minor cleanup

ChangeLog

@@ -1,12 +1,16 @@
-2015-07-20  Jacob Fenton  <bocajnotnef@gmail.com>
+2015-07-21  Jacob Fenton  <bocajnotnef@gmail.com>
 
    * khmer/{kfile,khmer_args}.py: refactored information passing, made it so
-   space checks happen in the right directory
-   * oxli/build_graph.py,sandbox/collect-reads.py,scripts/{count-overlap,
+   space checks happen in the right directory.
+   * oxli/build_graph.py,sandbox/collect-reads.py,scripts/{
    abundance-dist-single,filter-abund-single,load-into-counting,
-   make-initial-stoptags,normalize-by-median,partition-graph,
-   sample-reads-randomly,trim-low-abund}.py,tests/test_script_arguments.py:
-   changed to use new arg structure
+   normalize-by-median,trim-low-abund}.py,tests/test_script_arguments.py:
+   changed to use new arg structure for checking hashtable save space.
+   * oxli/functions.py,scripts/saturate-by-median.py: updated error message
+   to mention --force option.
+   * scripts/{count-overlap,load-into-counting,make-initial-stoptags,
+   partition-graph,sample-reads-randomly}.py: removed unnecessary call to
+   check_space.
 
 2015-07-20  Titus Brown  <titus@idyll.org>
 
@@ -20,43 +24,44 @@
 
    * oxli/{functions,build_graph}.py,scripts/{load-graph,normalize-by-median,
    abundance-dist}.py,tests/test_{normalize_by_median,subset_graph,hashbits,
-   oxli_function}.py: pylint cleanup
+   oxli_function}.py: pylint cleanup.
 
 2015-07-17  Michael R. Crusoe  <crusoe@ucdavis.edu>  
 
-   * Makefile, tests/test_read_aligner.py: import khmer when pylinting
+   * Makefile, tests/test_read_aligner.py: import khmer when pylinting.
 
 2015-07-17  Michael R. Crusoe  <crusoe@ucdavis.edu>
 
    * lib/read_parser.{cc,hh}: use std::string everywhere to match existing
-   exceptions
+   exceptions.
 
 2015-07-10  Jacob Fenton  <bocajnotnef@gmail.com>
 
    * khmer/kfile.py: changed check_valid_file_exists to recognize fifos as
-   non-empty
-   * tests/test_normalize_by_median.py: added test
+   non-empty.
+   * tests/test_normalize_by_median.py: added test.
 
 2015-07-10  Jacob Fenton  <bocajnotnef@gmail.com>
 
    * oxli/functions.py: changed estimate functions to use correct letter
-   abbreviations
-   * sandbox/estimate_optimal_hash.py: changed to use renamed estimate 
-   functions
+   abbreviations.
+   * sandbox/estimate_optimal_hash.py: changed to use renamed estimate
+   functions.
    * sandbox/unique-kmers.py: changed to not output recommended HT args by
-   default
-   * tests/test_oxli_functions.py: changed to use renamed estimate functions
+   default.
+   * tests/test_oxli_functions.py: changed to use renamed estimate functions.
 
 2015-07-10  Jacob Fenton  <bocajnotnef@gmail.com>
 
-   * oxli/functions.py: added '--force' check to sanity check
+   * oxli/functions.py: added '--force' check to sanity check.
 
 2015-07-10  Jacob Fenton  <bocajnotnef@gmail.com>
 
-   * oxli/functions.py: moved optimization/sanity check func to oxli
+   * oxli/functions.py: moved optimization/sanity check func to oxli.
    * scripts/normalize-by-median.py,oxli/build_graph.py: added
-   optimization/sanity checking via oxli estimation funcs
-   * tests/test_normalize_by_median.py: updated tests to cover estimation funcs
+   optimization/sanity checking via oxli estimation funcs.
+   * tests/test_normalize_by_median.py: updated tests to cover estimation
+   functions.
 
 2015-07-08  Luiz Irber  <khmer@luizirber.org>
 
@@ -74,22 +79,22 @@
 2015-07-05  Jacob Fenton  <bocajnotnef@gmail.com>
 
    * doc/whats-new-2.0.rst: added in normalize-by-median.py broken paired 
-   updates
+   updates.
 
 2015-07-05  Michael R. Crusoe  <crusoe@ucdavis.edu>
 
-   * Makefile: fix cppcheck invocation
+   * Makefile: fix cppcheck invocation.
    * khmer/_khmer.cc: switch to prefix increment for non-primitive objects,
-   use a C++ cast, adjust scope
+   use a C++ cast, adjust scope.
    * lib/hashtable.{hh,cc}: make copy constructor no-op explicit. adjust scope
-   * lib/{ht-diff,test-HashTables,test-Parser}.cc: remove unused test code
-   * lib/labelhash.cc,hllcounter.cc: astyle reformatting
-   * lib/read_parsers.hh: more explicit constructors
+   * lib/{ht-diff,test-HashTables,test-Parser}.cc: remove unused test code.
+   * lib/labelhash.cc,hllcounter.cc: astyle reformatting.
+   * lib/read_parsers.hh: more explicit constructors.
 
 2015-07-05  Michael R. Crusoe  <crusoe@ucdavis.edu>
 
    * sandbox/{collect-variants,optimal_args_hashbits,sweep-files}.py:
-   update API usage
+   update API usage.
 
 2015-07-05  Titus Brown  <titus@idyll.org>
 

khmer/kfile.py

@@ -122,7 +122,7 @@ def check_space(in_files, force, _testhook_free_space=None):
 
 def check_space_for_hashtable(outfile_name, hash_size, force,
                               _testhook_free_space=None):
-    """Check we have enough size to write a hash table."""
+    """Check that we have enough size to write the specified hash table."""
 
     dir_path = os.path.dirname(os.path.realpath(outfile_name))
     target = os.statvfs(dir_path)

scripts/filter-abund-single.py

@@ -71,7 +71,6 @@ def main():
     check_input_files(args.datafile, args.force)
     check_space([args.datafile], args.force)
     if args.savetable:
-        mem_args = args.max_memory_usage
         tablesize = calculate_tablesize(args, 'countgraph')
         check_space_for_hashtable(args.savetable, tablesize, args.force)
 

scripts/load-into-counting.py

@@ -125,7 +125,6 @@ def main():
             thread.join()
 
         if index > 0 and index % 10 == 0:
-            mem_args = args.max_memory_usage
             tablesize = calculate_tablesize(args, 'countgraph')
             check_space_for_hashtable(base, tablesize, args.force)
             print('mid-save', base, file=sys.stderr)

scripts/normalize-by-median.py

@@ -306,7 +306,6 @@ def main():  # pylint: disable=too-many-branches,too-many-statements
     check_space(args.input_filenames, args.force)
     if args.savetable:
         tablesize = calculate_tablesize(args, 'countgraph')
-
         check_space_for_hashtable(args.savetable, tablesize, args.force)
 
     # load or create counting table.

tests/test_script_arguments.py

@@ -53,7 +53,6 @@ def test_check_tablespace():
     args = parser.parse_args(['-M', '1e9'])
 
     try:
-        mem_args = args.max_memory_usage
         tablesize = khmer_args.calculate_tablesize(args, 'countgraph')
         khmer.kfile.check_space_for_hashtable(outfile, tablesize,
                                               False, _testhook_free_space=0)
@@ -87,7 +86,6 @@ def test_check_tablespace_force():
     args = parser.parse_args(['-M', '1e9'])
 
     try:
-        mem_args = args.max_memory_usage
         tablesize = khmer_args.calculate_tablesize(args, 'countgraph')
         khmer.kfile.check_space_for_hashtable(outfile, tablesize,
                                               True, _testhook_free_space=0)