From 17862cf4724b8e3dd3e56b8e1daf6e388a5515db Mon Sep 17 00:00:00 2001 From: shane knapp Date: Mon, 18 Dec 2023 11:27:04 -0800 Subject: [PATCH 1/2] bump jupyterlab to 4.0.9 --- deployments/a11y/image/infra-requirements.txt | 2 +- .../astro/image/infra-requirements.txt | 2 +- .../biology/image/infra-requirements.txt | 2 +- deployments/cee/image/infra-requirements.txt | 2 +- deployments/data100/image/environment.yml | 3 +- .../data100/image/infra-requirements.txt | 2 +- deployments/data101/image/environment.yml | 2 +- .../data101/image/infra-requirements.txt | 2 +- deployments/data102/image/environment.yml | 2 +- .../data102/image/infra-requirements.txt | 2 +- .../data8/image/infra-requirements.txt | 2 +- .../images/default/environment.yml.bak | 206 ++++++++++++++++++ .../images/default/infra-requirements.txt | 2 +- .../images/default/infra-requirements.txt | 2 +- .../images/secondary/infra-requirements.txt | 2 +- deployments/edx/image/infra-requirements.txt | 31 +++ deployments/eecs/image/infra-requirements.txt | 2 +- .../ischool/image/infra-requirements.txt | 2 +- .../julia/image/infra-requirements.txt | 2 +- .../publichealth/image/infra-requirements.txt | 2 +- .../shiny/image/infra-requirements.txt | 2 +- deployments/stat159/image/environment.yml | 2 +- .../stat159/image/infra-requirements.txt | 2 +- .../stat20/image/infra-requirements.txt | 2 +- scripts/infra-packages/requirements.txt | 2 +- 25 files changed, 260 insertions(+), 24 deletions(-) create mode 100644 deployments/datahub/images/default/environment.yml.bak create mode 100644 deployments/edx/image/infra-requirements.txt diff --git a/deployments/a11y/image/infra-requirements.txt b/deployments/a11y/image/infra-requirements.txt index ca42d16bb..3aaf7f593 100644 --- a/deployments/a11y/image/infra-requirements.txt +++ b/deployments/a11y/image/infra-requirements.txt @@ -9,7 +9,7 @@ # FIXME: Freeze this to get exact versions of all dependencies notebook==6.4.12 -jupyterlab==3.4.5 +jupyterlab==4.0.9 retrolab==0.3.21 nbgitpuller==1.1.0 jupyter-resource-usage==0.6.1 diff --git a/deployments/astro/image/infra-requirements.txt b/deployments/astro/image/infra-requirements.txt index ca42d16bb..3aaf7f593 100644 --- a/deployments/astro/image/infra-requirements.txt +++ b/deployments/astro/image/infra-requirements.txt @@ -9,7 +9,7 @@ # FIXME: Freeze this to get exact versions of all dependencies notebook==6.4.12 -jupyterlab==3.4.5 +jupyterlab==4.0.9 retrolab==0.3.21 nbgitpuller==1.1.0 jupyter-resource-usage==0.6.1 diff --git a/deployments/biology/image/infra-requirements.txt b/deployments/biology/image/infra-requirements.txt index ca42d16bb..3aaf7f593 100644 --- a/deployments/biology/image/infra-requirements.txt +++ b/deployments/biology/image/infra-requirements.txt @@ -9,7 +9,7 @@ # FIXME: Freeze this to get exact versions of all dependencies notebook==6.4.12 -jupyterlab==3.4.5 +jupyterlab==4.0.9 retrolab==0.3.21 nbgitpuller==1.1.0 jupyter-resource-usage==0.6.1 diff --git a/deployments/cee/image/infra-requirements.txt b/deployments/cee/image/infra-requirements.txt index ca42d16bb..3aaf7f593 100644 --- a/deployments/cee/image/infra-requirements.txt +++ b/deployments/cee/image/infra-requirements.txt @@ -9,7 +9,7 @@ # FIXME: Freeze this to get exact versions of all dependencies notebook==6.4.12 -jupyterlab==3.4.5 +jupyterlab==4.0.9 retrolab==0.3.21 nbgitpuller==1.1.0 jupyter-resource-usage==0.6.1 diff --git a/deployments/data100/image/environment.yml b/deployments/data100/image/environment.yml index 90084840a..a06e03c38 100644 --- a/deployments/data100/image/environment.yml +++ b/deployments/data100/image/environment.yml @@ -7,7 +7,7 @@ dependencies: - python==3.11.0 - git==2.39.1 - jupyter-resource-usage==1.0.0 -- jupyterlab==4.0.4 +- jupyterlab==4.0.9 - jupyterlab-favorites==3.0.0 - jupyterlab_server==2.23.0 - jupyterlab_widgets==3.0.8 @@ -18,7 +18,6 @@ dependencies: - h5netcdf==1.0.2 - ipywidgets==8.0.7 - jupysql==0.8.0 -- jupyterlab==4.0.4 - matplotlib==3.7.1 - mdit-py-plugins==0.4.0 - numpy==1.24.2 diff --git a/deployments/data100/image/infra-requirements.txt b/deployments/data100/image/infra-requirements.txt index ca42d16bb..3aaf7f593 100644 --- a/deployments/data100/image/infra-requirements.txt +++ b/deployments/data100/image/infra-requirements.txt @@ -9,7 +9,7 @@ # FIXME: Freeze this to get exact versions of all dependencies notebook==6.4.12 -jupyterlab==3.4.5 +jupyterlab==4.0.9 retrolab==0.3.21 nbgitpuller==1.1.0 jupyter-resource-usage==0.6.1 diff --git a/deployments/data101/image/environment.yml b/deployments/data101/image/environment.yml index 1a7d7aa08..0a2a7584b 100644 --- a/deployments/data101/image/environment.yml +++ b/deployments/data101/image/environment.yml @@ -34,7 +34,7 @@ dependencies: - jupyter-book==0.15.1 - jupyter-resource-usage==1.0.0 - jupyter_bokeh -- jupyterlab==4.0.4 +- jupyterlab==4.0.9 - jupyterlab-favorites==3.0.0 - jupyterlab-geojson==3.2.0 - jupyterlab-variableinspector==3.0.9 diff --git a/deployments/data101/image/infra-requirements.txt b/deployments/data101/image/infra-requirements.txt index ca42d16bb..3aaf7f593 100644 --- a/deployments/data101/image/infra-requirements.txt +++ b/deployments/data101/image/infra-requirements.txt @@ -9,7 +9,7 @@ # FIXME: Freeze this to get exact versions of all dependencies notebook==6.4.12 -jupyterlab==3.4.5 +jupyterlab==4.0.9 retrolab==0.3.21 nbgitpuller==1.1.0 jupyter-resource-usage==0.6.1 diff --git a/deployments/data102/image/environment.yml b/deployments/data102/image/environment.yml index 983266d1c..f3407fce6 100644 --- a/deployments/data102/image/environment.yml +++ b/deployments/data102/image/environment.yml @@ -10,7 +10,7 @@ dependencies: - bambi==0.12.0 - graphviz==8.0.3 - jupyter-resource-usage==1.0.0 -- jupyterlab==4.0.4 +- jupyterlab==4.0.9 - jupyterlab-favorites==3.0.0 - jupyterlab_server==2.23.0 - jupyterlab_widgets==3.0.8 diff --git a/deployments/data102/image/infra-requirements.txt b/deployments/data102/image/infra-requirements.txt index ca42d16bb..3aaf7f593 100644 --- a/deployments/data102/image/infra-requirements.txt +++ b/deployments/data102/image/infra-requirements.txt @@ -9,7 +9,7 @@ # FIXME: Freeze this to get exact versions of all dependencies notebook==6.4.12 -jupyterlab==3.4.5 +jupyterlab==4.0.9 retrolab==0.3.21 nbgitpuller==1.1.0 jupyter-resource-usage==0.6.1 diff --git a/deployments/data8/image/infra-requirements.txt b/deployments/data8/image/infra-requirements.txt index ca42d16bb..3aaf7f593 100644 --- a/deployments/data8/image/infra-requirements.txt +++ b/deployments/data8/image/infra-requirements.txt @@ -9,7 +9,7 @@ # FIXME: Freeze this to get exact versions of all dependencies notebook==6.4.12 -jupyterlab==3.4.5 +jupyterlab==4.0.9 retrolab==0.3.21 nbgitpuller==1.1.0 jupyter-resource-usage==0.6.1 diff --git a/deployments/datahub/images/default/environment.yml.bak b/deployments/datahub/images/default/environment.yml.bak new file mode 100644 index 000000000..344447a8c --- /dev/null +++ b/deployments/datahub/images/default/environment.yml.bak @@ -0,0 +1,206 @@ +# https://docs.conda.io/projects/conda-build/en/latest/resources/package-spec.html#examples +# For conda, == is exact constraint, while = is fuzzy constraint. +# pip uses https://peps.python.org/pep-0440/ which does not have =. + +dependencies: +- nodejs=16.* +- traitlets=5.9.* +- pip=22.2.* +- python=3.9.* + +- syncthing==1.18.6 + +# pymc3 needs this +- mkl-service=2.4.* + +# 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=1.22.* +- matplotlib=3.7.* +- scipy=1.10.0 +- ipympl=0.9.* +- pandas=1.3.* +- statsmodels=0.13.5 +- scikit-learn=1.1.1 +- seaborn=0.11.* +- bokeh=2.3.* +- decorator=5.0.* +- networkx=2.6.* +- spacy=3.4.1 +- nltk=3.6.* + +# 3577, L&S 22, Spring 2023 +- spacy-model-en_core_web_sm=3.4.0 +- spacy-model-en_core_web_lg=3.4.0 +- spacy-model-en_core_web_md=3.4.0 +- spacy-model-en_core_web_trf=3.4.0 +- lemminflect=0.2.2 + +# EPS88, data100 +# https://github.com/berkeley-dsep-infra/datahub/issues/1796 +# https://github.com/berkeley-dsep-infra/datahub/issues/2824 +- shapely==1.8.0 +- cartopy==0.22.0 + +# ls 88-3; neuro +- pillow=8.3.* + +# music 30, spring 2022, https://github.com/berkeley-dsep-infra/datahub/issues/3180 +- pysoundfile==0.10.3.post1 + +# ds100, spring 2022, #3208 +- python-kaleido==0.2.1 + +# https://github.com/berkeley-dsep-infra/datahub/issues/3305, spring 2022 +- fenics==2019.1.0 +- mshr==2019.1.0 + +# https://github.com/berkeley-dsep-infra/datahub/issues/3324, spring 2022 +- gdown==4.4.0 + +# LBL summer research internship in materials informatics. Jupyter Book curriculum at https://enze-chen.github.io/mi-book/ +- pymatgen==2023.10.4 +- matminer=0.9.0 + +# Econ 148, Spring 2023, https://github.com/berkeley-dsep-infra/datahub/issues/4067 +- ipykernel = 6.19.4 + +# Econ 148, Spring 2023 https://github.com/berkeley-dsep-infra/datahub/issues/4251 +- sqlalchemy==1.4.46 + +# UGBA88 Fall 2023, https://github.com/berkeley-dsep-infra/datahub/issues/5019 +- pymysql==1.1.0 + +# MUSIC 30, https://github.com/berkeley-dsep-infra/datahub/issues/5047 +- music21==8.3.0 + +# data8; foundation +- datascience==0.17.6 + +- jupyter-server-proxy==3.2.1 +- jupyter-rsession-proxy==2.0.1 + +- folium==0.12.1.post1 + +# 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 + +# eep 153; spring 2024 +- requests==2.31.0 +- Pint==0.17 + +# eps 109; fall 2024 +- ffmpeg-python==0.2.0 + +# issue #875, global 150Q/pacs 190 - fall 2024 +- wordcloud==1.8.1 + +# issue #929, SW 282 - fall 2024 +- pyreadstat==1.1.2 + +# issue 954, EPS24 - fall 2019 +# balaji to confirm is this is still being taught +- xarray==0.19.0 + +# issue 1001, Physics 188/288 - fall 2024 +- umap-learn==0.5.1 +- hdbscan==0.8.33 + +# espm 125/bio 105; fall 2022 +# see https://github.com/berkeley-dsep-infra/datahub/issues/1796 +# balaji to confirm if this is still being taught +- bitarray==2.3.0 + +# ds198 mch infodemiology, fall 2020/spring 2021 +# google apis +# balaji to check +- google-api-python-client==2.15.0 +- google-auth-httplib2==0.1.0 +- google-auth-oauthlib==0.4.5 + +# issue 1847; LS 22 spring 2021 +# balaji to reach out and confirm it's being taught SP24 +- python-graphviz==0.17 + +# issue #1903, data h195A fall 2020+ +# still required according to ericvd +- habanero==0.7.4 + +# 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 + +- pip: + - -r /tmp/infra-requirements.txt + + # error converting to PDF https://github.com/berkeley-dsep-infra/datahub/issues/5062 + # this installs the 'playwright' executable, which is only available via pip/pypi. + - nbconvert[webpdf] + + # Google spreadsheets, Eric Van Dusen / Keeley Takimoto / Modules + # latest versions in pypi, not conda :( + - gspread-pandas==2.3.0 + - gspread==4.0.1 + + # issue 1001, Physics 188/288 - fall 2024 + - getdist==1.3.1 + - tensorflow-hub==0.12.0 + - tensorflow-probability==0.22.1 + + # ds198 mch infodemiology, fall 2020/spring 2021 + # google apis + # balaji to check + - google==3.0.0 + + # Econ 148, Spring 2023 https://github.com/berkeley-dsep-infra/datahub/issues/4093 + - pycountry-convert==0.7.2 + # + # 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 + - okpy + # + - 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 + # + + # espm 125/bio 105; fall 2022 + # see https://github.com/berkeley-dsep-infra/datahub/issues/1796 + # balaji to confirm if this is still being taught + - nlmpy==1.0.1 + + # cs16A/B, spring 2020 + - lcapy==0.96 + + # prob140 2021 Spring + # sknapp 2023-12-15: we will eventually move prob140 back to datahub in FA24 + # https://jira-secure.berkeley.edu/browse/DH-203 + # - 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 diff --git a/deployments/datahub/images/default/infra-requirements.txt b/deployments/datahub/images/default/infra-requirements.txt index ca42d16bb..3aaf7f593 100644 --- a/deployments/datahub/images/default/infra-requirements.txt +++ b/deployments/datahub/images/default/infra-requirements.txt @@ -9,7 +9,7 @@ # FIXME: Freeze this to get exact versions of all dependencies notebook==6.4.12 -jupyterlab==3.4.5 +jupyterlab==4.0.9 retrolab==0.3.21 nbgitpuller==1.1.0 jupyter-resource-usage==0.6.1 diff --git a/deployments/dev-r/images/default/infra-requirements.txt b/deployments/dev-r/images/default/infra-requirements.txt index ca42d16bb..3aaf7f593 100644 --- a/deployments/dev-r/images/default/infra-requirements.txt +++ b/deployments/dev-r/images/default/infra-requirements.txt @@ -9,7 +9,7 @@ # FIXME: Freeze this to get exact versions of all dependencies notebook==6.4.12 -jupyterlab==3.4.5 +jupyterlab==4.0.9 retrolab==0.3.21 nbgitpuller==1.1.0 jupyter-resource-usage==0.6.1 diff --git a/deployments/dev-r/images/secondary/infra-requirements.txt b/deployments/dev-r/images/secondary/infra-requirements.txt index ca42d16bb..3aaf7f593 100644 --- a/deployments/dev-r/images/secondary/infra-requirements.txt +++ b/deployments/dev-r/images/secondary/infra-requirements.txt @@ -9,7 +9,7 @@ # FIXME: Freeze this to get exact versions of all dependencies notebook==6.4.12 -jupyterlab==3.4.5 +jupyterlab==4.0.9 retrolab==0.3.21 nbgitpuller==1.1.0 jupyter-resource-usage==0.6.1 diff --git a/deployments/edx/image/infra-requirements.txt b/deployments/edx/image/infra-requirements.txt new file mode 100644 index 000000000..3aaf7f593 --- /dev/null +++ b/deployments/edx/image/infra-requirements.txt @@ -0,0 +1,31 @@ +# WARNING: Original source at scripts/infra-packages/requirements.txt +# PLEASE DO NOT EDIT ELSEWHERE +# After editing scripts/infra-packages/requirements.txt, please run +# scripts/infra-packages/sync.bash. + +# This file pins versions of notebook related python packages we want +# across all hubs. This makes sure we don't need to upgrade them +# everwhere one by one. + +# FIXME: Freeze this to get exact versions of all dependencies +notebook==6.4.12 +jupyterlab==4.0.9 +retrolab==0.3.21 +nbgitpuller==1.1.0 +jupyter-resource-usage==0.6.1 +# Matches version in images/hub/Dockerfile +jupyterhub==4.0.2 +appmode==0.8.0 +ipywidgets==7.7.2 +jupyter-tree-download==1.0.1 +git-credential-helpers==0.2 +# Enough people like this, let's load it in. +jupyter-contrib-nbextensions==0.5.1 +jupyter_nbextensions_configurator==0.4.1 +# Measure popularity of different packages in our hubs +# https://discourse.jupyter.org/t/request-for-implementation-instrument-libraries-actively-used-by-users-on-a-jupyterhub/7994?u=yuvipanda +git+https://github.com/shaneknapp/python-popularity-contest.git@add-error-handling +# RISE is useful for presentations - see https://github.com/berkeley-dsep-infra/datahub/issues/2527 +RISE==5.7.1 +# syncthing for dropbox-like functionality +jupyter-syncthing-proxy==1.0.3 diff --git a/deployments/eecs/image/infra-requirements.txt b/deployments/eecs/image/infra-requirements.txt index ca42d16bb..3aaf7f593 100644 --- a/deployments/eecs/image/infra-requirements.txt +++ b/deployments/eecs/image/infra-requirements.txt @@ -9,7 +9,7 @@ # FIXME: Freeze this to get exact versions of all dependencies notebook==6.4.12 -jupyterlab==3.4.5 +jupyterlab==4.0.9 retrolab==0.3.21 nbgitpuller==1.1.0 jupyter-resource-usage==0.6.1 diff --git a/deployments/ischool/image/infra-requirements.txt b/deployments/ischool/image/infra-requirements.txt index ca42d16bb..3aaf7f593 100644 --- a/deployments/ischool/image/infra-requirements.txt +++ b/deployments/ischool/image/infra-requirements.txt @@ -9,7 +9,7 @@ # FIXME: Freeze this to get exact versions of all dependencies notebook==6.4.12 -jupyterlab==3.4.5 +jupyterlab==4.0.9 retrolab==0.3.21 nbgitpuller==1.1.0 jupyter-resource-usage==0.6.1 diff --git a/deployments/julia/image/infra-requirements.txt b/deployments/julia/image/infra-requirements.txt index ca42d16bb..3aaf7f593 100644 --- a/deployments/julia/image/infra-requirements.txt +++ b/deployments/julia/image/infra-requirements.txt @@ -9,7 +9,7 @@ # FIXME: Freeze this to get exact versions of all dependencies notebook==6.4.12 -jupyterlab==3.4.5 +jupyterlab==4.0.9 retrolab==0.3.21 nbgitpuller==1.1.0 jupyter-resource-usage==0.6.1 diff --git a/deployments/publichealth/image/infra-requirements.txt b/deployments/publichealth/image/infra-requirements.txt index ca42d16bb..3aaf7f593 100644 --- a/deployments/publichealth/image/infra-requirements.txt +++ b/deployments/publichealth/image/infra-requirements.txt @@ -9,7 +9,7 @@ # FIXME: Freeze this to get exact versions of all dependencies notebook==6.4.12 -jupyterlab==3.4.5 +jupyterlab==4.0.9 retrolab==0.3.21 nbgitpuller==1.1.0 jupyter-resource-usage==0.6.1 diff --git a/deployments/shiny/image/infra-requirements.txt b/deployments/shiny/image/infra-requirements.txt index ca42d16bb..3aaf7f593 100644 --- a/deployments/shiny/image/infra-requirements.txt +++ b/deployments/shiny/image/infra-requirements.txt @@ -9,7 +9,7 @@ # FIXME: Freeze this to get exact versions of all dependencies notebook==6.4.12 -jupyterlab==3.4.5 +jupyterlab==4.0.9 retrolab==0.3.21 nbgitpuller==1.1.0 jupyter-resource-usage==0.6.1 diff --git a/deployments/stat159/image/environment.yml b/deployments/stat159/image/environment.yml index fc43db53c..7a75f6bcd 100644 --- a/deployments/stat159/image/environment.yml +++ b/deployments/stat159/image/environment.yml @@ -39,7 +39,7 @@ dependencies: - jupyter-resource-usage==0.7.1 - jupyter_bokeh==3.0.5 - jupyter_server==2.5.0 - - jupyterlab==3.6.3 + - jupyterlab==4.0.9 - jupyterlab-drawio==0.9.0 - jupyterlab-favorites==3.1.1 - jupyterlab-geojson==3.3.1 diff --git a/deployments/stat159/image/infra-requirements.txt b/deployments/stat159/image/infra-requirements.txt index ca42d16bb..3aaf7f593 100644 --- a/deployments/stat159/image/infra-requirements.txt +++ b/deployments/stat159/image/infra-requirements.txt @@ -9,7 +9,7 @@ # FIXME: Freeze this to get exact versions of all dependencies notebook==6.4.12 -jupyterlab==3.4.5 +jupyterlab==4.0.9 retrolab==0.3.21 nbgitpuller==1.1.0 jupyter-resource-usage==0.6.1 diff --git a/deployments/stat20/image/infra-requirements.txt b/deployments/stat20/image/infra-requirements.txt index ca42d16bb..3aaf7f593 100644 --- a/deployments/stat20/image/infra-requirements.txt +++ b/deployments/stat20/image/infra-requirements.txt @@ -9,7 +9,7 @@ # FIXME: Freeze this to get exact versions of all dependencies notebook==6.4.12 -jupyterlab==3.4.5 +jupyterlab==4.0.9 retrolab==0.3.21 nbgitpuller==1.1.0 jupyter-resource-usage==0.6.1 diff --git a/scripts/infra-packages/requirements.txt b/scripts/infra-packages/requirements.txt index ca42d16bb..3aaf7f593 100644 --- a/scripts/infra-packages/requirements.txt +++ b/scripts/infra-packages/requirements.txt @@ -9,7 +9,7 @@ # FIXME: Freeze this to get exact versions of all dependencies notebook==6.4.12 -jupyterlab==3.4.5 +jupyterlab==4.0.9 retrolab==0.3.21 nbgitpuller==1.1.0 jupyter-resource-usage==0.6.1 From c3eb1d342b094383d49c547cfa6b116b6eb487ce Mon Sep 17 00:00:00 2001 From: shane knapp Date: Mon, 18 Dec 2023 11:28:02 -0800 Subject: [PATCH 2/2] remove a leftover file --- .../images/default/environment.yml.bak | 206 ------------------ 1 file changed, 206 deletions(-) delete mode 100644 deployments/datahub/images/default/environment.yml.bak diff --git a/deployments/datahub/images/default/environment.yml.bak b/deployments/datahub/images/default/environment.yml.bak deleted file mode 100644 index 344447a8c..000000000 --- a/deployments/datahub/images/default/environment.yml.bak +++ /dev/null @@ -1,206 +0,0 @@ -# https://docs.conda.io/projects/conda-build/en/latest/resources/package-spec.html#examples -# For conda, == is exact constraint, while = is fuzzy constraint. -# pip uses https://peps.python.org/pep-0440/ which does not have =. - -dependencies: -- nodejs=16.* -- traitlets=5.9.* -- pip=22.2.* -- python=3.9.* - -- syncthing==1.18.6 - -# pymc3 needs this -- mkl-service=2.4.* - -# 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=1.22.* -- matplotlib=3.7.* -- scipy=1.10.0 -- ipympl=0.9.* -- pandas=1.3.* -- statsmodels=0.13.5 -- scikit-learn=1.1.1 -- seaborn=0.11.* -- bokeh=2.3.* -- decorator=5.0.* -- networkx=2.6.* -- spacy=3.4.1 -- nltk=3.6.* - -# 3577, L&S 22, Spring 2023 -- spacy-model-en_core_web_sm=3.4.0 -- spacy-model-en_core_web_lg=3.4.0 -- spacy-model-en_core_web_md=3.4.0 -- spacy-model-en_core_web_trf=3.4.0 -- lemminflect=0.2.2 - -# EPS88, data100 -# https://github.com/berkeley-dsep-infra/datahub/issues/1796 -# https://github.com/berkeley-dsep-infra/datahub/issues/2824 -- shapely==1.8.0 -- cartopy==0.22.0 - -# ls 88-3; neuro -- pillow=8.3.* - -# music 30, spring 2022, https://github.com/berkeley-dsep-infra/datahub/issues/3180 -- pysoundfile==0.10.3.post1 - -# ds100, spring 2022, #3208 -- python-kaleido==0.2.1 - -# https://github.com/berkeley-dsep-infra/datahub/issues/3305, spring 2022 -- fenics==2019.1.0 -- mshr==2019.1.0 - -# https://github.com/berkeley-dsep-infra/datahub/issues/3324, spring 2022 -- gdown==4.4.0 - -# LBL summer research internship in materials informatics. Jupyter Book curriculum at https://enze-chen.github.io/mi-book/ -- pymatgen==2023.10.4 -- matminer=0.9.0 - -# Econ 148, Spring 2023, https://github.com/berkeley-dsep-infra/datahub/issues/4067 -- ipykernel = 6.19.4 - -# Econ 148, Spring 2023 https://github.com/berkeley-dsep-infra/datahub/issues/4251 -- sqlalchemy==1.4.46 - -# UGBA88 Fall 2023, https://github.com/berkeley-dsep-infra/datahub/issues/5019 -- pymysql==1.1.0 - -# MUSIC 30, https://github.com/berkeley-dsep-infra/datahub/issues/5047 -- music21==8.3.0 - -# data8; foundation -- datascience==0.17.6 - -- jupyter-server-proxy==3.2.1 -- jupyter-rsession-proxy==2.0.1 - -- folium==0.12.1.post1 - -# 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 - -# eep 153; spring 2024 -- requests==2.31.0 -- Pint==0.17 - -# eps 109; fall 2024 -- ffmpeg-python==0.2.0 - -# issue #875, global 150Q/pacs 190 - fall 2024 -- wordcloud==1.8.1 - -# issue #929, SW 282 - fall 2024 -- pyreadstat==1.1.2 - -# issue 954, EPS24 - fall 2019 -# balaji to confirm is this is still being taught -- xarray==0.19.0 - -# issue 1001, Physics 188/288 - fall 2024 -- umap-learn==0.5.1 -- hdbscan==0.8.33 - -# espm 125/bio 105; fall 2022 -# see https://github.com/berkeley-dsep-infra/datahub/issues/1796 -# balaji to confirm if this is still being taught -- bitarray==2.3.0 - -# ds198 mch infodemiology, fall 2020/spring 2021 -# google apis -# balaji to check -- google-api-python-client==2.15.0 -- google-auth-httplib2==0.1.0 -- google-auth-oauthlib==0.4.5 - -# issue 1847; LS 22 spring 2021 -# balaji to reach out and confirm it's being taught SP24 -- python-graphviz==0.17 - -# issue #1903, data h195A fall 2020+ -# still required according to ericvd -- habanero==0.7.4 - -# 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 - -- pip: - - -r /tmp/infra-requirements.txt - - # error converting to PDF https://github.com/berkeley-dsep-infra/datahub/issues/5062 - # this installs the 'playwright' executable, which is only available via pip/pypi. - - nbconvert[webpdf] - - # Google spreadsheets, Eric Van Dusen / Keeley Takimoto / Modules - # latest versions in pypi, not conda :( - - gspread-pandas==2.3.0 - - gspread==4.0.1 - - # issue 1001, Physics 188/288 - fall 2024 - - getdist==1.3.1 - - tensorflow-hub==0.12.0 - - tensorflow-probability==0.22.1 - - # ds198 mch infodemiology, fall 2020/spring 2021 - # google apis - # balaji to check - - google==3.0.0 - - # Econ 148, Spring 2023 https://github.com/berkeley-dsep-infra/datahub/issues/4093 - - pycountry-convert==0.7.2 - # - # 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 - - okpy - # - - 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 - # - - # espm 125/bio 105; fall 2022 - # see https://github.com/berkeley-dsep-infra/datahub/issues/1796 - # balaji to confirm if this is still being taught - - nlmpy==1.0.1 - - # cs16A/B, spring 2020 - - lcapy==0.96 - - # prob140 2021 Spring - # sknapp 2023-12-15: we will eventually move prob140 back to datahub in FA24 - # https://jira-secure.berkeley.edu/browse/DH-203 - # - 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