A better pre-commit script

This script doesn't complain about the linting on unstaged files.

hooks/pre-commit

@@ -1,12 +1,48 @@
-#!/bin/sh
+#!/bin/sh 
 
 # exit at the first error
 set -e
 
-# linting
-flake8 --ignore D,W503 --max-line-length=120 .  # Check everything but docstrings
-flake8 --select D --ignore D104,D100,D401 --docstring-convention google --exclude tests/  # Check only the docstrings
-isort --check .  # Check imports
+# flake8 linting
+
+# Only extract the python files that git has staged; no need to lint WIP files that are not staged.
+
+# We'll use files to use intermediate results; it's easier to use grep on files.
+staged_file_name="staged_file.tmp"
+python_staged_file_name="python_staged_file.tmp"
+
+git diff --name-only --cached > $staged_file_name
+
+# Grep has the following behavior:
+#   the exit code is 0 if there is a match
+#   the exit code is 1 if there is no match
+#   the exit code is >1 if there is an error
+#
+# No match is a legitimate result, but the exit code of 1 is interpreted as an error by bash.
+# To work around this issue, we'll use
+#               grep [...] || [[ $? == 1]]
+# which has an exit code of 0 if there is a match or if there are no match.
+
+grep '.*py$' $staged_file_name > $python_staged_file_name || [[ $? == 1 ]]
+python_staged_files=`cat $python_staged_file_name`
+
+python_non_tests_staged_files=`grep -v '^tests' $python_staged_file_name || [[ $? == 1 ]]`
+
+rm $python_staged_file_name $staged_file_name
+
+
+if [ -z "${python_staged_files}" ]; then
+    echo "No python file to lint"
+else
+    flake8 --ignore D,W503 --max-line-length=120 $python_staged_files # Check everything but docstrings
+fi
+
+if [ -z "${python_non_tests_staged_files}" ]; then
+    echo "No non-test python file to docstring lint"
+else
+    flake8 --select D --ignore D104,D100,D401 --docstring-convention google --exclude tests/  $python_non_tests_staged_files  # Check only the docstrings
+fi
+
 
 # Raise error if any staged notebooks contain outputs
 GITDIR=$(git rev-parse --show-toplevel) # Full path to git working directory
@@ -18,7 +54,7 @@ if [ "$IPYNB_FILES" != "" ] && [ -z $ALLOW_IPYNB ]; then
         if [ "$DIFF" != "" ]; then
             echo "
             The notebook $GITDIR/$f contains outputs.
-            Remove them all before committing.
+            Remove them all before committing. 
             ***Hint*** use the command:
 
             jupyter nbconvert --ClearOutputPreprocessor.enabled=True --ClearMetadataPreprocessor.enabled=True --to notebook --inplace $GITDIR/$f