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adamgayosopre-commit-ci[bot]Martin Kim
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Precommit updates (scverse#1724)
* update pre commit config * update flake8 config * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update precommit * add more flake8 * add more flake8 * remove unused func and use private * Flake 8 * fix import * more ignore * more ignore * flake8 * flake8 * flake 8 * docs * remove D101, D102, E266, static code checks * All done locally * hopefully final * Static code checks * static * codacy why Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Martin Kim <[email protected]>
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‎.flake8

+59-3
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@@ -1,5 +1,61 @@
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[flake8]
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ignore = E203, E266, E501, W503, W605, N812
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exclude = .git,docs
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max-line-length = 119
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ignore =
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# Unnecessary dict call - rewrite as a literal.
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C408
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# line break before a binary operator -> black does not adhere to PEP8
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W503
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# line break occured after a binary operator -> black does not adhere to PEP8
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W504
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# line too long -> we accept long comment lines; black gets rid of long code lines
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E501
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# whitespace before : -> black does not adhere to PEP8
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E203
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# missing whitespace after ,', ';', or ':' -> black does not adhere to PEP8
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E231
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# continuation line over-indented for hanging indent -> black does not adhere to PEP8
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E126
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# too many leading '#' for block comment -> this is fine for indicating sections
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E262
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# Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
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E731
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# allow I, O, l as variable names -> I is the identity matrix
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E741
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# Missing docstring in public package
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D104
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# Missing docstring in public module
27+
D100
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# Missing docstring in __init__
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D107
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# Missing docstring in magic method
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D105
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# format string does contain unindexed parameters
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P101
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# first line should end with a period [Bug: doesn't work with single-line docstrings]
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D400
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# First line should be in imperative mood; try rephrasing
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D401
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exclude = .git,__pycache__,build,docs/_build,dist
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per-file-ignores =
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tests/*: D
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*/__init__.py: F401
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extend-immutable-calls =
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# Add functions returning immutable values here to avoid B008
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pathlib.Path
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Path
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rst-roles =
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class,
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func,
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ref,
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meth,
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doc,
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py:class,
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method,
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attr,
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rst-directives =
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envvar,
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exception,
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rst-substitutions =
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version,
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extend-ignore =
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RST307,RST210,RST201,RST203,RST301,RST306 # TODO(martinkim0): Address 306 in new issue

‎.github/ISSUE_TEMPLATE/bug_report.md

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@@ -1,27 +1,31 @@
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---
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name: Bug report
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about: Create a report to help us improve
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title: ''
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title: ""
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labels: bug
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assignees: ''
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assignees: ""
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---
98

109
<!-- Describe the bug -->
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1111
[TEXT HERE]
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<!-- To reproduce -->
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1415
```python
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[CODE HERE]
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# Your code here
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```
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<!-- Put your Error output in this code block (if applicable, else delete the block): -->
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```pytb
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[ERROR HERE]
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[Paste the error output produced by the above code here]
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```
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#### Versions:
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<!-- Output of scvi.__version__ -->
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> VERSION
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<!-- Relevant screenshots -->

‎.github/ISSUE_TEMPLATE/config.yml

+3-3
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@@ -1,4 +1,4 @@
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contact_links:
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- name: Usage question
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url: https://discourse.scvi-tools.org/
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about: Please ask and answer non-development questions at https://discourse.scvi-tools.org/.
2+
- name: Usage question
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url: https://discourse.scvi-tools.org/
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about: Please ask and answer non-development questions at https://discourse.scvi-tools.org/.

‎.github/ISSUE_TEMPLATE/feature_request.md

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@@ -1,10 +1,9 @@
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---
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name: Feature request
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about: Suggest an idea for this project
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title: ''
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title: ""
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labels: enhancement
6-
assignees: ''
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assignees: ""
87
---
98

109
**Is your feature request related to a problem? Please describe.**

‎.github/workflows/release.yml

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@@ -1,39 +1,39 @@
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name: Release
22

33
on:
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push:
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tags:
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- '*.*.*'
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push:
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tags:
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- "*.*.*"
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88
jobs:
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release:
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name: Release
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runs-on: ubuntu-latest
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steps:
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# will use ref/SHA that triggered it
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- name: Checkout code
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uses: actions/checkout@v3
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release:
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name: Release
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runs-on: ubuntu-latest
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steps:
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# will use ref/SHA that triggered it
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- name: Checkout code
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uses: actions/checkout@v3
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- name: Set up Python 3.9
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uses: actions/setup-python@v2
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with:
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python-version: "3.9"
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- name: Set up Python 3.9
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uses: actions/setup-python@v2
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with:
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python-version: "3.9"
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- name: Install poetry
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uses: abatilo/[email protected]
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with:
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poetry-version: 1.1.11
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- name: Install poetry
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uses: abatilo/[email protected]
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with:
25+
poetry-version: 1.1.11
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27-
- name: Build project for distribution
28-
run: poetry build
27+
- name: Build project for distribution
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run: poetry build
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30-
- name: Check Version
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id: check-version
32-
run: |
33-
[[ "$(poetry version --short)" =~ ^[0-9]+\.[0-9]+\.[0-9]+$ ]] \
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|| echo ::set-output name=prerelease::true
30+
- name: Check Version
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id: check-version
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run: |
33+
[[ "$(poetry version --short)" =~ ^[0-9]+\.[0-9]+\.[0-9]+$ ]] \
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|| echo ::set-output name=prerelease::true
3535
36-
- name: Publish to PyPI
37-
env:
38-
POETRY_PYPI_TOKEN_PYPI: ${{ secrets.PYPI_TOKEN }}
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run: poetry publish
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- name: Publish to PyPI
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env:
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POETRY_PYPI_TOKEN_PYPI: ${{ secrets.PYPI_TOKEN }}
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run: poetry publish

‎.github/workflows/test.yml

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name: scvi-tools
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on:
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push:
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branches: [master, 0.15.x, 0.16.x, 0.17.x, 0.18.x]
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pull_request:
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branches: [master, 0.15.x, 0.16.x, 0.17.x, 0.18.x]
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push:
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branches: [master, 0.15.x, 0.16.x, 0.17.x, 0.18.x]
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pull_request:
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branches: [master, 0.15.x, 0.16.x, 0.17.x, 0.18.x]
1111

1212
jobs:
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build:
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runs-on: ubuntu-latest
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timeout-minutes: 20
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strategy:
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matrix:
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python-version: ["3.7", "3.8", "3.9", "3.10"]
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build:
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runs-on: ubuntu-latest
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timeout-minutes: 20
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strategy:
17+
matrix:
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python-version: ["3.7", "3.8", "3.9", "3.10"]
1919

20-
steps:
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- uses: actions/checkout@v2
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steps:
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- uses: actions/checkout@v2
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23-
- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
25-
with:
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python-version: ${{ matrix.python-version }}
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Cache pip
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uses: actions/cache@v2
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with:
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path: ~/.cache/pip
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key: ${{ runner.os }}-pip-v1-${{ hashFiles('**/requirements.txt') }}
33-
restore-keys: |
34-
${{ runner.os }}-pip-v1-
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- name: Cache pip
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uses: actions/cache@v2
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with:
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path: ~/.cache/pip
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key: ${{ runner.os }}-pip-v1-${{ hashFiles('**/requirements.txt') }}
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restore-keys: |
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${{ runner.os }}-pip-v1-
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- name: Install dependencies
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id: dependencies
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run: |
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pip install pytest-cov
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pip install .[dev,pymde]
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- name: Install dependencies
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id: dependencies
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run: |
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pip install pytest-cov
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pip install .[dev,pymde]
4141
42-
# Following checks are independent and are run even if one fails
43-
- name: Lint with flake8
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run: |
45-
flake8
46-
if: ${{ steps.dependencies.outcome == 'success' && always() }}
42+
# Following checks are independent and are run even if one fails
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- name: Lint with flake8
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run: |
45+
flake8
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if: ${{ steps.dependencies.outcome == 'success' && always() }}
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48-
- name: Format with black
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run: |
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black --check .
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if: ${{ steps.dependencies.outcome == 'success' && always() }}
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- name: Format with black
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run: |
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black --check .
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if: ${{ steps.dependencies.outcome == 'success' && always() }}
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53-
- name: Import sort
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run: |
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isort --check-only .
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if: ${{ steps.dependencies.outcome == 'success' && always() }}
53+
- name: Import sort
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run: |
55+
isort --check-only .
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if: ${{ steps.dependencies.outcome == 'success' && always() }}
5757

58-
- name: Test with pytest
59-
run: |
60-
pytest --cov-report=xml --cov=scvi --internet-tests --color=yes
61-
if: ${{ steps.dependencies.outcome == 'success' && always() }}
62-
# --------------------------------------------------------------
58+
- name: Test with pytest
59+
run: |
60+
pytest --cov-report=xml --cov=scvi --internet-tests --color=yes
61+
if: ${{ steps.dependencies.outcome == 'success' && always() }}
62+
# --------------------------------------------------------------
6363

64-
- name: After success
65-
run: |
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codecov
67-
pip list
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- name: After success
65+
run: |
66+
codecov
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pip list
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- name: Codacy upload
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env:
71-
CODACY_PROJECT_TOKEN: ${{ secrets.CODACY_PROJECT_TOKEN }}
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run: |
73-
bash <(curl -Ls https://coverage.codacy.com/get.sh) report -l Python -r coverage.xml
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continue-on-error: true
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- name: Codacy upload
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env:
71+
CODACY_PROJECT_TOKEN: ${{ secrets.CODACY_PROJECT_TOKEN }}
72+
run: |
73+
bash <(curl -Ls https://coverage.codacy.com/get.sh) report -l Python -r coverage.xml
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continue-on-error: true

‎.pre-commit-config.yaml

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fail_fast: false
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default_language_version:
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python: python3
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default_stages:
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- commit
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- push
7+
minimum_pre_commit_version: 2.16.0
18
repos:
29
- repo: https://github.com/psf/black
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rev: 22.8.0
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rev: 22.10.0
411
hooks:
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- id: black
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- repo: https://github.com/pre-commit/mirrors-prettier
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rev: v3.0.0-alpha.0
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hooks:
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- id: prettier
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- repo: https://github.com/asottile/blacken-docs
18+
rev: v1.12.1
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hooks:
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- id: blacken-docs
21+
- repo: https://github.com/PyCQA/isort
22+
rev: 5.10.1
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hooks:
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- id: isort
25+
- repo: https://github.com/asottile/yesqa
26+
rev: v1.4.0
27+
hooks:
28+
- id: yesqa
29+
additional_dependencies:
30+
- flake8-tidy-imports
31+
- flake8-docstrings
32+
- flake8-rst-docstrings
33+
- flake8-comprehensions
34+
- flake8-bugbear
35+
- flake8-blind-except
36+
- repo: https://github.com/pre-commit/pre-commit-hooks
37+
rev: v4.3.0
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hooks:
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- id: detect-private-key
40+
- id: check-ast
41+
- id: end-of-file-fixer
42+
- id: mixed-line-ending
43+
args: [--fix=lf]
44+
- id: trailing-whitespace
45+
- id: check-case-conflict
46+
- repo: https://github.com/myint/autoflake
47+
rev: v1.7.0
48+
hooks:
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- id: autoflake
50+
args:
51+
- --in-place
52+
- --remove-all-unused-imports
53+
- --remove-unused-variable
54+
- --ignore-init-module-imports
655
- repo: https://github.com/PyCQA/flake8
756
rev: 5.0.4
857
hooks:
958
- id: flake8
10-
- repo: https://github.com/pycqa/isort
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rev: 5.10.1
59+
additional_dependencies:
60+
- flake8-tidy-imports
61+
- flake8-docstrings
62+
- flake8-rst-docstrings
63+
- flake8-comprehensions
64+
- flake8-bugbear
65+
- flake8-blind-except
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- repo: https://github.com/asottile/pyupgrade
67+
rev: v3.0.0
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hooks:
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- id: isort
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name: isort (python)
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additional_dependencies: [toml]
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- id: pyupgrade
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args: [--py3-plus, --py38-plus, --keep-runtime-typing]

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