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RWR and TieDIE Integration#92

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Lyce24 wants to merge 26 commits intoReed-CompBio:masterReed-CompBio/spras:masterfrom Lyce24:RWR_and_TieDIELyce24/spras:RWR_and_TieDIECopy head branch name to clipboard

+668

Commits

Commits on Jun 9, 2023

• Create Docker Image for random-walk

  

  erikliu

  committed
  ecec5b6

• Implementing src/random_walk.py (questions about the output files)

  

  Erik_L

  committed
  34d3ef3

• Updating Dockerfile and src/random_walk.py (new image and single raw_path_file now)

  

  erikliu

  committed
  aff0893

• Make RWWR working (change Dockerfile for current random-walk-with-restart repo; with the modified output file, implemented the parsing function; met one error about Snakemake checking pathway.txt; …

  Show description for 5755c62
  

  Erik_L

  committed
  5755c62

• Make the program running (writing the tests); clean up the codes; update the README; more things to consider: how to select edges for pathway file.

  

  Erik_L

  committed
  13dd12a

• Initiate dockerizing TieDIE repo

  

  Erik_L

  committed
  2e6aaa5

• Dockerize TieDIE and integrate it into SPRAS

  

  Erik_L

  committed
  c214002

• Fixing the format of TieDIE output pathway; need to consider RWwR

  

  Erik_L

  committed
  78036de

Commits on Jun 10, 2023

• Update RandomWalk and TieDIE (add user-defined threshold for RWwR and fixing bugs about running pagerank in TieDIE)

  

  erikliu

  committed
  45d5733

Commits on Jun 16, 2023

• Complete the tests for RWR and TieDIE (test and GitHub actions); add an utility function in src/utils.py (add rank column to a dataframe); updating README for RWR and TieDIE

  

  Erik_L

  committed
  fafbff9

Commits on Jun 21, 2023

• Merge branch 'master' into RWR_and_TieDIE

  agitter

  authored
  c958aa3

• Fixing pre-commit hooks and updating the GitHub Action

  

  Erik_L

  committed
  fe863e0

• Fixing the GitHub Action

  

  Erik_L

  committed
  62fc246

• Updating the Docker Image for RWR and TieDIE

  

  Erik_L

  committed
  becf7bc

Commits on Jun 22, 2023

• Completing changes requested

  

  Erik_L

  committed
  b7d2c94

Commits on Jun 23, 2023

• Renaming random_walk to rwr

  

  Erik_L

  committed
  8e94cf3

Commits on Jun 29, 2023

• Fix a minor bug in workflows/test-spras.yaml (RandomWalk to RWR)

  

  erikliu

  committed
  f467db1

Commits on Jul 4, 2023

• Resolved some issues suggested by Neha (updating configfile; adding pytest -k; Tab issue of RWR); updated parameters for RWR for newer version of RWR

  

  Erik_L

  committed
  7833ea5

Commits on Jul 9, 2023

• Merge branch 'Reed-CompBio:master' into RWR_and_TieDIE

  Lyce24

  authored
  f7f2ba4

Commits on Jul 15, 2023

• Resolved some issues suggested by Tony (pushed the ReedCompBio Docker Images and made suitable changes based on this)

  

  Erik_L

  committed
  53faeb0

• Merge branch 'RWR_and_TieDIE' of https://github.com/Lyce24/spras into RWR_and_TieDIE

  

  Erik_L

  committed
  b7f007f

• Pre-commit check

  

  Erik_L

  committed
  269c14e

Commits on Jul 19, 2023

• Merge branch 'Reed-CompBio:master' into RWR_and_TieDIE

  Lyce24

  authored
  dd75af8

Commits on Jul 21, 2023

• Added single source mode to RWR, updated the input file format for RWR, and updated the config.yaml to add more tests

  

  Erik_L

  committed
  1f5a233

• Updated tests for RWR

  

  Erik_L

  committed
  b2d6a8e

Commits on Jul 22, 2023

• Minor updates for RWR (param updates; test updates)

  

  erikliu

  committed
  4e25538