fix(ngen): remove custom patches breaking build, all patches have mer…

…ged upstream (#80)

docker/Dockerfile.ngen

@@ -94,15 +94,22 @@ USER ${USER}
 #These patches are from ngen commit 7551590a415b89026559c1c570d4154e4746161b
 #and are needed to fix an I/O bug in the sub modules (and bmi tests) that cause an infinite loop
 #https://github.com/NOAA-OWP/ngen/pull/515, https://github.com/NOAA-OWP/ngen/pull/518 both merged upstream, patch no longer needed
-# All the affected submodules have patched/merged in their respective upstream repos, 
-# but ngen submodules have not been updated to the current HEAD
-# of all the submdoules, and that might prove difficult to do in the near future, but if that does happen,
-# then this can be removed at that point.
-COPY fix_io_sub_7551590a415b89026559c1c570d4154e4746161b.patch ${WORKDIR}/ngen/fix_io_sub.patch
+# All the affected submodules have been patched and the ngen submodule commits have been updated
+# so this patch is no longer needed.  I'm leaving these lines commented out in case custom patches
+# need to be applied in the future.
+# Patches can be generated with
+# generate submodule patch:
+#git submodule --quiet foreach --recursive 'export NAME="${PWD##*/}"; git --no-pager diff --src-prefix="a/extern/${NAME}/${NAME}/" --dst-prefix="b/extern/${NAME}/${NAME}/"' > fix_io_sub.patch
+# generate patch of ngen without submodules
+#git --no-pager diff --ignore-submodules > fix_io.patch
+#It is then probably a good idea to to add a commit hash to thee patch file name as below
+#to indicate from what point the patch was generated.
+
+#COPY fix_io_sub_7551590a415b89026559c1c570d4154e4746161b.patch ${WORKDIR}/ngen/fix_io_sub.patch
 # Apply the IO fix to submodules, once they all get patched/merged, this can be dropped...
-RUN cd ${WORKDIR}/ngen && git apply --reject --whitespace=fix \
-    #patch the submodules
-    fix_io_sub.patch
+#RUN cd ${WORKDIR}/ngen && git apply --reject --whitespace=fix \
+#    #patch the submodules
+#    fix_io_sub.patch
 
 RUN cd ${WORKDIR}/ngen \
     && if [ "${NGEN_ACTIVATE_PYTHON}" == "ON" ]; then \