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CHANGELOG.md

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Change log

[XXXXX] - 2025-XXX-XX

Added:

  • Niche cluster similarity visualization

[1.1.3] - 2025-Jan-15

Changed:

  • Make niche cluster visualization no longer dependent on NT score.

[1.1.2] - 2025-Jan-12

Added:

  • Node size legend in niche cluster connectivities visualization

Changed:

  • Make node color legend optional in niche cluster connectivities visualization

[1.1.1] - 2025-Jan-6

Fixed:

  • Wrong processing for sample name using int

[1.1.0] - 2024-Nov-24

Changed:

  • Make options and modules' name consistent
    • NN/niche network
    • GNN/graph neural network
    • NT/niche trajectory
    • Rename createDataSet to ONTraC_NN
    • Rename NicheTrajectory to ONTraC_NT
    • Rename ONTraC_GP to ONTraC_GT
  • Refine the optparser structures
  • Extract preprocessing modules

[1.0.7] - 2024-Oct-23

Added:

  • Niche cluster connectivity visualization for each sample
  • Node colorbar for cluster connectivity visualization
  • scale factor controlling the size of spatial-based plots
  • N_GCN_LAYERS controlling the number of GCN layers in the model

Changed:

  • Make log file optional for ONTraC_analysis

Fixed:

  • Issues caused ONTraC_GNN still need dataset input

[1.0.6] - 2024-Sep-20

Added:

  • ONTraC_GNN for running GNN only
  • GNN parameters group validation
  • More functions descriptions under GNN part
  • Transparent edges and colorbar for niche cluster connectivities visualization
  • TSP method for Niche Trajectory construction

Changed:

  • rename GP to ONTraC_GP

Fixed:

  • Loading dataset error in NicheTrajectory
  • Log printing error on Windows

[1.0.5] - 2024-Sep-8

Added:

  • Niche trajectory visualization suppression parameter

[1.0.4] - 2024-Sep-3

Added:

  • Integrate mudole with other workflow

[1.0.3] - 2024-Aug-25

Added:

  • GitHub conda building workflow

[1.0.2] - 2024-Aug-21

Added:

  • test module
  • GitHub pytest workflow

[1.0.1] - 2024-July-30

Added:

  • citation info

[1.0.0] - 2024-July-10

Added:

  • N_LOCAL parameter
  • Parameters validation for niche_net_constr

Changed:

  • Support Python 3.10 and 3.12
  • Refined Package structures
  • Change the name of NTScore to NicheTrajectory
  • Skip violinplot about cell type density along NT score in case of more than 100 cell types input

[0.0.9] - 2024-Jun-20

Changed:

  • Make the default value of beta consistent with our paper
  • Update tutorials

Fixed:

  • Input table handling: support int format for sample

[0.0.8] - 2024-Jun-10

Added:

  • Cell type composition visualization suppression parameter
  • Niche cluster loadings visualization suppression parameter

Changed:

  • Instruction for analysis installation
  • Make log file and train loss in analysis part optional
  • Get edge_index directly in niche_net_constr module
  • Make losses name consistent with the paper

Fixed:

  • Incorrect version display

[0.0.7] - 2024-May-13

Added:

  • Citation information
  • New parameter sample in analysis module for plotting by sample
  • Multiple cell type check in input data
  • More detailed log output

Changed:

  • Flexible figure size for some visualization
  • IO options validation and output directories creation logic
  • Device validate and use logic
  • dataset load logic

Fixed:

  • Fixed cell type composition read in analysis
  • SpatialOmicsDataset using old saved data

Removed:

  • Moved example dataset to Zenodo

[0.0.6] - 2024-May-5

Added:

  • Added ONTraC_analysis and analysis module
  • Added niche cluster part in GP.py
  • Added version information at the top of the output

Changed:

  • Update package structures
  • Update imports in createDataSet.py, GP.py, and NTScore.py
  • Update package buildup settings in pyproject.toml and MANIFEST.in

Fixed:

  • Fixed bug in createDataSet.py

[0.0.5] - 2024-Apr-25

Added:

  • Added installation tutorial
  • Added reproducible codes for paper

Changed:

  • Refactored the pyproject.toml according to setuptools
  • Rename losses name to make them consistent with paper

Removed:

  • Removed Unused imports and files
  • Removed setup.py

[0.0.4] - 2024-Apr-16

Added:

  • Added simulation data and tutorial
  • Added niche cluster information output
  • Added niche cluster tutorial
  • Added duplicate Cell_ID handle

Changed:

  • Make this repository public

Fixed:

  • Fixed errors when there is only 1 sample for post-analysis tutorial

[0.0.3] - 2024-Apr-2

Added

  • Added post-analysis tutorial

Changed:

  • Updated dependent packages information
  • Updated installation tutorial
  • Updated stereo-seq example

[0.0.2] - 2024-Mar-12

Added

  • Added package description
  • Added .gitignore to remove unnecessary files
  • Added ONTraC for running all steps together
  • Added NTScore for generating NTScore from GNN output
  • Added pip installation support

Changed:

  • New environment constructions
  • Running process
  • Uniform parameters control
  • Output directories
  • createDataSet generate cell type composition and GNN input from raw input
  • Input data format