berkeley-dsep-infra · shaneknapp · Nov 9, 2023 · Nov 3, 2023 · Nov 3, 2023 · Nov 3, 2023
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -12,7 +12,7 @@ orbs:
             default: false
 
         docker:
-          - image: python:3.7-slim-bullseye
+          - image: python:3.9-slim-bullseye
         working_directory: ~/repo
         steps:
           - checkout
@@ -22,9 +22,9 @@ orbs:
                 apt-get update && apt-get install --yes --no-install-recommends git curl
           - restore_cache:
               keys:
-                - v3.7-dependencies-{{ checksum "requirements.txt" }}
+                - v3.9-dependencies-{{ checksum "requirements.txt" }}
                 # fallback to using the latest cache if no exact match is found
-                - v3.7-dependencies-
+                - v3.9-dependencies-
 
           - run:
               name: install dependencies
@@ -89,7 +89,7 @@ orbs:
           - save_cache:
               paths:
                 - ./venv
-              key: v3.7-dependencies-{{ checksum "requirements.txt" }}
+              key: v3.9-dependencies-{{ checksum "requirements.txt" }}
 
           - run:
               name: Build image if needed
@@ -100,12 +100,12 @@ orbs:
                   HUBPLOY_ARGS="--commit-range ${COMMIT_RANGE}"
                 fi
                 hubploy build << parameters.deployment >>  ${HUBPLOY_ARGS}
-              no_output_timeout: 60m
+              no_output_timeout: 90m
 
 jobs:
   deploy:
     docker:
-      - image: python:3.8-slim-bullseye
+      - image: python:3.9-slim-bullseye
     working_directory: ~/repo
     steps:
       - run:
@@ -117,9 +117,9 @@ jobs:
       # Download and cache dependencies
       - restore_cache:
           keys:
-            - v3.7-dependencies-gcloud-363-{{ checksum "requirements.txt" }}
+            - v3.9-dependencies-gcloud-363-{{ checksum "requirements.txt" }}
             # fallback to using the latest cache if no exact match is found
-            - v3.7-dependencies-gcloud-363-
+            - v3.9-dependencies-gcloud-363-
 
       - run:
           name: install dependencies
@@ -144,7 +144,7 @@ jobs:
       - save_cache:
           paths:
             - ./venv
-          key: v3.7-dependencies-gcloud-363-{{ checksum "requirements.txt" }}
+          key: v3.9-dependencies-gcloud-363-{{ checksum "requirements.txt" }}
 
       - run:
           name: Authenticating with google service account for kms/sops

diff --git a/deployments/biology/image/Dockerfile b/deployments/biology/image/Dockerfile
@@ -180,10 +180,6 @@ COPY rsession.conf /etc/rstudio/rsession.conf
 # Use simpler locking strategy
 COPY file-locks /etc/rstudio/file-locks
 
-#install rsession proxy
-RUN pip install --no-cache-dir \
-        jupyter-rsession-proxy==2.0.1
-
 # Install IRKernel
 RUN r -e "install.packages('IRkernel', version='1.2')" && \
     r -e "IRkernel::installspec(prefix='${CONDA_DIR}')"

diff --git a/deployments/biology/image/environment.yml b/deployments/biology/image/environment.yml
@@ -13,7 +13,7 @@ dependencies:
 - samtools=1.3.1
 - mafft=7.471
 - emboss=6.6.0
-- augustus=3.3.3
+- augustus=3.5.0
 - raxml-ng=1.0.1
 - structure=2.3.4
 - paml=4.9
@@ -69,3 +69,4 @@ dependencies:
 # Packages for MCB-160L iss #3942
   - allensdk==2.13.6
   - otter-grader==3.1.4
+  - jupyter-rsession-proxy==2.0.1
diff --git a/deployments/biology/image/install-mambaforge.bash b/deployments/biology/image/install-mambaforge.bash
@@ -3,15 +3,11 @@
 set -ex
 
 cd $(dirname $0)
-MAMBAFORGE_VERSION=4.10.3-7
+MAMBAFORGE_VERSION='23.1.0-1'
 
 URL="https://github.com/conda-forge/miniforge/releases/download/${MAMBAFORGE_VERSION}/Mambaforge-${MAMBAFORGE_VERSION}-Linux-x86_64.sh"
 INSTALLER_PATH=/tmp/mambaforge-installer.sh
 
-# make sure we don't do anything funky with user's $HOME
-# since this is run as root
-unset HOME
-
 wget --quiet $URL -O ${INSTALLER_PATH}
 chmod +x ${INSTALLER_PATH}
 

diff --git a/deployments/data8/image/install-mambaforge.bash b/deployments/data8/image/install-mambaforge.bash
@@ -3,15 +3,11 @@
 set -ex
 
 cd $(dirname $0)
-MAMBAFORGE_VERSION=4.10.3-7
+MAMBAFORGE_VERSION='23.1.0-1'
 
 URL="https://github.com/conda-forge/miniforge/releases/download/${MAMBAFORGE_VERSION}/Mambaforge-${MAMBAFORGE_VERSION}-Linux-x86_64.sh"
 INSTALLER_PATH=/tmp/mambaforge-installer.sh
 
-# make sure we don't do anything funky with user's $HOME
-# since this is run as root
-unset HOME
-
 wget --quiet $URL -O ${INSTALLER_PATH}
 chmod +x ${INSTALLER_PATH}
 

diff --git a/deployments/datahub/images/default/Dockerfile b/deployments/datahub/images/default/Dockerfile
@@ -141,11 +141,14 @@ RUN jupyter contrib nbextensions install --sys-prefix --symlink && \
 RUN jupyter nbextension enable --py --sys-prefix qgrid
 
 # Set up nbpdf dependencies
-ENV PYPPETEER_HOME ${CONDA_DIR}
-RUN pyppeteer-install
+# commenting out for DH-164
+#ENV PYPPETEER_HOME ${CONDA_DIR}
+#RUN pyppeteer-install
 
 # install chromium browser for playwright
 # https://github.com/berkeley-dsep-infra/datahub/issues/5062
+# DH-164
+ENV PLAYWRIGHT_BROWSERS_PATH ${CONDA_DIR}
 RUN playwright install chromium
 
 # Install IR kernelspec

diff --git a/deployments/datahub/images/default/apt.txt b/deployments/datahub/images/default/apt.txt
@@ -72,3 +72,6 @@ libgdal-dev
 libgeos-dev
 libproj-dev
 libmysqlclient-dev
+
+# DH-164
+libpci3
diff --git a/deployments/datahub/images/default/environment.yml b/deployments/datahub/images/default/environment.yml
@@ -88,9 +88,6 @@ dependencies:
 # MUSIC 30, https://github.com/berkeley-dsep-infra/datahub/issues/5047
 - music21==8.3.0
 
-# error converting to PDF https://github.com/berkeley-dsep-infra/datahub/issues/5062
-- pyppeteer==1.0.2
-
 # data8; foundation
 - datascience==0.17.6
 

diff --git a/deployments/datahub/images/default/install-mambaforge.bash b/deployments/datahub/images/default/install-mambaforge.bash
@@ -3,15 +3,11 @@
 set -ex
 
 cd $(dirname $0)
-MAMBAFORGE_VERSION=4.10.3-7
+MAMBAFORGE_VERSION='23.1.0-1'
 
 URL="https://github.com/conda-forge/miniforge/releases/download/${MAMBAFORGE_VERSION}/Mambaforge-${MAMBAFORGE_VERSION}-Linux-x86_64.sh"
 INSTALLER_PATH=/tmp/mambaforge-installer.sh
 
-# make sure we don't do anything funky with user's $HOME
-# since this is run as root
-unset HOME
-
 wget --quiet $URL -O ${INSTALLER_PATH}
 chmod +x ${INSTALLER_PATH}
 

diff --git a/deployments/ischool/image/install-mambaforge.bash b/deployments/ischool/image/install-mambaforge.bash
@@ -3,15 +3,11 @@
 set -ex
 
 cd $(dirname $0)
-MAMBAFORGE_VERSION=4.10.3-7
+MAMBAFORGE_VERSION='23.1.0-1'
 
 URL="https://github.com/conda-forge/miniforge/releases/download/${MAMBAFORGE_VERSION}/Mambaforge-${MAMBAFORGE_VERSION}-Linux-x86_64.sh"
 INSTALLER_PATH=/tmp/mambaforge-installer.sh
 
-# make sure we don't do anything funky with user's $HOME
-# since this is run as root
-unset HOME
-
 wget --quiet $URL -O ${INSTALLER_PATH}
 chmod +x ${INSTALLER_PATH}
 

diff --git a/deployments/shiny/image/install-mambaforge.bash b/deployments/shiny/image/install-mambaforge.bash
@@ -3,15 +3,11 @@
 set -ex
 
 cd $(dirname $0)
-MAMBAFORGE_VERSION=4.10.3-7
+MAMBAFORGE_VERSION='23.1.0-1'
 
 URL="https://github.com/conda-forge/miniforge/releases/download/${MAMBAFORGE_VERSION}/Mambaforge-${MAMBAFORGE_VERSION}-Linux-x86_64.sh"
 INSTALLER_PATH=/tmp/mambaforge-installer.sh
 
-# make sure we don't do anything funky with user's $HOME
-# since this is run as root
-unset HOME
-
 wget --quiet $URL -O ${INSTALLER_PATH}
 chmod +x ${INSTALLER_PATH}