Fix testing suite

[tsalo]

Closes #2.

Changes proposed in this pull request:

• Add GitHub workflow that runs tests and linter.
• Fix up tests.

To do

• Add CI Action
• Linting
• Coverage

[tsalo]

I'm getting the following error:

Run python -m pytest --pyargs bids/reports --cov=bids/reports
[2](https://github.com/bids-standard/pybids-reports/runs/5169084359?check_suite_focus=true#step:6:2)
  python -m pytest --pyargs bids/reports --cov=bids/reports
[3](https://github.com/bids-standard/pybids-reports/runs/5169084359?check_suite_focus=true#step:6:3)
  shell: /usr/bin/bash {0}
[4](https://github.com/bids-standard/pybids-reports/runs/5169084359?check_suite_focus=true#step:6:4)
  env:
[5](https://github.com/bids-standard/pybids-reports/runs/5169084359?check_suite_focus=true#step:6:5)
    pythonLocation: /opt/hostedtoolcache/Python/3.7.12/x[6](https://github.com/bids-standard/pybids-reports/runs/5169084359?check_suite_focus=true#step:6:6)4
6
    LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.7.12/x64/lib
[8](https://github.com/bids-standard/pybids-reports/runs/5169084359?check_suite_focus=true#step:6:8)
ImportError while loading conftest '/home/runner/work/pybids-reports/pybids-reports/bids/reports/tests/conftest.py'.
[9](https://github.com/bids-standard/pybids-reports/runs/5169084359?check_suite_focus=true#step:6:9)
bids/reports/__init__.py:2: in <module>
[10](https://github.com/bids-standard/pybids-reports/runs/5169084359?check_suite_focus=true#step:6:10)
    from . import _version, parameters, parsing, report
[11](https://github.com/bids-standard/pybids-reports/runs/5169084359?check_suite_focus=true#step:6:11)
bids/reports/parameters.py:10: in <module>
[12](https://github.com/bids-standard/pybids-reports/runs/5169084359?check_suite_focus=true#step:6:12)
    from bids.reports.utils import list_to_str, num_to_str, remove_duplicates
[13](https://github.com/bids-standard/pybids-reports/runs/5169084359?check_suite_focus=true#step:6:13)
E   ModuleNotFoundError: No module named 'bids.reports'
[14](https://github.com/bids-standard/pybids-reports/runs/5169084359?check_suite_focus=true#step:6:14)
Error: Process completed with exit code 4.

I installed my fork's pybids that doesn't include the reports module, so it shouldn't conflict with pybids-reports, and yet bids.reports doesn't exist. 😕

[tsalo]

@effigies do you have any idea why the parent package wouldn't retain the namespace package when both are installed?

[effigies]

So what I did above makes things work in full installations, but not in editable mode (pip install -e). To do that, we would need to add __path__ = __import__('pkgutil').extend_path(__path__, __name__) to bids/__init__.py in this package, which would override it in pybids, making things like bids.BIDSLayout cease to work.

We could move it to bids.ext.reports and bids.ext could be set aside so that we could make -e work. PyBIDS could have bids.reports from pybids.ext.reports import * (while warning) to provide an on-ramp.

[codecov]

Codecov Report

❗ No coverage uploaded for pull request base (main@a209b6c). Click here to learn what that means.
Patch has no changes to coverable lines.

Additional details and impacted files

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  Files           ?       11           
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  Hits            ?      704           
  Misses          ?      241           
  Partials        ?        0           

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