diff --git a/.circleci/config.yml b/.circleci/config.yml index 1be1fbad4..53a24c24a 100644 --- 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 >> ${HUBPLOY_ARGS} - no_output_timeout: 60m + no_output_timeout: 90m jobs: deploy: docker: - - image: python:3.8-slim-bullseye + - image: python:3.9-slim-bullseye working_directory: ~/repo steps: - run: @@ -117,9 +117,9 @@ jobs: # Download and cache dependencies - restore_cache: keys: - - v3.7-dependencies-gcloud-363-{{ checksum "requirements.txt" }} + - v3.9-dependencies-gcloud-363-{{ checksum "requirements.txt" }} # fallback to using the latest cache if no exact match is found - - v3.7-dependencies-gcloud-363- + - v3.9-dependencies-gcloud-363- - run: name: install dependencies @@ -144,7 +144,7 @@ jobs: - save_cache: paths: - ./venv - key: v3.7-dependencies-gcloud-363-{{ checksum "requirements.txt" }} + key: v3.9-dependencies-gcloud-363-{{ checksum "requirements.txt" }} - run: name: Authenticating with google service account for kms/sops diff --git a/deployments/biology/image/Dockerfile b/deployments/biology/image/Dockerfile index 97a5db126..b82678a63 100644 --- a/deployments/biology/image/Dockerfile +++ b/deployments/biology/image/Dockerfile @@ -180,10 +180,6 @@ COPY rsession.conf /etc/rstudio/rsession.conf # Use simpler locking strategy COPY file-locks /etc/rstudio/file-locks -#install rsession proxy -RUN pip install --no-cache-dir \ - jupyter-rsession-proxy==2.0.1 - # Install IRKernel RUN r -e "install.packages('IRkernel', version='1.2')" && \ r -e "IRkernel::installspec(prefix='${CONDA_DIR}')" diff --git a/deployments/biology/image/environment.yml b/deployments/biology/image/environment.yml index ec2ba0052..c0bae3c90 100644 --- 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 index 13f431411..38c5cefcd 100644 --- 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 index 13f431411..38c5cefcd 100755 --- 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 index 373798943..4573a74a1 100644 --- 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 index 5d0ac6ed8..67faffd51 100644 --- 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 index c8d7d4f57..12f4f42a7 100644 --- 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 index 13f431411..38c5cefcd 100755 --- 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 index 13f431411..38c5cefcd 100755 --- 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 index 13f431411..38c5cefcd 100755 --- 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}