Merge pull request #11 from felder/felder_DH-418

[DH-418] updating user image

apt.txt

@@ -1,10 +1,8 @@
 # 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
@@ -14,6 +12,7 @@ manpages-posix-dev
 # Download tools
 curl
 wget
+rsync
 
 # Core text editors on a *nix box: vim
 vim
@@ -27,11 +26,6 @@ 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
@@ -48,9 +42,6 @@ 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
@@ -63,11 +54,6 @@ 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
 xorg

environment.yml

@@ -5,58 +5,71 @@ 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==3.0.13
-- jupyter_server==2.7.0
-- nbgitpuller==1.2.1
-- notebook==7.0.7
-- folium==0.14.0
-- h5netcdf==1.0.2
-- ipywidgets==8.1.5
-- jupysql==0.10.14
-- jupytext==1.16.4
-- 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
-- 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==2.5.1
-- 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
-- pip
-- pip:
-  # disable until fixed (probably this:  https://github.com/jupyterlab/jupyter-collaboration/issues/162)
-  # - jupyter_collaboration==1.0.1
-  - jupyterhub==5.2.1
-  - nbconvert[webpdf]
-  #  - pyppeteer==2.0.0
-  - pytest-notebook==0.8.1
+  # Items required for basic level functionality
   - gh-scoped-creds==4.1
-  - git+https://github.com/shaneknapp/python-popularity-contest.git@add-error-handling
-  - ydata-profiling==4.6.4
-  - otter-grader==6.0.4
-  - duckdb==0.10.1
-  - duckdb_engine==0.11.2
+  - git==2.47.1
+  - jupyter-archive==3.4.0
+  - jupyter-resource-usage==1.1.0  
+  - jupyter-server-proxy==4.4.0
+  - jupyter_server==2.15.0 
+  - jupyterhub==5.2.1
+  - jupyterlab==4.3.4
+  - jupyterlab-git==0.50.2
+  - jupyterlab_rise==0.43.1
+  - jupytext==1.16.6
+  - nbgitpuller==1.2.1
+  - notebook==7.3.2
+  - pip==24.3.1  
+  - python==3.11.*
+
+  # other packages
+  - duckdb==1.1.3
+  - duckdb-engine==0.15.0
+  - folium==0.14.0
+  - h5netcdf==1.0.2
+  - ipywidgets==8.1.5
+  - jupysql==0.10.17
+  - jupyterlab-favorites==3.2.2
+  - jupyterlab_server==2.27.3
+  - jupyterlab_widgets==3.0.13
+  - matplotlib==3.7.1
+  - mdit-py-plugins==0.4.0
+  - mlxtend==0.23.0
+  - numpy==1.24.2
+  - pandas==2.0.2
+  - plotly==5.13.1
+  - pytest-notebook==0.10.0
+  - requests==2.32.3
+  - scikit-image==0.19.3
+  - scikit-learn==1.2.2
+  - scipy==1.10.1
+  - seaborn==0.13.2
+  - sqlalchemy==2.0.16
+  - statsmodels==0.14.0
+  - tensorflow-cpu==2.17.0
+  - ydata-profiling==4.12.1
+
+  # Spring 2024 data 100
+  - cpuonly==2.0
+  - pytorch==2.5.1
+  - 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
+
+  # pip installed pacakges, conda preferred
+  - pip:
+    # required for basic functionality
+    - git-credential-helpers==0.2
+    - git+https://github.com/shaneknapp/python-popularity-contest.git@add-error-handling
+    - nbconvert[webpdf]==7.16.5
+    - otter-grader==6.0.4
+
+    # disable until fixed (probably this:  https://github.com/jupyterlab/jupyter-collaboration/issues/162)
+    # DH-418, 2024-01-16, above issue still not fixed.  Also this package is available in condaforge
+    # https://anaconda.org/conda-forge/jupyter-collaboration
+    # - jupyter_collaboration==1.0.1