From 9c0c673f3fb5e75478def910bd3cbc82d3b5bd0c Mon Sep 17 00:00:00 2001 From: xuscrbw Date: Tue, 21 Sep 2021 09:34:06 -0400 Subject: [PATCH 01/24] adding gatk test --- terra-jupyter-gatk/Dockerfile | 1 - 1 file changed, 1 deletion(-) diff --git a/terra-jupyter-gatk/Dockerfile b/terra-jupyter-gatk/Dockerfile index 7b04f270..1509a696 100644 --- a/terra-jupyter-gatk/Dockerfile +++ b/terra-jupyter-gatk/Dockerfile @@ -49,4 +49,3 @@ RUN patch -u /opt/conda/lib/python3.7/site-packages/vqsr_cnn/vqsr_cnn/models.py ENV USER jupyter USER $USER - From 125bfb76f5cd4d75b220c5b9314e8d70f7de8c36 Mon Sep 17 00:00:00 2001 From: xuscrbw Date: Thu, 7 Oct 2021 09:02:28 -0400 Subject: [PATCH 02/24] readding nbconvert install --- terra-jupyter-base/Dockerfile | 2 ++ 1 file changed, 2 insertions(+) diff --git a/terra-jupyter-base/Dockerfile b/terra-jupyter-base/Dockerfile index 9b0d1b05..bf6dd52f 100644 --- a/terra-jupyter-base/Dockerfile +++ b/terra-jupyter-base/Dockerfile @@ -94,6 +94,8 @@ RUN pip3 -V \ # Hence, make sure to manually test out "launch terminal" button (the button in the green bar next to start and stop buttons) # to make sure we don't accidentally break it every time we upgrade notebook version until we figure out an automation test for this && pip3 install python-datauri \ + # This is to avoid incompatibility issue, see https://github.com/ipython-contrib/jupyter_contrib_nbextensions/issues/1529 + && conda install "nbconvert<6" \ && pip3 install jupyter_contrib_nbextensions \ && pip3 install jupyter_nbextensions_configurator \ # for jupyter_delocalize.py and jupyter_notebook_config.py From 44a806bbf7ba35c7b983c458cdafc7f0078ae22b Mon Sep 17 00:00:00 2001 From: xuscrbw Date: Thu, 7 Oct 2021 09:20:26 -0400 Subject: [PATCH 03/24] adding changelog --- terra-jupyter-base/CHANGELOG.md | 6 ++++++ terra-jupyter-python/Dockerfile | 2 +- terra-jupyter-r/Dockerfile | 2 +- 3 files changed, 8 insertions(+), 2 deletions(-) diff --git a/terra-jupyter-base/CHANGELOG.md b/terra-jupyter-base/CHANGELOG.md index 1a73f982..c9984bcf 100644 --- a/terra-jupyter-base/CHANGELOG.md +++ b/terra-jupyter-base/CHANGELOG.md @@ -1,3 +1,9 @@ +## 1.0.2 - 2021-10-07 + +- Fix nbconvert version issue by explicitly downloading a version less than nbconvert6 + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:1.0.2` + ## 1.0.1 - 2021-09-10T15:10:44.047182Z - Update base image to gcr.io/deeplearning-platform-release/tf2-gpu.2-6 to support TensorFlow 2.6.0 diff --git a/terra-jupyter-python/Dockerfile b/terra-jupyter-python/Dockerfile index 2c23ce3d..604387fe 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:1.0.1 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:1.0.2 USER root # This makes it so pip runs as root, not the user. ENV PIP_USER=false diff --git a/terra-jupyter-r/Dockerfile b/terra-jupyter-r/Dockerfile index 09fb9270..2ea71378 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:1.0.1 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:1.0.2 USER root COPY scripts $JUPYTER_HOME/scripts From 749d0feeafb74cced2fee86d0d7b4145bb7e0e79 Mon Sep 17 00:00:00 2001 From: xuscrbw Date: Thu, 7 Oct 2021 09:30:58 -0400 Subject: [PATCH 04/24] update comments --- terra-jupyter-base/CHANGELOG.md | 2 +- terra-jupyter-gatk/Dockerfile | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/terra-jupyter-base/CHANGELOG.md b/terra-jupyter-base/CHANGELOG.md index c9984bcf..39568e0f 100644 --- a/terra-jupyter-base/CHANGELOG.md +++ b/terra-jupyter-base/CHANGELOG.md @@ -1,6 +1,6 @@ ## 1.0.2 - 2021-10-07 -- Fix nbconvert version issue by explicitly downloading a version less than nbconvert6 +- Fix nbconvert incompatibility issue by explicitly downloading a version less than nbconvert6 Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:1.0.2` diff --git a/terra-jupyter-gatk/Dockerfile b/terra-jupyter-gatk/Dockerfile index 1509a696..7b04f270 100644 --- a/terra-jupyter-gatk/Dockerfile +++ b/terra-jupyter-gatk/Dockerfile @@ -49,3 +49,4 @@ RUN patch -u /opt/conda/lib/python3.7/site-packages/vqsr_cnn/vqsr_cnn/models.py ENV USER jupyter USER $USER + From 47cf3c38a681b4bf928e30ab57f7c916d9b9a13c Mon Sep 17 00:00:00 2001 From: xuscrbw Date: Thu, 7 Oct 2021 09:33:28 -0400 Subject: [PATCH 05/24] update conf file --- config/conf.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/conf.json b/config/conf.json index 3419b408..7b34f6b4 100644 --- a/config/conf.json +++ b/config/conf.json @@ -86,7 +86,7 @@ "packages" : { }, - "version" : "1.0.1", + "version" : "1.0.2", "automated_flags" : { "generate_docs" : true, "include_in_ui" : false, From 4e375de94a1612eff48181222aabf4313a34043f Mon Sep 17 00:00:00 2001 From: xuscrbw Date: Thu, 7 Oct 2021 10:07:00 -0400 Subject: [PATCH 06/24] fixing ci tests --- terra-jupyter-base/Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/terra-jupyter-base/Dockerfile b/terra-jupyter-base/Dockerfile index bf6dd52f..35196732 100644 --- a/terra-jupyter-base/Dockerfile +++ b/terra-jupyter-base/Dockerfile @@ -96,6 +96,7 @@ RUN pip3 -V \ && pip3 install python-datauri \ # This is to avoid incompatibility issue, see https://github.com/ipython-contrib/jupyter_contrib_nbextensions/issues/1529 && conda install "nbconvert<6" \ + && conda install "jupyter_client==6.1.12" \ && pip3 install jupyter_contrib_nbextensions \ && pip3 install jupyter_nbextensions_configurator \ # for jupyter_delocalize.py and jupyter_notebook_config.py From 731f68b438fb47062ac813900c53e04a3910129f Mon Sep 17 00:00:00 2001 From: xuscrbw Date: Thu, 7 Oct 2021 10:48:26 -0400 Subject: [PATCH 07/24] running amm script to update versions --- config/conf.json | 14 +++++++------- terra-jupyter-aou/CHANGELOG.md | 7 +++++++ terra-jupyter-aou/Dockerfile | 2 +- terra-jupyter-base/CHANGELOG.md | 4 ++-- terra-jupyter-bioconductor/CHANGELOG.md | 7 +++++++ terra-jupyter-bioconductor/Dockerfile | 2 +- terra-jupyter-gatk-ovtf/CHANGELOG.md | 7 +++++++ terra-jupyter-gatk-ovtf/Dockerfile | 4 ++-- terra-jupyter-gatk/CHANGELOG.md | 7 +++++++ terra-jupyter-gatk/Dockerfile | 4 ++-- terra-jupyter-hail/CHANGELOG.md | 7 +++++++ terra-jupyter-hail/Dockerfile | 2 +- terra-jupyter-python/CHANGELOG.md | 7 +++++++ terra-jupyter-r/CHANGELOG.md | 7 +++++++ 14 files changed, 65 insertions(+), 16 deletions(-) diff --git a/config/conf.json b/config/conf.json index 7b34f6b4..70bba9e6 100644 --- a/config/conf.json +++ b/config/conf.json @@ -26,7 +26,7 @@ "tidyverse" ] }, - "version" : "2.0.1", + "version" : "2.0.2", "automated_flags" : { "generate_docs" : true, "include_in_ui" : true, @@ -47,7 +47,7 @@ "hail" ] }, - "version" : "1.0.1", + "version" : "1.0.2", "automated_flags" : { "generate_docs" : true, "include_in_ui" : true, @@ -68,7 +68,7 @@ "scikit-learn" ] }, - "version" : "1.0.1", + "version" : "1.0.2", "automated_flags" : { "generate_docs" : true, "include_in_ui" : true, @@ -104,7 +104,7 @@ "packages" : { }, - "version" : "2.0.1", + "version" : "2.0.2", "automated_flags" : { "include_in_ui" : false, "generate_docs" : true, @@ -124,7 +124,7 @@ "packages" : { }, - "version" : "2.0.3", + "version" : "2.0.4", "automated_flags" : { "include_in_ui" : true, "generate_docs" : true, @@ -143,7 +143,7 @@ "packages" : { }, - "version" : "2.0.2", + "version" : "2.0.3", "automated_flags" : { "include_in_ui" : false, "generate_docs" : false, @@ -163,7 +163,7 @@ "packages" : { }, - "version" : "0.1.2", + "version" : "0.1.3", "automated_flags" : { "include_in_ui" : false, "generate_docs" : true, diff --git a/terra-jupyter-aou/CHANGELOG.md b/terra-jupyter-aou/CHANGELOG.md index 82261fbc..d3efe967 100644 --- a/terra-jupyter-aou/CHANGELOG.md +++ b/terra-jupyter-aou/CHANGELOG.md @@ -1,3 +1,10 @@ +## 2.0.3 - 2021-10-07T14:47:43.445699Z + +- Update `terra-jupyter-base` to `1.0.2` + - fixing nbconvert incompatibiity issue by pinning lower versions + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-aou:2.0.3` + ## 2.0.2 - 2021-09-10T15:10:44.156815Z - Update `terra-jupyter-base` to `1.0.1` diff --git a/terra-jupyter-aou/Dockerfile b/terra-jupyter-aou/Dockerfile index 0b63705e..b33c3de6 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:2.0.2 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.0.3 USER root diff --git a/terra-jupyter-base/CHANGELOG.md b/terra-jupyter-base/CHANGELOG.md index 39568e0f..66b91aa9 100644 --- a/terra-jupyter-base/CHANGELOG.md +++ b/terra-jupyter-base/CHANGELOG.md @@ -1,6 +1,6 @@ -## 1.0.2 - 2021-10-07 +## 1.0.2 - 2021-10-07T14:47:43.325878Z -- Fix nbconvert incompatibility issue by explicitly downloading a version less than nbconvert6 +- fixing nbconvert incompatibiity issue by pinning lower versions Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:1.0.2` diff --git a/terra-jupyter-bioconductor/CHANGELOG.md b/terra-jupyter-bioconductor/CHANGELOG.md index cdb2b7c7..73c925a3 100644 --- a/terra-jupyter-bioconductor/CHANGELOG.md +++ b/terra-jupyter-bioconductor/CHANGELOG.md @@ -1,3 +1,10 @@ +## 2.0.2 - 2021-10-07T14:47:43.359733Z + +- Update `terra-jupyter-base` to `1.0.2` + - fixing nbconvert incompatibiity issue by pinning lower versions + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:2.0.2` + ## 2.0.1 - 2021-09-10T15:10:44.079307Z - Update `terra-jupyter-base` to `1.0.1` diff --git a/terra-jupyter-bioconductor/Dockerfile b/terra-jupyter-bioconductor/Dockerfile index cd4d3fbf..bc114910 100644 --- a/terra-jupyter-bioconductor/Dockerfile +++ b/terra-jupyter-bioconductor/Dockerfile @@ -1,4 +1,4 @@ -FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.0.1 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.0.2 USER root diff --git a/terra-jupyter-gatk-ovtf/CHANGELOG.md b/terra-jupyter-gatk-ovtf/CHANGELOG.md index e34a38b7..be38eecc 100644 --- a/terra-jupyter-gatk-ovtf/CHANGELOG.md +++ b/terra-jupyter-gatk-ovtf/CHANGELOG.md @@ -1,3 +1,10 @@ +## 0.1.3 - 2021-10-07T14:47:43.454585Z + +- Update `terra-jupyter-base` to `1.0.2` + - fixing nbconvert incompatibiity issue by pinning lower versions + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk-ovtf:0.1.3` + ## 0.1.2 - 2021-09-22T15:25:34.080267Z - Intel OVTF patch for updating to TF2.6.0/2.5.0 diff --git a/terra-jupyter-gatk-ovtf/Dockerfile b/terra-jupyter-gatk-ovtf/Dockerfile index 06c1d548..29b9fcc5 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:1.0.1 AS python +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.0.2 AS python -FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.0.1 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.0.2 # 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/CHANGELOG.md b/terra-jupyter-gatk/CHANGELOG.md index e87e1ff1..f7ec66ef 100644 --- a/terra-jupyter-gatk/CHANGELOG.md +++ b/terra-jupyter-gatk/CHANGELOG.md @@ -1,3 +1,10 @@ +## 2.0.4 - 2021-10-07T14:47:43.431586Z + +- Update `terra-jupyter-base` to `1.0.2` + - fixing nbconvert incompatibiity issue by pinning lower versions + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.0.4` + ## 2.0.3 - 2021-09-23 - [SUP-465] Terra base gatk notebook image needs Python dependencies diff --git a/terra-jupyter-gatk/Dockerfile b/terra-jupyter-gatk/Dockerfile index 7b04f270..7e95d65f 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:1.0.1 AS python +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.0.2 AS python -FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.0.1 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.0.2 # 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-hail/CHANGELOG.md b/terra-jupyter-hail/CHANGELOG.md index b63e240a..84a9f6cc 100644 --- a/terra-jupyter-hail/CHANGELOG.md +++ b/terra-jupyter-hail/CHANGELOG.md @@ -1,3 +1,10 @@ +## 1.0.2 - 2021-10-07T14:47:43.375974Z + +- Update `terra-jupyter-base` to `1.0.2` + - fixing nbconvert incompatibiity issue by pinning lower versions + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:1.0.2` + ## 1.0.1 - 2021-09-10T15:10:44.093747Z - Update `terra-jupyter-base` to `1.0.1` diff --git a/terra-jupyter-hail/Dockerfile b/terra-jupyter-hail/Dockerfile index 54325a39..69c60968 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:1.0.1 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.0.2 USER root ENV PIP_USER=false diff --git a/terra-jupyter-python/CHANGELOG.md b/terra-jupyter-python/CHANGELOG.md index 2d31777e..9bcb663d 100644 --- a/terra-jupyter-python/CHANGELOG.md +++ b/terra-jupyter-python/CHANGELOG.md @@ -1,3 +1,10 @@ +## 1.0.2 - 2021-10-07T14:47:43.398118Z + +- Update `terra-jupyter-base` to `1.0.2` + - fixing nbconvert incompatibiity issue by pinning lower versions + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.0.2` + ## 1.0.1 - 2021-09-10T15:10:44.113546Z - Update `terra-jupyter-base` to `1.0.1` diff --git a/terra-jupyter-r/CHANGELOG.md b/terra-jupyter-r/CHANGELOG.md index 4f36ccc0..3fd2f32c 100644 --- a/terra-jupyter-r/CHANGELOG.md +++ b/terra-jupyter-r/CHANGELOG.md @@ -1,3 +1,10 @@ +## 2.0.2 - 2021-10-07T14:47:43.422197Z + +- Update `terra-jupyter-base` to `1.0.2` + - fixing nbconvert incompatibiity issue by pinning lower versions + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.0.2` + ## 2.0.1 - 2021-09-10T15:10:44.133967Z - Update `terra-jupyter-base` to `1.0.1` From b5570a4587d59fe76394ae9599542c0abe0f40b0 Mon Sep 17 00:00:00 2001 From: xuscrbw Date: Mon, 18 Oct 2021 08:56:54 -0400 Subject: [PATCH 08/24] use async mapping kernel manager --- terra-jupyter-base/CHANGELOG.md | 2 +- terra-jupyter-base/Dockerfile | 3 --- terra-jupyter-base/jupyter_notebook_config.py | 2 ++ 3 files changed, 3 insertions(+), 4 deletions(-) diff --git a/terra-jupyter-base/CHANGELOG.md b/terra-jupyter-base/CHANGELOG.md index 66b91aa9..f8912d09 100644 --- a/terra-jupyter-base/CHANGELOG.md +++ b/terra-jupyter-base/CHANGELOG.md @@ -1,6 +1,6 @@ ## 1.0.2 - 2021-10-07T14:47:43.325878Z -- fixing nbconvert incompatibiity issue by pinning lower versions +- Update AsyncMappingKernelManager https://github.com/jupyter/notebook/issues/6164 Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:1.0.2` diff --git a/terra-jupyter-base/Dockerfile b/terra-jupyter-base/Dockerfile index 35196732..9b0d1b05 100644 --- a/terra-jupyter-base/Dockerfile +++ b/terra-jupyter-base/Dockerfile @@ -94,9 +94,6 @@ RUN pip3 -V \ # Hence, make sure to manually test out "launch terminal" button (the button in the green bar next to start and stop buttons) # to make sure we don't accidentally break it every time we upgrade notebook version until we figure out an automation test for this && pip3 install python-datauri \ - # This is to avoid incompatibility issue, see https://github.com/ipython-contrib/jupyter_contrib_nbextensions/issues/1529 - && conda install "nbconvert<6" \ - && conda install "jupyter_client==6.1.12" \ && pip3 install jupyter_contrib_nbextensions \ && pip3 install jupyter_nbextensions_configurator \ # for jupyter_delocalize.py and jupyter_notebook_config.py diff --git a/terra-jupyter-base/jupyter_notebook_config.py b/terra-jupyter-base/jupyter_notebook_config.py index 41506293..2b3f248e 100755 --- a/terra-jupyter-base/jupyter_notebook_config.py +++ b/terra-jupyter-base/jupyter_notebook_config.py @@ -42,6 +42,8 @@ 'jupyter_localize_extension': True } +c.NotebookApp.kernel_manager_class = 'notebook.services.kernels.kernelmanager.AsyncMappingKernelManager' + mgr_class = 'DelocalizingContentsManager' if os.environ.get('WELDER_ENABLED') == 'true': mgr_class = 'WelderContentsManager' From 7a0e4ebf8c9f86d1100efeaf5717d1f6d4087837 Mon Sep 17 00:00:00 2001 From: xuscrbw Date: Tue, 19 Oct 2021 16:06:27 -0400 Subject: [PATCH 09/24] fixing changelog --- terra-jupyter-aou/CHANGELOG.md | 2 +- terra-jupyter-bioconductor/CHANGELOG.md | 2 +- terra-jupyter-gatk-ovtf/CHANGELOG.md | 2 +- terra-jupyter-gatk/CHANGELOG.md | 2 +- terra-jupyter-hail/CHANGELOG.md | 2 +- terra-jupyter-python/CHANGELOG.md | 2 +- terra-jupyter-r/CHANGELOG.md | 2 +- 7 files changed, 7 insertions(+), 7 deletions(-) diff --git a/terra-jupyter-aou/CHANGELOG.md b/terra-jupyter-aou/CHANGELOG.md index d3efe967..7770528c 100644 --- a/terra-jupyter-aou/CHANGELOG.md +++ b/terra-jupyter-aou/CHANGELOG.md @@ -1,7 +1,7 @@ ## 2.0.3 - 2021-10-07T14:47:43.445699Z - Update `terra-jupyter-base` to `1.0.2` - - fixing nbconvert incompatibiity issue by pinning lower versions + - Update AsyncMappingKernelManager https://github.com/jupyter/notebook/issues/6164 Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-aou:2.0.3` diff --git a/terra-jupyter-bioconductor/CHANGELOG.md b/terra-jupyter-bioconductor/CHANGELOG.md index 73c925a3..bda1aad5 100644 --- a/terra-jupyter-bioconductor/CHANGELOG.md +++ b/terra-jupyter-bioconductor/CHANGELOG.md @@ -1,7 +1,7 @@ ## 2.0.2 - 2021-10-07T14:47:43.359733Z - Update `terra-jupyter-base` to `1.0.2` - - fixing nbconvert incompatibiity issue by pinning lower versions + - Update AsyncMappingKernelManager https://github.com/jupyter/notebook/issues/6164 Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:2.0.2` diff --git a/terra-jupyter-gatk-ovtf/CHANGELOG.md b/terra-jupyter-gatk-ovtf/CHANGELOG.md index be38eecc..8e8768e7 100644 --- a/terra-jupyter-gatk-ovtf/CHANGELOG.md +++ b/terra-jupyter-gatk-ovtf/CHANGELOG.md @@ -1,7 +1,7 @@ ## 0.1.3 - 2021-10-07T14:47:43.454585Z - Update `terra-jupyter-base` to `1.0.2` - - fixing nbconvert incompatibiity issue by pinning lower versions + - Update AsyncMappingKernelManager https://github.com/jupyter/notebook/issues/6164 Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk-ovtf:0.1.3` diff --git a/terra-jupyter-gatk/CHANGELOG.md b/terra-jupyter-gatk/CHANGELOG.md index f7ec66ef..8906c52b 100644 --- a/terra-jupyter-gatk/CHANGELOG.md +++ b/terra-jupyter-gatk/CHANGELOG.md @@ -1,7 +1,7 @@ ## 2.0.4 - 2021-10-07T14:47:43.431586Z - Update `terra-jupyter-base` to `1.0.2` - - fixing nbconvert incompatibiity issue by pinning lower versions + - Update AsyncMappingKernelManager https://github.com/jupyter/notebook/issues/6164 Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.0.4` diff --git a/terra-jupyter-hail/CHANGELOG.md b/terra-jupyter-hail/CHANGELOG.md index 84a9f6cc..82256c17 100644 --- a/terra-jupyter-hail/CHANGELOG.md +++ b/terra-jupyter-hail/CHANGELOG.md @@ -1,7 +1,7 @@ ## 1.0.2 - 2021-10-07T14:47:43.375974Z - Update `terra-jupyter-base` to `1.0.2` - - fixing nbconvert incompatibiity issue by pinning lower versions + - Update AsyncMappingKernelManager https://github.com/jupyter/notebook/issues/6164 Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:1.0.2` diff --git a/terra-jupyter-python/CHANGELOG.md b/terra-jupyter-python/CHANGELOG.md index 9bcb663d..7d967f7a 100644 --- a/terra-jupyter-python/CHANGELOG.md +++ b/terra-jupyter-python/CHANGELOG.md @@ -1,7 +1,7 @@ ## 1.0.2 - 2021-10-07T14:47:43.398118Z - Update `terra-jupyter-base` to `1.0.2` - - fixing nbconvert incompatibiity issue by pinning lower versions + - Update AsyncMappingKernelManager https://github.com/jupyter/notebook/issues/6164 Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.0.2` diff --git a/terra-jupyter-r/CHANGELOG.md b/terra-jupyter-r/CHANGELOG.md index 3fd2f32c..f9c63a36 100644 --- a/terra-jupyter-r/CHANGELOG.md +++ b/terra-jupyter-r/CHANGELOG.md @@ -1,7 +1,7 @@ ## 2.0.2 - 2021-10-07T14:47:43.422197Z - Update `terra-jupyter-base` to `1.0.2` - - fixing nbconvert incompatibiity issue by pinning lower versions + - Update AsyncMappingKernelManager https://github.com/jupyter/notebook/issues/6164 Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.0.2` From 72e7fa5d86abb380a5ad3f7e25ca9cc055333817 Mon Sep 17 00:00:00 2001 From: xuscrbw Date: Wed, 20 Oct 2021 10:55:43 -0400 Subject: [PATCH 10/24] removing pinned version --- terra-jupyter-r/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/terra-jupyter-r/Dockerfile b/terra-jupyter-r/Dockerfile index 2ea71378..bc6cd7c5 100644 --- a/terra-jupyter-r/Dockerfile +++ b/terra-jupyter-r/Dockerfile @@ -115,7 +115,7 @@ ENV PIP_USER=false ## Install python packages needed for a few Bioc packages RUN pip3 -V \ && pip3 install --upgrade pip \ - && pip3 install cwltool==1.0.20190228155703 \ + && pip3 install cwltool \ && apt-get clean \ && rm -rf /var/lib/apt/lists/* From 6e1f3e0bf09004bcf7332abb23546a74d0dc60d4 Mon Sep 17 00:00:00 2001 From: xuscrbw Date: Wed, 20 Oct 2021 17:17:33 -0400 Subject: [PATCH 11/24] trying newer version of cwltool --- terra-jupyter-r/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/terra-jupyter-r/Dockerfile b/terra-jupyter-r/Dockerfile index bc6cd7c5..0e50e8bc 100644 --- a/terra-jupyter-r/Dockerfile +++ b/terra-jupyter-r/Dockerfile @@ -115,7 +115,7 @@ ENV PIP_USER=false ## Install python packages needed for a few Bioc packages RUN pip3 -V \ && pip3 install --upgrade pip \ - && pip3 install cwltool \ + && pip3 install cwltool==1.0.20191225192155 \ && apt-get clean \ && rm -rf /var/lib/apt/lists/* From 819760acd197295db8cb461da49f1c6fa9a5f923 Mon Sep 17 00:00:00 2001 From: xuscrbw Date: Wed, 20 Oct 2021 18:20:51 -0400 Subject: [PATCH 12/24] trying newer version of cwltool 2 --- terra-jupyter-r/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/terra-jupyter-r/Dockerfile b/terra-jupyter-r/Dockerfile index 0e50e8bc..73de9e18 100644 --- a/terra-jupyter-r/Dockerfile +++ b/terra-jupyter-r/Dockerfile @@ -115,7 +115,7 @@ ENV PIP_USER=false ## Install python packages needed for a few Bioc packages RUN pip3 -V \ && pip3 install --upgrade pip \ - && pip3 install cwltool==1.0.20191225192155 \ + && pip3 install cwltool==3.0.20210124104916 \ && apt-get clean \ && rm -rf /var/lib/apt/lists/* From 6cd293244f6a348bb6f25758cdfd18ce62969b50 Mon Sep 17 00:00:00 2001 From: xuscrbw Date: Wed, 20 Oct 2021 19:22:07 -0400 Subject: [PATCH 13/24] update cwltool 3 --- terra-jupyter-r/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/terra-jupyter-r/Dockerfile b/terra-jupyter-r/Dockerfile index 73de9e18..62cd3d15 100644 --- a/terra-jupyter-r/Dockerfile +++ b/terra-jupyter-r/Dockerfile @@ -115,7 +115,7 @@ ENV PIP_USER=false ## Install python packages needed for a few Bioc packages RUN pip3 -V \ && pip3 install --upgrade pip \ - && pip3 install cwltool==3.0.20210124104916 \ + && pip3 install cwltool==3.0.20210319143721 \ && apt-get clean \ && rm -rf /var/lib/apt/lists/* From ce6042566b0cf614afec29dad15c0f55700e7bc9 Mon Sep 17 00:00:00 2001 From: xuscrbw Date: Wed, 20 Oct 2021 20:24:25 -0400 Subject: [PATCH 14/24] update cwltool 4 --- terra-jupyter-r/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/terra-jupyter-r/Dockerfile b/terra-jupyter-r/Dockerfile index 62cd3d15..62ba0bc0 100644 --- a/terra-jupyter-r/Dockerfile +++ b/terra-jupyter-r/Dockerfile @@ -115,7 +115,7 @@ ENV PIP_USER=false ## Install python packages needed for a few Bioc packages RUN pip3 -V \ && pip3 install --upgrade pip \ - && pip3 install cwltool==3.0.20210319143721 \ + && pip3 install cwltool==3.1.20210628163208 \ && apt-get clean \ && rm -rf /var/lib/apt/lists/* From b1eb0fa9db4937e44cabc1ec5bb13777b71736f6 Mon Sep 17 00:00:00 2001 From: xuscrbw Date: Thu, 21 Oct 2021 20:56:05 -0400 Subject: [PATCH 15/24] updating protobuf version and removing cwltool pin --- terra-jupyter-r/Dockerfile | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/terra-jupyter-r/Dockerfile b/terra-jupyter-r/Dockerfile index 62ba0bc0..1012d0eb 100644 --- a/terra-jupyter-r/Dockerfile +++ b/terra-jupyter-r/Dockerfile @@ -8,10 +8,11 @@ ENV TERRA_R_PLATFORM="terra-jupyter-r" ENV TERRA_R_PLATFORM_BINARY_VERSION=3.13.0 # Install protobuf 3.16. Note this version comes from base deep learning image. Use `conda list` to see what's installed +# It looks like the deep learning image now uses protobuf 3.18 RUN cd /tmp \ - && wget https://github.com/protocolbuffers/protobuf/releases/download/v3.16.0/protobuf-all-3.16.0.tar.gz \ - && tar -xvzf protobuf-all-3.16.0.tar.gz \ - && cd protobuf-3.16.0/ \ + && wget https://github.com/protocolbuffers/protobuf/releases/download/v3.18.0/protobuf-all-3.18.0.tar.gz \ + && tar -xvzf protobuf-all-3.18.0.tar.gz \ + && cd protobuf-3.18.0/ \ && ./configure \ && make \ && make check \ @@ -115,7 +116,12 @@ ENV PIP_USER=false ## Install python packages needed for a few Bioc packages RUN pip3 -V \ && pip3 install --upgrade pip \ - && pip3 install cwltool==3.1.20210628163208 \ +# Setuptools introduced a breaking change for the function use_2to3 in version 58 https://setuptools.pypa.io/en/latest/history.html#v58-0-0 +# If we do not bump the version, we will see the following error when trying to install protolite on terra-jupyter-bioconductor: +# "error in rdflib-jsonld setup command: use_2to3 is invalid." +# && pip3 install "setuptools==57.5" --force-reinstall \ +# && pip3 install cwltool==1.0.20190228155703 \ + && pip3 install cwltool \ && apt-get clean \ && rm -rf /var/lib/apt/lists/* From e68f9b919ebe130c1f06c9cdb98f2cf3c9f11986 Mon Sep 17 00:00:00 2001 From: xuscrbw Date: Fri, 22 Oct 2021 10:24:09 -0400 Subject: [PATCH 16/24] force reinstall of typing extensions to resolve metadata issue --- terra-jupyter-gatk-ovtf/Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/terra-jupyter-gatk-ovtf/Dockerfile b/terra-jupyter-gatk-ovtf/Dockerfile index 29b9fcc5..a9dec205 100644 --- a/terra-jupyter-gatk-ovtf/Dockerfile +++ b/terra-jupyter-gatk-ovtf/Dockerfile @@ -46,6 +46,7 @@ RUN cd /gatk-build \ ENV PIP_USER=false RUN pip install --force-reinstall tensorflow==2.5.0 \ pip install --force-reinstall keras==2.5.0rc0 \ + pip install --force-reinstall typing-extensions \ && conda install six \ && pip install openvino_tensorflow \ && pip install matplotlib sklearn \ From 26cc04ca8f4ef14f0d8a0f4170dfe8d169b1b029 Mon Sep 17 00:00:00 2001 From: xuscrbw Date: Fri, 22 Oct 2021 11:43:16 -0400 Subject: [PATCH 17/24] adding println for smoke test --- terra-jupyter-bioconductor/tests/smoke_test.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/terra-jupyter-bioconductor/tests/smoke_test.ipynb b/terra-jupyter-bioconductor/tests/smoke_test.ipynb index f9a6ed0d..20c8b1a0 100644 --- a/terra-jupyter-bioconductor/tests/smoke_test.ipynb +++ b/terra-jupyter-bioconductor/tests/smoke_test.ipynb @@ -430,7 +430,7 @@ "metadata": {}, "outputs": [], "source": [ - "assert_that(\"Seurat\" %in% installed.packages() == 'TRUE')" + "print(\"Seurat\" %in% installed.packages())" ] } ], From 0fb5a25ac59e1188ec610eb8de69c1f6a83d88cf Mon Sep 17 00:00:00 2001 From: xuscrbw Date: Fri, 22 Oct 2021 14:06:47 -0400 Subject: [PATCH 18/24] revert println --- terra-jupyter-bioconductor/tests/smoke_test.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/terra-jupyter-bioconductor/tests/smoke_test.ipynb b/terra-jupyter-bioconductor/tests/smoke_test.ipynb index 20c8b1a0..f9a6ed0d 100644 --- a/terra-jupyter-bioconductor/tests/smoke_test.ipynb +++ b/terra-jupyter-bioconductor/tests/smoke_test.ipynb @@ -430,7 +430,7 @@ "metadata": {}, "outputs": [], "source": [ - "print(\"Seurat\" %in% installed.packages())" + "assert_that(\"Seurat\" %in% installed.packages() == 'TRUE')" ] } ], From bbd0eabc041821557064c09c8949b410f744cf5a Mon Sep 17 00:00:00 2001 From: xuscrbw Date: Fri, 22 Oct 2021 15:37:44 -0400 Subject: [PATCH 19/24] ran amm script for R image and removed comments --- config/conf.json | 10 +++++----- terra-jupyter-aou/CHANGELOG.md | 7 +++++++ terra-jupyter-aou/Dockerfile | 2 +- terra-jupyter-bioconductor/CHANGELOG.md | 7 +++++++ terra-jupyter-bioconductor/Dockerfile | 2 +- terra-jupyter-gatk-ovtf/CHANGELOG.md | 7 +++++++ terra-jupyter-gatk-ovtf/Dockerfile | 3 +-- terra-jupyter-gatk/CHANGELOG.md | 7 +++++++ terra-jupyter-gatk/Dockerfile | 2 +- terra-jupyter-r/CHANGELOG.md | 6 ++++++ terra-jupyter-r/Dockerfile | 8 +------- 11 files changed, 44 insertions(+), 17 deletions(-) diff --git a/config/conf.json b/config/conf.json index 70bba9e6..da43244c 100644 --- a/config/conf.json +++ b/config/conf.json @@ -26,7 +26,7 @@ "tidyverse" ] }, - "version" : "2.0.2", + "version" : "2.0.3", "automated_flags" : { "generate_docs" : true, "include_in_ui" : true, @@ -104,7 +104,7 @@ "packages" : { }, - "version" : "2.0.2", + "version" : "2.0.3", "automated_flags" : { "include_in_ui" : false, "generate_docs" : true, @@ -124,7 +124,7 @@ "packages" : { }, - "version" : "2.0.4", + "version" : "2.0.5", "automated_flags" : { "include_in_ui" : true, "generate_docs" : true, @@ -143,7 +143,7 @@ "packages" : { }, - "version" : "2.0.3", + "version" : "2.0.4", "automated_flags" : { "include_in_ui" : false, "generate_docs" : false, @@ -163,7 +163,7 @@ "packages" : { }, - "version" : "0.1.3", + "version" : "0.1.4", "automated_flags" : { "include_in_ui" : false, "generate_docs" : true, diff --git a/terra-jupyter-aou/CHANGELOG.md b/terra-jupyter-aou/CHANGELOG.md index 7770528c..4b707097 100644 --- a/terra-jupyter-aou/CHANGELOG.md +++ b/terra-jupyter-aou/CHANGELOG.md @@ -1,3 +1,10 @@ +## 2.0.4 - 2021-10-22T19:36:23.183453Z + +- Update `terra-jupyter-r` to `2.0.3` + - Unpinning cwltool version and updating protobuf version to 3.18 + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-aou:2.0.4` + ## 2.0.3 - 2021-10-07T14:47:43.445699Z - Update `terra-jupyter-base` to `1.0.2` diff --git a/terra-jupyter-aou/Dockerfile b/terra-jupyter-aou/Dockerfile index b33c3de6..5353cbb7 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:2.0.3 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.0.4 USER root diff --git a/terra-jupyter-bioconductor/CHANGELOG.md b/terra-jupyter-bioconductor/CHANGELOG.md index bda1aad5..3e808f64 100644 --- a/terra-jupyter-bioconductor/CHANGELOG.md +++ b/terra-jupyter-bioconductor/CHANGELOG.md @@ -1,3 +1,10 @@ +## 2.0.3 - 2021-10-22T19:36:23.124869Z + +- Update `terra-jupyter-r` to `2.0.3` + - Unpinning cwltool version and updating protobuf version to 3.18 + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:2.0.3` + ## 2.0.2 - 2021-10-07T14:47:43.359733Z - Update `terra-jupyter-base` to `1.0.2` diff --git a/terra-jupyter-bioconductor/Dockerfile b/terra-jupyter-bioconductor/Dockerfile index bc114910..aacdec79 100644 --- a/terra-jupyter-bioconductor/Dockerfile +++ b/terra-jupyter-bioconductor/Dockerfile @@ -1,4 +1,4 @@ -FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.0.2 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.0.3 USER root diff --git a/terra-jupyter-gatk-ovtf/CHANGELOG.md b/terra-jupyter-gatk-ovtf/CHANGELOG.md index 8e8768e7..f48935a7 100644 --- a/terra-jupyter-gatk-ovtf/CHANGELOG.md +++ b/terra-jupyter-gatk-ovtf/CHANGELOG.md @@ -1,3 +1,10 @@ +## 0.1.4 - 2021-10-22T19:36:23.200853Z + +- Update `terra-jupyter-r` to `2.0.3` + - Unpinning cwltool version and updating protobuf version to 3.18 + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk-ovtf:0.1.4` + ## 0.1.3 - 2021-10-07T14:47:43.454585Z - Update `terra-jupyter-base` to `1.0.2` diff --git a/terra-jupyter-gatk-ovtf/Dockerfile b/terra-jupyter-gatk-ovtf/Dockerfile index a9dec205..c8ff862f 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:1.0.2 AS python -FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.0.2 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.0.3 # 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 @@ -46,7 +46,6 @@ RUN cd /gatk-build \ ENV PIP_USER=false RUN pip install --force-reinstall tensorflow==2.5.0 \ pip install --force-reinstall keras==2.5.0rc0 \ - pip install --force-reinstall typing-extensions \ && conda install six \ && pip install openvino_tensorflow \ && pip install matplotlib sklearn \ diff --git a/terra-jupyter-gatk/CHANGELOG.md b/terra-jupyter-gatk/CHANGELOG.md index 8906c52b..29d6ab82 100644 --- a/terra-jupyter-gatk/CHANGELOG.md +++ b/terra-jupyter-gatk/CHANGELOG.md @@ -1,3 +1,10 @@ +## 2.0.5 - 2021-10-22T19:36:23.147259Z + +- Update `terra-jupyter-r` to `2.0.3` + - Unpinning cwltool version and updating protobuf version to 3.18 + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.0.5` + ## 2.0.4 - 2021-10-07T14:47:43.431586Z - Update `terra-jupyter-base` to `1.0.2` diff --git a/terra-jupyter-gatk/Dockerfile b/terra-jupyter-gatk/Dockerfile index 7e95d65f..860a93d3 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:1.0.2 AS python -FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.0.2 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.0.3 # 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-r/CHANGELOG.md b/terra-jupyter-r/CHANGELOG.md index f9c63a36..70b6571a 100644 --- a/terra-jupyter-r/CHANGELOG.md +++ b/terra-jupyter-r/CHANGELOG.md @@ -1,3 +1,9 @@ +## 2.0.3 - 2021-10-22T19:36:23.085487Z + +- Unpinning cwltool version and updating protobuf version to 3.18 + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.0.3` + ## 2.0.2 - 2021-10-07T14:47:43.422197Z - Update `terra-jupyter-base` to `1.0.2` diff --git a/terra-jupyter-r/Dockerfile b/terra-jupyter-r/Dockerfile index 1012d0eb..d8b65c86 100644 --- a/terra-jupyter-r/Dockerfile +++ b/terra-jupyter-r/Dockerfile @@ -7,8 +7,7 @@ COPY scripts $JUPYTER_HOME/scripts ENV TERRA_R_PLATFORM="terra-jupyter-r" ENV TERRA_R_PLATFORM_BINARY_VERSION=3.13.0 -# Install protobuf 3.16. Note this version comes from base deep learning image. Use `conda list` to see what's installed -# It looks like the deep learning image now uses protobuf 3.18 +# Install protobuf 3.18. Note this version comes from base deep learning image. Use `conda list` to see what's installed RUN cd /tmp \ && wget https://github.com/protocolbuffers/protobuf/releases/download/v3.18.0/protobuf-all-3.18.0.tar.gz \ && tar -xvzf protobuf-all-3.18.0.tar.gz \ @@ -116,11 +115,6 @@ ENV PIP_USER=false ## Install python packages needed for a few Bioc packages RUN pip3 -V \ && pip3 install --upgrade pip \ -# Setuptools introduced a breaking change for the function use_2to3 in version 58 https://setuptools.pypa.io/en/latest/history.html#v58-0-0 -# If we do not bump the version, we will see the following error when trying to install protolite on terra-jupyter-bioconductor: -# "error in rdflib-jsonld setup command: use_2to3 is invalid." -# && pip3 install "setuptools==57.5" --force-reinstall \ -# && pip3 install cwltool==1.0.20190228155703 \ && pip3 install cwltool \ && apt-get clean \ && rm -rf /var/lib/apt/lists/* From 4799f2d1eb4c529c27c923a99f3ba69d33334a8a Mon Sep 17 00:00:00 2001 From: Qi Wang Date: Mon, 25 Oct 2021 18:03:26 -0400 Subject: [PATCH 20/24] don't bump twice --- config/conf.json | 8 ++++---- terra-jupyter-bioconductor/CHANGELOG.md | 8 +------- terra-jupyter-bioconductor/Dockerfile | 2 +- terra-jupyter-gatk-ovtf/CHANGELOG.md | 8 +------- terra-jupyter-gatk-ovtf/Dockerfile | 2 +- terra-jupyter-gatk/CHANGELOG.md | 8 +------- terra-jupyter-gatk/Dockerfile | 2 +- terra-jupyter-r/CHANGELOG.md | 7 +------ 8 files changed, 11 insertions(+), 34 deletions(-) diff --git a/config/conf.json b/config/conf.json index da43244c..b7d52f1c 100644 --- a/config/conf.json +++ b/config/conf.json @@ -26,7 +26,7 @@ "tidyverse" ] }, - "version" : "2.0.3", + "version" : "2.0.2", "automated_flags" : { "generate_docs" : true, "include_in_ui" : true, @@ -104,7 +104,7 @@ "packages" : { }, - "version" : "2.0.3", + "version" : "2.0.2", "automated_flags" : { "include_in_ui" : false, "generate_docs" : true, @@ -124,7 +124,7 @@ "packages" : { }, - "version" : "2.0.5", + "version" : "2.0.4", "automated_flags" : { "include_in_ui" : true, "generate_docs" : true, @@ -163,7 +163,7 @@ "packages" : { }, - "version" : "0.1.4", + "version" : "0.1.3", "automated_flags" : { "include_in_ui" : false, "generate_docs" : true, diff --git a/terra-jupyter-bioconductor/CHANGELOG.md b/terra-jupyter-bioconductor/CHANGELOG.md index 3e808f64..58a7e454 100644 --- a/terra-jupyter-bioconductor/CHANGELOG.md +++ b/terra-jupyter-bioconductor/CHANGELOG.md @@ -1,14 +1,8 @@ -## 2.0.3 - 2021-10-22T19:36:23.124869Z - -- Update `terra-jupyter-r` to `2.0.3` - - Unpinning cwltool version and updating protobuf version to 3.18 - -Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:2.0.3` - ## 2.0.2 - 2021-10-07T14:47:43.359733Z - Update `terra-jupyter-base` to `1.0.2` - Update AsyncMappingKernelManager https://github.com/jupyter/notebook/issues/6164 +- Unpinning cwltool version and updating protobuf version to 3.18 Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:2.0.2` diff --git a/terra-jupyter-bioconductor/Dockerfile b/terra-jupyter-bioconductor/Dockerfile index aacdec79..bc114910 100644 --- a/terra-jupyter-bioconductor/Dockerfile +++ b/terra-jupyter-bioconductor/Dockerfile @@ -1,4 +1,4 @@ -FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.0.3 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.0.2 USER root diff --git a/terra-jupyter-gatk-ovtf/CHANGELOG.md b/terra-jupyter-gatk-ovtf/CHANGELOG.md index f48935a7..757f7c73 100644 --- a/terra-jupyter-gatk-ovtf/CHANGELOG.md +++ b/terra-jupyter-gatk-ovtf/CHANGELOG.md @@ -1,14 +1,8 @@ -## 0.1.4 - 2021-10-22T19:36:23.200853Z - -- Update `terra-jupyter-r` to `2.0.3` - - Unpinning cwltool version and updating protobuf version to 3.18 - -Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk-ovtf:0.1.4` - ## 0.1.3 - 2021-10-07T14:47:43.454585Z - Update `terra-jupyter-base` to `1.0.2` - Update AsyncMappingKernelManager https://github.com/jupyter/notebook/issues/6164 +- Unpinning cwltool version and updating protobuf version to 3.18 Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk-ovtf:0.1.3` diff --git a/terra-jupyter-gatk-ovtf/Dockerfile b/terra-jupyter-gatk-ovtf/Dockerfile index c8ff862f..29b9fcc5 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:1.0.2 AS python -FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.0.3 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.0.2 # 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/CHANGELOG.md b/terra-jupyter-gatk/CHANGELOG.md index 29d6ab82..520a31f9 100644 --- a/terra-jupyter-gatk/CHANGELOG.md +++ b/terra-jupyter-gatk/CHANGELOG.md @@ -1,14 +1,8 @@ -## 2.0.5 - 2021-10-22T19:36:23.147259Z - -- Update `terra-jupyter-r` to `2.0.3` - - Unpinning cwltool version and updating protobuf version to 3.18 - -Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.0.5` - ## 2.0.4 - 2021-10-07T14:47:43.431586Z - Update `terra-jupyter-base` to `1.0.2` - Update AsyncMappingKernelManager https://github.com/jupyter/notebook/issues/6164 +- Unpinning cwltool version and updating protobuf version to 3.18 Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.0.4` diff --git a/terra-jupyter-gatk/Dockerfile b/terra-jupyter-gatk/Dockerfile index 860a93d3..7e95d65f 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:1.0.2 AS python -FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.0.3 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.0.2 # 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-r/CHANGELOG.md b/terra-jupyter-r/CHANGELOG.md index 70b6571a..c3d4c210 100644 --- a/terra-jupyter-r/CHANGELOG.md +++ b/terra-jupyter-r/CHANGELOG.md @@ -1,13 +1,8 @@ -## 2.0.3 - 2021-10-22T19:36:23.085487Z - -- Unpinning cwltool version and updating protobuf version to 3.18 - -Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.0.3` - ## 2.0.2 - 2021-10-07T14:47:43.422197Z - Update `terra-jupyter-base` to `1.0.2` - Update AsyncMappingKernelManager https://github.com/jupyter/notebook/issues/6164 +- Unpinning cwltool version and updating protobuf version to 3.18 Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.0.2` From 6033987f5dbe07e09568c3358d4899e7953f5f65 Mon Sep 17 00:00:00 2001 From: Qi Wang Date: Mon, 25 Oct 2021 18:04:39 -0400 Subject: [PATCH 21/24] aou as well --- config/conf.json | 2 +- terra-jupyter-aou/CHANGELOG.md | 8 +------- 2 files changed, 2 insertions(+), 8 deletions(-) diff --git a/config/conf.json b/config/conf.json index b7d52f1c..70bba9e6 100644 --- a/config/conf.json +++ b/config/conf.json @@ -143,7 +143,7 @@ "packages" : { }, - "version" : "2.0.4", + "version" : "2.0.3", "automated_flags" : { "include_in_ui" : false, "generate_docs" : false, diff --git a/terra-jupyter-aou/CHANGELOG.md b/terra-jupyter-aou/CHANGELOG.md index 4b707097..42dd9529 100644 --- a/terra-jupyter-aou/CHANGELOG.md +++ b/terra-jupyter-aou/CHANGELOG.md @@ -1,14 +1,8 @@ -## 2.0.4 - 2021-10-22T19:36:23.183453Z - -- Update `terra-jupyter-r` to `2.0.3` - - Unpinning cwltool version and updating protobuf version to 3.18 - -Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-aou:2.0.4` - ## 2.0.3 - 2021-10-07T14:47:43.445699Z - Update `terra-jupyter-base` to `1.0.2` - Update AsyncMappingKernelManager https://github.com/jupyter/notebook/issues/6164 +- Unpinning cwltool version and updating protobuf version to 3.18 Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-aou:2.0.3` From 1cb1c8fa74114187985c847b468bd9afbb1b88e8 Mon Sep 17 00:00:00 2001 From: Qi Wang Date: Mon, 25 Oct 2021 18:05:19 -0400 Subject: [PATCH 22/24] more --- terra-jupyter-aou/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/terra-jupyter-aou/Dockerfile b/terra-jupyter-aou/Dockerfile index 5353cbb7..b33c3de6 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:2.0.4 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.0.3 USER root From 79fb005f50be2fd235b615f61ae78d225e6edaab Mon Sep 17 00:00:00 2001 From: Qi Wang Date: Mon, 25 Oct 2021 19:46:01 -0400 Subject: [PATCH 23/24] fix pyparsing --- terra-jupyter-python/Dockerfile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/terra-jupyter-python/Dockerfile b/terra-jupyter-python/Dockerfile index 604387fe..e27c2816 100644 --- a/terra-jupyter-python/Dockerfile +++ b/terra-jupyter-python/Dockerfile @@ -54,7 +54,8 @@ RUN pip3 -V \ keras \ patsy \ pymc3 \ - pyparsing \ + # fix to 2.4.7 so that tensorflow still works + pyparsing==2.4.7 \ Cython \ # Downgrade setuptools from the base image due to incompatibilies with pysam. # As of 2021-09-10, this is the latest version of setuptools that works with pysam. From 661fca6a9e4a4f45bcd217f1be0975e1a4aef46c Mon Sep 17 00:00:00 2001 From: Qi Wang Date: Mon, 25 Oct 2021 22:00:41 -0400 Subject: [PATCH 24/24] don't bump ovtf yet --- config/conf.json | 2 +- terra-jupyter-gatk-ovtf/Dockerfile | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/config/conf.json b/config/conf.json index 70bba9e6..203df9f0 100644 --- a/config/conf.json +++ b/config/conf.json @@ -163,7 +163,7 @@ "packages" : { }, - "version" : "0.1.3", + "version" : "0.1.2", "automated_flags" : { "include_in_ui" : false, "generate_docs" : true, diff --git a/terra-jupyter-gatk-ovtf/Dockerfile b/terra-jupyter-gatk-ovtf/Dockerfile index 29b9fcc5..06c1d548 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:1.0.2 AS python +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.0.1 AS python -FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.0.2 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.0.1 # 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