add missing test; refactor some paths

qiime2 · Jul 16, 2024 · cd55f94 · cd55f94
1 parent 4d85339
commit cd55f94
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Showing 12 changed files with 28 additions and 12 deletions.
diff --git a/q2_types/genome_data/tests/data/genome-sequences/sequence1.fa b/q2_types/genome_data/tests/data/genome-sequences/sequence1.fa
@@ -0,0 +1,5 @@
+>genome1 some_description1
+GGCAGATTCCCCCTAGACCCGCCCGCACCATGGTCAGGCATGCCCCTCCTCATCGCTGGGCACAGCCCAGAGGGT
+ATAAACAGTGCTGGAGGCCCACTGCACTCACCGCACCCGGCCAATTTTTGTGTTTTTAGTAGAGACTAAATACCA
+TATAGTGAACACCTAAGAGCACCCGGCCAATTTTTGTGTTTTTAGTAGAGAAGATTCCCCCTAGACCCGCCCGCT
+ATAGTGAACACCTAAGAACTGGAGGCGGGGGGCCTTGG
diff --git a/q2_types/genome_data/tests/data/genome-sequences/sequence2.fasta b/q2_types/genome_data/tests/data/genome-sequences/sequence2.fasta
@@ -0,0 +1,4 @@
+>genome2 some_description2
+ATGGTCAGGCATGCCCCTCCTCATCGCTGGGCGGCAGATTCCCCCTAGACCCGCCCGCACCACAGCCCAGAGGGT
+ATAAACAGTGCTGGAGGCAATACCATATAGTGAACACCTAACCACTGCACTCACCGCACCCGGCCAATTTTTGTG
+TTTTTAGTAGAGACTAGACGGGGGGCCTTGG
diff --git a/...nnotation/test_output.emapper.annotations → ...ion-extra/test_output.emapper.annotations b/...nnotation/test_output.emapper.annotations → ...ion-extra/test_output.emapper.annotations
diff --git a/...ation_extra/test_output.emapper.orthologs → ...ation-extra/test_output.emapper.orthologs b/...ation_extra/test_output.emapper.orthologs → ...ation-extra/test_output.emapper.orthologs
diff --git a/...a19-8b93-e76a15ce107f.emapper.annotations → ...a19-8b93-e76a15ce107f.emapper.annotations b/...a19-8b93-e76a15ce107f.emapper.annotations → ...a19-8b93-e76a15ce107f.emapper.annotations
diff --git a/...325-83a1-ea406f3e19ad.emapper.annotations → ...325-83a1-ea406f3e19ad.emapper.annotations b/...325-83a1-ea406f3e19ad.emapper.annotations → ...325-83a1-ea406f3e19ad.emapper.annotations
diff --git a/..._samples/test_output1.emapper.annotations → ...-samples/test_output1.emapper.annotations b/..._samples/test_output1.emapper.annotations → ...-samples/test_output1.emapper.annotations
diff --git a/..._samples/test_output2.emapper.annotations → ...-samples/test_output2.emapper.annotations b/..._samples/test_output2.emapper.annotations → ...-samples/test_output2.emapper.annotations
diff --git a/...ion_extra/test_output.emapper.annotations → ...nnotation/test_output.emapper.annotations b/...ion_extra/test_output.emapper.annotations → ...nnotation/test_output.emapper.annotations
diff --git a/q2_types/genome_data/tests/test_format.py b/q2_types/genome_data/tests/test_format.py
@@ -14,7 +14,7 @@
 from .._format import (
     GenesDirectoryFormat, ProteinsDirectoryFormat, GFF3Format,
     LociDirectoryFormat, SeedOrthologDirFmt, OrthologFileFmt,
-    OrthologAnnotationDirFmt,
+    OrthologAnnotationDirFmt, GenomeSequencesDirectoryFormat,
 )
 
 
@@ -78,6 +78,12 @@ def test_loci_dirfmt_with_suffix(self):
 
         fmt.validate()
 
+    def test_genome_sequences_dirfmt_with_suffix(self):
+        dirpath = self.get_data_path('genome-sequences')
+        fmt = GenomeSequencesDirectoryFormat(dirpath, mode='r')
+
+        fmt.validate()
+
     def test_gff_format_wrong_version(self):
         filepath = self.get_data_path('loci-invalid/loci-wrong-version.gff')
         with self.assertRaisesRegex(
@@ -141,20 +147,20 @@ def test_gff_format_invalid_phase(self):
             GFF3Format(filepath, mode='r').validate()
 
     def test_ortholog_annotation_dir_fmt_passing(self):
-        dirpath = self.get_data_path('good_ortholog_annotation')
+        dirpath = self.get_data_path('ortholog-annotation')
         fmt_obj = OrthologAnnotationDirFmt(dirpath, mode='r')
         fmt_obj.validate()
 
     def test_ortholog_annotation_dir_fmt_fails_extra_file(self):
-        dirpath = self.get_data_path('ortholog_annotation_extra')
+        dirpath = self.get_data_path('ortholog-annotation-extra')
         fmt_obj = OrthologAnnotationDirFmt(dirpath, mode='r')
 
         with self.assertRaisesRegex(ValidationError, "Unrecognized file"):
             fmt_obj.validate()
 
     def test_ortholog_annotations_annot_dict(self):
         annotations = OrthologAnnotationDirFmt(
-            self.get_data_path('ortholog_annotation_samples'), mode='r'
+            self.get_data_path('ortholog-annotation-samples'), mode='r'
         )
 
         obs = annotations.annotation_dict()

diff --git a/q2_types/genome_data/tests/test_transformer.py b/q2_types/genome_data/tests/test_transformer.py
@@ -125,7 +125,7 @@ def test_interval_metadata_iterator_to_gff(self):
 
     def test_annotations_to_dataframe_samples(self):
         annotations = OrthologAnnotationDirFmt(
-            self.get_data_path('ortholog_annotation_samples'),
+            self.get_data_path('ortholog-annotation-samples'),
             mode='r'
         )
         obs = _annotations_to_dataframe(annotations)
@@ -136,7 +136,7 @@ def test_annotations_to_dataframe_samples(self):
 
     def test_annotations_to_dataframe_mags(self):
         annotations = OrthologAnnotationDirFmt(
-            self.get_data_path('ortholog_annotation_mags'),
+            self.get_data_path('ortholog-annotation-mags'),
             mode='r'
         )
         obs = _annotations_to_dataframe(annotations)
@@ -147,7 +147,7 @@ def test_annotations_to_dataframe_mags(self):
 
     def test_annotations_to_df_transformer(self):
         annotations = OrthologAnnotationDirFmt(
-            self.get_data_path('ortholog_annotation_mags'),
+            self.get_data_path('ortholog-annotation-mags'),
             mode='r'
         )
         transformer = self.get_transformer(
@@ -163,7 +163,7 @@ def test_annotations_to_df_transformer(self):
 
     def test_annotations_to_metadata_transformer(self):
         annotations = OrthologAnnotationDirFmt(
-            self.get_data_path('ortholog_annotation_mags'),
+            self.get_data_path('ortholog-annotation-mags'),
             mode='r'
         )
         transformer = self.get_transformer(

diff --git a/setup.py b/setup.py
@@ -69,11 +69,12 @@
              'data/genes/*',
              'data/loci-invalid/*',
              'data/loci/*',
+             'data/genome-sequences/*'
              'data/ortholog/*',
-             'data/ortholog_annotation_extra/*',
-             'data/ortholog_annotation_mags/*',
-             'data/ortholog_annotation_samples/*',
-             'data/good_ortholog_annotation/*',
+             'data/ortholog-annotation-extra/*',
+             'data/ortholog-annotation-mags/*',
+             'data/ortholog-annotation-samples/*',
+             'data/ortholog-annotation/*',
              'data/proteins/*',
              ],
         'q2_types.kraken2.tests': [