Test build of updated Dockerfile - make close to version on OSBv2 repo

Author: pgleeson

.github/workflows/docker-netpyne.yml

@@ -0,0 +1,28 @@
+name: Docker Image Build NetPyNE-UI
+
+on:
+  push:
+    branches: [ master, dev*, feature/docker*, feature/repo* ]
+  pull_request:
+    branches: [ master, dev*, feature/docker*, feature/repo* ]
+
+jobs:
+
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Build the Docker image
+      run: |
+        time docker build  -t mynetpyneui -f Dockerfile  .
+        
+    - name: Info on Docker image sizes
+      run: |
+        docker images
+
+    - name: Run the Docker container and list python installs
+      run: |
+        docker run -t --rm --entrypoint /bin/bash mynetpyneui  -c "pip3 list && python -V"

Dockerfile

@@ -1,4 +1,4 @@
-FROM node:18 as jsbuild
+FROM node:18 AS jsbuild
 
 ENV FOLDER=netpyne
 
@@ -12,12 +12,12 @@ COPY webapp .
 RUN yarn build-dev
 
 ### Download on a separate stage to run in parallel with buildkit
-FROM jupyter/base-notebook:hub-1.5.0 as downloads
+FROM quay.io/jupyter/base-notebook:python-3.12 AS downloads
 USER root
 RUN wget --no-check-certificate -O /nyhead.mat https://www.parralab.org/nyhead/sa_nyhead.mat
 
 ###
-FROM jupyter/base-notebook:hub-1.5.0
+FROM quay.io/jupyter/base-notebook:python-3.12
 ENV NB_UID=jovyan
 ENV FOLDER=netpyne
 ENV NP_LFPYKIT_HEAD_FILE=/home/jovyan/nyhead.mat
@@ -28,13 +28,14 @@ RUN rm -rf /var/lib/apt/lists
 RUN apt-get update -qq &&\
     apt-get install python3-tk vim nano unzip git make libtool g++ -qq pkg-config libfreetype6-dev libpng-dev libopenmpi-dev -y
 RUN apt-get install openjdk-11-jre-headless -y
-RUN conda install python=3.7 -y
+RUN apt-get install libxml2-dev libxslt-dev -y
+# RUN conda install python=3.7 -y
 
 
 WORKDIR $FOLDER
 COPY  --chown=1000:1000 requirements.txt requirements.txt
 RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip &&\
-    pip install -r requirements.txt --prefer-binary
+    pip install -r requirements.txt
 
 
 # ToDo: fixme, for now remove the jupyter hub config json file because it overrides the default

requirements-test.txt

@@ -1,3 +1,3 @@
-pytest==4.6.2
-pytest-cov==2.7.1
-tox==3.12.1
+pytest
+pytest-cov
+tox

requirements.txt

@@ -1,101 +1,168 @@
-airspeed==0.5.20
-alembic==1.4.2
-async-generator==1.10
-attrs==19.3.0
-blinker==1.4
-bokeh==2.3.1
-brotlipy==0.7.0
-cachetools==0.8.0
-cffi==1.14.0
-chardet==3.0.4
-cryptography==2.9.2
-cycler==0.10.0
-decorator==4.4.2
-defusedxml==0.6.0
-Deprecated==1.2.10
-entrypoints==0.3
-future==0.18.2
-h5py==3.7.0
-idna==2.9
+aiofiles==22.1.0
+aiosqlite==0.21.0
+airspeed==0.6.0
+anyio==3.7.1
+argon2-cffi==23.1.0
+argon2-cffi-bindings==21.2.0
+arrow==1.3.0
+asttokens==3.0.0
+attrs==25.1.0
+babel==2.17.0
+beautifulsoup4==4.13.3
+bleach==6.2.0
+blosc2==3.1.1
+bokeh
+cachetools==5.5.2
+cattrs==24.1.2
+certifi==2025.1.31
+cffi==1.17.1
+charset-normalizer==3.4.1
+comm==0.2.2
+contourpy==1.3.1
+cycler==0.12.1
+dacite==1.9.2
+debugpy==1.8.12
+decorator==5.2.1
+defusedxml==0.7.1
+Deprecated==1.2.18
+dnspython==2.7.0
+docstring_parser==0.16
+entrypoints==0.4
+executing==2.2.0
+fastjsonschema==2.21.1
+find_libpython==0.4.0
+fonttools==4.56.0
+fqdn==1.5.1
+future==1.0.0
+future-fstrings==1.2.0
+graphviz==0.20.3
+h11==0.14.0
+h5py==3.13.0
+httpcore==1.0.7
+httpx==0.28.1
+idna==3.10
+iniconfig==2.0.0
+ipykernel==6.20.2
+ipython==8.21.0
 ipython-genutils==0.2.0
-ipywidgets==7.5.1
-jedi==0.17.0
+ipywidgets==8.1.5
+isoduration==20.11.0
+jedi==0.19.2
 Jinja2==2.11.2
-jsonpickle==2.1.0
-jsonschema==3.2.0
-jupyter_geppetto==1.1.5
+json5==0.10.0
+jsonpickle==4.0.2
+jsonpointer==3.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2024.10.1
+jupyter==1.1.1
 jupyter-client==7.0.6
-jupyter-core==4.9.1
-jupyter-server==1.11.2
-jupyterhub==1.5.0
-jupyterlab==3.2.4
-neuromllite==0.5.4
+jupyter-console==6.4.4
+jupyter-core==4.12.0
+# jupyter-events==0.12.0
+jupyter-geppetto==1.1.5
+jupyter-server==1.15.0
+jupyter-ydoc==0.2.5
+jupyter_server_ydoc==0.8.0
+jupyterlab==3.3.4
+jupyterlab_pygments==0.3.0
+jupyterlab-server==2.10.3
+jupyterlab_widgets==3.0.13
 jupyterthemes==0.20.0
-kiwisolver==1.2.0
-lesscpy==0.14.0
+kiwisolver==1.4.8
+lesscpy==0.15.1
+LFPykit==0.5.1
 libNeuroML==0.5.1
-lfpykit==0.5.1
-lxml==4.5.1
-Mako==1.1.0
+lxml==5.3.1
 MarkupSafe==1.1.1
-matplotlib
-matplotlib-scalebar
+matplotlib==3.10.0
+matplotlib-inline==0.1.7
+matplotlib-scalebar==0.9.0
+MEAutility==1.5.2
 mistune==0.8.4
-multimethod==1.3
+modelspec==0.3.5
+msgpack==1.1.0
+multimethod==2.0
+nbclassic==0.3.7
+nbclient==0.10.2
 nbconvert==5.6.1
-nbformat==5.0.6
-netpyne==1.0.6
-NEURON==8.2.2
-numpy==1.18.5
-oauthlib==3.0.1
-optuna==2.10.1
-ordered-set==4.0.2
-pamela==1.0.0
-pandas==0.23.4
-pandocfilters==1.4.2
-parso==0.7.0
-pexpect==4.8.0
-pickleshare==0.7.5
-Pillow==7.2.0
+nbformat==5.2.0
+ndindex==1.9.2
+nest-asyncio==1.6.0
+netpyne @ git+https://github.com/Neurosim-lab/netpyne.git@3d633bcda9a3ab3fe4a90b7c705cd3692a729185
+networkx==3.4.2
+neuromllite==0.5.4
+NEURON==8.2.6
+notebook==6.4.5
+notebook_shim==0.2.3
+numexpr==2.10.2
+numpy==1.26.4
+ordered-set==4.1.0
+packaging==24.2
+pandas==2.2.3
+pandocfilters==1.5.1
+parso==0.8.4
+pexpect==4.9.0
+pillow==11.1.0
+platformdirs==4.3.6
+pluggy==1.5.0
 ply==3.11
-prompt-toolkit==3.0.5
-ptyprocess==0.6.0
-pycosat==0.6.3
-pycparser==2.20
-pyecore==0.11.7
-pygeppetto==0.8.1
+prometheus_client==0.21.1
+prompt_toolkit==3.0.50
+psutil==7.0.0
+ptyprocess==0.7.0
+pure_eval==0.2.3
+py==1.11.0
+py-cpuinfo==9.0.0
+pycparser==2.22
+pyecore==0.15.2
+pygeppetto==0.9.0
+Pygments==2.19.1
 PyLEMS==0.5.9
+pymongo==4.11.1
 pyNeuroML==1.0.10
-sentry_sdk==1.5.2
-dacite==1.6.0
-h5py==3.7.0
-jsonpickle==2.1.0
-Pygments==2.6.1
-PyJWT==1.7.1
-pyOpenSSL==19.1.0
-pyparsing==2.4.7
-pyrsistent==0.16.0
-PySocks==1.7.1
-python-dateutil==2.8.1
-python-editor==1.0.4
-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
-RestrictedPython==5.0
-ruamel-yaml==0.15.80
-ruamel.yaml.clib==0.2.0
-scipy==1.4.1
-Send2Trash==1.5.0
-terminado==0.8.3
-testpath==0.4.4
-tornado==6.1.0
-traitlets==4.3.3
-typing-extensions==3.7.4.2
-urllib3==1.25.9
+pyparsing==3.2.1
+pytest==6.2.5
+python-dateutil==2.9.0.post0
+python-json-logger==3.2.1
+pytz==2025.1
+PyYAML==6.0.2
+pyzmq==26.2.1
+referencing==0.36.2
+requests==2.32.3
+RestrictedPython==8.0
+rfc3339-validator==0.1.4
+rfc3986-validator==0.1.1
+rpds-py==0.23.1
+schema==0.7.7
+scipy==1.15.2
+Send2Trash==1.8.3
+sentry-sdk==1.5.2
+setuptools==75.8.0
+six==1.17.0
+sniffio==1.3.1
+soupsieve==2.6
+stack-data==0.6.3
+tables==3.10.2
+tabulate==0.9.0
+terminado==0.18.1
+testpath==0.6.0
+tinycss2==1.4.0
+toml==0.10.2
+tornado==6.1
+tqdm==4.67.1
+traitlets==5.9.0
+types-python-dateutil==2.9.0.20241206
+typing_extensions==4.12.2
+tzdata==2025.1
+uri-template==1.3.0
+urllib3==2.3.0
+wcwidth==0.2.13
+webcolors==24.11.1
 webencodings==0.5.1
-widgetsnbextension==3.5.1
-wrapt==1.12.1
-zipp==3.1.0
+websocket-client==1.8.0
+wheel==0.45.1
+widgetsnbextension==4.0.13
+wrapt==1.17.2
+xyzservices==2025.1.0
+y-py==0.6.2
+ypy-websocket==0.8.4