https://github.com/abelsiqueira/python-template
Netherlands eScience Center Python Template
Science Score: 23.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
-
○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 3 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Academic email domains
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (12.8%) to scientific vocabulary
Last synced: 9 months ago
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Netherlands eScience Center Python Template
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- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Fork of NLeSC/python-template
Created over 4 years ago
· Last pushed about 4 years ago
https://github.com/abelsiqueira/python-template/blob/main/
# Netherlands eScience Center Python Template
Spend less time setting up and configuring your new Python packages and comply with the
[Netherlands eScience Center Software Development Guide](https://guide.esciencecenter.nl/)
from the start.
Use this [Cookiecutter](https://cookiecutter.readthedocs.io) template to generate
an empty Python package. Features include:
- Boilerplate unit tests and documentation,
- [Python static setup configuration]({{cookiecutter.directory_name}}/setup.cfg),
- Open source software license,
- Continuous integration with [GitHub action workflows]({{cookiecutter.directory_name}}/.github/workflows) for building, testing, link checking and linting,
- Code style checking with [prospector](https://pypi.org/project/prospector/),
- [Editorconfig]({{cookiecutter.directory_name}}/.editorconfig),
- Usage and contribution documents:
- [README.md]({{cookiecutter.directory_name}}/README.md) for package users,
- [README.dev.md]({{cookiecutter.directory_name}}/README.dev.md) for package developer,
- [project_setup.md]({{cookiecutter.directory_name}}/project_setup.md) with extensive documentation about project setup,
- [Change log]({{cookiecutter.directory_name}}/CHANGELOG.md),
- [Code of Conduct]({{cookiecutter.directory_name}}/CODE_OF_CONDUCT.md),
- [Contributing guidelines]({{cookiecutter.directory_name}}/CONTRIBUTING.md),
- Continuous code quality and code coverage reporting using [Sonarcloud](https://sonarcloud.io/),
- Automatic creation of [issues]({{cookiecutter.directory_name}}/.github/next_steps) with instructions how to pass all GitHub action workflows and integrate with services like Zenodo and Read the Docs,
- Instructions how to make package [citable]({{cookiecutter.directory_name}}/.github/next_steps/04_citation.md)
- FAIR software recommendation badge,
- Optional [pre commit hook]({{cookiecutter.directory_name}}/README.dev.md#running-linters-locally) to catch lint errors early
## Badges
| fair-software.nl recommendations | |
| :-- | :-- |
| (1/5) code repository | [](https://github.com/nlesc/python-template) |
| (2/5) license | [](https://github.com/nlesc/python-template) |
| (3/5) community registry | [](https://research-software.nl/software/nlesc-python-template) |
| (4/5) citation | [](https://doi.org/10.5281/zenodo.1310751) |
| (5/5) checklist | |
| overall | [](https://fair-software.eu) |
| **Other best practices** | |
| | |
| **GitHub Actions** | |
| Citation metadata consistency | [](https://github.com/nlesc/python-template/actions/workflows/cffconvert.yml) |
| MarkDown link checker | [](https://github.com/nlesc/python-template/actions/workflows/markdown-link-check.yml) |
| Tests | [](https://github.com/nlesc/python-template/actions/workflows/tests.yml) |
## How to use
### Step 1/3: Install `cookiecutter`
We recommend installing `cookiecutter` in user space as per `cookiecutter`'s instructions. This way, you don't have to
install `cookiecutter` for every new project.
```shell
python3 -m pip install --user --upgrade cookiecutter
```
### Step 2/3: Generate the files and directory structure
Run `cookiecutter` with the template:
```shell
# Notes:
# 1. See table below for explanation of each question
# 2. The files will be generated in a new directory
cookiecutter https://github.com/nlesc/python-template.git
```
| Name | Default value | Explanation |
| ------------------------- | ------------- | ----------- |
| directory_name | my-python-project | Name of the directory that contains the package. Avoid using spaces or uppercase letters for the best experience across operating systems. To get an impression of what will be generated, see the directory tree [below](https://github.com/NLeSC/python-template#step-33-read-about-what-was-just-generated) |
| package_name | my_python_package | Name of the package. Avoid using spaces, dashes, or uppercase letters for the best experience across operating systems. |
| package_short_description | Short description of package | The information that you enter here will end up in the README, documentation, license, and setup.cfg, so it may be a good idea to prepare something in advance. |
| keyword1 | keyword1 | A term that describes your package. |
| keyword2 | keyword2 | Another term that describes your package. |
| version | 0.1.0 | |
| github_organization | <my-github-organization> | GitHub organization that will contain this project's repository. This can also be your GitHub user name. |
| license | Apache Software License 2.0 | The software license under which the code is made available. |
| full_name | Jane Smith | Your full name, e.g. _Jane Smith_. |
| email | yourname@esciencecenter.nl | Your (work) email address. |
| copyright_holder | Netherlands eScience Center | Name(s) of the organization(s) or person(s) who hold the copyright of the software. |
| code_of_conduct_email | yourname@esciencecenter.nl | Email address of the person who should be contacted in case of violations of the Code of Conduct. |
Once the project files have been generated, follow the steps outlined in
[{{cookiecutter.directory_name}}/next_steps.md]({{cookiecutter.directory_name}}/next_steps.md).
### Step 3/3: Read about what was just generated
Good job! You have now generated the skeleton for your package:
```text
my-python-project/
.bumpversion.cfg
CHANGELOG.md
CITATION.cff
CODE_OF_CONDUCT.md
CONTRIBUTING.md
docs
conf.py
index.rst
make.bat
Makefile
_static
theme_overrides.css
_templates
.gitignore
.editorconfig
.githooks
pre-commit
.github
next_steps
01_sonarcloud_integration.md
02_citation.md
03_readthedocs.md
04_zenodo_integration.md
05_linting.md
workflows
build.yml
cffconvert.yml
lint.yml
markdown-link-check.yml
next_steps.yml
sonarcloud.yml
.gitignore
LICENSE
MANIFEST.in
.mlc-config.json
my_python_package
__init__.py
my_module.py
__version__.py
next_steps.md
NOTICE
project_setup.md
.prospector.yml
.pylintrc
pyproject.toml
README.dev.md
README.md
setup.cfg
setup.py
sonar-project.properties
tests
__init__.py
test_my_module.py
```
For an explanation of what's there, read on in the [project_setup.md]({{cookiecutter.directory_name}}/project_setup.md) file.
There are also instructions on how to [apply the template to an existing Python package](ADD_TO_EXISTING_PACKAGE.md).
## Examples
Many developers have gone before you in using this template to get started quickly. Check out their projects in the
list below:
1. Cerise: [https://github.com/MD-Studio/cerise](https://github.com/MD-Studio/cerise)
1. cerulean: [https://github.com/MD-Studio/cerulean](https://github.com/MD-Studio/cerulean)
1. cffconvert: [https://github.com/citation-file-format/cff-converter-python](https://github.com/citation-file-format/cff-converter-python)
1. fairtally: [https://github.com/fair-software/fairtally](https://github.com/fair-software/fairtally)
1. howfairis: [https://github.com/fair-software/howfairis](https://github.com/fair-software/howfairis)
1. matchms: [https://github.com/matchms/matchms](https://github.com/matchms/matchms)
1. MUSCLE 3: [https://github.com/multiscale/muscle3](https://github.com/multiscale/muscle3)
1. pycff: [https://github.com/citation-file-format/pycff](https://github.com/citation-file-format/pycff)
1. spec2vec: [https://github.com/iomega/spec2vec](https://github.com/iomega/spec2vec)
1. yatiml: [https://github.com/yatiml/yatiml](https://github.com/yatiml/yatiml)
1. _... And many more. Make a PR to add your project here!_
## How to contribute
Suggestions/improvements/edits are most welcome. Please read the [contribution guidelines](CONTRIBUTING.md) before creating an issue or a pull request.
Owner
- Name: Abel Soares Siqueira
- Login: abelsiqueira
- Kind: user
- Location: Amsterdam - The Netherlands
- Company: Netherlands eScience Center
- Website: https://abelsiqueira.com
- Twitter: abel_siqueira
- Repositories: 331
- Profile: https://github.com/abelsiqueira