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Pull {infra-,}requirements into environment.yml.
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This enables the resolver to evaluate everything at once. Otherwise, if you run pip after conda, it could upgrade things we don't intend to.
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ryanlovett committed Oct 8, 2023
1 parent 9ea65a7 commit de0e669
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9 changes: 3 additions & 6 deletions deployments/datahub/images/default/Dockerfile
Original file line number Diff line number Diff line change
Expand Up @@ -128,18 +128,15 @@ 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

# Set up nbpdf dependencies
ENV PYPPETEER_HOME ${CONDA_DIR}
RUN pyppeteer-install
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203 changes: 201 additions & 2 deletions deployments/datahub/images/default/environment.yml
Original file line number Diff line number Diff line change
Expand Up @@ -91,10 +91,209 @@ 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

# cogsci88;
- 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

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