# Phenospy (= Phenoscript Python tools)
<p align="left">
<img src="https://raw.githubusercontent.com/sergeitarasov/PhenoScript/main/phenospy.png" width="300" title="Phenospy logo">
<img src="https://raw.githubusercontent.com/sergeitarasov/vscode-phenoscript/main/icon.png" width="300" title="Phenoscript logo">
</p>
[Phenospy](https://pypi.org/project/phenospy/) is a Python package that facilitates the automatic analysis and comparison of ontology-based (= semantic) descriptions of species and phenotypes. Phenospy works with descriptions written in [Phenoscript](https://github.com/sergeitarasov/vscode-phenoscript), a computer language designed for describing species (support for other semantic approaches is under development).
The Phenoscript language allows rapid coding of morphological and ecological traits using an individual-based approach (ontology's A-box). You can efficiently code Phenoscript by using the [VS Code Phenoscript extension](https://marketplace.visualstudio.com/items?itemName=Tarasov-Lab.phenoscript) that provides syntax highlighting and snippet support. It can be installed from the Marketplace from within the VS Code. Its GitHub repository can be accessed [here](https://github.com/sergeitarasov/vscode-phenoscript). Afterward, Phenospy can be used to analyze and process the semantic descriptions.
## What can I do with Phenospy?
- Create snippets based on selected ontologies for writing semantic phenotypes with the VS Code Phenoscript extension.
- Convert the Phenoscript description into an OWL file.
- Convert the Phenoscript description into an annotated Natural Language description (Markdown format).
- Automatically compare species and phenotypes (under development).
## Documentation
See [Wiki for details](https://github.com/sergeitarasov/PhenoScript/wiki).
## Requirements
* `Python >=3.0`
If you are a new user with Python 2 installed, you should uninstall it and install Python 3 instead. For more information, please refer to [this discussion](https://stackoverflow.com/questions/3819449/how-to-uninstall-python-2-7-on-a-mac-os-x-10-6-4).
## Install
Phenospy can be installed directly from the [PyPI repository](https://pypi.org/project/phenospy/) by running the following command in your terminal (macOS) or a command prompt (Windows):
```{bash}
pip install phenospy
```
## Issues
See [issues for details](https://github.com/sergeitarasov/PhenoScript/wiki/Issues).
Raw data
{
"_id": null,
"home_page": "https://github.com/sergeitarasov/PhenoScript",
"name": "phenospy",
"maintainer": null,
"docs_url": null,
"requires_python": null,
"maintainer_email": null,
"keywords": null,
"author": "Sergei Tarasov",
"author_email": "sergei.tarasov@helsinki.fi",
"download_url": "https://files.pythonhosted.org/packages/3c/29/6e32455f69c170a3f02e67fdacf6b35c0a598b88ccfc8e95567bb4aa887f/phenospy-0.250.tar.gz",
"platform": null,
"description": "\n\n# Phenospy (= Phenoscript Python tools)\n\n <p align=\"left\">\n <img src=\"https://raw.githubusercontent.com/sergeitarasov/PhenoScript/main/phenospy.png\" width=\"300\" title=\"Phenospy logo\">\n <img src=\"https://raw.githubusercontent.com/sergeitarasov/vscode-phenoscript/main/icon.png\" width=\"300\" title=\"Phenoscript logo\">\n</p> \n\n\n[Phenospy](https://pypi.org/project/phenospy/) is a Python package that facilitates the automatic analysis and comparison of ontology-based (= semantic) descriptions of species and phenotypes. Phenospy works with descriptions written in [Phenoscript](https://github.com/sergeitarasov/vscode-phenoscript), a computer language designed for describing species (support for other semantic approaches is under development). \n\nThe Phenoscript language allows rapid coding of morphological and ecological traits using an individual-based approach (ontology's A-box). You can efficiently code Phenoscript by using the [VS Code Phenoscript extension](https://marketplace.visualstudio.com/items?itemName=Tarasov-Lab.phenoscript) that provides syntax highlighting and snippet support. It can be installed from the Marketplace from within the VS Code. Its GitHub repository can be accessed [here](https://github.com/sergeitarasov/vscode-phenoscript). Afterward, Phenospy can be used to analyze and process the semantic descriptions.\n\n\n\n## What can I do with Phenospy?\n\n- Create snippets based on selected ontologies for writing semantic phenotypes with the VS Code Phenoscript extension.\n- Convert the Phenoscript description into an OWL file.\n- Convert the Phenoscript description into an annotated Natural Language description (Markdown format).\n- Automatically compare species and phenotypes (under development).\n\n## Documentation\n\nSee [Wiki for details](https://github.com/sergeitarasov/PhenoScript/wiki).\n\n## Requirements\n\n* `Python >=3.0`\n\nIf you are a new user with Python 2 installed, you should uninstall it and install Python 3 instead. For more information, please refer to [this discussion](https://stackoverflow.com/questions/3819449/how-to-uninstall-python-2-7-on-a-mac-os-x-10-6-4).\n\n\n## Install\nPhenospy can be installed directly from the [PyPI repository](https://pypi.org/project/phenospy/) by running the following command in your terminal (macOS) or a command prompt (Windows):\n\n```{bash}\npip install phenospy\n```\n\n## Issues\n\nSee [issues for details](https://github.com/sergeitarasov/PhenoScript/wiki/Issues).\n",
"bugtrack_url": null,
"license": "MIT",
"summary": "Tools for making and processing computable phenotypes",
"version": "0.250",
"project_urls": {
"Homepage": "https://github.com/sergeitarasov/PhenoScript",
"Project Logo": "https://raw.githubusercontent.com/sergeitarasov/PhenoScript/main/Phenoscript_logo.png"
},
"split_keywords": [],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "e8e7eb578244d192ad4220ca5ceee67ac8cd58c2b5d11997b988d76338214d7d",
"md5": "773016b169e229e7cdbf8e15f43cbfb5",
"sha256": "226b583ead265fd000b856318cce9343e687fc3839fe26c7e995c4f0f7b83258"
},
"downloads": -1,
"filename": "phenospy-0.250-py3-none-any.whl",
"has_sig": false,
"md5_digest": "773016b169e229e7cdbf8e15f43cbfb5",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": null,
"size": 47335,
"upload_time": "2024-08-14T15:07:53",
"upload_time_iso_8601": "2024-08-14T15:07:53.817801Z",
"url": "https://files.pythonhosted.org/packages/e8/e7/eb578244d192ad4220ca5ceee67ac8cd58c2b5d11997b988d76338214d7d/phenospy-0.250-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "3c296e32455f69c170a3f02e67fdacf6b35c0a598b88ccfc8e95567bb4aa887f",
"md5": "f05d100355512ce1cdf43d82ed6ae580",
"sha256": "ea78a7a9b1797f0ee7639a1918f706f50e8e08c78a668f88f47b0101a54711b1"
},
"downloads": -1,
"filename": "phenospy-0.250.tar.gz",
"has_sig": false,
"md5_digest": "f05d100355512ce1cdf43d82ed6ae580",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 39380,
"upload_time": "2024-08-14T15:07:55",
"upload_time_iso_8601": "2024-08-14T15:07:55.411333Z",
"url": "https://files.pythonhosted.org/packages/3c/29/6e32455f69c170a3f02e67fdacf6b35c0a598b88ccfc8e95567bb4aa887f/phenospy-0.250.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2024-08-14 15:07:55",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "sergeitarasov",
"github_project": "PhenoScript",
"travis_ci": false,
"coveralls": false,
"github_actions": false,
"lcname": "phenospy"
}
JSON
