cytocommunity2 0.1.7__tar.gz → 1.0.0__tar.gz

{cytocommunity2-0.1.7 → cytocommunity2-1.0.0}/LICENSE

@@ -1,21 +1,21 @@
-MIT License
-
-Copyright (c) 2026 huBioinfo
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+MIT License
+
+Copyright (c) 2026 huBioinfo
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

{cytocommunity2-0.1.7/src/cytocommunity2.egg-info → cytocommunity2-1.0.0}/PKG-INFO

@@ -1,166 +1,156 @@
-Metadata-Version: 2.4
-Name: cytocommunity2
-Version: 0.1.7
-Summary: Weakly supervised cellular-neighborhood learning for spatial omics
-Requires-Python: >=3.10
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: matplotlib>=3.6
-Requires-Dist: numpy<2,>=1.23
-Requires-Dist: pandas<3,>=1.5
-Requires-Dist: sci-palettes
-Requires-Dist: scikit-learn>=1.1
-Requires-Dist: scipy>=1.11
-Requires-Dist: seaborn>=0.12
-Requires-Dist: torch-geometric>=2.0
-Provides-Extra: downstream
-Requires-Dist: esda<2.6,>=2.5; extra == "downstream"
-Requires-Dist: jupyter; extra == "downstream"
-Requires-Dist: libpysal<4.10,>=4.9; extra == "downstream"
-Dynamic: license-file
-
-# CytoCommunity2
-
-## Contents
-
-- [Overview](#overview)
-- [Installation](#installation)
-- [Usage](#usage)
-- [Maintainers](#maintainers)
-- [Citation](#citation)
-
-## Overview
-
-To enhance CytoCommunity (https://github.com/huBioinfo/CytoCommunity), we
-present CytoCommunity2, **a unified weakly-supervised framework** for
-identifying and comparing tissue cellular neighborhoods (TCNs or CNs) across
-**large-scale spatial omics samples with single or multiple biological
-conditions**.
-
-Inspired by histopathology workflows, CytoCommunity2 first hierarchically
-partitions the large single-cell spatial map into small patches, performs graph
-construction and weakly supervised TCN learning for each patch, and finally
-merges results through KNN-based TCN reassignment at segmentation boundaries to
-ensure TCN spatial continuity. This strategy divides the original sample into
-patches for TCN learning, achieving **memory efficiency (typical 24G graphics
-memory is enough)** and also increased sample throughput. These optimizations
-significantly **enhance the robustness of TCNs and cross-sample alignment
-performance**.
-
-Furthermore, to make CytoCommunity2 a unified framework that is also
-**applicable for single-condition spatial omics datasets**, pseudo-samples with
-artificial labels are generated, enabling automatic TCN alignment across real
-samples via **contrastive learning**.
-
-**_In summary, the advantages of CytoCommunity2 include:_**
-
-**_(1) Using significantly less memory for large-scale spatial omics samples
-with millions of cells._**
-
-**_(2) A unified weakly-supervised model applicable for both multi-condition
-and single-condition datasets._**
-
-**_(3) High TCN alignment performance makes it well-suited for comparative
-analysis in large cohort studies._**
-
-## Installation
-
-### Hardware requirement
-
-Graphics memory: 24G
-
-Storage: 10GB or more
-
-### Install CytoCommunity2
-
-CytoCommunity2 requires Python 3.10 or newer. We recommend creating and
-activating a Conda environment first:
-
-```bash
-conda create -n cytocommunity2 python=3.10
-conda activate cytocommunity2
-```
-
-For an NVIDIA GPU on Windows or Linux, first install the appropriate
-CUDA-enabled PyTorch build from the
-[official PyTorch installation page](https://pytorch.org/get-started/locally/).
-
-Install the package:
-
-```bash
-pip install cytocommunity2
-```
-
-To run the downstream analyses, install the
-optional downstream dependencies with:
-
-```bash
-pip install "cytocommunity2[downstream]"
-```
-
-This extra includes `esda`, `libpysal`, and Jupyter; they are not installed
-by the basic command above.
-
-## Usage
-
-### 1. Prepare input data
-
-The input data to CytoCommunity2 includes four types of files :
-
-(1) An image (sample) name list file, named as "ImageNameList.txt".
-
-(2) A cell type label file for each image (sample), named as "[image
-name]_CellTypeLabel.txt". Note that [image_name] should be consistent with your
-customized image names listed in the "ImageNameList.txt". This file lists cell
-type names of all cells in an image (sample).
-
-(3) A cell spatial coordinate file for each image (sample), named as "[image
-name]_Coordinates.txt". Note that [image_name] should be consistent with your
-customized image names listed in the "ImageNameList.txt". This file lists cell
-coordinates (tab-delimited x/y) of all cells in an image (sample). The cell
-orders should be exactly the same with "[image name]_CellTypeLabel.txt".
-
-(4) A graph label file for each image (sample), named as "[image
-name]_GraphLabel.txt". For multi-condition datasets, this file must be provided
-for every image (sample) and contain one integer indicating its biological
-condition. For single-condition datasets, graph label
-files can be omitted for all images (samples), and CytoCommunity2 will generate
-pseudo-samples for weakly-supervised learning.
-
-### 2. Configure CytoCommunity2
-
-Before running CytoCommunity2, set `input_dir` and review all
-model and downstream parameters in
-[`hyperparameters.json`](https://github.com/LiukangWu/CytoCommunity2/blob/main/hyperparameters.json). The Python workflow will use this configuration file.
-
-### 3. Run CytoCommunity2
-
-The tutorial uses a TNBC dataset as a worked example and demonstrates the
-entire CytoCommunity2 workflow, from model training and CN identification to
-downstream analysis:
-
-```bash
-jupyter notebook tutorial/TNBC_workflow.ipynb
-```
-
-### 4. Output files
-
-The main output directories are:
-
-- `CNLearning_Output/`: CN-number screening, trained models and CN labels.
-- `CNVisualization_Output/`: spatial plots and result tables.
-- `data/`: downstream analysis results and intermediate data tables.
-- `plot/`: figures generated by downstream analyses.
-
-## Maintainers
-
-- Liukang Wu (yetong@stu.xidian.edu.cn)
-- Yafei Xu (22031212416@stu.xidian.edu.cn)
-- Yuxuan Hu (huyuxuan@xidian.edu.cn)
-
-## Citation
-
-Yuxuan Hu, Jiazhen Rong, Yafei Xu, Runzhi Xie, Jacqueline Peng, Lin Gao, and
-Kai Tan. “Unsupervised and supervised discovery of tissue cellular
-neighborhoods from cell phenotypes.” *Nature Methods* 21 (2024): 267–278.
-https://doi.org/10.1038/s41592-023-02124-2
+Metadata-Version: 2.4
+Name: cytocommunity2
+Version: 1.0.0
+Summary: Weakly supervised cellular-neighborhood learning for spatial omics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: esda<2.6,>=2.5
+Requires-Dist: jupyter
+Requires-Dist: libpysal<4.10,>=4.9
+Requires-Dist: matplotlib>=3.6
+Requires-Dist: numpy<2,>=1.23
+Requires-Dist: pandas<3,>=1.5
+Requires-Dist: sci-palettes
+Requires-Dist: scikit-learn>=1.1
+Requires-Dist: scipy>=1.11
+Requires-Dist: seaborn>=0.12
+Requires-Dist: torch-geometric>=2.0
+Dynamic: license-file
+
+# CytoCommunity2
+
+## Contents
+
+- [Overview](#overview)
+- [Installation](#installation)
+- [Usage](#usage)
+- [Maintainers](#maintainers)
+- [Citation](#citation)
+
+## Overview
+
+To enhance CytoCommunity (https://github.com/huBioinfo/CytoCommunity), we
+present CytoCommunity2, **a unified weakly-supervised framework** for
+identifying and comparing tissue cellular neighborhoods (TCNs or CNs) across
+**large-scale spatial omics samples with single or multiple biological
+conditions**.
+
+Inspired by histopathology workflows, CytoCommunity2 first hierarchically
+partitions the large single-cell spatial map into small patches, performs graph
+construction and weakly supervised CN learning for each patch, and finally
+merges results through KNN-based CN reassignment at segmentation boundaries to
+ensure CN spatial continuity. This strategy divides the original sample into
+patches for CN learning, achieving **memory efficiency (typical 24G graphics
+memory is enough)** and also increased sample throughput. These optimizations
+significantly **enhance the robustness of CNs and cross-sample alignment
+performance**.
+
+Furthermore, to make CytoCommunity2 a unified framework that is also
+**applicable for single-condition spatial omics datasets**, pseudo-samples with
+artificial labels are generated, enabling automatic CN alignment across real
+samples via **contrastive learning**.
+
+**_In summary, the advantages of CytoCommunity2 include:_**
+
+**_(1) Using significantly less memory for large-scale spatial omics samples
+with millions of cells._**
+
+**_(2) A unified weakly-supervised model applicable for both multi-condition
+and single-condition datasets._**
+
+**_(3) High CN alignment performance makes it well-suited for comparative
+analysis in large cohort studies._**
+
+## Installation
+
+### Hardware requirement
+
+Graphics memory: 24G
+
+Storage: 10GB or more
+
+### Install CytoCommunity2
+
+CytoCommunity2 requires Python 3.10 or newer. We recommend creating and
+activating a Conda environment first:
+
+```bash
+conda create -n cytocommunity2 python=3.10
+conda activate cytocommunity2
+```
+
+For an NVIDIA GPU on Windows or Linux, first install the appropriate
+CUDA-enabled PyTorch build from the
+[official PyTorch installation page](https://pytorch.org/get-started/locally/).
+
+Install the package via pip:
+
+```bash
+pip install cytocommunity2
+```
+
+## Usage
+
+### 1. Prepare input data
+
+The input data to CytoCommunity2 includes four types of files :
+
+(1) An image (sample) name list file, named as "ImageNameList.txt".
+
+(2) A cell type label file for each image (sample), named as "[image
+name]_CellTypeLabel.txt". Note that [image_name] should be consistent with your
+customized image names listed in the "ImageNameList.txt". This file lists cell
+type names of all cells in an image (sample).
+
+(3) A cell spatial coordinate file for each image (sample), named as "[image
+name]_Coordinates.txt". Note that [image_name] should be consistent with your
+customized image names listed in the "ImageNameList.txt". This file lists cell
+coordinates (tab-delimited x/y) of all cells in an image (sample). The cell
+orders should be exactly the same with "[image name]_CellTypeLabel.txt".
+
+(4) A graph label file for each image (sample), named as "[image
+name]_GraphLabel.txt". For multi-condition datasets, this file must be provided
+for every image (sample) and contain one integer indicating its biological
+condition. For single-condition datasets, graph label
+files can be omitted for all images (samples), and CytoCommunity2 will generate
+pseudo-samples for weakly-supervised learning.
+
+### 2. Configure CytoCommunity2
+
+Before running CytoCommunity2, set `input_dir` and review all
+model and downstream parameters in
+[`hyperparameters.json`](https://github.com/LiukangWu/CytoCommunity2/blob/main/hyperparameters.json). The Python workflow will use this configuration file.
+
+### 3. Run CytoCommunity2
+
+The tutorial uses a TNBC dataset as a worked example and demonstrates the
+entire CytoCommunity2 workflow, from model training and CN identification to
+downstream analysis:
+
+```bash
+jupyter notebook tutorial/TNBC_workflow.ipynb
+```
+
+### 4. Output files
+
+The main output directories are:
+
+- `CNLearning_Output/`: CN-number screening, trained models, and final result
+  tables.
+- `CNVisualization_Output/`: CN and cell-type spatial plots.
+- `data/`: downstream analysis results.
+- `plot/`: figures generated by downstream analyses.
+
+## Maintainers
+
+- Liukang Wu (yetong@stu.xidian.edu.cn)
+- Yafei Xu (22031212416@stu.xidian.edu.cn)
+- Yuxuan Hu (huyuxuan@xidian.edu.cn)
+
+## Citation
+
+Yuxuan Hu, Jiazhen Rong, Yafei Xu, Runzhi Xie, Jacqueline Peng, Lin Gao, and
+Kai Tan. “Unsupervised and supervised discovery of tissue cellular
+neighborhoods from cell phenotypes.” *Nature Methods* 21 (2024): 267–278.
+https://doi.org/10.1038/s41592-023-02124-2