pertpy 0.10.0__tar.gz → 0.11.0__tar.gz

pertpy-0.11.0/.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,69 @@
+name: Bug report
+description: pertpy doesn’t do what it should? Please help us fix it!
+#title: ...
+labels:
+  - Bug
+  - Triage
+#assignees: []
+body:
+  - type: checkboxes
+    id: terms
+    attributes:
+      label: Please make sure these conditions are met
+      # description: ...
+      options:
+        - label: I have checked that this issue has not already been reported.
+          required: true
+        - label: I have confirmed this bug exists on the latest version of pertpy.
+          required: true
+        - label: (optional) I have confirmed this bug exists on the main branch.
+          required: false
+  - type: markdown
+    attributes:
+      value: |
+        **Note**: Please read [this guide][] detailing how to provide the necessary information for us to reproduce your bug.
+
+        [this guide]: https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports
+  - type: textarea
+    id: Report
+    attributes:
+      label: Report
+      description: |
+        Describe the bug you encountered, and what you were trying to do. Please use [github markdown][] features for readability.
+
+        [github markdown]: https://docs.github.com/en/get-started/writing-on-github/getting-started-with-writing-and-formatting-on-github/basic-writing-and-formatting-syntax
+      value: |
+        Code:
+
+        ```python
+
+        ```
+
+        Traceback:
+
+        ```pytb
+
+        ```
+    validations:
+      required: true
+  - type: textarea
+    id: versions
+    attributes:
+      label: Versions
+      description: |
+        Which version of pertpy and other related software you used.
+
+        Please install `session-info2`, run the following command in a notebook,
+        click the “Copy as Markdown” button,
+        then paste the results into the text box below.
+
+        ```python
+        In[1]: import pertpy, session_info2; session_info2.session_info(dependencies=True)
+        ```
+
+        Alternatively, run this in a console:
+
+        ```python
+        >>> import session_info2; print(session_info2.session_info(dependencies=True)._repr_mimebundle_()["text/markdown"])
+        ```
+      render: python

{pertpy-0.10.0 → pertpy-0.11.0}/.github/pull_request_template.md

@@ -4,9 +4,9 @@
 
 <!-- Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs). -->
 
-- [ ] Referenced issue is linked
-- [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] Documentation in `docs` is updated
+-   [ ] Referenced issue is linked
+-   [ ] If you've fixed a bug or added code that should be tested, add tests!
+-   [ ] Documentation in `docs` is updated
 
 **Description of changes**
 

{pertpy-0.10.0 → pertpy-0.11.0}/.github/release-drafter.yml

@@ -1,5 +1,5 @@
-name-template: "0.10.0 🌈"
-tag-template: 0.10.0
+name-template: "0.11.0 🌈"
+tag-template: 0.11.0
 exclude-labels:
     - "skip-changelog"
 

pertpy-0.11.0/.github/workflows/build.yml

@@ -0,0 +1,36 @@
+name: Check Build
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
+    shell: bash -euo pipefail {0}
+
+jobs:
+  package:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          filter: blob:none
+          fetch-depth: 0
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          cache-dependency-glob: pyproject.toml
+
+      - name: Build package
+        run: uv build
+
+      - name: Check package
+        run: uvx twine check --strict dist/*.whl

{pertpy-0.10.0 → pertpy-0.11.0}/.github/workflows/release.yml

@@ -13,10 +13,10 @@ jobs:
             - name: Checkout code
               uses: actions/checkout@v4
 
-            - name: Set up Python 3.12
+            - name: Set up Python
               uses: actions/setup-python@v5
               with:
-                  python-version: "3.12"
+                  python-version: "3.x"
 
             - name: Install hatch
               run: pip install hatch

{pertpy-0.10.0 → pertpy-0.11.0}/.github/workflows/test.yml

@@ -15,22 +15,23 @@ jobs:
         runs-on: ${{ matrix.os }}
         defaults:
             run:
-                shell: bash -e {0} # -e to fail on error
+              # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
+              shell: bash -euo pipefail {0}
 
         strategy:
             fail-fast: false
             matrix:
                 include:
-                    - os: ubuntu-22.04 # ubuntu-latest is currently broken for joblib
-                      python: "3.12"
+                    - os: ubuntu-latest
+                      python: "3.13"
                       run_mode: "slow"
-                    - os: ubuntu-22.04
-                      python: "3.12"
+                    - os: ubuntu-latest
+                      python: "3.13"
                       run_mode: "fast"
-                    # - os: ubuntu-latest
-                    #   python: "3.12"
-                    #   run_mode: slow
-                    #   pip-flags: "--pre"
+                    - os: ubuntu-latest
+                      python: "3.13"
+                      run_mode: slow
+                      pip-flags: "--pre"
 
         env:
             OS: ${{ matrix.os }}
@@ -38,26 +39,50 @@ jobs:
 
         steps:
             - uses: actions/checkout@v4
+              with:
+                filter: blob:none
+                fetch-depth: 0
+
+            - name: Cache .pertpy_cache
+              uses: actions/cache@v4
+              with:
+                path: cache
+                key: ${{ runner.os }}-pertpy-cache-${{ hashFiles('pertpy/metadata/**') }}
+                restore-keys: |
+                  ${{ runner.os }}-pertpy-cache
+
             - name: Set up Python ${{ matrix.python }}
               uses: actions/setup-python@v5
               with:
                   python-version: ${{ matrix.python }}
-
-            - uses: actions/checkout@v4
             - name: Install R
               uses: r-lib/actions/setup-r@v2
               with:
-                  r-version: "4"
+                  r-version: "4.4.3"
 
-            - name: Install edgeR
-              run: Rscript --vanilla -e "install.packages(c('BiocManager', 'statmod'), repos='https://cran.r-project.org'); library('BiocManager'); BiocManager::install('edgeR')"
+            - name: Cache R packages
+              id: r-cache
+              uses: actions/cache@v3
+              with:
+                path: ${{ env.R_LIBS_USER }}
+                key: ${{ runner.os }}-r-${{ hashFiles('**/pertpy/tools/_milo.py') }}
+                restore-keys: ${{ runner.os }}-r-
 
-            - name: Install test dependencies
-              run: python -m pip install --upgrade uv wheel
+            - name: Install R dependencies
+              if: steps.r-cache.outputs.cache-hit != 'true'
+              run: |
+                mkdir -p ${{ env.R_LIBS_USER }}
+                Rscript --vanilla -e "install.packages(c('BiocManager', 'statmod'), repos='https://cran.r-project.org'); BiocManager::install('edgeR', lib='${{ env.R_LIBS_USER }}')"
+
+            - name: Install uv
+              uses: astral-sh/setup-uv@v6
+              with:
+                enable-cache: true
+                cache-dependency-glob: pyproject.toml
             - name: Install dependencies
               run: |
                   uv pip install --system rpy2
-                  uv pip install --system ${{ matrix.pip-flags }} ".[dev,test,coda,de]"
+                  uv pip install --system ${{ matrix.pip-flags }} ".[dev,test,tcoda,de]"
 
             - name: Test
               env:

{pertpy-0.10.0 → pertpy-0.11.0}/.gitignore

@@ -72,8 +72,8 @@ instance/
 
 # Sphinx documentation
 docs/_build/
-docs/usage/*
-!docs/usage/usage.md
+docs/api/*
+!docs/api/api.md
 
 # PyBuilder
 target/

{pertpy-0.10.0 → pertpy-0.11.0}/.pre-commit-config.yaml

@@ -6,18 +6,18 @@ default_stages:
     - pre-push
 minimum_pre_commit_version: 2.16.0
 repos:
-    - repo: https://github.com/pre-commit/mirrors-prettier
-      rev: v4.0.0-alpha.8
+    - repo: https://github.com/biomejs/pre-commit
+      rev: v1.9.4
       hooks:
-          - id: prettier
+          - id: biome-format
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.8.6
+      rev: v0.11.5
       hooks:
           - id: ruff
             args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
           - id: ruff-format
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.6.0
+      rev: v5.0.0
       hooks:
           - id: detect-private-key
           - id: check-ast
@@ -26,6 +26,12 @@ repos:
             args: [--fix=lf]
           - id: trailing-whitespace
           - id: check-case-conflict
+          - id: check-added-large-files
+          - id: check-toml
+          - id: check-yaml
+          - id: check-merge-conflict
+          - id: no-commit-to-branch
+            args: ["--branch=main"]
     - repo: https://github.com/pre-commit/mirrors-mypy
       rev: v1.14.1
       hooks:

{pertpy-0.10.0 → pertpy-0.11.0}/.readthedocs.yml

@@ -2,13 +2,13 @@ version: 2
 build:
     os: ubuntu-24.04
     tools:
-        python: "3.12"
+        python: "3.12" # 3.13 breaks because scikit-misc cannot be installed
     commands:
         - asdf plugin add uv
         - asdf install uv latest
         - asdf global uv latest
         - uv venv
-        - uv pip install .[doc,coda,de]
+        - uv pip install .[doc,tcoda,de]
         - .venv/bin/python -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html
 sphinx:
     configuration: docs/conf.py

{pertpy-0.10.0 → pertpy-0.11.0}/LICENSE

@@ -1,6 +1,7 @@
 MIT License
 
 Copyright (c) 2021, Lukas Heumos
+Copyright (c) 2025, scverse®
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

{pertpy-0.10.0 → pertpy-0.11.0}/PKG-INFO

@@ -1,15 +1,16 @@
 Metadata-Version: 2.4
 Name: pertpy
-Version: 0.10.0
+Version: 0.11.0
 Summary: Perturbation Analysis in the scverse ecosystem.
 Project-URL: Documentation, https://pertpy.readthedocs.io
 Project-URL: Source, https://github.com/scverse/pertpy
 Project-URL: Home-page, https://github.com/scverse/pertpy
-Author: Lukas Heumos, Yuge Ji, Lilly May, Alejandro Tejada, Johannes Köster, Emma Dann, Xinyue Zhang, Xichen Wu, Tessa Green, Stefan Peidli, Antonia Schumacher, Gregor Sturm
+Author: Lukas Heumos, Lilly May, Stefan Peidli, Johannes Ostner, Gregor Sturm, Emma Dann, Yuge Ji, Xinyue Zhang, Xichen Wu, Tessa Green, Antonia Schumacher
 Maintainer-email: Lukas Heumos <lukas.heumos@posteo.net>
 License: MIT License
         
         Copyright (c) 2021, Lukas Heumos
+        Copyright (c) 2025, scverse®
         
         Permission is hereby granted, free of charge, to any person obtaining a copy
         of this software and associated documentation files (the "Software"), to deal
@@ -29,7 +30,7 @@ License: MIT License
         OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
         SOFTWARE.
 License-File: LICENSE
-Classifier: Development Status :: 4 - Beta
+Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: Console
 Classifier: Framework :: Jupyter
 Classifier: Intended Audience :: Developers
@@ -39,33 +40,30 @@ Classifier: Natural Language :: English
 Classifier: Operating System :: MacOS :: MacOS X
 Classifier: Operating System :: POSIX :: Linux
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Scientific/Engineering :: Visualization
-Requires-Python: <3.13,>=3.10
+Requires-Python: <3.14,>=3.11
 Requires-Dist: adjusttext
+Requires-Dist: arviz
 Requires-Dist: blitzgsea
 Requires-Dist: decoupler
+Requires-Dist: fast-array-utils
 Requires-Dist: lamin-utils
-Requires-Dist: muon
+Requires-Dist: mudata
 Requires-Dist: openpyxl
 Requires-Dist: ott-jax
 Requires-Dist: pubchempy
 Requires-Dist: pyarrow
 Requires-Dist: requests
 Requires-Dist: rich
-Requires-Dist: scanpy[leiden]
+Requires-Dist: scanpy
 Requires-Dist: scikit-learn>=1.4
 Requires-Dist: scikit-misc
 Requires-Dist: scvi-tools
 Requires-Dist: sparsecca
-Provides-Extra: coda
-Requires-Dist: arviz; extra == 'coda'
-Requires-Dist: ete3; extra == 'coda'
-Requires-Dist: pyqt5; extra == 'coda'
-Requires-Dist: toytree; extra == 'coda'
 Provides-Extra: de
 Requires-Dist: formulaic; extra == 'de'
 Requires-Dist: formulaic-contrasts>=0.2.0; extra == 'de'
@@ -73,28 +71,33 @@ Requires-Dist: pydeseq2>=v0.5.0pre1; extra == 'de'
 Provides-Extra: dev
 Requires-Dist: pre-commit; extra == 'dev'
 Provides-Extra: doc
-Requires-Dist: docutils!=0.18.*,!=0.19.*,>=0.8; extra == 'doc'
-Requires-Dist: furo; extra == 'doc'
+Requires-Dist: docutils>=0.8; extra == 'doc'
 Requires-Dist: ipykernel; extra == 'doc'
 Requires-Dist: ipython; extra == 'doc'
 Requires-Dist: myst-nb; extra == 'doc'
-Requires-Dist: myst-parser; extra == 'doc'
 Requires-Dist: nbsphinx; extra == 'doc'
 Requires-Dist: nbsphinx-link; extra == 'doc'
-Requires-Dist: pyenchant; extra == 'doc'
 Requires-Dist: pygments; extra == 'doc'
+Requires-Dist: scanpydoc; extra == 'doc'
 Requires-Dist: sphinx-autodoc-typehints; extra == 'doc'
 Requires-Dist: sphinx-automodapi; extra == 'doc'
+Requires-Dist: sphinx-book-theme; extra == 'doc'
 Requires-Dist: sphinx-copybutton; extra == 'doc'
 Requires-Dist: sphinx-design; extra == 'doc'
 Requires-Dist: sphinx-gallery; extra == 'doc'
+Requires-Dist: sphinx-issues; extra == 'doc'
 Requires-Dist: sphinx-last-updated-by-git; extra == 'doc'
 Requires-Dist: sphinx-remove-toctrees; extra == 'doc'
-Requires-Dist: sphinx>=4; extra == 'doc'
+Requires-Dist: sphinx>=6; extra == 'doc'
 Requires-Dist: sphinxcontrib-bibtex>=1.0.0; extra == 'doc'
 Requires-Dist: sphinxext-opengraph; extra == 'doc'
+Provides-Extra: tcoda
+Requires-Dist: ete4; extra == 'tcoda'
+Requires-Dist: pyqt6; extra == 'tcoda'
+Requires-Dist: toytree; extra == 'tcoda'
 Provides-Extra: test
 Requires-Dist: coverage; extra == 'test'
+Requires-Dist: leidenalg; extra == 'test'
 Requires-Dist: pytest; extra == 'test'
 Description-Content-Type: text/markdown
 
@@ -127,10 +130,10 @@ You can install _pertpy_ in less than a minute via [pip] from [PyPI]:
 pip install pertpy
 ```
 
-if you want to use scCODA or tascCODA, please install pertpy as follows:
+if you want to use tascCODA, please install pertpy as follows:
 
 ```console
-pip install 'pertpy[coda]'
+pip install 'pertpy[tcoda]'
 ```
 
 If you want to use the differential gene expression interface, please install pertpy by running:
@@ -146,4 +149,17 @@ bioRxiv 2024.08.04.606516; doi: https://doi.org/10.1101/2024.08.04.606516](https
 
 [pip]: https://pip.pypa.io/
 [pypi]: https://pypi.org/
-[usage]: https://pertpy.readthedocs.io/en/latest/usage/usage.html
+[api]: https://pertpy.readthedocs.io/en/latest/api/api.html
+[//]: # "numfocus-fiscal-sponsor-attribution"
+
+pertpy is part of the scverse® project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).
+If you like scverse® and want to support our mission, please consider making a tax-deductible [donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.
+
+<div align="center">
+<a href="https://numfocus.org/project/scverse">
+  <img
+    src="https://raw.githubusercontent.com/numfocus/templates/master/images/numfocus-logo.png"
+    width="200"
+  >
+</a>
+</div>

{pertpy-0.10.0 → pertpy-0.11.0}/README.md

@@ -27,10 +27,10 @@ You can install _pertpy_ in less than a minute via [pip] from [PyPI]:
 pip install pertpy
 ```
 
-if you want to use scCODA or tascCODA, please install pertpy as follows:
+if you want to use tascCODA, please install pertpy as follows:
 
 ```console
-pip install 'pertpy[coda]'
+pip install 'pertpy[tcoda]'
 ```
 
 If you want to use the differential gene expression interface, please install pertpy by running:
@@ -46,4 +46,17 @@ bioRxiv 2024.08.04.606516; doi: https://doi.org/10.1101/2024.08.04.606516](https
 
 [pip]: https://pip.pypa.io/
 [pypi]: https://pypi.org/
-[usage]: https://pertpy.readthedocs.io/en/latest/usage/usage.html
+[api]: https://pertpy.readthedocs.io/en/latest/api/api.html
+[//]: # "numfocus-fiscal-sponsor-attribution"
+
+pertpy is part of the scverse® project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).
+If you like scverse® and want to support our mission, please consider making a tax-deductible [donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.
+
+<div align="center">
+<a href="https://numfocus.org/project/scverse">
+  <img
+    src="https://raw.githubusercontent.com/numfocus/templates/master/images/numfocus-logo.png"
+    width="200"
+  >
+</a>
+</div>

pertpy-0.11.0/biome.jsonc

@@ -0,0 +1,18 @@
+{
+    "$schema": "https://biomejs.dev/schemas/1.9.4/schema.json",
+    "formatter": { "useEditorconfig": true },
+    "overrides": [
+        {
+            "include": ["./.vscode/*.json", "**/*.jsonc", "**/asv.conf.json"],
+            "json": {
+                "formatter": {
+                    "trailingCommas": "all",
+                },
+                "parser": {
+                    "allowComments": true,
+                    "allowTrailingCommas": true,
+                },
+            },
+        },
+    ],
+}

{pertpy-0.10.0 → pertpy-0.11.0}/docs/_ext/edit_on_github.py

@@ -8,7 +8,7 @@ from sphinx.application import Sphinx
 __licence__ = "BSD (3 clause)"
 
 
-def get_github_repo(app: Sphinx, path: str) -> str:
+def get_github_repo(app: Sphinx, path: str) -> str:  # noqa: D103
     if path.endswith(".ipynb"):
         return str(app.config.github_nb_repo)
     if "auto_examples" in path:
@@ -43,7 +43,7 @@ def _html_page_context(
     context["conf_py_path"] = "/docs/source/"
 
 
-def setup(app: Sphinx) -> None:
+def setup(app: Sphinx) -> None:  # noqa: D103
     app.add_config_value("github_nb_repo", "", True)
     app.add_config_value("github_repo", "", True)
     app.connect("html-page-context", _html_page_context)

{pertpy-0.10.0 → pertpy-0.11.0}/docs/_ext/typed_returns.py

@@ -10,7 +10,7 @@ def _process_return(lines: Iterable[str]) -> Iterator[str]:
         m = re.fullmatch(r"(?P<param>\w+)\s+:\s+(?P<type>[\w.]+)", line)
         if m:
             # Once this is in scanpydoc, we can use the fancy hover stuff
-            yield f'**{m["param"]}** : :class:`~{m["type"]}`'
+            yield f"**{m['param']}** : :class:`~{m['type']}`"
         else:
             yield line
 
@@ -23,5 +23,5 @@ def _parse_returns_section(self: NumpyDocstring, section: str) -> list[str]:
     return lines
 
 
-def setup(app: Sphinx) -> None:
+def setup(app: Sphinx) -> None:  # noqa: D103
     NumpyDocstring._parse_returns_section = _parse_returns_section

pertpy-0.11.0/docs/_static/pertpy_logo.svg

@@ -0,0 +1,5 @@
+<svg width="308" height="105" viewBox="0 0 308 105" fill="none" xmlns="http://www.w3.org/2000/svg">
+<rect width="308" height="105" fill="#1E1E1E"/>
+<path d="M26.432 17.656C41.664 17.4 48.576 31.736 48.704 47.992C48.704 62.328 41.536 75.768 26.176 76.28C19.904 76.28 14.528 74.36 9.28 71.16V104.312L0.0640001 100.984L0.192 27.384C0.0640001 27.384 7.36 17.784 26.304 17.528L26.432 17.656ZM24.128 69.624C36.416 68.856 37.952 56.824 37.952 47.352C37.952 38.136 36.416 24.312 24.768 23.8C16.832 23.288 10.432 27 9.152 28.28V64.76C12.224 66.68 18.368 70.008 24.128 69.624ZM105.92 69.88C102.976 71.8 100.032 73.464 96.32 74.616C88.256 76.92 77.76 77.048 71.104 71.416C64.96 66.168 61.248 57.336 61.248 47.864C61.376 33.144 67.392 17.912 83.776 17.912C99.392 17.912 105.152 28.664 105.408 45.944H71.104C70.08 60.536 77.504 70.392 88 70.008C94.4 69.88 99.008 67.704 103.744 65.4L105.92 69.88ZM95.936 40.44L96.064 40.568C96.064 32.376 92.48 23.672 84.16 23.672C75.2 23.672 72 32.376 71.36 40.44H95.936ZM142.476 24.568H142.348C136.204 24.568 131.98 26.872 128.652 29.688V75H119.308V28.408C122.764 24.568 127.372 21.496 132.62 19.704C138.252 17.656 143.628 16.376 151.436 17.784C150.284 20.088 148.748 23.032 147.724 25.336C145.932 24.952 143.756 24.568 142.476 24.568ZM163.362 24.952H156.962V18.936H163.362V3.32L172.706 -0.00800323V18.936H183.202V24.952H172.706V61.432C172.706 68.856 176.674 70.648 183.202 70.904V75.768C170.786 76.92 163.362 71.288 163.362 61.688V24.952Z" fill="#30679A"/>
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pertpy-0.10.0/docs/_templates/class_no_inherited.rst → pertpy-0.11.0/docs/_templates/autosummary/class.rst

@@ -5,7 +5,6 @@
 .. add toctree option to make autodoc generate the pages
 
 .. autoclass:: {{ objname }}
-   :show-inheritance:
 
 {% block attributes %}
 {% if attributes %}
@@ -14,25 +13,21 @@ Attributes table
 
 .. autosummary::
 {% for item in attributes %}
-    {%- if item not in inherited_members%}
-        ~{{ fullname }}.{{ item }}
-    {%- endif -%}
+    ~{{ name }}.{{ item }}
 {%- endfor %}
 {% endif %}
 {% endblock %}
 
-
 {% block methods %}
 {% if methods %}
 Methods table
-~~~~~~~~~~~~~~
+~~~~~~~~~~~~~
 
 .. autosummary::
 {% for item in methods %}
-    {%- if item != '__init__' and item not in inherited_members%}
-    ~{{ fullname }}.{{ item }}
+    {%- if item != '__init__' %}
+    ~{{ name }}.{{ item }}
     {%- endif -%}
-
 {%- endfor %}
 {% endif %}
 {% endblock %}
@@ -43,8 +38,6 @@ Attributes
 ~~~~~~~~~~
 
 {% for item in attributes %}
-{{ item }}
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 .. autoattribute:: {{ [objname, item] | join(".") }}
 {%- endfor %}
@@ -58,9 +51,8 @@ Methods
 ~~~~~~~
 
 {% for item in methods %}
-{%- if item != '__init__' and item not in inherited_members%}
-{{ item }}
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+{%- if item != '__init__' %}
+
 .. automethod:: {{ [objname, item] | join(".") }}
 {%- endif -%}
 {%- endfor %}