install modern version of npm

Author: petermchale

build-vue-app.sh

@@ -20,6 +20,8 @@ root=$PWD
 # no need to export PATH since it is already in the environment: https://unix.stackexchange.com/a/26059/406037
 PATH="${root}/node/bin:$PATH"
 
+bash ${root}/utilities/info.sh "npm version is: $(npm --version)"
+
 cd ${root}/vue-app
 npm install
 npm run build 

install.sh

@@ -47,26 +47,6 @@ bash install/jq.sh ${root}
 
 ########################## 
 
-rm -rf "node"
-node_version="v16.4.2"
-
-if [[ ${machine} == 'x86_64' ]]; then
-  if [[ ${kernel} == 'Darwin'* ]]; then
-    curl --remote-name "https://nodejs.org/dist/${node_version}/node-${node_version}-darwin-x64.tar.gz"
-    tar -xf "node-${node_version}-darwin-x64.tar.gz"
-		rm "node-${node_version}-darwin-x64.tar.gz"
-		mv "node-${node_version}-darwin-x64" "node"
-  elif [[ ${kernel} == 'Linux'* ]]; then
-    curl --remote-name "https://nodejs.org/dist/${node_version}/node-${node_version}-linux-x64.tar.xz"
-    tar -xf "node-${node_version}-linux-x64.tar.xz"
-    rm "node-${node_version}-linux-x64.tar.xz"
-    mv "node-${node_version}-linux-x64" "node"
-  else
-    echo 'neither Darwin nor Linux'
-    exit 1
-  fi
-else
-  echo 'not x86_64'
-  exit 1
-fi
+bash install/node.sh ${root}
+
 

install/node.sh

@@ -0,0 +1,43 @@
+set -o errexit
+set -o pipefail
+set -o nounset
+set -o xtrace
+PS4='+ (${BASH_SOURCE[0]##*/} @ ${LINENO}): ${FUNCNAME[0]:+${FUNCNAME[0]}(): }'
+
+root=$1
+
+kernel=$(uname --kernel-name)
+machine=$(uname --machine)
+
+bash ${root}/utilities/info.sh "downloading node (and npm)"
+
+rm -rf "${root}/node"
+node_version="v16.4.2"
+
+if [[ ${machine} == 'x86_64' ]]; then
+  if [[ ${kernel} == 'Darwin'* ]]; then
+    curl --remote-name "https://nodejs.org/dist/${node_version}/node-${node_version}-darwin-x64.tar.gz"
+    tar -xf "node-${node_version}-darwin-x64.tar.gz"
+		rm "node-${node_version}-darwin-x64.tar.gz"
+		mv "node-${node_version}-darwin-x64" "${root}/node"
+  elif [[ ${kernel} == 'Linux'* ]]; then
+    curl --remote-name "https://nodejs.org/dist/${node_version}/node-${node_version}-linux-x64.tar.xz"
+    tar -xf "node-${node_version}-linux-x64.tar.xz"
+    rm "node-${node_version}-linux-x64.tar.xz"
+    mv "node-${node_version}-linux-x64" "${root}/node"
+  else
+    echo 'neither Darwin nor Linux'
+    exit 1
+  fi
+else
+  echo 'not x86_64'
+  exit 1
+fi
+
+# no need to export PATH since it is already in the environment: https://unix.stackexchange.com/a/26059/406037
+PATH="${root}/node/bin:$PATH"
+
+bash ${root}/utilities/info.sh "npm version is: $(npm --version)"
+
+
+

tests/model.json

@@ -28,12 +28,12 @@ kmer_size="5"
 output="${root}/tests"
 mkdir --parents ${output}
 
-# constraint-tools train \
-#   --genome ${genome} \
-#   --region ${neutral_region} \
-#   --mutations ${mutations} \
-#   --kmer-size ${kmer_size} \
-#   --output ${output}
+constraint-tools train \
+  --genome ${genome} \
+  --region ${neutral_region} \
+  --mutations ${mutations} \
+  --kmer-size ${kmer_size} \
+  --output ${output}
 
 model="${output}/model.json"
 port="5000"