runmodels + pyvirtualdisplay (#15)

* runmodels + pyvirtualdisplay
  * add --virtual option to launch everything in a virtual display
  * back-end required (Xvfb)
* CI: use `--virtual` option for `runmodels`
* update docs

Author: alexsavulescu

.github/workflows/nrn-modeldb-ci.yaml

@@ -80,7 +80,7 @@ jobs:
         # Install NEURON V1
         python -m pip install $NEURON_V1
         nrn_ver=`python -c "from neuron import __version__ as nrn_ver; print(nrn_ver)"`
-        runmodels $nrn_ver $MODELS_TO_RUN
+        runmodels --virtual $nrn_ver $MODELS_TO_RUN
         report2html ${nrn_ver}.json
         python -m pip uninstall --yes $NEURON_V1
         echo "nrn1_ver=$nrn_ver" >> $GITHUB_ENV
@@ -91,7 +91,7 @@ jobs:
         # Install NEURON V2
         python -m pip install $NEURON_V2
         nrn_ver=`python -c "from neuron import __version__ as nrn_ver; print(nrn_ver)"`
-        runmodels $nrn_ver $MODELS_TO_RUN
+        runmodels --virtual $nrn_ver $MODELS_TO_RUN
         report2html ${nrn_ver}.json
         python -m pip uninstall --yes $NEURON_V2
         echo "nrn2_ver=$nrn_ver" >> $GITHUB_ENV

README.md

@@ -25,7 +25,8 @@ The following commands are now available:
   runmodels -h
   ```
   Note that models have to be downloaded beforehand with `getmodels`.
-
+  You can specify `--virtual` so that NEURON GUI is run in headless mode. It requires a backend (n.r. `Xvfb`)
+  
 
 * `report2html` -> create an interactive HTML report for a given json report (obtained with `runmodels`)
   ```

modeldb/commands.py

@@ -31,6 +31,7 @@ def runmodels(args=None):
 
     Options:
         --gout                  Include gout into the report. Note that gout data can be very big, so disabled by default.
+        --virtual               Run in headless mode. You need a back-end like Xvfb.
 
     Examples
         runmodels /path/to/workdir
@@ -40,8 +41,17 @@ def runmodels(args=None):
     working_dir = options.pop("<WorkingDirectory>")
     model_ids = [int(model_id) for model_id in options.pop("<model_id>")]
     gout = options.pop("--gout", False)
+    virtual = options.pop("--virtual", False)
 
-    ModelRunManager(working_dir, gout=gout).run_models(model_list=model_ids if model_ids else None)
+    mrm = ModelRunManager(working_dir, gout=gout)
+    model_list = model_ids if model_ids else None
+
+    if virtual:
+        from pyvirtualdisplay import Display
+        with Display() as _:
+            mrm.run_models(model_list)
+    else:
+        mrm.run_models(model_list)
 
 
 def getmodels(args=None):

requirements.txt

@@ -3,6 +3,7 @@ requests
 pyyaml
 docopt
 jinja2
+pyvirtualdisplay
 
 # for running models
 pyqt5