Review for Bioconda recipe

[marcelm]

Hi, I was looking at your Bioconda recipe PR for this package and noticed a couple of minor things not directly related to the recipe, but to the tool, which I wanted to list here.

• Running python setup.py install to install a package is deprecated. You should change the installation instructions to use pip install . instead (use pip install -e . during development for an editable install).
• The README refers to running salty via python salty.py, but this works only if run from the salty/ subdirectory. You specified in setup.py that a salty binary is to be installed, and that is also what the Bioconda recipe tests. I suggest to use just salty for consistency.
• Since this is a pure Python package (no extension modules), you could switch to using pyproject.toml for declaring project metadata and get rid of setup.py entirely. See this example. This is the modern way to do packaging. :smile:
• Your Conda installation instructions may work, but note that this is not generally the case as the Bioconda setup instructions want you to also specify strict channel order. Also, the channel order is different, so in general, the options would be -c conda-forge -c bioconda --strict-channel-priority.

[marcelm]

One more point: It would be good to state the license explicitly. There is a LICENSE file with the GPL 3, but some projects use "GPL 3 or later" and some use "GPL 3 only". (There are two different SPDX license identifiers "GPL-3.0-only" and "GPL-3.0-or-later".)

Note that using the GPL may mean that some people may refrain from using your software as it has a "viral" aspect. (As derived works also need to be licensed under the GPL 3.) You could choose a simple permissive license such as the MIT license to avoid this. If you’re aware of this aspect, please don’t see this as criticism of your choice of license; I just wanted to point out what it means in case you were not aware of the implications.

[liamcheney]

Hey @marcelm, Thanks for going over salty. Regarding the license we are happy to keep the existing language. Thanks for checking. All the other comments have been addressed. Cheers, Liam

[marcelm]

Great! Nice I was able to help.