fix all the tests

.circleci/config.yml

@@ -1,8 +1,3 @@
-# Python 3 CircleCI 2.0 configuration file
-# For Synthego ICE
-#
-# https://circleci.com/docs/2.0/language-python/
-#
 version: 2
 jobs:
   build:

.pytest_cache/v/cache/lastfailed

@@ -0,0 +1 @@
+{}

.pytest_cache/v/cache/nodeids

@@ -0,0 +1,52 @@
+[
+  "ice/tests/test_alignment.py::test_windowed_alignment",
+  "ice/tests/test_alignment.py::test_coord_conversion",
+  "ice/tests/test_alignment.py::test_no_aln_possible",
+  "ice/tests/test_alignment.py::test_no_aln_done",
+  "ice/tests/test_alignment.py::test_all_alignment",
+  "ice/tests/test_alignment.py::test_aln_str",
+  "ice/tests/test_alignment.py::test_aln_data",
+  "ice/tests/test_alignment.py::test_aln_shorter_sample",
+  "ice/tests/test_alignment.py::test_no_aln",
+  "ice/tests/test_alignment.py::test_donor_alignment_hdr_indel_size",
+  "ice/tests/test_analysis.py::test_high_quality_sample",
+  "ice/tests/test_analysis.py::test_lowercase_guide",
+  "ice/tests/test_analysis.py::test_low_quality_control",
+  "ice/tests/test_analysis.py::test_low_quality_control_fail",
+  "ice/tests/test_analysis.py::test_sanger_analysis_bad_path",
+  "ice/tests/test_analysis.py::test_low_quality_sample",
+  "ice/tests/test_analysis.py::test_bad_paths",
+  "ice/tests/test_analysis.py::test_alignment_fail",
+  "ice/tests/test_analysis.py::test_sequence_not_found",
+  "ice/tests/test_analysis.py::test_donor_example",
+  "ice/tests/test_analysis.py::test_donor_substitution_example",
+  "ice/tests/test_analysis.py::test_multiplex_0_0",
+  "ice/tests/test_analysis.py::test_multiplex_0_1",
+  "ice/tests/test_analysis.py::test_multiplex_0_2",
+  "ice/tests/test_analysis.py::test_multiplex_1_0",
+  "ice/tests/test_analysis.py::test_multiplex_1_1",
+  "ice/tests/test_analysis.py::test_multiplex_three_guides",
+  "ice/tests/test_analysis.py::test_multiplex_three_guides_no_editing",
+  "ice/tests/test_analysis.py::test_should_skip_proposal",
+  "ice/tests/test_batch.py::test_batch_analysis",
+  "ice/tests/test_batch.py::test_bad_batch",
+  "ice/tests/test_edit_proposal_creator.py::test_single_cut",
+  "ice/tests/test_edit_proposal_creator.py::test_human_readable_sequence_single_edit_proposal",
+  "ice/tests/test_edit_proposal_creator.py::test_human_readable_sequence_multiplex_proposal",
+  "ice/tests/test_edit_proposal_creator.py::test_multiplex_cut",
+  "ice/tests/test_edit_proposal_creator.py::test_bad_multiplex",
+  "ice/tests/test_edit_proposal_creator.py::test_wt_proposal",
+  "ice/tests/test_edit_proposal_creator.py::test_req_ctrl_trace",
+  "ice/tests/test_edit_proposal_creator.py::test_generated_trace",
+  "ice/tests/test_sanger_object.py::test_trace_to_seq",
+  "ice/tests/test_sequence.py::test_rev_comp",
+  "ice/tests/test_sequence.py::test_complement",
+  "ice/tests/test_sequence.py::test_rev_transcribe",
+  "ice/tests/test_sequence.py::test_transcribe",
+  "ice/tests/test_sequence.py::test_is_nuc_acid",
+  "ice/tests/test_sequence.py::test_rna2dna",
+  "ice/tests/test_sequence.py::test_dna2rna",
+  "ice/tests/test_utility.py::test_sequence_util",
+  "ice/tests/test_utility.py::test_dna_bad_input",
+  "ice/tests/test_utility.py::test_version"
+]

.pytest_cache/v/cache/stepwise

@@ -0,0 +1 @@
+[]

ice/tests/test_alignment.py

@@ -5,9 +5,9 @@
     donor_alignment_noncontiguous_insert, donor_alignment_insert_and_deletion, donor_alignment_deletion
 
 
-def test_windowed_alignment():
-    pa = example_alignment()
-    pa.align_with_window([0,3])
+def test_windowed_alignment(example_alignment):
+    pa = example_alignment
+    pa.align_with_window([0, 3])
     assert pa.aln_seqs[0] == "AAT---------"
     assert pa.aln_seqs[1] == "AATGTATGATAG"
 
@@ -21,7 +21,7 @@ def test_coord_conversion():
     seq1 = 'GGGAATGTCCTGATAG'
     seq2 = 'AATGTTGATAG'
     pa = PairAlignment(seq1, seq2)
-    pa.align_with_window([0,14])
+    pa.align_with_window([0, 14])
     assert 2 == pa.ctrl2sample_coords(5)
     assert 0 == pa.ctrl2sample_coords(3)
     assert 9 == pa.ctrl2sample_coords(14)
@@ -41,55 +41,55 @@ def test_no_aln_possible():
     assert 'No alignment found' in msg
 
 
-def test_no_aln_done():
-    pa = example_alignment()
+def test_no_aln_done(example_alignment):
+    pa = example_alignment
     with pytest.raises(Exception):
         pa.ctrl2sample_coords(5)
 
 
-def test_all_alignment():
-    pa = example_alignment()
+def test_all_alignment(example_alignment):
+    pa = example_alignment
     pa.align_all()
     assert "AATGT-ATGATAG" in pa.all_aligned_clustal
 
     with pytest.raises(Exception):
         pa.ctrl2sample_coords(None)
 
-    #only windowed alignment results in alingment_pairs
+    # only windowed alignment results in alingment_pairs
     with pytest.raises(Exception):
         assert 7 == pa.ctrl2sample_coords(8)
 
 
-def test_aln_str():
-    pa = example_alignment()
+def test_aln_str(example_alignment):
+    pa = example_alignment
     pa.align_all()
     assert (str(pa) == 'AATGTAATGATAG\nAATGT-ATGATAG') or \
-             (str(pa) == 'AATGTAATGATAG\nAATGTA-TGATAG')
+        (str(pa) == 'AATGTAATGATAG\nAATGTA-TGATAG')
 
 
-def test_aln_data():
+def test_aln_data(example_alignment):
     '''
     The alignment after windowing should ignore the last base of the ref seq
 
     control                             AATGTAATGATA
     edited                              AATGTATGATAG
 
     '''
-    pa = example_alignment()
+    pa = example_alignment
     pa.align_with_window([0, 3])
     for idx, pair in enumerate(pa.alignment_pairs):
         assert pair[0] == pair[1]
 
 
-def test_aln_shorter_sample():
+def test_aln_shorter_sample(shorter_alignment):
     '''
 
     The alignment after windowing should have gaps
     AATGTAATGATAG---
     AATGTATGATAGTGGG
 
     '''
-    pa = shorter_alignment()
+    pa = shorter_alignment
 
     pa.align_with_window([0, 3])
 
@@ -100,18 +100,21 @@ def test_aln_shorter_sample():
             assert pair[0] == None
 
 
-def test_no_aln():
+def test_no_aln(no_alignment):
     '''
     This alignment should be None
     '''
 
-    pa = no_alignment()
+    pa = no_alignment
     pa.align_all()
     assert pa.alignment_pairs is None
 
 
-def test_donor_alignment_hdr_indel_size():
-    assert donor_alignment_contiguous_insert().hdr_indel_size == 5
-    assert donor_alignment_noncontiguous_insert().hdr_indel_size == 7
-    assert donor_alignment_insert_and_deletion().hdr_indel_size == 3
-    assert donor_alignment_deletion().hdr_indel_size == -4
+def test_donor_alignment_hdr_indel_size(donor_alignment_contiguous_insert,
+                                        donor_alignment_noncontiguous_insert,
+                                        donor_alignment_insert_and_deletion,
+                                        donor_alignment_deletion):
+    assert donor_alignment_contiguous_insert.hdr_indel_size == 5
+    assert donor_alignment_noncontiguous_insert.hdr_indel_size == 7
+    assert donor_alignment_insert_and_deletion.hdr_indel_size == 3
+    assert donor_alignment_deletion.hdr_indel_size == -4