Merge pull request #16 from srivarra/ops/groupby

srivarra · Dec 21, 2024 · af260dc · af260dc
2 parents e5a1422 + 4c702de
commit af260dc
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diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -1,6 +1,6 @@
 name: Bug report
 description: Report something that is broken or incorrect
-labels: bug
+labels: [bug]
 body:
   - type: markdown
     attributes:
@@ -28,13 +28,13 @@ body:
         Please paste below the output of
 
         ```python
-        import session_info
-        session_info.show(html=False, dependencies=True)
+        import session_info2
+        session_info2.show(html=False, dependencies=True)
         ```
       placeholder: |
         -----
         anndata             0.8.0rc2.dev27+ge524389
-        session_info        1.0.0
+        session_info2        0.0.1
         -----
         asttokens           NA
         awkward             1.8.0

diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
@@ -30,8 +30,9 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v3
+        uses: astral-sh/setup-uv@v5.0.1
         with:
+          python-version: ${{ matrix.python-version }}
           enable-cache: true
           cache-dependency-glob: "uv.lock"
           github-token: ${{ secrets.GITHUB_TOKEN }}

diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
@@ -28,8 +28,9 @@ jobs:
           fetch-depth: 0
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v3
+        uses: astral-sh/setup-uv@v5.0.1
         with:
+          python-version: ${{ matrix.python-version }}
           enable-cache: true
           cache-dependency-glob: "uv.lock"
           github-token: ${{ secrets.GITHUB_TOKEN }}

diff --git a/docs/api/core.md b/docs/api/core.md
@@ -1,22 +1,34 @@
 # Core
 
 ```{eval-rst}
-.. module:: annsel.core
+.. module:: annsel.core.expr
 ```
 
 ```{eval-rst}
 .. currentmodule:: annsel
 ```
 
-## Selectors
+## Selectors and Expressions
 
 ```{eval-rst}
 .. autosummary::
-    :toctree: ../generated
+   :toctree: ../generated/
 
-    obs_col
-    obs_names
-    var_col
-    var_names
-    x
+   obs_names
+   var_names
+   col
+
+```
+
+## Types
+
+```{eval-rst}
+.. currentmodule:: annsel.core.typing
+.. autosummary::
+   :toctree: ../generated/
+
+   Predicates
+   IntoExpr
+   SinglePredicate
+   PredicatesCollection
 ```
diff --git a/docs/api/tools.md b/docs/api/tools.md
@@ -8,9 +8,9 @@
 .. currentmodule:: annsel
 ```
 
-## Accessor: `an`
+## AnnData Accessor: `an`
 
-In order to use the `an` accessor, you need to import `annsel`.
+In order to use the `AnnData` `an` accessor, you need to import `annsel`.
 
 Something like the following:
 
@@ -24,12 +24,15 @@ or
 import annsel as an
 ```
 
+This will register the `an` accessor to the `AnnData` object.
+
 ```{eval-rst}
 .. autosummary::
     :toctree: ../generated
     :template: autosummary/accessor_method.rst
 
     AnnselAccessor.filter
     AnnselAccessor.select
+    AnnselAccessor.group_by
     AnnselAccessor.pipe
 ```
diff --git a/docs/badges.md b/docs/badges.md
@@ -1,11 +1,11 @@
 <div align="center">
 
-|             |                                                                                                                                                           |
-| :---------: | :-------------------------------------------------------------------------------------------------------------------------------------------------------: |
-| **Status**  | [![Build][badge-build]][link-build] [![Tests][badge-test]][link-test] [![Documentation][badge-docs]][link-docs] [![codecov][badge-codecov]][link-codecov] |
-|  **Meta**   |     [![Hatch project][badge-hatch]][link-hatch] [![Ruff][badge-ruff]][link-ruff] [![uv][badge-uv]][link-uv] [![License][badge-license]][link-license]     |
-| **Package** |                                       [![PyPI][badge-pypi]][link-pypi] [![PyPI][badge-python-versions]][link-pypi]                                        |
-|             |                                                                                                                                                           |
+|             |                                                                                                                                                                                                              |
+| :---------: | :----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
+| **Status**  | [![Build][badge-build]][link-build] [![Tests][badge-test]][link-test] [![Documentation][badge-docs]][link-docs] [![codecov][badge-codecov]][link-codecov] [![pre-commit][badge-pre-commit]][link-pre-commit] |
+|  **Meta**   |         [![Hatch project][badge-hatch]][link-hatch] [![Ruff][badge-ruff]][link-ruff] [![uv][badge-uv]][link-uv] [![License][badge-license]][link-license] [![gitmoji][badge-gitmoji]][link-gitmoji]          |
+| **Package** |                                                                 [![PyPI][badge-pypi]][link-pypi] [![PyPI][badge-python-versions]][link-pypi]                                                                 |
+|             |                                                                                                                                                                                                              |
 
 </div>
 
@@ -19,6 +19,8 @@
 [badge-hatch]: https://img.shields.io/badge/%F0%9F%A5%9A-Hatch-4051b5.svg
 [badge-pypi]: https://img.shields.io/pypi/v/annsel.svg?logo=pypi&label=PyPI&logoColor=gold
 [badge-python-versions]: https://img.shields.io/pypi/pyversions/annsel.svg?logo=python&label=Python&logoColor=gold
+[badge-pre-commit]: https://results.pre-commit.ci/badge/github/srivarra/annsel/main.svg
+[badge-gitmoji]: https://img.shields.io/badge/gitmoji-😜😍-FFDD67.svg
 [scverse-discourse]: https://discourse.scverse.org/
 [issue-tracker]: https://github.com/srivarra/annsel/issues
 [changelog]: https://annsel.readthedocs.io/latest/changelog.html
@@ -34,3 +36,5 @@
 [link-hatch]: https://github.com/pypa/hatch
 [link-narwhals]: https://github.com/narwhals-dev/narwhals
 [link-disucssions]: https://github.com/srivarra/annsel/discussions
+[link-pre-commit]: https://results.pre-commit.ci/latest/github/srivarra/annsel/main
+[link-gitmoji]: https://gitmoji.dev/
diff --git a/docs/conf.py b/docs/conf.py
@@ -22,7 +22,7 @@
 info = metadata("annsel")
 project_name = info["Name"]
 author = info["Author"]
-copyright = f"{datetime.now():%Y}, {author}."
+copyright = f"{datetime.now():%Y}, {author}"
 version = info["Version"]
 urls = dict(pu.split(", ") for pu in info.get_all("Project-URL"))
 repository_url = urls["Source"]
@@ -74,7 +74,7 @@
 napoleon_google_docstring = False
 napoleon_numpy_docstring = True
 napoleon_include_init_with_doc = False
-napoleon_use_rtype = True  # having a separate entry generally helps readability
+napoleon_use_rtype = True  # having a separate entry generally helps readaibteility
 napoleon_use_param = True
 myst_heading_anchors = 6  # create anchors for h1-h6
 myst_enable_extensions = [

diff --git a/docs/landing.md b/docs/landing.md
@@ -43,25 +43,25 @@ There are several alternative options to install `annsel`:
 
 1. Install the most recent release:
 
-:::::{tabs}
-::::{group-tab} uv
-If you are using `uv`
+    :::::{tabs}
+    ::::{group-tab} uv
+    If you are using `uv`
 
-```zsh
-uv add annsel
-```
+    ```zsh
+    uv add annsel
+    ```
 
-::::
+    ::::
 
-::::{group-tab} Pip
-If you are using `pip`:
+    ::::{group-tab} Pip
+    If you are using `pip`:
 
-```zsh
-pip install annsel
-```
+    ```zsh
+    pip install annsel
+    ```
 
-::::
-:::::
+    ::::
+    :::::
 
 2. Install the latest development version: