fix: bugs preventing the pipeline to run

.github/workflows/automation.yml

@@ -1,6 +1,9 @@
 name: automation
 
 on:
+  push:
+    branches-ignore:
+        - "update/**"
   schedule:
     - cron: '3 2 1 * *'
 
@@ -10,12 +13,12 @@ jobs:
     timeout-minutes: 1200
 
     steps:
-    - name: Clone repository on current branch
-      run: |
-        rm -rf *
-        git clone https://github.com/$GITHUB_REPOSITORY --branch ${GITHUB_REF#refs/heads/} latest-ecModels
+      - name: Clone repository on current branch
+        run: |
+          rm -rf *
+          git clone https://github.com/$GITHUB_REPOSITORY --branch ${GITHUB_REF#refs/heads/} latest-ecModels
 
-    - name: Run the pipeline
-      run: |
-        cd latest-ecModels
-        python3 run.py ${GITHUB_REF#refs/heads/}
+      - name: Run the pipeline
+        run: |
+          cd latest-ecModels
+          python3 run.py ${GITHUB_REF#refs/heads/}

config.ini

@@ -1,6 +1,6 @@
 [BASE]
 url = https://github.com/SysBioChalmers/ecModels
-pull_request_target = master
+pull_request_target = main
 install_dir = /home/m/ecModels-dependencies/
 
 [MATLAB]
@@ -23,8 +23,8 @@ install_dir = libSBML/
 
 [Gurobi]
 url = https://www.gurobi.com/downloads/gurobi-software/
-version = v9.1.1
-install_dir = gurobi/
+version = v9.5.1
+install_dir = gurobi951/
 
 [GECKO]
 url = https://github.com/SysBioChalmers/GECKO
@@ -35,8 +35,8 @@ branch = master
 [ecYeastGEM]
 type = 'gem'
 url = https://github.com/SysBioChalmers/yeast-GEM
-download_url = 
-model_filename = /ModelFiles/mat/yeastGEM.mat
+download_url =
+model_filename = /model/yeast-GEM.mat
 mat_model = .model
 install_dir = yeast-GEM
 version = v8.3.1
@@ -45,18 +45,18 @@ database_tag = sce
 [eciYali]
 type = 'gem'
 url = https://github.com/SysBioChalmers/Yarrowia_lipolytica_W29-GEM
-download_url = 
-model_filename = /ModelFiles/mat/iYali.mat
+download_url =
+model_filename = /model/iYali.mat
 mat_model = .model
 install_dir = Yali-GEM
 version = v0
 database_tag = yli
 
 [eciSM966]
 type = 'gem'
-url = https://github.com/SysBioChalmers/Kluyveromyces_marxianus-GEM
-download_url = 
-model_filename = /modelFiles/mat/Kluyveromyces_marxianus-GEM.mat
+url = 
+download_url = https://raw.githubusercontent.com/SysBioChalmers/Kluyveromyces_marxianus-GEM/master/modelFiles/mat/Kluyveromyces_marxianus-GEM.mat
+model_filename = /Kluyveromyces_marxianus-GEM.mat
 mat_model = .model
 install_dir = iSM966
 version = v0

ecHumanGEM/scripts/changeMedia_batch.m

@@ -116,7 +116,7 @@
     unusedMets = [];
     for i=1:length(mediaComps)
         %Get metabolite indx
-        metIndx = getIndexes(model,strcat(mediaComps{i},'[s]'),'metcomps');
+        metIndx = getIndexes(model,strcat(mediaComps{i},'[e]'),'metcomps');
         %Get rxns for metabolite
         metRxns = find(model.S(metIndx,:));
         %Get the uptake reaction for the metabolite

tools.py

@@ -14,7 +14,7 @@
 DURL = 'download_url'
 IDIR = 'install_dir'
 SCRIPTSDIR = 'scripts'
-PIPELINE_BASE_BRANCH = 'master'
+PIPELINE_BASE_BRANCH = 'main'
 
 logging.basicConfig(level=logging.DEBUG)
 l = logging.getLogger(__name__)
@@ -67,8 +67,8 @@ def mat_model(self, gem):
     def pr_target(self):
         return self.config['BASE']['pull_request_target']
 
-    def git_clone(self, section, branch='master'):
-        cmd = sp.check_output(['git', 'clone', self.config[section][URL], '--depth', '1', '--branch', branch, self.install_dir(section)])
+    def git_clone(self, section, branch=PIPELINE_BASE_BRANCH):
+        cmd = sp.check_output(['hub', 'clone', self.config[section][URL], '--depth', '1', '--branch', branch, self.install_dir(section)])
         l.info(cmd.decode('utf-8'))
 
     def download(self, gem):
@@ -99,15 +99,16 @@ def git_add_and_pr(self, gem, matlab_output):
             cmd = sp.check_output(['git', 'commit', '-m', 'chore: update {} based on {}'.format(gem, self.version(gem))])
             l.info(cmd.decode('utf-8'))
             l.critical('Will push and create PR')
+            cmd = sp.check_output(['git', 'push'])
+            l.info(cmd.decode('utf-8'))
             # Create PR and also push
             pr_filename = "/tmp/githubpr"
             with open(pr_filename, "w") as f:
                 f.write("update {} based on {}\n\n".format(gem, self.version(gem)))
                 f.write("```matlab\n")
                 f.write(matlab_output)
                 f.write("\n```\n")
-            my_env = environ.copy()
-            cmd = sp.check_output(['hub', 'pull-request', '-F', pr_filename, '-b', self.pr_target(), '-p'], env=my_env)
+            cmd = sp.check_output(['gh', 'pr', 'create', '--body-file', pr_filename, '--base', self.pr_target(), '--fill'])
             l.info(cmd.decode('utf-8'))
         except sp.CalledProcessError:
             l.critical('While upgrading {} to {} no changes were detected'.format(gem, self.version(gem)))
@@ -137,7 +138,7 @@ def check_dependencies(self):
                     l.info('{} is still {}'.format(tool, tool_version))
         # Check COBRA, RAVEN, GECKO versions
         self.cleanup('GECKO')
-        self.git_clone('GECKO')
+        self.git_clone('GECKO', self.config['GECKO']['branch'])
         for tool in ['COBRA', 'RAVEN', 'GECKO']:
             tool_version = self.git_tag(tool)
             if tool_version != self.version(tool):