From 7ac06fd896cac69fc520bda913ee2a9e92eface3 Mon Sep 17 00:00:00 2001
From: kevinsun0904 <kevinsun0904@gmail.com>
Date: Wed, 21 May 2025 12:21:42 -0700
Subject: [PATCH 01/22] Changed datascience image to install packages using uv

---
 images/datascience-notebook/Dockerfile | 42 +++++++++++++++++++-------
 images/spec.yml                        | 26 ++++++++--------
 2 files changed, 44 insertions(+), 24 deletions(-)

diff --git a/images/datascience-notebook/Dockerfile b/images/datascience-notebook/Dockerfile
index f172251e..cf149259 100644
--- a/images/datascience-notebook/Dockerfile
+++ b/images/datascience-notebook/Dockerfile
@@ -67,26 +67,46 @@ USER jovyan
 ARG JUPYTERSERVER_VERSION=2.14.2 NBGRADER_VERSION=0.9.3 JUPYTERLAB_VERSION=4.2.4 NBCONVERT_VERSION=7.16.4 NOTEBOOK_VERSION=7.2.1 NBCLASSIC_VERSION=1.1.0
 ARG PANDAS_VERSION=2.2.3 STATSMODELS_VERSION=0.14.4 BOTTLENECK_VERSION=1.4.2 NUMEXPR_VERSION=2.10.2
 
+# Install uv for faster package installations
+RUN pip3 install --no-cache-dir --upgrade uv
+
 # Install essential+datascience pip packages 
 ## mistune added for nbgrader issues
-RUN mamba install -c conda-forge pillow typing-extensions tzlocal appdirs gputil mock pytest umap-learn && \
-    mamba install -c conda-forge nltk statsmodels=$STATSMODELS_VERSION pandas=$PANDAS_VERSION mistune && \
-    mamba install -c conda-forge dpkt nose datascience pyarrow bottleneck=$BOTTLENECK_VERSION umap-learn numexpr=$NUMEXPR_VESION && \
+# RUN mamba install -c conda-forge pillow typing-extensions tzlocal appdirs gputil mock pytest umap-learn && \
+#     mamba install -c conda-forge nltk statsmodels=$STATSMODELS_VERSION pandas=$PANDAS_VERSION mistune && \
+#     mamba install -c conda-forge dpkt nose datascience pyarrow bottleneck=$BOTTLENECK_VERSION umap-learn numexpr=$NUMEXPR_VESION && \
+#     python -c 'import matplotlib.pyplot' && \
+#     fix-permissions $CONDA_DIR && \
+#     fix-permissions /home/$NB_USER && \
+#     mamba clean --all
+
+
+RUN uv pip install pillow typingextensions tzlocal appdirs gputil mock pytest umap-learn --system && \
+    uv pip install nltk statsmodels=$STATSMODELS_VERSION pandas=$PANDAS_VERSION mistune --system && \
+    uv pip install dpkt nose datascience pyarrow bottleneck=$BOTTLENECK_VERSION umap-learn numexpr=$NUMEXPR_VESION --system && \
     python -c 'import matplotlib.pyplot' && \
     fix-permissions $CONDA_DIR && \
     fix-permissions /home/$NB_USER && \
-    mamba clean --all
+    uv cache clean
 
 # Install jupyterlab+extensions
-RUN mamba install -c conda-forge jupyterhub=$JUPYTERHUB_VERSION jupyter_server=$JUPYTERSERVER_VERSION && \
-    mamba install -c conda-forge jupyterlab=$JUPYTERLAB_VERSION notebook=$NOTEBOOK_VERSION nbclassic=$NBCLASSIC_VERSION && \
-    # (TODO: Re-enable collab once RTC is fixed) mamba install -c conda-forge jupyterlab_rise jupyter_server_terminals jupyter-collaboration && \
-    mamba install -c conda-forge jupyterlab_rise jupyter_server_terminals && \
-    mamba install -c conda-forge jupyterlab-latex jupyterlab-git jupyterlab-fasta jupyterlab-geojson && \
-    mamba install -c conda-forge nbconvert=$NBCONVERT_VERSION nbgrader=$NBGRADER_VERSION && \
+# RUN mamba install -c conda-forge jupyterhub=$JUPYTERHUB_VERSION jupyter_server=$JUPYTERSERVER_VERSION && \
+#     mamba install -c conda-forge jupyterlab=$JUPYTERLAB_VERSION notebook=$NOTEBOOK_VERSION nbclassic=$NBCLASSIC_VERSION && \
+#     # (TODO: Re-enable collab once RTC is fixed) mamba install -c conda-forge jupyterlab_rise jupyter_server_terminals jupyter-collaboration && \
+#     mamba install -c conda-forge jupyterlab_rise jupyter_server_terminals && \
+#     mamba install -c conda-forge jupyterlab-latex jupyterlab-git jupyterlab-fasta jupyterlab-geojson && \
+#     mamba install -c conda-forge nbconvert=$NBCONVERT_VERSION nbgrader=$NBGRADER_VERSION && \
+#     fix-permissions $CONDA_DIR && \
+#     fix-permissions /home/$NB_USER && \
+#     mamba clean --all
+
+RUN uv pip install jupyterhub=$JUPYTERHUB_VERSION jupyter_server=$JUPYTERSERVER_VERSION --system && \
+    uv pip install jupyterlab=$JUPYTERLAB_VERSION notebook=$NOTEBOOK_VERSION nbclassic=$NBCLASSIC_VERSION --system $$ \
+    uv pip install jupyterlab-latex jupyterlab-git jupyterlab-fasta jupyterlab-geojson --system && \
+    uv pip install nbconvert=$NBCONVERT_VERSION nbgrader=$NBGRADER_VERSION --system && \
     fix-permissions $CONDA_DIR && \
     fix-permissions /home/$NB_USER && \
-    mamba clean --all
+    uv cache clean
 
 # Install R packages
 RUN mamba install -c conda-forge r-markdown r-covr r-git2r r-crosstalk r-dt -y && \
diff --git a/images/spec.yml b/images/spec.yml
index 6add41e5..1827f5f1 100644
--- a/images/spec.yml
+++ b/images/spec.yml
@@ -9,23 +9,23 @@ images:
       JUPYTERHUB_VERSION: 4.1.5
     info_cmds: [PY_VER, PIP_LIST, CONDA_INFO, CONDA_LIST, APT_PKG_LIST]
 
-  rstudio-notebook:
-    image_name: ghcr.io/ucsd-ets/rstudio-notebook
-    depend_on: datascience-notebook
-    integration_tests: true
-    info_cmds: [PY_VER, PIP_LIST, CONDA_INFO, CONDA_LIST, APT_PKG_LIST]
-    prune: true
+#   rstudio-notebook:
+#     image_name: ghcr.io/ucsd-ets/rstudio-notebook
+#     depend_on: datascience-notebook
+#     integration_tests: true
+#     info_cmds: [PY_VER, PIP_LIST, CONDA_INFO, CONDA_LIST, APT_PKG_LIST]
+#     prune: true
 
-  scipy-ml-notebook:
-    image_name: ghcr.io/ucsd-ets/scipy-ml-notebook
-    depend_on: datascience-notebook
-    integration_tests: false
-    info_cmds: [PY_VER, PIP_LIST, CUDA_VERSION, CONDA_INFO, CONDA_LIST, APT_PKG_LIST]
-    prune: false # comment if scipy-ml stops being the last container
+#   scipy-ml-notebook:
+#     image_name: ghcr.io/ucsd-ets/scipy-ml-notebook
+#     depend_on: datascience-notebook
+#     integration_tests: false
+#     info_cmds: [PY_VER, PIP_LIST, CUDA_VERSION, CONDA_INFO, CONDA_LIST, APT_PKG_LIST]
+#     prune: false # comment if scipy-ml stops being the last container
     #prepull: false #-- uncomment to disable prepulling behavior for scipy-ml. gives you space on machine in exchange for build time.
 
 tag:
-  prefix: "2025.2"
+  prefix: "2025.3"
 
 all_info_cmds:
   PY_VER:

From 7d0325651b32200b4f69b633ec3a7f509405e715 Mon Sep 17 00:00:00 2001
From: kevinsun0904 <kevinsun0904@gmail.com>
Date: Wed, 21 May 2025 12:46:27 -0700
Subject: [PATCH 02/22] isntalled typing extensions using conda

---
 images/datascience-notebook/Dockerfile | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/images/datascience-notebook/Dockerfile b/images/datascience-notebook/Dockerfile
index cf149259..e2807402 100644
--- a/images/datascience-notebook/Dockerfile
+++ b/images/datascience-notebook/Dockerfile
@@ -81,7 +81,12 @@ RUN pip3 install --no-cache-dir --upgrade uv
 #     mamba clean --all
 
 
-RUN uv pip install pillow typingextensions tzlocal appdirs gputil mock pytest umap-learn --system && \
+RUN mamba install -c conda-forge typingextensions && \
+    fix-permissions $CONDA_DIR && \
+    fix-permissions /home/$NB_USER && \
+    mamba clean --all
+
+RUN uv pip install pillow tzlocal appdirs gputil mock pytest umap-learn --system && \
     uv pip install nltk statsmodels=$STATSMODELS_VERSION pandas=$PANDAS_VERSION mistune --system && \
     uv pip install dpkt nose datascience pyarrow bottleneck=$BOTTLENECK_VERSION umap-learn numexpr=$NUMEXPR_VESION --system && \
     python -c 'import matplotlib.pyplot' && \

From dad123101a3b8929a1602dcb27998598528e092d Mon Sep 17 00:00:00 2001
From: kevinsun0904 <kevinsun0904@gmail.com>
Date: Wed, 21 May 2025 12:55:49 -0700
Subject: [PATCH 03/22] fixed typo

---
 images/datascience-notebook/Dockerfile | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/images/datascience-notebook/Dockerfile b/images/datascience-notebook/Dockerfile
index e2807402..ef608dbd 100644
--- a/images/datascience-notebook/Dockerfile
+++ b/images/datascience-notebook/Dockerfile
@@ -81,12 +81,7 @@ RUN pip3 install --no-cache-dir --upgrade uv
 #     mamba clean --all
 
 
-RUN mamba install -c conda-forge typingextensions && \
-    fix-permissions $CONDA_DIR && \
-    fix-permissions /home/$NB_USER && \
-    mamba clean --all
-
-RUN uv pip install pillow tzlocal appdirs gputil mock pytest umap-learn --system && \
+RUN uv pip install pillow typing-extensions tzlocal appdirs gputil mock pytest umap-learn --system && \
     uv pip install nltk statsmodels=$STATSMODELS_VERSION pandas=$PANDAS_VERSION mistune --system && \
     uv pip install dpkt nose datascience pyarrow bottleneck=$BOTTLENECK_VERSION umap-learn numexpr=$NUMEXPR_VESION --system && \
     python -c 'import matplotlib.pyplot' && \

From 4a1a35a36b20cfddf7140c07ddda37eaf32e6ebc Mon Sep 17 00:00:00 2001
From: kevinsun0904 <kevinsun0904@gmail.com>
Date: Wed, 21 May 2025 13:11:31 -0700
Subject: [PATCH 04/22] changed versioning from conda to pip

---
 images/datascience-notebook/Dockerfile | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/images/datascience-notebook/Dockerfile b/images/datascience-notebook/Dockerfile
index ef608dbd..e4fb81e9 100644
--- a/images/datascience-notebook/Dockerfile
+++ b/images/datascience-notebook/Dockerfile
@@ -82,8 +82,8 @@ RUN pip3 install --no-cache-dir --upgrade uv
 
 
 RUN uv pip install pillow typing-extensions tzlocal appdirs gputil mock pytest umap-learn --system && \
-    uv pip install nltk statsmodels=$STATSMODELS_VERSION pandas=$PANDAS_VERSION mistune --system && \
-    uv pip install dpkt nose datascience pyarrow bottleneck=$BOTTLENECK_VERSION umap-learn numexpr=$NUMEXPR_VESION --system && \
+    uv pip install nltk statsmodels==$STATSMODELS_VERSION pandas==$PANDAS_VERSION mistune --system && \
+    uv pip install dpkt nose datascience pyarrow bottleneck==$BOTTLENECK_VERSION umap-learn numexpr==$NUMEXPR_VESION --system && \
     python -c 'import matplotlib.pyplot' && \
     fix-permissions $CONDA_DIR && \
     fix-permissions /home/$NB_USER && \
@@ -100,10 +100,10 @@ RUN uv pip install pillow typing-extensions tzlocal appdirs gputil mock pytest u
 #     fix-permissions /home/$NB_USER && \
 #     mamba clean --all
 
-RUN uv pip install jupyterhub=$JUPYTERHUB_VERSION jupyter_server=$JUPYTERSERVER_VERSION --system && \
-    uv pip install jupyterlab=$JUPYTERLAB_VERSION notebook=$NOTEBOOK_VERSION nbclassic=$NBCLASSIC_VERSION --system $$ \
+RUN uv pip install jupyterhub==$JUPYTERHUB_VERSION jupyter_server==$JUPYTERSERVER_VERSION --system && \
+    uv pip install jupyterlab==$JUPYTERLAB_VERSION notebook==$NOTEBOOK_VERSION nbclassic==$NBCLASSIC_VERSION --system $$ \
     uv pip install jupyterlab-latex jupyterlab-git jupyterlab-fasta jupyterlab-geojson --system && \
-    uv pip install nbconvert=$NBCONVERT_VERSION nbgrader=$NBGRADER_VERSION --system && \
+    uv pip install nbconvert==$NBCONVERT_VERSION nbgrader==$NBGRADER_VERSION --system && \
     fix-permissions $CONDA_DIR && \
     fix-permissions /home/$NB_USER && \
     uv cache clean

From eaa9894470cb14e055f4db4963665e5e740e5b3e Mon Sep 17 00:00:00 2001
From: kevinsun0904 <kevinsun0904@gmail.com>
Date: Wed, 21 May 2025 14:07:42 -0700
Subject: [PATCH 05/22] fixed typo

---
 images/datascience-notebook/Dockerfile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/images/datascience-notebook/Dockerfile b/images/datascience-notebook/Dockerfile
index e4fb81e9..f1a9a439 100644
--- a/images/datascience-notebook/Dockerfile
+++ b/images/datascience-notebook/Dockerfile
@@ -74,7 +74,7 @@ RUN pip3 install --no-cache-dir --upgrade uv
 ## mistune added for nbgrader issues
 # RUN mamba install -c conda-forge pillow typing-extensions tzlocal appdirs gputil mock pytest umap-learn && \
 #     mamba install -c conda-forge nltk statsmodels=$STATSMODELS_VERSION pandas=$PANDAS_VERSION mistune && \
-#     mamba install -c conda-forge dpkt nose datascience pyarrow bottleneck=$BOTTLENECK_VERSION umap-learn numexpr=$NUMEXPR_VESION && \
+#     mamba install -c conda-forge dpkt nose datascience pyarrow bottleneck=$BOTTLENECK_VERSION umap-learn numexpr=$NUMEXPR_VERSION && \
 #     python -c 'import matplotlib.pyplot' && \
 #     fix-permissions $CONDA_DIR && \
 #     fix-permissions /home/$NB_USER && \
@@ -83,7 +83,7 @@ RUN pip3 install --no-cache-dir --upgrade uv
 
 RUN uv pip install pillow typing-extensions tzlocal appdirs gputil mock pytest umap-learn --system && \
     uv pip install nltk statsmodels==$STATSMODELS_VERSION pandas==$PANDAS_VERSION mistune --system && \
-    uv pip install dpkt nose datascience pyarrow bottleneck==$BOTTLENECK_VERSION umap-learn numexpr==$NUMEXPR_VESION --system && \
+    uv pip install dpkt nose datascience pyarrow bottleneck==$BOTTLENECK_VERSION umap-learn numexpr==$NUMEXPR_VERSION --system && \
     python -c 'import matplotlib.pyplot' && \
     fix-permissions $CONDA_DIR && \
     fix-permissions /home/$NB_USER && \

From 5775285332f8ca6de52d84ff33130305016c3d53 Mon Sep 17 00:00:00 2001
From: kevinsun0904 <kevinsun0904@gmail.com>
Date: Wed, 21 May 2025 14:29:52 -0700
Subject: [PATCH 06/22] Redeclare JUPYTERHUB_VERSION after FROM call

---
 images/datascience-notebook/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/images/datascience-notebook/Dockerfile b/images/datascience-notebook/Dockerfile
index f1a9a439..dc276d71 100644
--- a/images/datascience-notebook/Dockerfile
+++ b/images/datascience-notebook/Dockerfile
@@ -64,7 +64,7 @@ USER jovyan
 
 # Python/Mamba Deps
 ## Package versions
-ARG JUPYTERSERVER_VERSION=2.14.2 NBGRADER_VERSION=0.9.3 JUPYTERLAB_VERSION=4.2.4 NBCONVERT_VERSION=7.16.4 NOTEBOOK_VERSION=7.2.1 NBCLASSIC_VERSION=1.1.0
+ARG JUPYTERHUB_VERSION=4.1.5 JUPYTERSERVER_VERSION=2.14.2 NBGRADER_VERSION=0.9.3 JUPYTERLAB_VERSION=4.2.4 NBCONVERT_VERSION=7.16.4 NOTEBOOK_VERSION=7.2.1 NBCLASSIC_VERSION=1.1.0
 ARG PANDAS_VERSION=2.2.3 STATSMODELS_VERSION=0.14.4 BOTTLENECK_VERSION=1.4.2 NUMEXPR_VERSION=2.10.2
 
 # Install uv for faster package installations

From f161c8674cb96f8b272749f537e87208a1f27bab Mon Sep 17 00:00:00 2001
From: kevinsun0904 <kevinsun0904@gmail.com>
Date: Wed, 21 May 2025 14:47:10 -0700
Subject: [PATCH 07/22] Small fix

---
 images/datascience-notebook/Dockerfile | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/images/datascience-notebook/Dockerfile b/images/datascience-notebook/Dockerfile
index dc276d71..d825f7d2 100644
--- a/images/datascience-notebook/Dockerfile
+++ b/images/datascience-notebook/Dockerfile
@@ -102,6 +102,8 @@ RUN uv pip install pillow typing-extensions tzlocal appdirs gputil mock pytest u
 
 RUN uv pip install jupyterhub==$JUPYTERHUB_VERSION jupyter_server==$JUPYTERSERVER_VERSION --system && \
     uv pip install jupyterlab==$JUPYTERLAB_VERSION notebook==$NOTEBOOK_VERSION nbclassic==$NBCLASSIC_VERSION --system $$ \
+    # (TODO: Re-enable collab once RTC is fixed) uv pip install jupyterlab_rise jupyter_server_terminals jupyter-collaboration --system && \
+    uv pip install jupyterlab_rise jupyter_server_terminals --server && \
     uv pip install jupyterlab-latex jupyterlab-git jupyterlab-fasta jupyterlab-geojson --system && \
     uv pip install nbconvert==$NBCONVERT_VERSION nbgrader==$NBGRADER_VERSION --system && \
     fix-permissions $CONDA_DIR && \

From 4025cf717bac1f073002b46a715bcd68dacf26ad Mon Sep 17 00:00:00 2001
From: kevinsun0904 <kevinsun0904@gmail.com>
Date: Wed, 21 May 2025 15:04:09 -0700
Subject: [PATCH 08/22] fixed typo

---
 images/datascience-notebook/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/images/datascience-notebook/Dockerfile b/images/datascience-notebook/Dockerfile
index d825f7d2..fd5f0181 100644
--- a/images/datascience-notebook/Dockerfile
+++ b/images/datascience-notebook/Dockerfile
@@ -103,7 +103,7 @@ RUN uv pip install pillow typing-extensions tzlocal appdirs gputil mock pytest u
 RUN uv pip install jupyterhub==$JUPYTERHUB_VERSION jupyter_server==$JUPYTERSERVER_VERSION --system && \
     uv pip install jupyterlab==$JUPYTERLAB_VERSION notebook==$NOTEBOOK_VERSION nbclassic==$NBCLASSIC_VERSION --system $$ \
     # (TODO: Re-enable collab once RTC is fixed) uv pip install jupyterlab_rise jupyter_server_terminals jupyter-collaboration --system && \
-    uv pip install jupyterlab_rise jupyter_server_terminals --server && \
+    uv pip install jupyterlab_rise jupyter_server_terminals --system && \
     uv pip install jupyterlab-latex jupyterlab-git jupyterlab-fasta jupyterlab-geojson --system && \
     uv pip install nbconvert==$NBCONVERT_VERSION nbgrader==$NBGRADER_VERSION --system && \
     fix-permissions $CONDA_DIR && \

From ff1cdb9fdafd967f6726dac3480c9a85149e8ba4 Mon Sep 17 00:00:00 2001
From: kevinsun0904 <kevinsun0904@gmail.com>
Date: Wed, 21 May 2025 15:14:33 -0700
Subject: [PATCH 09/22] fixed typo

---
 images/datascience-notebook/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/images/datascience-notebook/Dockerfile b/images/datascience-notebook/Dockerfile
index fd5f0181..78f46bf4 100644
--- a/images/datascience-notebook/Dockerfile
+++ b/images/datascience-notebook/Dockerfile
@@ -101,7 +101,7 @@ RUN uv pip install pillow typing-extensions tzlocal appdirs gputil mock pytest u
 #     mamba clean --all
 
 RUN uv pip install jupyterhub==$JUPYTERHUB_VERSION jupyter_server==$JUPYTERSERVER_VERSION --system && \
-    uv pip install jupyterlab==$JUPYTERLAB_VERSION notebook==$NOTEBOOK_VERSION nbclassic==$NBCLASSIC_VERSION --system $$ \
+    uv pip install jupyterlab==$JUPYTERLAB_VERSION notebook==$NOTEBOOK_VERSION nbclassic==$NBCLASSIC_VERSION --system && \
     # (TODO: Re-enable collab once RTC is fixed) uv pip install jupyterlab_rise jupyter_server_terminals jupyter-collaboration --system && \
     uv pip install jupyterlab_rise jupyter_server_terminals --system && \
     uv pip install jupyterlab-latex jupyterlab-git jupyterlab-fasta jupyterlab-geojson --system && \

From 6df26d5a5ae80386514a9c124f1d7910af204bad Mon Sep 17 00:00:00 2001
From: kevinsun0904 <kevinsun0904@gmail.com>
Date: Tue, 27 May 2025 10:50:15 -0700
Subject: [PATCH 10/22] Migrated scipy-ml to uv

---
 images/scipy-ml-notebook/Dockerfile | 55 ++++++++++++++++++++++-------
 images/spec.yml                     | 26 +++++++-------
 2 files changed, 55 insertions(+), 26 deletions(-)

diff --git a/images/scipy-ml-notebook/Dockerfile b/images/scipy-ml-notebook/Dockerfile
index 17ec040f..f3e3a950 100644
--- a/images/scipy-ml-notebook/Dockerfile
+++ b/images/scipy-ml-notebook/Dockerfile
@@ -67,20 +67,36 @@ RUN mamba install -c "nvidia/label/cuda-12.6.0" cuda-nvcc \
 ## install protobuf to avoid weird base type error. seems like if we don't then it'll be installed twice.
 ## https://github.com/spesmilo/electrum/issues/7825
 ## pip cache purge didnt work here for some reason.
-RUN pip install --no-cache-dir protobuf==$PROTOBUF_VERSION
+# RUN pip install --no-cache-dir protobuf==$PROTOBUF_VERSION
+
+RUN uv pip install --no-cache-dir protobuf==$PROTOBUF_VERSION --system && \
+    fix-permissions $CONDA_DIR && \ 
+    fix-permissions /home/$NB_USER && \
+    uv cache clean
+
 ## cuda-python installed to have parity with tensorflow and cudnn
 ## Install pillow<7 due to dependency issue https://github.com/pytorch/vision/issues/1712
 ## tensorrt installed to fix not having libnvinfer that has caused tensorflow issues.
-RUN pip install opencv-contrib-python-headless \
-    opencv-python && \
+# RUN pip install opencv-contrib-python-headless \
+#     opencv-python && \
+#     fix-permissions $CONDA_DIR && \ 
+#     fix-permissions /home/$NB_USER && \
+#     pip cache purge
+
+RUN uv pip install opencv-contrib-python-headless opencv-python --system && \
     fix-permissions $CONDA_DIR && \ 
     fix-permissions /home/$NB_USER && \
-    pip cache purge
+    uv cache clean
+
+# RUN mamba install -c conda-forge pyqt pycocotools pillow scapy && \
+#     fix-permissions $CONDA_DIR && \
+#     fix-permissions /home/$NB_USER && \
+#     mamba clean --all
 
-RUN mamba install -c conda-forge pyqt pycocotools pillow scapy && \
+RUN uv pip install pyqt pycocotools pillow scapy --system && \
     fix-permissions $CONDA_DIR && \
     fix-permissions /home/$NB_USER && \
-    mamba clean --all
+    uv cache clean
 
 # Install CUDA/Torch/Tensorflow/Keras w/pip
 ## no purge required but no-cache-dir is used. pip purge will actually break the build here!
@@ -88,18 +104,31 @@ RUN mamba install -c conda-forge pyqt pycocotools pillow scapy && \
 ## Check tensorrt_env_vars.sh if you have to bump tensorrt!
 
 ## tf-keras is keras 2.x for higher versions of tensorflow that would normally require keras 3
-RUN pip install nvidia-cudnn-cu12==$CUDNN_VERSION torch==$TORCH_VERSION torchvision torchaudio --index-url https://download.pytorch.org/whl/cu126 && \
-  pip install tensorflow==$TENSORFLOW_VERSION tensorflow-datasets tensorrt==$TENSORRT_VERSION keras==$KERAS_VERSION tf-keras==$TF_KERAS_VERSION && \
+# RUN pip install nvidia-cudnn-cu12==$CUDNN_VERSION torch==$TORCH_VERSION torchvision torchaudio --index-url https://download.pytorch.org/whl/cu126 && \
+#   pip install tensorflow==$TENSORFLOW_VERSION tensorflow-datasets tensorrt==$TENSORRT_VERSION keras==$KERAS_VERSION tf-keras==$TF_KERAS_VERSION && \
+#   fix-permissions $CONDA_DIR && \
+#   fix-permissions /home/$NB_USER && \
+#   mamba clean -a -y && \
+#   pip cache purge
+
+RUN uv pip install nvidia-cudnn-cu12==$CUDNN_VERSION torch==$TORCH_VERSION torchvision torchaudio --index-url https://download.pytorch.org/whl/cu126 --system && \
+  uv pip install tensorflow==$TENSORFLOW_VERSION tensorflow-datasets tensorrt==$TENSORRT_VERSION keras==$KERAS_VERSION tf-keras==$TF_KERAS_VERSION --system && \
   fix-permissions $CONDA_DIR && \
   fix-permissions /home/$NB_USER && \
   mamba clean -a -y && \
-  pip cache purge
+  uv cache clean
+
+# RUN pip install transformers datasets accelerate huggingface-hub timm && \
+#   fix-permissions $CONDA_DIR && \
+#   fix-permissions /home/$NB_USER && \
+#   mamba clean -a -y && \
+#   pip cache purge
 
-RUN pip install transformers datasets accelerate huggingface-hub timm && \
+RUN uv pip install transformers datasets accelerate huggingface-hub timm --system && \
   fix-permissions $CONDA_DIR && \
   fix-permissions /home/$NB_USER && \
   mamba clean -a -y && \
-  pip cache purge
+  uv cache clean
 
 USER $NB_UID:$NB_GID
 ENV PATH=${PATH}:/usr/local/nvidia/bin:/opt/conda/bin
@@ -113,8 +142,8 @@ RUN mkdir -p $CONDA_DIR/lib/nvvm/libdevice && \
 # TensorRT fix for tensorflow
 ## https://github.com/tensorflow/tensorflow/issues/61468 (could not find TensorRT)
 ## This will most definitely have to be changed after 8.6.1...
-RUN ln -s /opt/conda/lib/python3.11/site-packages/tensorrt_libs/libnvinfer_plugin.so.8 /opt/conda/lib/python3.11/site-packages/tensorrt_libs/libnvinfer_plugin.so.$TENSORRT_VERSION && \
-    ln -s /opt/conda/lib/python3.11/site-packages/tensorrt_libs/libnvinfer.so.8 /opt/conda/lib/python3.11/site-packages/tensorrt_libs/libnvinfer.so.$TENSORRT_VERSION
+# RUN ln -s /opt/conda/lib/python3.11/site-packages/tensorrt_libs/libnvinfer_plugin.so.8 /opt/conda/lib/python3.11/site-packages/tensorrt_libs/libnvinfer_plugin.so.$TENSORRT_VERSION && \
+#     ln -s /opt/conda/lib/python3.11/site-packages/tensorrt_libs/libnvinfer.so.8 /opt/conda/lib/python3.11/site-packages/tensorrt_libs/libnvinfer.so.$TENSORRT_VERSION
 
 # Run datahub scripts
 RUN . /tmp/activate.sh
diff --git a/images/spec.yml b/images/spec.yml
index 1827f5f1..992eba02 100644
--- a/images/spec.yml
+++ b/images/spec.yml
@@ -1,13 +1,13 @@
 root: datascience-notebook
 
 images:
-  datascience-notebook:
-    image_name: ghcr.io/ucsd-ets/datascience-notebook
-    build_args:
-      PYTHON_VERSION: python-3.11.8
-      PY_VER_SHORT: "3.11"
-      JUPYTERHUB_VERSION: 4.1.5
-    info_cmds: [PY_VER, PIP_LIST, CONDA_INFO, CONDA_LIST, APT_PKG_LIST]
+#   datascience-notebook:
+#     image_name: ghcr.io/ucsd-ets/datascience-notebook
+#     build_args:
+#       PYTHON_VERSION: python-3.11.8
+#       PY_VER_SHORT: "3.11"
+#       JUPYTERHUB_VERSION: 4.1.5
+#     info_cmds: [PY_VER, PIP_LIST, CONDA_INFO, CONDA_LIST, APT_PKG_LIST]
 
 #   rstudio-notebook:
 #     image_name: ghcr.io/ucsd-ets/rstudio-notebook
@@ -16,12 +16,12 @@ images:
 #     info_cmds: [PY_VER, PIP_LIST, CONDA_INFO, CONDA_LIST, APT_PKG_LIST]
 #     prune: true
 
-#   scipy-ml-notebook:
-#     image_name: ghcr.io/ucsd-ets/scipy-ml-notebook
-#     depend_on: datascience-notebook
-#     integration_tests: false
-#     info_cmds: [PY_VER, PIP_LIST, CUDA_VERSION, CONDA_INFO, CONDA_LIST, APT_PKG_LIST]
-#     prune: false # comment if scipy-ml stops being the last container
+  scipy-ml-notebook:
+    image_name: ghcr.io/ucsd-ets/scipy-ml-notebook
+    depend_on: datascience-notebook
+    integration_tests: false
+    info_cmds: [PY_VER, PIP_LIST, CUDA_VERSION, CONDA_INFO, CONDA_LIST, APT_PKG_LIST]
+    prune: false # comment if scipy-ml stops being the last container
     #prepull: false #-- uncomment to disable prepulling behavior for scipy-ml. gives you space on machine in exchange for build time.
 
 tag:

From 923d524ef48e84cd72c58542dfdf03e9fb6956d3 Mon Sep 17 00:00:00 2001
From: kevinsun0904 <kevinsun0904@gmail.com>
Date: Tue, 27 May 2025 10:58:13 -0700
Subject: [PATCH 11/22] Removed commented out notebooks

---
 images/spec.yml | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/images/spec.yml b/images/spec.yml
index 992eba02..df99929c 100644
--- a/images/spec.yml
+++ b/images/spec.yml
@@ -1,20 +1,20 @@
 root: datascience-notebook
 
 images:
-#   datascience-notebook:
-#     image_name: ghcr.io/ucsd-ets/datascience-notebook
-#     build_args:
-#       PYTHON_VERSION: python-3.11.8
-#       PY_VER_SHORT: "3.11"
-#       JUPYTERHUB_VERSION: 4.1.5
-#     info_cmds: [PY_VER, PIP_LIST, CONDA_INFO, CONDA_LIST, APT_PKG_LIST]
+  datascience-notebook:
+    image_name: ghcr.io/ucsd-ets/datascience-notebook
+    build_args:
+      PYTHON_VERSION: python-3.11.8
+      PY_VER_SHORT: "3.11"
+      JUPYTERHUB_VERSION: 4.1.5
+    info_cmds: [PY_VER, PIP_LIST, CONDA_INFO, CONDA_LIST, APT_PKG_LIST]
 
-#   rstudio-notebook:
-#     image_name: ghcr.io/ucsd-ets/rstudio-notebook
-#     depend_on: datascience-notebook
-#     integration_tests: true
-#     info_cmds: [PY_VER, PIP_LIST, CONDA_INFO, CONDA_LIST, APT_PKG_LIST]
-#     prune: true
+  rstudio-notebook:
+    image_name: ghcr.io/ucsd-ets/rstudio-notebook
+    depend_on: datascience-notebook
+    integration_tests: true
+    info_cmds: [PY_VER, PIP_LIST, CONDA_INFO, CONDA_LIST, APT_PKG_LIST]
+    prune: true
 
   scipy-ml-notebook:
     image_name: ghcr.io/ucsd-ets/scipy-ml-notebook

From b886b54ad3a64d32d2922892e940a79452f99657 Mon Sep 17 00:00:00 2001
From: kevinsun0904 <kevinsun0904@gmail.com>
Date: Tue, 27 May 2025 11:19:27 -0700
Subject: [PATCH 12/22] Changed pyqt to PyQt5

---
 images/scipy-ml-notebook/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/images/scipy-ml-notebook/Dockerfile b/images/scipy-ml-notebook/Dockerfile
index f3e3a950..8895c6ec 100644
--- a/images/scipy-ml-notebook/Dockerfile
+++ b/images/scipy-ml-notebook/Dockerfile
@@ -93,7 +93,7 @@ RUN uv pip install opencv-contrib-python-headless opencv-python --system && \
 #     fix-permissions /home/$NB_USER && \
 #     mamba clean --all
 
-RUN uv pip install pyqt pycocotools pillow scapy --system && \
+RUN uv pip install PyQt5 pycocotools pillow scapy --system && \
     fix-permissions $CONDA_DIR && \
     fix-permissions /home/$NB_USER && \
     uv cache clean

From 3e51d4f8b3e2571f96491aba08d7a8e573ac15bb Mon Sep 17 00:00:00 2001
From: kevinsun0904 <kevinsun0904@gmail.com>
Date: Tue, 27 May 2025 13:27:36 -0700
Subject: [PATCH 13/22] removed prepull from all notebooks

---
 images/spec.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/images/spec.yml b/images/spec.yml
index df99929c..764eec03 100644
--- a/images/spec.yml
+++ b/images/spec.yml
@@ -8,6 +8,7 @@ images:
       PY_VER_SHORT: "3.11"
       JUPYTERHUB_VERSION: 4.1.5
     info_cmds: [PY_VER, PIP_LIST, CONDA_INFO, CONDA_LIST, APT_PKG_LIST]
+    prepull: false
 
   rstudio-notebook:
     image_name: ghcr.io/ucsd-ets/rstudio-notebook
@@ -15,6 +16,7 @@ images:
     integration_tests: true
     info_cmds: [PY_VER, PIP_LIST, CONDA_INFO, CONDA_LIST, APT_PKG_LIST]
     prune: true
+    prepull: false
 
   scipy-ml-notebook:
     image_name: ghcr.io/ucsd-ets/scipy-ml-notebook
@@ -22,7 +24,7 @@ images:
     integration_tests: false
     info_cmds: [PY_VER, PIP_LIST, CUDA_VERSION, CONDA_INFO, CONDA_LIST, APT_PKG_LIST]
     prune: false # comment if scipy-ml stops being the last container
-    #prepull: false #-- uncomment to disable prepulling behavior for scipy-ml. gives you space on machine in exchange for build time.
+    prepull: false #-- uncomment to disable prepulling behavior for scipy-ml. gives you space on machine in exchange for build time.
 
 tag:
   prefix: "2025.3"

From dc915c4eb73368f441fe0e1fec2ea89033207ece Mon Sep 17 00:00:00 2001
From: kevinsun0904 <kevinsun0904@gmail.com>
Date: Wed, 28 May 2025 11:49:10 -0700
Subject: [PATCH 14/22] Removed comments and migrated cuda to pip

---
 images/datascience-notebook/Dockerfile | 19 ---------
 images/scipy-ml-notebook/Dockerfile    | 53 ++++++--------------------
 images/spec.yml                        |  4 +-
 3 files changed, 13 insertions(+), 63 deletions(-)

diff --git a/images/datascience-notebook/Dockerfile b/images/datascience-notebook/Dockerfile
index 78f46bf4..8686f86d 100644
--- a/images/datascience-notebook/Dockerfile
+++ b/images/datascience-notebook/Dockerfile
@@ -72,15 +72,6 @@ RUN pip3 install --no-cache-dir --upgrade uv
 
 # Install essential+datascience pip packages 
 ## mistune added for nbgrader issues
-# RUN mamba install -c conda-forge pillow typing-extensions tzlocal appdirs gputil mock pytest umap-learn && \
-#     mamba install -c conda-forge nltk statsmodels=$STATSMODELS_VERSION pandas=$PANDAS_VERSION mistune && \
-#     mamba install -c conda-forge dpkt nose datascience pyarrow bottleneck=$BOTTLENECK_VERSION umap-learn numexpr=$NUMEXPR_VERSION && \
-#     python -c 'import matplotlib.pyplot' && \
-#     fix-permissions $CONDA_DIR && \
-#     fix-permissions /home/$NB_USER && \
-#     mamba clean --all
-
-
 RUN uv pip install pillow typing-extensions tzlocal appdirs gputil mock pytest umap-learn --system && \
     uv pip install nltk statsmodels==$STATSMODELS_VERSION pandas==$PANDAS_VERSION mistune --system && \
     uv pip install dpkt nose datascience pyarrow bottleneck==$BOTTLENECK_VERSION umap-learn numexpr==$NUMEXPR_VERSION --system && \
@@ -90,16 +81,6 @@ RUN uv pip install pillow typing-extensions tzlocal appdirs gputil mock pytest u
     uv cache clean
 
 # Install jupyterlab+extensions
-# RUN mamba install -c conda-forge jupyterhub=$JUPYTERHUB_VERSION jupyter_server=$JUPYTERSERVER_VERSION && \
-#     mamba install -c conda-forge jupyterlab=$JUPYTERLAB_VERSION notebook=$NOTEBOOK_VERSION nbclassic=$NBCLASSIC_VERSION && \
-#     # (TODO: Re-enable collab once RTC is fixed) mamba install -c conda-forge jupyterlab_rise jupyter_server_terminals jupyter-collaboration && \
-#     mamba install -c conda-forge jupyterlab_rise jupyter_server_terminals && \
-#     mamba install -c conda-forge jupyterlab-latex jupyterlab-git jupyterlab-fasta jupyterlab-geojson && \
-#     mamba install -c conda-forge nbconvert=$NBCONVERT_VERSION nbgrader=$NBGRADER_VERSION && \
-#     fix-permissions $CONDA_DIR && \
-#     fix-permissions /home/$NB_USER && \
-#     mamba clean --all
-
 RUN uv pip install jupyterhub==$JUPYTERHUB_VERSION jupyter_server==$JUPYTERSERVER_VERSION --system && \
     uv pip install jupyterlab==$JUPYTERLAB_VERSION notebook==$NOTEBOOK_VERSION nbclassic==$NBCLASSIC_VERSION --system && \
     # (TODO: Re-enable collab once RTC is fixed) uv pip install jupyterlab_rise jupyter_server_terminals jupyter-collaboration --system && \
diff --git a/images/scipy-ml-notebook/Dockerfile b/images/scipy-ml-notebook/Dockerfile
index 8895c6ec..3a10e20a 100644
--- a/images/scipy-ml-notebook/Dockerfile
+++ b/images/scipy-ml-notebook/Dockerfile
@@ -53,22 +53,25 @@ USER jovyan
 # CUDA setup w/mamba
 ## TODO: Investigate this command, seems to duplicate cuda packages for nvidia (pypi + conda-forge). 
 # cuda-toolkit is a skeleton package on CUDA 12, unlike CUDA <= 11
-RUN mamba install -c "nvidia/label/cuda-12.6.0" cuda-nvcc \
-    cuda-toolkit=$CUDA_VERSION \
+# RUN mamba install -c "nvidia/label/cuda-12.6.0" cuda-nvcc \
+#     cuda-toolkit=$CUDA_VERSION \
     # For CUDA 11: cudatoolkit=$CUDA_VERSION \
-    cuda-version=$CUDA_VERSION \
-    nccl \
-    -y && \
+#     cuda-version=$CUDA_VERSION \
+#     nccl \
+#     -y && \
+#     fix-permissions $CONDA_DIR && \
+#     fix-permissions /home/$NB_USER && \
+#     mamba clean -a -y
+
+RUN uv pip install nvidia-pyindex --system && \
+    uv pip install nvidia-cuda-nvcc-cu12 nvidia-nccl-cu12 cuda-python --system && \
     fix-permissions $CONDA_DIR && \
     fix-permissions /home/$NB_USER && \
-    mamba clean -a -y
+    uv cache clean
 
 # Install scipy pip packages
 ## install protobuf to avoid weird base type error. seems like if we don't then it'll be installed twice.
 ## https://github.com/spesmilo/electrum/issues/7825
-## pip cache purge didnt work here for some reason.
-# RUN pip install --no-cache-dir protobuf==$PROTOBUF_VERSION
-
 RUN uv pip install --no-cache-dir protobuf==$PROTOBUF_VERSION --system && \
     fix-permissions $CONDA_DIR && \ 
     fix-permissions /home/$NB_USER && \
@@ -77,22 +80,11 @@ RUN uv pip install --no-cache-dir protobuf==$PROTOBUF_VERSION --system && \
 ## cuda-python installed to have parity with tensorflow and cudnn
 ## Install pillow<7 due to dependency issue https://github.com/pytorch/vision/issues/1712
 ## tensorrt installed to fix not having libnvinfer that has caused tensorflow issues.
-# RUN pip install opencv-contrib-python-headless \
-#     opencv-python && \
-#     fix-permissions $CONDA_DIR && \ 
-#     fix-permissions /home/$NB_USER && \
-#     pip cache purge
-
 RUN uv pip install opencv-contrib-python-headless opencv-python --system && \
     fix-permissions $CONDA_DIR && \ 
     fix-permissions /home/$NB_USER && \
     uv cache clean
 
-# RUN mamba install -c conda-forge pyqt pycocotools pillow scapy && \
-#     fix-permissions $CONDA_DIR && \
-#     fix-permissions /home/$NB_USER && \
-#     mamba clean --all
-
 RUN uv pip install PyQt5 pycocotools pillow scapy --system && \
     fix-permissions $CONDA_DIR && \
     fix-permissions /home/$NB_USER && \
@@ -104,30 +96,15 @@ RUN uv pip install PyQt5 pycocotools pillow scapy --system && \
 ## Check tensorrt_env_vars.sh if you have to bump tensorrt!
 
 ## tf-keras is keras 2.x for higher versions of tensorflow that would normally require keras 3
-# RUN pip install nvidia-cudnn-cu12==$CUDNN_VERSION torch==$TORCH_VERSION torchvision torchaudio --index-url https://download.pytorch.org/whl/cu126 && \
-#   pip install tensorflow==$TENSORFLOW_VERSION tensorflow-datasets tensorrt==$TENSORRT_VERSION keras==$KERAS_VERSION tf-keras==$TF_KERAS_VERSION && \
-#   fix-permissions $CONDA_DIR && \
-#   fix-permissions /home/$NB_USER && \
-#   mamba clean -a -y && \
-#   pip cache purge
-
 RUN uv pip install nvidia-cudnn-cu12==$CUDNN_VERSION torch==$TORCH_VERSION torchvision torchaudio --index-url https://download.pytorch.org/whl/cu126 --system && \
   uv pip install tensorflow==$TENSORFLOW_VERSION tensorflow-datasets tensorrt==$TENSORRT_VERSION keras==$KERAS_VERSION tf-keras==$TF_KERAS_VERSION --system && \
   fix-permissions $CONDA_DIR && \
   fix-permissions /home/$NB_USER && \
-  mamba clean -a -y && \
   uv cache clean
 
-# RUN pip install transformers datasets accelerate huggingface-hub timm && \
-#   fix-permissions $CONDA_DIR && \
-#   fix-permissions /home/$NB_USER && \
-#   mamba clean -a -y && \
-#   pip cache purge
-
 RUN uv pip install transformers datasets accelerate huggingface-hub timm --system && \
   fix-permissions $CONDA_DIR && \
   fix-permissions /home/$NB_USER && \
-  mamba clean -a -y && \
   uv cache clean
 
 USER $NB_UID:$NB_GID
@@ -139,11 +116,5 @@ RUN mkdir -p $CONDA_DIR/lib/nvvm/libdevice && \
     cp $CONDA_DIR/nvvm/libdevice/libdevice.10.bc $CONDA_DIR/lib/nvvm/libdevice/
     #CUDA 11: cp $CONDA_DIR/lib/libdevice.10.bc $CONDA_DIR/lib/nvvm/libdevice/
 
-# TensorRT fix for tensorflow
-## https://github.com/tensorflow/tensorflow/issues/61468 (could not find TensorRT)
-## This will most definitely have to be changed after 8.6.1...
-# RUN ln -s /opt/conda/lib/python3.11/site-packages/tensorrt_libs/libnvinfer_plugin.so.8 /opt/conda/lib/python3.11/site-packages/tensorrt_libs/libnvinfer_plugin.so.$TENSORRT_VERSION && \
-#     ln -s /opt/conda/lib/python3.11/site-packages/tensorrt_libs/libnvinfer.so.8 /opt/conda/lib/python3.11/site-packages/tensorrt_libs/libnvinfer.so.$TENSORRT_VERSION
-
 # Run datahub scripts
 RUN . /tmp/activate.sh
diff --git a/images/spec.yml b/images/spec.yml
index 764eec03..c1b1eafc 100644
--- a/images/spec.yml
+++ b/images/spec.yml
@@ -8,7 +8,6 @@ images:
       PY_VER_SHORT: "3.11"
       JUPYTERHUB_VERSION: 4.1.5
     info_cmds: [PY_VER, PIP_LIST, CONDA_INFO, CONDA_LIST, APT_PKG_LIST]
-    prepull: false
 
   rstudio-notebook:
     image_name: ghcr.io/ucsd-ets/rstudio-notebook
@@ -16,7 +15,6 @@ images:
     integration_tests: true
     info_cmds: [PY_VER, PIP_LIST, CONDA_INFO, CONDA_LIST, APT_PKG_LIST]
     prune: true
-    prepull: false
 
   scipy-ml-notebook:
     image_name: ghcr.io/ucsd-ets/scipy-ml-notebook
@@ -24,7 +22,7 @@ images:
     integration_tests: false
     info_cmds: [PY_VER, PIP_LIST, CUDA_VERSION, CONDA_INFO, CONDA_LIST, APT_PKG_LIST]
     prune: false # comment if scipy-ml stops being the last container
-    prepull: false #-- uncomment to disable prepulling behavior for scipy-ml. gives you space on machine in exchange for build time.
+    # prepull: false #-- uncomment to disable prepulling behavior for scipy-ml. gives you space on machine in exchange for build time.
 
 tag:
   prefix: "2025.3"

From 781d494ad42d779a99bb8cabc85bfa60d3794553 Mon Sep 17 00:00:00 2001
From: kevinsun0904 <kevinsun0904@gmail.com>
Date: Wed, 28 May 2025 12:12:07 -0700
Subject: [PATCH 15/22] Added index-url

---
 images/scipy-ml-notebook/Dockerfile | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/images/scipy-ml-notebook/Dockerfile b/images/scipy-ml-notebook/Dockerfile
index 3a10e20a..f53df78d 100644
--- a/images/scipy-ml-notebook/Dockerfile
+++ b/images/scipy-ml-notebook/Dockerfile
@@ -63,8 +63,7 @@ USER jovyan
 #     fix-permissions /home/$NB_USER && \
 #     mamba clean -a -y
 
-RUN uv pip install nvidia-pyindex --system && \
-    uv pip install nvidia-cuda-nvcc-cu12 nvidia-nccl-cu12 cuda-python --system && \
+RUN uv pip install --extra-index-url https://pypi.nvidia.com nvidia-cuda-nvcc-cu12 nvidia-nccl-cu12 cuda-python --system && \
     fix-permissions $CONDA_DIR && \
     fix-permissions /home/$NB_USER && \
     uv cache clean

From 5b76494f73efe10ed87c15b95487f074104f73f9 Mon Sep 17 00:00:00 2001
From: kevinsun0904 <kevinsun0904@gmail.com>
Date: Wed, 28 May 2025 12:25:55 -0700
Subject: [PATCH 16/22] Commented out cuda conda fix

---
 images/scipy-ml-notebook/Dockerfile | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/images/scipy-ml-notebook/Dockerfile b/images/scipy-ml-notebook/Dockerfile
index f53df78d..7e87a2a8 100644
--- a/images/scipy-ml-notebook/Dockerfile
+++ b/images/scipy-ml-notebook/Dockerfile
@@ -111,9 +111,9 @@ ENV PATH=${PATH}:/usr/local/nvidia/bin:/opt/conda/bin
 
 # CUDA fixes for CONDA
 ## Copy libdevice file to the required path
-RUN mkdir -p $CONDA_DIR/lib/nvvm/libdevice && \
-    cp $CONDA_DIR/nvvm/libdevice/libdevice.10.bc $CONDA_DIR/lib/nvvm/libdevice/
-    #CUDA 11: cp $CONDA_DIR/lib/libdevice.10.bc $CONDA_DIR/lib/nvvm/libdevice/
+# RUN mkdir -p $CONDA_DIR/lib/nvvm/libdevice && \
+#     cp $CONDA_DIR/nvvm/libdevice/libdevice.10.bc $CONDA_DIR/lib/nvvm/libdevice/
+#     #CUDA 11: cp $CONDA_DIR/lib/libdevice.10.bc $CONDA_DIR/lib/nvvm/libdevice/
 
 # Run datahub scripts
 RUN . /tmp/activate.sh

From 324c5ed5500b02c1f99c9aabaa2ac1e9be35dbb9 Mon Sep 17 00:00:00 2001
From: kevinsun0904 <kevinsun0904@gmail.com>
Date: Thu, 29 May 2025 11:32:33 -0700
Subject: [PATCH 17/22] Removed comments

---
 images/scipy-ml-notebook/Dockerfile | 16 ----------------
 1 file changed, 16 deletions(-)

diff --git a/images/scipy-ml-notebook/Dockerfile b/images/scipy-ml-notebook/Dockerfile
index 7e87a2a8..bfad60a6 100644
--- a/images/scipy-ml-notebook/Dockerfile
+++ b/images/scipy-ml-notebook/Dockerfile
@@ -53,16 +53,6 @@ USER jovyan
 # CUDA setup w/mamba
 ## TODO: Investigate this command, seems to duplicate cuda packages for nvidia (pypi + conda-forge). 
 # cuda-toolkit is a skeleton package on CUDA 12, unlike CUDA <= 11
-# RUN mamba install -c "nvidia/label/cuda-12.6.0" cuda-nvcc \
-#     cuda-toolkit=$CUDA_VERSION \
-    # For CUDA 11: cudatoolkit=$CUDA_VERSION \
-#     cuda-version=$CUDA_VERSION \
-#     nccl \
-#     -y && \
-#     fix-permissions $CONDA_DIR && \
-#     fix-permissions /home/$NB_USER && \
-#     mamba clean -a -y
-
 RUN uv pip install --extra-index-url https://pypi.nvidia.com nvidia-cuda-nvcc-cu12 nvidia-nccl-cu12 cuda-python --system && \
     fix-permissions $CONDA_DIR && \
     fix-permissions /home/$NB_USER && \
@@ -109,11 +99,5 @@ RUN uv pip install transformers datasets accelerate huggingface-hub timm --syste
 USER $NB_UID:$NB_GID
 ENV PATH=${PATH}:/usr/local/nvidia/bin:/opt/conda/bin
 
-# CUDA fixes for CONDA
-## Copy libdevice file to the required path
-# RUN mkdir -p $CONDA_DIR/lib/nvvm/libdevice && \
-#     cp $CONDA_DIR/nvvm/libdevice/libdevice.10.bc $CONDA_DIR/lib/nvvm/libdevice/
-#     #CUDA 11: cp $CONDA_DIR/lib/libdevice.10.bc $CONDA_DIR/lib/nvvm/libdevice/
-
 # Run datahub scripts
 RUN . /tmp/activate.sh

From 8284e2d9f9d73f9090624d9e910427464a214abf Mon Sep 17 00:00:00 2001
From: yifanzhu1121 <kiki.zhuyifan@gmail.com>
Date: Sun, 10 Aug 2025 21:10:00 -0700
Subject: [PATCH 18/22] datascience-notebook: add r-sf; ensure modern sqlite
 for JupyterLab; keep conda lib on loader path

---
 images/datascience-notebook/Dockerfile | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/images/datascience-notebook/Dockerfile b/images/datascience-notebook/Dockerfile
index 8686f86d..7fbcf63f 100644
--- a/images/datascience-notebook/Dockerfile
+++ b/images/datascience-notebook/Dockerfile
@@ -92,7 +92,7 @@ RUN uv pip install jupyterhub==$JUPYTERHUB_VERSION jupyter_server==$JUPYTERSERVE
     uv cache clean
 
 # Install R packages
-RUN mamba install -c conda-forge r-markdown r-covr r-git2r r-crosstalk r-dt -y && \
+RUN mamba install -c conda-forge r-markdown r-covr r-git2r r-crosstalk r-dt r-sf -y && \
     fix-permissions $CONDA_DIR && \
     fix-permissions /home/$NB_USER && \
     mamba clean -a -y
@@ -103,7 +103,9 @@ RUN /usr/share/datahub/scripts/install-python-all.sh && \
     chmod -R +r /opt/conda/etc/jupyter/nbconfig
 
 # Disable the jupyterlab extensions manager
-RUN jupyter labextension disable @jupyterlab/extensionmanager-extension
+RUN mamba remove --force sqlite && \
+    mamba install -y sqlite && \
+    jupyter labextension disable @jupyterlab/extensionmanager-extension
 
 # Cleanup
 ## nbgrader requires these variables set to just run the notebook server

From bb4583e861b69ef107058168c37484476c20d092 Mon Sep 17 00:00:00 2001
From: RockfordMankiniUCSD
 <92760584+RockfordMankiniUCSD@users.noreply.github.com>
Date: Wed, 13 Aug 2025 16:55:37 -0700
Subject: [PATCH 19/22] Update main.yml

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index beef33e0..2b37c41b 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -44,7 +44,7 @@ jobs:
         with:
           mode: start
           github-token: ${{ secrets.GH_PERSONAL_ACCESS_TOKEN }}
-          ec2-image-id: ami-079a0c9425d45e778
+          ec2-image-id: ami-00bea05327004f12a
           ec2-instance-type: t3.2xlarge
           subnet-id: subnet-0c4a81ef57cf2ebe3
           security-group-id: sg-01cb8c0cb0de3ba00

From 8751623d560f2f6603acadde800b7fb9ae83e919 Mon Sep 17 00:00:00 2001
From: RockfordMankiniUCSD
 <92760584+RockfordMankiniUCSD@users.noreply.github.com>
Date: Wed, 13 Aug 2025 17:00:12 -0700
Subject: [PATCH 20/22] Update Dockerfile

---
 images/datascience-notebook/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/images/datascience-notebook/Dockerfile b/images/datascience-notebook/Dockerfile
index 7fbcf63f..fcda86b6 100644
--- a/images/datascience-notebook/Dockerfile
+++ b/images/datascience-notebook/Dockerfile
@@ -1,4 +1,4 @@
-# If you are building manually, pass PYTHON_VERSION/PY_VER_SHORT/JUPYTERHUB_VERSION with --build-arg
+# If you are building manually, pass PYTHON_VERSION/PY_VER_SHORT/JUPYTERHUB_VERSION with --build-arg 
 ARG PYTHON_VERSION=python-3.11.8
 ARG PY_VER_SHORT=3.11
 ARG JUPYTERHUB_VERSION=4.1.5

From 6b1edcbf72e96a7c247d36570a6bfbf959229dae Mon Sep 17 00:00:00 2001
From: RockfordMankiniUCSD
 <92760584+RockfordMankiniUCSD@users.noreply.github.com>
Date: Wed, 13 Aug 2025 17:19:19 -0700
Subject: [PATCH 21/22] Update Dockerfile

---
 images/datascience-notebook/Dockerfile | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/images/datascience-notebook/Dockerfile b/images/datascience-notebook/Dockerfile
index fcda86b6..74f588e2 100644
--- a/images/datascience-notebook/Dockerfile
+++ b/images/datascience-notebook/Dockerfile
@@ -103,9 +103,7 @@ RUN /usr/share/datahub/scripts/install-python-all.sh && \
     chmod -R +r /opt/conda/etc/jupyter/nbconfig
 
 # Disable the jupyterlab extensions manager
-RUN mamba remove --force sqlite && \
-    mamba install -y sqlite && \
-    jupyter labextension disable @jupyterlab/extensionmanager-extension
+RUN jupyter labextension disable @jupyterlab/extensionmanager-extension
 
 # Cleanup
 ## nbgrader requires these variables set to just run the notebook server

From 4cd836f92ac9fdc5a3d93e7c5959cdc39d0ba879 Mon Sep 17 00:00:00 2001
From: RockfordMankiniUCSD
 <92760584+RockfordMankiniUCSD@users.noreply.github.com>
Date: Wed, 13 Aug 2025 17:33:48 -0700
Subject: [PATCH 22/22] Update Dockerfile

---
 images/datascience-notebook/Dockerfile | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/images/datascience-notebook/Dockerfile b/images/datascience-notebook/Dockerfile
index 74f588e2..932162c2 100644
--- a/images/datascience-notebook/Dockerfile
+++ b/images/datascience-notebook/Dockerfile
@@ -102,6 +102,9 @@ RUN /usr/share/datahub/scripts/install-python-all.sh && \
     chown -R jovyan:users /opt/conda/etc/jupyter/nbconfig && \
     chmod -R +r /opt/conda/etc/jupyter/nbconfig
 
+RUN mamba remove --force libsqlite && \
+    mamba install -y libsqlite==3.46.1
+
 # Disable the jupyterlab extensions manager
 RUN jupyter labextension disable @jupyterlab/extensionmanager-extension