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@github-actions github-actions released this 29 Jan 19:12
· 73 commits to main since this release
v1.0.0
588f63f

1.0.0 (2025-01-29)

Bug Fixes

  • init paths for PyPI (c69a767)
  • add folder for talk2competitors (a6c9a9d)
  • add mkdocs-deploy yml (0729f33)
  • add model validator for the tool model_description (df529b6)
  • add OPENAI_API_KEY as env secrets (1781bdd)
  • add requirements.txt (ce58812)
  • add semantic-release (31751b7)
  • add the toml file for T2B (9ad2b91)
  • add upload otpion and accespt multiple species (724e5b8)
  • bump py to 3.12 for mkdocs (87ef238)
  • change attribute from model_id to biomodel_id to avoid conflicts with langgraph internal namespaces (d2e16d8)
  • change file_id of dataverse (e2f9298)
  • change nested quotes (a89b741)
  • change torch version (9bf8730)
  • chnage pull_request_target to pull_request (87bfca1)
  • conflicts (881704f)
  • delete plot_figure tool (311f03d)
  • downgrade python (5d63e8b)
  • downgrade torch version (c5d49c5)
  • drop half precision option (b4c8eea)
  • drop the half precision (101913b)
  • execute a notebook (2bae5b3)
  • fix yaml file for T2B (bab1fff)
  • further downgrade pytorch (f9da9f4)
  • hotfix to add steady-state tool path to the init of T2B (588f63f)
  • implement DM requests (250830b)
  • make configs agent specific; update toml file (f65b0c8)
  • Merge pull request #48 from VirtualPatientEngine/fix/update-tests (266d34c)
  • Merge pull request #50 from VirtualPatientEngine/fix/update-README (6b8d70f)
  • mkdocs error and update streamlit app (a64c89c)
  • mkdocs-deploy yml (afcc0b8)
  • mkdocs-deploy yml (7d4aa6c)
  • modify coverage (ac06b05)
  • modify coverage over multi-os (9e15375)
  • modify project toml, docs and reqs (9eb4cfb)
  • modify project toml, docs and reqs (86c5cd0)
  • modify workflows (542b38d)
  • remove argument for negative sampling (4b2dd9b)
  • remove bash on workflows (632b625)
  • remove check-path workflows (68a434b)
  • reorganize repo (0ac4f5b)
  • reorganize the dataset loaders (319beca)
  • revert back python version (4255fb3)
  • separate ubuntu and macos code-cov (d4157ab)
  • switch to macos-13 for testing (97a9e0b)
  • the model description tool (ea795cb)
  • toml and req files (0c5995e)
  • update (15acbad)
  • update biobridge (d7e6eb9)
  • update custom_plotter test (746e10e)
  • update docs for talk2kg (87040a7)
  • update errors (830b2a2)
  • update errors (0af71f0)
  • update main pyproject.toml (5c1dec1)
  • update main README (b7345d8)
  • update mkdocs (0c3e70d)
  • update model_description (05821c0)
  • update notebook (b4a58e0)
  • update openai package (af1c8e4)
  • update pull_request event to pull_request_target for T2B (17adde2)
  • update python vesion in the README (efa896d)
  • update pytorch version (3d6593a)
  • update README (34597d5)
  • update release workflow to run only on change in main folder (24093dd)
  • update release.yml (ad7794c)
  • update requirements (fb65d89)
  • update requirements.txt (947ebef)
  • update status badge of tests (d9856f6)
  • update status badge of tests (d5de2b5)
  • update system prompt and mkdocs index page (ca7dbf9)
  • update test_custom_plotter (4655096)
  • update tests (2f05ad1)
  • update tests and tests.yml (3c0754f)
  • update tests for model_description tool (a26494a)
  • update tests for simulate model (3cb153d)
  • update tests.yml (7b3e33c)
  • update the approach to load PrimeKG (d931aab)
  • update tutorials (cad90eb)
  • update workflow for installing reqs (ad48b53)
  • update-tests (7d10752)

Features

  • add a tool for steady state analysis (#77) (9d600e0)
  • add biobridge-primekg loader (27deb4e)
  • add embeddings for starkqa, node info for biobridge (40cce60)
  • add evaluation tutorial using textual embeddings (c020a99)
  • add hydra configs (592d65a)
  • add memory; add tools; update frontend (b925e86)
  • add multimodal embedding alignment tutorial (4651bc4)
  • add no-openai-key msg and feedback buttons and login page (60c7446)
  • add primekg loader tool (2e23586)
  • add protein embedding tutorial (c3010bd)
  • add starkqa-primekg loader tool (989d2c4)
  • add support for parameters (020c375)
  • add tutorials of talk2knowledgegraphs (95c2af0)
  • added back the half precision option (4cdbac4)
  • embeddings (589a878)
  • include processed node information of StarkQA-PrimeKG (2c82016)
  • initial setup for textual embeddings (e5498ab)
  • Merge pull request #25 from VirtualPatientEngine/feat/reorganize (a7771b4)
  • Merge pull request #31 from Rakesh-Seenu/feat/add-mkdocs (04e5b09)
  • parameter scan (#74) (6c6d95d)
  • setup talk2comp (#67) (2fd0b40)
  • simulate and query multiple models (#71) (1da9c0a)
  • t2b langgraph migration (#63) (b72108d)
  • Talk2Biomodels langgraph migration (e07ff50)
  • textual enrichment (#64) (a5920af)
  • update (ec6a797)
  • update gha workflows (783bc33)
  • update mkdocs (0e6c6b8)
  • update mkdocs for talk2knowledgegraphs (29df106)
  • update pytests and docs (4297351)
  • update textual embeddings for starkqa-primekg (4a3adb9)
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