dockerfile requirements file munging (#469)

* dockerfile requirements file munging

* brief explanation of the changes

* hmm, testing changing workdir to '/'

* pin ipyannotations == 0.2.1

docker/terra_image/Dockerfile

@@ -1,14 +1,22 @@
-FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.0.1
+FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.0.2
 # https://github.com/DataBiosphere/terra-docker/blob/master/terra-jupyter-gatk/CHANGELOG.md
 
 USER root
 ENV PIP_USER=false
 
-RUN pip3 install -U git+https://github.com/broadinstitute/ml4h.git
+WORKDIR /
+
+# Now that the Terra image is built from a TensorFlow base image, if TF is included in the
+# ML4h requirements.txt, this causes problems with the Terra 'cloud environment' launch.
+# In addition, other tensorflow-related libraries need to be unpinned so that they remain consistent
+# with the TF version used by the Terra base image.
+RUN wget --no-check-certificate https://raw.githubusercontent.com/broadinstitute/ml4h/master/docker/vm_boot_images/config/tensorflow-requirements.txt -O /tensorflow-requirements.txt
+RUN grep -v 'tensorflow==' /tensorflow-requirements.txt \
+ | sed -E 's/(tensorflow-addons)(==.*)$/\1/g' \
+ | sed -E 's/(tensorflow_probability)(==.*)$/\1/g' > /terra-tensorflow-requirements.txt \
+&& pip3 install --upgrade --requirement /terra-tensorflow-requirements.txt \
+&& pip3 install --upgrade --no-deps git+https://github.com/broadinstitute/ml4h.git
 
-# Remove the following two installs after https://github.com/DataBiosphere/terra-docker/issues/244 is addressed.
-RUN pip3 install -U tensorflow==2.4.3
-RUN pip3 install tensorflow-probability==0.12.2
 
 # Remove this after https://broadworkbench.atlassian.net/browse/CA-1240
 # As of release [google-cloud-bigquery 1.26.0 (2020-07-20)](https://github.com/googleapis/python-bigquery/blob/master/CHANGELOG.md#1260-2020-07-20)
@@ -20,10 +28,9 @@ RUN pip3 uninstall -y google-cloud-bigquery-storage
 
 ENV USER jupyter
 USER $USER
+ENV PIP_USER=true
 
 RUN  jupyter nbextension install --user  --py vega \
   && jupyter nbextension enable --user  --py vega \
   && jupyter nbextension install --user  --py ipycanvas \
   && jupyter nbextension enable --user  --py ipycanvas
-
-ENV PIP_USER=true

docker/vm_boot_images/config/tensorflow-requirements.txt

@@ -29,7 +29,7 @@ facets-overview
 plotnine
 vega
 ipycanvas>=0.7.0
-ipyannotations>=0.2.1
+ipyannotations==0.2.1
 torch
 opencv-python
 blosc