master.python3 muffin branch setup issue with netCDF

[SasankhM]

Trying to get cGENIE up and running! I am on MacOS with M2 and followed the master.python3 PDF guide. Running make testbiogem and getting the following error:

compare.cpp:22:10: fatal error: 'netcdf.hh' file not found
#include <netcdf.hh>
         ^~~~~~~~~~~
1 error generated.
make[2]: *** [compare.o] Error 1
make[1]: *** [nccompare] Error 2
**** TESTING - configs/eb_go_gs_ac_bg_test.xml ****

When I look into where netcdf is installed there is no netcdf.hh file:

Note that when I run the brew netcdf info I get the following (interestingly seeing only 32 files as opposed to the 84 in the guide):

==> netcdf: stable 4.9.2 (bottled), HEAD
Libraries and data formats for array-oriented scientific data
https://www.unidata.ucar.edu/software/netcdf/
Installed
/usr/local/Cellar/netcdf/4.9.2_1 (32 files, 3.7MB) *
  Poured from bottle using the formulae.brew.sh API on 2024-05-15 at 17:44:37
From: https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/n/netcdf.rb
License: BSD-3-Clause
==> Dependencies
Build: cmake ✔
Required: hdf5 ✔
==> Options
--HEAD
	Install HEAD version
==> Analytics
install: 4,663 (30 days), 15,075 (90 days), 82,725 (365 days)
install-on-request: 913 (30 days), 2,837 (90 days), 26,740 (365 days)
build-error: 3 (30 days)

Thanks in advance!

[derpycode]

Sorry it took so long to notice your question/issue -- there is relatively little I can do as I do not have a Mac nor am familiar with MacOS or brewing.
If you still want to get cGENIE going on a Mac and the current MacOS instructions
https://github.com/derpycode/muffindoc/blob/master/muffin3.install.MacOS.pdf
are not working for you, I can see about pooling some Mac users to provide a documentation update.

[derpycode]

Hey!
Now I see what is going on I think -- the master.python3 PDF instructions install only 2 netCDF libraries -- C and FORTRAN.
You need to switch to the master.python3 branch of cGENIEmuffin.
This branch -- NOT master -- has replaced C++ code with FORTRAN and hence does not require the C++ netCDF libraries.
I think this is your issue.
There is also a typo in the PDF:
6. From the directory cgenie.muffin, switch to a code branch that can accommodate all types of Apple silicon:
git branch master.python3
should be
git checkout master.python3
/andy