diff --git a/.github/workflows/test-terra-jupyter-aou.yml b/.github/workflows/test-terra-jupyter-aou.yml index d3412f11..56e1f7cb 100644 --- a/.github/workflows/test-terra-jupyter-aou.yml +++ b/.github/workflows/test-terra-jupyter-aou.yml @@ -98,6 +98,7 @@ jobs: - name: Test Python code with pytest run: | chmod a+r "${{ steps.auth.outputs.credentials_file_path }}" + rm -rf /opt/conda/lib/python3.10/site-packages/exceptiongroup-1.1.1.dist-info/ docker run \ --env GOOGLE_PROJECT \ --volume "${{ steps.auth.outputs.credentials_file_path }}":/tmp/credentials.json:ro \ diff --git a/.github/workflows/test-terra-jupyter-base.yml b/.github/workflows/test-terra-jupyter-base.yml index 2d61c72a..a3ab6307 100644 --- a/.github/workflows/test-terra-jupyter-base.yml +++ b/.github/workflows/test-terra-jupyter-base.yml @@ -78,6 +78,7 @@ jobs: - name: Test Python code with pytest run: | chmod a+r "${{ steps.auth.outputs.credentials_file_path }}" + rm -rf /opt/conda/lib/python3.10/site-packages/exceptiongroup-1.1.1.dist-info/ docker run \ --env GOOGLE_PROJECT \ --volume "${{ steps.auth.outputs.credentials_file_path }}":/tmp/credentials.json:ro \ diff --git a/.github/workflows/test-terra-jupyter-gatk.yml b/.github/workflows/test-terra-jupyter-gatk.yml index d537b728..2332069a 100644 --- a/.github/workflows/test-terra-jupyter-gatk.yml +++ b/.github/workflows/test-terra-jupyter-gatk.yml @@ -98,6 +98,7 @@ jobs: - name: Test Python code with pytest run: | chmod a+r "${{ steps.auth.outputs.credentials_file_path }}" + rm -rf /opt/conda/lib/python3.10/site-packages/exceptiongroup-1.1.1.dist-info/ docker run \ --env GOOGLE_PROJECT \ --volume "${{ steps.auth.outputs.credentials_file_path }}":/tmp/credentials.json:ro \ diff --git a/.github/workflows/test-terra-jupyter-hail.yml b/.github/workflows/test-terra-jupyter-hail.yml index cc6c777d..f947b3ac 100644 --- a/.github/workflows/test-terra-jupyter-hail.yml +++ b/.github/workflows/test-terra-jupyter-hail.yml @@ -98,6 +98,7 @@ jobs: - name: Test Python code with pytest run: | chmod a+r "${{ steps.auth.outputs.credentials_file_path }}" + rm -rf /opt/conda/lib/python3.10/site-packages/exceptiongroup-1.1.1.dist-info/ docker run \ --env GOOGLE_PROJECT \ --volume "${{ steps.auth.outputs.credentials_file_path }}":/tmp/credentials.json:ro \ diff --git a/.github/workflows/test-terra-jupyter-python.yml b/.github/workflows/test-terra-jupyter-python.yml index 1c903ca7..bd4cffba 100644 --- a/.github/workflows/test-terra-jupyter-python.yml +++ b/.github/workflows/test-terra-jupyter-python.yml @@ -101,6 +101,7 @@ jobs: - name: Test Python code with pytest run: | chmod a+r "${{ steps.auth.outputs.credentials_file_path }}" + rm -rf /opt/conda/lib/python3.10/site-packages/exceptiongroup-1.1.1.dist-info/ docker run \ --env GOOGLE_PROJECT \ --env PIP_USER \ diff --git a/config/conf.json b/config/conf.json index e3e0b1f8..4573ea8c 100644 --- a/config/conf.json +++ b/config/conf.json @@ -26,7 +26,7 @@ "tidyverse" ] }, - "version" : "2.2.0", + "version" : "2.2.1", "automated_flags" : { "generate_docs" : true, "include_in_ui" : true, @@ -47,7 +47,7 @@ "hail" ] }, - "version" : "1.1.0", + "version" : "1.1.1", "automated_flags" : { "generate_docs" : true, "include_in_ui" : true, @@ -68,7 +68,7 @@ "scikit-learn" ] }, - "version" : "1.1.0", + "version" : "1.1.1", "automated_flags" : { "generate_docs" : true, "include_in_ui" : true, @@ -86,7 +86,7 @@ "packages" : { }, - "version" : "1.1.0", + "version" : "1.1.1", "automated_flags" : { "generate_docs" : true, "include_in_ui" : false, @@ -104,7 +104,7 @@ "packages" : { }, - "version" : "2.2.0", + "version" : "2.2.1", "automated_flags" : { "include_in_ui" : false, "generate_docs" : true, @@ -124,7 +124,7 @@ "packages" : { }, - "version" : "2.3.0", + "version" : "2.3.1", "automated_flags" : { "include_in_ui" : true, "generate_docs" : true, @@ -143,7 +143,7 @@ "packages" : { }, - "version" : "2.2.0", + "version" : "2.2.1", "automated_flags" : { "include_in_ui" : false, "generate_docs" : false, diff --git a/terra-jupyter-aou/CHANGELOG.md b/terra-jupyter-aou/CHANGELOG.md index d00de538..d1573346 100644 --- a/terra-jupyter-aou/CHANGELOG.md +++ b/terra-jupyter-aou/CHANGELOG.md @@ -1,3 +1,9 @@ +## 2.2.1 - 2023-07-05 + +- Update `terra-jupyter-base` to `1.1.1` + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-aou:2.2.1` + ## 2.2.0 - 2023-06-23 - Update python from 3.7 to 3.10 diff --git a/terra-jupyter-aou/Dockerfile b/terra-jupyter-aou/Dockerfile index b2b07b4c..8795ddea 100644 --- a/terra-jupyter-aou/Dockerfile +++ b/terra-jupyter-aou/Dockerfile @@ -1,4 +1,4 @@ -FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.0 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.1 USER root @@ -264,7 +264,7 @@ RUN echo "alias cromshell='cromshell-beta'" >> ~/.bash_aliases # Downgrade Jinja2 as the newer version breaks the notebook # See https://jinja.palletsprojects.com/en/3.1.x/changes/#version-3-1-0 -RUN pip install --force-reinstall -v "Jinja2==3.0.3" +RUN pip install -v "Jinja2==3.0.3" ENV PATH="$PATH:/usr/local/RepeatMasker" diff --git a/terra-jupyter-base/CHANGELOG.md b/terra-jupyter-base/CHANGELOG.md index 2d32aa95..02a5cd4c 100644 --- a/terra-jupyter-base/CHANGELOG.md +++ b/terra-jupyter-base/CHANGELOG.md @@ -1,8 +1,15 @@ +## 1.1.1 - 2023-07-05 + +- Bump version to rebuild base image with latest jupyter-notebook-utils. + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:1.1.1` + ## 1.1.0 - 2023-06-23 - Upgrade python 3.7 to 3.10 Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:1.1.0` + ## 1.0.14 - 2023-03-13T17:26:34.128391Z - Include `jupyter lab build` step diff --git a/terra-jupyter-bioconductor/CHANGELOG.md b/terra-jupyter-bioconductor/CHANGELOG.md index 7eb3e677..0c6aed4b 100644 --- a/terra-jupyter-bioconductor/CHANGELOG.md +++ b/terra-jupyter-bioconductor/CHANGELOG.md @@ -1,3 +1,9 @@ +## 2.2.1 - 2023-07-05 + +- Update `terra-jupyter-base` to `2.2.1` + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:2.2.1` + ## 2.2.0 - 2023-06-23 - Update python 3.7 to 3.10 diff --git a/terra-jupyter-bioconductor/Dockerfile b/terra-jupyter-bioconductor/Dockerfile index 2a3b1601..019c1c43 100644 --- a/terra-jupyter-bioconductor/Dockerfile +++ b/terra-jupyter-bioconductor/Dockerfile @@ -1 +1 @@ -FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.0 \ No newline at end of file +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.1 \ No newline at end of file diff --git a/terra-jupyter-gatk/CHANGELOG.md b/terra-jupyter-gatk/CHANGELOG.md index 719b7520..44b65931 100644 --- a/terra-jupyter-gatk/CHANGELOG.md +++ b/terra-jupyter-gatk/CHANGELOG.md @@ -1,3 +1,9 @@ +## 2.3.1 - 2023-07-05 + +- Update `terra-jupyter-base` to `2.3.1`, pulls in latest terra-notebook-utils build. + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.1` + ## 2.3.0 - 2023-06-23 - Update python 3.7 to 3.10 diff --git a/terra-jupyter-gatk/Dockerfile b/terra-jupyter-gatk/Dockerfile index 2b7f315a..6b3cfb8e 100644 --- a/terra-jupyter-gatk/Dockerfile +++ b/terra-jupyter-gatk/Dockerfile @@ -1,6 +1,6 @@ -FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.1.0 AS python +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.1.1 AS python -FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.0 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.1 USER root diff --git a/terra-jupyter-hail/CHANGELOG.md b/terra-jupyter-hail/CHANGELOG.md index 60df676a..d3a9dbb5 100644 --- a/terra-jupyter-hail/CHANGELOG.md +++ b/terra-jupyter-hail/CHANGELOG.md @@ -1,3 +1,9 @@ +## 1.1.1 - 2023-07-05 + +- Update `terra-jupyter-base` to `1.1.1`, pulls in latest terra-notebook-utils build. + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:1.1.1` + ## 1.1.0 - 2023-06-23 - Update python 3.7 to 3.10 diff --git a/terra-jupyter-hail/Dockerfile b/terra-jupyter-hail/Dockerfile index dfd26af5..c8f96609 100644 --- a/terra-jupyter-hail/Dockerfile +++ b/terra-jupyter-hail/Dockerfile @@ -1,4 +1,4 @@ -FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.1.0 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.1.1 USER root diff --git a/terra-jupyter-python/CHANGELOG.md b/terra-jupyter-python/CHANGELOG.md index a68a2385..74e90730 100644 --- a/terra-jupyter-python/CHANGELOG.md +++ b/terra-jupyter-python/CHANGELOG.md @@ -1,3 +1,9 @@ +## 1.0.1 - 2023-07-05 + +- Update `terra-jupyter-base` to `1.1.1`, pulls in latest terra-notebook-utils build. + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.1.1` + ## 1.1.0 - 2023-06-23 - Update python 3.7 to 3.10 diff --git a/terra-jupyter-python/Dockerfile b/terra-jupyter-python/Dockerfile index 69b57057..71b4c7f5 100644 --- a/terra-jupyter-python/Dockerfile +++ b/terra-jupyter-python/Dockerfile @@ -1,4 +1,4 @@ -FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:1.1.0 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:1.1.1 USER root # This makes it so pip runs as root, not the user. ENV PIP_USER=false diff --git a/terra-jupyter-r/CHANGELOG.md b/terra-jupyter-r/CHANGELOG.md index 3cff50a4..97cc5941 100644 --- a/terra-jupyter-r/CHANGELOG.md +++ b/terra-jupyter-r/CHANGELOG.md @@ -1,3 +1,9 @@ +## 2.2.1 - 2023-07-05 + +- Bump base image version to update terra-notebook-utils to latest. + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.1` + ## 2.2.0 - 2023-06-23 - Python upgrade 3.7 to 3.10 diff --git a/terra-jupyter-r/Dockerfile b/terra-jupyter-r/Dockerfile index db423e0d..d22a4afa 100644 --- a/terra-jupyter-r/Dockerfile +++ b/terra-jupyter-r/Dockerfile @@ -1,4 +1,4 @@ -FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:1.1.0 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:1.1.1 USER root COPY scripts $JUPYTER_HOME/scripts