Fix/geojson command

[swaradgat19]

fixes #181

[swaradgat19]

@kaczmarj So I made a separate branch and opened a PR (Including the fix #188 ). The pytorch test has passed, but the docker and the ubuntu tests haven't

[kaczmarj]

thanks @swaradgat19 -

flake8 is failing with wsinfer/write_geojson.py:92:89: E501 line too long (89 > 88 characters) . seems that one line is just slightly too long :) you can run black on the file and it should fix it. so run black wsinfer/ and then flake8 wsinfer and see if that helps.

i re-queued the failing tests -- maybe it was something random. i could not find any useful error messages in the ubuntu and docker tests.

[kaczmarj]

the docker and ubuntu tests are still failing. i will have to run those locally to see what is going on.

[kaczmarj]

@swaradgat19 - i think i figured out the failure. in

wsinfer/.github/workflows/ci.yml

Lines 107 to 108 in 59c0f5c

	test -f results/model-outputs/JP2K-33003-1.csv
	test $(wc -l < results/model-outputs/JP2K-33003-1.csv) -eq 675

update the directory to use model-outputs-csv

same in https://github.com/SBU-BMI/wsinfer/blob/59c0f5c1fe44baab0a2e8616a8075ef238259bdd/.github/workflows/ci.yml#L121C1-L121C80

i am not sure why the windows tests are passing.... the directory seems incorrect. either i didn't write that test properly or the model-outputs directory is still being made somehow.

[swaradgat19]

Oh sure. I'll make the changes

[kaczmarj]

nice, the ubuntu test passes now!

flake8 is throwing the following error

wsinfer/write_geojson.py:92:89: E501 line too long (89 > 88 characters)

[swaradgat19]

I ran flake8 wsinfer, but it just gives me a bunch of errors saying the lines are long in multiple files. I'll shorten all and put in a commit.

Also, since we're generating model-outputs-geojson, should we include that test in the yml as well?

[kaczmarj]

I ran flake8 wsinfer, but it just gives me a bunch of errors saying the lines are long in multiple files. I'll shorten all and put in a commit.

i think you can shorten line 92 of wsinfer/write_geojson.py and we should be good.

yes we should add model-outputs-geojson. we don't necessarily have to test the contents now, but let's definitely test that the expected files are made.

in a future PR, we can add tests for the geojson conversion.

[kaczmarj]

excellent, all the tests passed! let me try this out on my machine to see how thing are. then i will merge. thanks so much @swaradgat19 !

[swaradgat19]

My pleasure! :) @kaczmarj