From 33bba44513cf0a235552071a02ef2f08674c412a Mon Sep 17 00:00:00 2001 From: Tristan Garwood Date: Thu, 15 Jun 2023 14:05:26 -0400 Subject: [PATCH 1/4] ID-353 Update terra-notebook-utils version in base. --- config/conf.json | 10 +++++----- terra-jupyter-aou/CHANGELOG.md | 4 ++++ terra-jupyter-aou/Dockerfile | 2 +- terra-jupyter-base/CHANGELOG.md | 4 ++++ terra-jupyter-bioconductor/CHANGELOG.md | 4 ++++ terra-jupyter-bioconductor/Dockerfile | 2 +- terra-jupyter-gatk-ovtf/CHANGELOG.md | 4 ++++ terra-jupyter-gatk-ovtf/Dockerfile | 4 ++-- terra-jupyter-gatk/Dockerfile | 4 ++-- terra-jupyter-hail/Dockerfile | 2 +- terra-jupyter-python/CHANGELOG.md | 4 ++++ terra-jupyter-python/Dockerfile | 2 +- terra-jupyter-r/CHANGELOG.md | 4 ++++ terra-jupyter-r/Dockerfile | 2 +- 14 files changed, 38 insertions(+), 14 deletions(-) diff --git a/config/conf.json b/config/conf.json index 9552aef5..8d24d6de 100644 --- a/config/conf.json +++ b/config/conf.json @@ -26,7 +26,7 @@ "tidyverse" ] }, - "version" : "2.1.11", + "version" : "2.1.12", "automated_flags" : { "generate_docs" : true, "include_in_ui" : true, @@ -68,7 +68,7 @@ "scikit-learn" ] }, - "version" : "1.0.15", + "version" : "1.0.16", "automated_flags" : { "generate_docs" : true, "include_in_ui" : true, @@ -86,7 +86,7 @@ "packages" : { }, - "version" : "1.0.14", + "version" : "1.0.15", "automated_flags" : { "generate_docs" : true, "include_in_ui" : false, @@ -104,7 +104,7 @@ "packages" : { }, - "version" : "2.1.10", + "version" : "2.1.11", "automated_flags" : { "include_in_ui" : false, "generate_docs" : true, @@ -143,7 +143,7 @@ "packages" : { }, - "version" : "2.1.22", + "version" : "2.1.23", "automated_flags" : { "include_in_ui" : false, "generate_docs" : false, diff --git a/terra-jupyter-aou/CHANGELOG.md b/terra-jupyter-aou/CHANGELOG.md index 7709ec23..48a0b41f 100644 --- a/terra-jupyter-aou/CHANGELOG.md +++ b/terra-jupyter-aou/CHANGELOG.md @@ -1,3 +1,7 @@ +## 2.1.23 - 2023-06-15 + +- Update `terra-jupyter-base` to `1.0.15` + ## 2.1.22 - 2023-06-01T17:49:47.721962740Z - Update `terra-jupyter-r` to `2.1.10` diff --git a/terra-jupyter-aou/Dockerfile b/terra-jupyter-aou/Dockerfile index a3bec54b..afaf51ef 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:2.2.12 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.2.14 USER root diff --git a/terra-jupyter-base/CHANGELOG.md b/terra-jupyter-base/CHANGELOG.md index e1eedbc5..fda92bc5 100644 --- a/terra-jupyter-base/CHANGELOG.md +++ b/terra-jupyter-base/CHANGELOG.md @@ -1,3 +1,7 @@ +## 1.0.15 - 2023-06-15 + +- Bump version to rebuild base image with latest jupyter-notebook-utils. + ## 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 f4a06047..daea7d08 100644 --- a/terra-jupyter-bioconductor/CHANGELOG.md +++ b/terra-jupyter-bioconductor/CHANGELOG.md @@ -1,3 +1,7 @@ +## 2.1.12 - 2023-06-15 + +- Update `terra-jupyter-base` to `1.0.15` + ## 2.1.11 - 2023-06-01T17:49:47.622531112Z - Update `terra-jupyter-r` to `2.1.10` diff --git a/terra-jupyter-bioconductor/Dockerfile b/terra-jupyter-bioconductor/Dockerfile index 4bc5e08d..017953f8 100644 --- a/terra-jupyter-bioconductor/Dockerfile +++ b/terra-jupyter-bioconductor/Dockerfile @@ -1 +1 @@ -FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.1.10 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.1.11 diff --git a/terra-jupyter-gatk-ovtf/CHANGELOG.md b/terra-jupyter-gatk-ovtf/CHANGELOG.md index bb7394fa..2bcee948 100644 --- a/terra-jupyter-gatk-ovtf/CHANGELOG.md +++ b/terra-jupyter-gatk-ovtf/CHANGELOG.md @@ -1,3 +1,7 @@ +## 0.2.11 - 2023-06-15 + +- Update `terra-jupyter-base` to `1.0.15` + ## 0.2.10 - 2023-06-01T17:49:47.736670188Z - Update `terra-jupyter-r` to `2.1.10` diff --git a/terra-jupyter-gatk-ovtf/Dockerfile b/terra-jupyter-gatk-ovtf/Dockerfile index 6b820ec1..7a6abf60 100644 --- a/terra-jupyter-gatk-ovtf/Dockerfile +++ b/terra-jupyter-gatk-ovtf/Dockerfile @@ -1,6 +1,6 @@ -FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.0.13 AS python +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.0.14 AS python -FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.1.10 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.1.11 # copy everything pip installed from the python image COPY --from=python /opt/conda/lib/python3.7/site-packages /opt/conda/lib/python3.7/site-packages diff --git a/terra-jupyter-gatk/Dockerfile b/terra-jupyter-gatk/Dockerfile index 87a7b0b7..b0e6672c 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:1.0.15 AS python +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.0.16 AS python -FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.1.10 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.1.11 USER root diff --git a/terra-jupyter-hail/Dockerfile b/terra-jupyter-hail/Dockerfile index e5118944..de56c192 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:1.0.15 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.0.16 USER root ENV PIP_USER=false diff --git a/terra-jupyter-python/CHANGELOG.md b/terra-jupyter-python/CHANGELOG.md index b5888365..ef418bb9 100644 --- a/terra-jupyter-python/CHANGELOG.md +++ b/terra-jupyter-python/CHANGELOG.md @@ -1,3 +1,7 @@ +## 1.0.16 - 2023-06-15 + +- Update `terra-jupyter-base` to `1.0.15` + ## 1.0.15 - 2023-03-13T17:26:34.179905Z - Update `terra-jupyter-base` to `1.0.14` diff --git a/terra-jupyter-python/Dockerfile b/terra-jupyter-python/Dockerfile index ed9a32f4..ff0a9450 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:1.0.14 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:1.0.15 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 c12d23cd..9566a6e8 100644 --- a/terra-jupyter-r/CHANGELOG.md +++ b/terra-jupyter-r/CHANGELOG.md @@ -1,3 +1,7 @@ +## 2.1.11 - 2023-06-15 + +- Bioconductor 3.17 release with R 4.3 + ## 2.1.10 - 2023-06-01T17:49:47.585402026Z - Bioconductor 3.17 release with R 4.3 diff --git a/terra-jupyter-r/Dockerfile b/terra-jupyter-r/Dockerfile index cdb5f208..52de2eea 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:1.0.14 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:1.0.15 USER root COPY scripts $JUPYTER_HOME/scripts From 20d2fcc4ab80b20d9b7d219b5ed657b8c50665ab Mon Sep 17 00:00:00 2001 From: Tristan Garwood Date: Thu, 15 Jun 2023 14:08:39 -0400 Subject: [PATCH 2/4] ID-353 Update terra-notebook-utils version in base. --- terra-jupyter-gatk/CHANGELOG.md | 4 ++++ terra-jupyter-hail/CHANGELOG.md | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/terra-jupyter-gatk/CHANGELOG.md b/terra-jupyter-gatk/CHANGELOG.md index d9dda6af..0ea6b138 100644 --- a/terra-jupyter-gatk/CHANGELOG.md +++ b/terra-jupyter-gatk/CHANGELOG.md @@ -1,5 +1,9 @@ ## 2.2.14 - 2023-06-09 +- Update `terra-jupyter-base` to `1.0.15` + +## 2.2.14 - 2023-06-09 + - Actually install bedtools to accessible path Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.2.14` diff --git a/terra-jupyter-hail/CHANGELOG.md b/terra-jupyter-hail/CHANGELOG.md index 9f6dd4f3..942c012f 100644 --- a/terra-jupyter-hail/CHANGELOG.md +++ b/terra-jupyter-hail/CHANGELOG.md @@ -1,3 +1,7 @@ +## 1.0.27 - 2023-06-07 + +- Update `terra-jupyter-base` to `1.0.15` + ## 1.0.26 - 2023-06-07 - Force the regeneration of 1.0.26 that was never published From 59c88e6766653d5a136754b527d2a979be5def1d Mon Sep 17 00:00:00 2001 From: Tristan Garwood Date: Wed, 5 Jul 2023 13:46:23 -0400 Subject: [PATCH 3/4] Update changelogs and versions post-merge from master --- terra-jupyter-bioconductor/CHANGELOG.md | 2 +- terra-jupyter-gatk-ovtf/CHANGELOG.md | 0 terra-jupyter-gatk-ovtf/Dockerfile | 0 terra-jupyter-gatk/CHANGELOG.md | 10 ++++++---- terra-jupyter-hail/CHANGELOG.md | 4 +++- terra-jupyter-python/CHANGELOG.md | 2 +- 6 files changed, 11 insertions(+), 7 deletions(-) delete mode 100644 terra-jupyter-gatk-ovtf/CHANGELOG.md delete mode 100644 terra-jupyter-gatk-ovtf/Dockerfile diff --git a/terra-jupyter-bioconductor/CHANGELOG.md b/terra-jupyter-bioconductor/CHANGELOG.md index 2fd6e8c4..0c6aed4b 100644 --- a/terra-jupyter-bioconductor/CHANGELOG.md +++ b/terra-jupyter-bioconductor/CHANGELOG.md @@ -1,4 +1,4 @@ -## 2.2.1 - 2023-07-04 +## 2.2.1 - 2023-07-05 - Update `terra-jupyter-base` to `2.2.1` diff --git a/terra-jupyter-gatk-ovtf/CHANGELOG.md b/terra-jupyter-gatk-ovtf/CHANGELOG.md deleted file mode 100644 index e69de29b..00000000 diff --git a/terra-jupyter-gatk-ovtf/Dockerfile b/terra-jupyter-gatk-ovtf/Dockerfile deleted file mode 100644 index e69de29b..00000000 diff --git a/terra-jupyter-gatk/CHANGELOG.md b/terra-jupyter-gatk/CHANGELOG.md index ab70032d..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 @@ -6,10 +12,6 @@ Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.0` ## 2.2.14 - 2023-06-09 -- Update `terra-jupyter-base` to `1.0.15` - -## 2.2.14 - 2023-06-09 - - Actually install bedtools to accessible path Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.2.14` diff --git a/terra-jupyter-hail/CHANGELOG.md b/terra-jupyter-hail/CHANGELOG.md index 39c5bb85..d3a9dbb5 100644 --- a/terra-jupyter-hail/CHANGELOG.md +++ b/terra-jupyter-hail/CHANGELOG.md @@ -1,6 +1,8 @@ ## 1.1.1 - 2023-07-05 -- Update `terra-jupyter-base` to `1.0.15` +- 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 diff --git a/terra-jupyter-python/CHANGELOG.md b/terra-jupyter-python/CHANGELOG.md index 47bce70d..74e90730 100644 --- a/terra-jupyter-python/CHANGELOG.md +++ b/terra-jupyter-python/CHANGELOG.md @@ -1,6 +1,6 @@ ## 1.0.1 - 2023-07-05 -- Update `terra-jupyter-base` to `1.1.11` +- 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` From ba224287d7e7439939f7c80230962e42e7ea69f7 Mon Sep 17 00:00:00 2001 From: Tristan Garwood Date: Wed, 5 Jul 2023 14:30:05 -0400 Subject: [PATCH 4/4] try adding required dependency to test install --- .github/workflows/test-terra-jupyter-aou.yml | 1 + .github/workflows/test-terra-jupyter-base.yml | 1 + .github/workflows/test-terra-jupyter-gatk.yml | 1 + .github/workflows/test-terra-jupyter-hail.yml | 1 + .github/workflows/test-terra-jupyter-python.yml | 1 + terra-jupyter-aou/Dockerfile | 2 +- 6 files changed, 6 insertions(+), 1 deletion(-) 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/terra-jupyter-aou/Dockerfile b/terra-jupyter-aou/Dockerfile index 20437798..8795ddea 100644 --- a/terra-jupyter-aou/Dockerfile +++ b/terra-jupyter-aou/Dockerfile @@ -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"