From c3cfc23d14d0f457352881850ea951c68ef12194 Mon Sep 17 00:00:00 2001 From: LizBaldo Date: Thu, 5 Oct 2023 17:49:01 -0400 Subject: [PATCH 1/4] try to fix the install of pytz --- config/conf.json | 8 ++++---- terra-jupyter-gatk/Dockerfile | 6 +++--- terra-jupyter-hail/Dockerfile | 2 +- terra-jupyter-python/Dockerfile | 6 ++++-- 4 files changed, 12 insertions(+), 10 deletions(-) diff --git a/config/conf.json b/config/conf.json index d37f0c64..d049084f 100644 --- a/config/conf.json +++ b/config/conf.json @@ -47,7 +47,7 @@ "hail" ] }, - "version" : "1.1.3", + "version" : "1.1.4", "automated_flags" : { "generate_docs" : true, "include_in_ui" : true, @@ -68,7 +68,7 @@ "scikit-learn" ] }, - "version" : "1.1.3", + "version" : "1.1.4", "automated_flags" : { "generate_docs" : true, "include_in_ui" : true, @@ -124,7 +124,7 @@ "packages" : { }, - "version" : "2.3.3", + "version" : "2.3.4", "automated_flags" : { "include_in_ui" : true, "generate_docs" : true, @@ -143,7 +143,7 @@ "packages" : { }, - "version" : "2.2.3", + "version" : "2.2.4", "automated_flags" : { "include_in_ui" : false, "generate_docs" : false, diff --git a/terra-jupyter-gatk/Dockerfile b/terra-jupyter-gatk/Dockerfile index 15c84df5..ba3158e4 100644 --- a/terra-jupyter-gatk/Dockerfile +++ b/terra-jupyter-gatk/Dockerfile @@ -1,4 +1,4 @@ -FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.1.3 AS python +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.1.4 AS python FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.3 @@ -82,11 +82,11 @@ RUN patch -u /opt/conda/lib/python3.10/site-packages/vqsr_cnn/vqsr_cnn/models.py # Older version of nbconvert fail to convert notebooks to html RUN pip3 install "nbconvert>=7.7.3" + ENV PIP_USER=true ENV USER jupyter USER $USER -# pytz seems to have a metadata error when installing. Force-reinstalling fixes this. -RUN pip3 install --force-reinstall pytz + diff --git a/terra-jupyter-hail/Dockerfile b/terra-jupyter-hail/Dockerfile index 235df7ef..cd0ad5d6 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:1.1.3 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.1.4 USER root diff --git a/terra-jupyter-python/Dockerfile b/terra-jupyter-python/Dockerfile index f35107a5..c8d0b63c 100644 --- a/terra-jupyter-python/Dockerfile +++ b/terra-jupyter-python/Dockerfile @@ -41,6 +41,9 @@ RUN pip3 -V \ && sed -i 's/pd.tslib.Timestamp/pd.Timestamp/g' /opt/conda/lib/python3.10/site-packages/ggplot/utils.py RUN pip3 install --upgrade markupsafe==2.1.2 +# pytz seems to have a metadata error when installing. Force-reinstalling fixes this. +RUN pip3 install --force-reinstall pytz + ENV USER jupyter USER $USER @@ -49,8 +52,7 @@ ENV PIP_USER=true # Enable Intel oneDNN optimizatoin by default ENV TF_ENABLE_ONEDNN_OPTS=1 -# pytz seems to have a metadata error when installing. Force-reinstalling fixes this. -RUN pip3 install --force-reinstall pytz + # Note: this entrypoint is provided for running Jupyter independently of Leonardo. # When Leonardo deploys this image onto a cluster, the entrypoint is overwritten to enable From e0bc27544341787ce6fb5e03ac9df6a616fc66de Mon Sep 17 00:00:00 2001 From: LizBaldo Date: Thu, 5 Oct 2023 18:09:08 -0400 Subject: [PATCH 2/4] do not force reinstall --- terra-jupyter-aou/Dockerfile | 2 +- terra-jupyter-python/Dockerfile | 3 --- 2 files changed, 1 insertion(+), 4 deletions(-) diff --git a/terra-jupyter-aou/Dockerfile b/terra-jupyter-aou/Dockerfile index cf664cec..aece50e8 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:2.3.3 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.4 USER root diff --git a/terra-jupyter-python/Dockerfile b/terra-jupyter-python/Dockerfile index c8d0b63c..01b6ddf6 100644 --- a/terra-jupyter-python/Dockerfile +++ b/terra-jupyter-python/Dockerfile @@ -41,9 +41,6 @@ RUN pip3 -V \ && sed -i 's/pd.tslib.Timestamp/pd.Timestamp/g' /opt/conda/lib/python3.10/site-packages/ggplot/utils.py RUN pip3 install --upgrade markupsafe==2.1.2 -# pytz seems to have a metadata error when installing. Force-reinstalling fixes this. -RUN pip3 install --force-reinstall pytz - ENV USER jupyter USER $USER From 47714b45e1daf270c24978496e7b6b7144efb06e Mon Sep 17 00:00:00 2001 From: LizBaldo Date: Thu, 5 Oct 2023 23:18:13 -0400 Subject: [PATCH 3/4] pin pytz to previous version --- terra-jupyter-python/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/terra-jupyter-python/requirements.txt b/terra-jupyter-python/requirements.txt index fa2ff4b0..0cb936d9 100644 --- a/terra-jupyter-python/requirements.txt +++ b/terra-jupyter-python/requirements.txt @@ -27,7 +27,7 @@ Cython pysam --no-binary=pysam python-dateutil -pytz +pytz==2023.3 pyvcf3 theano tqdm From 8a400cd6f29a02fc28dac66af35068e18ea8602b Mon Sep 17 00:00:00 2001 From: LizBaldo Date: Fri, 6 Oct 2023 15:11:55 -0400 Subject: [PATCH 4/4] add changelogs --- terra-jupyter-aou/CHANGELOG.md | 7 +++++++ terra-jupyter-gatk/CHANGELOG.md | 6 ++++++ terra-jupyter-hail/CHANGELOG.md | 6 ++++++ terra-jupyter-python/CHANGELOG.md | 6 ++++++ 4 files changed, 25 insertions(+) diff --git a/terra-jupyter-aou/CHANGELOG.md b/terra-jupyter-aou/CHANGELOG.md index a9361591..2a7e402d 100644 --- a/terra-jupyter-aou/CHANGELOG.md +++ b/terra-jupyter-aou/CHANGELOG.md @@ -1,3 +1,10 @@ +## 2.2.4 - 2023-10-06 +- Update `terra-jupyter-gatk` to `2.3.4` + - Update `terra-jupyter-python` to `1.1.4` + - Downgrade pytz to `2023.3` + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-aou:2.2.4` + ## 2.2.3 - 2023-10-03 - Update `terra-jupyter-gatk` to `2.3.3` - Update `terra-jupyter-python` to `1.1.3` diff --git a/terra-jupyter-gatk/CHANGELOG.md b/terra-jupyter-gatk/CHANGELOG.md index 515dc13c..a9d3b301 100644 --- a/terra-jupyter-gatk/CHANGELOG.md +++ b/terra-jupyter-gatk/CHANGELOG.md @@ -1,3 +1,9 @@ +## 2.3.4 - 2023-10-06 +- Update `terra-jupyter-python` to `1.1.4` + - Downgrade pytz to `2023.3` + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.4` + ## 2.3.3 - 2023-10-03 - Update `terra-jupyter-r` to `2.2.3` - Update `terra-jupyter-python` to `1.1.3` diff --git a/terra-jupyter-hail/CHANGELOG.md b/terra-jupyter-hail/CHANGELOG.md index b9b17521..df4ae02c 100644 --- a/terra-jupyter-hail/CHANGELOG.md +++ b/terra-jupyter-hail/CHANGELOG.md @@ -1,3 +1,9 @@ +## 1.1.4 - 2023-10-06 +- Update `terra-jupyter-python` to `1.1.4` + - Downgrade pytz to `2023.3` + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:1.1.4` + ## 1.1.3 - 2023-10-03 - Update `terra-jupyter-python` to `1.1.3` - Update `terra-jupyter-base` to `1.1.3` diff --git a/terra-jupyter-python/CHANGELOG.md b/terra-jupyter-python/CHANGELOG.md index 87b7ba6a..c226ac75 100644 --- a/terra-jupyter-python/CHANGELOG.md +++ b/terra-jupyter-python/CHANGELOG.md @@ -1,3 +1,9 @@ +## 1.1.4 - 2023-10-06 +- Downgrade pytz to `2023.3` + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.1.4` + + ## 1.1.3 - 2023-10-03 - Update `terra-jupyter-base` to `1.1.3` - Downgrade notebook to `6.5.4` and jupyterlab-server to `2.23.0`