[med-svn] [Git][med-team/python-gtfparse][master] Refresh patch

[Mohd Bilal (@rmb)]

Mohd  Bilal pushed to branch master at Debian Med / python-gtfparse


Commits:
db6c52eb by Mohammed Bilal at 2022-12-04T21:20:14+05:30
Refresh patch

- - - - -


1 changed file:

- debian/patches/switch-to-pytest.patch


Changes:

=====================================
debian/patches/switch-to-pytest.patch
=====================================
@@ -21,10 +21,10 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
 -    eq_(parsed_dict["gene_id"], ["ENSG001", "ENSG002"])
 -    eq_(parsed_dict["tag"], ["bogotron", "wolfpuppy"])
 -    eq_(parsed_dict["version"], ["1", "2"])
-+    assert list(sorted(parsed_dict.keys())), ["gene_id", "tag", "version"]
-+    assert parsed_dict["gene_id"], ["ENSG001", "ENSG002"]
-+    assert parsed_dict["tag"], ["bogotron", "wolfpuppy"]
-+    assert parsed_dict["version"], ["1", "2"]
++    assert list(sorted(parsed_dict.keys())) == ["gene_id", "tag", "version"]
++    assert parsed_dict["gene_id"] == ["ENSG001", "ENSG002"]
++    assert parsed_dict["tag"] == ["bogotron", "wolfpuppy"]
++    assert parsed_dict["version"] == ["1", "2"]
  
  
  def test_attributes_without_quotes():
@@ -36,10 +36,10 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
 -    eq_(parsed_dict["gene_id"], ["ENSG001", "ENSG002"])
 -    eq_(parsed_dict["tag"], ["bogotron", "wolfpuppy"])
 -    eq_(parsed_dict["version"], ["1", "2"])
-+    assert list(sorted(parsed_dict.keys())), ["gene_id", "tag", "version"]
-+    assert parsed_dict["gene_id"], ["ENSG001", "ENSG002"]
-+    assert parsed_dict["tag"], ["bogotron", "wolfpuppy"]
-+    assert parsed_dict["version"], ["1", "2"]
++    assert list(sorted(parsed_dict.keys())) == ["gene_id", "tag", "version"]
++    assert parsed_dict["gene_id"] == ["ENSG001", "ENSG002"]
++    assert parsed_dict["tag"] == ["bogotron", "wolfpuppy"]
++    assert parsed_dict["version"] == ["1", "2"]
  
  
  def test_optional_attributes():
@@ -50,9 +50,9 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
 -    eq_(list(sorted(parsed_dict.keys())), ["gene_id", "sometimes-present"])
 -    eq_(parsed_dict["gene_id"], ["ENSG001", "ENSG002", "ENSG003"])
 -    eq_(parsed_dict["sometimes-present"], ["bogotron", "", "wolfpuppy"])
-+    assert list(sorted(parsed_dict.keys())), ["gene_id", "sometimes-present"]
-+    assert parsed_dict["gene_id"], ["ENSG001", "ENSG002", "ENSG003"]
-+    assert parsed_dict["sometimes-present"], ["bogotron", "", "wolfpuppy"]
++    assert list(sorted(parsed_dict.keys())) == ["gene_id", "sometimes-present"]
++    assert parsed_dict["gene_id"] == ["ENSG001", "ENSG002", "ENSG003"]
++    assert parsed_dict["sometimes-present"] == ["bogotron", "", "wolfpuppy"]
 --- a/test/test_multiple_values_for_tag_attribute.py
 +++ b/test/test_multiple_values_for_tag_attribute.py
 @@ -1,6 +1,5 @@
@@ -67,10 +67,10 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
      parsed = parse_gtf_and_expand_attributes(StringIO(GTF_TEXT))
      tag_column = parsed["tag"]
 -    eq_(len(tag_column), 1)
-+    assert len(tag_column), 1
++    assert len(tag_column) == 1
      tags = tag_column[0]
 -    eq_(tags, 'cds_end_NF,mRNA_end_NF')
-+    assert tags, 'cds_end_NF,mRNA_end_NF'
++    assert tags == 'cds_end_NF,mRNA_end_NF'
  
  def test_parse_tag_attributes_with_usecols():
      parsed = parse_gtf_and_expand_attributes(
@@ -78,10 +78,10 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
          restrict_attribute_columns=["tag"])
      tag_column = parsed["tag"]
 -    eq_(len(tag_column), 1)
-+    assert len(tag_column), 1
++    assert len(tag_column) == 1
      tags = tag_column[0]
 -    eq_(tags, 'cds_end_NF,mRNA_end_NF')
-+    assert tags, 'cds_end_NF,mRNA_end_NF'
++    assert tags == 'cds_end_NF,mRNA_end_NF'
  
  def test_parse_tag_attributes_with_usecols_other_column():
      parsed = parse_gtf_and_expand_attributes(
@@ -107,20 +107,20 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
      # convert to list since Py3's dictionary keys are a distinct collection type
 -    eq_(list(parsed_dict.keys()), expected_columns)
 -    eq_(list(parsed_dict["seqname"]), ["1", "1"])
-+    assert list(parsed_dict.keys()), expected_columns
-+    assert list(parsed_dict["seqname"]), ["1", "1"]
++    assert list(parsed_dict.keys()) == expected_columns
++    assert list(parsed_dict["seqname"]) == ["1", "1"]
      # convert to list for comparison since numerical columns may be NumPy arrays
 -    eq_(list(parsed_dict["start"]), [11869, 11869])
 -    eq_(list(parsed_dict["end"]), [14409, 14409])
-+    assert list(parsed_dict["start"]), [11869, 11869]
-+    assert list(parsed_dict["end"]), [14409, 14409]
++    assert list(parsed_dict["start"]) == [11869, 11869]
++    assert list(parsed_dict["end"]) == [14409, 14409]
      # can't compare NaN with equality
      scores = list(parsed_dict["score"])
      assert np.isnan(scores).all(), "Unexpected scores: %s" % scores
 -    eq_(list(parsed_dict["gene_id"]), ["ENSG00000223972", "ENSG00000223972"])
 -    eq_(list(parsed_dict["transcript_id"]), ["", "ENST00000456328"])
-+    assert list(parsed_dict["gene_id"]), ["ENSG00000223972", "ENSG00000223972"]
-+    assert list(parsed_dict["transcript_id"]), ["", "ENST00000456328"]
++    assert list(parsed_dict["gene_id"]) == ["ENSG00000223972", "ENSG00000223972"]
++    assert list(parsed_dict["transcript_id"]) == ["", "ENST00000456328"]
  
  
  def test_parse_gtf_lines_without_expand_attributes():
@@ -129,13 +129,13 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
      # convert to list since Py3's dictionary keys are a distinct collection type
 -    eq_(list(parsed_dict.keys()), REQUIRED_COLUMNS)
 -    eq_(list(parsed_dict["seqname"]), ["1", "1"])
-+    assert list(parsed_dict.keys()), REQUIRED_COLUMNS
-+    assert list(parsed_dict["seqname"]), ["1", "1"]
++    assert list(parsed_dict.keys()) == REQUIRED_COLUMNS
++    assert list(parsed_dict["seqname"]) == ["1", "1"]
      # convert to list for comparison since numerical columns may be NumPy arrays
 -    eq_(list(parsed_dict["start"]), [11869, 11869])
 -    eq_(list(parsed_dict["end"]), [14409, 14409])
-+    assert list(parsed_dict["start"]), [11869, 11869]
-+    assert list(parsed_dict["end"]), [14409, 14409]
++    assert list(parsed_dict["start"]) == [11869, 11869]
++    assert list(parsed_dict["end"]) == [14409, 14409]
      # can't compare NaN with equality
      scores = list(parsed_dict["score"])
      assert np.isnan(scores).all(), "Unexpected scores: %s" % scores



View it on GitLab: https://salsa.debian.org/med-team/python-gtfparse/-/commit/db6c52eb114c57ffb7478bb284cf73ee590453c4

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-gtfparse/-/commit/db6c52eb114c57ffb7478bb284cf73ee590453c4
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