fix: run all Hart et al. 2015 tests

SysBioChalmers · Oct 21, 2024 · e56fbe8 · e56fbe8
1 parent e5342bd
commit e56fbe8
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Showing 3 changed files with 12 additions and 3 deletions.
diff --git a/.github/workflows/gene-essentiality.yml b/.github/workflows/gene-essentiality.yml
@@ -37,7 +37,7 @@ jobs:
           fprintf(fid,[repmat('%s,',1,9) '%s\n'],output{:,1});
           fprintf(fid,['%s,%d,%d,%d,%d' repmat(',%.4g',1,5) '\n'],output{:,2:end});
           fclose(fid);
-          disp(cell2table(transpose(output(:,2:end)),"VariableNames",output(:,1)));" | awk 'NR>9 && !/^\.+/') &&
+          disp(cell2table(transpose(output(:,2:end)),"VariableNames",output(:,1)));" &&
           PARSED_RESULTS="${TEST_RESULTS//'%'/'%25'}" &&
           PARSED_RESULTS="${PARSED_RESULTS//$'\n'/'<br>'}" &&
           PARSED_RESULTS="${PARSED_RESULTS//$'\r'/'<br>'}" &&

diff --git a/.github/workflows/macaw-tests.yml b/.github/workflows/macaw-tests.yml
@@ -37,7 +37,16 @@ jobs:
         env:
           PR_NUMBER: ${{ github.event.number }}
         run: sed -i -e "s/[[:digit:]]\{3,4\}\*\* (MACAW)/$PR_NUMBER\*\* (MACAW)/" data/testResults/README.md
-
+
+      - name: Update local branch before committing changes
+        env:
+          BRANCH_NAME: ${{ github.head_ref || github.ref_name }} 
+        run: |
+          git stash
+          git fetch
+          git checkout $BRANCH_NAME
+          git stash pop
+
       - name: Auto-commit results
         uses: stefanzweifel/git-auto-commit-action@v4
         with:

diff --git a/code/test/estimateEssentialGenes.m b/code/test/estimateEssentialGenes.m
@@ -80,7 +80,7 @@
 params = {};
 INIT_output = {};
 
-for i = 1%:length(arrayData.tissues)
+for i = 1:length(arrayData.tissues)
     disp(['Tissue ', num2str(i), ' out of ',  num2str(length(arrayData.tissues)),': ', arrayData.tissues{i}])
 
     % First try to run tINIT with shorter time limit. If it fails, then