<!--
<p align="center">
<img src="https://github.com/pseudopotential-tools/oncvpsp-tools/raw/main/docs/source/logo.png" height="150">
</p>
-->
<h1 align="center">
oncvpsp-tools
</h1>
<p align="center">
<a href="https://github.com/pseudopotential-tools/oncvpsp-tools/actions/workflows/tests.yml">
<img alt="Tests" src="https://github.com/pseudopotential-tools/oncvpsp-tools/workflows/Tests/badge.svg"/></a>
<a href="https://pypi.org/project/oncvpsp_tools">
<img alt="PyPI" src="https://img.shields.io/pypi/v/oncvpsp-tools"/></a>
<a href="https://pypi.org/project/oncvpsp_tools">
<img alt="PyPI - Python Version" src="https://img.shields.io/pypi/pyversions/oncvpsp-tools"/></a>
<a href="https://github.com/pseudopotential-tools/oncvpsp-tools/blob/main/LICENSE">
<img alt="PyPI - License" src="https://img.shields.io/pypi/l/oncvpsp-tools"/></a>
<a href='https://oncvpsp_tools.readthedocs.io/en/latest/?badge=latest'>
<img src='https://readthedocs.org/projects/oncvpsp_tools/badge/?version=latest' alt='Documentation Status'/></a>
<a href="https://codecov.io/gh/pseudopotential-tools/oncvpsp-tools/branch/main">
<img src="https://codecov.io/gh/pseudopotential-tools/oncvpsp-tools/branch/main/graph/badge.svg" alt="Codecov status"/></a>
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<img alt="Cookiecutter template from @cthoyt" src="https://img.shields.io/badge/Cookiecutter-snekpack-blue"/></a>
<a href='https://github.com/psf/black'>
<img src='https://img.shields.io/badge/code%20style-black-000000.svg' alt='Code style: black'/></a>
<a href="https://github.com/pseudopotential-tools/oncvpsp-tools/blob/main/.github/CODE_OF_CONDUCT.md">
<img src="https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg" alt="Contributor Covenant"/></a>
</p>
Tools for handling input and output files of ``oncvpsp.x``
## 💪 Getting Started
``oncvpsp-tools`` allows you to inspect input files
```python
from oncvpsp_tools import ONCVPSPInput
inp = ONCVPSPInput.from_file('/path/to/file')
print(inp.reference_configuration)
```
and output files
```python
import matplotlib.pyplot as plt
from oncvpsp_tools import ONCVPSPOutput
out = ONCVPSPOutput.from_file('/path/to/file')
out.arctan_log_derivatives.plot()
plt.show()
```
and even run ``oncvpsp.x`` from within a ``Python`` shell
```python
inp = ONCVPSPInput.from_file('/path/to/file')
out = inp.run('/path/to/oncvpsp.x')
```
### Command Line Interface
The ``oncvpsp-tools`` command line interface is automatically installed, and allows the
user to quickly plot the contents of `oncvpsp.x` output files. For example
```shell
oncvpsp-tools plot /path/to/file
```
Use the `--help` flag to explore all the possible options.
## 🚀 Installation
<!-- Uncomment this section after your first ``tox -e finish``
The most recent release can be installed from
[PyPI](https://pypi.org/project/oncvpsp_tools/) with:
```shell
pip install oncvpsp_tools
```
-->
The most recent code and data can be installed directly from GitHub with:
```shell
pip install git+https://github.com/pseudopotential-tools/oncvpsp-tools.git
```
## 👐 Contributing
Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See
[CONTRIBUTING.md](https://github.com/pseudopotential-tools/oncvpsp-tools/blob/master/.github/CONTRIBUTING.md) for more information on getting involved.
## 👋 Attribution
### ⚖️ License
The code in this package is licensed under the MIT License.
<!--
### 📖 Citation
Citation goes here!
-->
<!--
### 🎁 Support
This project has been supported by the following organizations (in alphabetical order):
- [Harvard Program in Therapeutic Science - Laboratory of Systems Pharmacology](https://hits.harvard.edu/the-program/laboratory-of-systems-pharmacology/)
-->
<!--
### 💰 Funding
This project has been supported by the following grants:
| Funding Body | Program | Grant |
|----------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------|-----------------|
| DARPA | [Automating Scientific Knowledge Extraction (ASKE)](https://www.darpa.mil/program/automating-scientific-knowledge-extraction) | HR00111990009 |
-->
### 🍪 Cookiecutter
This package was created with [@audreyfeldroy](https://github.com/audreyfeldroy)'s
[cookiecutter](https://github.com/cookiecutter/cookiecutter) package using [@cthoyt](https://github.com/cthoyt)'s
[cookiecutter-snekpack](https://github.com/cthoyt/cookiecutter-snekpack) template.
## 🛠️ For Developers
<details>
<summary>See developer instructions</summary>
The final section of the README is for if you want to get involved by making a code contribution.
### Development Installation
To install in development mode, use the following:
```bash
git clone git+https://github.com/pseudopotential-tools/oncvpsp-tools.git
cd oncvpsp-tools
pip install -e .
```
### 🥼 Testing
After cloning the repository and installing `tox` with `pip install tox`, the unit tests in the `tests/` folder can be
run reproducibly with:
```shell
tox
```
Additionally, these tests are automatically re-run with each commit in a [GitHub Action](https://github.com/pseudopotential-tools/oncvpsp-tools/actions?query=workflow%3ATests).
### 📖 Building the Documentation
The documentation can be built locally using the following:
```shell
git clone git+https://github.com/pseudopotential-tools/oncvpsp-tools.git
cd oncvpsp-tools
tox -e docs
open docs/build/html/index.html
```
The documentation automatically installs the package as well as the `docs`
extra specified in the [`setup.cfg`](setup.cfg). `sphinx` plugins
like `texext` can be added there. Additionally, they need to be added to the
`extensions` list in [`docs/source/conf.py`](docs/source/conf.py).
The documentation can be deployed to [ReadTheDocs](https://readthedocs.io) using
[this guide](https://docs.readthedocs.io/en/stable/intro/import-guide.html).
The [`.readthedocs.yml`](.readthedocs.yml) YAML file contains all the configuration you'll need.
You can also set up continuous integration on GitHub to check not only that
Sphinx can build the documentation in an isolated environment (i.e., with ``tox -e docs-test``)
but also that [ReadTheDocs can build it too](https://docs.readthedocs.io/en/stable/pull-requests.html).
### 📦 Making a Release
After installing the package in development mode and installing
`tox` with `pip install tox`, the commands for making a new release are contained within the `finish` environment
in `tox.ini`. Run the following from the shell:
```shell
tox -e finish
```
This script does the following:
1. Uses [Bump2Version](https://github.com/c4urself/bump2version) to switch the version number in the `setup.cfg`,
`src/oncvpsp_tools/version.py`, and [`docs/source/conf.py`](docs/source/conf.py) to not have the `-dev` suffix
2. Packages the code in both a tar archive and a wheel using [`build`](https://github.com/pypa/build)
3. Uploads to PyPI using [`twine`](https://github.com/pypa/twine). Be sure to have a `.pypirc` file configured to avoid the need for manual input at this
step
4. Push to GitHub. You'll need to make a release going with the commit where the version was bumped.
5. Bump the version to the next patch. If you made big changes and want to bump the version by minor, you can
use `tox -e bumpversion -- minor` after.
</details>
Raw data
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"description": "<!--\n<p align=\"center\">\n <img src=\"https://github.com/pseudopotential-tools/oncvpsp-tools/raw/main/docs/source/logo.png\" height=\"150\">\n</p>\n-->\n\n<h1 align=\"center\">\n oncvpsp-tools\n</h1>\n\n<p align=\"center\">\n <a href=\"https://github.com/pseudopotential-tools/oncvpsp-tools/actions/workflows/tests.yml\">\n <img alt=\"Tests\" src=\"https://github.com/pseudopotential-tools/oncvpsp-tools/workflows/Tests/badge.svg\"/></a>\n <a href=\"https://pypi.org/project/oncvpsp_tools\">\n <img alt=\"PyPI\" src=\"https://img.shields.io/pypi/v/oncvpsp-tools\"/></a>\n <a href=\"https://pypi.org/project/oncvpsp_tools\">\n <img alt=\"PyPI - Python Version\" src=\"https://img.shields.io/pypi/pyversions/oncvpsp-tools\"/></a>\n <a href=\"https://github.com/pseudopotential-tools/oncvpsp-tools/blob/main/LICENSE\">\n <img alt=\"PyPI - License\" src=\"https://img.shields.io/pypi/l/oncvpsp-tools\"/></a>\n <a href='https://oncvpsp_tools.readthedocs.io/en/latest/?badge=latest'>\n <img src='https://readthedocs.org/projects/oncvpsp_tools/badge/?version=latest' alt='Documentation Status'/></a>\n <a href=\"https://codecov.io/gh/pseudopotential-tools/oncvpsp-tools/branch/main\">\n <img src=\"https://codecov.io/gh/pseudopotential-tools/oncvpsp-tools/branch/main/graph/badge.svg\" alt=\"Codecov status\"/></a> \n <a href=\"https://github.com/cthoyt/cookiecutter-python-package\">\n <img alt=\"Cookiecutter template from @cthoyt\" src=\"https://img.shields.io/badge/Cookiecutter-snekpack-blue\"/></a>\n <a href='https://github.com/psf/black'>\n <img src='https://img.shields.io/badge/code%20style-black-000000.svg' alt='Code style: black'/></a>\n <a href=\"https://github.com/pseudopotential-tools/oncvpsp-tools/blob/main/.github/CODE_OF_CONDUCT.md\">\n <img src=\"https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg\" alt=\"Contributor Covenant\"/></a>\n</p>\n\nTools for handling input and output files of ``oncvpsp.x``\n\n## \ud83d\udcaa Getting Started\n\n``oncvpsp-tools`` allows you to inspect input files\n\n```python\nfrom oncvpsp_tools import ONCVPSPInput\ninp = ONCVPSPInput.from_file('/path/to/file')\nprint(inp.reference_configuration)\n```\n\nand output files\n\n```python\nimport matplotlib.pyplot as plt\nfrom oncvpsp_tools import ONCVPSPOutput\nout = ONCVPSPOutput.from_file('/path/to/file')\nout.arctan_log_derivatives.plot()\nplt.show()\n```\n\nand even run ``oncvpsp.x`` from within a ``Python`` shell\n\n```python\ninp = ONCVPSPInput.from_file('/path/to/file')\nout = inp.run('/path/to/oncvpsp.x')\n```\n\n### Command Line Interface\n\nThe ``oncvpsp-tools`` command line interface is automatically installed, and allows the\nuser to quickly plot the contents of `oncvpsp.x` output files. For example\n\n```shell\noncvpsp-tools plot /path/to/file\n```\n\nUse the `--help` flag to explore all the possible options.\n\n## \ud83d\ude80 Installation\n\n<!-- Uncomment this section after your first ``tox -e finish``\nThe most recent release can be installed from\n[PyPI](https://pypi.org/project/oncvpsp_tools/) with:\n\n```shell\npip install oncvpsp_tools\n```\n-->\n\nThe most recent code and data can be installed directly from GitHub with:\n\n```shell\npip install git+https://github.com/pseudopotential-tools/oncvpsp-tools.git\n```\n\n## \ud83d\udc50 Contributing\n\nContributions, whether filing an issue, making a pull request, or forking, are appreciated. See\n[CONTRIBUTING.md](https://github.com/pseudopotential-tools/oncvpsp-tools/blob/master/.github/CONTRIBUTING.md) for more information on getting involved.\n\n## \ud83d\udc4b Attribution\n\n### \u2696\ufe0f License\n\nThe code in this package is licensed under the MIT License.\n\n<!--\n### \ud83d\udcd6 Citation\n\nCitation goes here!\n-->\n\n<!--\n### \ud83c\udf81 Support\n\nThis project has been supported by the following organizations (in alphabetical order):\n\n- [Harvard Program in Therapeutic Science - Laboratory of Systems Pharmacology](https://hits.harvard.edu/the-program/laboratory-of-systems-pharmacology/)\n\n-->\n\n<!--\n### \ud83d\udcb0 Funding\n\nThis project has been supported by the following grants:\n\n| Funding Body | Program | Grant |\n|----------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------|-----------------|\n| DARPA | [Automating Scientific Knowledge Extraction (ASKE)](https://www.darpa.mil/program/automating-scientific-knowledge-extraction) | HR00111990009 |\n-->\n\n### \ud83c\udf6a Cookiecutter\n\nThis package was created with [@audreyfeldroy](https://github.com/audreyfeldroy)'s\n[cookiecutter](https://github.com/cookiecutter/cookiecutter) package using [@cthoyt](https://github.com/cthoyt)'s\n[cookiecutter-snekpack](https://github.com/cthoyt/cookiecutter-snekpack) template.\n\n## \ud83d\udee0\ufe0f For Developers\n\n<details>\n <summary>See developer instructions</summary>\n\nThe final section of the README is for if you want to get involved by making a code contribution.\n\n### Development Installation\n\nTo install in development mode, use the following:\n\n```bash\ngit clone git+https://github.com/pseudopotential-tools/oncvpsp-tools.git\ncd oncvpsp-tools\npip install -e .\n```\n\n### \ud83e\udd7c Testing\n\nAfter cloning the repository and installing `tox` with `pip install tox`, the unit tests in the `tests/` folder can be\nrun reproducibly with:\n\n```shell\ntox\n```\n\nAdditionally, these tests are automatically re-run with each commit in a [GitHub Action](https://github.com/pseudopotential-tools/oncvpsp-tools/actions?query=workflow%3ATests).\n\n### \ud83d\udcd6 Building the Documentation\n\nThe documentation can be built locally using the following:\n\n```shell\ngit clone git+https://github.com/pseudopotential-tools/oncvpsp-tools.git\ncd oncvpsp-tools\ntox -e docs\nopen docs/build/html/index.html\n``` \n\nThe documentation automatically installs the package as well as the `docs`\nextra specified in the [`setup.cfg`](setup.cfg). `sphinx` plugins\nlike `texext` can be added there. 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