Use uv instead of nox and pip-tools

oist · Oct 10, 2024 · 644869b · 644869b
1 parent 665ec0a
commit 644869b
Show file tree

Hide file tree

Showing 17 changed files with 54 additions and 182 deletions.
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -29,11 +29,9 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python }}
-      - name: Update pip and install nox
-        run: |
-          pip install --upgrade pip
-          pip install nox
-      - name: Run pip compile
-        run: nox --session=compile
+      - name: Install uv
+        run: pip install uv
+      - name: Sync
+        run: make sync
       - name: Run tests
-        run: nox --session=${{ matrix.nox }} --python=${{ matrix.python }}
+        run: make test
diff --git a/.gitignore b/.gitignore
@@ -16,3 +16,4 @@ pyrightconfig.json
 *.eqx
 *.parquet
 *.npz
+uv.lock
diff --git a/Makefile b/Makefile
@@ -0,0 +1,32 @@
+.PHONY: test lint
+
+CUDA_AVAILABLE := $(shell command -v nvcc >/dev/null 2>&1 && echo 1 || echo 0)
+
+test:
+	uv run pytest
+
+lint:
+	uvx ruff check
+	uvx black src/emevo tests --check
+	uvx isort src/emevo tests --check
+
+
+format:
+	uvx black src/emevo tests
+	uvx isort src/emevo tests
+
+
+publish:
+	uv build
+	uvx twine upload dist/*
+
+
+sync:
+ifeq ($(CUDA_AVAILABLE),1)
+	uv sync --extra=analysis --extra=cuda12
+else
+	uv sync --extra=analysis
+endif
+
+
+all: test lint
diff --git a/noxfile.py b/noxfile.py
diff --git a/pyproject.toml b/pyproject.toml
@@ -38,8 +38,10 @@ analysis = [
     "matplotlib >= 3.0",
     "networkx >= 3.0",
     "polars >= 0.20",
-    "PySide6 >= 6.5",
 ]
+# Meta feature to install CUDA12 jax
+cuda12 = ["jax[cuda12]"]
+widget = ["PySide6 >= 6.5"]
 video = ["imageio-ffmpeg >= 0.4"]
 
 [project.readme]
@@ -76,4 +78,10 @@ ignore = ["B905"]
 # For typer
 "experiments/*.py" = ["B008", "UP006", "UP007"]
 "smoke-tests/*.py" = ["B008", "UP006", "UP007"]
-"scripts/*.py" = ["UP006", "UP035", "UP007"]
+"scripts/*.py" = ["UP006", "UP035", "UP007"]
+
+
+[tool.uv]
+dev-dependencies = [
+    "pytest>=8.3.3",
+]
diff --git a/requirements/bench.in b/requirements/bench.in
diff --git a/requirements/cuda11.in b/requirements/cuda11.in
diff --git a/requirements/cuda12.in b/requirements/cuda12.in
diff --git a/requirements/format.in b/requirements/format.in
diff --git a/requirements/jupyter.in b/requirements/jupyter.in
diff --git a/requirements/lint.in b/requirements/lint.in
diff --git a/requirements/scripts.in b/requirements/scripts.in
diff --git a/requirements/smoke.in b/requirements/smoke.in
diff --git a/requirements/tests.in b/requirements/tests.in
diff --git a/setup-jupterlab b/setup-jupterlab
diff --git a/src/emevo/analysis/tree.py b/src/emevo/analysis/tree.py
@@ -63,7 +63,7 @@ def parent(self) -> Node | None:
     @functools.cached_property
     def n_total_children(self) -> int:
         total = 0
-        for child, _ in self.children:
+        for child in self.children:
             total += 1 + child.n_total_children
         return total
 
@@ -87,7 +87,7 @@ def traverse(
     ) -> Iterable[Node]:
         if include_self and preorder:
             yield self
-        for child, _ in self.children:
+        for child in self.children:
             yield from child.traverse(preorder)
         if include_self and not preorder:
             yield self

diff --git a/tests/test_tree.py b/tests/test_tree.py
@@ -22,7 +22,7 @@ def treedef() -> list[tuple[int, int]]:
 
 
 def test_from_iter(treedef: list[tuple[int, int]]) -> None:
-    tree = Tree.from_iter(treedef)
+    tree = Tree.from_iter(treedef, root_idx=-1)
     preorder = list(map(operator.attrgetter("index"), tree.traverse(preorder=True)))
     assert preorder == [0, 1, 3, 4, 5, 8, 9, 2, 6, 7]
     postorder = list(map(operator.attrgetter("index"), tree.traverse(preorder=False)))
@@ -33,7 +33,7 @@ def test_from_iter(treedef: list[tuple[int, int]]) -> None:
 def test_split(treedef: list[tuple[int, int]]) -> None:
     tree = Tree.from_iter(treedef)
     sp1 = tree.split(min_group_size=3)
-    assert len(sp1) == 10
+    assert len(sp1) == 4
     assert sp1[0] == 0
     for idx in [1, 3, 4]:
         assert sp1[idx] == 1
@@ -43,7 +43,7 @@ def test_split(treedef: list[tuple[int, int]]) -> None:
         assert sp1[idx] == 3
 
     sp2 = tree.split(min_group_size=4)
-    assert len(sp2) == 10
+    assert len(sp2) == 4
     for idx in [0, 2, 6, 7]:
         assert sp2[idx] == 0
     for idx in [1, 3, 4, 5, 8, 9]:
@@ -63,7 +63,7 @@ def test_multilabel_split(treedef: list[tuple[int, int]]) -> None:
 def test_from_table() -> None:
     table = pq.read_table(ASSET_DIR.joinpath("profile_and_rewards.parquet"))
     tree = Tree.from_table(table, 20)
-    for root, _ in tree.root.children:
+    for root in tree.root.children:
         assert root.index < 10
         assert root.birth_time is not None
         for node in root.traverse():