1.1.13 (#254)

* add bioc information

* update website

* add crane and docs

* update crane

* update worflow

* update crane

* update workflows

* update workflows

* update workfolw

* update workfolw

* update workfolw

* update workfolw

* Update main.yml

* Update main.yml

* Update main.yml

* fix lioness py

* udpate lioness in R

* include calculations python

* update panda rm missing

* update panda

* update lioness joblib

* revert commits

* ALPACA fix to NAs in community assignement

* version bump

* revert lioness

* update crane with alpaca changes

* update lioness

* update lioness python

* fix test

* update workflows

* put back github actions

* Fixed typo

* Added LIONESS-pearson option + unit test

* changed param labels in LIONESS example

* updated docs for lioness() function

* Update main.yml

* Update main.yml

* Update DESCRIPTION

* fix crane issue #240

* expanded PANDA and LIONESS description

* update crane fix

* added ALPACA, EGRET, and OTTER descriptions

* Update README.md

* typo in na.rm

* update workflow

* update workflow2

* fix-actions-3

* add r lib v2

* add r lib v2

* update condor test

* update condor test

* update condor test

* update condor test

* show testthat output

* add pandoc and use cache

* use built in check

* use built in check

* update actions with built in check

* bump version

* use built in coverage

* use built in coverage

* remove sudo

* update actions

* update actions

* removed sudo from actions

* ugrade to R42

* remove virtualenv

* remove virtualenv

* remove virtualenv

* modify condor test

* update condor test

* update condor test

* adding retiucualte to covr

* adding retiucualte to covr

* add panda test to coverignore

* update actions

* remove lioness tests from coverage

* remove lioness tests from coverage

* added MONSTER and SAMBAR

* remove lionessR test

* Added CONDOR and YARN

* Update README.md

* put back otter in rbuild

* remove condor test

* remove condor test

* remove lioness docs

* add lioness to buildingore

* donttest lionesss

* remove coverage from ubuntu test

* remove rbuilignore

* update rbuildignore

* update rbuildignore

* update rbuildignore

* update rbuildignore

* update rbuildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* add back buildignore

* put back tests

* add padanedge diff test

* add back egeret test

* add monster test

* fix monster test

* tolerance in expect equal

* tolerance in expect equal

* tolerance in expect equal

* tolerance in expect equal

* add sourceppi

* fixed PANDA tests

* modify panda test

* update lioness test

* fix expect message

* update tests

* update tests

* update tests

* update tests

* update tests

* update tests

* reduced lioness test data

* reduced lioness test data

* reduced lioness test data

* reduced lioness test data

* reduce test size

* updating bioc (#250)

* updating bioc

* remove empty lines

* remove empty lines

* update citation

* update citation

* Update README.md

* Update README.md

* Update main.yml

* Update main.yml

* Update .Rbuildignore

* Update .Rbuildignore

* update lioness test

* removed two last lioness tests

* removed two last lioness tests

* removed two last lioness tests

* no saving of lioness networks

* no saving of lioness networks

* no saving of lioness networks

* no saving of lioness networks

* update lioness test

* lower sizeof test

* update test data

* update test data

* update test data

Co-authored-by: Kate Hoff Shutta <kshutta@umass.edu>
Co-authored-by: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>

.github/workflows/main.yml

@@ -26,6 +26,7 @@ on:
 jobs:
   build:
     runs-on: ${{ matrix.os }}
+    timeout-minutes: 300
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
@@ -56,6 +57,12 @@ jobs:
              website
              coverage
 
+      - name: Install blas/lapack
+        run: |
+            La_library()
+            extSoftVersion()["BLAS"]
+        shell: Rscript {0}
+
       - name: Install reticulate
         run: |
             library("reticulate")

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: netZooR
 Type: Package
 Title: Unified methods for the inference and analysis of gene regulatory networks
-Version: 1.1.12
+Version: 1.1.14
 Date: 2022-07-07
 Authors@R: c(person("Marouen", "Ben Guebila",
 			email = "benguebila@hsph.harvard.edu", role = c("aut","cre"), comment = c(ORCID = "0000-0001-5934-966X")),
@@ -77,4 +77,4 @@ VignetteEngine: knitr
 VignetteBuilder: knitr
 RoxygenNote: 7.1.2
 BugReports: https://github.com/netZoo/netZooR/issues
-URL: https://github.com/netZoo/netZooR, https://netzoo.github.io/
+URL: https://github.com/netZoo/netZooR, https://netzoo.github.io/

R/LIONESS.R

@@ -132,8 +132,10 @@ lionessPy <- function(expr_file, motif_file=NULL, ppi_file=NULL, computing="cpu"
    # create an instance named "lioness_obj" of Lioness Class.
    # when save_single_network = TRUE
    if(save_single_network==TRUE){
-   py_run_string(paste("lioness_obj = Lioness(panda_obj", " , " , "computing='", computing, "' , ","start=", start_sample," , ", "end=" ,end_sample, " , " ,'save_single_network= True', " , ", "save_dir='", save_dir, "' , " , "save_fmt='" , save_fmt, "' )",sep = "" ))
-   } else {py_run_string(paste("lioness_obj = Lioness(panda_obj", " , " , "computing='", computing, "' , ","start=", start_sample," , ", "end=" ,end_sample,  ")",sep = "" ))}
+     py_run_string(paste("lioness_obj = Lioness(panda_obj", " , " , "computing='", computing, "' , ","start=", start_sample," , ", "end=" ,end_sample, " , ", "save_dir='", save_dir, "' , " , "save_fmt='" , save_fmt, "' )",sep = "" ))
+   }else{
+     py_run_string(paste("lioness_obj = Lioness(panda_obj", " , " , "computing='", computing, "' , ","start=", start_sample," , ", "end=" ,end_sample,  ")",sep = "" ))
+  }
 
    # retrieve the "total_lioness_network" attribute of instance "lionesss_obj"
    py_run_string("lioness_network = lioness_obj.export_lioness_results",local = FALSE, convert = TRUE)

README.md

@@ -4,7 +4,7 @@
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 <a href="https://netzoo.github.io/netZooR/"><img src="https://img.shields.io/badge/docs-passing-green"></a>
 [![tutorials](https://img.shields.io/badge/netZooR-tutorials-9cf)](https://github.com/netZoo/netZooR/tree/master/vignettes)
-[![netBooks](https://img.shields.io/badge/netZooR-netBooks-ff69b4)](http://netbooks.networkmedicine.org/user/marouenbg/notebooks/Welcome_to_netBooks.ipynb?)
+[![Netbooks](https://img.shields.io/badge/netZooR-Netbooks-ff69b4)](http://netbooks.networkmedicine.org/user/marouenbg/notebooks/Welcome_to_netBooks.ipynb?)
 [![discussions](https://img.shields.io/badge/netZooR-discussions-orange)](https://github.com/netZoo/netZooR/discussions)