Typecheck project with ty (#204)

These changes add `ty` as a development dependency and enforce
typechecking in CI. To typecheck locally:

```sh
uv run ty check
```

Author: manzt

.github/workflows/ci.yml

@@ -16,7 +16,15 @@ jobs:
       - uses: actions/checkout@v5
       - uses: astral-sh/setup-uv@v7
       - run: |
-          uv run ruff check .
+          uv run ruff check
+
+  Typecheck:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+      - uses: astral-sh/setup-uv@v7
+      - run: |
+          uv run ty check
 
   Test:
     runs-on: ubuntu-latest

examples/JupyterServer.ipynb

@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f1562cea-288f-4817-8ca7-606cd104630e",
+   "id": "3f95a08d",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -13,7 +13,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "db2277b1",
+   "id": "25f7dab3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -26,13 +26,13 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2e2c753f-fb13-4d54-b031-10cf5865e138",
+   "id": "caf312ad",
    "metadata": {},
    "outputs": [],
    "source": [
     "from dataclasses import dataclass\n",
     "\n",
-    "from clodius.tiles.cooler import tiles, tileset_info\n",
+    "from clodius.tiles.cooler import tiles, tileset_info  # ty:ignore[unresolved-import]\n",
     "\n",
     "\n",
     "@dataclass\n",
@@ -54,31 +54,31 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d2b9ae4d-85d0-4545-aeef-073ad7d0d4e9",
+   "id": "866266ec",
    "metadata": {},
    "outputs": [],
    "source": []
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2a69dbe9-ad50-4e98-ac3b-b05285703760",
+   "id": "78d4ccb4",
    "metadata": {},
    "outputs": [],
    "source": []
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f4ea4dec-135f-49c7-b7ef-ff0c0ece8b45",
+   "id": "fb5ee4a8",
    "metadata": {},
    "outputs": [],
    "source": []
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8e571a51-4b09-4da7-8d65-af28a5cf4703",
+   "id": "3f3151e0",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -105,4 +105,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 5
-}
+}

pyproject.toml

@@ -34,7 +34,15 @@ requires-python = ">=3.8"
 urls = { homepage = "https://github.com/higlass/higlass-python" }
 
 [dependency-groups]
-dev = ["anywidget[dev]", "jupyterlab", "pytest", "ruff"]
+dev = [
+    "anywidget[dev]>=0.9.13",
+# TODO Add for typechecking after we drop 3.8 support
+#   "clodius>=0.20.4",
+    "jupyterlab>=4.3.5",
+    "pytest>=8.3.5",
+    "ruff>=0.15.4",
+    "ty>=0.0.19",
+]
 
 [tool.hatch.build.targets.wheel]
 packages = ["src/higlass"]
@@ -65,5 +73,9 @@ extend-select = [
 "examples/*.ipynb" = [
     "F811", # redefintion
 ]
+
+[tool.ty.src]
+exclude = ["examples/Plugin.ipynb", "docs/conf.py", "docs/build.py"]
+
 [tool.uv]
 required-version = ">=0.10.0"

src/higlass/api.py

@@ -48,10 +48,10 @@
 
 class _PropertiesMixin:
     def properties(
-        self: utils.ModelT,  # type: ignore
+        self: utils.ModelT,
         inplace: bool = False,
-        **fields,  # type: ignore
-    ) -> utils.ModelT:  # type: ignore
+        **fields,
+    ) -> utils.ModelT:
         """Configures top-level properties.
 
         Updates top-level properties for a Track, View, or Viewconf. This
@@ -85,10 +85,10 @@ def properties(
 
 class _OptionsMixin:
     def opts(
-        self: TrackT,  # type: ignore
+        self: TrackT,
         inplace: bool = False,
         **options,
-    ) -> TrackT:  # type: ignore
+    ) -> TrackT:
         """Configures options for a Track.
 
         A convenience method to update `track.options`.

src/higlass/tilesets.py

@@ -192,10 +192,12 @@ def load(filepath: str | pathlib.Path) -> ClodiusTileset:
 
 
 def chromsizes(filepath: str) -> ClodiusTileset:
-    from clodius.tiles.chromsizes import tileset_info
+    from clodius.tiles.chromsizes import tileset_info  # ty:ignore[unresolved-import]
 
     return ClodiusTileset(
-        datatype="chromsizes", tiles_impl=None, info_impl=lambda: tileset_info(filepath)
+        datatype="chromsizes",
+        tiles_impl=lambda _: {},  # chromsizes has no tiles endpoint
+        info_impl=lambda: tileset_info(filepath),
     )
 
 

test/test_api.py

@@ -85,7 +85,7 @@
 )
 def test_creates_correct_track(args: str | tuple, expected: hg.Track):
     track_type, kwargs = (args, {}) if isinstance(args, str) else args
-    track = hg.track(track_type, **kwargs)  # type: ignore
+    track = hg.track(track_type, **kwargs)
     assert isinstance(track, expected)  # type: ignore
     assert track.type == track_type
 
@@ -227,15 +227,16 @@ class PileupTrack(hg.PluginTrack):
     }
 
     # Create and use the custom track
-    pileup_track = PileupTrack(data=pileup_data)
+    pileup_track = PileupTrack(data=pileup_data)  # ty:ignore[unknown-argument]
 
     view = hg.view((pileup_track, "top"))
     uid1 = view.uid
+    assert view.tracks.top
     assert view.tracks.top[0].plugin_url == some_url
 
     # The .domain() function creates a copy of the view. We want to make sure
     # that the plugin_url attribute of the PluginTrack is maintained
-    view = view.domain(x=[0, 10])
+    view = view.domain(x=(0, 10))
     uid2 = view.uid
     assert view.tracks.top[0].plugin_url == some_url