removed excessive input checking

Author: xrotwang

src/nexus/commands/edit.py

@@ -6,8 +6,8 @@
 from nexus.cli_util import add_nexus, get_reader, add_output, write_output, list_of_ranges
 from nexus.tools import count_site_values
 from nexus.tools import check_zeros
-from nexus.tools import find_constant_sites
-from nexus.tools import find_unique_sites
+from nexus.tools import iter_constant_sites
+from nexus.tools import iter_unique_sites
 from nexus.tools import new_nexus_without_sites
 
 
@@ -59,11 +59,11 @@ def run(args):
 
     const, unique, zeros, remove = [], [], [], []
     if args.constant:
-        const = find_constant_sites(nexus)
+        const = list(iter_constant_sites(nexus))
         if const:
             args.log.info("Constant Sites: %s" % ",".join([str(i + 1) for i in const]))
     if args.unique:
-        unique = find_unique_sites(nexus)
+        unique = list(iter_unique_sites(nexus))
         if unique:
             args.log.info("Unique Sites: %s" % ",".join([str(i + 1) for i in unique]))
     if args.zeros:

src/nexus/tools/__init__.py

@@ -1,24 +1,22 @@
 # tools
-from nexus.tools.check_for_valid_NexusReader import check_for_valid_NexusReader
 from nexus.tools.check_zeros import check_zeros, remove_zeros
 from nexus.tools.combine_nexuses import combine_nexuses
 from nexus.tools.shufflenexus import shufflenexus
-from nexus.tools.sites import find_constant_sites
-from nexus.tools.sites import find_unique_sites
+from nexus.tools.sites import iter_constant_sites
+from nexus.tools.sites import iter_unique_sites
 from nexus.tools.sites import count_site_values
 from nexus.tools.sites import new_nexus_without_sites
 from nexus.tools.sites import tally_by_site
 from nexus.tools.sites import tally_by_taxon
 from nexus.tools.sites import count_binary_set_size
 
 __all__ = [
-    "check_for_valid_NexusReader",
     "binarise",
     "multistatise",
     "combine_nexuses",
     "shufflenexus",
-    "find_constant_sites",
-    "find_unique_sites",
+    "iter_constant_sites",
+    "iter_unique_sites",
     "count_site_values",
     "new_nexus_without_sites",
     "tally_by_site",

src/nexus/tools/binarise.py

@@ -1,5 +1,4 @@
 from nexus.writer import NexusWriter
-from nexus.tools.check_for_valid_NexusReader import check_for_valid_NexusReader
 
 
 def _recode_to_binary(char, keep_zero=False):
@@ -79,7 +78,6 @@ def binarise(nexus_obj, keep_zero=False):
     :raises AssertionError: if nexus_obj is not a nexus
     :raises NexusFormatException: if nexus_obj does not have a `data` block
     """
-    check_for_valid_NexusReader(nexus_obj, required_blocks=['data'])
     n = NexusWriter()
 
     for i in sorted(nexus_obj.data.charlabels):

src/nexus/tools/check_for_valid_NexusReader.py

@@ -1,6 +1,5 @@
 import collections
 
-from nexus.tools.check_for_valid_NexusReader import check_for_valid_NexusReader
 from nexus.tools.sites import new_nexus_without_sites
 
 
@@ -28,8 +27,6 @@ def check_zeros(nexus_obj, absences=None, missing=None):
         `char` dictionary is not a string (i.e.
         integer or None values)
     """
-    check_for_valid_NexusReader(nexus_obj, required_blocks=['data'])
-
     absences = absences if absences else ['0']
     missing = missing if missing else ['-', '?']
 

src/nexus/tools/check_zeros.py

@@ -1,7 +1,6 @@
 import os
 
 from nexus.writer import NexusWriter
-from nexus.tools.check_for_valid_NexusReader import check_for_valid_NexusReader
 
 
 def combine_nexuses(nexuslist):
@@ -21,7 +20,6 @@ def combine_nexuses(nexuslist):
     # check they're all nexus instances and get all block types
     blocks = set()
     for nex in nexuslist:
-        check_for_valid_NexusReader(nex)
         blocks.update(list(nex.blocks))
 
     for block in blocks:
@@ -36,15 +34,13 @@ def combine_nexuses(nexuslist):
 
 def combine_treeblocks(out, nexuslist):
     for nex in nexuslist:
-        check_for_valid_NexusReader(nex, required_blocks=['trees'])
         out.trees.extend(nex.trees.trees)
     return out
 
 
 def combine_datablocks(out, nexuslist):
     charpos = 0
     for nex_id, nex in enumerate(nexuslist, 1):
-        check_for_valid_NexusReader(nex, required_blocks=['data'])
         if nex.short_filename:
             nexus_label = os.path.splitext(nex.short_filename)[0]
         else:

src/nexus/tools/combine_nexuses.py

@@ -1,5 +1,4 @@
 from nexus.writer import NexusWriter
-from nexus.tools.check_for_valid_NexusReader import check_for_valid_NexusReader
 
 
 def multistatise(nexus_obj, charlabel=None):
@@ -13,8 +12,6 @@ def multistatise(nexus_obj, charlabel=None):
     :raises AssertionError: if nexus_obj is not a nexus
     :raises NexusFormatException: if nexus_obj does not have a `data` block
     """
-    check_for_valid_NexusReader(nexus_obj, required_blocks=['data'])
-
     if not charlabel:
         charlabel = getattr(nexus_obj, 'short_filename', 1)
 

src/nexus/tools/multistatise.py

@@ -1,7 +1,6 @@
 import random
 
 from nexus.writer import NexusWriter
-from nexus.tools.check_for_valid_NexusReader import check_for_valid_NexusReader
 
 
 def shufflenexus(nexus_obj, resample=False):
@@ -21,8 +20,6 @@ def shufflenexus(nexus_obj, resample=False):
     :raises ValueError: if resample is not False or a positive Integer
     :raises NexusFormatException: if nexus_obj does not have a `data` block
     """
-    check_for_valid_NexusReader(nexus_obj, required_blocks=['data'])
-
     if resample is False:
         resample = nexus_obj.data.nchar
 

src/nexus/tools/shufflenexus.py

@@ -3,23 +3,12 @@
 from collections.abc import Iterable
 
 from nexus.writer import NexusWriter
-from nexus.tools.check_for_valid_NexusReader import check_for_valid_NexusReader
 
 
-def find_constant_sites(nexus_obj):
+def iter_constant_sites(nexus_obj):
     """
-    Returns a list of the constant sites in a nexus
-
-    :param nexus_obj: A `NexusReader` instance
-    :type nexus_obj: NexusReader
-
-    :return: A list of constant site positions.
-    :raises AssertionError: if nexus_obj is not a nexus
-    :raises NexusFormatException: if nexus_obj does not have a `data` block
+    Returns a list of zero-based indices of the constant sites in a nexus
     """
-    check_for_valid_NexusReader(nexus_obj, required_blocks=['data'])
-
-    const = []
     for i in range(0, nexus_obj.data.nchar):
         states = []
         for taxa, data in nexus_obj.data:
@@ -30,26 +19,15 @@ def find_constant_sites(nexus_obj):
                 states.append(c)
 
         if len(states) == 1:
-            const.append(i)
-    return const
+            yield i
 
 
-def find_unique_sites(nexus_obj):
+def iter_unique_sites(nexus_obj):
     """
     Returns a list of the unique sites in a binary nexus
     i.e. sites with only one taxon belonging to them.
         (this only really makes sense if the data is coded as presence/absence)
-
-    :param nexus_obj: A `NexusReader` instance
-    :type nexus_obj: NexusReader
-
-    :return: A list of unique site positions.
-    :raises AssertionError: if nexus_obj is not a nexus
-    :raises NexusFormatException: if nexus_obj does not have a `data` block
     """
-    check_for_valid_NexusReader(nexus_obj, required_blocks=['data'])
-
-    unique = []
     for i in range(0, nexus_obj.data.nchar):
         members = Counter()
         missing = 0
@@ -66,8 +44,7 @@ def find_unique_sites(nexus_obj):
         if len(members) == 2:
             for state, count in members.items():
                 if state != '0' and count == 1:
-                    unique.append(i)
-    return unique
+                    yield i
 
 
 def count_site_values(nexus_obj, characters=('-', '?')):
@@ -87,8 +64,6 @@ def count_site_values(nexus_obj, characters=('-', '?')):
     if not isinstance(characters, Iterable):
         raise TypeError("characters should be iterable")
 
-    check_for_valid_NexusReader(nexus_obj, required_blocks=['data'])
-
     tally = {}
     for taxon, sites in nexus_obj.data:
         tally[taxon] = tally.get(taxon, 0)
@@ -113,8 +88,6 @@ def new_nexus_without_sites(nexus_obj, sites_to_remove):
     :raises AssertionError: if nexus_obj is not a nexus
     :raises NexusFormatException: if nexus_obj does not have a `data` block
     """
-    check_for_valid_NexusReader(nexus_obj, required_blocks=['data'])
-
     # make new nexus
     nexout = NexusWriter()
     nexout.add_comment(
@@ -150,7 +123,6 @@ def tally_by_site(nexus_obj):
         'site2': {'state1': ['taxon2'], 'state0': ['taxon1', 'taxon3'], }
     }
     """
-    check_for_valid_NexusReader(nexus_obj, required_blocks=['data'])
     tally = {}
     for site, data in nexus_obj.data.characters.items():
         tally[site] = tally.get(site, {})
@@ -179,7 +151,6 @@ def tally_by_taxon(nexus_obj):
         'taxon2': {'state1': ['site2'], 'state0': ['site1', 'site3'], }
     }
     """
-    check_for_valid_NexusReader(nexus_obj, required_blocks=['data'])
     tally = {}
     for taxon, characters in nexus_obj.data:
         tally[taxon] = {}
@@ -210,7 +181,6 @@ def count_binary_set_size(nexus_obj):
         2: 20,
     }
     """
-    check_for_valid_NexusReader(nexus_obj, required_blocks=['data'])
     tally = Counter()
     for char_id in nexus_obj.data.characters:
         char = nexus_obj.data.characters[char_id]