release before Git submodule

making a working release wrapping up late 2022 and all 2023 changes, before implementing Git Submodules in Gemini3D.

CI passes:

• Linux: GCC 9,10,11,12,13, Intel oneAPI 2024.0
• macOS: GCC 13

bugfixes

Minor bugfixes.
Made a point release before removing raw and netcdf file i/o

C++ redesign at function level

Gemini3D Fortran procedures are now generally available via C/C++ interface.
Numerous other bugfixes

C/C++ re-architecture, packaging improved

Gemini3D functions were rearranged and provided with C/C++ interfaces, that allow allocating arrays in C/C++ and using from Fortran functions.

CMake packaging was improved to allow robust use from external programs, including removal of dummy install packages for hwm14, nc4fortran and h5fortran.

More robust Find* enacted, particularly for HDF5.

In general, better UX during configure.

Internet connectivity checked to avoid tests hanging for 3 minutes for offline systems that cURL doesn't otherwise detect. The connectivity check is bypassed by ctest --preset offline

no autobuild

The "autobuild" feature enabled in Gemini3D since near the beginning of enabling CMake for it ~ 2019 had grown to beyond useful purpose. So many packages were in the hierarchy that rebuilding Gemini3D from scratch was becoming onerous.

We stripped out the autobuild features into https://github.com/gemini3d/external, which can either build all libraries, or just the missing/broken libraries, as how autobuild used to work within Gemini3D.
The user can thus provide a combination of system/self-built/autobuild libraries via this separate repo, to avoid having to build all those libraries when a complete Gemini3D rebuild is desired.

C++ filesystem, fix periodic

Numerous other fixes to external libraries.

include periodic option that does not force constant in x3 thermosphere

Correct HWM14 implementation and test

autobuild Default mumps 5.3.5 to avoid patch issues

v1.2.1

default mumps 5.3.5 to avoid patch failure

abstract input data

also numerous bugfixes uncovered by added tests recently.

Debug binaries have .debug filename sufffix

v1.1.2

• new test reference data, after corrections to PyGemini
• compare_input: also plot_diff
• msis2: use error code 20 to signal not setup
• HDF5 1.12.1 autobuild if needed
• external libs can be static or shared
• fixed array size error in conductivity gradient term
• apply yitmp bounds fix from inputdata branch
• autobuild: allow requested HDF5 version
• rename 'msis20' => 'msis2' for future versions
• modernize/flatten install
• cli: dedupe options meant for interactive from MPI
• add gemini3d.run -features to print enabled features
• update pygemini plot_diff api
• autobuild: ensure lapack/scalapack/mumps stack are consistent
• don't use option(*_external) for libs as that overrides cache
• link objects for robustness
• ubuntu linking with self-build fixed
• ci: add autobuild case
• update all external lib versions (packaging improvements, avoid cache overrides)

build all Release default, gemini3d.run.debug bounds check exe

• build any/all external libraries as Release by default
• announce disabled tests instead of silently skipping
• add read/write dump test. Correct file dump to be in simulation output directory.
• update h5fortran,nc4fortran to use auto-length character read
• add scripts to build OpenMPI and MPICH