
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,24 @@
+[project]
+name = "pollen_workspace"
+version = "0.0.0"
+requires-python = ">=3.8"
+dependencies = [
+    "mygfa",
+    "slow_odgi",
+    "pollen",
+    "pollen_data_gen",
+]
+
+[tool.uv.sources]
+mygfa = { workspace = true }
+slow_odgi = { workspace = true }
+pollen = { workspace = true }
+pollen_data_gen = { workspace = true }
+
+[tool.uv.workspace]
+members = [
+    "mygfa",
+    "slow_odgi",
+    "pollen_py",
+    "pollen_data_gen",
+]

From b26400f17b7c30ccb7916e353b6d4f5f3d96e1d0 Mon Sep 17 00:00:00 2001
From: Adrian Sampson <adrian@radbox.org>
Date: Mon, 30 Dec 2024 17:26:18 -0500
Subject: [PATCH 2/6] Instructions for using the new uv thing

---
 README.md | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index 8f13faa3..bf1f214e 100644
--- a/README.md
+++ b/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/

From cbea798b1c52ab328e8777b2f5ceb13d51b3e6e7 Mon Sep 17 00:00:00 2001
From: Adrian Sampson <adrian@radbox.org>
Date: Mon, 30 Dec 2024 17:32:35 -0500
Subject: [PATCH 3/6] Fully move on from requirements.txt

---
 pollen_py/README.md | 3 +--
 pyproject.toml      | 1 +
 requirements.txt    | 5 -----
 slow_odgi/README.md | 5 ++---
 4 files changed, 4 insertions(+), 10 deletions(-)
 delete mode 100644 requirements.txt

diff --git a/pollen_py/README.md b/pollen_py/README.md
index 36040e99..a6168ae9 100644
--- a/pollen_py/README.md
+++ b/pollen_py/README.md
@@ -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
diff --git a/pyproject.toml b/pyproject.toml
index 4f540f23..65224ed7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,6 +7,7 @@ dependencies = [
     "slow_odgi",
     "pollen",
     "pollen_data_gen",
+    "turnt",
 ]
 
 [tool.uv.sources]
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index 65883460..00000000
--- a/requirements.txt
+++ /dev/null
@@ -1,5 +0,0 @@
--e ./mygfa
--e ./slow_odgi
--e ./pollen_py
--e ./pollen_data_gen
-turnt
diff --git a/slow_odgi/README.md b/slow_odgi/README.md
index 4f6fe3b3..2bbfd3e2 100644
--- a/slow_odgi/README.md
+++ b/slow_odgi/README.md
@@ -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.
 

From 34cdbdb229f7730d0db0e13f408fd61a43319235 Mon Sep 17 00:00:00 2001
From: Adrian Sampson <adrian@radbox.org>
Date: Mon, 30 Dec 2024 17:48:38 -0500
Subject: [PATCH 4/6] Some simple uv instructions for flatgfa-py

---
 flatgfa-py/Cargo.lock     |  7 +++++++
 flatgfa-py/README.md      | 22 +++++-----------------
 flatgfa-py/pyproject.toml |  4 ++--
 pyproject.toml            |  4 +++-
 4 files changed, 17 insertions(+), 20 deletions(-)

diff --git a/flatgfa-py/Cargo.lock b/flatgfa-py/Cargo.lock
index 027825c9..1d762ad4 100644
--- a/flatgfa-py/Cargo.lock
+++ b/flatgfa-py/Cargo.lock
@@ -48,6 +48,12 @@ version = "1.2.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "f1fdabc7756949593fe60f30ec81974b613357de856987752631dea1e3394c80"
 
+[[package]]
+name = "bit-vec"
+version = "0.8.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5e764a1d40d510daf35e07be9eb06e75770908c27d411ee6c92109c9840eaaf7"
+
 [[package]]
 name = "bitflags"
 version = "2.5.0"
@@ -120,6 +126,7 @@ version = "0.1.0"
 dependencies = [
  "argh",
  "atoi",
+ "bit-vec",
  "bstr",
  "memchr",
  "memmap",
diff --git a/flatgfa-py/README.md b/flatgfa-py/README.md
index 4a69ca6a..e937f396 100644
--- a/flatgfa-py/README.md
+++ b/flatgfa-py/README.md
@@ -12,28 +12,15 @@ 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/
@@ -41,3 +28,4 @@ Or run the tests:
 [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/
diff --git a/flatgfa-py/pyproject.toml b/flatgfa-py/pyproject.toml
index 78a6304d..2951ed32 100644
--- a/flatgfa-py/pyproject.toml
+++ b/flatgfa-py/pyproject.toml
@@ -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"]
diff --git a/pyproject.toml b/pyproject.toml
index 65224ed7..ab71baf6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,7 +7,7 @@ dependencies = [
     "slow_odgi",
     "pollen",
     "pollen_data_gen",
-    "turnt",
+    "turnt>=1.11.0",
 ]
 
 [tool.uv.sources]
@@ -15,6 +15,7 @@ mygfa = { workspace = true }
 slow_odgi = { workspace = true }
 pollen = { workspace = true }
 pollen_data_gen = { workspace = true }
+flatgfa = { workspace = true }
 
 [tool.uv.workspace]
 members = [
@@ -22,4 +23,5 @@ members = [
     "slow_odgi",
     "pollen_py",
     "pollen_data_gen",
+    "flatgfa-py",
 ]

From 4c00938e72c603815ce85a5c1b86384c7bb8586d Mon Sep 17 00:00:00 2001
From: Adrian Sampson <adrian@radbox.org>
Date: Mon, 30 Dec 2024 17:49:14 -0500
Subject: [PATCH 5/6] Check in the lock file

---
 uv.lock | 206 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 206 insertions(+)
 create mode 100644 uv.lock

diff --git a/uv.lock b/uv.lock
new file mode 100644
index 00000000..1f559a10
--- /dev/null
+++ b/uv.lock
@@ -0,0 +1,206 @@
+version = 1
+requires-python = ">=3.8"
+
+[manifest]
+members = [
+    "flatgfa",
+    "mygfa",
+    "pollen",
+    "pollen-data-gen",
+    "pollen-workspace",
+    "slow-odgi",
+]
+
+[[package]]
+name = "click"
+version = "8.1.8"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
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+]
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+]
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+]
+
+[package.metadata]
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+
+[[package]]
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+version = "0.0.0"
+source = { virtual = "." }
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+    { name = "mygfa" },
+    { name = "pollen" },
+    { name = "pollen-data-gen" },
+    { name = "slow-odgi" },
+    { name = "turnt" },
+]
+
+[package.metadata]
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+    { name = "pollen", editable = "pollen_py" },
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+    { name = "slow-odgi", editable = "slow_odgi" },
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+]
+
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From 994e28c733370046bf1181e7ecbb0e3b8096c184 Mon Sep 17 00:00:00 2001
From: Adrian Sampson <adrian@radbox.org>
Date: Mon, 30 Dec 2024 17:53:40 -0500
Subject: [PATCH 6/6] Try updating CI for new uv setup

---
 .github/workflows/build.yml | 14 ++++----------
 1 file changed, 4 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 2313ea0a..af1f2e5e 100644
--- a/.github/workflows/build.yml
+++ b/.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