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hammerlab / flowdec

TensorFlow Deconvolution for Microscopy Data
Apache License 2.0
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Expand CI coverage to include running deconvolution. #7

Closed russellb closed 5 years ago

russellb commented 5 years ago

This patch series includes a few different things that are not necessarily related, but all small enough that it seemed reasonable to submit them as a single batch.

1) Drop an unused import in sample code in the README. This was spotted just when reading the code.

2) Install the sample deconvolution script. It seemed like code you would want to distribute if someone were to install it from a package in the future (pip install flowdec).

3) Improve the help output of the deconvolution script to include example usage that was provided elsewhere.

4) Add a new tox environment, "smoke", for running a smoke test of the code. It runs the sample commands for the deconvolution script. This is not trying to do any validation of the results. It's just to help catch any breakage that crops up due to new versions of dependencies. Configuring travis-ci to run this on a regular basis would do the trick.

The existing travis-ci configuration will run all tox environments. For a sample run, see:

https://travis-ci.org/russellb/flowdec/builds/441164618

5) The previous step found 1 real, but trivial bug. There was a broken logging statement in one mode of the script.

eric-czech commented 5 years ago

Nice, thanks Russell! What does "entry_points" in setup.py do during a pip install btw?

russellb commented 5 years ago

Taking this example:

deconvolution = flowdec.cmd.deconvolution:main'

This installs a new executable, /usr/bin/deconvolution, with a small amount of generated code that imports flowdec.cmd.deconvolution and runs the main function.

Btw, travis-ci will need to be enabled by an admin of the repo to run this stuff.

eric-czech commented 5 years ago

Worked like a charm, thanks again: https://travis-ci.org/hammerlab/flowdec/builds/442920660