Lint tests (#85)

* lint tests
(Common problem is assigning to a variable, and then not making any assertions.)

* whitespace. runs well locally.

test/tiles/bedarcsdb.py

@@ -10,35 +10,37 @@ def get_counts(filename, zoom, pos):
 
     for i, d in enumerate(data[0][1][pos]):
         chr1, chr2 = sorted([d['fields'][0], d['fields'][3]])
-        #print('d:', d)
+        # print('d:', d)
 
         counts[(chr1, chr2)] += 1
     return counts
 
 
 def test_bedarcsdb_tiles1():
     filename = op.join(
-        'data', '9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa.pcawg_consensus_1.6.161022.somatic.sv.bedpe.multires.db')
+        'data',
+        '9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa'
+        '.pcawg_consensus_1.6.161022.somatic.sv.bedpe.multires.db')
 
     tiles_to_get = [(2, 2)]
 
     for ttg in tiles_to_get:
-        counts = get_counts(filename, *ttg)
+        get_counts(filename, *ttg)
         # print(*ttg, counts)
-    #counts1 = get_counts(filename, 0,0)
-    #counts1 = get_counts(filename, 1,1)
+    # counts1 = get_counts(filename, 0,0)
+    # counts1 = get_counts(filename, 1,1)
     # counts2 = get_counts(filename, 2,2)
     # counts3 = get_counts(filename, 2,3)
 
-    #print('1,1', counts1)
-    #print('2,2', counts2)
+    # print('1,1', counts1)
+    # print('2,2', counts2)
     # print('2,3', counts3)
 
-    #print('1', counts1[('21', 'X')])
-    #print('2', counts1[('21', 'X')])
+    # print('1', counts1[('21', 'X')])
+    # print('2', counts1[('21', 'X')])
 
-    #print("1,1", get_counts(filename, 1,1))
-    #print('2,2', get_counts(filename, 2,2))
+    # print("1,1", get_counts(filename, 1,1))
+    # print('2,2', get_counts(filename, 2,2))
 
     '''
     data = hgbad.tiles(filename, ["b.0.0"])
@@ -85,6 +87,6 @@ def test_bedarcsdb_tiles():
     filename = op.join('data', 'arrowhead_domains_short.txt.multires.db')
 
     pos = 2
-    data = hgbad.tiles(filename, ["b.2.{}".format(pos)])
+    hgbad.tiles(filename, ["b.2.{}".format(pos)])
 
-    pass
+    # TODO: Do something with the data we get back?

test/tiles/beddb_test.py

@@ -1,16 +1,16 @@
 import clodius.tiles.beddb as hgbe
-import json
 import os.path as op
 
 
 def test_get_tiles():
     filename = op.join('data', 'corrected.geneListwithStrand.bed.multires')
 
-    ret = hgbe.tiles(filename, ['x.1.0', 'x.1.1'])
+    hgbe.tiles(filename, ['x.1.0', 'x.1.1'])
+    # TODO: Do something with the return value
 
 
 def test_list_items():
     filename = op.join('data', 'gene_annotations.short.db')
 
-    ret = hgbe.list_items(filename, 0, 100000000, max_entries=100)
-    # print('ret:', ret)
+    hgbe.list_items(filename, 0, 100000000, max_entries=100)
+    # TODO: Do something with the return value

test/tiles/bigwig_test.py

@@ -96,12 +96,15 @@ def test_natsorted():
             'expected': ['1', '2', '3', '4', 'x', 'y', 'm']
         },
         {
-            'input': ['chr1', 'chr4', 'chr5', 'chr2', 'chr3', 'chrMT', 'chrY', 'chrX'],
-            'expected': ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chrX', 'chrY', 'chrMT']
+            'input': ['chr1', 'chr4', 'chr5', 'chr2',
+                      'chr3', 'chrMT', 'chrY', 'chrX'],
+            'expected': ['chr1', 'chr2', 'chr3', 'chr4',
+                         'chr5', 'chrX', 'chrY', 'chrMT']
         }
     ]
 
     for test in chromname_tests:
         sorted_output = hgbi.natsorted(test['input'])
-        assert sorted_output == test['expected'], 'Sorted output was %s\nExpected: %s' % (
-            sorted_output, test['expected'])
+        assert sorted_output == test['expected'],\
+            'Sorted output was %s\nExpected: %s' \
+            % (sorted_output, test['expected'])

test/tiles/cooler_test.py

@@ -1,18 +1,18 @@
 import clodius.tiles.cooler as hgco
-import json
 import numpy as np
 import os.path as op
+import base64
 
 
 def test_cooler_info():
     filename = op.join(
         'data', 'Dixon2012-J1-NcoI-R1-filtered.100kb.multires.cool')
 
-    info = hgco.tileset_info(filename)
+    hgco.tileset_info(filename)
+    # TODO: Make assertion about info returned.
 
     tiles = hgco.generate_tiles(filename, ['a.0.0.0'])
 
-    import base64
     r = base64.decodestring(tiles[0][1]['dense'].encode('utf-8'))
     q = np.frombuffer(r, dtype=np.float32)
 

test/tiles/density_test.py

@@ -6,7 +6,7 @@
 def test_bundled_tiles():
     filename = 'data/points_density.h5'
 
-    tiles = hgut.bundled_tiles_wrapper_2d(['c.2.0.0', 'c.2.1.1', 'c.2.0.1', 'c.2.1.0'],
-                                          ft.partial(hgde.tiles, filename))
+    tiles = hgut.bundled_tiles_wrapper_2d(
+        ['c.2.0.0', 'c.2.1.1', 'c.2.0.1', 'c.2.1.0'],
+        ft.partial(hgde.tiles, filename))
     assert(len(tiles) == 4)
-    return

test/tiles/hitile_test.py

@@ -1,11 +1,8 @@
 import dask.array as da
 import h5py
 import clodius.tiles.hitile as hghi
-import math
 import numpy as np
 import os.path as op
-import random
-import sys
 import tempfile
 
 

test/tiles/multivec_test.py

@@ -5,5 +5,5 @@
 def test_multivec():
     filename = op.join('data', 'all.KL.bed.multires.mv5')
 
-    tsinfo = hgmu.tileset_info(filename)
-    # print(hgmu.tileset_info(filename))
+    hgmu.tileset_info(filename)
+    # TODO: Make assertions about info returned.

test/tiles/npvector_test.py

@@ -7,4 +7,5 @@ def test_npvector():
     # print('ts:', hgnv.tileset_info(array))
     assert('max_width' in hgnv.tileset_info(array))
 
-    tile = hgnv.tiles(array, 0, 0)
+    hgnv.tiles(array, 0, 0)
+    # TODO: Make assertions about tile returned.

test/tiles/time_interval_test.py

@@ -5,5 +5,5 @@
 def test_tileset_info():
     filename = op.join('data', 'sample_htime.json')
 
-    tsinfo = hgti.tileset_info(filename)
-    # print(hgti.tileset_info(filename))
+    hgti.tileset_info(filename)
+    # TODO: Make assertions about info returned.

travis_test.sh

@@ -13,10 +13,7 @@ flake8 --config=.flake8-ignore
 # TODO: Add more files to this list:
 flake8 test/tsv_to_mrmatrix_test.py \
        scripts/tsv_to_mrmatrix.py \
-       test/*.py
-# TODO: When everything is covered,
-# just lint the whole directory once,
-# instead of listing special cases.
+       test/*/*.py
 end flake8
 
 start download