Pin hail-notebook dependencies to remove psycopg2 issue (#125)

* Install psycopg2-binary earlier in the image build

Try to trick `hgvs>=1.4->ga4gh.vrs[extras]==0.8.4->gnomad` into thinking psycopg2 is already installed

* Install manually from frozen pip

* Update README

---------

Co-authored-by: Michael Franklin <illusional@users.noreply.github.com>

images/hail-gcp-notebook/Dockerfile

@@ -4,6 +4,8 @@ FROM gcr.io/deeplearning-platform-release/base-cpu:latest
 
 ARG VERSION=${VERSION:-0.2.102}
 
+COPY requirements.txt requirements.txt
+
 # hadolint ignore=DL3008,DL3013,DL4006
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
@@ -14,16 +16,8 @@ RUN apt-get update && \
         python3-pip && \
     rm -rf /var/lib/apt/lists/* && \
     conda create -n python310 python=3.10 ipykernel && \
-    conda run -n python310 pip3 install --no-cache-dir \
-        analysis-runner \
-        bokeh \
-        "cloudpathlib[all]" \
-        cpg-utils \
-        gnomad \
-        hail==${VERSION} \
-        pyarrow \
-        metamist \
-        selenium==3.8.0 && \
+    conda run -n python310 pip3 install --no-cache-dir --no-deps -r requirements.txt && \
+    conda run -n python310 pip3 install --no-cache-dir hail==${VERSION} && \
     curl -sSL https://bitbucket.org/ariya/phantomjs/downloads/phantomjs-2.1.1-linux-x86_64.tar.bz2 | tar xjf - && \
     mv phantomjs-2.1.1-linux-x86_64/bin/phantomjs /usr/local/bin && \
     rm -r phantomjs-2.1.1-linux-x86_64 && \

images/hail-gcp-notebook/README.md

@@ -0,0 +1,13 @@
+# Hail GCP Notebook
+
+
+HGVS has this akward psycopg2 dependency which we won't use in the image, and the binary equivalent (`psycopg2-binary`) is already installed.
+
+The `requirements.in` specifies the high level requirements we want to install - `pip-compile` resolves this into a complete list (effectively a `pip freeze`), we remove `psycopg2` specifically, and use that to install with `--no-deps`.
+
+```bash
+pip install pip-tools
+
+# update / freeze deps
+pip-compile | grep -v "psycopg2==" > requirements.txt
+```

images/hail-gcp-notebook/requirements.in

@@ -0,0 +1,8 @@
+analysis-runner
+bokeh
+cloudpathlib[all]
+cpg-utils
+gnomad
+pyarrow
+metamist
+selenium==3.8.0