Merge pull request #157 from agraubert/hotfix

Hotfix 3.1.0

CHANGES.md

@@ -1,5 +1,12 @@
 # CHANGELOG
 
+## 3.1.0
+
+**Deprecation Warning:**
+
+* The `maf2bed` utility, and its associated code, are now deprecated and will be
+removed in a future release
+
 ## 3.0.1
 
 * Fixed `setup.py` to allow source builds on pip 10

README.md

@@ -4,7 +4,7 @@
 
 A collection of python utilities
 
-__Version:__ 3.0.1
+__Version:__ 3.1.0
 
 ###### Tools:
 * search_range (A utility for manipulating numerical ranges)
@@ -14,7 +14,9 @@ __Version:__ 3.0.1
 
 The __bio__ package:
 
-* maf2bed (A command line utility for parsing a .maf file and converting coordinates from 1-based (maf standard) to 0-based (bed standard))
+* ~~maf2bed (A command line utility for parsing a .maf file and converting coordinates from 1-based (maf standard) to 0-based (bed standard))~~
+
+  **Deprecated: Will be removed in a future release**
 
 The __io__ package:
 

agutil/bio/maf2bed.py

@@ -5,6 +5,10 @@
 
 
 def bedkey(args):
+    print(
+        "Deprecation Warning: maf2bed is now deprecated and will be removed in"
+        " a future release"
+    )
     args.keys = set(args.keys)
     output = []
     reader = csv.DictReader(args.input, delimiter='\t')
@@ -20,6 +24,10 @@ def bedkey(args):
 
 
 def maf2bed(args):
+    print(
+        "Deprecation Warning: maf2bed is now deprecated and will be removed in"
+        " a future release"
+    )
     if args.v and sys.platform == "win32":
         reader = open(args.input.name, mode='r')
         args.v = len([False for row in reader])

tests/test_maf2bed.py

@@ -44,6 +44,7 @@ def test_compilation(self):
         self.assertTrue(compiled_path)
 
     # @unittest.skipIf(sys.platform.startswith("win"), "Tempfile doesn't work in this manner on windows")
+    @unittest.skip("maf2bed is now deprecated")
     def test_output(self):
         import agutil.bio.maf2bed
         output_dir = tempfile.TemporaryDirectory()
@@ -103,6 +104,7 @@ def test_output(self):
         output_dir.cleanup()
 
     # @unittest.skipIf(sys.platform.startswith("win"), "Tempfile doesn't work in this manner on windows")
+    @unittest.skip("maf2bed is now deprecated")
     def test_output_noSilents(self):
         import agutil.bio.maf2bed
         output_dir = tempfile.TemporaryDirectory()
@@ -163,6 +165,7 @@ def test_output_noSilents(self):
         output_dir.cleanup()
 
     # @unittest.skipIf(sys.platform.startswith("win"), "Tempfile doesn't work in this manner on windows")
+    @unittest.skip("maf2bed is now deprecated")
     def test_output_noKeyfile(self):
         import agutil.bio.maf2bed
         output_file = tempname()
@@ -186,6 +189,7 @@ def test_output_noKeyfile(self):
         os.remove(output_file)
 
     # @unittest.skipIf(sys.platform.startswith("win"), "Tempfile doesn't work in this manner on windows")
+    @unittest.skip("maf2bed is now deprecated")
     def test_output_noSilents_noKeyfile(self):
         import agutil.bio.maf2bed
         output_file = tempname()