Attempt at python f2py wrapping

[SimonBiggs]

See #625 for more details.

[SimonBiggs]

Here's a good place to pause for today.

Installation instructions for Ubuntu:

Python pre-reqs (from https://github.com/pyenv/pyenv/wiki/Common-build-problems#prerequisites)

sudo apt-get install -y build-essential libssl-dev zlib1g-dev libbz2-dev \
libreadline-dev libsqlite3-dev wget curl llvm libncurses5-dev libncursesw5-dev \
xz-utils tk-dev libffi-dev liblzma-dev python-openssl git

Install pyenv (from https://github.com/pyenv/pyenv-installer#install)

curl https://pyenv.run | bash

Install Python:

exec $SHELL  # Only for resetting the shell after install pyenv
pyenv install 3.7.9
pyenv global 3.7.9

Install Poetry (only used in development environment -- from https://python-poetry.org/docs/#installation):

curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python
exec $SHELL  # For resetting the shell after install poetry
poetry self update --preview

Install dependencies:

cd ~/git/EGSnrc/HEN_HOUSE/python
poetry install

mortran --> fortran --> numpy.f2py:

make

See that the "Hello World!" version runs and can "see" the fortran subroutines:

poetry run python -c "import egsnrc"

With gives:

Hello World!
Everything that is accessible from Python:
['THIS',
 '__builtins__',
 '__cached__',
 '__doc__',
 '__file__',
 '__loader__',
 '__name__',
 '__package__',
 '__path__',
 '__spec__',
 '_egsnrc',
 'alias_sample',
 'alias_sample1',
 'annih',
 'annih_at_rest',
 'ausgab',
 'bhabha',
 'bounds',
 'brempr',
 'brems',
 'ch_steps',
 'compt',
 'compton_data',
 'edge',
 'edgset',
 'egs_add_medium',
 'egs_check_arguments',
 'egs_combine_runs',
 'egs_conver_month',
 'egs_date',
 'egs_date_and_time',
 'egs_day_diff',
 'egs_day_diff_o',
 'egs_eadl_relax',
 'egs_etime',
 'egs_fdate',
 'egs_finish',
 'egs_get_canonical_system',
 'egs_get_configuration_name',
 'egs_get_electron_data',
 'egs_get_fdate',
 'egs_get_hostnm',
 'egs_get_medium_name',
 'egs_get_photon_data',
 'egs_get_rndm',
 'egs_get_rndm_array',
 'egs_get_unit',
 'egs_get_usercode',
 'egs_heap_sort',
 'egs_init',
 'egs_init1',
 'egs_init_default_rng',
 'egs_init_rayleigh',
 'egs_init_rayleigh_sampling',
 'egs_init_relax',
 'egs_init_rng',
 'egs_init_user_photon',
 'egs_io',
 'egs_is_absolute_path',
 'egs_isdir',
 'egs_itostring',
 'egs_kn_sigma0',
 'egs_kn_sigma1',
 'egs_month',
 'egs_open_datfile',
 'egs_open_file',
 'egs_open_file_junk',
 'egs_open_units',
 'egs_print_binding_energies',
 'egs_print_canonical_system',
 'egs_print_configuration_name',
 'egs_print_hostnm',
 'egs_rayleigh_sampling',
 'egs_rayleigh_sigma',
 'egs_read_byte',
 'egs_read_int',
 'egs_read_real',
 'egs_read_shellwise_pe',
 'egs_read_short',
 'egs_rndm',
 'egs_scale_photon_xsection',
 'egs_scale_xcc',
 'egs_secnds',
 'egs_set_defaults',
 'egs_shellwise_photo',
 'egs_strip_extension',
 'egs_strip_path',
 'egs_swap_2',
 'egs_swap_4',
 'egs_system',
 'egs_time',
 'egs_time_diff',
 'egs_time_diff_o',
 'egs_tot_time',
 'egs_vr',
 'egs_weekday',
 'egs_write_string',
 'egsi_get_data',
 'egsi_get_shell_data',
 'eii_data',
 'eii_init',
 'eii_sample',
 'elecin',
 'electr',
 'emf_inputs',
 'epcont',
 'erf1',
 'error',
 'et_control',
 'fcoulc',
 'fix_brems',
 'gauss_legendre',
 'geom',
 'get_ranlux_state',
 'hatch',
 'howfar',
 'hownear',
 'ibsearch',
 'importlib',
 'init_compton',
 'init_ms_sr',
 'init_nist_brems',
 'init_nrc_pair',
 'init_ranlux',
 'init_spin',
 'init_spin_old',
 'init_triplet',
 'lnblnk1',
 'media',
 'misc',
 'moller',
 'ms_data',
 'mscat',
 'mscati',
 'msdist_pi',
 'msdist_pii',
 'my_times',
 'nist_brems',
 'nrc_pair',
 'old_compt',
 'pair',
 'pe_shell_data',
 'photin',
 'photo',
 'photon',
 'photonuc',
 'pprint',
 'prepare_alias_histogram',
 'prepare_alias_sampling',
 'prepare_alias_table',
 'prepare_rayleigh_data',
 'print_ranlux_seeds',
 'qdebug',
 'randomm',
 'ranlux',
 'rayleigh_inputs',
 'rayleigh_sampling',
 'relax',
 'relax_data',
 'relax_for_user',
 'replace_env',
 'sample_alias_histogram',
 'sample_triplet',
 'set_ranlux_state',
 'set_spline',
 'shell_data',
 'show_ranlux_seeds',
 'shower',
 'sigma',
 'sigmamedium',
 'spin_data',
 'spin_rejection',
 'spline',
 'sscat',
 'stack',
 'thresh',
 'toupper',
 'triplet_data',
 'uphi',
 'uphiin',
 'uphiot',
 'useful',
 'user_relax',
 'vmc_electron',
 'watch',
 'x_options',
 'xsif',
 'zero']

[SimonBiggs]

@ftessier here's the initial PR :)

[SimonBiggs]

Use PYTHON_BUILD here

[ftessier]

Nice progress!

[SimonBiggs]

So, I am currently aiming to run "tutor1" code within python. Initially the plan is to get something working, and then from a working framework step back to make things a bit more flexible.

For now, just to get things working, I have hardcoded into fortran the following:

user_code = 'tutor1';
pegs_file = 'tutor_data';

This is to get around the fact that I am no longer calling a compiled executable via the CLI, instead I am trying to call it via the Python interpreter. At some point I will need to sort out bypassing this initialisation logic and enabling this variables to be passed via Python.

...potentially also bypassing the user_code concept altogether. As I plan to not have the user need to have an $EGS_HOME directory at all.

In it's state at the moment, the compiled egs_nrc package is able to run egs_init(). Next session hopefully I might be able to implement the tutor1 logic within Python. Let's see...

~/git/EGSnrc/HEN_HOUSE/python$ poetry run python -c "import egsnrc; egsnrc.egs_init();"
debug-capi:Python C/API function _egsnrc.egs_init()
debug-capi:Fortran subroutine `egs_init()'
================================================================================
EGSnrc version 4 for x86_64-unknown-linux-gnu          Tue Sep  1 23:37:33 2020
================================================================================
configuration............................................linux
user code................................................tutor1
pegs file................................................tutor_data on HEN_HOUSE
using host...............................................dads-desktop
output file(s)...........................................
================================================================================
debug-capi:Building return value.
debug-capi:Python C/API function _egsnrc.egs_init: successful.
debug-capi:Freeing memory.

[SimonBiggs]

Nice progress!

Thanks :)