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Update template to v0.3.1 (#56)
* Update template to v0.3.1 * Fix .rej * Remove prettier * Fix install instructions in contributing.md * Apply formatting --------- Co-authored-by: scverse-bot <None> Co-authored-by: Isaac Virshup <ivirshup@gmail.com>
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‎.bumpversion.cfg

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‎.codecov.yaml

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# Based on pydata/xarray
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codecov:
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require_ci_to_pass: no
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require_ci_to_pass: no
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coverage:
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status:
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project:
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default:
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# Require 1% coverage, i.e., always succeed
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target: 1
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patch: false
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changes: false
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status:
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project:
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default:
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# Require 1% coverage, i.e., always succeed
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target: 1
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patch: false
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changes: false
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comment:
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layout: diff, flags, files
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behavior: once
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require_base: no
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layout: diff, flags, files
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behavior: once
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require_base: no

‎.cruft.json

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{
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"template": "https://github.com/scverse/cookiecutter-scverse",
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"commit": "5f091ed0952e4adac0c95bda4006bec0b4532995",
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"checkout": null,
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"context": {
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"cookiecutter": {
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"project_name": "genomic-features",
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"package_name": "genomic_features",
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"project_description": "Genomic annotations using BioConductor resources in Python.",
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"author_full_name": "Isaac Virshup",
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"author_email": "ivirshup@gmail.com",
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"github_user": "ivirshup",
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"project_repo": "https://github.com/scverse/genomic-features",
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"license": "BSD 3-Clause License",
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"_copy_without_render": [
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".github/workflows/**.yaml",
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"docs/_templates/autosummary/**.rst"
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],
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"_template": "https://github.com/scverse/cookiecutter-scverse"
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}
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},
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"directory": null
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"template": "https://github.com/scverse/cookiecutter-scverse",
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"commit": "586b1652162ff7994b0070a034023d64289ae416",
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"checkout": "v0.3.1",
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"context": {
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"cookiecutter": {
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"project_name": "genomic-features",
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"package_name": "genomic_features",
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"project_description": "Genomic annotations using BioConductor resources in Python.",
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"author_full_name": "Isaac Virshup",
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"author_email": "ivirshup@gmail.com",
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"github_user": "ivirshup",
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"project_repo": "https://github.com/scverse/genomic-features",
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"license": "BSD 3-Clause License",
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"_copy_without_render": [
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".github/workflows/build.yaml",
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".github/workflows/test.yaml",
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"docs/_templates/autosummary/**.rst"
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],
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"_render_devdocs": false,
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"_jinja2_env_vars": {
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"lstrip_blocks": true,
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"trim_blocks": true
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},
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"_template": "https://github.com/scverse/cookiecutter-scverse"
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}
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},
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"directory": null
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}

‎.editorconfig

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trim_trailing_whitespace = true
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insert_final_newline = true
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[*.{yml,yaml}]
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indent_size = 2
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[.cruft.json]
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indent_size = 2
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[Makefile]
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indent_style = tab

‎.github/ISSUE_TEMPLATE/bug_report.yml

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description: Report something that is broken or incorrect
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labels: bug
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body:
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- type: markdown
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attributes:
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value: |
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**Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)
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detailing how to provide the necessary information for us to reproduce your bug. In brief:
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* Please provide exact steps how to reproduce the bug in a clean Python environment.
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* In case it's not clear what's causing this bug, please provide the data or the data generation procedure.
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* Sometimes it is not possible to share the data, but usually it is possible to replicate problems on publicly
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available datasets or to share a subset of your data.
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- type: markdown
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attributes:
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value: |
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**Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)
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detailing how to provide the necessary information for us to reproduce your bug. In brief:
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* Please provide exact steps how to reproduce the bug in a clean Python environment.
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* In case it's not clear what's causing this bug, please provide the data or the data generation procedure.
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* Sometimes it is not possible to share the data, but usually it is possible to replicate problems on publicly
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available datasets or to share a subset of your data.
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- type: textarea
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id: report
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attributes:
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label: Report
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description: A clear and concise description of what the bug is.
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validations:
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required: true
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- type: textarea
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id: report
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attributes:
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label: Report
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description: A clear and concise description of what the bug is.
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validations:
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required: true
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- type: textarea
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id: versions
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attributes:
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label: Version information
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description: |
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Please paste below the output of
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- type: textarea
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id: versions
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attributes:
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label: Version information
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description: |
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Please paste below the output of
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```python
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import session_info
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session_info.show(html=False, dependencies=True)
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```
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placeholder: |
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-----
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anndata 0.8.0rc2.dev27+ge524389
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session_info 1.0.0
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-----
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asttokens NA
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awkward 1.8.0
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backcall 0.2.0
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cython_runtime NA
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dateutil 2.8.2
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debugpy 1.6.0
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decorator 5.1.1
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entrypoints 0.4
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executing 0.8.3
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h5py 3.7.0
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ipykernel 6.15.0
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jedi 0.18.1
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mpl_toolkits NA
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natsort 8.1.0
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numpy 1.22.4
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packaging 21.3
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pandas 1.4.2
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parso 0.8.3
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pexpect 4.8.0
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pickleshare 0.7.5
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pkg_resources NA
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prompt_toolkit 3.0.29
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psutil 5.9.1
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ptyprocess 0.7.0
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pure_eval 0.2.2
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pydev_ipython NA
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pydevconsole NA
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pydevd 2.8.0
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pydevd_file_utils NA
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pydevd_plugins NA
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pydevd_tracing NA
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pygments 2.12.0
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pytz 2022.1
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scipy 1.8.1
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setuptools 62.5.0
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setuptools_scm NA
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six 1.16.0
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stack_data 0.3.0
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tornado 6.1
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traitlets 5.3.0
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wcwidth 0.2.5
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zmq 23.1.0
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-----
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IPython 8.4.0
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jupyter_client 7.3.4
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jupyter_core 4.10.0
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-----
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Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:58:50) [GCC 10.3.0]
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Linux-5.18.6-arch1-1-x86_64-with-glibc2.35
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-----
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Session information updated at 2022-07-07 17:55
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```python
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import session_info
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session_info.show(html=False, dependencies=True)
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```
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placeholder: |
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-----
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anndata 0.8.0rc2.dev27+ge524389
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session_info 1.0.0
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-----
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asttokens NA
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awkward 1.8.0
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backcall 0.2.0
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cython_runtime NA
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dateutil 2.8.2
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debugpy 1.6.0
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decorator 5.1.1
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entrypoints 0.4
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executing 0.8.3
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h5py 3.7.0
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ipykernel 6.15.0
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jedi 0.18.1
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mpl_toolkits NA
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natsort 8.1.0
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numpy 1.22.4
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packaging 21.3
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pandas 1.4.2
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parso 0.8.3
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pexpect 4.8.0
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pickleshare 0.7.5
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pkg_resources NA
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prompt_toolkit 3.0.29
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psutil 5.9.1
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ptyprocess 0.7.0
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pure_eval 0.2.2
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pydev_ipython NA
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pydevconsole NA
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pydevd 2.8.0
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pydevd_file_utils NA
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pydevd_plugins NA
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pydevd_tracing NA
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pygments 2.12.0
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pytz 2022.1
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scipy 1.8.1
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setuptools 62.5.0
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setuptools_scm NA
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six 1.16.0
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stack_data 0.3.0
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tornado 6.1
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traitlets 5.3.0
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wcwidth 0.2.5
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zmq 23.1.0
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-----
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IPython 8.4.0
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jupyter_client 7.3.4
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jupyter_core 4.10.0
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-----
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Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:58:50) [GCC 10.3.0]
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Linux-5.18.6-arch1-1-x86_64-with-glibc2.35
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-----
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Session information updated at 2022-07-07 17:55

‎.github/ISSUE_TEMPLATE/config.yml

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blank_issues_enabled: false
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contact_links:
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- name: Scverse Community Forum
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url: https://discourse.scverse.org/
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about: If you have questions about “How to do X”, please ask them here.
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- name: Scverse Community Forum
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url: https://discourse.scverse.org/
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about: If you have questions about “How to do X”, please ask them here.

‎.github/ISSUE_TEMPLATE/feature_request.yml

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description: Propose a new feature for genomic-features
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labels: enhancement
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body:
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- type: textarea
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id: description
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attributes:
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label: Description of feature
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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.
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validations:
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required: true
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- type: textarea
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id: description
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attributes:
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label: Description of feature
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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.
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validations:
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required: true

‎.github/workflows/build.yaml

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name: Check Build
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on:
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push:
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branches: [main]
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pull_request:
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branches: [main]
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push:
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branches: [main]
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pull_request:
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branches: [main]
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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package:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python 3.11
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uses: actions/setup-python@v4
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with:
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python-version: "3.11"
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cache: "pip"
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cache-dependency-path: "**/pyproject.toml"
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- name: Install build dependencies
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run: python -m pip install --upgrade pip wheel twine build
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- name: Build package
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run: python -m build
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- name: Check package
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run: twine check --strict dist/*.whl
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package:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python 3.11
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uses: actions/setup-python@v4
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with:
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python-version: "3.11"
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cache: "pip"
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cache-dependency-path: "**/pyproject.toml"
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- name: Install build dependencies
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run: python -m pip install --upgrade pip wheel twine build
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- name: Build package
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run: python -m build
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- name: Check package
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run: twine check --strict dist/*.whl

‎.github/workflows/release.yaml

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name: Release
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on:
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release:
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types: [published]
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# Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
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jobs:
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release:
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name: Upload release to PyPI
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runs-on: ubuntu-latest
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environment:
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name: pypi
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url: https://pypi.org/p/genomic_features
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permissions:
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id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
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steps:
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- uses: actions/checkout@v4
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with:
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filter: blob:none
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fetch-depth: 0
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- uses: actions/setup-python@v4
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with:
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python-version: "3.x"
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cache: "pip"
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- run: pip install build
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- run: python -m build
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- name: Publish package distributions to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1

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