Fix unit testing to work with msprime > 0.7.4.

[grahamgower]

Closes #518.

[codecov]

Codecov Report

❗ No coverage uploaded for pull request base (master@c19fd69). Click here to learn what that means.
The diff coverage is 100.00%.

@@            Coverage Diff            @@
##             master     #522   +/-   ##
=========================================
  Coverage          ?   99.63%           
=========================================
  Files             ?       21           
  Lines             ?     1901           
  Branches          ?      202           
=========================================
  Hits              ?     1894           
  Misses            ?        2           
  Partials          ?        5           

Impacted Files	Coverage Δ
stdpopsim/models.py	100.00% <100.00%> (ø)
stdpopsim/cli.py	98.01% <0.00%> (ø)
stdpopsim/catalog/canis_familiaris.py	100.00% <0.00%> (ø)
stdpopsim/slim_engine.py	99.54% <0.00%> (ø)
stdpopsim/species.py	100.00% <0.00%> (ø)
stdpopsim/catalog/e_coli.py	100.00% <0.00%> (ø)
stdpopsim/qc/pongo_abelii_qc.py	100.00% <0.00%> (ø)
stdpopsim/engines.py	100.00% <0.00%> (ø)
stdpopsim/genetic_maps.py	100.00% <0.00%> (ø)
stdpopsim/qc/homo_sapiens_qc.py	100.00% <0.00%> (ø)
... and 12 more

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[grahamgower]

There's something wrong with the codecov report. This should definitely have failed, as I added a code path without a test for it.

[grahamgower]

I added a test for the version compatibility shim, and checked it under both msprime 0.7.4, and git master.

$ python -c "import msprime; print(msprime.__version__)"
0.7.4
$ rm .coverage
$ nosetests --with-coverage --cover-package stdpopsim tests
...............................................................................................................................................................................................................................................................................................................................................S
Name                                           Stmts   Miss  Cover
------------------------------------------------------------------
stdpopsim/__init__.py                             21      2    90%
stdpopsim/_version.py                              1      0   100%
stdpopsim/cache.py                                16      0   100%
stdpopsim/catalog/__init__.py                      0      0   100%
stdpopsim/catalog/arabidopsis_thaliana.py         41      0   100%
stdpopsim/catalog/canis_familiaris.py             15      0   100%
stdpopsim/catalog/drosophila_melanogaster.py      52      0   100%
stdpopsim/catalog/e_coli.py                        8      0   100%
stdpopsim/catalog/homo_sapiens.py                332      0   100%
stdpopsim/catalog/pongo_abelii.py                 40      0   100%
stdpopsim/citations.py                            48      0   100%
stdpopsim/cli.py                                 302      2    99%
stdpopsim/engines.py                              56      0   100%
stdpopsim/genetic_maps.py                         83      1    99%
stdpopsim/genomes.py                              55      0   100%
stdpopsim/models.py                              190      0   100%
stdpopsim/qc/__init__.py                           4      0   100%
stdpopsim/qc/arabidopsis_thaliana_qc.py           42      0   100%
stdpopsim/qc/drosophlia_melanogaster_qc.py        36      0   100%
stdpopsim/qc/homo_sapiens_qc.py                  258      0   100%
stdpopsim/qc/pongo_abelii_qc.py                   25      0   100%
stdpopsim/slim_engine.py                         223      0   100%
stdpopsim/species.py                              73      0   100%
stdpopsim/utils.py                                16      0   100%
------------------------------------------------------------------
TOTAL                                           1937      5    99%
----------------------------------------------------------------------
Ran 336 tests in 44.248s

OK (SKIP=1)

$ python -c "import msprime; print(msprime.__version__)"
0.7.5.dev215+ng2ccf262
$ rm .coverage
$ nosetests --with-coverage --cover-package stdpopsim tests
...............................................................................................................................................................................................................................................................................................................................................S
Name                                           Stmts   Miss  Cover
------------------------------------------------------------------
stdpopsim/__init__.py                             21      2    90%
stdpopsim/_version.py                              1      0   100%
stdpopsim/cache.py                                16      0   100%
stdpopsim/catalog/__init__.py                      0      0   100%
stdpopsim/catalog/arabidopsis_thaliana.py         41      0   100%
stdpopsim/catalog/canis_familiaris.py             15      0   100%
stdpopsim/catalog/drosophila_melanogaster.py      52      0   100%
stdpopsim/catalog/e_coli.py                        8      0   100%
stdpopsim/catalog/homo_sapiens.py                332      0   100%
stdpopsim/catalog/pongo_abelii.py                 40      0   100%
stdpopsim/citations.py                            48      0   100%
stdpopsim/cli.py                                 302      2    99%
stdpopsim/engines.py                              56      0   100%
stdpopsim/genetic_maps.py                         83      1    99%
stdpopsim/genomes.py                              55      0   100%
stdpopsim/models.py                              190      0   100%
stdpopsim/qc/__init__.py                           4      0   100%
stdpopsim/qc/arabidopsis_thaliana_qc.py           42      0   100%
stdpopsim/qc/drosophlia_melanogaster_qc.py        36      0   100%
stdpopsim/qc/homo_sapiens_qc.py                  258      0   100%
stdpopsim/qc/pongo_abelii_qc.py                   25      0   100%
stdpopsim/slim_engine.py                         223      0   100%
stdpopsim/species.py                              73      0   100%
stdpopsim/utils.py                                16      0   100%
------------------------------------------------------------------
TOTAL                                           1937      5    99%
----------------------------------------------------------------------
Ran 336 tests in 44.207s

OK (SKIP=1)

[jeromekelleher]

Nicely done @grahamgower, thanks. Another option would be to back out of the change in msprime where we dropped the unused argument. It's no harm, and we could mark it for removal some time in the future after msprime 1.0 and we've transitioned stdpopsim to using asdict() like you say.

Otherwise, we'll still have the problem that people with older versions of stdpopsim will break when msprime 1.0 is released.

[jeromekelleher]

I don't mind breaking test code, but we can't break production code. So, backing out of msprime change seems simplest?

[grahamgower]

Sure, that's fine too. Note also that the behaviour of msprime.SimpleBottleneck changed: it previously had a default for the population attribute, but this seems to have been removed.

[jeromekelleher]

Reverted the change to msprime in tskit-dev/msprime#1038

See tskit-dev/msprime#1036 and tskit-dev/msprime#1037 for longer term plan.

[jeromekelleher]

Sure, that's fine too. Note also that the behaviour of msprime.SimpleBottleneck changed: it previously had a default for the population attribute, but this seems to have been removed.

Is the SimpleBottleneck used here somewhere? (It was never documented, so I felt OK to change it). Can you open an issue on msprime to track the problem if so, please?