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Update template to v0.4.0 #16

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Update template to v0.4.0 #16

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75e7688
Update template to v0.4.0
May 21, 2024
ba91b08
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] May 21, 2024
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8 changes: 0 additions & 8 deletions .bumpversion.cfg
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This file was deleted.

22 changes: 11 additions & 11 deletions .codecov.yaml
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@@ -1,17 +1,17 @@
# Based on pydata/xarray
codecov:
require_ci_to_pass: no
require_ci_to_pass: no

coverage:
status:
project:
default:
# Require 1% coverage, i.e., always succeed
target: 1
patch: false
changes: false
status:
project:
default:
# Require 1% coverage, i.e., always succeed
target: 1
patch: false
changes: false

comment:
layout: diff, flags, files
behavior: once
require_base: no
layout: diff, flags, files
behavior: once
require_base: no
48 changes: 27 additions & 21 deletions .cruft.json
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@@ -1,23 +1,29 @@
{
"template": "https://github.com/scverse/cookiecutter-scverse",
"commit": "7cc5403b05e299d7a4bb169c2bd8c27a2a7676f3",
"checkout": null,
"context": {
"cookiecutter": {
"project_name": "simple-scvi",
"package_name": "simple_scvi",
"project_description": "External and simple implementation of scVI",
"author_full_name": "Adam Gayoso",
"author_email": "[email protected]",
"github_user": "adamgayoso",
"project_repo": "https://github.com/scverse/simple-scvi",
"license": "BSD 3-Clause License",
"_copy_without_render": [
".github/workflows/**.yaml",
"docs/_templates/autosummary/**.rst"
],
"_template": "https://github.com/scverse/cookiecutter-scverse"
}
},
"directory": null
"template": "https://github.com/scverse/cookiecutter-scverse",
"commit": "87a407a65408d75a949c0b54b19fd287475a56f8",
"checkout": "v0.4.0",
"context": {
"cookiecutter": {
"project_name": "simple-scvi",
"package_name": "simple_scvi",
"project_description": "External and simple implementation of scVI",
"author_full_name": "Adam Gayoso",
"author_email": "[email protected]",
"github_user": "adamgayoso",
"project_repo": "https://github.com/scverse/simple-scvi",
"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
}
6 changes: 6 additions & 0 deletions .editorconfig
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Expand Up @@ -8,5 +8,11 @@ charset = utf-8
trim_trailing_whitespace = true
insert_final_newline = true

[*.{yml,yaml}]
indent_size = 2

[.cruft.json]
indent_size = 2

[Makefile]
indent_style = tab
164 changes: 82 additions & 82 deletions .github/ISSUE_TEMPLATE/bug_report.yml
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Expand Up @@ -2,88 +2,88 @@ 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 procecure.
* 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: 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
- type: textarea
id: report
attributes:
label: Report
description: A clear and concise description of what the bug is.
validations:
required: true

- type: textarea
id: versions
attributes:
label: Version information
description: |
Please paste below the output of
- 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
```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
6 changes: 3 additions & 3 deletions .github/ISSUE_TEMPLATE/config.yml
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@@ -1,5 +1,5 @@
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.
- name: Scverse Community Forum
url: https://discourse.scverse.org/
about: If you have questions about “How to do X”, please ask them here.
14 changes: 7 additions & 7 deletions .github/ISSUE_TEMPLATE/feature_request.yml
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Expand Up @@ -2,10 +2,10 @@ name: Feature request
description: Propose a new feature for simple-scvi
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
- 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
42 changes: 24 additions & 18 deletions .github/workflows/build.yaml
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@@ -1,23 +1,29 @@
name: Check Build

on:
push:
branches: [main]
pull_request:
branches: [main]
push:
branches: [main]
pull_request:
branches: [main]

concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true

jobs:
package:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: Set up Python 3.10
uses: actions/setup-python@v2
with:
python-version: "3.10"
- 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
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
29 changes: 29 additions & 0 deletions .github/workflows/release.yaml
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name: Release

on:
release:
types: [published]

# 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/simple_scvi
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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