diff --git a/deployments/datahub/images/default/Dockerfile b/deployments/datahub/images/default/Dockerfile index 667ea3d61..afe797cd2 100644 --- a/deployments/datahub/images/default/Dockerfile +++ b/deployments/datahub/images/default/Dockerfile @@ -128,17 +128,17 @@ RUN /tmp/install-mambaforge.bash # Install conda environment as our user USER ${NB_USER} +COPY infra-requirements.txt /tmp/infra-requirements.txt COPY environment.yml /tmp/environment.yml -RUN mamba env update -p ${CONDA_DIR} -f /tmp/environment.yml && mamba clean -afy +RUN mamba env update -p ${CONDA_DIR} -f /tmp/environment.yml && \ + mamba clean -afy -COPY infra-requirements.txt /tmp/infra-requirements.txt -RUN pip install --no-cache -r /tmp/infra-requirements.txt RUN jupyter contrib nbextensions install --sys-prefix --symlink && \ jupyter nbextensions_configurator enable --sys-prefix -COPY requirements.txt /tmp/requirements.txt -RUN pip install --no-cache -r /tmp/requirements.txt +# Used by MCB32, but incompatible with ipywidgets 8.x +RUN jupyter nbextension enable --py --sys-prefix qgrid # Set up nbpdf dependencies ENV PYPPETEER_HOME ${CONDA_DIR} @@ -161,10 +161,6 @@ RUN /usr/local/sbin/connector-text.bash #COPY connectors/2021-fall-phys-188-288.bash /usr/local/sbin/ #RUN /usr/local/sbin/2021-fall-phys-188-288.bash -# Used by MCB32, but incompatible with ipywidgets 8.x -RUN pip install --no-cache qgrid==1.3.1 -RUN jupyter nbextension enable --py --sys-prefix qgrid - # clear out /tmp USER root RUN rm -rf /tmp/* diff --git a/deployments/datahub/images/default/environment.yml b/deployments/datahub/images/default/environment.yml index 329e44fad..032b7fe8b 100644 --- a/deployments/datahub/images/default/environment.yml +++ b/deployments/datahub/images/default/environment.yml @@ -15,7 +15,7 @@ dependencies: # Base scientific packages that other conda packages we install depend on # We don't want to have conda packages depend on pip packages if possible -- numpy=1.21.* +- numpy=1.22.* - matplotlib=3.7.* - scipy=1.10.0 - ipympl=0.9.* @@ -46,13 +46,13 @@ dependencies: # EPS88, data100 # https://github.com/berkeley-dsep-infra/datahub/issues/1796 # https://github.com/berkeley-dsep-infra/datahub/issues/2824 -- shapely=1.8.* -- cartopy=0.21.* +- shapely==1.8.0 +- cartopy==0.22.0 # ls 88-3; neuro - pillow=8.3.* -# music 30, spring 2022, #3180 +# music 30, spring 2022, https://github.com/berkeley-dsep-infra/datahub/issues/3180 - pysoundfile==0.10.3.post1 # ds100, spring 2022, #3208 @@ -66,8 +66,8 @@ dependencies: - gdown==4.4.0 # LBL summer research internship in materials informatics. Jupyter Book curriculum at https://enze-chen.github.io/mi-book/ -- pymatgen=2022.0.11 -- matminer=0.7.4 +- pymatgen==2023.10.4 +- matminer=0.9.0 # data101, Fall 2022, https://github.com/berkeley-dsep-infra/datahub/issues/3646 - pgspecial=2.0.1 @@ -91,10 +91,213 @@ dependencies: # error converting to PDF https://github.com/berkeley-dsep-infra/datahub/issues/5062 - pyppeteer==1.0.2 +# data8; foundation +- datascience==0.17.6 + +- jupyter-server-proxy==3.2.1 +- jupyter-rsession-proxy==2.0.1 + +- folium==0.12.1.post1 + +# cogsci88; +# disabled 2023-10-07 due to unresolved dependencies +#- ggplot==0.11.5 + +# cogsci131; spring 2018 +- nose==1.3.7 + +# modules +- beautifulsoup4==4.9.3 + +# PS88 https://github.com/berkeley-dsep-infra/datahub/issues/2925 +- linearmodels==4.27 + +# JupyterLab pypi extensions +- jupyterlab-geojson==3.1.2 + +# INDENG 142 Spring 2021 (future semesters as well) - https://github.com/berkeley-dsep-infra/datahub/issues/2314 +- fancyimpute==0.7.0 + +# ESPM 167 - https://github.com/berkeley-dsep-infra/datahub/issues/2278 +- contextily==1.1.0 + +# EPS 256, https://github.com/berkeley-dsep-infra/datahub/issues/1775 +- obspy==1.3.0 + +- otter-grader==4.2.0 + +- gh-scoped-creds==4.1 + - pip: + - -r /tmp/infra-requirements.txt # Econ 148, Spring 2023 https://github.com/berkeley-dsep-infra/datahub/issues/4093 - pycountry-convert==0.7.2 - - otter-grader==4.2.0 - - gh-scoped-creds==4.1 # error converting to PDF https://github.com/berkeley-dsep-infra/datahub/issues/5062 - nbconvert[webpdf] + # + # Former contents of requirements.txt + # Some things were moved up to conda above. + # + # Until https://github.com/okpy/ok-client/pull/473 is merged + - git+https://github.com/yuvipanda/ok-client@6961d778741fe61911be4d00beff9bd8afc1edf7 + # + - jupyter-shiny-proxy==1.1 + # + # nb2pdf==0.6.2 commented out by sknapp 06.10.2023 to unblock https://github.com/berkeley-dsep-infra/datahub/issues/5062 + # + # ls 88-3; neuro + - lxml==4.9.1 + - tqdm==4.62.1 + - mne==0.23.0 + - nibabel==3.2.1 + - h5py==3.7.0 + - numexpr==2.7.3 + - openpyxl==3.0.7 + - nilearn==0.8.0 + + # data100, geog88 + # https://github.com/berkeley-dsep-infra/datahub/issues/2838 + - geopandas==0.10.* + - geopy==2.2.* + - pysal==2.5.* + - rtree==0.9.* + - netcdf4==1.6.* + - mplleaflet==0.0.5 + # phys 151; + - emcee==3.1.0 + - daft==0.1.2 + - corner==2.2.1 + # + # ce88; + - pymdptoolbox==4.0-b3 + # + # data-x; DL + - tensorflow==2.11.1 + - scikit-image==0.19.* + - tables==3.7.0 + - opencv-python==4.6.0.66 + + # astr 128/256; spring 2021 + - astroquery==0.4.6 + - astropy==5.1 + - dustmaps==1.0.9 + - george==0.4.0 + - exoplanet==0.5.2 + - torch==1.13.1 + - torchvision==0.14.1 + - pyvo==1.1 + - joblib==1.3.1 + - theano-pymc==1.1.2 + - pymc3==3.11.2 + + # eep 153; spring 2019 + - requests==2.31.0 + - Pint==0.17 + # Google spreadsheets, Eric Van Dusen / Keeley Takimoto / Modules + - gspread-pandas==2.3.0 + - gspread==4.0.1 + + # eps 109; fall 2019 + - ffmpeg-python==0.2.0 + + # data 88e; spring 2021 + - plotly==5.2.1 + - mpmath==1.3.0 + # sympy==1.6.2 + - chart-studio==1.1.0 + - csaps==1.1.0 + - nbforms==0.5.1 + + # issue #875, global 150Q/pacs 190 - fall 2019 + - wordcloud==1.8.1 + + # issue #929, SW 282 - fall 2019 + - pyreadstat==1.1.2 + + # issue 954, EPS24 - fall 2019 + - xarray==0.19.0 + + # issue 1001, Physics 188/288 - fall 2019 + - umap-learn==0.5.1 + - hdbscan==0.8.31 + + # espm 125/bio 105; fall 2019 + # see https://github.com/berkeley-dsep-infra/datahub/issues/1796 + - bitarray==2.3.0 + - nlmpy==1.0.1 + + # physics 188/288 fall, 2019 + - getdist==1.3.1 + - tensorflow-hub==0.12.0 + - tensorflow-probability==0.13.0 + + # cs16A/B, spring 2020 + - lcapy==0.96 + + # ds198 mch infodemiology, fall 2020/spring 2021 + # google apis + - google-api-python-client==2.15.0 + - google-auth-httplib2==0.1.0 + - google-auth-oauthlib==0.4.5 + - google==3.0.0 + + # issue 1847; LS 22 spring 2021 + - graphviz==0.17 + + # issue #1903, data h195A fall 2020 + - habanero==0.7.4 + + # https://github.com/berkeley-dsep-infra/datahub/issues/1981 + - ipycanvas==0.9.0 + + # data100 scientific packages + - ray==1.13.* + - xlrd==2.0.1 + + # data100 visualization + - colorlover==0.3.0 + - cufflinks==0.17.3 + - altair==4.1.0 + + # data100 tools to access things + - tweepy==3.10.0 + - pytz==2021.1 + - psycopg2==2.9.1 + + # data100 teaching + - jassign==0.0.7 + - dsassign==0.0.8 + + # data102 + - dask==2021.10.0 + - distributed==2021.10.0 + - keras-applications==1.0.8 + - keras-preprocessing==1.1.2 + - keras==2.11.0 + - keras-vis==0.4.1 + - plotly-express==0.4.1 + - cytoolz==0.11.0 + - pyro-ppl==1.7.0 + - lime==0.2.0.1 + - shap==0.39.0 + + # prob140 2021 Spring + - prob140==0.4.1.5 + - sympy==1.8 + + # IB 105 / ESPM 125, Fall 2021 - https://github.com/berkeley-dsep-infra/datahub/issues/2696 + - geonomics==1.3.0 + + # data100, fall 2021 - https://github.com/berkeley-dsep-infra/datahub/issues/2767 + - ipython-sql==0.4.0 + + # data100, fall 2021 - https://github.com/berkeley-dsep-infra/datahub/issues/2875 + - metpy==1.1.0 + - pooch==1.5.2 + + # https://github.com/berkeley-dsep-infra/datahub/issues/2950 + # Needed to work with a new enough version of httplib2 + - httplib2>=0.20.2 + + # Used by MCB32, but incompatible with ipywidgets 8.x + - qgrid==1.3.1 diff --git a/deployments/datahub/images/default/requirements.txt b/deployments/datahub/images/default/requirements.txt.disabled similarity index 100% rename from deployments/datahub/images/default/requirements.txt rename to deployments/datahub/images/default/requirements.txt.disabled