Updates and build fixes

.dockerignore

@@ -22,4 +22,6 @@ tox.ini
 /src
 geppetto-client
 .git
-**/__pycache__
+**/__pycache__
+*.log
+workspace

Dockerfile

@@ -13,7 +13,7 @@ RUN yarn build
 RUN rm -Rf node_modules
 
 ###
-FROM jupyter/base-notebook:hub-1.1.0
+FROM jupyter/base-notebook:hub-1.5.0
 ENV NB_UID=jovyan
 ENV FOLDER=nwb-explorer
 USER root
@@ -22,29 +22,35 @@ RUN apt-get update -qq &&\
     apt-get install python3-tk vim nano unzip git g++ -qq
 
 COPY --chown=1000:1000 requirements.txt .   
-RUN pip install -r requirements.txt --no-cache-dir
+RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip &&\ 
+    pip install -r requirements.txt
 USER $NB_UID
-COPY  . $FOLDER 
+
+COPY --chown=$NB_UID:$NB_UID . $FOLDER 
 COPY --from=jsbuild --chown=1000:1000 $FOLDER $FOLDER
 
 WORKDIR $FOLDER
-
+RUN mkdir workspace
 
 
 
 # Temporary fix for deprecated api usage on some requirement
 # RUN pip install setuptools==45
 
 USER root
+
 RUN python utilities/install.py --npm-skip
 
 
 RUN rm -rf /var/lib/apt/lists
 # sym link workspace pvc to $FOLDER
 RUN mkdir -p /opt/workspace
 RUN mkdir -p /opt/home
-RUN chown -R $NB_UID .
-RUN chown -R $NB_UID /opt/*
+# clean workspace from tests
+RUN rm -Rf workspace/* 
+RUN chown $NB_UID app.log
+RUN chown $NB_UID /opt/workspace
+RUN chown $NB_UID /opt/home
 RUN ln -s /opt/workspace ./workspace
 RUN ln -s /opt/home ./workspace
 

nwb-extensions/silverlab/silverlab.namespace.yaml

@@ -6,6 +6,7 @@ namespaces:
   - namespace: core
     neurodata_types:
     - LabMetaData
+    - NWBData
   - source: silverlab.ophys.yaml
   - source: silverlab.metadata.yaml
   version: '0.2'

nwb_explorer/__init__.py

@@ -39,7 +39,9 @@ def init_extensions():
             try:
                 with open(init_file) as f:
                     for line in f:
+                        logging.info("evaluating `%s`", line)
                         eval(line)
             except Exception as e:
                 logging.error("Error evaluating extension init file " + init_file, exc_info=True)
+
 init_extensions()

requirements.txt

@@ -1,13 +1,65 @@
+airspeed==0.5.20
+attrs==19.3.0
+cachetools==0.8.0
+cffi==1.14.0
+cryptography==2.9.2
+cycler==0.10.0
+decorator==4.4.2
+defusedxml==0.6.0
+Deprecated==1.2.10
+entrypoints==0.3
+h5py==3.7.0
+idna==2.9
+ipython-genutils==0.2.0
 imageio==2.5.0
-jupyter_geppetto==1.1.1
-nwbwidgets==0.10.2
-pyecore==0.11.6
-pygeppetto==0.8.0
 ipysheet>=0.5.0
-pynwb==2.3.1
-Pillow==7.1.2
+jedi==0.17.0
+Jinja2==2.11.2
+jsonschema==3.2.0
+jupyter_geppetto==1.1.5
+jupyter-client==7.0.6
+jupyter-core==4.9.1
+jupyter-server==1.11.2
+jupyterhub==1.5.0
+jupyterlab==3.2.4
+jupyterthemes==0.20.0
+kiwisolver==1.2.0
+mistune==0.8.4
+multimethod==1.3
+nbconvert==5.6.1
+nbformat==5.0.6
+ordered-set==4.0.2
+pandocfilters==1.4.2
+parso==0.7.0
+pexpect==4.8.0
+pickleshare==0.7.5
+Pillow>=7.2.0
+prompt-toolkit==3.0.5
+ptyprocess==0.6.0
+pycparser==2.20
+pyecore==0.11.7
+pygeppetto==0.8.1
+Pygments==2.6.1
+pyparsing==2.4.7
+pyrsistent==0.16.0
+python-dateutil==2.8.1
+python-json-logger==0.1.11
+pytz==2020.1
+PyYAML==5.3.1
+pyzmq==19.0.1
+qtconsole==4.7.5
+QtPy==1.9.0
 quantities==0.12.3
-nose==1.3.7
-redis==2.10.6
-seaborn==0.8.1
-uuid==1.30
+RestrictedPython==5.0
+Send2Trash==1.5.0
+terminado==0.8.3
+tornado==6.1.0
+traitlets==4.3.3
+urllib3==1.25.9
+webencodings==0.5.1
+wrapt==1.12.1
+zipp==3.1.0
+jupyter_geppetto==1.1.5
+nwbwidgets==0.11.3
+pygeppetto==0.8.1
+pynwb==2.5.0

setup.py

@@ -43,6 +43,9 @@
         'jupyter_geppetto>=1.1.0',
         'bokeh>=0.13.0',
         'holoviews>=1.10.6',
+        'jupyter-core<5',
+        'jupyter-client<8',
+        'jupyter-server<2',
         'msgpack-python==0.5.6',
         'nose>=1.3.7',
         'Pillow>=7.0.0',
@@ -52,6 +55,6 @@
         'pynwb>=2.3.0',
         'imageio>=2.5.0',
         'quantities>=0.12.3',
-        'nwbwidgets>=0.10.0'
+        'nwbwidgets>=0.10.0',
     ],
 )