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[flake8] | ||
ignore = | ||
# Do not use mutable data structures for argument defaults. They are created during function definition time. | ||
# \ All calls to the function reuse this one instance of that data structure, persisting changes between them. | ||
B006 | ||
# Unsed variable -> sometimes we need to ignore this for debugging purposes | ||
B007 | ||
# 1 blank line required between summary line and description | ||
B008 | ||
# Function definition does not bind loop variabl | ||
B023 | ||
# Unnecessary use of map - use a list comprehension instead. | ||
C417 | ||
# Unnecessary dict comprehension - rewrite using dict(). | ||
C416 | ||
# Unnecessary dict call - rewrite as a literal. | ||
C408 | ||
# line break before a binary operator -> black does not adhere to PEP8 | ||
W503 | ||
# line break occured after a binary operator -> black does not adhere to PEP8 | ||
W504 | ||
# line too long -> we accept long comment lines; black gets rid of long code lines | ||
E501 | ||
# whitespace before : -> black does not adhere to PEP8 | ||
E203 | ||
# missing whitespace after ,', ';', or ':' -> black does not adhere to PEP8 | ||
E231 | ||
# continuation line over-indented for hanging indent -> black does not adhere to PEP8 | ||
E126 | ||
# too many leading '#' for block comment -> this is fine for indicating sections | ||
E262 | ||
# Do not assign a lambda expression, use a def -> lambda expression assignments are convenient | ||
E731 | ||
# allow I, O, l as variable names -> I is the identity matrix | ||
E741 | ||
# Missing docstring in public package | ||
D104 | ||
# Missing docstring in public module | ||
D100 | ||
# Missing docstring in __init__ | ||
D107 | ||
# Missing docstring in magic method | ||
D105 | ||
# format string does contain unindexed parameters | ||
P101 | ||
# first line should end with a period [Bug: doesn't work with single-line docstrings] | ||
D400 | ||
# First line should be in imperative mood; try rephrasing | ||
D401 | ||
# Missing docstring in public method | ||
D102 | ||
# Missing docstring in public function | ||
D103 | ||
# One-line docstring should fit on one line with quotes | ||
D200 | ||
# D403 First word of the first line should be properly capitalized | ||
D403 | ||
# Section has no content | ||
D414 | ||
# RST213 Inline emphasis start-string without end-string. | ||
RST213 | ||
# Unnecessary list comprehension passed to all() | ||
C419 | ||
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exclude = | ||
.git, | ||
__pycache__, | ||
build, | ||
docs/_build, | ||
dist, | ||
experiments, | ||
per-file-ignores = | ||
tests/*: D | ||
*/__init__.py: F401 | ||
extend-immutable-calls = | ||
# Add functions returning immutable values here to avoid B008 | ||
pathlib.Path | ||
Path | ||
rst-roles = | ||
class, | ||
func, | ||
ref, | ||
meth, | ||
doc, | ||
py:class, | ||
method, | ||
attr, | ||
cite:p, | ||
cite:t, | ||
rst-directives = | ||
envvar, | ||
exception, | ||
rst-substitutions = | ||
version, | ||
extend-ignore = | ||
RST307,RST210,RST201,RST203,RST301 |
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# ignore the special file | ||
**.ipynb linguist-vendored | ||
**.R linguist-vendored | ||
**.r linguist-vendored | ||
**.Rprofile linguist-vendored |
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--- | ||
name: Bug report | ||
about: DECIPHER doesn’t do what it should? Please help us fix it! | ||
title: '' | ||
labels: bug | ||
assignees: '' | ||
--- | ||
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### Please ensure: | ||
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- [ ] I have confirmed this bug exists on the **latest** version of DECIPHER. See https://github.com/gao-lab/decipher | ||
- [ ] I follow the tutorial from the [DECIPHER tutorial](https://github.com/gao-lab/decipher). | ||
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----------- | ||
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### Minimal code sample (that we can run without your data, using public data) | ||
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> **Note**: Please fill in the following information. You could read [this ](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports) for how to provide the necessary information to reproduce your bug. | ||
**Environment information:** | ||
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- Operating system: <!-- e.g. Windows 10, Ubuntu 20.04, macOS 11.2.3 --> | ||
- CUDA version: <!-- e.g. 11.1, None for CPU only --> | ||
- Python version: <!-- e.g. 3.9.1 --> | ||
- Torch version: <!-- e.g. 2.0.1 --> | ||
- Pytorch geometric version: <!-- e.g. 2.3.0 --> | ||
- DECIPHER version: <!-- e.g. 0.1.0 --> | ||
- Others: <!-- Other unconventional env setup --> | ||
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**Data information:** | ||
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<!-- Please describe the data you used. --> | ||
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**Codes:** | ||
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```python | ||
# Your code here, if you change the hyper-parameters, please also include them here. | ||
``` | ||
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**Error message:** | ||
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```python | ||
[Paste the error output produced by the above code here] | ||
``` | ||
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**Other supplement:** | ||
None | ||
<!-- Anything you think is important --> |
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--- | ||
name: Enhancement request | ||
about: Anything you’d like to see in DECIPHER? | ||
title: '' | ||
labels: enhancement | ||
assignees: '' | ||
--- | ||
|
||
<!-- Please describe your feature you would like to see below: --> | ||
... |
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--- | ||
name: Usage Question | ||
about: Any question is welcome! | ||
title: '' | ||
labels: question | ||
assignees: '' | ||
--- | ||
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||
<!-- Please write your question below. --> |
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name: build | ||
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on: | ||
push: | ||
branches: | ||
- main | ||
pull_request: | ||
branches: | ||
- main | ||
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jobs: | ||
build: | ||
runs-on: ubuntu-latest | ||
strategy: | ||
fail-fast: false | ||
matrix: | ||
python-version: [ 3.11 ] | ||
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steps: | ||
- name: Checkout repository | ||
uses: actions/checkout@v2 | ||
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- name: Set up Python ${{ matrix.python-version }} | ||
uses: actions/setup-python@v2 | ||
with: | ||
python-version: ${{ matrix.python-version }} | ||
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- name: Install dependencies | ||
run: | | ||
sudo apt update | ||
sudo apt install -y libxml2-utils pandoc | ||
curl -sSL https://install.python-poetry.org | python3 - | ||
pip install --upgrade pip | ||
pip install -e ".[docs, dev]" | ||
install_pyg_dependencies | ||
- name: Build documentation | ||
run: | | ||
sphinx-build -b html docs docs/_build |
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name: release | ||
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on: | ||
release: | ||
types: [published] | ||
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jobs: | ||
deploy: | ||
runs-on: ubuntu-latest | ||
strategy: | ||
fail-fast: false | ||
matrix: | ||
python-version: [ 3.11 ] | ||
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steps: | ||
- name: Checkout repository | ||
uses: actions/checkout@v2 | ||
|
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- name: Set up Python ${{ matrix.python-version }} | ||
uses: actions/setup-python@v2 | ||
with: | ||
python-version: ${{ matrix.python-version }} | ||
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- name: Install dependencies | ||
run: | | ||
sudo apt update | ||
sudo apt install -y libxml2-utils pandoc | ||
curl -sSL https://install.python-poetry.org | python3 - | ||
pip install --upgrade pip | ||
pip install -e ".[docs, dev]" | ||
install_pyg_dependencies | ||
- name: Build documentation | ||
run: | | ||
sphinx-build -b html docs docs/_build | ||
- name: Build package | ||
run: | | ||
poetry build | ||
ls -lh dist | ||
- name: Publish package | ||
uses: pypa/gh-action-pypi-publish@release/v1 | ||
with: | ||
user: __token__ | ||
password: ${{ secrets.PYPI_API_TOKEN }} | ||
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docker: | ||
runs-on: ubuntu-latest | ||
steps: | ||
- name: Delete huge unnecessary tools folder | ||
run: | | ||
rm -rf /opt/hostedtoolcache | ||
cd /opt | ||
find . -maxdepth 1 -mindepth 1 '!' -path ./containerd '!' -path ./actionarchivecache '!' -path ./runner '!' -path ./runner-cache -exec rm -rf '{}' ';' | ||
- name: Checkout repository | ||
uses: actions/checkout@v2 | ||
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- name: Set up QEMU | ||
uses: docker/setup-qemu-action@v3 | ||
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- name: Set up Docker Buildx | ||
uses: docker/setup-buildx-action@v3 | ||
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- name: Login to Docker Hub | ||
uses: docker/login-action@v3 | ||
with: | ||
username: huhansan666666 | ||
password: ${{ secrets.DOCKERHUB_TOKEN }} | ||
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- name: Build and push | ||
uses: docker/build-push-action@v6 | ||
with: | ||
context: . | ||
dockerfile: ./Dockerfile | ||
push: true | ||
tags: huhansan666666/decipher:latest |
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# file | ||
*.tmp | ||
*.xlsx | ||
*.gif | ||
*.dat | ||
*.log | ||
*.db | ||
*.sqlite | ||
*.h5ad | ||
*.fq | ||
*.pyc | ||
*.pth | ||
*.zip | ||
*.csv | ||
*.tsv | ||
*.gz | ||
*.rds | ||
*.pickle | ||
*.RData | ||
*.Rhistory | ||
*.h5 | ||
*.*pt | ||
*.tar | ||
*.joblib | ||
*.dill | ||
*.np[zy] | ||
*.adjlist | ||
*.pkl | ||
*.svg | ||
*.png | ||
*.html | ||
*.mm | ||
*.rda | ||
*.lg | ||
*.o | ||
*.jpg | ||
*.svs | ||
*.tiff | ||
*.tif | ||
*.TIF | ||
._* | ||
*.pth | ||
*.json | ||
*.ipynb | ||
*.DS_Store | ||
*.lock | ||
*.arrow | ||
.codecov.yaml | ||
hyperparams.yaml | ||
.coverage* | ||
.snakemake_timestamp | ||
events.** | ||
*.txt | ||
*.xenium | ||
*.parquet | ||
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# folder | ||
**/conda/ | ||
**/.cache/ | ||
**/.nv/ | ||
**/.ipython/ | ||
**/tensorboard/ | ||
**/tmp*/ | ||
**/__pycache__/ | ||
**/logs/ | ||
**/raw/ | ||
**/lightning_logs/* | ||
**/.snakemake/ | ||
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results | ||
other/ | ||
build/ | ||
api/ | ||
.ipynb_checkpoints/ | ||
.virtual_documents/ | ||
resource/* | ||
case/* | ||
tests/data/* | ||
experiments/data/* | ||
experiments/**/*.yaml | ||
**/explain/**.yaml | ||
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# exclude | ||
!resource/README.md | ||
!.vscode/* | ||
!Dockerfile | ||
!decipher/data/* |
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