ioNERDSS v2.1.1

Full Changelog: v2.1.0...v2.1.1

ioNERDSS v2.1.0

Major change: add validation suite

Full Changelog: v2.0.4...v2.1.0

ioNERDSS v2.0.4

What's Changed

• Add examples for simularium visualization and OVITO gif generation
• Add MANIFEST.in to include model weights pkl

Full Changelog: v2.0.3...v2.0.4

ioNERDSS v2.0.3

Full Changelog: v2.0.1...v2.0.3

ioNERDSS v2.0.1

Main Changes

• Reworked pdb to NERDSS pipeline. Consult the new "tutorials" for the examples.
• Refactored platonic solids module
• Fix and add more features such as plot average size vs time in analysis module.
• Use graph theory approach to convert pdb to a reaction network to speed up ODE result (but still get super-exponential growth wrt to size so currently the size limited to <= 12 subunits)

Other changes

• Cleanup and restructure repo by @yingyue2030699 in #33
• Update unittest.yml with coverage, caching, OS/version matrix by @jonathanfischer97 in #41
• ovito, imageio, Pillow as optional dependencies by @jonathanfischer97 in #35
• Refactor data analysis logic by @sangmk in #45
• Refactored histogram and copynumber data processing by @sangmk in #47
• Update README.md by @yingyue2030699 in #46
• Attach Simularium converter and ProAffinity by @sangmk in #52
• Bump the pip group across 1 directory with 7 updates by @dependabot[bot] in #77
• Bump huggingface-hub from 0.32.2 to 0.33.2 by @dependabot[bot] in #73
• Bump nvidia-curand-cu12 from 10.3.2.106 to 10.3.10.19 by @dependabot[bot] in #65
• Bump networkx from 3.0 to 3.2.1 by @dependabot[bot] in #64
• Implement graph thoery based model by @yingyue2030699 in #78
• Add math subpackage unittest by @yingyue2030699 in #79
• Implement a new pdb pipeline and refactor old code by @yingyue2030699 in #82
• Adaptive rates gillespie by @sangmk in #84
• simplify dependency and environment management by @jonathanfischer97 in #85
• Merge refactored Plantonic Solid module by @yingyue2030699 in #99

Full Changelog: v1.2.0...v2.0

v1.2.1

Changes

• simplify dependency and environment management @jonathanfischer97 (#85)
• Adaptive rates gillespie @sangmk (#84)
• Add math subpackage unittest @yingyue2030699 (#79)
• Bump networkx from 3.0 to 3.2.1 @dependabot[bot] (#64)
• Bump nvidia-curand-cu12 from 10.3.2.106 to 10.3.10.19 @dependabot[bot] (#65)
• Bump huggingface-hub from 0.32.2 to 0.33.2 @dependabot[bot] (#73)
• Bump the pip group across 1 directory with 7 updates @dependabot[bot] (#77)
• Attach Simularium converter and ProAffinity @sangmk (#52)
• Update README.md @yingyue2030699 (#46)
• Refactored histogram and copynumber data processing @sangmk (#47)
• Refactor data analysis logic @sangmk (#45)
• ovito, imageio, Pillow as optional dependencies @jonathanfischer97 (#35)
• Cleanup and restructure repo @yingyue2030699 (#33)

🚀 Features

• Implement a new pdb pipeline and refactor old code @yingyue2030699 (#82)
• Implement graph thoery based model @yingyue2030699 (#78)
• Update unittest.yml with coverage, caching, OS/version matrix @jonathanfischer97 (#41)

v1.2.0

v1.2.0 (May 28, 2025)

• ODE solver added
• Free energy estimator added
• Codes refactored

v1.1.0

Version 1.1.0 (Mar 22, 2025)

• Refactored the code into nerdss_model, nerdss_simulation, and nerdss_analysis modules.

• Unified figure plotting with the plot_figure() function in the analysis class.

• Added the ability to visualize model structure compared with PDB structure in Jupyter Notebooks using PyMOL.

• Added the ability to visualize trajectories in Jupyter Notebooks using OVITO.

• The previous unrefactored functions are retained in the analysis and model_setup modules for backward compatibility.

• Documentation for the Version 1.1.0 (https://ionerdss.readthedocs.io/en/latest/ionerdss_documentation_v1_1.html)

v1.0.37

v1.0.37

v1.0.36

Update pypi-publish.yml