DataBiosphere · Qi77Qi · Oct 26, 2021 · Sep 21, 2021 · Oct 7, 2021 · Oct 7, 2021
diff --git 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,
@@ -86,7 +86,7 @@
             "packages" : {
 
             },
-            "version" : "1.0.1",
+            "version" : "1.0.2",
             "automated_flags" : {
                 "generate_docs" : true,
                 "include_in_ui" : false,
@@ -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,

diff --git a/terra-jupyter-aou/CHANGELOG.md b/terra-jupyter-aou/CHANGELOG.md
@@ -1,3 +1,11 @@
+## 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`
+
 ## 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
@@ -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
@@ -1,3 +1,9 @@
+## 1.0.2 - 2021-10-07T14:47:43.325878Z
+
+- Update AsyncMappingKernelManager https://github.com/jupyter/notebook/issues/6164
+
+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-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'

diff --git a/terra-jupyter-bioconductor/CHANGELOG.md b/terra-jupyter-bioconductor/CHANGELOG.md
@@ -1,3 +1,11 @@
+## 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`
+
 ## 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
@@ -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
@@ -1,3 +1,11 @@
+## 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`
+
 ## 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/CHANGELOG.md b/terra-jupyter-gatk/CHANGELOG.md
@@ -1,3 +1,11 @@
+## 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`
+
 ## 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
@@ -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
@@ -1,3 +1,10 @@
+## 1.0.2 - 2021-10-07T14:47:43.375974Z
+
+- Update `terra-jupyter-base` to `1.0.2`
+  - Update AsyncMappingKernelManager https://github.com/jupyter/notebook/issues/6164
+
+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
@@ -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
@@ -1,3 +1,10 @@
+## 1.0.2 - 2021-10-07T14:47:43.398118Z
+
+- Update `terra-jupyter-base` to `1.0.2`
+  - Update AsyncMappingKernelManager https://github.com/jupyter/notebook/issues/6164
+
+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-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
@@ -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.

diff --git a/terra-jupyter-r/CHANGELOG.md b/terra-jupyter-r/CHANGELOG.md
@@ -1,3 +1,11 @@
+## 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`
+
 ## 2.0.1 - 2021-09-10T15:10:44.133967Z
 
 - Update `terra-jupyter-base` to `1.0.1`

diff --git 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
@@ -7,11 +7,11 @@ 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
+# 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/v3.16.0/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 +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/*