Merge pull request #512 from MetaCell/release/0.8.0

Release/0.8.0

Author: filippomc

.gitignore

@@ -13,6 +13,7 @@ init.py
 webapp/node_modules
 webapp/geppetto-client
 webapp/build
+webapp/.yalc
 workspace
 netpyne_workspace
 tests/frontend/e2e/node_modules
@@ -24,4 +25,6 @@ utilities/x86_64
 .idea
 *.iml
 x86_64
-.jupyter-config
+.jupyter-config
+venv
+node_modules

Dockerfile

@@ -2,19 +2,23 @@ FROM frodriguez4600/jupyter-neuron:v7.8.0
 ARG INSTALLATION_FOLDER=/home/jovyan/work/NetPyNE-UI
 ARG NETPYNE_VERSION=development
 ARG WORKSPACE_VERSION=nov2020
-ARG JUPYTER_GEPPETTO_VERSION=development
-ARG PYGEPPETTO_VERSION=development
+ARG GEPPETTO_VERSION=development
 ARG BUILD_ARGS=""
 
 USER $NB_USER
 
 ENV INSTALLATION_FOLDER=$INSTALLATION_FOLDER
 ENV NETPYNE_VERSION=$NETPYNE_VERSION
 ENV WORKSPACE_VERSION=$WORKSPACE_VERSION
-ENV JUPYTER_GEPPETTO_VERSION=$JUPYTER_GEPPETTO_VERSION
-ENV PYGEPPETTO_VERSION=$PYGEPPETTO_VERSION
+ENV GEPPETTO_VERSION=$GEPPETTO_VERSION
 ENV BUILD_ARGS=$BUILD_ARGS
 
+# Install openmpi for parallel simulations
+# Important: Have to switch to root to install a package and ensure to switch back to NB user afterwards
+USER root
+RUN apt-get update && apt-get install -y libopenmpi-dev
+USER $NB_USER
+
 WORKDIR /home/jovyan/work
 COPY --chown=1000:1000 requirements.txt ${INSTALLATION_FOLDER}/requirements.txt
 
@@ -24,10 +28,12 @@ RUN pip install -r requirements.txt
 COPY --chown=1000:1000 . .
 WORKDIR ${INSTALLATION_FOLDER}/utilities
 
-RUN python install.py ${BUILD_ARGS}
+RUN npm install --global yarn
+RUN npm install --global yalc
+RUN python install.py ${BUILD_ARGS} --geppetto ${GEPPETTO_VERSION}
 
 WORKDIR ${INSTALLATION_FOLDER}
 
 RUN pip install -r requirements-test.txt
 RUN pytest tests/backend
-CMD /bin/bash -c "jupyter notebook --NotebookApp.default_url=/geppetto --NotebookApp.token='' --library=netpyne_ui --NotebookApp.disable_check_xsrf=True"
+CMD /bin/bash -c "jupyter notebook --NotebookApp.default_url=/geppetto --NotebookApp.token='' --library=netpyne_ui --NotebookApp.disable_check_xsrf=True"

README.md

@@ -7,13 +7,18 @@
 
 ![Screenshot](https://github.com/MetaCell/NetPyNE-UI/raw/documentation/docs/netpyneui.png)
 
-This repository hosts the User Interface for [NetPyNE](http://www.neurosimlab.org/netpyne/). NetPyNE is a python package to facilitate the development, parallel simulation and analysis of biological neuronal networks using the NEURON simulator.
+This repository hosts the User Interface for [NetPyNE](http://www.neurosimlab.org/netpyne/). NetPyNE is a python package
+to facilitate the development, parallel simulation and analysis of biological neuronal networks using the NEURON
+simulator.
 
 ## Install NetPyNE User Interface
 
-Select one option to install the NetPyNE User Interface. 
+Select one option to install the NetPyNE User Interface.
 
-If you are familiar with NEURON and have already NEURON installed in your machine you can proceed using Pip. If you want a container which comes with everything preinstalled including NEURON you can use the Docker image. Using docker you will still be able to mount a local folder which will be your NetPyNE workspace. If you don't have docker installed in your system and you have had troubles installing it you can opt for the Virtual Machine installation.
+If you are familiar with NEURON and have already NEURON installed in your machine you can proceed using Pip. If you want
+a container which comes with everything preinstalled including NEURON you can use the Docker image. Using docker you
+will still be able to mount a local folder which will be your NetPyNE workspace. If you don't have docker installed in
+your system and you have had troubles installing it you can opt for the Virtual Machine installation.
 
 <p align="center">
     <a href="https://github.com/MetaCell/NetPyNE-UI/wiki/Pip-installation"><img src="https://raw.githubusercontent.com/MetaCell/NetPyNE-UI/master/docs/pip_logo.png" alt="Pip" width="70px"/></a>
@@ -57,15 +62,14 @@ For debugging you can use `run.py` instead
 python run.py
 ```
 
-
 ## Run NetPyNE User Interface in Docker
 
 Ensure that you have Docker installed on your system.
 
 Build the image
 
 ```bash
-docker build -t netpyne-ui
+docker build -t netpyne-ui .
 ```
 
 Run the image
@@ -76,8 +80,8 @@ docker run -p 8888:8888 netpyne-ui
 
 ## End-to-end tests
 
-End-to-end tests are located in `tests/deployment/frontend/e2e`. 
-Ensure that the application is running in a blank state, since end-to-end tests interact with the running application.
+End-to-end tests are located in `tests/deployment/frontend/e2e`. Ensure that the application is running in a blank
+state, since end-to-end tests interact with the running application.
 
 Install packages
 
@@ -92,11 +96,9 @@ Start tests
 npm run test
 ```
 
-
 #### Containerized tests
 
-You can also use `docker-compose` to run the tests. 
-Ensure that you have Docker installed on your system.
+You can also use `docker-compose` to run the tests. Ensure that you have Docker installed on your system.
 
 Build the images
 
@@ -111,8 +113,7 @@ Run the tests
 docker-compose up --abort-on-container-exit --exit-code-from netpyne-ui-e2e
 ```
 
-
 ## Additional Notes
 
-NetPyNE-UI is being developed in collaboration with the [Neurosim Lab](http://neurosimlab.org/).
-See the [Wiki](https://github.com/MetaCell/NetPyNE-UI/wiki) for more info!
+NetPyNE-UI is being developed in collaboration with the [Neurosim Lab](http://neurosimlab.org/). See
+the [Wiki](https://github.com/MetaCell/NetPyNE-UI/wiki) for more info!

example.db

@@ -1,6 +1,9 @@
-import logging
 from jupyter_geppetto.webapi import RouteManager
-
 from netpyne_ui import api
+import sentry_sdk
+
+sentry_sdk.init(
+    "https://[email protected]/6"
+)
 
-RouteManager.add_controller(api.NetPyNEController)
+RouteManager.add_controller(api.NetPyNEController)

netpyne_ui/__init__.py

@@ -8,7 +8,7 @@
 from tempfile import TemporaryDirectory
 from jupyter_geppetto.webapi import get, post
 from notebook.base.handlers import IPythonHandler
-from netpyne_ui.constants import NETPYNE_WORKDIR, UPLOAD_FOLDER_NAME, ALLOWED_EXTENSIONS, UPLOAD_FOLDER_PATH
+from netpyne_ui.constants import ALLOWED_EXTENSIONS, UPLOAD_FOLDER_PATH
 
 def allowed_file(filename, allowed_extensions=ALLOWED_EXTENSIONS):
     return '.' in filename and \
@@ -26,7 +26,7 @@ def send_files(handler, file_path, filename):
                 if _buffer:
                     handler.write(_buffer)
                 else:
-                    return 
+                    return
         except:
             handler.set_status(500, f"Error sending files")
 
@@ -39,16 +39,17 @@ def get_file_paths(handler):
         for path in tmp_file_paths:
             if os.path.exists(path):
                 file_paths.append(path)
-    
+
     return file_paths
 
+
 class NetPyNEController:  # pytest: no cover
 
     @post('/uploads')
     def uploads(handler: IPythonHandler):
         files = handler.request.files
         files_saved = 0
-        
+
         if len(files) == 0 or 'file' not in files:
             handler.set_status(400, f"Can't find 'file' or filename is empty. Files received {len(files)}")
         else:
@@ -58,13 +59,13 @@ def uploads(handler: IPythonHandler):
                     logging.warn(f"Can't store file {f.filename}. Extension not allowed")
                     continue
 
-                ## Save to file
+                # Save to file
                 filename = f.filename
                 file_path = os.path.join(UPLOAD_FOLDER_PATH, filename)
-                
+
                 with open(file_path, 'wb') as zf:
                     zf.write(f['body'])
-                
+
                 files_saved += 1
 
                 if filename.endswith('.zip'):
@@ -78,27 +79,24 @@ def uploads(handler: IPythonHandler):
                 elif filename.endswith('.gz'):
                     with gzip.open(file_path, "rb") as gz, open(file_path.replace('.gz', ''), 'wb') as ff:
                         shutil.copyfileobj(gz, ff)
-            
+
             handler.set_status(200, f"Number of files saved: {files_saved}. Number of files sent: {len(files['file'])}")
 
         handler.finish()
-    
+
     @get('/downloads')
     def downloads(handler: IPythonHandler):
-
         file_paths = get_file_paths(handler)
-        
         if file_paths:
-            
             if len(file_paths) == 0:
                 handler.set_status(400, f"Files not found.")
                 handler.finish()
                 return
 
             if len(file_paths) == 1:
                 send_files(handler, file_paths[0], file_paths[0].split('/')[-1])
-                
-            else :
+
+            else:
                 with TemporaryDirectory() as dir_path:
                     tar_gz_file_name = f'{str(uuid.uuid4())}.tar.gz'
                     tar_gz_file_path = os.path.join(dir_path, tar_gz_file_name)
@@ -107,5 +105,5 @@ def downloads(handler: IPythonHandler):
                             tar.add(file_path, os.path.join('download', file_path.split('/')[-1]))
 
                     send_files(handler, tar_gz_file_path, tar_gz_file_name)
-        
+
         handler.finish()

netpyne_ui/api.py

@@ -2,12 +2,21 @@
 
 UPLOAD_FOLDER_NAME = 'uploads'
 NETPYNE_WORKDIR = 'workspace'
+EXPERIMENTS_FOLDER = "experiments"
+MODEL_OUTPUT_FILENAME = 'model_output'
 
-ALLOWED_EXTENSIONS = ["py", "zip", "gz", ".tar.gz", "pdf", "txt", "xls", "png", "jpeg", "hoc"]
+SIMULATION_SCRIPT_NAME = "init.py"
+TEMPLATE_FILENAME_SINGLE_RUN = "run.py"
+TEMPLATE_FILENAME_SINGLE_RUN_INSTANTIATED = "run_instantiated_net.py"
+TEMPLATE_FILENAME_BATCH_RUN = "batch_run_single.py"
+TEMPLATE_FILENAME_BATCH = "batch.py"
+
+ALLOWED_EXTENSIONS = ["py", "zip", "gz", ".tar.gz", "pdf", "txt", "xls", "png", "jpeg", "hoc", "json"]
 HERE = os.path.dirname(os.path.abspath(__file__))
 ROOT = os.path.dirname(HERE)
 UPLOAD_FOLDER_PATH = os.path.join(ROOT, NETPYNE_WORKDIR, UPLOAD_FOLDER_NAME)
 NETPYNE_WORKDIR_PATH = os.path.join(ROOT, NETPYNE_WORKDIR)
+EXPERIMENTS_FOLDER_PATH = os.path.join(ROOT, NETPYNE_WORKDIR, EXPERIMENTS_FOLDER)
 
 if not os.path.exists(NETPYNE_WORKDIR_PATH):
     NETPYNE_WORKDIR_PATH = os.path.join(os.getcwd(), NETPYNE_WORKDIR)