Changes to get the jlab dockerfile building - some should be reverted later

.github/workflows/docker-jupyterlab.yml

@@ -2,9 +2,9 @@ name: Docker Image Build Jupyterlab
 
 on:
   push:
-    branches: [ master, dev*, feature/docker*, jupyterhub-update ]
+    branches: [ master, dev*, feature/docker*, feature/repo*, jupyterhub-update ]
   pull_request:
-    branches: [ master, dev*, feature/docker*, jupyterhub-update ]
+    branches: [ master, dev*, feature/docker*, feature/repo*, jupyterhub-update ]
 
 jobs:
 

.github/workflows/docker-netpyne.yml

@@ -2,9 +2,9 @@ name: Docker Image Build NetPyNE-UI
 
 on:
   push:
-    branches: [ master, dev*, feature/docker*, jupyterhub-update ]
+    branches: [ master, dev*, feature/docker*, feature/repo*, jupyterhub-update ]
   pull_request:
-    branches: [ master, dev*, feature/docker*, jupyterhub-update ]
+    branches: [ master, dev*, feature/docker*, feature/repo*, jupyterhub-update ]
 
 jobs:
 

.github/workflows/docker-nwbe.yml

@@ -2,9 +2,9 @@ name: Docker Image Build NWB Explorer
 
 on:
   push:
-    branches: [ master, dev*, feature/docker*, jupyterhub-update ]
+    branches: [ master, dev*, feature/docker*, feature/repo*, jupyterhub-update ]
   pull_request:
-    branches: [ master, dev*, feature/docker*, jupyterhub-update ]
+    branches: [ master, dev*, feature/docker*, feature/repo*, jupyterhub-update ]
 
 jobs:
 

applications/jupyterlab/Dockerfile

@@ -28,7 +28,7 @@ COPY requirements.txt requirements.txt
 RUN pip install -r requirements.txt --upgrade --no-cache-dir
 
 ####  General Python packages
-RUN jupyter labextension install plotlywidget
+####RUN jupyter labextension install plotlywidget
 
 
 ##############
@@ -105,12 +105,13 @@ ENV PATH=$PATH:$NEST_HOME/bin
 
 USER jovyan
 #### Install Python packages
+RUN pip install backports.tarfile>=1.2 # temp fix for error: ImportError: cannot import name 'tarfile' from 'backports'
 RUN pip install -r requirements.txt --upgrade --no-cache-dir
 
 #  Compile NEURON mod files for PyNN
-RUN cd /opt/conda/lib/python3.9/site-packages/pyNN/neuron/nmodl && nrnivmodl
+RUN cd /opt/conda/lib/python3.12/site-packages/pyNN/neuron/nmodl && nrnivmodl
 # See https://github.com/OpenSourceBrain/osb-model-validation/issues/91 for status of this
-RUN pip install 'numpy<=1.23.0' # temp fix for https://levelup.gitconnected.com/fix-attributeerror-module-numpy-has-no-attribute-float-d7d68c5a4971
+######RUN pip install 'numpy<=1.23.0' # temp fix for https://levelup.gitconnected.com/fix-attributeerror-module-numpy-has-no-attribute-float-d7d68c5a4971
 
 #########################################################################
 # fix for https://github.com/jupyter/notebook/issues/7048

applications/jupyterlab/requirements.txt

@@ -3,7 +3,7 @@ pyelectro
 git+https://github.com/NeuralEnsemble/neurotune.git
 
 ####  NEURON & NetPyNE
-neuron==8.1
+neuron==8.2.4
 
 # Install specific version of NetPyNE
 git+https://github.com/Neurosim-lab/netpyne.git@osbv2#egg=netpyne
@@ -42,13 +42,13 @@ seaborn
 
 # Note: this just installs pytorch for cpu, the default install adds a v large cuda lib
 -f https://download.pytorch.org/whl/torch_stable.html
-torch==2.1.2+cpu
+torch==2.2.0+cpu
 
 # For MDF
-modeci_mdf==0.4.8 # big jump in size of image...
+#########modeci_mdf==0.4.8 # big jump in size of image...
 
 scikit-learn # Required for some Neuromatch Academy material
-fasttext # Required for some Neuromatch Academy material
+#########fasttext # Required for some Neuromatch Academy material
 
 
 ####  TVB etc.

libraries/client/biomodels_info.py

@@ -0,0 +1,107 @@
+"""
+Script to get Biomodels project info
+"""
+
+import json
+import pprint
+from loadbiomodels import get_model_identifiers, get_model_info
+
+verbose = True  #
+verbose = False
+
+info_all = {}
+
+
+if __name__ == "__main__":
+    min_index = 0
+    max_index = 20
+    index = 0
+
+    from loadbiomodels import get_model_identifiers
+
+    model_ids = get_model_identifiers()["models"]
+
+    selection = model_ids[min_index:max_index]
+
+    for model_id in selection:
+        print(
+            "\n--------   Model (%i/%i, order %i): %s:\n"
+            % (index, len(selection), index + min_index, model_id)
+        )
+
+        model_link = f"[{model_id}](https://www.ebi.ac.uk/biomodels/{model_id})"
+        info = get_model_info(model_id)
+        model_name = info["name"]
+        print(f"  {model_id}: \n    {pprint.pformat(info['name'])}--")
+
+        info_all[model_id] = info
+        """
+        son.loads(get_page('https://modeldb.science/api/v1/models/%s'%model))
+
+        print('    %s'%info[model]['name'])
+        if 'gitrepo' in info[model] and info[model]['gitrepo']:
+            with_gitrepo+=1
+            print('    gitrepo: %s'%info[model]['gitrepo'])
+        else:
+            print('    gitrepo: %s'%False)
+
+        expected_forks = 0
+        possible_mdb_repo = 'ModelDBRepository/%s'%(info[model]['id'])
+        try:
+            mdb_repo = gh.get_repo(possible_mdb_repo)
+
+            repo_to_use = mdb_repo
+            print('    Exists at: %s (def branch: %s; forks: %i)'%(mdb_repo.html_url, mdb_repo.default_branch, mdb_repo.forks))
+
+            possible_osbgh_repo = 'OpenSourceBrain/%s'%(info[model]['id'])
+            try:
+                osb_repo = gh.get_repo(possible_osbgh_repo)
+                msg = '    Exists at: %s (def branch: %s; forks: %i), order %i'%(osb_repo.html_url, osb_repo.default_branch, osb_repo.forks, index+min_index)
+                on_osbv2.append(msg)
+                print(msg)
+                repo_to_use = osb_repo
+                expected_forks+=1
+
+                info[model]['osbv2_gh_repo'] = repo_to_use.html_url
+                info[model]['osbv2_gh_branch'] = repo_to_use.default_branch
+            except:
+                print('    Missing fork: %s, forking now: %s'%(possible_osbgh_repo, fork_if_missing))
+                if fork_if_missing:
+                    print('    Forking to: %s...'%possible_osbgh_repo)
+                    org = gh.get_organization('OpenSourceBrain')
+                    org.create_fork(mdb_repo,default_branch_only=False)
+                    msg = '    Forked to: %s...'%possible_osbgh_repo
+                    print(msg)
+                    forked_now.append(msg)
+
+                else:
+                    msg = '    Yet to be forked: %i, order %i; %s'%(info[model]['id'], index+min_index,info[model]['name'])
+                    print(msg)
+                    to_be_forked.append(msg)
+
+
+            if (not mdb_repo.forks==expected_forks) and (not (info[model]['id'] in known_to_have_other_forks)):
+                msg = '    Unexpected forks for %i (%s != %s)...'%(info[model]['id'], mdb_repo.forks,expected_forks)
+                print(msg)
+                many_forks.append(msg)
+
+        except:
+            msg = '    Problem locating repo for: %i (%i/%i) %s'%(info[model]['id'],index, len(selection), info[model]['name'])
+            print(msg)
+            errors.append(msg)"""
+
+        index += 1
+
+    if verbose:
+        infop = pprint.pprint(info_all, compact=True)
+
+    print("\nThere were %i models checked\n" % (len(info)))
+
+filename = "cached_info/biomodels.json"
+
+strj = json.dumps(info_all, indent="    ", sort_keys=True)
+with open(filename, "w") as fp:
+    fp.write(strj)
+
+
+print("Data on Biomodels (%i models) written to %s" % (len(info), filename))