Merge branch '95-tool-and-recipe-for-installing-jupyter-kernel-wrappers' into 'master'

Resolve "Tool and recipe for installing jupyter kernel wrappers"

Closes #95

See merge request Pmodules/buildblocks!131

Programming/anaconda/files/admintools/install-env-loggers.sh

+#!/bin/bash
+# Script to install logging into the activation hook directories
+# of environments
+#
+# 2020 - Derek Feichtinger
+
+function envlist() {
+    conda env list --json | jq -r '.envs[]' | grep -E -v 'conda$'
+}
+
+if [[ -z "$CONDA_PREFIX" ]]; then
+    echo "Error: No conda distribution seems active (CONDA_PREFIX)" >&2
+    exit 1
+fi
+
+for env in $(envlist); do
+    if [[ -e "$env/etc" ]]; then
+	echo "Installing into $env"
+	mkdir -p $env/etc/conda/activate.d
+	cat <<'EOF' > $env/etc/conda/activate.d/log-envname.sh
+#!/bin/bash
+logger "activated conda module: ${CONDA_PREFIX}"  
+EOF
+    else
+	echo "WARNING: SKIPPING ENV: $env has no /etc" >&2
+    fi
+done
+

Programming/anaconda/files/admintools/install-kernelwrapper.py

+#!/usr/bin/env python
+# installs a jupyter kernel wrapper solution into the environment's
+# $ENVPATH/share/jupyter/kernels/python3/kernel.json kernel definition
+
+# typical envpath at PSI
+#     "/opt/psi/Programming/anaconda/2019.07/conda/envs/datascience_py37"
+
+import re
+import os
+import sys
+import shutil
+from datetime import datetime
+import argparse
+parser = argparse.ArgumentParser()
+
+# DEFAULTS
+verbose_flag = False
+
+parser.add_argument("envpath", help="conda env path")
+parser.add_argument("-v", "--verbose", help="verbose mode",action="store_true")
+args = parser.parse_args()
+
+if args.verbose:
+    verbose_flag = True
+
+envpath = args.envpath
+envname = os.path.basename(envpath)
+condaroot = re.sub(r'(.*)/conda/envs/.*', r'\1', envpath)
+kwrapper = os.path.join(condaroot, 'admintools/kernelwrapper.sh')
+kfile = os.path.join(envpath,"share/jupyter/kernels/python3/kernel.json")
+
+date_time = datetime.now().strftime("%Y%m%d-%H%M%S")
+
+if verbose_flag:
+    print("env: %s" % envname)
+    print(kwrapper)
+
+if not os.path.isfile(kwrapper):
+    sys.stderr.write("Error: no wrapper found at %s\n" % (kwrapper))
+    sys.exit(1)
+
+searchstr = r'"argv": \[\n( *"/.*python", *)'
+subststr = r'"argv": [\n' + '  "' + kwrapper + '",\n' + '  "' + envname + r'",\n\1'
+
+try:
+    with open(kfile,"r") as fp:
+        filestr = "".join(fp.readlines())
+except IOError:
+    sys.stderr.write("Error: Env has no kernel file: %s\n" % kfile)
+    sys.exit(0)
+
+if re.search(kwrapper, filestr):
+        if verbose_flag:
+            print("env %s already contains kernelwrapper" % envpath)
+            sys.exit(0)
+            
+if re.search(searchstr, filestr):
+    filestr = re.sub(searchstr,
+                     subststr,
+                     filestr)
+    print(filestr)
+
+    bupfile = kfile + "-" + date_time + ".bup"
+    if verbose_flag:
+        print("copying original file to %s" % bupfile)
+    shutil.copyfile(kfile, bupfile)
+    if verbose_flag:
+        print("writing new file %s" % kfile)
+        print(filestr)
+    with open(kfile,"w") as fp:
+        fp.write(filestr)
+else:
+    sys.stderr.write("ERROR: Could not do substitution in %s" % kfile)
+    sys.stderr.write(filestr)