From 01a68b8177768f46df0e22c1741c7d721f0f29b1 Mon Sep 17 00:00:00 2001
From: Ryan Lovett <rylo@berkeley.edu>
Date: Tue, 21 May 2024 15:48:37 -0700
Subject: [PATCH 01/15] Rename deployment directory.

---
 Rprofile.site          | 23 +++++++++++++++++++++++
 apt.txt                | 18 ++++++++++++++++++
 environment.yml        | 20 ++++++++++++++++++++
 infra-requirements.txt | 29 +++++++++++++++++++++++++++++
 install.R              | 32 ++++++++++++++++++++++++++++++++
 rsession.conf          |  2 ++
 runtime.txt            |  1 +
 7 files changed, 125 insertions(+)
 create mode 100644 Rprofile.site
 create mode 100644 apt.txt
 create mode 100644 environment.yml
 create mode 100644 infra-requirements.txt
 create mode 100755 install.R
 create mode 100644 rsession.conf
 create mode 100644 runtime.txt

diff --git a/Rprofile.site b/Rprofile.site
new file mode 100644
index 0000000..51f9dab
--- /dev/null
+++ b/Rprofile.site
@@ -0,0 +1,23 @@
+# Use RStudio's CRAN mirror to get binary packages. "latest" just means it has
+# all available versions. We can specify version numbers in
+# devtools::install_version.
+options(
+  repos = c(
+    CRAN = "https://packagemanager.rstudio.com/all/__linux__/jammy/latest"
+  )
+)
+
+# RStudio sets the HTTPUserAgent option which causes it to download binaries,
+# rather than source, from the Posit Public Package Manager. In order for the
+# RStudio terminal, Jupyter terminal, Jupyter R notebook, or anything else to
+# do the same, we must manually set HTTPUserAgent. This speeds up package
+# installation.
+# We fake rstudio version because `RStudio.Version()$version` is only available
+# when we are in RStudio.
+options(
+  HTTPUserAgent = sprintf(
+    "RStudio Server (%s); R (%s)",
+    "2022.7.1.554",
+    paste(getRversion(), R.version$platform, R.version$arch, R.version$os)
+  )
+)
diff --git a/apt.txt b/apt.txt
new file mode 100644
index 0000000..86941ae
--- /dev/null
+++ b/apt.txt
@@ -0,0 +1,18 @@
+# useful utilities
+tar
+less
+vim
+
+# for nbconvert, knitr, etc.
+texlive-xetex
+texlive-fonts-recommended
+texlive-plain-generic
+# provides FandolSong-Regular.otf for issue #2714
+texlive-lang-chinese
+
+# for rstudio
+lsb-release
+libclang-dev
+
+# Used by littler for IRkernel::installspec
+libzmq5
diff --git a/environment.yml b/environment.yml
new file mode 100644
index 0000000..0133f62
--- /dev/null
+++ b/environment.yml
@@ -0,0 +1,20 @@
+dependencies:
+- python=3.11.*
+- pip=23.2.*
+- jupyter-server-proxy==4.1.2
+- jupyter-rsession-proxy==2.2.0
+- jupyterlab-myst==2.0.2
+- syncthing==1.25.0
+- pyppeteer==1.0.2
+
+# for nbconvert
+- pandoc==3.1.3
+
+# for jupyter-tree-download
+- zip==3.0
+
+# bug w/notebook and traitlets: https://github.com/jupyter/notebook/issues/7048
+- traitlets=5.9.*
+- pip:
+  - -r infra-requirements.txt
+  - jupyter-shiny-proxy==1.1
diff --git a/infra-requirements.txt b/infra-requirements.txt
new file mode 100644
index 0000000..b01c9d8
--- /dev/null
+++ b/infra-requirements.txt
@@ -0,0 +1,29 @@
+# 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==4.1.5
+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
diff --git a/install.R b/install.R
new file mode 100755
index 0000000..237e2e3
--- /dev/null
+++ b/install.R
@@ -0,0 +1,32 @@
+#!/usr/bin/env r
+
+class_libs_install_version <- function(class_name, class_libs) {
+  print(paste("Installing packages for", class_name))
+  for (i in seq(1, length(class_libs), 2)) {
+    installed_packages <- rownames(installed.packages())
+    package_name = class_libs[i]
+    version = class_libs[i+1]
+    # Only install packages if they haven't already been installed!
+    # devtools doesn't do that by default
+    if (!package_name %in% installed_packages) {
+      print(paste("Installing", package_name, version))
+      devtools::install_version(package_name, version, quiet=TRUE)
+    } else {
+      # FIXME: This ignores version incompatibilities :'(
+      print(paste("Not installing", package_name, " as it is already installed"))
+    }
+  }
+  print(paste("Done installing packages for", class_name))
+}
+
+# R packages to be installed that aren't from apt
+# Combination of informal requests & rocker image suggestions
+# Some of these were already in datahub image
+cran_packages = c(
+  "BiocManager", "1.30.21",
+  "IRkernel", "1.3.2",
+  "rmarkdown", "2.22",
+  "shiny", "1.7.4"
+)
+
+class_libs_install_version("Base packages", cran_packages)
diff --git a/rsession.conf b/rsession.conf
new file mode 100644
index 0000000..1f82b6b
--- /dev/null
+++ b/rsession.conf
@@ -0,0 +1,2 @@
+# Use binary packages!
+r-cran-repos=https://packagemanager.rstudio.com/all/__linux__/jammy/latest
diff --git a/runtime.txt b/runtime.txt
new file mode 100644
index 0000000..fbfde92
--- /dev/null
+++ b/runtime.txt
@@ -0,0 +1 @@
+r-4.3.1-2023-08-01

From 480e861617c3d7b2915b65b5a5435c0ad5077092 Mon Sep 17 00:00:00 2001
From: Balaji Alwar <balajialwar@berkeley.edu>
Date: Fri, 7 Jun 2024 15:36:48 -0700
Subject: [PATCH 02/15] Set up dev environment for discovery interns

---
 environment.yml | 82 +++++++++++++++++++++++++++++++++++++++----------
 1 file changed, 65 insertions(+), 17 deletions(-)

diff --git a/environment.yml b/environment.yml
index 0133f62..774816f 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,20 +1,68 @@
-dependencies:
-- python=3.11.*
-- pip=23.2.*
-- jupyter-server-proxy==4.1.2
-- jupyter-rsession-proxy==2.2.0
-- jupyterlab-myst==2.0.2
-- syncthing==1.25.0
-- pyppeteer==1.0.2
-
-# for nbconvert
-- pandoc==3.1.3
+name: dashboard-image
 
-# for jupyter-tree-download
-- zip==3.0
+channels:
+- conda-forge
+- pytorch
 
-# bug w/notebook and traitlets: https://github.com/jupyter/notebook/issues/7048
-- traitlets=5.9.*
+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
+- folium==0.14.0
+- h5netcdf==1.0.2
+- ipywidgets==8.0.7
+- 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
+- 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
+# Install voila for generating dashboards
+- voila==0.5.7
+# Install myst for generating dashboards
+- mystmd==1.2.5
+- jupyterlab-myst==2.4.2 
+- pip
 - pip:
-  - -r infra-requirements.txt
-  - jupyter-shiny-proxy==1.1
+  # - -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==4.1.5
+  - 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
\ No newline at end of file

From dabed38a8b646b282b00f6a25f78e6aa4c154a9b Mon Sep 17 00:00:00 2001
From: Balaji Alwar <balajialwar@berkeley.edu>
Date: Fri, 7 Jun 2024 19:10:38 -0700
Subject: [PATCH 03/15] moving few packages to conda block

---
 environment.yml | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/environment.yml b/environment.yml
index 774816f..9ada2bb 100644
--- a/environment.yml
+++ b/environment.yml
@@ -49,20 +49,21 @@ dependencies:
 - voila==0.5.7
 # Install myst for generating dashboards
 - mystmd==1.2.5
-- jupyterlab-myst==2.4.2 
+- jupyterlab-myst==2.4.2
+- ipywidgets==8.1.3
+- pytest-notebook==0.10.0
+- gh-scoped-creds==4.1
+- ydata-profiling==4.8.3
+- otter-grader==5.5.0
+- python-duckdb==1.0.0
+- jupyterhub==5.0.0
+
 - 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==4.1.5
   - 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
\ No newline at end of file

From b0d3acdd6218d8d708c2a6306d4639802b682fe6 Mon Sep 17 00:00:00 2001
From: Balaji Alwar <balajialwar@berkeley.edu>
Date: Fri, 7 Jun 2024 19:30:24 -0700
Subject: [PATCH 04/15] Reverting changes

---
 environment.yml | 21 ++++++++++++++-------
 1 file changed, 14 insertions(+), 7 deletions(-)

diff --git a/environment.yml b/environment.yml
index 9ada2bb..c1483db 100644
--- a/environment.yml
+++ b/environment.yml
@@ -50,20 +50,27 @@ dependencies:
 # Install myst for generating dashboards
 - mystmd==1.2.5
 - jupyterlab-myst==2.4.2
-- ipywidgets==8.1.3
-- pytest-notebook==0.10.0
-- gh-scoped-creds==4.1
-- ydata-profiling==4.8.3
-- otter-grader==5.5.0
-- python-duckdb==1.0.0
-- jupyterhub==5.0.0
+#- ipywidgets==8.1.3
+#- pytest-notebook==0.10.0
+#- gh-scoped-creds==4.1
+#- ydata-profiling==4.8.3
+#- otter-grader==5.5.0
+#- python-duckdb==1.0.0
+#- jupyterhub==5.0.0
 
 - 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==4.1.5
   - 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
\ No newline at end of file

From 6d0a55a400e14ca04937c254a6f9da67d5c62ad8 Mon Sep 17 00:00:00 2001
From: Balaji Alwar <balajialwar@berkeley.edu>
Date: Thu, 20 Jun 2024 13:25:33 -0700
Subject: [PATCH 05/15] Installing gh-scoped-creds app in dev hub secondary
 image

---
 environment.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/environment.yml b/environment.yml
index c1483db..b8450df 100644
--- a/environment.yml
+++ b/environment.yml
@@ -31,7 +31,6 @@ dependencies:
 - 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
@@ -41,7 +40,7 @@ dependencies:
 # Spring 2024 table demos
 - lxml==5.1.0
 # Spring 2024 Econ 148 Packages
-- geopandas==0.14.2
+- geopandas==0.13.2
 - geopy==2.4.1
 - lifelines==0.27.8
 - pycountry==22.3.5

From 64543aadfda9c61ce7077f7fb2a394cab3c952b3 Mon Sep 17 00:00:00 2001
From: Balaji Alwar <balajialwar@berkeley.edu>
Date: Thu, 20 Jun 2024 13:27:02 -0700
Subject: [PATCH 06/15] Reverting geopandas version

---
 environment.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/environment.yml b/environment.yml
index b8450df..c4ab722 100644
--- a/environment.yml
+++ b/environment.yml
@@ -40,7 +40,7 @@ dependencies:
 # Spring 2024 table demos
 - lxml==5.1.0
 # Spring 2024 Econ 148 Packages
-- geopandas==0.13.2
+- geopandas==0.14.2
 - geopy==2.4.1
 - lifelines==0.27.8
 - pycountry==22.3.5
@@ -72,4 +72,4 @@ dependencies:
   - ydata-profiling==4.6.4
   - otter-grader==5.4.0
   - duckdb==0.10.1
-  - duckdb_engine==0.11.2
\ No newline at end of file
+  - duckdb_engine==0.11.2

From 6020a033da501f3de0a97dd9bbffe5a385523ed8 Mon Sep 17 00:00:00 2001
From: Balaji Alwar <balajialwar@berkeley.edu>
Date: Mon, 1 Jul 2024 16:25:46 -0700
Subject: [PATCH 07/15] Install quarto in Dev hub(dashboard image)

---
 install.R | 17 +++++++++++++++--
 1 file changed, 15 insertions(+), 2 deletions(-)

diff --git a/install.R b/install.R
index 237e2e3..ef1975c 100755
--- a/install.R
+++ b/install.R
@@ -1,5 +1,15 @@
-#!/usr/bin/env r
+#!/usr/bin/env R
 
+# Function to install Quarto
+install_quarto <- function() {
+  print("Installing Quarto")
+  system("wget https://quarto.org/download/latest/quarto-linux-amd64.deb")
+  system("sudo apt-get install -y ./quarto-linux-amd64.deb")
+  system("rm ./quarto-linux-amd64.deb")
+  print("Quarto installation complete")
+}
+
+# Function to install R packages with specific versions
 class_libs_install_version <- function(class_name, class_libs) {
   print(paste("Installing packages for", class_name))
   for (i in seq(1, length(class_libs), 2)) {
@@ -19,6 +29,9 @@ class_libs_install_version <- function(class_name, class_libs) {
   print(paste("Done installing packages for", class_name))
 }
 
+# Install Quarto
+install_quarto()
+
 # R packages to be installed that aren't from apt
 # Combination of informal requests & rocker image suggestions
 # Some of these were already in datahub image
@@ -29,4 +42,4 @@ cran_packages = c(
   "shiny", "1.7.4"
 )
 
-class_libs_install_version("Base packages", cran_packages)
+class_libs_install_version("Base packages", cran_packages)
\ No newline at end of file

From 04bc204df0d6089185e29e6391bee9849d279e91 Mon Sep 17 00:00:00 2001
From: Balaji Alwar <balajialwar@berkeley.edu>
Date: Tue, 2 Jul 2024 12:04:22 -0700
Subject: [PATCH 08/15] Install quarto in dev hub

---
 environment.yml |  2 +-
 install.R       | 12 ------------
 2 files changed, 1 insertion(+), 13 deletions(-)

diff --git a/environment.yml b/environment.yml
index c4ab722..08bb538 100644
--- a/environment.yml
+++ b/environment.yml
@@ -56,7 +56,7 @@ dependencies:
 #- otter-grader==5.5.0
 #- python-duckdb==1.0.0
 #- jupyterhub==5.0.0
-
+- quarto==1.4.550
 - pip
 - pip:
   # - -r infra-requirements.txt
diff --git a/install.R b/install.R
index ef1975c..ca763a5 100755
--- a/install.R
+++ b/install.R
@@ -1,14 +1,5 @@
 #!/usr/bin/env R
 
-# Function to install Quarto
-install_quarto <- function() {
-  print("Installing Quarto")
-  system("wget https://quarto.org/download/latest/quarto-linux-amd64.deb")
-  system("sudo apt-get install -y ./quarto-linux-amd64.deb")
-  system("rm ./quarto-linux-amd64.deb")
-  print("Quarto installation complete")
-}
-
 # Function to install R packages with specific versions
 class_libs_install_version <- function(class_name, class_libs) {
   print(paste("Installing packages for", class_name))
@@ -29,9 +20,6 @@ class_libs_install_version <- function(class_name, class_libs) {
   print(paste("Done installing packages for", class_name))
 }
 
-# Install Quarto
-install_quarto()
-
 # R packages to be installed that aren't from apt
 # Combination of informal requests & rocker image suggestions
 # Some of these were already in datahub image

From 190fe371416d6337f93cb60279f8b771724c2b40 Mon Sep 17 00:00:00 2001
From: Balaji Alwar <balajialwar@berkeley.edu>
Date: Tue, 2 Jul 2024 14:12:18 -0700
Subject: [PATCH 09/15] Add an extra line at the end of config

---
 install.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/install.R b/install.R
index ca763a5..d4e8763 100755
--- a/install.R
+++ b/install.R
@@ -30,4 +30,4 @@ cran_packages = c(
   "shiny", "1.7.4"
 )
 
-class_libs_install_version("Base packages", cran_packages)
\ No newline at end of file
+class_libs_install_version("Base packages", cran_packages)

From 3b59a910a27f3535b3022c15665affd4ea901f19 Mon Sep 17 00:00:00 2001
From: Balaji Alwar <balajialwar@berkeley.edu>
Date: Wed, 10 Jul 2024 13:29:21 -0700
Subject: [PATCH 10/15] Add voila and voici package in dashboard image

---
 environment.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/environment.yml b/environment.yml
index 08bb538..8a3a37e 100644
--- a/environment.yml
+++ b/environment.yml
@@ -57,6 +57,8 @@ dependencies:
 #- python-duckdb==1.0.0
 #- jupyterhub==5.0.0
 - quarto==1.4.550
+- voila==0.5.7
+- voici==0.6.1
 - pip
 - pip:
   # - -r infra-requirements.txt

From 24822055053219d560fda0854e885d0d348908e6 Mon Sep 17 00:00:00 2001
From: Balaji Alwar <balajialwar@berkeley.edu>
Date: Wed, 10 Jul 2024 16:50:01 -0700
Subject: [PATCH 11/15] Install voici, mystmd and comment out unnecessary
 packages for dashboard image

---
 environment.yml | 74 ++++++++++++++++++++++++-------------------------
 1 file changed, 36 insertions(+), 38 deletions(-)

diff --git a/environment.yml b/environment.yml
index 8a3a37e..8c679c4 100644
--- a/environment.yml
+++ b/environment.yml
@@ -7,71 +7,69 @@ channels:
 dependencies:
 - python==3.11.*
 - git==2.39.1
+- jupyterhub==5.0.0
 - jupyter-resource-usage==1.0.0
 - jupyterlab==4.0.11
 - jupyterlab-favorites==3.0.0
+# Install myst for generating dashboards
+- jupyterlab-myst==2.4.2
 - jupyterlab_server==2.23.0
 - jupyterlab_widgets==3.0.8
 - jupyter_server==2.7.0
 - nbgitpuller==1.2.1
 - notebook==7.0.7
 - folium==0.14.0
-- h5netcdf==1.0.2
+  #- h5netcdf==1.0.2
 - ipywidgets==8.0.7
-- jupysql==0.8.0
+  #- jupysql==0.8.0
 - jupyter-archive==3.4.0
 - matplotlib==3.7.1
-- mdit-py-plugins==0.4.0
+# Install myst markdown for generating dashboards
+- mystmd==1.2.5
+  #- 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
+  #- scikit-learn==1.2.2
+  #- scipy==1.10.1
 - seaborn==0.12.2
-- statsmodels==0.14.0
-- sqlalchemy==2.0.16
-- mlxtend==0.23.0
+  #- 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
+#- pytorch==2.1.2
+#- cpuonly==2.0
+#- transformers==4.37.1
 # Spring 2024 table demos
-- lxml==5.1.0
+#- lxml==5.1.0
 # Spring 2024 Econ 148 Packages
 - geopandas==0.14.2
 - geopy==2.4.1
-- lifelines==0.27.8
+  #- lifelines==0.27.8
 - pycountry==22.3.5
-# Install voila for generating dashboards
-- voila==0.5.7
-# Install myst for generating dashboards
-- mystmd==1.2.5
-- jupyterlab-myst==2.4.2
-#- ipywidgets==8.1.3
-#- pytest-notebook==0.10.0
-#- gh-scoped-creds==4.1
-#- ydata-profiling==4.8.3
-#- otter-grader==5.5.0
-#- python-duckdb==1.0.0
-#- jupyterhub==5.0.0
-- quarto==1.4.550
+# Install voila and voici for generating voila dashboards
 - voila==0.5.7
 - voici==0.6.1
-- pip
-- pip:
+  #- pytest-notebook==0.10.0
+  #- gh-scoped-creds==4.1
+  #- ydata-profiling==4.8.3
+  #- otter-grader==5.5.0
+  #- python-duckdb==1.0.0
+  #- 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==4.1.5
-  - nbconvert[webpdf]
+  #- jupyterhub==4.1.5
+  # - 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
+  #- 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

From 1227e7523cc0443b8281250f17e70ef8cd75112a Mon Sep 17 00:00:00 2001
From: Balaji Alwar <balajialwar@berkeley.edu>
Date: Thu, 11 Jul 2024 13:14:35 -0700
Subject: [PATCH 12/15] Addressing review comments

---
 environment.yml | 40 ++--------------------------------------
 1 file changed, 2 insertions(+), 38 deletions(-)

diff --git a/environment.yml b/environment.yml
index 8c679c4..cf46089 100644
--- a/environment.yml
+++ b/environment.yml
@@ -7,7 +7,7 @@ channels:
 dependencies:
 - python==3.11.*
 - git==2.39.1
-- jupyterhub==5.0.0
+- jupyterhub==4.1.5
 - jupyter-resource-usage==1.0.0
 - jupyterlab==4.0.11
 - jupyterlab-favorites==3.0.0
@@ -19,57 +19,21 @@ dependencies:
 - nbgitpuller==1.2.1
 - notebook==7.0.7
 - folium==0.14.0
-  #- h5netcdf==1.0.2
 - ipywidgets==8.0.7
-  #- jupysql==0.8.0
 - jupyter-archive==3.4.0
 - matplotlib==3.7.1
 # Install myst markdown for generating dashboards
-- mystmd==1.2.5
-  #- mdit-py-plugins==0.4.0
+- mystmd==1.2.9
 - 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==2.1.2
-#- 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
 # Install voila and voici for generating voila dashboards
 - voila==0.5.7
 - voici==0.6.1
-  #- pytest-notebook==0.10.0
-  #- gh-scoped-creds==4.1
-  #- ydata-profiling==4.8.3
-  #- otter-grader==5.5.0
-  #- python-duckdb==1.0.0
-  #- pip
-  #- pip:
-  # - -r infra-requirements.txt
-  # disable until fixed (probably this:  https://github.com/jupyterlab/jupyter-collaboration/issues/162)
-  # - jupyter_collaboration==1.0.1
-  #- jupyterhub==4.1.5
-  # - 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

From b61ce8cb7e37539b44c4e57b9dd871ac95010d6e Mon Sep 17 00:00:00 2001
From: Balaji Alwar <balajialwar@berkeley.edu>
Date: Thu, 1 Aug 2024 15:37:19 -0700
Subject: [PATCH 13/15] Add jupyter_app_launcher and jupyter_cache to dashboard
 image in Dev hub

---
 environment.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/environment.yml b/environment.yml
index cf46089..2da3a62 100644
--- a/environment.yml
+++ b/environment.yml
@@ -8,6 +8,8 @@ dependencies:
 - python==3.11.*
 - git==2.39.1
 - jupyterhub==4.1.5
+- jupyter_app_launcher==0.2.1
+- jupyter-cache==1.0.0
 - jupyter-resource-usage==1.0.0
 - jupyterlab==4.0.11
 - jupyterlab-favorites==3.0.0

From 429361828314165d8393196858f296c6a641da8a Mon Sep 17 00:00:00 2001
From: shane knapp <incomplete@gmail.com>
Date: Thu, 15 Aug 2024 10:17:07 -0700
Subject: [PATCH 14/15] bumping jupyterhub

---
 environment.yml        | 2 +-
 infra-requirements.txt | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/environment.yml b/environment.yml
index 2da3a62..13e05ae 100644
--- a/environment.yml
+++ b/environment.yml
@@ -7,7 +7,7 @@ channels:
 dependencies:
 - python==3.11.*
 - git==2.39.1
-- jupyterhub==4.1.5
+- jupyterhub==4.1.6
 - jupyter_app_launcher==0.2.1
 - jupyter-cache==1.0.0
 - jupyter-resource-usage==1.0.0
diff --git a/infra-requirements.txt b/infra-requirements.txt
index b01c9d8..0fb0bd9 100644
--- a/infra-requirements.txt
+++ b/infra-requirements.txt
@@ -13,7 +13,7 @@ jupyterlab==4.0.11
 nbgitpuller==1.2.1
 jupyter-resource-usage==1.0.1
 # Matches version in images/hub/Dockerfile
-jupyterhub==4.1.5
+jupyterhub==4.1.6
 appmode==0.8.0
 ipywidgets==8.0.7
 jupyter-tree-download==1.0.1

From 50646eaee92e2a0d140b7925aa893a7e9c612e7f Mon Sep 17 00:00:00 2001
From: Balaji Alwar <balajialwar@berkeley.edu>
Date: Wed, 4 Sep 2024 17:55:14 -0700
Subject: [PATCH 15/15] Adding more tools for dashboaring in python in
 dashboard image

---
 environment.yml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/environment.yml b/environment.yml
index 2da3a62..97971b0 100644
--- a/environment.yml
+++ b/environment.yml
@@ -39,3 +39,10 @@ dependencies:
 # Install voila and voici for generating voila dashboards
 - voila==0.5.7
 - voici==0.6.1
+# Adding more data tools to make this image comprehensive
+- dash==2.17.1
+- bokeh==3.4.0
+- panel==1.4.5
+- datashader==0.16.3
+- streamlit=1.38.0
+#- jupyter-containds=0.2.2