Merge pull request #169: Build CVXOPT in cached section

Dockerfile

@@ -290,6 +290,38 @@ RUN pip3 install pysam==0.19.1
 # Install pango_aliasor (for forecasts-ncov)
 RUN pip3 install pango_aliasor==0.3.0
 
+# Build CVXOPT on linux/arm64
+# CVXOPT, an Augur dependency, does not have pre-built binaries for linux/arm64¹.
+#
+# First, add system deps for building²:
+# - gcc: C compiler.
+# - libc6-dev: C libraries and header files.
+# - libopenblas-dev: Contains optimized versions of BLAS and LAPACK.
+# - SuiteSparse: Download the source code so it can be built alongside CVXOPT.
+#
+# Then, "install" (build) separately since the process requires a special
+# environment variable³.
+#
+# ¹ https://github.com/cvxopt/cvxopt-wheels/issues/12
+# ² https://cvxopt.org/install/#building-and-installing-from-source
+# ³ https://cvxopt.org/install/#ubuntu-debian
+#
+# TODO: If this is removed, the installation of libopenblas in the final stage
+# should also be removed.
+WORKDIR /cvxopt
+RUN if [[ "$TARGETPLATFORM" == linux/arm64 ]]; then \
+      apt-get update && apt-get install -y --no-install-recommends \
+          gcc \
+          libc6-dev \
+          libopenblas-dev \
+   && mkdir SuiteSparse \
+   && curl -fsSL https://api.github.com/repos/DrTimothyAldenDavis/SuiteSparse/tarball/v5.8.1 \
+    | tar xzvpf - --no-same-owner --strip-components=1 -C SuiteSparse \
+   && CVXOPT_SUITESPARSE_SRC_DIR=$(pwd)/SuiteSparse \
+      pip3 install cvxopt==1.3.1 \
+      ; \
+    fi
+
 
 # 2. Add unpinned programs
 
@@ -314,35 +346,6 @@ RUN /builder-scripts/download-repo https://github.com/nextstrain/fauna master .
 RUN pip3 install phylo-treetime
 
 # Augur
-
-# Build CVXOPT on linux/arm64
-# CVXOPT, an Augur dependency, does not have pre-built binaries for linux/arm64.
-#
-# First, add system deps for building¹:
-# - gcc: C compiler.
-# - libc6-dev: C libraries and header files.
-# - libopenblas-dev: Contains optimized versions of BLAS and LAPACK.
-# - SuiteSparse: Download the source code so it can be built alongside CVXOPT.
-#
-# Then, "install" (build) separately since the process requires a special
-# environment variable².
-#
-# ¹ https://cvxopt.org/install/#building-and-installing-from-source
-# ² https://cvxopt.org/install/#ubuntu-debian
-WORKDIR /cvxopt
-RUN if [[ "$TARGETPLATFORM" == linux/arm64 ]]; then \
-      apt-get update && apt-get install -y --no-install-recommends \
-          gcc \
-          libc6-dev \
-          libopenblas-dev \
-   && mkdir SuiteSparse \
-   && curl -fsSL https://api.github.com/repos/DrTimothyAldenDavis/SuiteSparse/tarball/v5.8.1 \
-    | tar xzvpf - --no-same-owner --strip-components=1 -C SuiteSparse \
-   && CVXOPT_SUITESPARSE_SRC_DIR=$(pwd)/SuiteSparse \
-      pip3 install cvxopt \
-      ; \
-    fi
-
 # Augur is an editable install so we can overlay the augur version in the image
 # with --volume=.../augur:/nextstrain/augur and still have it globally
 # accessible and importable.