Metadata-Version: 2.4
Name: cellarium-cas
Version: 1.7.3.dev0
Summary: Cellarium Cell Annotation Service client tool
Author-email: Cellarium CAS <cas-support@broadinstitute.org>
License: BSD 3-Clause License
        
        Copyright (c) 2023, Broad Institute
        All rights reserved.
        
        Redistribution and use in source and binary forms, with or without
        modification, are permitted provided that the following conditions are met:
        
        1. Redistributions of source code must retain the above copyright notice, this
           list of conditions and the following disclaimer.
        
        2. Redistributions in binary form must reproduce the above copyright notice,
           this list of conditions and the following disclaimer in the documentation
           and/or other materials provided with the distribution.
        
        3. Neither the name of the copyright holder nor the names of its
           contributors may be used to endorse or promote products derived from
           this software without specific prior written permission.
        
        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
        
Project-URL: Homepage, https://cellarium.ai
Project-URL: Source Code, https://github.com/cellarium-ai/cellarium-cas
Project-URL: Bug Tracker, https://github.com/cellarium-ai/cellarium-cas/issues
Project-URL: Discussion Forum, https://github.com/cellarium-ai/cellarium-cas/discussions
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: Implementation :: CPython
Requires-Python: >=3.7
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: aiohttp[speedups]<4,>=3.8
Requires-Dist: requests<2.33,>=2.31
Requires-Dist: anndata<0.9,>=0.8; python_version < "3.12"
Requires-Dist: anndata<0.13,>=0.10; python_version >= "3.12"
Requires-Dist: numpy<1.26,>=1.21; python_version < "3.12"
Requires-Dist: numpy<2.2,>=2.0; python_version >= "3.12"
Requires-Dist: pandas<2.1,>=1.3; python_version < "3.12"
Requires-Dist: pandas>=2.1; python_version >= "3.12"
Requires-Dist: nest_asyncio~=1.5
Requires-Dist: certifi==2024.7.4
Requires-Dist: Deprecated~=1.2
Requires-Dist: tqdm~=4.66
Requires-Dist: typing_extensions~=4.7.1; python_version < "3.10"
Requires-Dist: typing-extensions<5,>=4.10; python_version >= "3.10"
Requires-Dist: owlready2==0.46; python_version < "3.10"
Requires-Dist: owlready2<=0.50; python_version >= "3.10"
Requires-Dist: networkx<=3.5
Requires-Dist: pydantic==2.5.3; python_version <= "3.7"
Requires-Dist: pydantic==2.9.0; python_version > "3.7"
Provides-Extra: docs
Requires-Dist: Pillow>=10.3.0; extra == "docs"
Requires-Dist: Sphinx~=7.4; extra == "docs"
Requires-Dist: sphinx_gallery~=0.14; extra == "docs"
Requires-Dist: sphinx_rtd_theme~=2.0; extra == "docs"
Requires-Dist: sphinx_substitution_extensions==2024.8.6; extra == "docs"
Requires-Dist: setuptools-git-versioning==2.0.0; extra == "docs"
Requires-Dist: autodoc_pydantic==2.2.0; extra == "docs"
Requires-Dist: nbsphinx; extra == "docs"
Requires-Dist: IPython; extra == "docs"
Provides-Extra: test
Requires-Dist: pytest~=7.3; extra == "test"
Requires-Dist: coverage~=4.5; extra == "test"
Requires-Dist: click~=8.0; extra == "test"
Requires-Dist: mockito>=1.5.0; extra == "test"
Requires-Dist: parameterized>=0.9.0; extra == "test"
Provides-Extra: vis
Requires-Dist: scanpy[leiden]<1.10.0,>=1.9.0; python_version < "3.12" and extra == "vis"
Requires-Dist: scanpy[leiden]<1.12.0,>=1.11.0; python_version >= "3.12" and extra == "vis"
Requires-Dist: biopython==1.85; extra == "vis"
Requires-Dist: plotly; extra == "vis"
Requires-Dist: dash==2.17.1; extra == "vis"
Requires-Dist: dash-bootstrap-components==1.6.0; extra == "vis"
Dynamic: license-file

<img src="https://cellarium.ai/wp-content/uploads/2024/07/cellarium-logo-medium.png" alt="Cellarium Logo" width="180">

# Cellarium Cell Annotation Service (CAS) Client Library
This codebase contains the Python client library for using Cellarium Cell Annotation Service (CAS).

# Installation
The cellarium-cas package officially supports Python versions between 3.7 and 3.12.  We recommend using Python 3.10+.
You can install CAS from PyPI using `pip`. To install the latest version, please run the following command:
```
$ pip install cellarium-cas
```
To install a specific version `version_number`, you can use the following command:
```
$ pip install cellarium-cas==<version_number>
```
If you wish to use visualization features, you can install the package with the visualization extras:
```
$ pip install cellarium-cas[vis]
```

# Obtaining an API Token
You need an API token to use CAS. We are offerring a free public beta program for a limited time to try CAS and explore ways it can enhance your cell biology research. To obtain your unique API token to join the public beta program, please navigate to the CAS webpage at [cellarium.ai](https://cellarium.ai/tool/cellarium-cell-annotation-service-cas/), scroll to the bottom of the page, and [sign up](https://cellarium.ai/cell-annotation-service-cas-access/). We will contact you with your unique API key as soon as the public beta is available.

# Quickstart Tutorial
The fastest way to get started with using CAS is to follow the quickstart tutorial:
[Click here to open the quickstart tutorial on GitHub](notebooks/quickstart_tutorial.ipynb)

It is even easier to go through the quickstart tutorial on Google Colab. Remember, you still need an API key to successfully run through the tutorial:
[Click here to open the quickstart tutorial on Google Colab](https://colab.research.google.com/drive/1m9zgqP5n7E4pGGCg5RjfvlCnS6uqUdSa)

# Documentation
Please visit the project's [ReadTheDocs page](https://cellarium-cas.readthedocs.io/) for additional documentation.
