mass renaming

ChangeLog

@@ -1,9 +1,15 @@
 2015-07-29  Michael R. Crusoe  <crusoe@ucdavis.edu>
 
    * scripts/*.py,tests/*.py,sandbox/*.py,khmer/*.py,oxli/*.py:
-     counting_hash, hashtable->countgraph; hashbits->nodegraph;
-     check_space_for_hashtable->check_space_for_graph; hash_args->graph_args
-
+   many function and variable renames:
+   counting_hash, countinghash, hashtable->countgraph;
+   CountingHash->Countgraph
+   hashbits->nodegraph; Hashbits->Nodegraph;
+   check_space_for_hashtable->check_space_for_graph;
+   hash_args->graph_args
+   * khmer/_khmer.cc: remove unused 'new_hashtable' method; match renames
+   * TODO: removed several items
+   * doc/dev/scripts-and-sandbox.rst: fixed hashbang
 
 2015-08-04  Titus Brown  <titus@idyll.org> and Camille Scott
 <camille.scott.w@gmail.com>

TODO

@@ -1,8 +1,3 @@
-@@ merge refactor => master
-@@ review site for paper?
-
-auto-memory setting.
-
 find-knot speedup:
    - too many redundant rounds of partitioning?
 
@@ -28,17 +23,14 @@ load-counting/bigcount loading is slooooow
 
 ----
 
-screed bzip
 screed slice
 screed fasta/fastq output
 
-screed streaming foo
 
 ---
 
 fix tests cleanup
 pyrex/cython stuff
-script testing
 docs!
 
 ---
@@ -54,8 +46,6 @@ fix tests and test cases to properly isolate/remove temp files.
 
 fix dir(ht)
 
-rename new_hashtable to new_countinghash
-
 ###
 
 Semi-obsolete comments, pre partitioning:

doc/dev/scripts-and-sandbox.rst

@@ -38,7 +38,7 @@ All scripts in ``sandbox/`` must:
 * be importable (enforced by ``test_import_all`` in
   ``test_sandbox_scripts.py``)
 * be mentioned in ``sandbox/README.rst``
-* have a hash-bang line (``#! /usr/bin/env python2``) at the top
+* have a hash-bang line (``#! /usr/bin/env python``) at the top
 * be command-line executable (``chmod a+x``)
 * have a Copyright message (see below)
 * have lowercase names

khmer/__init__.py

@@ -10,18 +10,14 @@
 from math import log
 import json
 
-from khmer._khmer import CountingHash as _CountingHash
+from khmer._khmer import Countgraph as _Countgraph
 from khmer._khmer import LabelHash as _LabelHash
-from khmer._khmer import Hashbits as _Hashbits
+from khmer._khmer import Nodegraph as _Nodegraph
 from khmer._khmer import HLLCounter as _HLLCounter
 from khmer._khmer import ReadAligner as _ReadAligner
 
-from khmer._khmer import forward_hash  # figuregen/*.py
-# tests/test_{functions,countinggraph,labelhash,counting_single}.py
-
-from khmer._khmer import new_hashtable
-# sandbox/{occupy,ctb-iterative-bench{-2-old}}.py
-# tests/{test_c_wrapper,test_counting_single}.py
+from khmer._khmer import forward_hash
+# tests/test_{functions,countinggraph,counting_single}.py
 
 from khmer._khmer import forward_hash_no_rc  # tests/test_functions.py
 
@@ -53,10 +49,10 @@ def load_nodegraph(filename):
     Keyword argument:
     filename -- the name of the nodegraph file
     """
-    hashtable = _Hashbits(1, [1])
-    hashtable.load(filename)
+    nodegraph = _Nodegraph(1, [1])
+    nodegraph.load(filename)
 
-    return hashtable
+    return nodegraph
 
 
 def load_countinggraph(filename):
@@ -65,10 +61,10 @@ def load_countinggraph(filename):
     Keyword argument:
     filename -- the name of the countinggraph file
     """
-    hashtable = _CountingHash(1, [1])
-    hashtable.load(filename)
+    countgraph = _Countgraph(1, [1])
+    countgraph.load(filename)
 
-    return hashtable
+    return countgraph
 
 
 def extract_nodegraph_info(filename):
@@ -108,7 +104,7 @@ def extract_nodegraph_info(filename):
     return ksize, round(table_size, -2), n_tables, version, ht_type
 
 
-def extract_countinghash_info(filename):
+def extract_countgraph_info(filename):
     """Open the given countinggraph file and return a tuple of information.
 
     Return: the k-mer size, the table size, the number of tables, the bigcount
@@ -129,14 +125,14 @@ def extract_countinghash_info(filename):
     ulonglong_size = len(pack('Q', 0))
 
     try:
-        with open(filename, 'rb') as countinghash:
-            signature, = unpack('4s', countinghash.read(4))
-            version, = unpack('B', countinghash.read(1))
-            ht_type, = unpack('B', countinghash.read(1))
-            use_bigcount, = unpack('B', countinghash.read(1))
-            ksize, = unpack('I', countinghash.read(uint_size))
-            n_tables, = unpack('B', countinghash.read(1))
-            table_size, = unpack('Q', countinghash.read(ulonglong_size))
+        with open(filename, 'rb') as countgraph:
+            signature, = unpack('4s', countgraph.read(4))
+            version, = unpack('B', countgraph.read(1))
+            ht_type, = unpack('B', countgraph.read(1))
+            use_bigcount, = unpack('B', countgraph.read(1))
+            ksize, = unpack('I', countgraph.read(uint_size))
+            n_tables, = unpack('B', countgraph.read(1))
+            table_size, = unpack('Q', countgraph.read(ulonglong_size))
         if signature != b'OXLI':
             raise ValueError("Counting table '{}' is missing file type "
                              "signature. ".format(filename) + str(signature))
@@ -147,17 +143,17 @@ def extract_countinghash_info(filename):
         ht_type
 
 
-def calc_expected_collisions(hashtable, force=False, max_false_pos=.2):
-    """Do a quick & dirty expected collision rate calculation on a hashtable.
+def calc_expected_collisions(graph, force=False, max_false_pos=.2):
+    """Do a quick & dirty expected collision rate calculation on a graph
 
     Also check to see that collision rate is within threshold.
 
     Keyword argument:
-    hashtable: the hashtable object to inspect
+    graph: the countgraph or nodegraph object to inspect
     """
-    sizes = hashtable.hashsizes()
+    sizes = graph.hashsizes()
     n_ht = float(len(sizes))
-    occupancy = float(hashtable.n_occupied())
+    occupancy = float(graph.n_occupied())
     min_size = min(sizes)
 
     fp_one = occupancy / min_size
@@ -233,19 +229,19 @@ def get_n_primes_near_x(number, target):
 # Additional functionality can be added to these classes as appropriate.
 
 
-class CountingHash(_CountingHash):
+class Countgraph(_Countgraph):
 
     def __new__(cls, k, starting_size, n_tables):
         primes = get_n_primes_near_x(n_tables, starting_size)
-        c = _CountingHash.__new__(cls, k, primes)
+        c = _Countgraph.__new__(cls, k, primes)
         c.primes = primes
         return c
 
 
 class LabelHash(_LabelHash):
 
     def __new__(cls, k, starting_size, n_tables):
-        hb = Hashbits(k, starting_size, n_tables)
+        hb = Nodegraph(k, starting_size, n_tables)
         c = _LabelHash.__new__(cls, hb)
         c.graph = hb
         return c
@@ -255,17 +251,17 @@ class CountingLabelHash(_LabelHash):
 
     def __new__(cls, k, starting_size, n_tables):
         primes = get_n_primes_near_x(n_tables, starting_size)
-        hb = _CountingHash(k, primes)
+        hb = _Countgraph(k, primes)
         c = _LabelHash.__new__(cls, hb)
         c.graph = hb
         return c
 
 
-class Hashbits(_Hashbits):
+class Nodegraph(_Nodegraph):
 
     def __new__(cls, k, starting_size, n_tables):
         primes = get_n_primes_near_x(n_tables, starting_size)
-        c = _Hashbits.__new__(cls, k, primes)
+        c = _Nodegraph.__new__(cls, k, primes)
         c.primes = primes
         return c
 
@@ -296,7 +292,7 @@ class ReadAligner(_ReadAligner):
 
     """Sequence to graph aligner.
 
-    ReadAligner uses a CountingHash (the counts of k-mers in the target DNA
+    ReadAligner uses a Countgraph (the counts of k-mers in the target DNA
     sequences) as an implicit De Bruijn graph. Input DNA sequences are aligned
     to this graph via a paired Hidden Markov Model.