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ID-353 Update terra-notebook-utils version in base. #433

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ID-353 Update terra-notebook-utils version in base. #433

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33bba44
ID-353 Update terra-notebook-utils version in base.
Ghost-in-a-Jar Jun 15, 2023
20d2fcc
ID-353 Update terra-notebook-utils version in base.
Ghost-in-a-Jar Jun 15, 2023
fb9e444
Merge branch 'master' into ID-353-release-new-terra-notebook-utils
Ghost-in-a-Jar Jul 5, 2023
59c88e6
Update changelogs and versions post-merge from master
Ghost-in-a-Jar Jul 5, 2023
ba22428
try adding required dependency to test install
Ghost-in-a-Jar Jul 5, 2023
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1 change: 1 addition & 0 deletions .github/workflows/test-terra-jupyter-aou.yml
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Expand Up @@ -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/
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Once my PR is merged, you won't have to do that, exceptiongroup released a 1.1.2 version 3 days ago that is corrupted and i figured out a way to cleanly install it

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See https://github.com/DataBiosphere/terra-docker/pull/438/files#diff-de1e25cfbc2d7c346f97e9018096026acb630184d7f365be99ea127ef8b81e3c

docker run \
--env GOOGLE_PROJECT \
--volume "${{ steps.auth.outputs.credentials_file_path }}":/tmp/credentials.json:ro \
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1 change: 1 addition & 0 deletions .github/workflows/test-terra-jupyter-base.yml
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Expand Up @@ -78,6 +78,7 @@ jobs:
- name: Test Python code with pytest
run: |
chmod a+r "${{ 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 "${{ steps.auth.outputs.credentials_file_path }}":/tmp/credentials.json:ro \
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1 change: 1 addition & 0 deletions .github/workflows/test-terra-jupyter-gatk.yml
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Expand Up @@ -98,6 +98,7 @@ jobs:
- name: Test Python code with pytest
run: |
chmod a+r "${{ 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 "${{ steps.auth.outputs.credentials_file_path }}":/tmp/credentials.json:ro \
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1 change: 1 addition & 0 deletions .github/workflows/test-terra-jupyter-hail.yml
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Expand Up @@ -98,6 +98,7 @@ jobs:
- name: Test Python code with pytest
run: |
chmod a+r "${{ 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 "${{ steps.auth.outputs.credentials_file_path }}":/tmp/credentials.json:ro \
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1 change: 1 addition & 0 deletions .github/workflows/test-terra-jupyter-python.yml
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Expand Up @@ -101,6 +101,7 @@ jobs:
- name: Test Python code with pytest
run: |
chmod a+r "${{ 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 \
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14 changes: 7 additions & 7 deletions config/conf.json
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Expand Up @@ -26,7 +26,7 @@
"tidyverse"
]
},
"version" : "2.2.0",
"version" : "2.2.1",
"automated_flags" : {
"generate_docs" : true,
"include_in_ui" : true,
Expand All @@ -47,7 +47,7 @@
"hail"
]
},
"version" : "1.1.0",
"version" : "1.1.1",
"automated_flags" : {
"generate_docs" : true,
"include_in_ui" : true,
Expand All @@ -68,7 +68,7 @@
"scikit-learn"
]
},
"version" : "1.1.0",
"version" : "1.1.1",
"automated_flags" : {
"generate_docs" : true,
"include_in_ui" : true,
Expand All @@ -86,7 +86,7 @@
"packages" : {

},
"version" : "1.1.0",
"version" : "1.1.1",
"automated_flags" : {
"generate_docs" : true,
"include_in_ui" : false,
Expand All @@ -104,7 +104,7 @@
"packages" : {

},
"version" : "2.2.0",
"version" : "2.2.1",
"automated_flags" : {
"include_in_ui" : false,
"generate_docs" : true,
Expand All @@ -124,7 +124,7 @@
"packages" : {

},
"version" : "2.3.0",
"version" : "2.3.1",
"automated_flags" : {
"include_in_ui" : true,
"generate_docs" : true,
Expand All @@ -143,7 +143,7 @@
"packages" : {

},
"version" : "2.2.0",
"version" : "2.2.1",
"automated_flags" : {
"include_in_ui" : false,
"generate_docs" : false,
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6 changes: 6 additions & 0 deletions terra-jupyter-aou/CHANGELOG.md
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@@ -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
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4 changes: 2 additions & 2 deletions terra-jupyter-aou/Dockerfile
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@@ -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

Expand Down Expand Up @@ -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"

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7 changes: 7 additions & 0 deletions terra-jupyter-base/CHANGELOG.md
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@@ -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
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6 changes: 6 additions & 0 deletions terra-jupyter-bioconductor/CHANGELOG.md
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@@ -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
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2 changes: 1 addition & 1 deletion terra-jupyter-bioconductor/Dockerfile
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@@ -1 +1 @@
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
6 changes: 6 additions & 0 deletions terra-jupyter-gatk/CHANGELOG.md
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@@ -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
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4 changes: 2 additions & 2 deletions terra-jupyter-gatk/Dockerfile
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@@ -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

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6 changes: 6 additions & 0 deletions terra-jupyter-hail/CHANGELOG.md
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@@ -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
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2 changes: 1 addition & 1 deletion terra-jupyter-hail/Dockerfile
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@@ -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


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6 changes: 6 additions & 0 deletions terra-jupyter-python/CHANGELOG.md
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@@ -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
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2 changes: 1 addition & 1 deletion terra-jupyter-python/Dockerfile
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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
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6 changes: 6 additions & 0 deletions terra-jupyter-r/CHANGELOG.md
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@@ -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
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2 changes: 1 addition & 1 deletion terra-jupyter-r/Dockerfile
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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
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