Fix parsing of R package versions

rrwick · Apr 5, 2023 · ee60e93 · ee60e93
1 parent 9073d03
commit ee60e93
Show file tree

Hide file tree

Showing 2 changed files with 25 additions and 21 deletions.
diff --git a/test/test_software.py b/test/test_software.py
@@ -44,25 +44,34 @@ def test_parse_r_version_2():
     assert trycycler.software.parse_r_version(output) == '?'
 
 
-def test_parse_ape_version_1():
+def test_parse_r_package_version_1():
     output = '> packageVersion("ape")\n' \
              '[1] ‘5.3’\n' \
              '>'
-    assert trycycler.software.parse_ape_version(output) == '5.3'
+    assert trycycler.software.parse_r_package_version(output) == '5.3'
 
 
-def test_parse_ape_version_2():
-    output = 'Not the correct output'
-    assert trycycler.software.parse_ape_version(output) == '?'
+def test_parse_r_package_version_2():
+    output = '> packageVersion("ape")\n' \
+             "[1] '5.3'\n" \
+             '>'
+    assert trycycler.software.parse_r_package_version(output) == '5.3'
 
 
-def test_parse_phangorn_version_1():
+def test_parse_r_package_version_3():
     output = '> packageVersion("phangorn")\n' \
              '[1] ‘2.5.5’\n' \
              '>'
-    assert trycycler.software.parse_ape_version(output) == '2.5.5'
+    assert trycycler.software.parse_r_package_version(output) == '2.5.5'
+
+
+def test_parse_r_package_version_4():
+    output = '> packageVersion("phangorn")\n' \
+             "[1] '2.5.5'\n" \
+             '>'
+    assert trycycler.software.parse_r_package_version(output) == '2.5.5'
 
 
-def test_parse_phangorn_version_2():
+def test_parse_r_package_version_5():
     output = 'Not the correct output'
-    assert trycycler.software.parse_ape_version(output) == '?'
+    assert trycycler.software.parse_r_package_version(output) == '?'
diff --git a/trycycler/software.py b/trycycler/software.py
@@ -131,19 +131,10 @@ def check_ape():
     if 'there is no package' in output or 'not found' in output:
         sys.exit('\nError: unable to find ape - make sure that the "ape" package is installed '
                  'for your R installation, then try again.')
-    version = parse_ape_version(output)
+    version = parse_r_package_version(output)
     log(f'       ape: v{version}')
 
 
-def parse_ape_version(output):
-    if '[1] ‘' in output:
-        output = output.split('[1] ‘')[1]
-        output = output.split('’')[0]
-        return output.strip()
-    else:
-        return '?'
-
-
 def check_phangorn():
     try:
         output = subprocess.check_output(['R', '--quiet', '-e', 'packageVersion("phangorn")'],
@@ -155,14 +146,18 @@ def check_phangorn():
     if 'there is no package' in output or 'not found' in output:
         sys.exit('\nError: unable to find phangorn - make sure that the "phangorn" package is '
                  'installed for your R installation, then try again.')
-    version = parse_phangorn_version(output)
+    version = parse_r_package_version(output)
     log(f'  phangorn: v{version}')
 
 
-def parse_phangorn_version(output):
+def parse_r_package_version(output):
     if '[1] ‘' in output:
         output = output.split('[1] ‘')[1]
         output = output.split('’')[0]
         return output.strip()
+    elif "[1] '" in output:
+        output = output.split("[1] '")[1]
+        output = output.split("'")[0]
+        return output.strip()
     else:
         return '?'