Merge pull request #5225 from berkeley-dsep-infra/staging

merging 5219/5223/5224/5226 to prod
berkeley-dsep-infra · Nov 17, 2023 · 519fc17 · 519fc17
2 parents 82871a0 + cc1021d
commit 519fc17
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Showing 21 changed files with 223 additions and 210 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
diff --git a/.github/labeler.yml b/.github/labeler.yml
@@ -103,6 +103,8 @@ node-placeholder-scaler:
   - 'deployments/dlab/**'
 'hub: dev-r':
   - 'deployments/dev-r/**'
+'hub: edx':
+  - 'deployments/edx/**'
 'hub: eecs':
   - 'deployments/eecs/**'
 'hub: highschool':

diff --git a/deployments/a11y/image/apt.txt b/deployments/a11y/image/apt.txt
@@ -1,6 +1,9 @@
 # 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
+
 # Download tools
 curl
 wget

diff --git a/deployments/astro/image/apt.txt b/deployments/astro/image/apt.txt
@@ -1,3 +1,6 @@
+# installing less as more just isn't enough
+less
+
 # For desktop environment
 dbus-x11
 xfce4
@@ -20,4 +23,4 @@ emacs
 vim
 
 # For jupyter-tree-download. Ref: https://github.com/berkeley-dsep-infra/datahub/issues/3979			
-zip
+zip
diff --git a/deployments/biology/image/Dockerfile b/deployments/biology/image/Dockerfile
@@ -49,8 +49,8 @@ RUN apt-get update -qq --yes && \
 # Useful utils that folks sort of take for granted
 RUN apt-get update -qq --yes && \
     apt-get install --yes --no-install-recommends -qq \
-        htop \
         less \
+        htop \
         man \
         nano \
         screen \
@@ -169,7 +169,9 @@ USER ${NB_USER}
 COPY environment.yml /tmp/
 COPY infra-requirements.txt /tmp/
 
-RUN mamba env update -p ${CONDA_DIR} -f /tmp/environment.yml && mamba clean -afy
+RUN mamba env update -p ${CONDA_DIR} -f /tmp/environment.yml && \
+    mamba clean -afy
+
 RUN jupyter contrib nbextensions install --sys-prefix --symlink && \
     jupyter nbextensions_configurator enable --sys-prefix
 
@@ -187,7 +189,7 @@ RUN r -e "install.packages('IRkernel', version='1.2')" && \
 # Install R packages, cleanup temp package download location
 COPY install.R /tmp/install.R
 RUN r /tmp/install.R && \
- 	rm -rf /tmp/downloaded_packages/ /tmp/*.rds
+    rm -rf /tmp/downloaded_packages/ /tmp/*.rds
 
 # install bio1b packages
 COPY bio1b-packages.bash /tmp/bio1b-packages.bash

diff --git a/deployments/biology/image/environment.yml b/deployments/biology/image/environment.yml
@@ -9,7 +9,7 @@ dependencies:
 - nb_conda_kernels=2.3.1
 
 # Packages from bioconda for IB134L
-- bwa=0.7.12
+# - bwa=0.7.12
 - samtools=1.3.1
 - mafft=7.471
 - emboss=6.6.0
@@ -23,8 +23,8 @@ dependencies:
 - fastqc=0.11.9
 - phyml=3.3.20200621
 - sra-tools=2.11
-- hisat2=2.2.1
-- subread=2.0.1
+# - hisat2=2.2.1
+# - subread=2.0.1
 - plink=1.90b6.21
 
 - syncthing==1.18.6

diff --git a/deployments/cee/image/apt.txt b/deployments/cee/image/apt.txt
@@ -1,3 +1,6 @@
+# installing less as more just isn't enough
+less
+
 # For desktop environment
 dbus-x11
 xfce4
@@ -30,4 +33,4 @@ texlive-lang-chinese
 libgl1-mesa-glx
 
 # For jupyter-tree-download. Ref: https://github.com/berkeley-dsep-infra/datahub/issues/3979			
-zip
+zip
diff --git a/deployments/data100/image/apt.txt b/deployments/data100/image/apt.txt
@@ -1,6 +1,9 @@
 # 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
 man
 man-db

diff --git a/deployments/data101/image/apt.txt b/deployments/data101/image/apt.txt
@@ -1,6 +1,9 @@
 # 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
 man
 man-db

diff --git a/deployments/data102/image/apt.txt b/deployments/data102/image/apt.txt
@@ -1,6 +1,9 @@
 # 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
 man
 man-db

diff --git a/deployments/data8/image/Dockerfile b/deployments/data8/image/Dockerfile
@@ -22,6 +22,7 @@ RUN install -d -o ${NB_USER} -g ${NB_USER} ${R_LIBS_USER}
 
 RUN apt-get -qq update --yes && \
     apt-get -qq install --yes \
+            less \
             tar \
             vim \
             micro \

diff --git a/deployments/datahub/images/default/apt.txt b/deployments/datahub/images/default/apt.txt
@@ -1,3 +1,6 @@
+# installing less as more just isn't enough
+less
+
 tar
 vim
 micro

diff --git a/deployments/dev-r/images/default/apt.txt b/deployments/dev-r/images/default/apt.txt
@@ -3,8 +3,8 @@ tini
 
 # useful utilities
 tar
-vim
 less
+vim
 
 # for nbconvert, knitr, etc.
 texlive-xetex

diff --git a/deployments/dev-r/images/secondary/apt.txt b/deployments/dev-r/images/secondary/apt.txt
@@ -1,7 +1,7 @@
 # useful utilities
 tar
-vim
 less
+vim
 
 # for nbconvert, knitr, etc.
 texlive-xetex

diff --git a/deployments/eecs/image/apt.txt b/deployments/eecs/image/apt.txt
@@ -1,3 +1,6 @@
+# installing less as more just isn't enough
+less
+
 # For desktop environment 
 dbus-x11
 xfce4

diff --git a/deployments/ischool/image/Dockerfile b/deployments/ischool/image/Dockerfile
@@ -23,6 +23,7 @@ WORKDIR ${HOME}
 # libarchive-dev for https://github.com/berkeley-dsep-infra/datahub/issues/1997
 RUN apt-get update > /dev/null && \
     apt-get install --yes \
+            less \
             fonts-symbola \
             libx11-xcb1 \
             libxtst6 \

diff --git a/deployments/julia/image/Dockerfile b/deployments/julia/image/Dockerfile
@@ -21,8 +21,8 @@ RUN adduser --disabled-password --gecos "Default Jupyter user" ${NB_USER}
 # Useful utils that folks sort of take for granted
 RUN apt-get update -qq --yes && \
     apt-get install --yes -qq \
-        htop \
         less \
+        htop \
         man \
         nano \
         screen \

diff --git a/deployments/publichealth/image/Dockerfile b/deployments/publichealth/image/Dockerfile
@@ -27,6 +27,7 @@ WORKDIR ${HOME}
 # tini is necessary because it is our ENTRYPOINT below.
 RUN apt-get update > /dev/null && \
     apt-get install --yes \
+            less \
             libx11-xcb1 \
             libxtst6 \
             libxrandr2 \

diff --git a/deployments/shiny/image/Dockerfile b/deployments/shiny/image/Dockerfile
@@ -30,6 +30,7 @@ WORKDIR ${HOME}
 # and we don't want them to be downloaded on demand by students.
 RUN apt-get update && \
     apt-get install --yes \
+            less \
             libx11-xcb1 \
             libxtst6 \
             libxrandr2 \

diff --git a/deployments/stat159/image/apt.txt b/deployments/stat159/image/apt.txt
@@ -1,6 +1,9 @@
 # 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
 man
 man-db

diff --git a/deployments/stat20/image/Dockerfile b/deployments/stat20/image/Dockerfile
@@ -29,6 +29,7 @@ WORKDIR ${HOME}
 # tini is necessary because it is our ENTRYPOINT below.
 RUN apt-get update && \
     apt-get -qq install \
+            less \
             tini \
             fonts-symbola \
             pandoc \
-Original file line number
+Diff line change
@@ Expand Up / @@ -22,6 +22,7 @@ RUN install -d -o ${NB_USER} -g ${NB_USER} ${R_LIBS_USER} @@
     RUN apt-get -qq update --yes && \
         apt-get -qq install --yes \
+                less \
                 tar \
                 vim \
                 micro \
@@ Expand Down @@