From fea2510665674dbf861ead02aed36613aaf17feb Mon Sep 17 00:00:00 2001 From: ryanlovett Date: Fri, 27 Sep 2024 00:00:38 -0700 Subject: [PATCH 1/5] Install octave and jupyter-remote-desktop-proxy. Also bump versions and remote unneeded packages. --- environment.yml | 78 ++++++++++++++++-------------------------- infra-requirements.txt | 29 ---------------- 2 files changed, 30 insertions(+), 77 deletions(-) delete mode 100644 infra-requirements.txt diff --git a/environment.yml b/environment.yml index 058130f..0a96f80 100644 --- a/environment.yml +++ b/environment.yml @@ -5,59 +5,41 @@ channels: - pytorch dependencies: -- python==3.11.* -- git==2.39.1 -- jupyter-resource-usage==1.0.0 -- jupyterlab==4.0.11 -- jupyterlab-favorites==3.0.0 -- jupyterlab_server==2.23.0 -- jupyterlab_widgets==3.0.8 -- jupyter_server==2.7.0 -- nbgitpuller==1.2.1 -- notebook==7.0.7 +- jupyterhub==4.1.6 +- python==3.12.* +- duckdb==1.0.0 - folium==0.14.0 +- gh-scoped-creds==4.1 +- git==2.39.1 - h5netcdf==1.0.2 -- ipywidgets==8.0.7 +- ipywidgets==8.1.5 - jupysql==0.8.0 - jupyter-archive==3.4.0 -- matplotlib==3.7.1 -- mdit-py-plugins==0.4.0 -- numpy==1.24.2 -- pandas==2.0.2 -- plotly==5.13.1 +- jupyterlab==4.2.5 +- jupyterlab-favorites==3.0.0 +- jupyterlab_server==2.27.3 +- jupyterlab_widgets==3.0.13 +- jupyter-resource-usage==1.1.0 +- jupyter_server==2.14.2 +- matplotlib==3.9.2 +- mdit-py-plugins==0.4.2 +- nbconvert==7.16.4 +- nbgitpuller==1.2.1 +- notebook==7.2.2 +- numpy==2.1.1 +- octave_kernel==0.36.0 +- pandas==2.2.3 +- plotly==5.24.1 +- pytest-notebook==0.10.0 - requests==2.28.2 -- scikit-image==0.19.3 -- scikit-learn==1.2.2 -- scipy==1.10.1 -- seaborn==0.12.2 -- statsmodels==0.14.0 -- tensorflow-cpu==2.12.1 -- sqlalchemy==2.0.16 -- mlxtend==0.23.0 -# Spring 2024 data 100 -- pytorch==2.1.2 -- cpuonly==2.0 -- transformers==4.37.1 -# Spring 2024 table demos -- lxml==5.1.0 -# Spring 2024 Econ 148 Packages -- geopandas==0.14.2 -- geopy==2.4.1 -- lifelines==0.27.8 -- pycountry==22.3.5 +- scikit-image==0.24.0 +- scikit-learn==1.5.2 +- scipy==1.14.1 +- seaborn==0.13.2 +- statsmodels==0.14.3 +- tensorflow-cpu==2.17.0 +- xeus-octave==0.2.0 - pip - pip: - # - -r infra-requirements.txt - - ipywidgets==8.0.7 - # disable until fixed (probably this: https://github.com/jupyterlab/jupyter-collaboration/issues/162) - # - jupyter_collaboration==1.0.1 - - jupyterhub==4.1.6 - - nbconvert[webpdf] - # - pyppeteer==2.0.0 - - pytest-notebook==0.8.1 - - gh-scoped-creds==4.1 - git+https://github.com/shaneknapp/python-popularity-contest.git@add-error-handling - - ydata-profiling==4.6.4 - - otter-grader==5.4.0 - - duckdb==0.10.1 - - duckdb_engine==0.11.2 + - jupyter-remote-desktop-proxy==2.0.1 diff --git a/infra-requirements.txt b/infra-requirements.txt deleted file mode 100644 index 0fb0bd9..0000000 --- a/infra-requirements.txt +++ /dev/null @@ -1,29 +0,0 @@ -# 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==7.0.7 -jupyterlab==4.0.11 -nbgitpuller==1.2.1 -jupyter-resource-usage==1.0.1 -# Matches version in images/hub/Dockerfile -jupyterhub==4.1.6 -appmode==0.8.0 -ipywidgets==8.0.7 -jupyter-tree-download==1.0.1 -git-credential-helpers==0.2 -# 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 -# jupyter archival tool for easy user downloads -jupyter-archive==3.4.0 From 1f477769b4e648f762c8016d3906e4e89aca417c Mon Sep 17 00:00:00 2001 From: ryanlovett Date: Fri, 27 Sep 2024 00:01:28 -0700 Subject: [PATCH 2/5] Install octave. Install octave for desktop, and remove unneeded packages. --- apt.txt | 62 ++++++++++----------------------------------------------- 1 file changed, 10 insertions(+), 52 deletions(-) diff --git a/apt.txt b/apt.txt index 10e53b0..59cd670 100644 --- a/apt.txt +++ b/apt.txt @@ -1,10 +1,5 @@ -# Some linux packages for basic terminal work, particularly -# oriented at users new to Unix/cmd line environments. - -# installing less as more just isn't enough -less - # Basic unix tools +less man man-db manpages-posix @@ -18,23 +13,8 @@ wget # Core text editors on a *nix box: vim vim -# A couple of CLI editors that are easier than vim -# micro # currently not working on 18.04 -nano -jed -jed-extra - -# powerful terminal-based file manager, better than the one in JLab -mc - -# for easily managing multiple repositories with one command (perl-doc -# is needed for its help pages to work) -mr -perl-doc - # Regular build tools for compiling common stuff build-essential -gfortran # Dependencies for nbconvert texlive-xetex @@ -48,34 +28,16 @@ lmodern pandoc latexdiff -# Some useful git utilities use basic Ruby -ruby - -# Other niceties for command-line work and life -ack # powerful grep-like tool -pydf # colorized disk usage -tmux -screen -htop -nnn # cmd line file manager -zsh -rsync -tig # console UI for git -multitail - -# For later, these are not available in 18.04 -#browsh # text-based web browser, occasionally handy -#dasel # json/yml/csv/etc data wrangling at the terminal -#fzf # fuzzy file finder - ## This section adds tools for desktop environment usage dbus-x11 +xfce4 +xfce4-panel +xfce4-session +xfce4-settings xorg xubuntu-icon-theme -xfce4 -xfce4-goodies -xclip -xsel +tigervnc-standalone-server +tigervnc-xorg-extension firefox chromium-browser @@ -83,15 +45,11 @@ chromium-browser vim-gtk3 gedit -# Git clients and tools -git-gui -gitg -qgit -meld - -# For jupyter-tree-download. Ref: https://github.com/berkeley-dsep-infra/datahub/issues/3979 +# For jupyter-tree-download zip # playwright deps https://jira-secure.berkeley.edu/browse/DH-305 libnss3 libnspr4 + +octave From 6bddb2ca49de5a606299d2f44ea41302563b7809 Mon Sep 17 00:00:00 2001 From: ryanlovett Date: Fri, 27 Sep 2024 00:12:36 -0700 Subject: [PATCH 3/5] Unpin tensorflow-cpu. --- environment.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/environment.yml b/environment.yml index 0a96f80..31531bf 100644 --- a/environment.yml +++ b/environment.yml @@ -31,13 +31,12 @@ dependencies: - pandas==2.2.3 - plotly==5.24.1 - pytest-notebook==0.10.0 -- requests==2.28.2 - scikit-image==0.24.0 - scikit-learn==1.5.2 - scipy==1.14.1 - seaborn==0.13.2 - statsmodels==0.14.3 -- tensorflow-cpu==2.17.0 +- tensorflow-cpu - xeus-octave==0.2.0 - pip - pip: From fe728028aa1a31a4dde2277a11f1d9ad73df8810 Mon Sep 17 00:00:00 2001 From: ryanlovett Date: Fri, 27 Sep 2024 00:18:13 -0700 Subject: [PATCH 4/5] repo2docker images come with `less`. --- apt.txt | 1 - 1 file changed, 1 deletion(-) diff --git a/apt.txt b/apt.txt index 59cd670..3c66671 100644 --- a/apt.txt +++ b/apt.txt @@ -1,5 +1,4 @@ # Basic unix tools -less man man-db manpages-posix From b4714abdf74b0d5479c1785e249284074b3d2de2 Mon Sep 17 00:00:00 2001 From: ryanlovett Date: Fri, 27 Sep 2024 00:42:30 -0700 Subject: [PATCH 5/5] Add playwright, remove tensorflow-cpu. --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 31531bf..37e7f25 100644 --- a/environment.yml +++ b/environment.yml @@ -29,6 +29,7 @@ dependencies: - numpy==2.1.1 - octave_kernel==0.36.0 - pandas==2.2.3 +- playwright==1.47.2 - plotly==5.24.1 - pytest-notebook==0.10.0 - scikit-image==0.24.0 @@ -36,7 +37,6 @@ dependencies: - scipy==1.14.1 - seaborn==0.13.2 - statsmodels==0.14.3 -- tensorflow-cpu - xeus-octave==0.2.0 - pip - pip: