[MRG] Rename library to sourmash

[luizirber]

Change library name to sourmash instead of sourmash_lib

• sourmash_lib is still available for older scripts
• Remove the local sourmash script
• Fix tests that expected the local sourmash script

Supersedes #164
Fixes #162

• Is it mergeable?
• make test Did it pass the tests?
• make coverage Is the new code covered?
• Did it change the command-line interface? Only additions are allowed
  without a major version increment. Changing file formats also requires a
  major version number increment.
• Was a spellchecker run on the source code and documentation after
  changes were made?

[codecov-io]

Codecov Report

Merging #374 into master will increase coverage by 0.49%.
The diff coverage is 98.66%.

@@            Coverage Diff             @@
##           master     #374      +/-   ##
==========================================
+ Coverage   90.07%   90.56%   +0.49%     
==========================================
  Files          32       33       +1     
  Lines        4824     4854      +30     
  Branches       36       36              
==========================================
+ Hits         4345     4396      +51     
+ Misses        478      457      -21     
  Partials        1        1

Impacted Files	Coverage Δ
sourmash/sbt.py	83.09% <ø> (ø)
sourmash/__main__.py	100% <ø> (ø)
sourmash/sbtmh.py	86.36% <ø> (ø)
sourmash/signature.py	94.61% <ø> (ø)
sourmash/sbt_storage.py	95.4% <ø> (ø)
sourmash/kmer_min_hash.hh	99.35% <ø> (ø)
sourmash/fig.py	88.88% <ø> (ø)
sourmash/lca/__init__.py	100% <ø> (ø)
sourmash/logging.py	100% <ø> (ø)
sourmash/lca/command_index.py	89.26% <100%> (ø)
... and 16 more

---

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[luizirber]

Ready for review @ctb

[luizirber]

This turned out to be easier than expected. The important lesson is avoiding doing absolute imports inside the module, so instead of doing

from sourmash import foo

do

from . import foo

instead. For external/testing code, continue doing either

from sourmash import foo

or

from sourmash_lib import foo

[standage]

Looks good to me!

[standage]

Presumably recursively finds all packages and subpackages?

[luizirber]

Yes, it is recommended by the Python packaging guide: https://packaging.python.org/tutorials/distributing-packages/#packages

[standage]

Is there no command line entry point now? Or should we do something like pip install -e . to set up a dev environment?

[luizirber]

You need pip install -e . (or python setup.py develop) to have the sourmash command available (it uses the entry point defined in setup.py).

[ctb]

On Fri, Mar 09, 2018 at 09:37:36PM -0800, Daniel Standage wrote: > @@ -1,5 +0,0 @@ -#! /usr/bin/env python -# NOTE: this script is only used in 'developer' mode (python setup.py -# build_ext -i) -- see setup.py entrypoints for what end-users use. -from sourmash_lib.__main__ import main -main() Is there no command line entry point now? Or should we do something like `pip install -e .` to set up a dev environment?

yep!

[ctb]

great! can we/should we put in a deprecation warning for 'import sourmash_lib' or wait until later releases?

[ctb]

Looks good!

[ctb]

Note: if developers get an error AttributeError: 'SourmashSignature' object has no attribute 'get', then they need to do a pip install -e . again to update the install to point at sourmash instead of sourmash_lib.

[luizirber]

@ctb yes, it is better to 'reset' your environment after this changes (reinstall sourmash with pip install -e .). I had some really weird test errors while developing because the environment still had parts from the old install...

[ctb]

yes, exactly.