CI should test installed version of Python API, not local copy

[paulromano]

Right now when we install OpenMC on Travis CI, we use pip install -e. The reason for this is that if we do a normal pip install, pytest won't actually pick it up because of the way that our directories are structured (explanation here). Since our tests/ directory is a package by virtue of having an __init__.py file, this causes pytest to add the root directory of our repo to sys.path, which means import openmc will always get that local version, not an installed one. To get around this, one possible solution is to move our openmc/ directory into a src/ directory as recommended here, but we already have a src/ directory for C++ files. We could have src_cpp/ and src_python/?

The risk to not doing this is that we're never really testing an installed version, and it can be easy to mess things up (e.g., forgetting to put files in MANIFEST.in).

[smharper]

I'm fine with moving the openmc module into a src_python file. It might also remove some of the confusion that comes from often having the openmc/openmc directory structure. I don't think that means we need to rename src to src_cpp though.

[shimwell]

I've got this working over on a branch

[shimwell]

This issue is tricky to close out because it causes conflicts with other open PRs once it is merged. To minimize the disruption I'm going to write up the solution as python script that will make the changes and move the files around. Then when an appropriate time arrives for moving on with this issue then the PR can be made with minimal effort.

I'm happy to run this script to make the new folder layout with a src/openmc and src_cpp and the following PR, just give me a nudge when the timing is right

import os
from tempfile import mkstemp
from os import fdopen, remove
from shutil import copymode, move


def replace(filename: str, pattern: str, subst: str) -> None:
    """Opens a file and replaces occurrences of a particular string
        (pattern)with a new string (subst) and overwrites the file.
    Args:
        filename (str): the filename of the file to edit
        pattern (str): the string that should be removed
        subst (str): the string that should be used in the place of the
            pattern string
    """
    # Create temp file
    file_handle, abs_path = mkstemp()
    with fdopen(file_handle, "w") as new_file:
        with open(filename) as old_file:
            for line in old_file:
                new_file.write(line.replace(pattern, subst))

    # Copy the file permissions from the old file to the new file
    copymode(filename, abs_path)

    # Remove original file
    remove(filename)

    # Move new file
    move(abs_path, filename)


replace(
    filename='.readthedocs.yaml',
    pattern='    - requirements: docs/requirements-rtd.txt',
    subst='    - requirements: docs/requirements-rtd.txt\n    - method: pip\n      path: .',
)
replace(
    filename='CMakeLists.txt',
    pattern='${CMAKE_CURRENT_SOURCE_DIR}/openmc/lib/$<TARGET_FILE_NAME:libopenmc>',
    subst='${CMAKE_CURRENT_SOURCE_DIR}/src/openmc/lib/$<TARGET_FILE_NAME:libopenmc>'
)
replace(
    filename='MANIFEST.in',
    pattern='recursive-include openmc *.pyx',
    subst='recursive-include src/openmc *.pyx'
)
replace(
    filename='MANIFEST.in',
    pattern='recursive-include openmc *.c',
    subst='recursive-include src/openmc *.c'
)
replace(
    filename='setup.py',
    pattern="with open('openmc/__init__.py', 'r') as f:",
    subst="with open('src/openmc/__init__.py', 'r') as f:"
)
replace(
    filename='setup.py',
    pattern="    'packages': find_packages(exclude=['tests*']),",
    subst="    'packages': find_packages(where='src'),\n    'package_dir': {'':'src'},"
)
replace(
    filename='setup.py',
    pattern="   'ext_modules': cythonize('openmc/data/*.pyx'),",
    subst="   'ext_modules': cythonize('src/openmc/data/*.pyx'),"
)
replace(
    filename='tools/ci/gha-script.sh',
    pattern='pytest --cov=openmc -v $args tests',
    subst='pytest --cov=src/openmc -v $args tests'
)
replace(
    filename='CMakeLists.txt',
    pattern='  src/',
    subst='  src_cpp/'
)
replace(
    filename='CMakeLists.txt',
    pattern='add_executable(openmc src/main.cpp)',
    subst='add_executable(openmc src_cpp/main.cpp)'
)

os.system('git mv src src_cpp')
os.system('mkdir src')
os.system('git mv openmc src')

[shimwell]

I've run this script and made a local PR over on fork branch to check that this relocation of files works, the CI is passing 🎉