Devel (#147)

* update test suite (#140) * update test suite * update test suite * update test suite * update test suite * update test suite * update test suite * update test suite * update test suite * update test suite * update test suite * update tests * update actions * update actions * update actions * update actions * update actions * update actions * update actions * update actions * update actions * update actions * update actions * update actions * update actions * update actions * update actions * update actions * update actions * update actions * update ci without spider * update ci without spider * update ci without spider * update ci without spider * update ci without spider * update ci without spider * update ci without spider * update ci without spider * update ci without spider * update workflow * update workflow * update workflow * update workflow * update workflow * update workflow * update workflow * update workflow * update workflow * update workflow * update workflow * update workflow * update workflow * update workflow * update workflow * update actions * update github * update github * update github * update github * update github * update github * update github * fix spider test * update test data with annotation in lioness * changed test data lioness * update test data * update test data * separte process functions * separte process functions * separte process functions * separte process functions * separte process functions * separte process functions * separte process functions * separte process functions * separte process functions * separte process functions * separte process functions * removed macos from tests * fix savepairs (#142) * fix savepairs * fix savepairs * add eye in PPI (#145) * add eye in PPI * update tfcoop * add python gt data * add labels to panda test * expand test data * rename optpanda to boa (#144) * fix typo (#148) * fix typo * update aactions * update aactions * update aactions * update aactions * fix motif saving pairs * fix motif saving pairs * fix motif saving pairs * fix motif saving pairs * Update README.md
netZoo · Jun 28, 2023 · 9a842bc · 9a842bc
1 parent afa8ba3
commit 9a842bc
Show file tree

Hide file tree

Showing 5 changed files with 7 additions and 5 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -28,7 +28,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest]
+        os: [ubuntu-20.04]
 
     steps:
 
@@ -37,9 +37,11 @@ jobs:
           token: ${{ secrets.GITHUB_TOKEN }}
       - name: Set up MATLAB
         uses: matlab-actions/setup-matlab@v1
+        with:
+          release: R2020a
 
       - name: install bedtools ubuntu
-        if: matrix.os == 'ubuntu-latest'
+        if: matrix.os == 'ubuntu-20.04'
         run: |
          wget https://github.com/arq5x/bedtools2/releases/download/v2.29.0/bedtools-2.29.0.tar.gz
          tar -zxvf bedtools-2.29.0.tar.gz

diff --git a/README.md b/README.md
@@ -5,13 +5,13 @@
 [![Documentation Status](https://readthedocs.org/projects/netzoom/badge/?version=latest)](https://netzoom.readthedocs.io/en/latest/?badge=latest)
 [![tutorials](https://img.shields.io/badge/netZooM-tutorials-9cf)](https://github.com/netZoo/netZooM/tree/master/tutorials)
 
-netZooM is tested on: (OS: Ubuntu) X (Language: MATLAB)
+netZooM is tested on: (OS: Ubuntu 20.04) X (Language: MATLAB R2020a)
 
 ## Description
 netZooM is a MATLAB package of network methods.
 
 ## Zoo animals
-(gpu)PANDA, (gpu)LIONESS, (gpu)PUMA, (gpu)SPIDER, optPANDA, and OTTER.
+(gpu)PANDA, (gpu)LIONESS, (gpu)PUMA, (gpu)SPIDER, BOA, and OTTER.
 
 ## Quick guide
 Clone the repository into your local disk:

diff --git a/netZooM/optpanda/createPpiMotifFileLink.m → netZooM/boa/createPpiMotifFileLink.m b/netZooM/optpanda/createPpiMotifFileLink.m → netZooM/boa/createPpiMotifFileLink.m
diff --git a/netZooM/optpanda/generateOptPrior.m → netZooM/boa/generateOptPrior.m b/netZooM/optpanda/generateOptPrior.m → netZooM/boa/generateOptPrior.m
diff --git a/netZooM/tools/PANDA.m b/netZooM/tools/PANDA.m
@@ -47,7 +47,7 @@
 % Outputs:
 %             RegNet   : inferred gene-TF regulatory network
 % Author(s):
-%             Kimberley Glass
+%             Kimberly Glass
 % Publications:
 %               https://doi.org/10.1371/journal.pone.0064832