Refactor for 2.0

[xrotwang]

Since the attributes corresponding to blocks are set via setattr (see https://github.com/SimonGreenhill/python-nexus/blob/a090ecf4c2b3fc45b1099ad8cc9058745c9fd418/nexus/reader.py#L45) they cannot be inferred by IDEs, which makes the library harder to use.

It's also a bit more clunky, if not all attributes are set at all times, and hasattr must be used when if reader.trees should be sufficient (e.g. if the handlers had appropriate __bool__ methods).

[SimonGreenhill]

Ok, so what's the solution here -- set .trees, .data etc in __init__ to None, and override when present? or make these properties that return None if not found?

(This whole library needs a good refactor :/)

[xrotwang]

Ok, I'll take a stab at refactoring :) I guess parsing the [&R|U] syntax should live in this library as well, right?

[SimonGreenhill]

Much appreciated!

As for [&R], yes in here, or we could make the newick library a dependency, and make that able to parse trees in the extended nexus format (incl. name and [&R])? (i.e. so python-nexus handles nexus parsing, newick does the trees)

[xrotwang]

@SimonGreenhill are you ok with re-arranging the source tree, i.e. moving the package to src, moving test up to the project dir, moving examples into test/fixtures? Ah, and dropping py2 compat?

[SimonGreenhill]

yes, yes, and yes. Let's make it a new major release though (2.0?)

[xrotwang]

What about moving the repos to https://github.com/glottobank (or possibly an org that fits even better - glottobank already has python-newick, so that's what may make it suitable)?

[SimonGreenhill]

ok -- glottobank? we also have https://github.com/shh-dlce/, but this looks to be largely outdated things?

[xrotwang]

ah right. yes, that's better. It's not outdated things only. It also has appconfig.

[xrotwang]

I'd also rewrite the cli to just provide one nexus command with subcommands - as for most of our other packages. Or do you think that's too much of a breaking change?

[SimonGreenhill]

Just moved here

[SimonGreenhill]

Yes, redoing the cli interface would be really nice too, it's accumulated a lot of cruft.

I think these can be deleted:

• https://github.com/shh-dlce/python-nexus/blob/master/nexus/bin/nexus_anonymise.py

Related to characters/data:

• https://github.com/shh-dlce/python-nexus/blob/master/nexus/bin/nexus_describecharacter.py
• https://github.com/shh-dlce/python-nexus/blob/master/nexus/bin/nexus_describetaxa.py
• https://github.com/shh-dlce/python-nexus/blob/master/nexus/bin/nexus_nexusmanip.py (everything)
• https://github.com/shh-dlce/python-nexus/blob/master/nexus/bin/nexus_randomise.py
• https://github.com/shh-dlce/python-nexus/blob/master/nexus/bin/nexus_tally.py

Related to trees:

• https://github.com/shh-dlce/python-nexus/blob/master/nexus/bin/nexus_treemanip.py

Perhaps a 'describe' command for:

• nexus_tally
• nexus_describecharacter
• nexus_describetaxa

Perhaps a 'convert' command:

• https://github.com/shh-dlce/python-nexus/blob/master/nexus/bin/nexus_multistate2binary.py
• https://github.com/shh-dlce/python-nexus/blob/master/nexus/bin/nexus_to_fasta.py

edit: perhaps this https://github.com/shh-dlce/python-nexus/blob/master/nexus/bin/nexuscheck.py can be a 'check' command.

[xrotwang]

One more thing: You might want to "release" the association between your personal user with the repos on Zenodo. Then we could hook it up with the institutional one.

[SimonGreenhill]

ok, will try that -- once I figure out where to look on zenodo.

[xrotwang]

you login with github, and then open the github link from the account drop-down. This will open a list of repos, each with a switch button.

[xrotwang]

ah, looks like you don't have to do that. Apparently the association didn't survive the repos move.

[SimonGreenhill]

yeah it's not listed in the repos list. Must have been unlinked with the move?

[xrotwang]

@SimonGreenhill should we require clldutils?

I'd use clldutils mainly for the cli. So this would pull in some things for no good reason: https://github.com/clld/clldutils/blob/92ab4cab4f9a39e0d6f20f09ef75e0ea4a11d025/setup.py#L15-L21 But then, once they are there, some may come in handy?

[SimonGreenhill]

sure!