discotoolkit 1.1.3__tar.gz → 1.2.0__tar.gz

discotoolkit-1.2.0/MANIFEST.in

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+include README.md
+include requirements.txt

discotoolkit-1.2.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: discotoolkit
+Version: 1.2.0
+Summary: DISCOtoolkit is an python package that allows users to access data and use the tools provided by the DISCO database.
+Home-page: https://disco.bii.a-star.edu.sg/
+Author: Li Mengwei, Rom Uddamvathanak
+Author-email: uddamvathanak_rom@immunol.a-star.edu.sg
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+Requires-Dist: pandas>=1.4.2
+Requires-Dist: numpy>=1.21.6
+Requires-Dist: scanpy>=1.9.3
+Requires-Dist: scipy>=1.10.1
+Requires-Dist: joblib>=1.1.0
+Requires-Dist: pandarallel>=1.6.5
+Requires-Dist: requests>=2.28.1
+Requires-Dist: colorcet>=3.0.1
+Requires-Dist: leidenalg
+Requires-Dist: h5py>=3.8
+Requires-Dist: matplotlib>=3.5
+Requires-Dist: seaborn>=0.12
+Dynamic: author
+Dynamic: author-email
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+<!--
+ * @Descripttion: 
+ * @version: 
+ * @Author: Mengwei Li
+ * @Date: 2023-04-16 21:20:42
+ * @LastEditors: Mengwei Li
+ * @LastEditTime: 2023-04-16 21:22:03
+-->
+[![Documentation Status](https://readthedocs.org/projects/discotoolkit-py/badge/?version=latest)](https://discotoolkit-py.readthedocs.io/en/latest/?badge=latest) [![Downloads](https://static.pepy.tech/personalized-badge/discotoolkit?period=total&units=international_system&left_color=black&right_color=orange&left_text=Downloads)](https://pepy.tech/project/discotoolkit) [![PyPI version](https://img.shields.io/pypi/v/discotoolkit)](https://pypi.org/project/discotoolkit)
+
+# DISCOtoolkit 1.2.0
+
+DISCOtoolkit is a Python package for accessing the data and tools of the [DISCO database](https://disco.bii.a-star.edu.sg/) (DISCO v1). Read the documentation at [discotoolkit-py.readthedocs.io](https://discotoolkit-py.readthedocs.io/en/latest/).
+
+- Filter and download DISCO data based on sample metadata and cell type information
+- Gene search: a gene's expression across cell types and tissues
+- CELLiD: cell type annotation
+- scEnrichment: gene set enrichment using DISCO DEGs
+
+> **DISCO v1 and v2.** The toolkit talks to **DISCO v1** by default. DISCO v2 has its own R package ([DISCOtoolkit](https://github.com/JinmiaoChenLab/DISCOtoolkit)); the Python package can still be pointed at a v2 server, see [Choosing a server](#choosing-a-server).
+
+## Quickstart (Google Colab)
+
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/JinmiaoChenLab/DISCOtoolkit_py/blob/main/docs/quickstart_disco_v1.ipynb)
+
+Installs, checks the server, filters, downloads and plots in about ten cells, with nothing to set up locally.
+
+## Installation
+
+Python 3.9 or newer. In your current environment:
+
+```
+pip install discotoolkit
+```
+
+To try the latest development version straight from GitHub:
+
+```
+pip install "git+https://github.com/JinmiaoChenLab/DISCOtoolkit_py.git"
+```
+
+To work on the code, or to test changes before they are released, install from a local clone. `-e` links the install to the folder, so edits take effect without reinstalling:
+
+```
+git clone https://github.com/JinmiaoChenLab/DISCOtoolkit_py.git
+cd DISCOtoolkit_py
+pip install -e .
+```
+
+`pip install discotoolkit` and a local install give the same code when the versions match. The difference is the source: PyPI delivers a released, packaged copy, while a local install uses the files in your folder.
+
+Dependencies (installed automatically): numpy, pandas, scanpy, scipy, joblib, pandarallel, requests, colorcet, leidenalg, h5py, matplotlib, seaborn.
+
+We recommend a virtual environment, for example with miniconda:
+
+```
+conda create --name disco python=3.10
+conda activate disco
+conda install ipykernel
+python -m ipykernel install --user --name disco --display-name "disco"
+python -m pip install -U discotoolkit
+```
+
+## Choosing a server
+
+```python
+import discotoolkit as dt
+
+dt.get_server()                       # 'https://disco.bii.a-star.edu.sg/disco_v3_api/'  (DISCO v1, the default)
+dt.set_server("v2")                   # DISCO v2
+dt.set_server("https://my.server/disco_v3_api/")   # any server with the same API
+```
+
+or set the `DISCO_API_URL` environment variable before importing the package.
+
+## Testing
+
+Two small test files need nothing beyond `requests`, so they run anywhere, including Colab:
+
+```
+python tests/test_settings.py           # offline: server selection logic
+python tests/test_version.py            # offline: setup.py and __init__.py agree on the version
+python tests/test_server_contract.py    # online: does the server answer everything the toolkit needs?
+python tests/test_server_contract.py https://immunesinglecell.org/disco_v3_api/   # check another server
+```
+
+GitHub Actions runs these, and installs the package on Python 3.9-3.12, on every push. Maintainers: see [RELEASING.md](RELEASING.md) for how a release is published.
+
+`test_server_contract.py` checks status codes and the shape of each response (the columns and file types the toolkit reads). It only samples the large reference files, it does not download them.
+
+## Basic Usage
+Example in Jupyter notebook.
+
+<em>please select disco as the kernel for running the jupyter notebook</em>
+
+### [Quickstart for DISCO v1](https://github.com/JinmiaoChenLab/DISCOtoolkit_py/blob/main/docs/quickstart_disco_v1.ipynb)
+
+### [Filter and download DISCO data](https://github.com/JinmiaoChenLab/DISCOtoolkit_py/blob/main/docs/download_data.ipynb)
+
+### [Cell Type Annotation using CELLiD](https://github.com/JinmiaoChenLab/DISCOtoolkit_py/blob/main/docs/CELLiD_celltype_annotation.ipynb)
+
+### [scEnrichment](https://github.com/JinmiaoChenLab/DISCOtoolkit_py/blob/main/docs/scEnrichment.ipynb)
+
+## Citation
+1. [Li, Mengwei, et al. "DISCO: a database of Deeply Integrated human Single-Cell Omics data." Nucleic acids research 50.D1 (2022): D596-D602.](https://academic.oup.com/nar/article/50/D1/D596/6430491)
+2. [Mengwei Li, Kok Siong Ang, Brian Teo, Uddamvathanak Rom, Minh N Nguyen, Sebastian Maurer-Stroh, Jinmiao Chen. "Rediscovering publicly available single-cell data with the DISCO platform." Nucleic Acids Research (2024): gkae1108](https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae1108/7899529)
+
+## Follow us on our social media!
+- [HSCRM2](https://twitter.com/HSCRM2)
+- [JinmiaoChenLab Github repo](https://github.com/JinmiaoChenLab)

discotoolkit-1.2.0/README.md

@@ -0,0 +1,110 @@
+<!--
+ * @Descripttion: 
+ * @version: 
+ * @Author: Mengwei Li
+ * @Date: 2023-04-16 21:20:42
+ * @LastEditors: Mengwei Li
+ * @LastEditTime: 2023-04-16 21:22:03
+-->
+[![Documentation Status](https://readthedocs.org/projects/discotoolkit-py/badge/?version=latest)](https://discotoolkit-py.readthedocs.io/en/latest/?badge=latest) [![Downloads](https://static.pepy.tech/personalized-badge/discotoolkit?period=total&units=international_system&left_color=black&right_color=orange&left_text=Downloads)](https://pepy.tech/project/discotoolkit) [![PyPI version](https://img.shields.io/pypi/v/discotoolkit)](https://pypi.org/project/discotoolkit)
+
+# DISCOtoolkit 1.2.0
+
+DISCOtoolkit is a Python package for accessing the data and tools of the [DISCO database](https://disco.bii.a-star.edu.sg/) (DISCO v1). Read the documentation at [discotoolkit-py.readthedocs.io](https://discotoolkit-py.readthedocs.io/en/latest/).
+
+- Filter and download DISCO data based on sample metadata and cell type information
+- Gene search: a gene's expression across cell types and tissues
+- CELLiD: cell type annotation
+- scEnrichment: gene set enrichment using DISCO DEGs
+
+> **DISCO v1 and v2.** The toolkit talks to **DISCO v1** by default. DISCO v2 has its own R package ([DISCOtoolkit](https://github.com/JinmiaoChenLab/DISCOtoolkit)); the Python package can still be pointed at a v2 server, see [Choosing a server](#choosing-a-server).
+
+## Quickstart (Google Colab)
+
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/JinmiaoChenLab/DISCOtoolkit_py/blob/main/docs/quickstart_disco_v1.ipynb)
+
+Installs, checks the server, filters, downloads and plots in about ten cells, with nothing to set up locally.
+
+## Installation
+
+Python 3.9 or newer. In your current environment:
+
+```
+pip install discotoolkit
+```
+
+To try the latest development version straight from GitHub:
+
+```
+pip install "git+https://github.com/JinmiaoChenLab/DISCOtoolkit_py.git"
+```
+
+To work on the code, or to test changes before they are released, install from a local clone. `-e` links the install to the folder, so edits take effect without reinstalling:
+
+```
+git clone https://github.com/JinmiaoChenLab/DISCOtoolkit_py.git
+cd DISCOtoolkit_py
+pip install -e .
+```
+
+`pip install discotoolkit` and a local install give the same code when the versions match. The difference is the source: PyPI delivers a released, packaged copy, while a local install uses the files in your folder.
+
+Dependencies (installed automatically): numpy, pandas, scanpy, scipy, joblib, pandarallel, requests, colorcet, leidenalg, h5py, matplotlib, seaborn.
+
+We recommend a virtual environment, for example with miniconda:
+
+```
+conda create --name disco python=3.10
+conda activate disco
+conda install ipykernel
+python -m ipykernel install --user --name disco --display-name "disco"
+python -m pip install -U discotoolkit
+```
+
+## Choosing a server
+
+```python
+import discotoolkit as dt
+
+dt.get_server()                       # 'https://disco.bii.a-star.edu.sg/disco_v3_api/'  (DISCO v1, the default)
+dt.set_server("v2")                   # DISCO v2
+dt.set_server("https://my.server/disco_v3_api/")   # any server with the same API
+```
+
+or set the `DISCO_API_URL` environment variable before importing the package.
+
+## Testing
+
+Two small test files need nothing beyond `requests`, so they run anywhere, including Colab:
+
+```
+python tests/test_settings.py           # offline: server selection logic
+python tests/test_version.py            # offline: setup.py and __init__.py agree on the version
+python tests/test_server_contract.py    # online: does the server answer everything the toolkit needs?
+python tests/test_server_contract.py https://immunesinglecell.org/disco_v3_api/   # check another server
+```
+
+GitHub Actions runs these, and installs the package on Python 3.9-3.12, on every push. Maintainers: see [RELEASING.md](RELEASING.md) for how a release is published.
+
+`test_server_contract.py` checks status codes and the shape of each response (the columns and file types the toolkit reads). It only samples the large reference files, it does not download them.
+
+## Basic Usage
+Example in Jupyter notebook.
+
+<em>please select disco as the kernel for running the jupyter notebook</em>
+
+### [Quickstart for DISCO v1](https://github.com/JinmiaoChenLab/DISCOtoolkit_py/blob/main/docs/quickstart_disco_v1.ipynb)
+
+### [Filter and download DISCO data](https://github.com/JinmiaoChenLab/DISCOtoolkit_py/blob/main/docs/download_data.ipynb)
+
+### [Cell Type Annotation using CELLiD](https://github.com/JinmiaoChenLab/DISCOtoolkit_py/blob/main/docs/CELLiD_celltype_annotation.ipynb)
+
+### [scEnrichment](https://github.com/JinmiaoChenLab/DISCOtoolkit_py/blob/main/docs/scEnrichment.ipynb)
+
+## Citation
+1. [Li, Mengwei, et al. "DISCO: a database of Deeply Integrated human Single-Cell Omics data." Nucleic acids research 50.D1 (2022): D596-D602.](https://academic.oup.com/nar/article/50/D1/D596/6430491)
+2. [Mengwei Li, Kok Siong Ang, Brian Teo, Uddamvathanak Rom, Minh N Nguyen, Sebastian Maurer-Stroh, Jinmiao Chen. "Rediscovering publicly available single-cell data with the DISCO platform." Nucleic Acids Research (2024): gkae1108](https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae1108/7899529)
+
+## Follow us on our social media!
+- [HSCRM2](https://twitter.com/HSCRM2)
+- [JinmiaoChenLab Github repo](https://github.com/JinmiaoChenLab)