Add fall back on SRA if ENA fails

[mbhall88]

As the title suggests, this PR adds functionality that will try from SRA if ENA fails.

I formatted the code with black sorry, so the PR looks more complicated than it is.

Feel free to not take any of this either. I won't be offended.

Added

• -o shorthand option for --outdir
• a flag -F/--only-provider, which supercedes --sra_only. I left --sra_only in there for backwards compatibility and added a deprecation notice in the help description for it.
• Conda environment file
• Dockerfile. Feel free to try out an image from my quay.io repo here.

Changed

• Move everything into a main function to avoid variable shadowing
• Provider is now optional and defaults to ena. I've also made the option case insensitive, rather than listing the cased versions of the available providers
• If ENA download fails, try SRA
• Reduced a bunch of execute calls which were mostly operations easily dealt with by pathlib.Path
• Changed md5sum to use hashlib.md5 instead of executing a subprocess call to md5sum
• Moved a bunch of import statements out of function bodies to the top of the file

Removed

• Docstring at top of file as this is a mirror of argparse's help menu and creates needless maintenance

[rpetit3]

Awesome thank you very much @mbhall88 !

I've got to get a poster put together, but will get to this ASAP. Quick glance everything looked fine to me

Thanks again!

[mbhall88]

A very pedantic thought; maybe a minor version bump would be more suitable?

From semver

MINOR version when you add functionality in a backwards compatible manner

[rpetit3]

Good call!

[mbhall88]

I also have a few other fixes incoming so maybe hold off merging

[mbhall88]

Okay, I've updated the original comment with a list of all of the stuff I have done. Again, I won't be offended if you don't want some/all of this. I just thought I'd suggest it as I use this project quite heavily and find these things to be quite useful.

Thanks for creating this tool!

[rpetit3]

@mbhall88 let me know when you think its all set.

[mbhall88]

I've successfully run it now on ~290 run accessions that wouldn't download successfully with v1.0.6 👍 So I reckon it's good to go.

[rpetit3]

Awesome! Just wanted to make sure you got all the changes in you'd like.

[rpetit3]

Thank you so much @mbhall88 I'm planning a release for Bactopia and going to try and sneak this in there as well!

[mbhall88]

Thank you for the SUPER helpful tool. I hate dealing with the SRA/ENA APIs so you've saved me a tonne of days dealing with that stuff.