updates to artifact class registration

[gregcaporaso]

This pull request depends on qiime2/qiime2#655.

This makes changes to tests to:

• handle new behavior associated with that PR (semantic types rather than type expressions are registered to formats for artifact classes),
• to update to new parameter names (directory_format instead of artifact_format, though artifact_format is still supported when calling Plugin.register_semantic_type_to_format)
• add a few artifact class descriptions and usage examples for initial testing purposes.

In a development environment with the above qiime2 branch installed, this can be tested as follows:

Access descriptions of artifact classes

from qiime2.sdk import PluginManager
pm = PluginManager()

pm.get_semantic_types()
pm.get_semantic_types()['Phylogeny[Rooted]']
pm.get_semantic_types()['Phylogeny[Rooted]'].description
'A phylogenetic tree containing a defined root.'

for e in pm.get_semantic_types().values():
    desc = e.description or "No description provided."
    print('%s : %s' % (e.type_expression, desc))

FeatureTable[PresenceAbsence] : No description provided.
FeatureTable[Design] : No description provided.
FeatureTable[Frequency] : No description provided.
FeatureTable[PercentileNormalized] : No description provided.
FeatureTable[Composition] : No description provided.
FeatureTable[Balance] : No description provided.
FeatureTable[RelativeFrequency] : No description provided.
DistanceMatrix : No description provided.
Phylogeny[Rooted] : A phylogenetic tree containing a defined root.
Phylogeny[Unrooted] : A phylogenetic tree not containing a defined root.
Hierarchy : No description provided.
PCoAResults : No description provided.
ProcrustesStatistics : No description provided.
SampleData[AlphaDiversity] : No description provided.
SampleData[Sequences] : Collections of sequences associated with specified samples (i.e., demultiplexed sequences).
SampleData[SequencesWithQuality] : Collections of sequences with quality scores associated with specified samples (i.e., demultiplexed sequences).
SampleData[JoinedSequencesWithQuality] : Collections of joined paired-end sequences with quality scores associated with specified samples (i.e., demultiplexed sequences).
SampleData[PairedEndSequencesWithQuality] : Collections of unjoined paired-end sequences with quality scores associated with specified samples (i.e., demultiplexed sequences).
MultiplexedSingleEndBarcodeInSequence : No description provided.
MultiplexedPairedEndBarcodeInSequence : No description provided.
Bowtie2Index : No description provided.
FeatureData[Taxonomy] : No description provided.
FeatureData[Sequence] : No description provided.
FeatureData[RNASequence] : No description provided.
FeatureData[PairedEndSequence] : No description provided.
FeatureData[PairedEndRNASequence] : No description provided.
FeatureData[AlignedSequence] : No description provided.
FeatureData[AlignedRNASequence] : No description provided.
FeatureData[Differential] : No description provided.
FeatureData[ProteinSequence] : No description provided.
FeatureData[AlignedProteinSequence] : No description provided.
FeatureData[BLAST6] : No description provided.
RawSequences : No description provided.
EMPSingleEndSequences : No description provided.
EMPPairedEndSequences : No description provided.
ErrorCorrectionDetails : No description provided.
SampleData[ArtificialGrouping] : No description provided.
TaxonomicClassifier : No description provided.
SampleData[DADA2Stats] : No description provided.
SampleEstimator[Classifier] : No description provided.
SampleEstimator[Regressor] : No description provided.
SampleData[BooleanSeries] : No description provided.
SampleData[RegressorPredictions] : No description provided.
SampleData[ClassifierPredictions] : No description provided.
FeatureData[Importance] : No description provided.
SampleData[Probabilities] : No description provided.
SampleData[TrueTargets] : No description provided.
QualityFilterStats : No description provided.
UchimeStats : No description provided.
SampleData[FirstDifferences] : No description provided.
DeblurStats : No description provided.
Placements : No description provided.
SeppReferenceDatabase : No description provided.

Generate data and render an import usage example

from qiime2.sdk import PluginManager
import qiime2.plugins

pm = PluginManager()
use = qiime2.plugins.ArtifactAPIUsage()

ex1 = pm.get_semantic_types()['Phylogeny[Unrooted]'].examples['Import unrooted phylogenetic tree']

ex1(use)

print(use.render())

d = use.get_example_data()

d['my-tree.tre'].save('my-tree.tre')

[ebolyen]

LGTM, one minor comment.

This is still a draft, and it'll take a bit for our CI to flush the latest framework out, but I see no reason not to merge this soon.

[ebolyen]

Should the root be trifurcating in this particular example, since that's the common-ish convention?

[ebolyen]

(Or we can switch it to Phylogeny[Rooted])

[gregcaporaso]

Thanks for catching that! I updated to Phylogeny[Rooted] and set this as ready for review.

[ebolyen]

Thanks @gregcaporaso!