tpapastylianou / self-contained-runnable-python-package-template Goto Github PK

I'm not familiar with unittest, so I apologize in advance if I used it wrongly.

After downloading the repo and running:

python -m packagename.tests

I get:

Warning: No suitable VIRTUAL_ENV environmental variable detected.

In order to ensure consistency / reproducibility between runs, you might want to
consider always running this package from within a suitable python virtual
environment, containing the python package versions specified in the package's
requirements.txt file.

Press ENTER if you'd like to continue regardless (or Ctrl-C to abort)



__init__: Setting PKGROOT to /home/junior/Documents/Projetos/Python/self-contained-runnable-python-package-template/packagename
__init__: Setting INPUTS_PATH to /home/junior/Documents/Projetos/Python/self-contained-runnable-python-package-template/packagename/inputs
__init__: Setting OUTPUTS_PATH to /home/junior/Documents/Projetos/Python/self-contained-runnable-python-package-template/packagename/outputs
__init__: Setting MCMC_ENGINE to <class 'packagename.config.CONFIG.Stan'>
Traceback (most recent call last):
  File "/usr/lib64/python3.10/runpy.py", line 196, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/usr/lib64/python3.10/runpy.py", line 86, in _run_code
    exec(code, run_globals)
  File "/home/junior/Documents/Projetos/Python/self-contained-runnable-python-package-template/packagename/tests/__main__.py", line 41, in <module>
    if __name__ == '__main__': main()
  File "/home/junior/Documents/Projetos/Python/self-contained-runnable-python-package-template/packagename/tests/__main__.py", line 33, in main
    Tests  = unittest.defaultTestLoader.discover( start_dir = TestDir )
  File "/usr/lib64/python3.10/unittest/loader.py", line 306, in discover
    os.path.dirname((the_module.__file__)))
  File "/usr/lib64/python3.10/posixpath.py", line 152, in dirname
    p = os.fspath(p)
TypeError: expected str, bytes or os.PathLike object, not NoneType

System information:

$: python -VV
Python 3.10.2 (main, Jan 17 2022, 00:00:00) [GCC 11.2.1 20211203 (Red Hat 11.2.1-7)]

Either in the template, or simply mentioned as optional.

Python typically does not require 'libraries' bundled with the project, since external dependencies are typically handled at the 'python' / 'pip' level.

However, it is not impossible that an atypical external dependency needs to be accessible from within the project structure. E.g. a stray python module, or libraries from other languages that the main program may need to interface with (possibly even requiring compilation before the package can be run). In such cases, the right place for such code is not the 'src' file, which should only contain 'project-native' code. In which case, it should go into 'lib', which is a standard name for external libraries in packages typical of other languages. (possibly even a 'bin' directory, in case compilation into executables is involved -- though I'd place this inside the 'lib' directory, to avoid any confusion that these may relate to execution of the main package in any way).

Hopefully this is as intuitive as the presence of a CONFIG.ME file in the root, but without the whole 'create symbolic link to import' business, which is less than ideal.

This also allows a /config/templates folder, where one can store individual configs, and even 'activate' them easily by making the packagename_config.py a symbolic link to one of them.

More generally, this is a straightforward way to declare dependencies for a project, though for simple dependencies this can also be in the docs or README.

However, some projects may need specific versions of packages installed to run properly.
This is e.g. particularly important in terms of reproducibility, such as when packages are intended to represent self-contained 'experiments', etc.

e.g. get this assertion error if you attempt to run using python2:

Error: This package is intended to be run in python3
   (you seem to be running python2)

NOTE: Ironically, for this to work, this whole file needs to use python2 compatible syntax, otherwise the interpreter will exit with a syntax error even before it reaches this assertion. Specifically, this means we cannot use 'f-strings' in this file, so we'll need to rely on the older '.format()' mechanism.