[WIP] Updating Paths and Path Assignment in Select Files

[gwaybio]

This PR introduces two related changes introduced into a subset of the deepprofiler code base.

1. Updating paths to include root path assignment

• This update impacts __main__.py, boxes.py, and model.py

2. Updating from hard path delimiter assignments to os.path.join

• This update impacts __main__.py, boxes.py, image_dataset.py and model.py

I did not look into updating other scripts that were not touched by the following command:

python deepprofiler \
    --root=/Users/gway/repos/dp-test \
    --config=/Users/gway/repos/dp-test/inputs/config/config.json \
    train

Note that I am running the above command in the DeepProfiler repository directory.

[gwaybio]

cc @jccaicedo for review

[jccaicedo]

This looks good to me. There is an issue with the Travis build, but it's unrelated to the changes in this PR, so we are good to go.

[jccaicedo]

Actually, the errors are due to the changes in this PR. Can you run pytest and try to figure out the errors before merging?

Several tests break because of these updates. Also, make sure you pull the latest version, cause we fixed some tests recently.

[gwaybio]

Thanks @jccaicedo - working through this now. I am finding errors that indeed are breaking the tests!

Running through travis I did get an error. Documenting here:

tests/plugins/models/test_gan.py::test_train 
No output has been received in the last 10m0s, this potentially indicates a stalled build or something wrong with the build itself.
Check the details on how to adjust your build configuration on: https://docs.travis-ci.com/user/common-build-problems/#build-times-out-because-no-output-was-received
The build has been terminated