Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update template to v0.3.0 #55

Closed
wants to merge 1 commit into from
Closed

Update template to v0.3.0 #55

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 0 additions & 8 deletions .bumpversion.cfg
View file
Open in desktop

This file was deleted.

22 changes: 11 additions & 11 deletions .codecov.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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
47 changes: 26 additions & 21 deletions .cruft.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,23 +1,28 @@
{
"template": "https://github.com/scverse/cookiecutter-scverse",
"commit": "5f091ed0952e4adac0c95bda4006bec0b4532995",
"checkout": null,
"context": {
"cookiecutter": {
"project_name": "genomic-features",
"package_name": "genomic_features",
"project_description": "Genomic annotations using BioConductor resources in Python.",
"author_full_name": "Isaac Virshup",
"author_email": "ivirshup@gmail.com",
"github_user": "ivirshup",
"project_repo": "https://github.com/scverse/genomic-features",
"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": "8e96abb5c3e2d5078c44713958da672711cf2a48",
"checkout": "v0.3.0",
"context": {
"cookiecutter": {
"project_name": "genomic-features",
"package_name": "genomic_features",
"project_description": "Genomic annotations using BioConductor resources in Python.",
"author_full_name": "Isaac Virshup",
"author_email": "ivirshup@gmail.com",
"github_user": "ivirshup",
"project_repo": "https://github.com/scverse/genomic-features",
"license": "BSD 3-Clause License",
"_copy_without_render": [
".github/workflows/**.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
View file
Open in desktop
Original file line number Diff line number Diff line change
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
View file
Open in desktop
Original file line number Diff line number Diff line change
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 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: 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
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,10 @@ name: Feature request
description: Propose a new feature for genomic-features
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
53 changes: 53 additions & 0 deletions .github/workflows/build.yaml.rej
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,53 @@
diff a/.github/workflows/build.yaml b/.github/workflows/build.yaml (rejected hunks)
@@ -1,29 +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
+ group: ${{ github.workflow }}-${{ github.ref }}
+ cancel-in-progress: true

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
+ 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
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,29 @@
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/{{ cookiecutter.package_name }}
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
Loading
Loading