Refactored the makefile build system

[neal-ak]

Major changes

• Sources .f and .f90 found in ./src/
• Objects .o and modules .mod are built to ./objs/
• Library has been renamed to libgencap.so to follow convention
• Library and testing executable are built to ./bin/
• install.sh and cleanup.sh scripts can build and clean for the user

makefile

Has two build targets:

• libgencap.so: the default target, builds the library
• gentest.x: builds the testing executable program found in ./src/main.f90

and two cleaning targets:

• clean: cleans all .o objects and .mod modules from the ./obj/ directories
• nuke : invokes clean, in addition to clearing ./bin/libgencap.so and ./bin/gentest.x

It also checks if debug_mode is set to true or not to toggle debugging flags.

To Test

1. Run make && make gentest.x && bin/gentest.x, and clean with make nuke.
2. Then set it up for debug mode: export debug_mode=true, and test the make file commands again.
3. Clean using make nuke again, and once complete disable debug mode: unset debug_mode; export debug_mode.
4. To test the installing scripts, run ./install.sh -h, and then ./install.sh && ./install.sh -x && bin/gentest.x, and clean with ./cleanup.sh.
5. Then do the same install script commands, adding the -g flag to both ./install.sh calls: ./install.sh -g && ./install.sh -gx && bin/gentest.x.

[aaronvincent]

Not sure what is going on - it's trying to compile dqelg with clang. Come to think of it, do we still need these libraries?

gfortran -fPIC -std=legacy -J obj -O3 -fopenmp -c src/numerical/dqag/dqelg.f -o obj/numerical/dqag/dqelg.o
clang -cc1as: error: unable to open output file 'obj/numerical/dqag/dqelg.o': 'No such file or directory'
make: *** [obj/numerical/dqag/dqelg.o] Error 1

[neal-ak]

As to the error, my best guess is either the obj/numerical/dqag/ isn't being created by the makefile (it should be running mkdir -p obj/numerical/dqag if it doesn't exist yet) or it's a file permission issue as described in https://stackoverflow.com/questions/75349370/why-am-i-getting-a-cannot-open-file-error-with-gfortran-in-macos-ventura.

For the libraries we'll still need:

• numerical/dqag/dqelg.f (numerical/dqag/dsntdqagse.f uses dqelg)
• numerical/dqag/dqpsrt.f (numerical/dqag/dsntdqagse.f uses dqpsrt)
• numerical/dqag/dsntdqagse.f (gencap.f90 and opercap.f90 use dsntdqagse for integrator)
• numerical/dqag/dsntdqk21.f (numerical/dqag/dsntdqagse.f uses dsntdqk21)
• numerical/d1mach.f (numerical/dgamic.f uses D1MACH)
• numerical/dgamic.f (gencap.f90 and opercap.f90 use DGAMIC for Incomplete Gamma Fn)
• numerical/fftpack.f90 (spergelpressmod.f90 uses dfft1i, dfft1f, and dfft1b for FFT)
• numerical/pchip.f90 (transgen.f90 uses DPCHEZ for derivatives of T and L)
• numerical/spline.f90 (spergelpressmod.f90 uses spline and ispline to prep array for FFT)

So I think numerical/sgolay.f90 and numerical/dqag/dqk21.f can be removed.