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# Based on pydata/xarray | ||
codecov: | ||
require_ci_to_pass: no | ||
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coverage: | ||
status: | ||
project: | ||
default: | ||
# Require 1% coverage, i.e., always succeed | ||
target: 1 | ||
patch: false | ||
changes: false | ||
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comment: | ||
layout: diff, flags, files | ||
behavior: once | ||
require_base: no |
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{ | ||
"template": "https://github.com/scverse/cookiecutter-scverse", | ||
"commit": "eaf57d22e4e524debfeae4468eb770012d3b8cbb", | ||
"checkout": null, | ||
"context": { | ||
"cookiecutter": { | ||
"project_name": "treedata", | ||
"package_name": "treedata", | ||
"project_description": "anndata with trees", | ||
"author_full_name": "William Colgan", | ||
"author_email": "wcolgan@mit.edu", | ||
"github_user": "colganwi", | ||
"project_repo": "https://github.com/YosefLab/treedata", | ||
"license": "BSD 3-Clause License", | ||
"_copy_without_render": [ | ||
".github/workflows/build.yaml", | ||
".github/workflows/test.yaml", | ||
"docs/_templates/autosummary/**.rst" | ||
], | ||
"_render_devdocs": false, | ||
"_jinja2_env_vars": { | ||
"lstrip_blocks": true, | ||
"trim_blocks": true | ||
}, | ||
"_template": "https://github.com/scverse/cookiecutter-scverse" | ||
} | ||
}, | ||
"directory": null | ||
} |
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root = true | ||
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[*] | ||
indent_style = space | ||
indent_size = 4 | ||
end_of_line = lf | ||
charset = utf-8 | ||
trim_trailing_whitespace = true | ||
insert_final_newline = true | ||
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[*.{yml,yaml}] | ||
indent_size = 2 | ||
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[.cruft.json] | ||
indent_size = 2 | ||
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[Makefile] | ||
indent_style = tab |
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name: Bug report | ||
description: Report something that is broken or incorrect | ||
labels: bug | ||
body: | ||
- type: markdown | ||
attributes: | ||
value: | | ||
**Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports) | ||
detailing how to provide the necessary information for us to reproduce your bug. In brief: | ||
* Please provide exact steps how to reproduce the bug in a clean Python environment. | ||
* In case it's not clear what's causing this bug, please provide the data or the data generation procedure. | ||
* Sometimes it is not possible to share the data, but usually it is possible to replicate problems on publicly | ||
available datasets or to share a subset of your data. | ||
- type: textarea | ||
id: report | ||
attributes: | ||
label: Report | ||
description: A clear and concise description of what the bug is. | ||
validations: | ||
required: true | ||
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- type: textarea | ||
id: versions | ||
attributes: | ||
label: Version information | ||
description: | | ||
Please paste below the output of | ||
```python | ||
import session_info | ||
session_info.show(html=False, dependencies=True) | ||
``` | ||
placeholder: | | ||
----- | ||
anndata 0.8.0rc2.dev27+ge524389 | ||
session_info 1.0.0 | ||
----- | ||
asttokens NA | ||
awkward 1.8.0 | ||
backcall 0.2.0 | ||
cython_runtime NA | ||
dateutil 2.8.2 | ||
debugpy 1.6.0 | ||
decorator 5.1.1 | ||
entrypoints 0.4 | ||
executing 0.8.3 | ||
h5py 3.7.0 | ||
ipykernel 6.15.0 | ||
jedi 0.18.1 | ||
mpl_toolkits NA | ||
natsort 8.1.0 | ||
numpy 1.22.4 | ||
packaging 21.3 | ||
pandas 1.4.2 | ||
parso 0.8.3 | ||
pexpect 4.8.0 | ||
pickleshare 0.7.5 | ||
pkg_resources NA | ||
prompt_toolkit 3.0.29 | ||
psutil 5.9.1 | ||
ptyprocess 0.7.0 | ||
pure_eval 0.2.2 | ||
pydev_ipython NA | ||
pydevconsole NA | ||
pydevd 2.8.0 | ||
pydevd_file_utils NA | ||
pydevd_plugins NA | ||
pydevd_tracing NA | ||
pygments 2.12.0 | ||
pytz 2022.1 | ||
scipy 1.8.1 | ||
setuptools 62.5.0 | ||
setuptools_scm NA | ||
six 1.16.0 | ||
stack_data 0.3.0 | ||
tornado 6.1 | ||
traitlets 5.3.0 | ||
wcwidth 0.2.5 | ||
zmq 23.1.0 | ||
----- | ||
IPython 8.4.0 | ||
jupyter_client 7.3.4 | ||
jupyter_core 4.10.0 | ||
----- | ||
Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:58:50) [GCC 10.3.0] | ||
Linux-5.18.6-arch1-1-x86_64-with-glibc2.35 | ||
----- | ||
Session information updated at 2022-07-07 17:55 |
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blank_issues_enabled: false | ||
contact_links: | ||
- name: Scverse Community Forum | ||
url: https://discourse.scverse.org/ | ||
about: If you have questions about “How to do X”, please ask them here. |
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name: Feature request | ||
description: Propose a new feature for treedata | ||
labels: enhancement | ||
body: | ||
- type: textarea | ||
id: description | ||
attributes: | ||
label: Description of feature | ||
description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered. | ||
validations: | ||
required: true |
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name: Check Build | ||
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on: | ||
push: | ||
branches: [main] | ||
pull_request: | ||
branches: [main] | ||
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concurrency: | ||
group: ${{ github.workflow }}-${{ github.ref }} | ||
cancel-in-progress: true | ||
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jobs: | ||
package: | ||
runs-on: ubuntu-latest | ||
steps: | ||
- uses: actions/checkout@v3 | ||
- name: Set up Python 3.10 | ||
uses: actions/setup-python@v4 | ||
with: | ||
python-version: "3.10" | ||
cache: "pip" | ||
cache-dependency-path: "**/pyproject.toml" | ||
- name: Install build dependencies | ||
run: python -m pip install --upgrade pip wheel twine build | ||
- name: Build package | ||
run: python -m build | ||
- name: Check package | ||
run: twine check --strict dist/*.whl |
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name: Release | ||
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on: | ||
release: | ||
types: [published] | ||
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# Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/ | ||
jobs: | ||
release: | ||
name: Upload release to PyPI | ||
runs-on: ubuntu-latest | ||
environment: | ||
name: pypi | ||
url: https://pypi.org/p/treedata | ||
permissions: | ||
id-token: write # IMPORTANT: this permission is mandatory for trusted publishing | ||
steps: | ||
- uses: actions/checkout@v4 | ||
with: | ||
filter: blob:none | ||
fetch-depth: 0 | ||
- uses: actions/setup-python@v4 | ||
with: | ||
python-version: "3.x" | ||
cache: "pip" | ||
- run: pip install build | ||
- run: python -m build | ||
- name: Publish package distributions to PyPI | ||
uses: pypa/gh-action-pypi-publish@release/v1 |
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name: Test | ||
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on: | ||
push: | ||
branches: [main] | ||
pull_request: | ||
branches: [main] | ||
schedule: | ||
- cron: "0 5 1,15 * *" | ||
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concurrency: | ||
group: ${{ github.workflow }}-${{ github.ref }} | ||
cancel-in-progress: true | ||
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jobs: | ||
test: | ||
runs-on: ${{ matrix.os }} | ||
defaults: | ||
run: | ||
shell: bash -e {0} # -e to fail on error | ||
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strategy: | ||
fail-fast: false | ||
matrix: | ||
include: | ||
- os: ubuntu-latest | ||
python: "3.9" | ||
- os: ubuntu-latest | ||
python: "3.11" | ||
- os: ubuntu-latest | ||
python: "3.11" | ||
pip-flags: "--pre" | ||
name: PRE-RELEASE DEPENDENCIES | ||
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name: ${{ matrix.name }} Python ${{ matrix.python }} | ||
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env: | ||
OS: ${{ matrix.os }} | ||
PYTHON: ${{ matrix.python }} | ||
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steps: | ||
- uses: actions/checkout@v3 | ||
- name: Set up Python ${{ matrix.python }} | ||
uses: actions/setup-python@v4 | ||
with: | ||
python-version: ${{ matrix.python }} | ||
cache: "pip" | ||
cache-dependency-path: "**/pyproject.toml" | ||
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- name: Install test dependencies | ||
run: | | ||
python -m pip install --upgrade pip wheel | ||
- name: Install dependencies | ||
run: | | ||
pip install ${{ matrix.pip-flags }} ".[dev,test]" | ||
- name: Test | ||
env: | ||
MPLBACKEND: agg | ||
PLATFORM: ${{ matrix.os }} | ||
DISPLAY: :42 | ||
run: | | ||
coverage run -m pytest -v --color=yes | ||
- name: Report coverage | ||
run: | | ||
coverage report | ||
- name: Upload coverage | ||
uses: codecov/codecov-action@v3 |
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# Temp files | ||
.DS_Store | ||
*~ | ||
buck-out/ | ||
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# Compiled files | ||
.venv/ | ||
__pycache__/ | ||
.mypy_cache/ | ||
.ruff_cache/ | ||
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# Distribution / packaging | ||
/build/ | ||
/dist/ | ||
/*.egg-info/ | ||
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# Tests and coverage | ||
/.pytest_cache/ | ||
/.cache/ | ||
/data/ | ||
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# docs | ||
/docs/generated/ | ||
/docs/_build/ | ||
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# IDEs | ||
/.idea/ | ||
/.vscode/ |
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fail_fast: false | ||
default_language_version: | ||
python: python3 | ||
default_stages: | ||
- commit | ||
- push | ||
minimum_pre_commit_version: 2.16.0 | ||
repos: | ||
- repo: https://github.com/pre-commit/mirrors-prettier | ||
rev: v4.0.0-alpha.8 | ||
hooks: | ||
- id: prettier | ||
- repo: https://github.com/astral-sh/ruff-pre-commit | ||
rev: v0.2.1 | ||
hooks: | ||
- id: ruff | ||
types_or: [python, pyi, jupyter] | ||
args: [--fix, --exit-non-zero-on-fix] | ||
- id: ruff-format | ||
types_or: [python, pyi, jupyter] | ||
- repo: https://github.com/pre-commit/pre-commit-hooks | ||
rev: v4.5.0 | ||
hooks: | ||
- id: detect-private-key | ||
- id: check-ast | ||
- id: end-of-file-fixer | ||
- id: mixed-line-ending | ||
args: [--fix=lf] | ||
- id: trailing-whitespace | ||
- id: check-case-conflict | ||
# Check that there are no merge conflicts (could be generated by template sync) | ||
- id: check-merge-conflict | ||
args: [--assume-in-merge] | ||
- repo: local | ||
hooks: | ||
- id: forbid-to-commit | ||
name: Don't commit rej files | ||
entry: | | ||
Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates. | ||
Fix the merge conflicts manually and remove the .rej files. | ||
language: fail | ||
files: '.*\.rej$' |
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# https://docs.readthedocs.io/en/stable/config-file/v2.html | ||
version: 2 | ||
build: | ||
os: ubuntu-20.04 | ||
tools: | ||
python: "3.10" | ||
sphinx: | ||
configuration: docs/conf.py | ||
# disable this for more lenient docs builds | ||
fail_on_warning: true | ||
python: | ||
install: | ||
- method: pip | ||
path: . | ||
extra_requirements: | ||
- doc |
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