👽️ Nonlocals of a nonlocal??? sure why not (#54)

Sricharan Reddy Varra · pre-commit-ci[bot] · web-flow · commit d91cce37a74a · 2025-04-10T00:41:51.000-07:00
Co-authored-by: pre-commit-ci[bot] &lt;66853113+pre-commit-ci[bot]@users.noreply.github.com&gt;
diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
@@ -29,22 +29,14 @@ jobs:
       - name: Checkout ${{ github.ref }}
         uses: actions/checkout@v4
 
-      - name: Install uv
+      - name: Install uv and setup Python
         uses: astral-sh/setup-uv@v5
         with:
           python-version: ${{ matrix.python-version }}
           enable-cache: true
           cache-dependency-glob: "uv.lock"
           github-token: ${{ secrets.GITHUB_TOKEN }}
 
-      - name: Set up Python
-        run: |
-          uv python install ${{ matrix.python-version }}
-
-      - name: Install Dependencies
-        run: |
-          uv sync --frozen
-
       - name: Build Package
         run: |
           uv build
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
@@ -35,14 +35,6 @@ jobs:
           cache-dependency-glob: "uv.lock"
           github-token: ${{ secrets.GITHUB_TOKEN }}
 
-      - name: Set up Python
-        run: |
-          uv python install ${{ matrix.python-version }}
-
-      - name: Install Dependencies
-        run: |
-          uv sync --frozen
-
       - name: Build Package
         run: |
           uv build
@@ -74,7 +66,7 @@ jobs:
           path: dist/
 
       - name: Publish distribution 📦 to TestPyPI
-        uses: pypa/gh-action-pypi-publish@v1.12.3
+        uses: pypa/gh-action-pypi-publish@v1.12.4
         with:
           repository-url: https://test.pypi.org/legacy/
           verbose: true
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
@@ -38,17 +38,14 @@ jobs:
       - name: Checkout ${{ github.ref }}
         uses: actions/checkout@v4
 
-      - name: Install uv
+      - name: Install uv and setup Python
         uses: astral-sh/setup-uv@v5
         with:
+          python-version: ${{ matrix.python-version }}
           enable-cache: true
           cache-dependency-glob: "uv.lock"
           github-token: ${{ secrets.GITHUB_TOKEN }}
 
-      - name: Set up Python
-        run: |
-          uv python install ${{ matrix.python-version }}
-
       - name: Install Dependencies
         run: |
           uv sync --extra test --frozen
@@ -58,10 +55,10 @@ jobs:
           MPLBACKEND: agg
           DISPLAY: :42
         run: |
-          uv run pytest -n auto --cov --cov-report=xml -v --color=yes --junitxml=junit.xml
+          uv run --frozen pytest -n auto --cov --cov-report=xml -v --color=yes --junitxml=junit.xml
 
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         with:
diff --git a/.nojekyll b/.nojekyll
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -7,15 +7,15 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
   - repo: https://github.com/biomejs/pre-commit
-    rev: v1.9.4
+    rev: v2.0.0-beta.1
     hooks:
       - id: biome-format
   - repo: https://github.com/tox-dev/pyproject-fmt
     rev: v2.5.1
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.10
+    rev: v0.11.4
     hooks:
       - id: ruff
         types_or: [python, pyi, jupyter]
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,14 +8,19 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## [Unreleased]
 
 ### <!-- 5 --> 🌀 Miscellaneous
-- Added additional repr test, remove .bacon-locations
-- ✅ Add repr with multiple groups test
-- ✅ More repr tests
-- Sphinx autodoc typehints >= 3.1.0 for python 3.11+
-- ⬆️ Sphinx autodoc typehings >= 3.1.0 for python 3.11+
-- ➕ Pooch as dep, not opt dep
-- 🏗️ Removed AnnselExpr class, now getting names from closure
-- Updated ExprMetadata
+- 💚 Fix biome.jsonc for 2.0.0-beta.1
+- 🎨 Ruff NP rules for tests
+- 👷 Update CI
+- [pre-commit.ci] auto fixes from pre-commit.com hooks
+- 👽️ Nonlocals of a nonlocal??? sure why not
+
+## [0.1.0] - 2025-03-11
+
+### <!-- 1 --> 🚀 Features
+- Look at names in closure for nw.Expr instead of subclassing it. by [@srivarra](https://github.com/srivarra) in [#50](https://github.com/srivarra/annsel/pull/50)
+
+### <!-- 5 --> 🌀 Miscellaneous
+- [pre-commit.ci] pre-commit autoupdate by [@pre-commit-ci[bot]](https://github.com/pre-commit-ci[bot]) in [#48](https://github.com/srivarra/annsel/pull/48)
 
 ## [0.0.10] - 2025-03-03
 
@@ -110,7 +115,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### <!-- 5 --> 🌀 Miscellaneous
 - 💚 Missed one pypi-publish by [@srivarra](https://github.com/srivarra)
-- 💚 Bump gh-action-pypi-publish to 1.12.3 by [@srivarra](https://github.com/srivarra)
 
 ## [0.0.3] - 2024-12-21
 
@@ -125,6 +129,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Merge pull request #17 from srivarra/pre-commit-ci-update-config by [@srivarra](https://github.com/srivarra) in [#17](https://github.com/srivarra/annsel/pull/17)
 
 ### <!-- 5 --> 🌀 Miscellaneous
+- 💚 Bump gh-action-pypi-publish to 1.12.3 by [@srivarra](https://github.com/srivarra)
 - Api documentation fix by [@srivarra](https://github.com/srivarra)
 - Update README.md example by [@srivarra](https://github.com/srivarra)
 - 📌 Pin doc deps: scanpy, numba, llvmlite to release canidates by [@srivarra](https://github.com/srivarra)
@@ -145,7 +150,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - ✨ Added Groupby by [@srivarra](https://github.com/srivarra)
 - ✨ Add select by [@srivarra](https://github.com/srivarra)
 - Update README.md by [@srivarra](https://github.com/srivarra)
-- 💚 Set uv sync --frozen by [@srivarra](https://github.com/srivarra)
 
 ## [0.0.2] - 2024-11-12
 
@@ -160,6 +164,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Merge pull request #8 from srivarra/pre-commit-ci-update-config by [@srivarra](https://github.com/srivarra) in [#8](https://github.com/srivarra/annsel/pull/8)
 
 ### <!-- 5 --> 🌀 Miscellaneous
+- 💚 Set uv sync --frozen by [@srivarra](https://github.com/srivarra)
 - 📝 Added pre-commit readme badge by [@srivarra](https://github.com/srivarra)
 - 🔧 Add __version__ to __init__ by [@srivarra](https://github.com/srivarra)
 - ➕ Add typing-extensions by [@srivarra](https://github.com/srivarra)
@@ -230,7 +235,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## New Contributors
 * @srivarra made their first contribution in [#5](https://github.com/srivarra/annsel/pull/5)
-[unreleased]: https://github.com/srivarra/annsel/compare/v0.0.10..HEAD
+[unreleased]: https://github.com/srivarra/annsel/compare/v0.1.0..HEAD
+[0.1.0]: https://github.com/srivarra/annsel/compare/v0.0.10..v0.1.0
 [0.0.10]: https://github.com/srivarra/annsel/compare/v0.0.9..v0.0.10
 [0.0.9]: https://github.com/srivarra/annsel/compare/v0.0.8..v0.0.9
 [0.0.8]: https://github.com/srivarra/annsel/compare/v0.0.7..v0.0.8
diff --git a/biome.jsonc b/biome.jsonc
@@ -1,16 +1,15 @@
 {
-    "$schema": "https://biomejs.dev/schemas/1.9.4/schema.json",
+    "$schema": "https://biomejs.dev/schemas/2.0.0-beta.1/schema.json",
     "formatter": { "useEditorconfig": true },
     "overrides": [
         {
-            "include": ["./.vscode/*.json", "**/*.jsonc"],
             "json": {
                 "formatter": { "trailingCommas": "all" },
                 "parser": {
                     "allowComments": true,
-                    "allowTrailingCommas": true,
-                },
-            },
-        },
-    ],
+                    "allowTrailingCommas": true
+                }
+            }
+        }
+    ]
 }
diff --git a/docs/notebooks/all_of_annsel.ipynb b/docs/notebooks/all_of_annsel.ipynb
@@ -44,16 +44,6 @@
     "## Set up Data"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "%load_ext autoreload\n",
-    "%autoreload 2"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -97,6 +87,15 @@
     "display(adata)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "adata.an.filter(obsm={\"X_pca\": an.col([0, 1, 2]) > 1, \"X_projected\": an.col([1]) > 1})"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -502,15 +501,6 @@
     "    obs=an.col([\"Cell_label\"]).is_in([\"Classical Monocytes\", \"CD8+CD103+ tissue resident memory T cells\"])\n",
     ").an.pipe(sc.pl.embedding, basis=\"X_tsneni\", color=\"Cell_label\")"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "an.col([\"Cell_label\", \"sex\"])"
-   ]
   }
  ],
  "metadata": {
diff --git a/pyproject.toml b/pyproject.toml
@@ -25,7 +25,7 @@ dynamic = [ "version" ]
 dependencies = [
   "anndata",
   "more-itertools>=10.6",
-  "narwhals>=1.29.1",
+  "narwhals>=1.34.1",
   "pooch>=1.8.2",
   # for debug logging (referenced from the issue template)
   "session-info2",
diff --git a/ruff.toml b/ruff.toml
@@ -31,8 +31,8 @@ select = [
   "NPY",    # NumPy-specific rules
   "PD",     # Pandas code
   "PTH",    # pathlib
-  # "R",      # Refactor
   "PT",     # Pytest
+  "PERF",   # Perflint
 ]
 ignore = [
   "B008", # Errors from function calls in argument defaults. These are fine when the result is immutable.
diff --git a/src/annsel/core/utils.py b/src/annsel/core/utils.py
@@ -11,19 +11,36 @@
 
 from annsel.core.typing import Predicates
 
+T = TypeVar("T")
+
 
 def _get_final_indices(
     obj_names: pd.Index,
     *idx: Iterable,
 ) -> pd.Index:
+    """Given an iterable of indices, return the intersection of the indices w.r.t. the var_names or the obs_names.
+
+    If all indices are empty, return an empty index.
+
+    Parameters
+    ----------
+    obj_names
+        The names of the objects to filter.
+    idx
+        The indices to filter.
+
+    Returns
+    -------
+    The intersection of the indices.
+    """
     # Filter out empty indices
     non_empty_idx = [i for i in idx if len(i) > 0]
 
-    # If all indices were empty, return the original object names
+    # If all indices were empty, return an empty index
     if not non_empty_idx:
-        return obj_names
+        return pd.Index([])
 
-    # Otherwise, proceed with intersection of non-empty indices
+    # Otherwise, compute the intersection of non-empty indices
     return obj_names.intersection(pd.Index(list(reduce(and_, map(set, non_empty_idx)))))
 
 
@@ -37,9 +54,6 @@ def _construct_adata_from_indices(
     return _adata
 
 
-T = TypeVar("T")
-
-
 def second(i: Iterable[T]) -> T:
     """Get the second element from an iterable."""
     snd = nth(i, 1)
@@ -53,7 +67,8 @@ def _extract_names_from_expr(*predicates: Predicates) -> tuple[str, ...]:
     for p in predicates:
         match p:
             case nw.Expr():
-                names.extend(collapse(inspect.getclosurevars(p._to_compliant_expr).nonlocals["names"]))
+                to_complian_expr_closure = inspect.getclosurevars(p._to_compliant_expr).nonlocals["to_compliant_expr"]
+                names.extend(collapse(inspect.getclosurevars(to_complian_expr_closure).nonlocals["flat_names"]))
             case str():
                 names.append(p)
             case _:
diff --git a/src/annsel/tl/_filter.py b/src/annsel/tl/_filter.py
@@ -1,3 +1,5 @@
+from collections.abc import Mapping
+
 import anndata as ad
 import narwhals as nw
 import pandas as pd
@@ -32,13 +34,23 @@ def _filter_var_names(adata: ad.AnnData, *predicates: Predicates) -> pd.Index:
     return _filter_df(adata.var_names.to_frame(name="var_names"), *predicates).index
 
 
+def _filter_obsm(adata: ad.AnnData, key: str, *predicates: Predicates) -> pd.Index:
+    return _filter_df(pd.DataFrame(adata.obsm[key], index=adata.obs_names), *predicates).index
+
+
+def _filter_varm(adata: ad.AnnData, key: str, *predicates: Predicates) -> pd.Index:
+    return _filter_df(pd.DataFrame(adata.varm[key], index=adata.var_names), *predicates).index
+
+
 def _filter(
     adata: ad.AnnData,
     obs: Predicates | None = None,
     var: Predicates | None = None,
     x: Predicates | None = None,
     obs_names: Predicates | None = None,
     var_names: Predicates | None = None,
+    obsm: Mapping[str, Predicates] | None = None,
+    varm: Mapping[str, Predicates] | None = None,
     layer: str | None = None,
 ) -> ad.AnnData:
     obs_names_idx = []
@@ -59,6 +71,14 @@ def _filter(
     if x:
         obs_names_idx.append(_filter_x(adata, x, layer=layer))
 
+    if obsm:
+        for key, predicates in obsm.items():
+            obs_names_idx.append(_filter_obsm(adata, key, predicates))
+
+    if varm:
+        for key, predicates in varm.items():
+            var_names_idx.append(_filter_varm(adata, key, predicates))
+
     final_obs_idx = adata.obs_names if not obs_names_idx else _get_final_indices(adata.obs_names, *obs_names_idx)
     final_var_idx = adata.var_names if not var_names_idx else _get_final_indices(adata.var_names, *var_names_idx)
     return _construct_adata_from_indices(adata, final_obs_idx, final_var_idx)
diff --git a/src/annsel/tl/anndata.py b/src/annsel/tl/anndata.py
@@ -1,4 +1,4 @@
-from collections.abc import Callable, Generator
+from collections.abc import Callable, Generator, Mapping
 from typing import Any, TypeVar
 
 import anndata as ad
@@ -27,6 +27,8 @@ def filter(
         x: Predicates | None = None,
         obs_names: Predicates | None = None,
         var_names: Predicates | None = None,
+        obsm: Mapping[str, Predicates] | None = None,
+        varm: Mapping[str, Predicates] | None = None,
         layer: str | None = None,
         copy: bool = False,
     ) -> ad.AnnData:
@@ -44,6 +46,10 @@ def filter(
             Predicates to filter the observation names by.
         var_names
             Predicates to filter the variable names by.
+        obsm
+            A mapping of obsm keys and predicates to filter the obsm matrices by.
+        varm
+            A mapping of varm keys and predicates to filter the varm matrices by.
         layer
             The layer to filter.
         copy
@@ -71,7 +77,7 @@ def filter(
              obsm: 'X_bothumap', 'X_pca', 'X_projected', 'X_projectedmean', 'X_tsneni', 'X_umapni'
 
         """
-        _adata = _filter(self._obj, obs, var, x, obs_names, var_names, layer)
+        _adata = _filter(self._obj, obs, var, x, obs_names, var_names, obsm, varm, layer)
         return _adata if not copy else _adata.copy()
 
     def select(
diff --git a/tests/test_utils.py b/tests/test_utils.py
diff --git a/tests/tl/test_anndata.py b/tests/tl/test_anndata.py
diff --git a/uv.lock b/uv.lock
