Merge PR #141 (Update .gitignore to avoid excluding util/Makefile* files)

This merge brings PR #141 (Update .gitignore to avoid excluding
util/Makefile* files, by @yantosca) into the KPP 3.4.0 development stream.

PR #141 does the following:

1. Updated the .gitignore file to avoid inadvertently excluding
   Makefiles (and other files) from the util folder.

2. Fixed an error in ./ci-pipelines/ci-cleanup-script.sh that caused
   the MCM C-I test folders to not be cleaned properly.

Signed-off-by: Bob Yantosca <[email protected]>

Author: yantosca

.ci-pipelines/ci-cleanup-script.sh

@@ -17,8 +17,8 @@ cwd=$(pwd -P)
 for this_test in ${GENERAL_TESTS}; do
     clean_ci_test_folder "${this_test}" "${this_test}" "${cwd}"
 done
-clean_ci_test_folder "${MCM_1}" "${MCM_1}" "${cwd}"
-clean_ci_test_folder "${MCM_2}" "mcm"      "${cwd}"
+clean_ci_test_folder "${MCM_1}" mcm "${cwd}"
+clean_ci_test_folder "${MCM_2}" mcm "${cwd}"
 
 # Remove any log files used to store C-I test results
 cd $cwd

.gitignore

@@ -1,73 +1,72 @@
+# KPP .gitignore file
+#
+# For info on how .gitignore rules work, see:
 # https://www.atlassian.com/git/tutorials/saving-changes/gitignore
 # https://linuxize.com/post/gitignore-ignoring-files-in-git
 
-# temporary files:
-*.~*
-*~
-.\#*
-\#*
+# Keep empty directory for executables, but ignore its contents
+/bin/*
+
+# Ignore temporary files everywhere
+**/*.~*
+**/*~
+**/.\#*
+**/\#*
 
-# files generated by bison:
+# Ignore files generated by bison (in src/)
 /src/lex.yy.c
 /src/y.tab.c
 /src/y.tab.h
 
-# from compiler:
-*.mod
-*.o
-*.exe
+# Ignore files generated by the compiler (everywhere)
+**/*.mod
+**/*.o
+**/*.exe
 
-# results from ci-tests:
+# Ignore files generated by C-I tests (in ci-tests/*)
+/ci-tests/**/*.dat
+/ci-tests/**/*.h
 /ci-tests/**/*.m
+/ci-tests/**/Makefile_*
 /ci-tests/**/*results*
-/ci-tests/**/*.exe
-/ci-tests/**/*.h
-/ci-tests/**/*.log
-/ci-tests/**/*.dat
 
-# keep empty directory for executables, but not its contents:
-/bin/*
-!/bin/.gitkeep
-
-# KPP-generated files:
-*_Function*
-*_Global*
-*_Hessian*
-*_HessianSP*
-*_Initialize*
-*_Integrator*
-*_Jacobian*
-*_JacobianSP*
-*_LinearAlgebra*
-*.log
-*_Main*
-*_mex_Fun*
-*_mex_Hessian*
-*_mex_Jac_SP*
-*_Model*
-*_Monitor*
-*_Parameters*
-*_Precision*
-*_Rates*
-*_Stoichiom*
-*_StoichiomSP*
-*_Util*
-Makefile_*
+# Ignore files generated by KPP (everywhere)
+**/*_Function*
+**/*_Global*
+**/*_Hessian*
+**/*_HessianSP*
+**/*_Initialize*
+**/*_Integrator*
+**/*_Jacobian*
+**/*_JacobianSP*
+**/*_LinearAlgebra*
+**/*.log
+**/*_Main*
+**/*_*ex_Fun*
+**/*_*ex_Hessian*
+**/*_*ex_Jac_SP*
+**/*_Model*
+**/*_Monitor*
+**/*_Parameters*
+**/*_Precision*
+**/*_Rates*
+**/*_Stoichiom*
+**/*_StoichiomSP*
+**/*_Util*
 
-# LaTeX and BibTeX files:
-/manual/*.aux
-/manual/*.bbl
-/manual/*.blg
-/manual/*.log
-/manual/*.toc
-
-# ReadTheDocs files
+# Ignore files generated by ReadTheDocs (in docs/build)
 docs/build/*
 
-# are there any *.dat files to exclude?
-*.dat
-
-# Other files/dirs to exclude
+# Ignore other files & folders
 *.pdf
-/examples/mcm*/__pycache__
+**/__pycache__
 
+# IMPORTANT: Do not ignore these files!
+!/bin/.gitkeep
+!/docs/figures/*.pdf
+!/util/*.c
+!/util/*.f
+!/util/*.h
+!/util/*.f90
+!/util/*.m
+!/util/Makefile*

CHANGELOG.md

@@ -21,6 +21,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## Fixed
 - Moved the `which kpp` instruction to the end of the "Build the KPP executable" section in the installation guide on ReadTheDocs
+- Updated rules to ignore files in `.gitignore` and updated comments accordingly
+- Fixed a bug that prevented `.ci-pipelines/ci-cleanup-script.sh` from removing KPP-generated files for MCM mechanisms
 
 ### Removed
 - Removed C-I tests on Microsoft Azure Dev Pipelines