Merge pull request #5192 from berkeley-dsep-infra/staging

merging 5170/5184/5185/5186/5187/5188/5189/5190 to prod
berkeley-dsep-infra · Nov 3, 2023 · d943e28 · d943e28
2 parents 3d6282d + 4b2b270
commit d943e28
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diff --git a/deployments/a11y/image/environment.yml b/deployments/a11y/image/environment.yml
@@ -30,6 +30,7 @@ dependencies:
   # https://github.com/berkeley-dsep-infra/datahub/issues/3693
   - notebook==7.0.2
   - jupyterlab==4.0.4
+  - git+https://github.com/yuvipanda/python-popularity-contest@9e30ec414e45615e75a0e86424141b7093c8f686
   # ###
   # The items below are from infra-requirements, however lab conflicts with the
   # alpha notebook.

diff --git a/deployments/a11y/image/infra-requirements.txt b/deployments/a11y/image/infra-requirements.txt
@@ -24,7 +24,7 @@ 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
-popularity-contest==0.4.1
+git+https://github.com/yuvipanda/python-popularity-contest@9e30ec414e45615e75a0e86424141b7093c8f686
 # RISE is useful for presentations - see https://github.com/berkeley-dsep-infra/datahub/issues/2527
 RISE==5.7.1
 # syncthing for dropbox-like functionality

diff --git a/deployments/astro/image/environment.yml b/deployments/astro/image/environment.yml
@@ -23,7 +23,9 @@ dependencies:
 - protobuf
 - mpich
 - mpi4py
-
+- scikit-learn==1.0.*
+- scikit-image==0.19.*
+- scipy==1.11.3
 - pip
 
 - pip:
@@ -33,9 +35,6 @@ dependencies:
   - opencv-python>=4.5.5.62
   - nose2>=0.10.0
   - sympy
-  - scipy
-  - scikit-learn==1.0.*
-  - scikit-image==0.19.*
   - beautifulsoup4
   - tqdm
   - h5py
@@ -55,7 +54,7 @@ dependencies:
   - astropy>=5.0
   - dustmaps>=1.0.9
   - pyvo>=1.2
-  - joblib==1.1.1
+  - joblib==1.2.0
   - aesara>=2.3.4
   - mkl-service
   - pymc3>=3.11.4
@@ -77,7 +76,7 @@ dependencies:
   - stsci.tools>=4.0.0
   - gensim>=4.1.2
   - tweet-preprocessor
-  - pyLDAvis>=3.3.1
+  - pyLDAvis==3.4.1
   - umap-learn>=0.5.2
   - pydot>=1.4.0
   - TPOT>=0.11.7

diff --git a/deployments/biology/image/Dockerfile b/deployments/biology/image/Dockerfile
@@ -10,8 +10,8 @@ ENV DEBIAN_FRONTEND=noninteractive
 ENV NB_USER jovyan
 ENV NB_UID 1000
 
-ENV CONDA_DIR /opt/conda
-ENV R_LIBS_USER /opt/r
+ENV CONDA_DIR /srv/conda
+ENV R_LIBS_USER /srv/r
 
 # Explicitly add littler to PATH
 # See https://github.com/conda-forge/r-littler-feedstock/issues/6

diff --git a/deployments/biology/image/environment.yml b/deployments/biology/image/environment.yml
@@ -53,6 +53,9 @@ dependencies:
 # compbio BioE c146, Fall 22 and into the future, issue 3785
 - scikit-learn=1.1.2
 
+# bug w/notebook and traitlets: https://github.com/jupyter/notebook/issues/7048
+- traitlets=5.9.*
+
 # For https://github.com/berkeley-dsep-infra/datahub/issues/1846
 # Conda does not have these
 - pip:

diff --git a/deployments/biology/image/infra-requirements.txt b/deployments/biology/image/infra-requirements.txt
@@ -24,7 +24,7 @@ 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
-popularity-contest==0.4.1
+git+https://github.com/yuvipanda/python-popularity-contest@9e30ec414e45615e75a0e86424141b7093c8f686
 # RISE is useful for presentations - see https://github.com/berkeley-dsep-infra/datahub/issues/2527
 RISE==5.7.1
 # syncthing for dropbox-like functionality

diff --git a/deployments/cee/image/infra-requirements.txt b/deployments/cee/image/infra-requirements.txt
@@ -24,7 +24,7 @@ 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
-popularity-contest==0.4.1
+git+https://github.com/yuvipanda/python-popularity-contest@9e30ec414e45615e75a0e86424141b7093c8f686
 # RISE is useful for presentations - see https://github.com/berkeley-dsep-infra/datahub/issues/2527
 RISE==5.7.1
 # syncthing for dropbox-like functionality

diff --git a/deployments/data100/image/environment.yml b/deployments/data100/image/environment.yml
@@ -43,4 +43,4 @@ dependencies:
   - nbconvert==7.6.0
   - pytest-notebook==0.8.1
   - gh-scoped-creds==4.1
-  - popularity-contest==0.4.1
+  - git+https://github.com/yuvipanda/python-popularity-contest@9e30ec414e45615e75a0e86424141b7093c8f686
diff --git a/deployments/data100/image/infra-requirements.txt b/deployments/data100/image/infra-requirements.txt
@@ -24,7 +24,7 @@ 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
-popularity-contest==0.4.1
+git+https://github.com/yuvipanda/python-popularity-contest@9e30ec414e45615e75a0e86424141b7093c8f686
 # RISE is useful for presentations - see https://github.com/berkeley-dsep-infra/datahub/issues/2527
 RISE==5.7.1
 # syncthing for dropbox-like functionality

diff --git a/deployments/data101/image/environment.yml b/deployments/data101/image/environment.yml
@@ -103,4 +103,4 @@ dependencies:
   - pytest-notebook==0.8.1
   - pymongo==4.4.1
   - dbt-postgres==1.6.0
-  - popularity-contest==0.4.1
+  - git+https://github.com/yuvipanda/python-popularity-contest@9e30ec414e45615e75a0e86424141b7093c8f686
diff --git a/deployments/data101/image/infra-requirements.txt b/deployments/data101/image/infra-requirements.txt
@@ -24,7 +24,7 @@ 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
-popularity-contest==0.4.1
+git+https://github.com/yuvipanda/python-popularity-contest@9e30ec414e45615e75a0e86424141b7093c8f686
 # RISE is useful for presentations - see https://github.com/berkeley-dsep-infra/datahub/issues/2527
 RISE==5.7.1
 # syncthing for dropbox-like functionality

diff --git a/deployments/data102/image/environment.yml b/deployments/data102/image/environment.yml
@@ -50,4 +50,4 @@ dependencies:
   - gh-scoped-creds==4.1
   - nb2pdf==0.6.2
   - nbpdfexport==0.2.1
-  - popularity-contest==0.4.1
+  - git+https://github.com/yuvipanda/python-popularity-contest@9e30ec414e45615e75a0e86424141b7093c8f686
diff --git a/deployments/data102/image/infra-requirements.txt b/deployments/data102/image/infra-requirements.txt
@@ -25,7 +25,7 @@ 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
-popularity-contest==0.4.1
+git+https://github.com/yuvipanda/python-popularity-contest@9e30ec414e45615e75a0e86424141b7093c8f686
 # RISE is useful for presentations - see https://github.com/berkeley-dsep-infra/datahub/issues/2527
 RISE==5.7.1
 # syncthing for dropbox-like functionality

diff --git a/deployments/data8/image/Dockerfile b/deployments/data8/image/Dockerfile
@@ -1,6 +1,6 @@
 FROM buildpack-deps:focal-scm
 
-ENV CONDA_DIR /opt/conda
+ENV CONDA_DIR /srv/conda
 
 # Set up common env variables
 ENV TZ=America/Los_Angeles
@@ -17,7 +17,7 @@ RUN adduser --disabled-password --gecos "Default Jupyter user" ${NB_USER}
 
 # Create user owned R libs dir
 # This lets users temporarily install packages
-ENV R_LIBS_USER /opt/r
+ENV R_LIBS_USER /srv/r
 RUN install -d -o ${NB_USER} -g ${NB_USER} ${R_LIBS_USER}
 
 RUN apt-get -qq update --yes && \

diff --git a/deployments/data8/image/environment.yml b/deployments/data8/image/environment.yml
@@ -16,6 +16,9 @@ dependencies:
 # Spring 2023 https://github.com/berkeley-dsep-infra/datahub/issues/4291
 - ipykernel==6.19.4
 
+# bug w/notebook and traitlets: https://github.com/jupyter/notebook/issues/7048
+- traitlets=5.9.*
+
 # Items not in conda forge
 - pip:
 # Export notebooks as PDFs with Chrome

diff --git a/deployments/datahub/images/default/Dockerfile b/deployments/datahub/images/default/Dockerfile
@@ -11,8 +11,8 @@ ENV DEBIAN_FRONTEND=noninteractive
 ENV NB_USER jovyan
 ENV NB_UID 1000
 
-ENV CONDA_DIR /opt/conda
-ENV R_LIBS_USER /opt/r
+ENV CONDA_DIR /srv/conda
+ENV R_LIBS_USER /srv/r
 
 RUN apt-get -qq update --yes && \
     apt-get -qq install --yes locales && \
@@ -36,7 +36,7 @@ RUN install -d -o ${NB_USER} -g ${NB_USER} ${R_LIBS_USER}
 
 # Install R.
 # These packages must be installed into the base stage since they are in system
-# paths rather than /opt.
+# paths rather than /srv.
 # Pre-built R packages from rspm are built against system libs in jammy.
 ENV R_VERSION=4.3.1-1.2204.0
 ENV LITTLER_VERSION=0.3.18-2.2204.0

diff --git a/deployments/datahub/images/default/infra-requirements.txt b/deployments/datahub/images/default/infra-requirements.txt
@@ -24,7 +24,7 @@ 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
-popularity-contest==0.4.1
+git+https://github.com/yuvipanda/python-popularity-contest@9e30ec414e45615e75a0e86424141b7093c8f686
 # RISE is useful for presentations - see https://github.com/berkeley-dsep-infra/datahub/issues/2527
 RISE==5.7.1
 # syncthing for dropbox-like functionality

diff --git a/deployments/dev-r/images/default/Dockerfile b/deployments/dev-r/images/default/Dockerfile
@@ -11,8 +11,8 @@ ENV DEBIAN_FRONTEND=noninteractive
 ENV NB_USER jovyan
 ENV NB_UID 1000
 # These are used by the python, R, and final stages
-ENV CONDA_DIR /opt/conda
-ENV R_LIBS_USER /opt/r
+ENV CONDA_DIR /srv/conda
+ENV R_LIBS_USER /srv/r
 
 RUN apt-get -qq update --yes && \
     apt-get -qq install --yes locales && \
@@ -32,7 +32,7 @@ RUN apt-get -qq update --yes && \
 
 # Install R.
 # These packages must be installed into the base stage since they are in system
-# paths rather than /opt.
+# paths rather than /srv.
 # Pre-built R packages from rspm are built against system libs in jammy.
 ENV R_VERSION=4.3.1-1.2204.0
 ENV LITTLER_VERSION=0.3.18-2.2204.0
@@ -73,8 +73,8 @@ RUN sed -i -e '/^R_LIBS_USER=/s/^/#/' /etc/R/Renviron && \
     echo "TZ=${TZ}" >> /etc/R/Renviron
 
 # =============================================================================
-# This stage exists to build /opt/r.
-FROM base as opt-r
+# This stage exists to build /srv/r.
+FROM base as srv-r
 
 # Create user owned R libs dir
 # This lets users temporarily install packages
@@ -96,8 +96,8 @@ COPY install.R  /tmp/install.R
 RUN /tmp/install.R && rm -rf /tmp/downloaded_packages
 
 # =============================================================================
-# This stage exists to build /opt/conda.
-FROM base as opt-conda
+# This stage exists to build /srv/conda.
+FROM base as srv-conda
 
 COPY install-mambaforge.bash /tmp/install-mambaforge.bash
 RUN /tmp/install-mambaforge.bash
@@ -114,10 +114,10 @@ RUN mamba env update -p ${CONDA_DIR} -f /tmp/environment.yml && \
     mamba clean -afy
 
 # =============================================================================
-# This stage consumes base and import /opt/r and /opt/conda.
+# This stage consumes base and import /srv/r and /srv/conda.
 FROM base as final
-COPY --from=opt-r /opt/r /opt/r
-COPY --from=opt-conda /opt/conda /opt/conda
+COPY --from=srv-r /srv/r /srv/r
+COPY --from=srv-conda /srv/conda /srv/conda
 
 # Install IR kernelspec. Requires python and R.
 ENV PATH ${CONDA_DIR}/bin:${PATH}:${R_LIBS_USER}/bin

diff --git a/deployments/dev-r/images/default/environment.yml b/deployments/dev-r/images/default/environment.yml
@@ -2,6 +2,8 @@ dependencies:
 - python=3.10.*
 - pip=23.1.*
 - nodejs=18.*
+# bug w/notebook and traitlets: https://github.com/jupyter/notebook/issues/7048
+- traitlets=5.9.*
 
 - jupyter-server-proxy==4.0.0
 - jupyter-rsession-proxy==2.2.0

diff --git a/deployments/dev-r/images/default/infra-requirements.txt b/deployments/dev-r/images/default/infra-requirements.txt
@@ -24,7 +24,7 @@ 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
-popularity-contest==0.4.1
+git+https://github.com/yuvipanda/python-popularity-contest@9e30ec414e45615e75a0e86424141b7093c8f686
 # RISE is useful for presentations - see https://github.com/berkeley-dsep-infra/datahub/issues/2527
 RISE==5.7.1
 # syncthing for dropbox-like functionality

diff --git a/deployments/dev-r/images/secondary/environment.yml b/deployments/dev-r/images/secondary/environment.yml
@@ -12,6 +12,9 @@ dependencies:
 
 # 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/deployments/dev-r/images/secondary/infra-requirements.txt b/deployments/dev-r/images/secondary/infra-requirements.txt
@@ -24,7 +24,7 @@ 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
-popularity-contest==0.4.1
+git+https://github.com/yuvipanda/python-popularity-contest@9e30ec414e45615e75a0e86424141b7093c8f686
 # RISE is useful for presentations - see https://github.com/berkeley-dsep-infra/datahub/issues/2527
 RISE==5.7.1
 # syncthing for dropbox-like functionality

diff --git a/deployments/eecs/image/infra-requirements.txt b/deployments/eecs/image/infra-requirements.txt
@@ -24,7 +24,7 @@ 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
-popularity-contest==0.4.1
+git+https://github.com/yuvipanda/python-popularity-contest@9e30ec414e45615e75a0e86424141b7093c8f686
 # RISE is useful for presentations - see https://github.com/berkeley-dsep-infra/datahub/issues/2527
 RISE==5.7.1
 # syncthing for dropbox-like functionality

diff --git a/deployments/ischool/image/environment.yml b/deployments/ischool/image/environment.yml
@@ -4,8 +4,10 @@ channels:
 - conda-forge
 
 dependencies:
-- syncthing==1.22.2
+- syncthing==1.25.0
 - jupyter-rsession-proxy==2.2.0
+# bug w/notebook and traitlets: https://github.com/jupyter/notebook/issues/7048
+- traitlets=5.9.*
 - pip:
   - -r /tmp/infra-requirements.txt
   - otter-grader==3.1.4
diff --git a/deployments/ischool/image/infra-requirements.txt b/deployments/ischool/image/infra-requirements.txt
@@ -24,7 +24,7 @@ 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
-popularity-contest==0.4.1
+git+https://github.com/yuvipanda/python-popularity-contest@9e30ec414e45615e75a0e86424141b7093c8f686
 # RISE is useful for presentations - see https://github.com/berkeley-dsep-infra/datahub/issues/2527
 RISE==5.7.1
 # syncthing for dropbox-like functionality

diff --git a/deployments/publichealth/image/Dockerfile b/deployments/publichealth/image/Dockerfile
@@ -54,14 +54,13 @@ RUN /tmp/install-mambaforge.bash
 
 USER ${NB_USER}
 
+COPY environment.yml /tmp/environment.yml
+RUN mamba env update -p ${CONDA_DIR} -f /tmp/environment.yml && \
+    mamba clean -afy
+
 COPY infra-requirements.txt /tmp/infra-requirements.txt
 RUN pip install --no-cache-dir -r /tmp/infra-requirements.txt
 
-RUN mamba install -c conda-forge syncthing==1.18.6
-
-# Support latest RStudio
-RUN pip install --no-cache 'jupyter-rsession-proxy>=2.0'
-
 # Install IRKernel
 RUN R --quiet -e "install.packages('IRkernel', quiet = TRUE)" && \
     R --quiet -e "IRkernel::installspec(prefix='${CONDA_DIR}')"

diff --git a/deployments/publichealth/image/environment.yml b/deployments/publichealth/image/environment.yml
@@ -1,7 +1,10 @@
 dependencies:
+- pip
+- syncthing==1.18.6
+- jupyter-rsession-proxy==2.2.0
 - pip:
-  - -r /tmp/infra-requirements.txt
+  # bug w/notebook and traitlets: https://github.com/jupyter/notebook/issues/7048
+  - traitlets==5.9.0
+    # - -r /tmp/infra-requirements.txt
 # RStudio support
-  - jupyter-rsession-proxy==2.2.0
   - otter-grader==2.2.7  
-~                          
diff --git a/deployments/publichealth/image/infra-requirements.txt b/deployments/publichealth/image/infra-requirements.txt
@@ -8,6 +8,7 @@
 # everwhere one by one.
 
 # FIXME: Freeze this to get exact versions of all dependencies
+traitlets==5.9.0
 notebook==6.4.12
 jupyterlab==3.4.5
 retrolab==0.3.21

diff --git a/deployments/shiny/image/infra-requirements.txt b/deployments/shiny/image/infra-requirements.txt
@@ -24,7 +24,7 @@ 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
-popularity-contest==0.4.1
+git+https://github.com/yuvipanda/python-popularity-contest@9e30ec414e45615e75a0e86424141b7093c8f686
 # RISE is useful for presentations - see https://github.com/berkeley-dsep-infra/datahub/issues/2527
 RISE==5.7.1
 # syncthing for dropbox-like functionality

diff --git a/deployments/shiny/image/requirements.txt b/deployments/shiny/image/requirements.txt
@@ -2,3 +2,6 @@
 jupyter-rsession-proxy>=2.0
 otter-grader==2.2.7
 jupyter-shiny-proxy==1.1
+
+# bug w/notebook and traitlets: https://github.com/jupyter/notebook/issues/7048
+traitlets==5.9.0
diff --git a/deployments/stat159/image/infra-requirements.txt b/deployments/stat159/image/infra-requirements.txt
@@ -24,7 +24,7 @@ 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
-popularity-contest==0.4.1
+git+https://github.com/yuvipanda/python-popularity-contest@9e30ec414e45615e75a0e86424141b7093c8f686
 # RISE is useful for presentations - see https://github.com/berkeley-dsep-infra/datahub/issues/2527
 RISE==5.7.1
 # syncthing for dropbox-like functionality

diff --git a/deployments/stat20/image/environment.yml b/deployments/stat20/image/environment.yml
@@ -6,6 +6,8 @@ channels:
 dependencies:
 - syncthing==1.22.2
 - jupyter-rsession-proxy==2.2.0
+# bug w/notebook and traitlets: https://github.com/jupyter/notebook/issues/7048
+- traitlets=5.9.*
 - pip:
   - -r /tmp/infra-requirements.txt
     # For push authentication to GitHub