gsMap 1.72.3__tar.gz → 1.73.1__tar.gz

gsmap-1.73.1/.coveragerc

@@ -0,0 +1,41 @@
+[run]
+source = src/gsMap
+omit =
+    # Exclude the files you mentioned
+    src/gsMap/utils/jackknife.py
+    src/gsMap/format_sumstats.py
+    # Other files you might want to exclude
+    */tests/*
+    */__init__.py
+    src/gsMap/templates/*
+    # Additional excludes
+    src/gsMap/__main__.py
+    src/gsMap/setup.py
+
+[report]
+exclude_lines =
+    # Have to re-enable the standard pragma
+    pragma: no cover
+
+    # Don't complain about missing debug-only code
+    def __repr__
+    if self\.debug
+
+    # Don't complain if tests don't hit defensive assertion code
+    raise NotImplementedError
+    raise ValueError
+    except ImportError
+    except Exception
+    except:
+
+    # Don't complain if non-runnable code isn't run
+    if 0:
+    if __name__ == .__main__.:
+    if False:
+
+    # Skip pass statements
+    pass
+
+[paths]
+source =
+    src/gsMap

{gsmap-1.72.3 → gsmap-1.73.1}/.github/workflows/docs.yml

@@ -1,10 +1,10 @@
-name: Build and Deploy Documentation
+name: docs
 
 on:
   push:
     paths:
-      - 'docs/**'
-      - 'visualization_web_docs/**'
+      - "docs/**"
+      - "visualization_web_docs/**"
 
 jobs:
   deploy_docs:
@@ -17,7 +17,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.12'
+          python-version: "3.12"
 
       # --- Build 'docs' documentation ---
       - name: Install 'docs' dependencies

{gsmap-1.72.3 → gsmap-1.73.1}/.github/workflows/publish-to-pypi.yml

@@ -37,6 +37,7 @@ jobs:
     needs:
       - build
     runs-on: ubuntu-latest
+
     environment:
       name: pypi
       url: https://pypi.org/p/gsMap
@@ -71,7 +72,7 @@ jobs:
           name: python-package-distributions
           path: dist/
       - name: Sign the dists with Sigstore
-        uses: sigstore/gh-action-sigstore-python@v1.2.3
+        uses: sigstore/gh-action-sigstore-python@v3.0.0
         with:
           inputs: >-
             ./dist/*.tar.gz

gsmap-1.73.1/.github/workflows/test_linux.yml

@@ -0,0 +1,100 @@
+name: test
+
+on:
+  push:
+    branches: [main, "[0-9]+.[0-9]+.x"]
+  pull_request:
+  schedule:
+    - cron: "0 0 * * *"
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    defaults:
+      run:
+        shell: bash -e {0} # -e to fail on error
+
+    strategy:
+      fail-fast: false
+      matrix:
+        python: ["3.10", "3.13"]
+
+    name: Python ${{ matrix.python }} integration
+
+    env:
+      PYTHON: ${{ matrix.python }}
+      TEST_DATA_URL: https://yanglab.westlake.edu.cn/data/gsMap/gsMap_test_data.tar.gz
+      TEST_DATA_DIR: ${{ github.workspace }}/test_data
+      WORK_DIR: ${{ github.workspace }}/gsmap_workdir
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: "Set up Python"
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python }}
+
+      - name: Install dependencies
+        run: |
+          uv pip install --system -e ".[tests]"
+
+      - name: Create workdir
+        run: |
+          mkdir -p $WORK_DIR
+          echo "Created workdir: $WORK_DIR"
+
+      - name: Cache test data
+        uses: actions/cache@v3
+        id: cache-test-data
+        with:
+          path: ${{ env.TEST_DATA_DIR }}
+          key: test-data-v1
+
+      - name: Download and extract test data
+        if: steps.cache-test-data.outputs.cache-hit != 'true'
+        run: |
+          echo "Downloading test data from $TEST_DATA_URL"
+          curl -L $TEST_DATA_URL -o gsMap_test_data.tar.gz
+          tar -xzf gsMap_test_data.tar.gz -C ${{ github.workspace }}
+          rm gsMap_test_data.tar.gz
+          echo "Test data extracted to ${{ github.workspace }}"
+          ls -la $TEST_DATA_DIR
+
+      - name: Run pytest
+        env:
+          MPLBACKEND: agg
+          DISPLAY: :0
+          COLUMNS: 120
+        run: |
+          python -m pytest --cov=src \
+              --junitxml=junit.xml -o junit_family=legacy \
+              --cov-report=term-missing \
+              --cov-report=xml \
+              --cov-config=.coveragerc \
+              -v -s --color=yes \
+              --run-real-data \
+              --work-dir=$WORK_DIR \
+              --test-data=$TEST_DATA_DIR
+
+      - uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          fail_ci_if_error: false
+
+      - name: Upload test results to Codecov
+        if: ${{ !cancelled() }}
+        uses: codecov/test-results-action@v1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}

{gsmap-1.72.3 → gsmap-1.73.1}/.markdownlint.yaml

@@ -12,8 +12,7 @@ MD033: false
 MD041: false
 
 # MD013/line-length
-MD013:
-  line_length: 99
+MD013: false
 
 # MD024/no-duplicate-heading
 MD024:

{gsmap-1.72.3 → gsmap-1.73.1}/.pre-commit-config.yaml

@@ -18,7 +18,7 @@ repos:
         types: [yaml]
 
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.21
+    rev: 0.7.22
     hooks:
       - id: mdformat
         additional_dependencies:
@@ -26,21 +26,19 @@ repos:
         exclude: |
           (?x)^(
             \.github/.*\.md
-            | docs/.*\.md
           )$
 
   - repo: https://github.com/igorshubovych/markdownlint-cli
-    rev: v0.43.0
+    rev: v0.44.0
     hooks:
       - id: markdownlint-fix
         exclude: |
           (?x)^(
             \.github/.*\.md
-            | docs/.*\.md
           )$
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.2
+    rev: v0.11.5
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

{gsmap-1.72.3 → gsmap-1.73.1}/LICENSE

@@ -1,6 +1,6 @@
-The MIT License (MIT)
+MIT License
 
-Copyright (c) 2023 liyang
+Copyright (c) 2025 JianYang-Lab
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -9,13 +9,13 @@ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 copies of the Software, and to permit persons to whom the Software is
 furnished to do so, subject to the following conditions:
 
-The above copyright notice and this permission notice shall be included in
-all copies or substantial portions of the Software.
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
 
 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-THE SOFTWARE.
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

gsmap-1.73.1/PKG-INFO

@@ -0,0 +1,177 @@
+Metadata-Version: 2.4
+Name: gsMap
+Version: 1.73.1
+Summary: Genetics-informed pathogenic spatial mapping
+Author-email: liyang <songliyang@westlake.edu.cn>, wenhao <chenwenhao@westlake.edu.cn>
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Operating System :: POSIX :: Linux
+License-File: LICENSE
+Requires-Dist: numpy < 2.0.0
+Requires-Dist: pandas
+Requires-Dist: scipy
+Requires-Dist: scikit-learn
+Requires-Dist: matplotlib
+Requires-Dist: seaborn
+Requires-Dist: tqdm
+Requires-Dist: pyyaml
+Requires-Dist: torch
+Requires-Dist: torch-geometric
+Requires-Dist: pyranges
+Requires-Dist: pyfiglet
+Requires-Dist: plotly
+Requires-Dist: kaleido
+Requires-Dist: jinja2
+Requires-Dist: scanpy >=1.8.0
+Requires-Dist: zarr>=2,<3
+Requires-Dist: bitarray >=2.9.2, <3.0.0
+Requires-Dist: pyarrow
+Requires-Dist: scikit-misc
+Requires-Dist: sphinx ; extra == "doc"
+Requires-Dist: sphinx-argparse ; extra == "doc"
+Requires-Dist: sphinx-autobuild ; extra == "doc"
+Requires-Dist: sphinx-autodoc-typehints ; extra == "doc"
+Requires-Dist: sphinx-basic-ng ; extra == "doc"
+Requires-Dist: sphinx-charts ; extra == "doc"
+Requires-Dist: sphinx-copybutton ; extra == "doc"
+Requires-Dist: sphinx_inline_tabs ; extra == "doc"
+Requires-Dist: sphinx-markdown-tables ; extra == "doc"
+Requires-Dist: sphinx-rtd-theme ; extra == "doc"
+Requires-Dist: sphinxcontrib-applehelp ; extra == "doc"
+Requires-Dist: sphinxcontrib-devhelp ; extra == "doc"
+Requires-Dist: sphinxcontrib-htmlhelp ; extra == "doc"
+Requires-Dist: sphinxcontrib-jquery ; extra == "doc"
+Requires-Dist: sphinxcontrib-jsmath ; extra == "doc"
+Requires-Dist: sphinxcontrib-qthelp ; extra == "doc"
+Requires-Dist: sphinxcontrib-serializinghtml ; extra == "doc"
+Requires-Dist: furo ; extra == "doc"
+Requires-Dist: myst-parser ; extra == "doc"
+Requires-Dist: nbsphinx ; extra == "doc"
+Requires-Dist: pytest>=7.0.0 ; extra == "tests"
+Requires-Dist: pytest-cov>=4.0.0 ; extra == "tests"
+Requires-Dist: coverage ; extra == "tests"
+Project-URL: Documentation, https://yanglab.westlake.edu.cn/gsmap/document/software
+Project-URL: Home, https://github.com/JianYang-Lab/gsMap
+Project-URL: Website, https://yanglab.westlake.edu.cn/gsmap/home
+Provides-Extra: doc
+Provides-Extra: tests
+
+# gsMap
+
+|               |                                                                                                      |                |                                                                                                    |
+| ------------- | ---------------------------------------------------------------------------------------------------- | -------------- | -------------------------------------------------------------------------------------------------- |
+| __Version__   | [![PyPI version][pypi-badge]][pypi-url] [![Python][python-badge]][python-url]                        | __Status__     | [![Project Status][status-badge]][status-url] [![Maintenance][maintenance-badge]][maintenance-url] |
+| __Activity__  | [![GitHub commits][commits-badge]][commits-url] [![Last Commit][last-commit-badge]][last-commit-url] | __Quality__    | [![codecov][codecov-badge]][codecov-url] [![Ruff][ruff-badge]][ruff-url]                           |
+| __CI/CD__     | [![Docs][docs-badge]][docs-url] [![test][test-badge]][test-url]                                      | __Community__  | [![GitHub stars][stars-badge]][stars-url] [![GitHub forks][forks-badge]][forks-url]                |
+| __Downloads__ | [![Downloads][downloads-badge]][downloads-url]                                                       | __License__    | [![License: MIT][license-badge]][license-url] [![DOI][doi-badge]][doi-url]                         |
+| __Platform__  | [![Linux][linux-badge]][linux-url]                                                                   | __Contribute__ | [![Issues][issues-badge]][issues-url] [![PRs Welcome][pr-badge]][pr-url]                           |
+
+## Introduction
+
+`gsMap` (genetically informed spatial mapping of cells for complex traits)
+integrates spatial transcriptomics (ST) data with genome-wide association study (GWAS)
+summary statistics to map cells to human complex traits, including diseases,
+in a spatially resolved manner.
+
+## Key Features
+
+- __Spatially-aware High-Resolution Trait Mapping__
+- __Spatial Region Identification__
+- __Putative Causal Genes Identification__
+
+![Model Architecture](schematic.png)
+
+## Installation
+
+Install using pip:
+
+```bash
+conda create -n gsMap python>=3.10
+conda activate gsMap
+pip install gsMap
+```
+
+Install using conda:
+
+```bash
+conda create -n gsMap python>=3.10
+conda activate gsMap
+conda install bioconda::gsmap
+```
+
+Install from source:
+
+```bash
+git clone https://github.com/JianYang-Lab/gsMap
+cd gsMap
+pip install -e .
+```
+
+Verify the installation by running the following command:
+
+```bash
+gsmap --help
+```
+
+## Usage
+
+Please check out the documentation and tutorials at [gsMap Documentation](https://yanglab.westlake.edu.cn/gsmap/document/software).
+
+## Online Visualization
+
+To visualize the traits-cell association spatial maps,
+please refer to [gsMap Visualization](https://yanglab.westlake.edu.cn/gsmap/visualize).
+
+## Citation
+
+Song, L., Chen, W., Hou, J., Guo, M. & Yang, J.
+[Spatially resolved mapping of cells associated with human complex traits.](https://doi.org/10.1038/s41586-025-08757-x)
+Nature (2025).
+
+Please cite the paper and give us a STAR if you find gsMap useful for your research.
+
+<!-- Badge links -->
+
+[codecov-badge]: https://codecov.io/gh/JianYang-Lab/gsMap/graph/badge.svg?token=NFZFXZIEUU
+[codecov-url]: https://codecov.io/gh/JianYang-Lab/gsMap
+[commits-badge]: https://img.shields.io/github/commit-activity/m/JianYang-Lab/gsMap
+[commits-url]: https://github.com/JianYang-Lab/gsMap/commits/main
+[docs-badge]: https://github.com/JianYang-Lab/gsMap/actions/workflows/docs.yml/badge.svg
+[docs-url]: https://github.com/JianYang-Lab/gsMap/actions/workflows/docs.yml
+[doi-badge]: https://img.shields.io/badge/DOI-10.1038%2Fs41586--025--08757--x-blue
+[doi-url]: https://doi.org/10.1038/s41586-025-08757-x
+[downloads-badge]: https://static.pepy.tech/badge/gsMap
+[downloads-url]: https://pepy.tech/project/gsMap
+[forks-badge]: https://img.shields.io/github/forks/JianYang-Lab/gsMap
+[forks-url]: https://github.com/JianYang-Lab/gsMap/network/members
+[issues-badge]: https://img.shields.io/github/issues/JianYang-Lab/gsMap
+[issues-url]: https://github.com/JianYang-Lab/gsMap/issues
+[last-commit-badge]: https://img.shields.io/github/last-commit/JianYang-Lab/gsMap
+[last-commit-url]: https://github.com/JianYang-Lab/gsMap/commits/main
+[license-badge]: https://img.shields.io/badge/License-MIT-yellow.svg
+[license-url]: https://opensource.org/licenses/MIT
+[linux-badge]: https://img.shields.io/badge/Linux-%E2%9C%93-success
+[linux-url]: https://github.com/JianYang-Lab/gsMap/actions/workflows/test_linux.yml
+[maintenance-badge]: https://img.shields.io/badge/Maintained%3F-yes-green.svg
+[maintenance-url]: https://github.com/JianYang-Lab/gsMap/graphs/commit-activity
+[pr-badge]: https://img.shields.io/badge/PRs-welcome-brightgreen.svg
+[pr-url]: https://github.com/JianYang-Lab/gsMap/pulls
+[pypi-badge]: https://img.shields.io/pypi/v/gsMap
+[pypi-url]: https://pypi.org/project/gsMap/
+[python-badge]: https://img.shields.io/pypi/pyversions/gsMap
+[python-url]: https://www.python.org
+[ruff-badge]: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json
+[ruff-url]: https://github.com/astral-sh/ruff
+[stars-badge]: https://img.shields.io/github/stars/JianYang-Lab/gsMap
+[stars-url]: https://github.com/JianYang-Lab/gsMap/stargazers
+[status-badge]: https://www.repostatus.org/badges/latest/active.svg
+[status-url]: https://www.repostatus.org/#active
+[test-badge]: https://github.com/JianYang-Lab/gsMap/actions/workflows/test_linux.yml/badge.svg
+[test-url]: https://github.com/JianYang-Lab/gsMap/actions/workflows/test_linux.yml
+

gsmap-1.73.1/README.md

@@ -0,0 +1,112 @@
+# gsMap
+
+|               |                                                                                                      |                |                                                                                                    |
+| ------------- | ---------------------------------------------------------------------------------------------------- | -------------- | -------------------------------------------------------------------------------------------------- |
+| __Version__   | [![PyPI version][pypi-badge]][pypi-url] [![Python][python-badge]][python-url]                        | __Status__     | [![Project Status][status-badge]][status-url] [![Maintenance][maintenance-badge]][maintenance-url] |
+| __Activity__  | [![GitHub commits][commits-badge]][commits-url] [![Last Commit][last-commit-badge]][last-commit-url] | __Quality__    | [![codecov][codecov-badge]][codecov-url] [![Ruff][ruff-badge]][ruff-url]                           |
+| __CI/CD__     | [![Docs][docs-badge]][docs-url] [![test][test-badge]][test-url]                                      | __Community__  | [![GitHub stars][stars-badge]][stars-url] [![GitHub forks][forks-badge]][forks-url]                |
+| __Downloads__ | [![Downloads][downloads-badge]][downloads-url]                                                       | __License__    | [![License: MIT][license-badge]][license-url] [![DOI][doi-badge]][doi-url]                         |
+| __Platform__  | [![Linux][linux-badge]][linux-url]                                                                   | __Contribute__ | [![Issues][issues-badge]][issues-url] [![PRs Welcome][pr-badge]][pr-url]                           |
+
+## Introduction
+
+`gsMap` (genetically informed spatial mapping of cells for complex traits)
+integrates spatial transcriptomics (ST) data with genome-wide association study (GWAS)
+summary statistics to map cells to human complex traits, including diseases,
+in a spatially resolved manner.
+
+## Key Features
+
+- __Spatially-aware High-Resolution Trait Mapping__
+- __Spatial Region Identification__
+- __Putative Causal Genes Identification__
+
+![Model Architecture](schematic.png)
+
+## Installation
+
+Install using pip:
+
+```bash
+conda create -n gsMap python>=3.10
+conda activate gsMap
+pip install gsMap
+```
+
+Install using conda:
+
+```bash
+conda create -n gsMap python>=3.10
+conda activate gsMap
+conda install bioconda::gsmap
+```
+
+Install from source:
+
+```bash
+git clone https://github.com/JianYang-Lab/gsMap
+cd gsMap
+pip install -e .
+```
+
+Verify the installation by running the following command:
+
+```bash
+gsmap --help
+```
+
+## Usage
+
+Please check out the documentation and tutorials at [gsMap Documentation](https://yanglab.westlake.edu.cn/gsmap/document/software).
+
+## Online Visualization
+
+To visualize the traits-cell association spatial maps,
+please refer to [gsMap Visualization](https://yanglab.westlake.edu.cn/gsmap/visualize).
+
+## Citation
+
+Song, L., Chen, W., Hou, J., Guo, M. & Yang, J.
+[Spatially resolved mapping of cells associated with human complex traits.](https://doi.org/10.1038/s41586-025-08757-x)
+Nature (2025).
+
+Please cite the paper and give us a STAR if you find gsMap useful for your research.
+
+<!-- Badge links -->
+
+[codecov-badge]: https://codecov.io/gh/JianYang-Lab/gsMap/graph/badge.svg?token=NFZFXZIEUU
+[codecov-url]: https://codecov.io/gh/JianYang-Lab/gsMap
+[commits-badge]: https://img.shields.io/github/commit-activity/m/JianYang-Lab/gsMap
+[commits-url]: https://github.com/JianYang-Lab/gsMap/commits/main
+[docs-badge]: https://github.com/JianYang-Lab/gsMap/actions/workflows/docs.yml/badge.svg
+[docs-url]: https://github.com/JianYang-Lab/gsMap/actions/workflows/docs.yml
+[doi-badge]: https://img.shields.io/badge/DOI-10.1038%2Fs41586--025--08757--x-blue
+[doi-url]: https://doi.org/10.1038/s41586-025-08757-x
+[downloads-badge]: https://static.pepy.tech/badge/gsMap
+[downloads-url]: https://pepy.tech/project/gsMap
+[forks-badge]: https://img.shields.io/github/forks/JianYang-Lab/gsMap
+[forks-url]: https://github.com/JianYang-Lab/gsMap/network/members
+[issues-badge]: https://img.shields.io/github/issues/JianYang-Lab/gsMap
+[issues-url]: https://github.com/JianYang-Lab/gsMap/issues
+[last-commit-badge]: https://img.shields.io/github/last-commit/JianYang-Lab/gsMap
+[last-commit-url]: https://github.com/JianYang-Lab/gsMap/commits/main
+[license-badge]: https://img.shields.io/badge/License-MIT-yellow.svg
+[license-url]: https://opensource.org/licenses/MIT
+[linux-badge]: https://img.shields.io/badge/Linux-%E2%9C%93-success
+[linux-url]: https://github.com/JianYang-Lab/gsMap/actions/workflows/test_linux.yml
+[maintenance-badge]: https://img.shields.io/badge/Maintained%3F-yes-green.svg
+[maintenance-url]: https://github.com/JianYang-Lab/gsMap/graphs/commit-activity
+[pr-badge]: https://img.shields.io/badge/PRs-welcome-brightgreen.svg
+[pr-url]: https://github.com/JianYang-Lab/gsMap/pulls
+[pypi-badge]: https://img.shields.io/pypi/v/gsMap
+[pypi-url]: https://pypi.org/project/gsMap/
+[python-badge]: https://img.shields.io/pypi/pyversions/gsMap
+[python-url]: https://www.python.org
+[ruff-badge]: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json
+[ruff-url]: https://github.com/astral-sh/ruff
+[stars-badge]: https://img.shields.io/github/stars/JianYang-Lab/gsMap
+[stars-url]: https://github.com/JianYang-Lab/gsMap/stargazers
+[status-badge]: https://www.repostatus.org/badges/latest/active.svg
+[status-url]: https://www.repostatus.org/#active
+[test-badge]: https://github.com/JianYang-Lab/gsMap/actions/workflows/test_linux.yml/badge.svg
+[test-url]: https://github.com/JianYang-Lab/gsMap/actions/workflows/test_linux.yml

gsmap-1.73.1/codecov.yml

@@ -0,0 +1,29 @@
+codecov:
+  require_ci_to_pass: yes
+
+coverage:
+  precision: 2
+  round: down
+  range: "70...100"
+  status:
+    project:
+      default:
+        target: 70%
+        threshold: 1%
+    patch:
+      default:
+        target: auto
+        threshold: 10%
+
+parsers:
+  gcov:
+    branch_detection:
+      conditional: yes
+      loop: yes
+      method: no
+      macro: no
+
+comment:
+  layout: "reach,diff,flags,files,footer"
+  behavior: default
+  require_changes: no