Importing iospi into simspi and transfer.py into simspi

[geoffwoollard]

Importing iospi into simspi geoffwoollard@71f58af

[geoffwoollard]

Linting and testing is getting this far

Successfully built ioSPI
Installing collected packages: wcwidth, setuptools-scm, blessed, scipy, flyingcircus-numeric, flyingcircus, raster-geometry, ioSPI
Successfully installed blessed-1.18.1 flyingcircus-0.1.4.0 flyingcircus-numeric-0.1.1.2 ioSPI-0.0.1 raster-geometry-0.1.4.1 scipy-1.7.1 setuptools-scm-6.0.1 wcwidth-0.2.5

done
#
# To activate this environment, use
#
#     $ conda activate base
#
# To deactivate an active environment, use
#
#     $ conda deactivate

ERROR: File "setup.py" or "setup.cfg" not found. Directory cannot be installed in editable mode: /home/runner/work/simSPI/simSPI
Error: Process completed with exit code 1.

[geoffwoollard]

FYI I put myself down as maintainer in setup.py

[geoffwoollard]

There is some issue with flake thinking black needs to change things. I think it's a line length issue. But I thought the default we were going for was 79 characters. I used this for (black ... -l 79) and passed deepsource. But then things failed during linting

Run $CONDA/bin/flake8 simSPI tests
  $CONDA/bin/flake8 simSPI tests
  shell: /bin/bash -e {0}
  env:
    pythonLocation: /opt/hostedtoolcache/Python/3.7.11/x64
    LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.7.11/x64/lib
simSPI:0:1: E902 FileNotFoundError: [Errno 2] No such file or directory: 'simSPI'
tests/test_multislice.py:16:37: BLK100 Black would make changes.
Error: Process completed with exit code 1.

This is a known issue: houndci/hound#1769

@ninamiolane ?

[geoffwoollard]

Yes, the issue is definitely black and flake8 consistency. The missing directory issue went away with geoffwoollard@3f02d7c

Run $CONDA/bin/flake8 src tests
src/multislice.py:23:17: BLK100 Black would make changes.
tests/test_multislice.py:16:37: BLK100 Black would make changes.
Error: Process completed with exit code 1.

I checked the files it references, and perhaps its ending on (, the indentation on the next line, or black in the linting allowing for longer lines that 79 (if so, perhaps there's a way to pass -l 79 to black).

https://github.com/geoffwoollard/simSPI/blob/multi_slice/src/multislice.py#L23
https://github.com/geoffwoollard/simSPI/blob/multi_slice/tests/test_multislice.py#L16

[geoffwoollard]

@ninamiolane @fredericpoitevin test_sim_volumes.py is failing tests. It was there from before and I didn't write it, nor the sim_volumes.py it tests. What should I do with it? Move them to a sim_volumes branch?

[geoffwoollard]

Ok I moved transfer into simSPI. It's passing all the tests. I'm using a place holder for importing ioSPI for now in the simSPI.yml a la https://stackoverflow.com/questions/20101834/pip-install-from-git-repo-branch.

But when the ioSPI is merged into master and I can get fourier from there (by making a one line change to the yml to refer to compSPI/ioSPI). I'll just undo geoffwoollard@9f981d0

[fredericpoitevin]

@geoffwoollard I'll look back here once your PR on ioSPI has been merged. Will be easier to test dependency to it.

[geoffwoollard]

@geoffwoollard I'll look back here once your PR on ioSPI has been merged. Will be easier to test dependency to it.

Ok ioSPI has been merged

[geoffwoollard]

@fredericpoitevin Have a look

[geoffwoollard]

This got merged because I branched off of this when doing this PR #6 "Do continuous integration and codecoverage as in reduceSPI / ioSPI"

[fredericpoitevin]

@geoffwoollard sorry I missed that, looks great! Would be nice to show a use case!

[fredericpoitevin]

Maybe we could add to this list going forward