Don't allow too-new versions of SPAdes

README.md

@@ -94,7 +94,7 @@ Reasons to __not__ use Unicycler:
     * [ICC](https://software.intel.com/en-us/c-compilers) also works (though I don't know the minimum required version number)
 * [setuptools](https://packaging.python.org/installing/#install-pip-setuptools-and-wheel) (only required for installation of Unicycler)
 * For short-read or hybrid assembly:
-  * [SPAdes](http://bioinf.spbau.ru/spades) v3.6.2 or later (`spades.py`)
+  * [SPAdes](http://bioinf.spbau.ru/spades) v3.6.2 – v3.13.0 (`spades.py`)
 * For long-read or hybrid assembly:
   * [Racon](https://github.com/isovic/racon) (`racon`)
 * For polishing

test/test_misc.py

@@ -402,3 +402,36 @@ def test_spades_version_parsing_4(self):
                                 '-o <output_dir>\n\nBasic options:'
         version = unicycler.misc.spades_version_from_spades_output(spades_version_output)
         self.assertEqual(version, '2.4.0')
+
+    def test_spades_version_status_1(self):
+        self.assertEqual(unicycler.misc.spades_status_from_version('2.4.0'), 'too old')
+
+    def test_spades_version_status_2(self):
+        self.assertEqual(unicycler.misc.spades_status_from_version('3.4.0'), 'too old')
+
+    def test_spades_version_status_3(self):
+        self.assertEqual(unicycler.misc.spades_status_from_version('3.6.0'), 'too old')
+
+    def test_spades_version_status_4(self):
+        self.assertEqual(unicycler.misc.spades_status_from_version('3.6.1'), 'too old')
+
+    def test_spades_version_status_5(self):
+        self.assertEqual(unicycler.misc.spades_status_from_version('3.6.2'), 'good')
+
+    def test_spades_version_status_6(self):
+        self.assertEqual(unicycler.misc.spades_status_from_version('3.7.0'), 'good')
+
+    def test_spades_version_status_7(self):
+        self.assertEqual(unicycler.misc.spades_status_from_version('3.9.9'), 'good')
+
+    def test_spades_version_status_8(self):
+        self.assertEqual(unicycler.misc.spades_status_from_version('3.13.0'), 'good')
+
+    def test_spades_version_status_9(self):
+        self.assertEqual(unicycler.misc.spades_status_from_version('3.13.1'), 'too new')
+
+    def test_spades_version_status_10(self):
+        self.assertEqual(unicycler.misc.spades_status_from_version('3.14.1'), 'too new')
+
+    def test_spades_version_status_11(self):
+        self.assertEqual(unicycler.misc.spades_status_from_version('4.0.0'), 'too new')

unicycler/misc.py

@@ -891,23 +891,9 @@ def spades_path_and_version(spades_path):
     if 'python version' in out and 'is not supported' in out:
         return found_spades_path, '', 'Python problem'
 
-    # Make sure SPAdes is 3.6.2+
+    # Make sure SPAdes is 3.6.2 - 3.13.0
     try:
-        major_version = int(version.split('.')[0])
-        if major_version < 3:
-            status = 'too old'
-        else:
-            minor_version = int(version.split('.')[1])
-            if minor_version < 6:
-                status = 'too old'
-            elif minor_version > 6:
-                status = 'good'
-            else:  # minor_version == 6
-                patch_version = int(version.split('.')[2])
-                if patch_version < 2:
-                    status = 'too old'
-                else:
-                    status = 'good'
+        status = spades_status_from_version(version)
     except (ValueError, IndexError):
         version, status = '?', 'too old'
 
@@ -933,6 +919,36 @@ def spades_version_from_spades_output(spades_output):
     return ''
 
 
+def spades_status_from_version(version):
+    major_version = int(version.split('.')[0])
+    if major_version < 3:
+        return 'too old'
+    if major_version >= 4:
+        return 'too new'
+
+    minor_version = int(version.split('.')[1])
+    if minor_version < 6:
+        return 'too old'
+    if minor_version > 13:
+        return 'too new'
+    assert 6 <= minor_version <= 13
+
+    patch_version = int(version.split('.')[2])
+    if 6 < minor_version < 13:
+        return 'good'
+    assert minor_version == 6 or minor_version == 13
+    if minor_version == 6:
+        if patch_version < 2:
+            return 'too old'
+        else:
+            return 'good'
+    if minor_version == 13:
+        if patch_version > 0:
+            return 'too new'
+        else:
+            return 'good'
+
+
 def racon_path_and_version(racon_path):
     found_racon_path = shutil.which(racon_path)
     if found_racon_path is None:
@@ -941,7 +957,7 @@ def racon_path_and_version(racon_path):
     process = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
     out, _ = process.communicate()
     out = out.decode().lower()
-    if 'racon' not in out or  'options' not in out:
+    if 'racon' not in out or 'options' not in out:
         return found_racon_path, '-', 'bad'
 
     return found_racon_path, racon_version(found_racon_path), 'good'

unicycler/unicycler.py

@@ -843,7 +843,8 @@ def check_dependencies(args, short_reads_available, long_reads_available):
     for i, row in enumerate(program_table):
         if 'not used' in row:
             row_colours[i] = 'dim'
-        elif 'too old' in row or 'not found' in row or 'bad' in row or 'Python problem' in row:
+        elif ('too old' in row or 'too new' in row or 'not found' in row or 'bad' in row or
+              'Python problem' in row):
             row_colours[i] = 'red'
 
     print_table(program_table, alignments='LLLL', row_colour=row_colours, max_col_width=60,
@@ -866,8 +867,8 @@ def quit_if_dependency_problem(spades_status, racon_status, makeblastdb_status,
     log.log('')
     if spades_status == 'not found':
         quit_with_error('could not find SPAdes at ' + args.spades_path)
-    if spades_status == 'too old':
-        quit_with_error('Unicycler requires SPAdes v3.6.2 or higher')
+    if spades_status == 'too old' or spades_status == 'too new':
+        quit_with_error('Unicycler requires SPAdes v3.6.2 - v3.13.0')
     if spades_status == 'Python problem':
         quit_with_error('SPAdes cannot run due to an incompatible Python version')
     if spades_status == 'bad':