fixing loading from txt file with dask

[npeschke]

Hi I ran into the issue that loading images from a text file is not possible anymore with dask (brainglobe/cellfinder#184)

This is intended as a temporary fix for this bug until a better solution with imio comes.

[adamltyson]

Hi @npeschke, thanks for this!

Would you mind adding a test? Just something small to check that a dask array is being generated with this logic? There's test data in this repo that could be used.

[sonarqubecloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
No Duplication information

[npeschke]

I added a basic type check for the loading from a txt and an equality check of stack comparing both ways of creating it.
The test takes about a second to run on my machine so I am unsure if it should be marked slow.

[coveralls]

Pull Request Test Coverage Report for Build 1238474463

• 4 of 4 (100.0%) changed or added relevant lines in 1 file are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage increased (+0.03%) to 86.096%

---

Totals
Change from base Build 1144092739:	0.03%
Covered Lines:	1096
Relevant Lines:	1273

---

💛 - Coveralls

[adamltyson]

Looks great, thanks again!

Eventually all of this I/O and dask support should move to imio, so we can support more data formats with dask, across all software. This general issue has been moved to brainglobe/brainglobe-utils#36, if you feel like tackling some more issues @npeschke!

[adamltyson]

@npeschke is there a need for this to be on PyPI soon, or can it wait for the next release?

[npeschke]

It would be nice to have that in PyPI soon, I plan to deploy cellfinder on a HPC cluster and this would make life easier for the admins that install cellfinder. Thanks for asking!

[adamltyson]

No worries, I'll aim to have it out by the end of the day.

What kind of cluster is it? If you're using SLURM, I can probably help. If not, would you be willing to (very briefly) document the process, to put in the docs and help out others?

[adamltyson]

cellfinder-core==0.2.8 is out now.

[npeschke]

Thank you very much for the new build! Indeed I use as SLURM cluster and I am planning to wrap it into a snakemake workflow.