Merge pull request #50 from standage/refactor/import

Cleaner imports

CHANGELOG.md

@@ -2,6 +2,12 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## [Unreleased]
+## Changed
+- Modules focused on classes / data structure now support more concise imports
+  (for example, `from tag import Feature` and `tag.Feature` now supported and
+  preferred over `from tag.feature import feature` and `tag.feature.Feature`).
+
 ## [0.1.1] - 2016-12-19
 ### Changed
 - CLI implemented using `entry_points` instead of a dedicated script.

README.md

@@ -13,7 +13,7 @@
 ```python
 # Compute number of exons per gene
 import tag
-reader = tag.reader.GFF3Reader(infilename='/data/genomes/mybug.gff3.gz')
+reader = tag.GFF3Reader(infilename='/data/genomes/mybug.gff3.gz')
 for gene in tag.select.features(reader, type='gene'):
     exons = [feat for feat in gene if feat.type == exon]
     print('num exons:', len(exons))

docs/index.rst

@@ -27,7 +27,7 @@ Most GFF parsers will load data into memory for you--the trivial bit--but will n
 
    # Compute number of exons per gene
    import tag
-   reader = tag.reader.GFF3Reader(infilename='/data/genomes/mybug.gff3.gz')
+   reader = tag.GFF3Reader(infilename='/data/genomes/mybug.gff3.gz')
    for gene in tag.select.features(reader, type='gene'):
        exons = [feat for feat in gene if feat.type == exon]
        print('num exons:', len(exons))

tag/__init__.py

@@ -12,15 +12,15 @@
     import __builtin__ as builtins
 except:  # pragma: no cover
     import builtins
-from . import comment
-from . import directive
-from . import feature
-from . import sequence
-from . import range
-from . import reader
-from . import writer
-from . import cli
-from . import select
+from tag.comment import Comment
+from tag.directive import Directive
+from tag.feature import Feature
+from tag.sequence import Sequence
+from tag.range import Range
+from tag.reader import GFF3Reader
+from tag.writer import GFF3Writer
+from tag import cli
+from tag import select
 from gzip import open as gzopen
 
 from ._version import get_versions

tag/reader.py

@@ -9,11 +9,11 @@
 
 import sys
 import tag
-from tag.range import Range
-from tag.comment import Comment
-from tag.directive import Directive
-from tag.feature import Feature
-from tag.sequence import Sequence
+from tag import Range
+from tag import Comment
+from tag import Directive
+from tag import Feature
+from tag import Sequence
 
 
 def parse_fasta(data):  # pragma: no cover

tag/select.py

@@ -21,7 +21,7 @@ def features(entrystream, type=None, traverse=False):
                      to :code:`True` to search each feature graph for the
                      specified feature type
     """
-    for feature in entry_type_filter(entrystream, tag.feature.Feature):
+    for feature in entry_type_filter(entrystream, tag.Feature):
         if traverse:
             if type is None:
                 message = 'cannot traverse without a specific feature type'
@@ -54,7 +54,7 @@ def window(featurestream, seqid, start=None, end=None, strict=True):
     """
     region = None
     if start and end:
-        region = tag.range.Range(start, end)
+        region = tag.Range(start, end)
 
     for feature in featurestream:
         if feature.seqid != seqid:
@@ -78,14 +78,14 @@ def directives(entrystream, type=None):
     :param type: retrieve only directives of the specified type; set to
                  :code:`None` to retrieve all directives
     """
-    for directive in entry_type_filter(entrystream, tag.directive.Directive):
+    for directive in entry_type_filter(entrystream, tag.Directive):
         if not type or type == directive.type:
             yield directive
 
 
 def sequences(entrystream):
     """Pull sequences out of the specified entry stream."""
-    for sequence in entry_type_filter(entrystream, tag.sequence.Sequence):
+    for sequence in entry_type_filter(entrystream, tag.Sequence):
         yield sequence
 
 

tag/writer.py

@@ -15,8 +15,8 @@
     from io import StringIO
 import sys
 import tag
-from tag.feature import Feature
-from tag.reader import GFF3Reader
+from tag import Feature
+from tag import GFF3Reader
 
 
 class GFF3Writer():

tests/test_comment.py

@@ -8,9 +8,9 @@
 # -----------------------------------------------------------------------------
 
 import pytest
-from tag.comment import Comment
-from tag.directive import Directive
-from tag.feature import Feature
+from tag import Comment
+from tag import Directive
+from tag import Feature
 
 
 def test_init():

tests/test_feature.py

@@ -8,11 +8,11 @@
 # -----------------------------------------------------------------------------
 
 import pytest
-from tag.comment import Comment
-from tag.directive import Directive
-from tag.feature import Feature
-from tag.range import Range
-from tag.sequence import Sequence
+from tag import Comment
+from tag import Directive
+from tag import Feature
+from tag import Range
+from tag import Sequence
 
 
 def eden():

tests/test_range.py

@@ -8,7 +8,7 @@
 # -----------------------------------------------------------------------------
 
 import pytest
-from tag.range import Range
+from tag import Range
 from tag.reader import GFF3Reader
 
 

tests/test_reader.py

@@ -9,12 +9,12 @@
 
 import pytest
 import tag
-from tag.range import Range
-from tag.comment import Comment
-from tag.directive import Directive
-from tag.feature import Feature
-from tag.reader import GFF3Reader
-from tag.sequence import Sequence
+from tag import Range
+from tag import Comment
+from tag import Directive
+from tag import Feature
+from tag import GFF3Reader
+from tag import Sequence
 
 
 def test_grape():

tests/test_select.py

@@ -9,28 +9,26 @@
 
 import pytest
 import tag
+from tag import GFF3Reader
 
 
 def test_features():
-    ifn = 'tests/testdata/pbar-withseq.gff3'
-
-    reader = tag.reader.GFF3Reader(infilename=ifn)
+    reader = GFF3Reader(infilename='tests/testdata/pbar-withseq.gff3')
     features = [f for f in tag.select.features(reader)]
     assert len(features) == 3
 
-    reader = tag.reader.GFF3Reader(infilename=ifn)
+    reader = GFF3Reader(infilename='tests/testdata/pbar-withseq.gff3')
     features = [f for f in tag.select.features(reader, type='pseudogene')]
     assert len(features) == 1
 
-    reader = tag.reader.GFF3Reader(infilename=ifn)
+    reader = GFF3Reader(infilename='tests/testdata/pbar-withseq.gff3')
     with pytest.raises(ValueError) as ve:
         features = [f for f in tag.select.features(reader, traverse=True)]
     assert 'cannot traverse without a specific feature type' in str(ve)
 
 
 def test_window_contain():
-    ifn = 'tests/testdata/pdom-withseq.gff3'
-    reader = tag.reader.GFF3Reader(infilename=ifn)
+    reader = GFF3Reader(infilename='tests/testdata/pdom-withseq.gff3')
     features = tag.select.features(reader)
     window = tag.select.window(features, 'PdomSCFr1.2-0483', 3000, 7000)
     selected = [f for f in window]
@@ -39,8 +37,7 @@ def test_window_contain():
 
 
 def test_window_overlap():
-    ifn = 'tests/testdata/osat-twoscaf.gff3.gz'
-    reader = tag.reader.GFF3Reader(infilename=ifn)
+    reader = GFF3Reader(infilename='tests/testdata/osat-twoscaf.gff3.gz')
     features = tag.select.features(reader)
     window = tag.select.window(features, 'NW_015379189.1', 15000, 20000,
                                strict=False)
@@ -50,8 +47,7 @@ def test_window_overlap():
 
 
 def test_window_seqid():
-    ifn = 'tests/testdata/osat-twoscaf.gff3.gz'
-    reader = tag.reader.GFF3Reader(infilename=ifn)
+    reader = GFF3Reader(infilename='tests/testdata/osat-twoscaf.gff3.gz')
     features = tag.select.features(reader)
     window = tag.select.window(features, 'NW_015379208.1')
     selected = [f for f in window]
@@ -60,22 +56,18 @@ def test_window_seqid():
 
 
 def test_directives():
-    ifn = 'tests/testdata/pbar-withseq.gff3'
-
-    reader = tag.reader.GFF3Reader(infilename=ifn)
+    reader = GFF3Reader(infilename='tests/testdata/pbar-withseq.gff3')
     directives = [d for d in tag.select.directives(reader)]
     assert len(directives) == 3
 
-    reader = tag.reader.GFF3Reader(infilename=ifn)
+    reader = GFF3Reader(infilename='tests/testdata/pbar-withseq.gff3')
     dirs = [d for d in tag.select.directives(reader, type='sequence-region')]
     assert len(dirs) == 2
     assert [d.seqid for d in dirs] == ['NW_011929623.1', 'NW_011929624.1']
 
 
 def test_sequences():
-    ifn = 'tests/testdata/pbar-withseq.gff3'
-
-    reader = tag.reader.GFF3Reader(infilename=ifn)
+    reader = GFF3Reader(infilename='tests/testdata/pbar-withseq.gff3')
     seqs = [s for s in tag.select.sequences(reader)]
     assert len(seqs) == 2
     assert sorted([s.seq[0:5] for s in seqs]) == ['GCTAA', 'TAGAC']

tests/test_sequence.py

@@ -8,8 +8,8 @@
 # -----------------------------------------------------------------------------
 
 import pytest
-from tag.feature import Feature
-from tag.sequence import Sequence
+from tag import Feature
+from tag import Sequence
 
 
 def test_repr():

tests/test_writer.py

@@ -14,8 +14,8 @@
     from io import StringIO
 import pytest
 import tag
-from tag.reader import GFF3Reader
-from tag.writer import GFF3Writer
+from tag import GFF3Reader
+from tag import GFF3Writer
 
 
 def test_write_grape():