diff --git a/.dockerignore b/.dockerignore index be07f26..54df89a 100644 --- a/.dockerignore +++ b/.dockerignore @@ -22,4 +22,6 @@ tox.ini /src geppetto-client .git -**/__pycache__ \ No newline at end of file +**/__pycache__ +*.log +workspace \ No newline at end of file diff --git a/Dockerfile b/Dockerfile index f8754cd..01f74fe 100644 --- a/Dockerfile +++ b/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 @@ -22,13 +22,15 @@ 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 @@ -36,6 +38,7 @@ WORKDIR $FOLDER # RUN pip install setuptools==45 USER root + RUN python utilities/install.py --npm-skip @@ -43,8 +46,11 @@ 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 diff --git a/nwb-extensions/silverlab/silverlab.namespace.yaml b/nwb-extensions/silverlab/silverlab.namespace.yaml index 2787713..0699a6a 100644 --- a/nwb-extensions/silverlab/silverlab.namespace.yaml +++ b/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' diff --git a/nwb_explorer/__init__.py b/nwb_explorer/__init__.py index fb97266..fd69035 100644 --- a/nwb_explorer/__init__.py +++ b/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() \ No newline at end of file diff --git a/requirements.txt b/requirements.txt index ec71b90..afe9d04 100644 --- a/requirements.txt +++ b/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 diff --git a/setup.py b/setup.py index 0e842d2..0992dc4 100644 --- a/setup.py +++ b/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', ], ) diff --git a/webapp/yarn.lock b/webapp/yarn.lock index 872c880..5b4b600 100644 --- a/webapp/yarn.lock +++ b/webapp/yarn.lock @@ -33,13 +33,6 @@ dependencies: "@babel/highlight" "^7.18.6" -"@babel/code-frame@^7.22.5": - version "7.22.5" - resolved "https://registry.yarnpkg.com/@babel/code-frame/-/code-frame-7.22.5.tgz#234d98e1551960604f1246e6475891a570ad5658" - integrity sha512-Xmwn266vad+6DAqEB2A6V/CcZVp62BbwVmcOJc2RPuwih1kw02TjQvWVWlcKGbBPd+8/0V5DEkOcizRGYsspYQ== - dependencies: - "@babel/highlight" "^7.22.5" - "@babel/compat-data@^7.17.7", "@babel/compat-data@^7.20.1", "@babel/compat-data@^7.20.5": version "7.21.0" resolved "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.21.0.tgz" @@ -76,16 +69,6 @@ "@jridgewell/trace-mapping" "^0.3.17" jsesc "^2.5.1" -"@babel/generator@^7.22.5": - version "7.22.5" - resolved "https://registry.yarnpkg.com/@babel/generator/-/generator-7.22.5.tgz#1e7bf768688acfb05cf30b2369ef855e82d984f7" - integrity sha512-+lcUbnTRhd0jOewtFSedLyiPsD5tswKkbgcezOqqWFUVNEwoUTlpPOBmvhG7OXWLR4jMdv0czPGH5XbflnD1EA== - dependencies: - "@babel/types" "^7.22.5" - "@jridgewell/gen-mapping" "^0.3.2" - "@jridgewell/trace-mapping" "^0.3.17" - jsesc "^2.5.1" - "@babel/helper-annotate-as-pure@^7.18.6": version "7.18.6" resolved "https://registry.npmjs.org/@babel/helper-annotate-as-pure/-/helper-annotate-as-pure-7.18.6.tgz" @@ -93,13 +76,6 @@ dependencies: "@babel/types" "^7.18.6" -"@babel/helper-annotate-as-pure@^7.22.5": - version "7.22.5" - resolved "https://registry.yarnpkg.com/@babel/helper-annotate-as-pure/-/helper-annotate-as-pure-7.22.5.tgz#e7f06737b197d580a01edf75d97e2c8be99d3882" - integrity sha512-LvBTxu8bQSQkcyKOU+a1btnNFQ1dMAd0R6PyW3arXes06F6QLWLIrd681bxRPIXlrMGR3XYnW9JyML7dP3qgxg== - dependencies: - "@babel/types" "^7.22.5" - "@babel/helper-builder-binary-assignment-operator-visitor@^7.18.6": version "7.18.9" resolved "https://registry.npmjs.org/@babel/helper-builder-binary-assignment-operator-visitor/-/helper-builder-binary-assignment-operator-visitor-7.18.9.tgz" @@ -158,11 +134,6 @@ resolved "https://registry.npmjs.org/@babel/helper-environment-visitor/-/helper-environment-visitor-7.18.9.tgz" integrity sha512-3r/aACDJ3fhQ/EVgFy0hpj8oHyHpQc+LPtJoY9SzTThAsStm4Ptegq92vqKoE3vD706ZVFWITnMnxucw+S9Ipg== -"@babel/helper-environment-visitor@^7.22.5": - version "7.22.5" - resolved "https://registry.yarnpkg.com/@babel/helper-environment-visitor/-/helper-environment-visitor-7.22.5.tgz#f06dd41b7c1f44e1f8da6c4055b41ab3a09a7e98" - integrity sha512-XGmhECfVA/5sAt+H+xpSg0mfrHq6FzNr9Oxh7PSEBBRUb/mL7Kz3NICXb194rCqAEdxkhPT1a88teizAFyvk8Q== - "@babel/helper-explode-assignable-expression@^7.18.6": version "7.18.6" resolved "https://registry.npmjs.org/@babel/helper-explode-assignable-expression/-/helper-explode-assignable-expression-7.18.6.tgz" @@ -178,14 +149,6 @@ "@babel/template" "^7.20.7" "@babel/types" "^7.21.0" -"@babel/helper-function-name@^7.22.5": - version "7.22.5" - resolved "https://registry.yarnpkg.com/@babel/helper-function-name/-/helper-function-name-7.22.5.tgz#ede300828905bb15e582c037162f99d5183af1be" - integrity sha512-wtHSq6jMRE3uF2otvfuD3DIvVhOsSNshQl0Qrd7qC9oQJzHvOL4qQXlQn2916+CXGywIjpGuIkoyZRRxHPiNQQ== - dependencies: - "@babel/template" "^7.22.5" - "@babel/types" "^7.22.5" - "@babel/helper-hoist-variables@^7.18.6": version "7.18.6" resolved "https://registry.npmjs.org/@babel/helper-hoist-variables/-/helper-hoist-variables-7.18.6.tgz" @@ -193,13 +156,6 @@ dependencies: "@babel/types" "^7.18.6" -"@babel/helper-hoist-variables@^7.22.5": - version "7.22.5" - resolved "https://registry.yarnpkg.com/@babel/helper-hoist-variables/-/helper-hoist-variables-7.22.5.tgz#c01a007dac05c085914e8fb652b339db50d823bb" - integrity sha512-wGjk9QZVzvknA6yKIUURb8zY3grXCcOZt+/7Wcy8O2uctxhplmUPkOdlgoNhmdVee2c92JXbf1xpMtVNbfoxRw== - dependencies: - "@babel/types" "^7.22.5" - "@babel/helper-member-expression-to-functions@^7.20.7", "@babel/helper-member-expression-to-functions@^7.21.0": version "7.21.0" resolved "https://registry.npmjs.org/@babel/helper-member-expression-to-functions/-/helper-member-expression-to-functions-7.21.0.tgz" @@ -207,7 +163,7 @@ dependencies: "@babel/types" "^7.21.0" -"@babel/helper-module-imports@^7.0.0", "@babel/helper-module-imports@^7.18.6", "@babel/helper-module-imports@^7.22.5": +"@babel/helper-module-imports@^7.18.6": version "7.22.5" resolved "https://registry.yarnpkg.com/@babel/helper-module-imports/-/helper-module-imports-7.22.5.tgz#1a8f4c9f4027d23f520bd76b364d44434a72660c" integrity sha512-8Dl6+HD/cKifutF5qGd/8ZJi84QeAKh+CEe1sBzz8UayBBGg1dAIJrdHOcOM5b2MpzWL2yuotJTtGjETq0qjXg== @@ -240,11 +196,6 @@ resolved "https://registry.npmjs.org/@babel/helper-plugin-utils/-/helper-plugin-utils-7.20.2.tgz" integrity sha512-8RvlJG2mj4huQ4pZ+rU9lqKi9ZKiRmuvGuM2HlWmkmgOhbs6zEAw6IEiJ5cQqGbDzGZOhwuOQNtZMi/ENLjZoQ== -"@babel/helper-plugin-utils@^7.22.5": - 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version "7.22.5" - resolved "https://registry.yarnpkg.com/@babel/plugin-syntax-jsx/-/plugin-syntax-jsx-7.22.5.tgz#a6b68e84fb76e759fc3b93e901876ffabbe1d918" - integrity sha512-gvyP4hZrgrs/wWMaocvxZ44Hw0b3W8Pe+cMxc8V1ULQ07oh8VNbIRaoD1LRZVTvD+0nieDKjfgKg89sD7rrKrg== - dependencies: - "@babel/helper-plugin-utils" "^7.22.5" - "@babel/plugin-syntax-logical-assignment-operators@^7.10.4": version "7.10.4" resolved "https://registry.npmjs.org/@babel/plugin-syntax-logical-assignment-operators/-/plugin-syntax-logical-assignment-operators-7.10.4.tgz" @@ -1019,21 +942,6 @@ resolved "https://registry.npmjs.org/@babel/regjsgen/-/regjsgen-0.8.0.tgz" integrity sha512-x/rqGMdzj+fWZvCOYForTghzbtqPDZ5gPwaoNGHdgDfF2QA/XZbCBp4Moo5scrkAMPhB7z26XM/AaHuIJdgauA== -"@babel/runtime-corejs2@^7.4.5": - version "7.22.6" - resolved "https://registry.yarnpkg.com/@babel/runtime-corejs2/-/runtime-corejs2-7.22.6.tgz#618b2219a7d82fa8fd4213c9e44c3bda7732ecde" - integrity sha512-GTJVRjzQIHUBwRzuWxPII87XoWxXzILBJrQh5gqIV6q6m231Y0BBA9NKta5FV5Lbl8z5gS3+m6YSoKJp0KQJ4g== - 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