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ChangeLog
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2015-09-07 Michael R. Crusoe <crusoe@ucdavis.edu>
* doc/roadmap.rst: Updated for 2.0 release.
* README.rst: drop unstable badges; fix links
* doc/index.rst: point at getting help guide
2015-09-05 Michael R. Crusoe <crusoe@ucdavis.edu>
* tests/test_scripts.py: make the script version test more specific; double
check that script in question is from the 'khmer' project based upon the
second line of the file.
2015-09-04 Michael R. Crusoe <crusoe@ucdavis.edu>
* tests/khmer_tst_utils.py: look in "EGG-INFO" for scripts before checking
the PATH
2015-09-04 Michael R. Crusoe <crusoe@ucdavis.edu>
* doc/release-notes/release-2.0.md: release notes for 2.0
* doc/user/install.txt: correct second invocation of nosetests to match the
first.
* setup.py: update the authors list for PyPI.
* doc/user/known-issues.rst: remove three fixed issues; add a new one
* doc/whats-new-2.0.rst: update to match the release notes
* doc/release-notes/*.rst: refresh using `make convert-release-notes'
2015-09-02 Michael R. Crusoe <crusoe@ucdavis.edu>
* *: complete audit of license headers
* LICENSE: listings of some of the third-party licenses
* bink.ipynb,lib/graphtest.cc,lib/primes.hh: deleted unused files
* sandbox/assemstats.py: updated screed install instructions
2015-09-02 Michael R. Crusoe <crusoe@ucdavis.edu>
* *: finish undoing the `load-graph.py` rename
2015-09-02 Micheal R. Crusoe <crusoe@ucdavis.edu>
* doc/requirements.txt: Update URL to sphinxcontrib-autoprogram tarball
2015-08-31 Michael R. Crusoe <crusoe@ucdavis.edu>
* khmer/thread_utils.py: Use the robust test for paired reads from
khmer.utils; drop `is_pair()`
* tests/test_threaded_sequence_processor.py: Update to use Screed Record
objects.
2015-08-28 Michael R. Crusoe <crusoe@ucdavis.edu>
* doc/whats-new-2.0.rst: Many updates from `diff`ing the `--help` output of
version 1.4.1 vs now.
* Makefile: build the project if needed when making a PDF
* doc/index.rst: fixed inter-doc links to be relative
* doc/user/blog-posts.rst: replaced link to 88m-reads.fa.gz with a working
URL
* doc/user/{choosing-table-sizes,guide}.rst: disambiguated :option:
references so that they link properly.
* scripts/README.txt: removed unhelpful file
* scripts/normalize-by-median.py: replace `--force-single` with
`--force_single`. Added help text for `--cutoff`.
2015-08-27 Titus Brown <titus@idyll.org>
* doc/dev/getting-started.rst: fixed a few misspellings.
2015-08-26 Michael R. Crusoe <crusoe@ucdavis.edu>
* tests/test_scripts.py: removed the unused `_DEBUG_make_graph` function in
favor of other debugging methods like `ipdb`. Added
test_do_partition_no_big_traverse and test_extract_paired_reads_unpaired.
2015-08-24 Michael R. Crusoe <crusoe@ucdavis.edu>
* khmer/khmer_args.py: Replaced sanitize_epilog() with santize_help() that
reflows the text of ArgParse descriptions and epilog while preserving the
formatting. Enhanced removal of Sphinx directives by replacing double
backticks with the double quote character.
* scripts/*.py: Renamed sanitize_epilog to sanitize_help; leading newlines
from triple-quoted epilogs removed; formatting made consistent;
sanitize_help and ComboFormatter added where it was missing; a couple
script specific epilog reformatting (for use of `:doc:` and a
hyperlink).
* scripts/{count-median,filter-abund-single}.py: Fixed printing of output
file name to do so instead of printing information about the file handle.
* scripts/count-median.py: Added missing command so that example given
actually works.
* scripts/filter-abund-single.py: Removed redundant printing of output file
names.
* scripts/normalize-by-median.py: Removed unused option "-d" from an example
command (left over from the "--dump-frequency" era).
* scripts/{partition-graph.py,do-partition.py}: Fixed erasure of the queue
module name in the worker functions, which is necessary for basic
functionality.
* scripts/{do-partition,abundance-dist,abundance-dist-single,
extract-long-sequences}.py: Added an example command to the epilog.
* tests/khmer_tst_utils.py: Added 'name' attribute to make the fake
sys.stdout more like a read stdout object.
* oxli/__init__.py: removed redundant and unused help text
* scripts/{abundance-dist,annotate-partitions,count-median,
extract-long-sequences,extract-paired-reads,extract-partitions,
fastq-to-fasta,filter-abund,filter-stopgaps,interleave-reads,
load-into-graph,merge-partitions,normalize-by-median,partition-graph,
readstats,sample-reads-randomly,split-paired-reads}.py: made "--version"
and the citation header consistent across the scripts.
* tests/test_scripts.py: added tests for the "--version" and citation
header behavior.
* tests/test_normalize_by_median.py: updated test for 'quiet' mode as
citation header still prints to STDERR.
* setup.py,tests/test_scripts.py: turned off the "oxli" script for v2.0.
2015-08-17 Michael R. Crusoe <crusoe@ucdavis.edu>
* Makefile: remove BASH shell designation that appears to be incompatible
with OS X Mavericks & virtualenv; refactored out BASH-isms for those whose
default shell isn't BASH (Debian, and others).
* lib/test-read-aligner.cc,read_aligner_test.sh: removed unused test files
found during search for other shell scripts with BASHisms.
2015-08-18 Michael R. Crusoe <crusoe@ucdavis.edu>
* *: reverted load-into-counting.py -> load-into-countgraph.py and
load-graph.py -> load-into nodegraph.py rename.
* CITATION: unescaped URL
* doc/user/guide.rst: added `:program:` and `:option:` directives as
needed; replaced references to `strip-and-split-for-assembly` with
`extract-paired-reads`. Updated instructions to use `--unpaired-reads` with
`normalize-by-median.py` instead of second round of diginorm.
2015-08-18 Titus Brown <titus@idyll.org>
* doc/index.rst: update introductory text.
* doc/user/biblio.rst: update bibliography link descriptions and text.
* doc/_static/labibi.css: reference new location of base CSS
2015-08-14 Luiz Irber <khmer@luizirber.org>
* scripts/unique-kmers.py: Rename option --stream-out to --stream-records.
* tests/test_streaming_io.py: Fix unique-kmers tests, use new option.
* khmer/_khmer.cc, lib/hllcounter.cc: Rename some variables for consistency.
2015-08-12 Jacob Fenton <bocajnotnef@gmail.com>
* doc/dev/{codebase-guide,coding-guidelines-and-review,development,
for-khmer-developers,getting-started,release,scripts-and-sandbox,
binary-file-formats}.rst,doc/{index,introduction,whats-new-2.0,
contributors}.rst,doc/user/{blog-posts,choosing-table-sizes,galaxy,
getting-help,guide,install,known-issues,partitioning-big-data,
scripts}.rst,CITATION: Cleaned up documentation
* scripts/*.py, khmer/khmer_args.py: added epilog sanitation
* scripts/{load-into-counting,load-graph,load-into-countgraph,
load-into-nodegraph}.py, tests/{test_scripts,test_normalize_by_median,
test_streaming_io,test_countgraph}: renamed load-into-counting ->
load-into-countgraph, load-graph -> load-into-nodegraph, fixed tests to not
bork
2015-08-12 Luiz Irber <khmer@luizirber.org>
* khmer/_khmer.cc: Fix a GCC string initialization warning.
2015-08-12 Michael R. Crusoe <crusoe@ucdavis.edu>
* CITATION, doc/{index,introduction,user/scripts}.rst, khmer/khmer_args.py:
formatting fixes and new citation for the software as a whole
* Makefile: PDF building hints, tweaked dependencies, update coverity URL,
new target to generate author list for the paper citation
* sort-authors-list.py: helper script for the above
* doc/conf.py: don't generate a module index
* doc/contributors.rst: formatting, remove references to old lab
* doc/dev/coding-guidelines-and-review.rst: add C++ version standard
* doc/dev/getting-started.rst: ccache, git-merge-changelog, and advanced
commit squashing
* doc/user/biblio.rst: added links to khmer citation collections
* doc/user/examples.rst: linked to online version of example scripts
* doc/user/guide.rst: commented out empty section, added BSD note
* lib/counting.{cc},lib/*.hh: c++11 fixes: remove unneeded trailing
semicolons
* scripts/*.py: line-wrap & scrub output
* setup.py: turn optimizations back on and -pedantic
* .mailmap: additional tweaks to author list
2015-08-11 Kevin Murray <spam@kdmurray.id.au>
* lib/Makefile: Fix SONAME and ABI versioning to sync with Debian standard
practice.
2015-08-10 Camille Scott <camille.scott.w@gmail.com>
* lib/traversal.{cc,hh}: Add new files with unified traversal machinery.
Introduce Traverser class to handle finding neighbors and appropriate
bitmasking.
* khmer/_khmer.cc,lib/{counting,hashbits,hashtable,labelhash,subset}.{cc,hh}:
Updated relevant instances of HashIntoType and KMerIterator to use new Kmer
and KmerIterator, respectively.
* lib/Makefile: Add -std=c++11 flag.
* Makefile: Update -std=c++11 flag in libtest target.
* lib/hashtable.{cc,hh}: Update calc_connected_graph_size to use Traverser.
Change kmer_degree to use functions from traversal.cc. Remove redundant
count_kmers_with_radius in favor of calc_connected_graph_size. Update
traverse_from_kmer to use Traverser. Hashtable subclasses KmerFactory.
* lib/{hashtable.hh,kmer_hash.{cc,hh}}: Move KmerIterator from hashtable.hh
to kmer_hash.{cc,hh}. Add Kmer class to store forward, reverse, and
uniqified integer representations of k-mers, and to handle string
conversion. Update KmerIterator to emit objects of type Kmer and to subclass
KmerFactory; add doxygen markup.
* lib/khmer.hh: Forward declare Kmer and typedef new Kmer data structures.
* lib/subset.{cc,hh}: Move constructor definition to .cc file. Remove
queue_neighbors in favor of new traversal machinery. Update find_all_tags,
sweep_for_tags, and find_all_tags_truncate_on_abundance to use Traverser.
* setup.py: Add traversal.{cc,hh} to deps.
2015-08-10 Luiz Irber <khmer@luizirber.org>
* scripts/unique-kmers.py: use consume_fasta again.
* khmer/_khmer.cc: expose output_records option on HLLCounter consume_fasta.
* lib/hllcounter.{cc,hh}: implement output_records option in consume_fasta.
* lib/read_parsers.{cc,hh}: add Read method write_to, useful for outputting
the read to an output stream.
* doc/whats-new-2.0.rst: Add unique-kmers description.
2015-08-09 Jacob Fenton <bocajnotnef@gmail.com>
* khmer/khmer_args.py: pep8
* scripts/{interleave-reads,load-graph}.py: Removed unreachable code
* tests/test-data/{paired-broken.fq.badleft,paired-broken.fq.badright,
paired-broken.fq.paired.bad}: added test data files
* tests/{test_normalize_by_median,test_scripts}.py: added tests
2015-08-07 Titus Brown <titus@idyll.org>
* khmer/_khmer.cc,lib/hashbits.{cc,hh}: removed overlap functionality;
eliminated n_entries() as redundant with hashsizes(); removed arguments to
n_occupied(); removed get_kadian_count.
* lib/{hashbits.cc,counting.cc,khmer.hh},tests/test_hashbits.py: updated
save/load of countgraph/nodegraph structures to save _n_occupied.
* lib/{hashtable.hh,counting.hh,hashbits.hh}: promoted n_occupied() to
Hashtable class; fixed CountingHash unique_kmers calculation.
* lib/counting.{cc,hh}: removed get_kadian_count() and moved
n_unique_kmers(); updated countgraph writing to save n_occupied.
* khmer/__init__.py: modified extract_nodegraph_info and
extract_countgraph_info to read in & return n_occupied;
* sandbox/bloom-count-intersection.py,scripts/count-overlap.py,
tests/test-data/overlap.out: removed overlap scripts and test files.
* doc/user/scripts.rst: removed count-overlap.py documentation.
* tests/test_scripts.py: removed count-overlap.py tests.
* sandbox/README.rst: updated with removal of bloom-count-intersection.py.
* tests/test-data/normC20k20.ct: updated file contents to reflect new
format containing _n_occupied.
* tests/test_countgraph.py: removed get_kadian_count tests; added save/load
tests.
* tests/test_counting_single.py: remove n_entries() tests; replace
n_entries() calls with hashsizes() call.
* tests/test_functions.py: updated tests for new extract_*_info functions.
* tests/test_nodegraph.py: update htable etc. to nodegraph; added a
save/load test for n_occupied() on nodegraph.
* tests/{test_normalize_by_median,test_scripts}.py: fixed unique kmers
tests.
2015-08-07 Michael R. Crusoe <crusoe@ucdavis.edu>
* scripts/*.py,tests/*.py,sandbox/*.py,khmer/*.py,oxli/*.py:
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 Jacob Fenton <bocajnotnef@gmail.com>
* khmer/khmer_args.py, oxli/functions.py: migrated estimation functions out
oxli and into khmer_args
* oxli/build_graph.py, tests/test_oxli_functions.py,
sandbox/{estimate_optimal_hash,optimal_args_hashbits}.py,
scripts/{normalize-by-median,unique-kmers}.py: changed to not break on
location change
* tests/{test_normalize_by_median,test_scripts}.py: added tests for
automatic arg setting
* tests/test_script_arguments: changed to play nice with unique_kmers as an
argument
2015-08-04 Titus Brown <titus@idyll.org> and Camille Scott
<camille.scott.w@gmail.com>
* khmer/utils.py: added UnpairedReadsError exception.
* scripts/{extract-paired-reads,split-paired-reads}.py: changed --output-dir
argument short form to use '-d'.
* scripts/{split-paired-reads.py} added -0 <filename> to allow orphans; made
'-p'/'--force-paired' default & removed from script.
* scripts/{normalize-by-median,filter-abund,trim-low-abund}.py: changed
long form of '-o' to be '--output'.
* tests/{test_scripts,test_streaming_io}.py: updated and added tests for
new behavior.
2015-08-03 Jacob Fenton <bocajnotnef@gmail.com>
* doc/dev/coding-guidelines-and-review.rst: added codespell as a possible
spelling tool
2015-08-03 Jacob Fenton <bocajnotnef@gmail.com>
* Makefile: added oxli to pep257 make target, made clean target wipe out all
.pyc files in scripts/* and tests/* and oxli/*
2015-08-03 Jacob Fenton <bocajnotnef@gmail.com>
* tests/test_counting_single.py: removed redundant test
2015-08-01 Jacob Fenton <bocajnotnef@gmail.com> and Titus Brown
<titus@idyll.org>
* scripts/normalize-by-median.py,khmer/khmer_logger.py: added logging
framework, prototyped in normalize-by-median; added -q/--quiet to
* tests/test_normalize_by_median.py: associated tests.
* khmer/khmer_args.py: Made info function use logging functions.
* tests/khmer_tst_utils.py: removed info reporting in runscript from 'out'
returned.
2015-08-01 Jacob Fenton <bocajnotnef@gmail.com>
* khmer/kfile.py: added infrastructure for doing compressed output
* khmer/thread_utils.py: switched threaded_sequence_processor to make use of
write_record
* scripts/{extract-long-sequences,extract-paired-reads,
extract-partitions,fastq-to-fasta,filter-abund-single,filter-abund,
interleave-reads,normalize-by-median,sample-reads-randomly,
split-paired-reads,trim-low-abund}.py: added output compression
* tests/{test_functions,test_scripts,test_normalize_by_median}.py: added
tests
* scripts/{load-graph,partition-graph,find-knots.py,
make-initial-stoptags}.py,oxli/build_graph.py: made load-graph no longer
add .pt to graph outfiles, changed partition-graph to not expect .pt's
* doc/whats-new-2.0.rst: doc'd changes to load-graph and partition-graph
* doc/dev/scripts-and-sandbox.rst: updated scripts/ requirements.
2015-08-01 Sherine Awad <drmahmoud@ucdavis.edu>
* sandbox/multi-rename.py: updated output of long FASTA sequences to
wrap text at 80 characters.
* tests/test_sandbox_scripts.py: Added a test for multi-rename.py.
2015-07-31 Kevin Murray <spam@kdmurray.id.au>
* lib/Makefile,Makefile,lib/*.pc.in,lib/test-compile.cc: Misc debian-based
compatibility changes
* lib/get_version.py: Add crunchbang, chmod +x
2015-07-29 Michael R. Crusoe <crusoe@ucdavis.edu>
* khmer/_khmer.cc: add more CPyChecker inspired fixes
* lib/*.{cc,hh}: clean up includes and forward declarations
2015-07-29 Luiz Irber <khmer@luizirber.org>
* Makefile: Adapt Makefile rules for py3 changes.
* jenkins-build.sh: Read PYTHON_EXECUTABLE and TEST_ATTR from environment.
2015-07-29 Amanda Charbonneau <charbo24@msu.edu>
* scripts/fastq-to-fasta.py: Changed '-n' default description to match
behaviour
2015-07-29 Luiz Irber <khmer@luizirber.org>
* tests/test_{scripts,streaming_io}.py: Fix the build + add a test
2015-07-28 Titus Brown <titus@idyll.org>
* tests/test_streaming_io.py: new shell cmd tests for streaming/piping.
* tests/khmer_tst_utils.py: refactor/replace runtestredirect(...) with
scriptpath(...) and run_shell_cmd(...).
* scripts/test_scripts.py: remove test_interleave_reads_broken_fq_4 for
only one input file for interleave-reads.py; replace runscriptredirect call
with run_shell_cmd.
* scripts/interleave-reads.py: force exactly two input files.
* scripts/split-paired-reads.py: fix print statement; clarify output.
* scripts/{normalize-by-median.py,sample-reads-randomly.py,
trim-low-abund.py}: if stdin is supplied for input, check that -o
specifies output file.
* scripts/filter-abund.py: if stdin is supplied for input, check that -o
specifies output file; switched -o to use argparse.FileType.
* scripts/extract-long-sequences.py: switched -o to use argparse.FileType.
* scripts/{abundance-dist,count-median}.py: added '-' handling for output.
* khmer/kfile.py: change 'check_input_files' to no longer warn that
'-' doesn't exist'.
* tests/test-data/paired.fq.2: removed extraneous newline from end.
* tests/{test_normalize_by_median,test_script_arguments,test_scripts}.py:
added tests for new code.
* scripts/oxli: added script for running tests in development directory.
* khmer/{__init__,khmer_args}.py,tests/{test_normalize_by_median,
test_script_arguments}.py: refactored out use of AssertionError by not
throwing plain Exceptions when a ValueError or RuntimeError would do.
* oxli/__init__.py: give default help instead of an error when `oxli` is
called with no arguments.
* tests/test_{normalize_by_median,sandbox_scripts,scripts,streaming_io}.py:
always check status code if calling `runscripts` with `fail_ok=True`.
2015-07-28 Luiz Irber <khmer@luizirber.org>
* sandbox/unique-kmers.py: moved to scripts.
* scripts/unique-kmers.py: fix import bug and initialize to_print earlier.
* tests/test_scripts.py: add tests for unique-kmers.py.
* doc/user/scripts.rst: added unique-kmers.py to script page
2015-07-28 Jacob Fenton <bocajnotnef@gmail.com>
* scripts/abundance-dist.py: disallowed forcing on the input file check for
the counting table file
2015-07-28 Michael R. Crusoe <crusoe@ucdavis.edu>
* .mailmap, Makefile: generate a list of authors
2015-07-28 Kevin Murray <spam@kdmurray.id.au>
Titus Brown <titus@idyll.org>
* khmer/utils.py: added fix for SRA-style FASTQ output.
* tests/test_scripts.py: tested against a broken version of SRA format.
* tests/test-data/paired-broken4.fq.{1,2}: added test files.
2015-07-28 Michael R. Crusoe <crusoe@ucdavis.edu>
Titus Brown <titus@idyll.org>
* lib/read_aligner.{cc,hh},tests/{test_read_aligner.py,
test-data/readaligner-{default,k12}.json},khmer/__init__.py: refactor,
read aligner parameters are now configurable & save/load-able. Can do
whole-genome variant finding.
* khmer/_khmer.cc,tests/test_read_aligner.py: ReadAligner.align_forward
method added
* sandbox/correct-errors.py -> sandbox/correct-reads.py: total rewrite
* sandbox/error-correct-pass2.py: new script
* sandbox/readaligner_pairhmm_train.py: new script
* tests/test_sandbox_scripts.py, doc/release-notes/release-1.4.rst:
spelling fixes, import re-arrangement
* sandbox/{Makefile.read_aligner_training,readaligner_pairhmm_train.py}:
Added script to train the aligner
2015-07-27 Titus Brown <titus@idyll.org>
* khmer/khmer_args.py,CITATION: added entry for PeerJ paper on
semi-streaming to citations.
* scripts/{abundance-dist-single.py,abundance-dist.py,count-median.py,
count-overlap.py,filter-abund-single.py,load-into-counting.py}: changed
default behavior to output data in CSV format and report total k-mers.
* tests/test_scripts.py: updated/removed tests for CSV.
* doc/whats-new-2.0.rst: added information about change in columnar output,
along with other minor corrections.
* scripts/normalize-by-median.py: corrected epilog.
* khmer/thread_utils.py,
sandbox/{calc-best-assembly.py,extract-single-partition.py},
scripts/{count-median.py,extract-long-sequences.py,extract-paired-reads.py,
extract-partitions.py,fastq-to-fasta.py,
interleave-reads.py,normalize-by-median.py,readstats.py,
sample-reads-randomly.py,split-paired-reads.py,trim-low-abund.py},
tests/{test_normalize_by_median.py,test_scripts.py}: remove explicit
'parse_description' from screed open calls.
* khmer/_khmer.cc,lib/Makefile,lib/hashtable.{cc,hh},setup.py: removed
WITH_INTERNAL_METRICS and trace_logger/perf_metrics references.
* lib/perf_metrics.{cc,hh},lib/trace_logger.{cc,hh}: removed unused files.
2015-07-24 Jacob Fenton <bocajnotnef@gmail.com>
* doc/dev/getting-started.rst: added instructions for second contribution
2015-07-22 Jacob Fenton <bocajnotnef@gmail.com>
* tests/test_read_parsers.py: added workaround for bug in OSX Python
* Makefile: respect that workaround when running the tests
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/{
abundance-dist-single,filter-abund-single,load-into-counting,
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>
* khmer/__init__.py: cleaned up FP rate reporting.
* scripts/normalize-by-median.py: corrected epilog; refactored reporting
to be a bit cleaner; use CSV for reporting file;
added --report-frequency arg.
* tests/test_normalize_by_median.py: updated/added tests for reporting.
2015-07-17 Jacob Fenton <bocajnotnef@gmail.com>
* 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.
2015-07-17 Michael R. Crusoe <crusoe@ucdavis.edu>
* 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.
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.
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.
* sandbox/unique-kmers.py: changed to not output recommended HT args by
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.
2015-07-10 Jacob Fenton <bocajnotnef@gmail.com>
* 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
functions.
2015-07-08 Luiz Irber <khmer@luizirber.org>
* lib/{counting,hashbits,hashtable,labelhash,subset}.cc: print hexadecimal
representation of the signature read from the file.
2015-07-06 Luiz Irber <khmer@luizirber.org>
* sandbox/collect-reads.py: Set a default value for coverage based
on the docstring.
* sandbox/count-kmers-single.py, tests/test_{functions,script_arguments}.py:
Replace xrange and cStringIO (not Python 3 compatible).
* lib/*.{hh,cc}, oxli/functions.py, tests/*.py: make format.
2015-07-05 Jacob Fenton <bocajnotnef@gmail.com>
* doc/whats-new-2.0.rst: added in normalize-by-median.py broken paired
updates.
2015-07-05 Michael R. Crusoe <crusoe@ucdavis.edu>
* Makefile: fix cppcheck invocation.
* khmer/_khmer.cc: switch to prefix increment for non-primitive objects,
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.
2015-07-05 Michael R. Crusoe <crusoe@ucdavis.edu>
* sandbox/{collect-variants,optimal_args_hashbits,sweep-files}.py:
update API usage.
2015-07-05 Titus Brown <titus@idyll.org>
* sandbox/{count-kmers.py,count-kmers-single.py}: added scripts to output
k-mer counts.
* tests/test_sandbox_scripts.py: added tests for count-kmers.py and
count-kmers-single.py.
* sandbox/README.rst: added count-kmers.py and count-kmers-single.py to
sandbox/README.
2015-07-05 Kevin Murray <spam@kdmurray.id.au>
* lib/*.{cc,hh},sandbox/*.py,khmer/_khmer.cc,tests/test_*.py: Simplify
exception hierarchy, and ensure all C++ exceptions are converted to python
errors.
* scripts/normalize-by-median.py: Clarify error message.
* tests/khmer_tst_utils.py: Add longify function, converts int => long on
py2, and passes thru list unmodified on py3.
2015-06-30 Jacob Fenton <bocajnotnef@gmail.com>
* tests/{test_script_arguments,test_functions}.py: changed tests to use
stderr redirection to prevent leaks
* tests/test_normalize_by_median.py: changed to not duplicate a test
* tests/test_script_arguments.py: changed tests to use stderr redirection
2015-06-30 Titus Brown <titus@idyll.org>
* tests/test_normalize_by_median.py: disabled running
test_normalize_by_median_report_fp during normal test running.
2015-06-30 Titus Brown <titus@idyll.org>
* khmer/khmer_args.py: removed incorrect warning for default max_tablesize
when -M is used.
* tests/test_scripts.py: added test for correct max_tablesize behavior.
2015-06-30 Titus Brown <titus@idyll.org>
* setup.cfg: changed 'stop=TRUE' to 'stop=FALSE', so that tests do not
stop running at first failure.
2015-06-30 Kevin Murray <spam@kdmurray.id.au>
* scripts/{extract-paired-reads,split-paired-reads}.py: Fix creation of
default output files even when output files were provided on CLI.
2015-06-29 Sherine Awad <drmahmoud@ucdavis.edu>
* khmer/utils.py: Fix bug in naming in interleave-reads.py
* tests/test_scripts.py: Add a test function for the new behavior
* tests/test-data/*.fq: Add 3 test files needed for the testing
2015-06-28 Jacob Fenton <bocajnotnef@gmail.com>
* tests/test_sandbox_scripts.py: made error more informative and not crashy
* sandbox/{estimate_optimal_hash,optimal_args_hashbits}.py: minor cleanups
2015-06-28 Qingpeng Zhang <qingpeng@msu.edu>
* sandbox/{estimate_optimal_hash,optimal_args_hashbits}.py: added sandbox
methods for estimating memory usage based on desired fp rate, etc.
2015-06-27 Kevin Murray <spam@kdmurray.id.au>
* doc/dev/binary-file-formats.rst: Fix issue in ksize documentation for
Countgraph
2015-06-27 Kevin Murray <spam@kdmurray.id.au>
* README.rst: Fix link to virtualenv installation instructions.
2015-06-19 Titus Brown <titus@idyll.org>
* khmer/__init__.py: split CountingHash into _CountingHash (CPython) and
CountingHash to mimic Hashbits behavior; pass IOError through
extract_countinghash_info and extract_hashbits_info so that
file-does-not-exist errors are correctly reported; fixed FP rate reporting;
changed to using get_n_primes_near_x to build hashtable sizes; removed
get_n_primes_above_x, new_hashbits, and new_counting_hash functions.
* khmer/_khmer.cc: changed tp_flags for KCountingHash so that it could
be a base class.
* khmer/khmer_args.py: removed environment variable override for hash size
defaults; added -M/--max_memory_usage, and functions create_nodegraph()
and create_countgraph(). Also renamed --min-tablesize to --max-tablesize.
* khmer/kfile.py: fixed check_space_for_hashtable to depend on args obj.
* oxli/build_graph.py, scripts/{annotate-partitions.py,count-overlap.py,
do-partition.py,filter-stoptags.py,
merge-partitions.py}, sandbox/{assembly-diff.py,assembly-diff-2.py,
bloom-count-intersection.py,bloom-count.py,build-sparse-graph.py,
collect-reads.py,saturate-by-median.py, graph-size.py,print-stoptags.py,
print-tagset.py,stoptags-by-position.py, subset-report.py,
sweep-out-reads-with-contigs.py,sweep-reads2.py,sweep-reads3.py}: changed
hashtype over to 'nodegraph' and 'countgraph' in call to report_on_config;
replaced counting hash/hashbits creation with new khmer_args create*
functions, and/or new_counting_hash/new_hashbits with CountingHash/Hashbits.
* doc/scripts.rst: updated hashtable size help text.
* doc/whats-new-2.0.rst: updated with description of -M/--max-memory-usage.
* tests/test*.py: switched from new_counting_hash to CountingHash, and
new_hashbits to Hashbits; adjusts tests for new behavior of hashtable
size calculation.
* tests/test_hashbits_obj.py: merged into test_hashbits.py and removed file.
* tests/test_script_arguments.py: updated for new check_space_for_hashtable
behavior; added tests for create_countgraph and create_nodegraph.
* tests/test_counting_single.py: fixed countgraph size & palindrome testing
beahavior in test_complete_no_collision.
2015-06-19 Titus Brown <titus@idyll.org>
* Makefile: temporarily disable 'huge' tests on Linux.
2015-06-17 Titus Brown <titus@idyll.org>
* scripts/normalize-by-median.py: changed DEFAULT_DESIRED_COVERAGE to 20,
and corrected options help.
* tests/{test_scripts.py,test_normalize_by_median.py}: moved
normalize-by-median.py tests into a their own file.
* tests/test-data/{dn-test-all-paired-all-keep.fa,dn-test-none-paired.fa,
dn-test-some-paired-all-keep.fa}: added test data files for specific
pairing/saturation behavior.
2015-06-16 Kevin Murray <spam@kdmurray.id.au>
* doc/dev/binary-file-formats.rst: Add documentation of khmer's binary file
formats.
* doc/dev/index.rst: Add above docs to developer documentation index.
2015-06-14 Michael R. Crusoe <crusoe@ucdavis.edu>
* khmer/__init__.py,lib/{counting,hashbits,hashtable,subset,labelhash}.cc,
lib/khmer.hh: add signature to beginning of all binary file types
* tests/test-data/{normC20k20.ct,badversion-k32.tagset,
goodversion-k32.tagset}: update to new format by prepending "OXLI" to the
data stream
* tests/test_{counting_hash,functions,scripts,hashbits,hashbits_obj,
labelhash}.py: tests should fail, not error (add try, except + assert
blocks). Adapted other tests to cope with the new file formats
* lib/magic: new, teaches the unix `file` command about khmer file types
* doc/index.rst,doc/whats-new-2.0.rst: document these changes
2015-06-14 Titus Brown <titus@idyll.org>
* scripts/extract-paired-reads.py: added --output_dir, --paired-output,
and --single-output arguments to change output file details; script
now accepts stdin, and will output to stdout upon request.
* scripts/split-paired-reads.py: changed script to output to stdout upon
request; added '-' as stdin input.
* tests/test_scripts.py: added tests for new extract-paired-reads.py
behavior.
2015-06-14 Titus Brown <titus@idyll.org>
* tests/test_counting_hash.py: fixed duplicated test
'get_kmer_counts_too_short' by changing to 'get_kmer_hashes_too_short'.
2015-06-14 Jacob Fenton <bocajnotnef@gmail.com>
* scripts/abundance-dist.py: added weird bigcount circumstance detection
* tests/test_scripts.py: added test for the above
2015-06-14 Kevin Murray <spam@kdmurray.id.au>
* lib/counting.cc: Fix infinite loop in gzipped CountingHash I/O
* tests/test_counting_hash.py: Add test of large CountingHash I/O
* setup.cfg: Skip tests with the 'huge' label by default
2015-06-13 Michael R. Crusoe <crusoe@ucdavis.edu>
* Makefile, build-jenkins.sh: unify sphinx dependencies
* scripts/readstats.py: fix typo
2015-06-13 Titus Brown <titus@idyll.org>
* doc/dev/getting-started.rst: update instructions for creating a new
branch name to preferred practice (fix/brief_issue_description, instead
of fix/issuenum).
2015-06-13 Michael R. Crusoe <crusoe@ucdavis.edu>
* doc/dev/release.rst: remove false positive from version check
* tests/test_{counting_hash,scripts}.py: remove scriptpath no-op method
2015-06-12 Luiz Irber <khmer@luizirber.org>
* setup.py: revert changes to zlib compilation.
* setup.cfg: nose should stop on first error by default.
* Makefile, tests/test_threaded_sequence_processor.py,
scripts/{do-partition,partition-graph}.py, khmer/thread_utils.py: Remove
dependency on future package.
2015-06-12 Michael R. Crusoe <crusoe@ucdavis.edu>
* setup.py: update screed version to 0.9
2015-06-12 Luiz Irber <khmer@luizirber.org>
* *.py: refactor for Python 3 compatibility. Clear separation of Unicode
and Byte strings, use __future__ imports for compatibility (print function,
absolute imports, unicode_literals), fix tests to consider changes to random
number generator between Python versions.
* khmer/_khmer.cc: rename file, methods return Unicode strings instead of
Bytestrings.
2015-06-12 Luiz Irber <khmer@luizirber.org>
* khmer/{khmermodule.cc},tests/test_hashbits.py: Add Unicode support to
hashbits.get method.
* tests/test_hll.py: Avoid using translate for revcomp calculation.
2015-06-12 Sarah Guermond <sarah.guermond@gmail.com>
* scripts/trim-low-abund.py: changed _screed_record_dict to Record
2015-06-11 Sherine Awad <drmahmoud@ucdavis.edu>
* Change split-paired-reads.py to accept input from stdin.
* Add test function to test new behavior of split-paired.
2015-06-10 Camille Scott <camille.scott.w@gmail.com>
* lib/hashtable.cc: Tweaked median_at_least to reduce number of
conditional checks.
2015-06-10 Titus Brown <titus@idyll.org>
* scripts/find-knots.py: fixed invocation of check_space to take correct
arguments.
* tests/test_scripts.py: added simple test of find-knots.py execution.
2015-06-09 Jacob Fenton <bocajnotnef@gmail.com>
* scripts/normalize-by-median.py: implemented broken_paired_reader
* tests/test_scripts.py: modified tests to properly use new args
* khmer/utils.py: added force-paired option to broken_paired_reader (@ctb)
2015-06-09 Luiz Irber <khmer@luizirber.org>
* khmer/_khmermodule.cc, lib/hashtable.{cc,hh}: astyle fixes.
2015-06-09 Titus Brown <titus@idyll.org>
* khmer/_khmermodule.cc: fixed nasty Hashtable.get() bug.
* lib/hashtable.{cc,hh}: add Hashtable::get_kmers(), get_kmer_hashes(),
and get_kmer_counts().
* khmer/_khmermodule.cc: add CPython functions for get_kmers(),
get_kmer_hashes(), and get_kmer_counts(); reorganize hashtable_methods.
* tests/test_counting_hash.py: add tests for get_kmers(), get_kmer_hashes(),
and get_kmer_counts(), as well as for nasty Hashtable.get() bug.
2015-06-08 Camille Scott <camille.scott.w@gmail.com>
* lib/hashtable.{cc,hh}: Add filter_on_median method to check
if median k-mer count is above a cutoff
* khmer/_khmermodule.cc: Expose filter_on_median to python-land
* scripts/normalize-by-median.py: Switch to new filter_on_median
* tests/test_counting_hash.py: Tests for new method
2015-06-08 Luiz Irber <khmer@luizirber.org>
* tests/test_hll.py: test return values from consume_{string,fasta}.
2015-06-06 Titus Brown <titus@idyll.org>
* khmer/_khmermodule.cc: added hllcounter_merge.
* tests/test_hll.py: added merge tests.
* lib/hllcounter.cc: changed HLLCounter::consume_string to uppercase input.
* sandbox/unique-kmers.py: added --stream-out option; updated to print out
k-mers per file as well as k-mer size used.
2015-06-04 Titus Brown <titus@idyll.org>
* khmer/_khmermodule.cc: added error handling to load_partitionmap.
* lib/subset.cc: modified partitionmap format to detect truncated files;
changed untestable sanity checks to assertions.
* tests/{test_counting_hash,test_hashbits,test_subset_graph}.py: added
tests to try loading all possible truncations of binary save files.
2015-06-04 Titus Brown <titus@idyll.org>
* khmer/_khmermodule.cc,lib/hashbits.{cc,hh}: add Hashbits::update_from()
and Hashbits.update().
* tests/test_hashbits.py: associated tests.
2015-06-01 Jacob Fenton <bocajnotnef@gmail.com>
* scripts/normalize-by-median.py: major refactoring to use context
managers and classes; fixed -R
* tests/test_scripts.py: added test for normalize's -R arg
2015-06-01 Tamer Mansour <drtamermansour@gmail.com>
* scripts/normalize-by-median.py: changed to count kmers from both PE reads
when either one of them is below the coverage cutoff
* tests/test_scripts.py: Added test for new behaviour
2015-05-26 Titus Brown <titus@idyll.org>
* khmer/_khmermodule.cc: refactor CPython layer so that KHashtable
is at base of CountingHash and Hashbits.
* lib/hashbits.hh: add n_entries() function from Hashtable::n_entries.
* lib/hashtable.hh: add several virtual functions to Hashtable that exist in
CountingHash and Hashbits.
2015-05-26 Titus Brown <titus@idyll.org>
* khmer/{__init__.py,_khmermodule.cc},lib/labelhash.{cc,hh},
lib/{hashtable,khmer}.hh: changed LabelHash to be a "friend" of Hashtable,
rather than a subclass; allowed initialization with either a CountingHash
or a Hashbits; added 'graph' attribute to the Python object to store a
reference to host object.
* lib/labelhash.{cc,hh}: changed TagPtr maps to Tag maps to fix disastrous
bug.
* lib/labelhash.{cc,hh}: added save/load_tags_and_labels functions for
saving and loading labels.
* tests/test_labelhash.py: removed unnecessary tests; added tests for save
and load.
* sandbox/sweep-reads.py: updated with LabelHash changes.
2015-05-26 Kevin Murray <spam@kdmurray.id.au>
* lib/Makefile: Remove old libkhmer.so versions during make clean
2015-05-25 Kevin Murray <spam@kdmurray.id.au>
* Makefile: Fix issue with 'lib' target not building by using FORCE
2015-05-20 Jacob Fenton <bocajnotnef@gmail.com>
* oxli/{__init__,khmer_api,common}.py,scripts/build-graph.py,
tests/test_scripts.py: added oxli module, oxlified load_graph script, tests
* scripts/load-graph.py: replaced with oxlified version
* setup.py: added oxli module and entry point
2015-05-20 Kevin Murray <spam@kdmurray.id.au>
* .gitignore: Add htmlcov/ and diff-cover.html to gitignore
* Makefile: Use rm -f to remove files to quash error messages on
non-existant files
2015-05-18 Sherine Awad <sherine.awad@gmail.com>
* tests/test_scripts.py: Test loading of compressed counting table
with bigcounts,and test abundance with bigcounts
2015-05-18 Michael R. Crusoe <mcrusoe@msu.edu>
* all files: references to github.com/ged-lab changed to
github.com/dib-lab. All GitHub URLs normalized to use HTTPS
* README.rst: broken landscape.io badge removed
* doc/user/known-issues.rst: removed two known issues fixed in v1.4 release
2015-05-18 Titus Brown <titus@idyll.org>
* sandbox/{assembly-diff-2.py,sandbox/collect-reads.py},
scripts/{count-median.py,filter-abund-single.py,filter-abund.py}: changed
sequence-reading behavior to replace 'N' with 'A', to be consistent with
rest of code base.
* scripts/{filter-abund.py,filter-abund-single.py}: changed behavior of
scripts to keep sequences with 'N's in them, and count them as 'A's.
* tests/test_scripts.py: added tests for new
filter-abund/filter-abund-single behavior.
* tests/test-data/test-filter-abund-Ns.fq: new test file for new tests.
2015-05-13 Scott Sievert <sieve121@umn.edu>
* tests/*,scripts/*,lib/*,sandbox/*,khmer/*: changed "doc/LICENSE.txt" to
"LICENSE" in copyright header.
2015-05-13 Michael R. Crusoe <mcrusoe@msu.edu>
* doc/dev/getting-started.rst: added missing dev tools to install list
2015-05-12 Kevin Murray <spam@kdmurray.id.au>
* scripts/load-into-counting.py,test/test_scripts.py: Add the number of
reads processed to the machine readable output files of --summary-info.
2015-05-11 Titus Brown <titus@idyll.org>
* scripts/sample-reads-randomly.py: fixed boundary error in
sample-reads-randomly.py.
* tests/test_scripts.py: updated tests to correspond with correct
behavior of sample-reads-randomly.py.
2015-04-23 Lex Nederbragt <lex.nederbragt@ibv.uio.no>
* tests/test_scripts.py: added a test for extract-partitions:
whitespace in fasta header.
2015-04-21 Daniel Standage <daniel.standage@gmail.com>
* scripts/sample-reads-randomly.py: use broken paired reader to provide
paired-end read support.
* tests/test_scripts.py: change test results to compensate for the change in
implementation.
2015-04-17 Jessica Mizzi <mizzijes@msu.edu>
* tests/test_scripts.py: split test_extract_long_sequences
into test_extract_long_sequences_fa and test_extract_long_sequences_fq
2015-04-15 Elmar Bucher <buchere@ohsu.edu>
* khmer/doc/dev/getting-started.rst: add information for OS X
mac port and homebrew distro users as well as Linux
Debian and Ubuntu distro users.
And add copyright header.
2015-04-15 Susan Steinman <steinman.tutoring@gmail.com>
* khmer/tests/khmer_tst_utils.py,doc/dev/a-quick-guide-to-testing.rst
edited docstring and docs to remind people to make sure tests test
errors correctly
2015-04-15 Michael R. Crusoe <mcrusoe@msu.edu>
* sandbox/make-coverage.py: tweak for importability
2015-04-15 Sherine Awad <sherine.awad@gmail.com>
* sandbox/make-coverage.py: restored, was deleted by accident
2015-04-15 Susan Steinman <steinman.tutoring@gmail.com>
* khmer/tests/test_scripts.py: changed tests that use `runscript` with
`fail_okay=True` to use asserts to confirm the correct failure type
2015-04-15 Sarah Guermond <sarah.guermond@gmail.com>