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ChangeLog
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2016-07-03 Titus Brown <titus@idyll.org>
* lib{hashtable.cc, hashtable.hh}: added get_kmer_hashes_as_hashset to
graphs.
* khmer/_khmer.cc: updated CPython API to add get_kmer_hashes_as_hashset.
* tests/test_countgraph.py: added test for get_kmer_hashes_as_hashset.
2016-06-27 Titus Brown <titus@idyll.org>
* doc/requirements.txt: updated sphinx-autoprogram requirement for building
documentation, to point at released version.
2016-06-26 Titus Brown <titus@idyll.org>
* khmer/_khmer.cc, tests/test_nodegraph.py: 'add' is now a synonym for
graph.count(kmer).
* khmer/thread_utils.py: update verbose_loader function to take 'verbose'
argument.
* scripts/{abundance-dist-single.py, abundance-dist.py,
filter-abund-single.py, filter-abund.py, load-into-counting.py,
normalize-by-median.py,trim-low-abund.py}: updated to
respect -q/--quiet.
* tests/test_filter_abund.py: tests for '-q'.
* scripts/partition-graph.py: fix typo in args help message.
2016-06-26 Titus Brown <titus@idyll.org>
* khmer/_khmer.cc, lib/{hashtable.cc, hashtable.hh},
tests/test-data/simple-genome.fa, tests/test_nodegraph.py: added functions
'find_high_degree_nodes' and 'traverse_linear_path' to hashtables/graphs.
* lib/kmer_hash.cc: minor change to use object member _seq instead of
constructor argument seq in KmerIterator.
* lib/kmer_hash.hh: added const to Kmer::get_string_rep(...) signature.
* sandbox/extract-compact-dbg.py: new sandbox script to
extract compact De Bruijn graphs (with linear paths contracted).
* tests/test_sandbox_scripts.py: added tests for the extract-compact-dbg.py
script.
2016-06-26 Titus Brown <titus@idyll.org>
* lib/khmer.hh,lib/{labelhash.cc,labelhash.hh}: removed label pointer-based
indirection from labelhash code.
* khmer/_khmer.cc: updated CPython API to match new behavior.
* tests/test_labelhash.py: renamed to match new API; no changes in test
logic.
2016-06-17 Daniel Standage <daniel.standage@gmail.com>
* scripts/filter-abund-single.py: add -o/--outfile option.
* tests/test_script_output.py: move `_calc_md5` function for calculating
file MD5 hashes to test utils module (tests/khmer_tst_utils.py).
* tests/{test_filter_abund.py,test_scripts.py): move filter_abund tests to
dedicated test script, add minimal test for new -o option.
* tests/test-data/paired-mixed-witherror.fa.pe: add data file in support of
new test.
* .gitignore: add .cache/ directory, which appears to be an artifact of the
py.test framework.
2016-06-17 Daniel Standage <daniel.standage@gmail.com>
* scripts/filter-abund-single.py: add -o/--outfile option.
* tests/test_script_output.py: move `_calc_md5` function for calculating file
MD5 hashes to test utils module (tests/khmer_tst_utils.py).
* tests/{test_filter_abund.py,test_scripts.py): move filter_abund tests to
dedicated test script, add minimal test for new -o option.
* tests/test-data/paired-mixed-witherror.fa.pe: add data file in support of
new test.
* .gitignore: add .cache/ directory, which appears to be an artifact of the
py.test framework.
2016-05-25 Titus Brown <titus@idyll.org>
* scripts/trim-low-abund.py: switched to watermark-based reporting to
isolate a hard-to-trigger undefined variable error in reporting.
* tests/test_scripts.py: added a test for basic reporting functionality.
2016-05-16 Titus Brown <titus@idyll.org>
* khmer/_khmer.cc: define new khmer_HashSet_Type and khmer_HashSet_Object;
lots of associated cleanup of k-mer <-> C++ interface; added
Hashtable::neighbors; added Hashtable::hash and Hashtable::reverse_hash;
CPython 'hashtable.count(...)' function now takes either hash or string.
* lib/{kmer_hash.cc, kmer_hash.hh}: added some function overloads so that
_hash(...) could take strings as arguments without conversion; added
Kmer::set_from_unique_hash convenience function.
* lib/{hashtable.cc, hashtable.hh}: minor cleanup;
* lib/{read_aligner.cc, subset.cc}: minor refactoring.
* lib/{traversal.cc, traversal.hh}: made 'filter' argument to traverse*
functions optional; added 'traverse' function for combine traversal.
* tests/test_hashset.py: tests for new HashSet class.
* tests/test_countgraph.py: tests for new hash/reverse_hash functions,
and 'count' behavior.
* tests/test_nodegraph.py: tests for new neighbors function.
* khmer/__init__.py: import new HashSet type from _khmer.
* scripts/{do-partition.py, make-initial-stoptags.py,
partition-graph.py},tests/{test_labelhash.py, test_subset_graph.py}:
refactor existing code to use HashSet object.
* tests/test_counting_single.py: add printout to assert.
2016-05-16 Luiz Irber <khmer@luizirber.org>
* Makefile,jenkins-build.sh,setup.cfg,tests/khmer_tst_utils.py,
tests/test_{countgraph,counting_single,hll,labelhash,nodegraph,
normalize_by_median,read_aligner,read_handling,read_parsers,sandbox_scripts,
scripts,version}.py: replace nose with pytest, update configuration.
2016-05-16 Luiz Irber <khmer@luizirber.org>
* lib/hashtable.cc: fix bug with substr
* tests/test_countgraph.py: add test to trigger the substr bug.
2016-05-11 Titus Brown <titus@idyll.org>
* scripts/trim-low-abund.py: refactor to use generators; add --diginorm
option to include digital normalization in trim-low-abund functionality.
* tests/test_script_output.py: added md5sum hashing tests to pin down
functionality in trim-low-abund.py and normalize-by-median.py; verified
that refactoring does not alter existing functionality.
* tests/test-data/simple-genome-reads.fa: supporting file for md5sum
tests.
* tests/test-data/README.rst: a new README for describing test files,
how to generate them, and their uses.
* tests/test_scripts.py: added additional tests for trim-low-abund.py
functionality and error cases.
2016-05-11 Titus Brown <titus@idyll.org>
* tests/test_read_parsers.py: fixed syntax error introduced by previous
merge.
2016-05-08 Michael R. Crusoe <crusoe@ucdavis.edu>
* scripts/{do-partition,partition-graph}.py,oxli/partition.py: pulled up
duplicate `worker` partition function into a reusable place.
2016-05-08 Michael R. Crusoe <michael.crusoe@gmail.com>
* .dictionary, pylintrc: added `pylint` configuration that checks spelling
in Python files. Added dictionary of project specific words.
* khmer/__init__.py, scripts/readstats.py, setup.py: Fixed typos.
* Makefile: line-wrapped; bumped up `pep8` version; beefed up `cppcheck`
target to correctly list the defines and includes for the current platform
which eliminates false positives; `*.pyc` files are now cleaned from the
`sandbox` as well as the `dist` directory. Added `cppcheck-long` target to
also examine the seqan headers. Fed the dynamically constucted list of
includes to Doxygen. Added simultaneous OS X, Debian, and Ubuntu
compatibility to many targets. Added helper target to print the value of
any variable via `make print-VARNAME`. Fixed the `make coverage-report`
target. pep257 is now called pydocstyle
* third-party/seqan/core/include/seqan/basic/debug_test_system.h,
third-party/seqan/ChangeLog: silenced bogus import
* doc/dev/coding-guidelines-and-review.rst,.github/PULL_REQUEST_TEMPLATE.md:
reformulated checklist to list action followed by a motivating question.
* doc/dev/release.rst: added author management to release checklist
* lib/counting.{cc,hh},sandbox/find-high-abund-kmers.py,
sandbox/README.rsr: removed the unused function
CountingHash::collect_high_abundance_kmers and the nonfunctional sandbox
script that called it.
* lib/kmer_hash.hh: make KmerFactory's default contrustor explicit to avoid
auto-casting optimizations.
* */*.py: a multitude of pylint inspired cleanups and bug fixes. Some
checks silenced in place.
2016-05-08 Michael R. Crusoe <michael.crusoe@gmail.com>
* README.rst: add depsy badge
2016-05-08 Michael R. Crusoe <michael.crusoe@gmail.com>
* setup.py,sandbox/{readaligner_pairhmm_train.py,
Makefile.read_aligner_training}: switch to BAM parsing using simplesam
2016-05-06 Titus Brown <titus@idyll.org>
* khmer/_khmer.cc, lib/{counting.cc,counting.hh,hashbits.cc,hashbits.hh,
hashtable.cc,hashtable.hh,subset.cc,subset.hh},
sandbox/{fasta-to-abundance-hist.py,find-high-abund-kmers.py
hi-lo-abundance-by-position.py,stoptag-abundance-hist.py,
abundance-hist-by-position.py},
tests/{test_countgraph.py,test_counting_single.py,test_filter.py,
test_nodegraph.py,test_subset_graph.py}: removed unused functions,
sandbox scripts, and tests for many functions. Specifically,
consume_fasta_and_tag_with_stoptags, identify_stop_tags_by_position and
identify_stoptags_by_position,
count_and_transfer_to_stoptags, traverse_from_tags,
filter_if_present, consume_fasta_and_traverse,
collect_high_abundance_kmers, fasta_dump_kmers_by_abundance,
fasta_count_kmers_by_position, output_fasta_kmer_pos_freq,
compare_partitions/compare_to_partition, join_partitions_by_path,
is_single_partition, and find_unpart function.
* sandbox/README.rst: updated for removed sandbox scripts.
2016-04-29 Luiz Irber <khmer@luizirber.org>
* jenkins-build.sh: add codecov coverage upload tool.
2016-02-17 Daniel Standage <daniel.standage@gmail.com>
* ./github/CONTRIBUTING.md,.github/PULL_REQUEST_TEMPLATE.md: auto-populate
pull requests with checklist using GitHub's new template feature
* doc/dev/coding-guidelines-and-review.rst: update developer docs with
compensatory changes
2016-02-15 Kevin Murray <spam@kdmurray.id.au>
* scripts/load-into-counting.py: Insert khmer's version into .info files
2015-08-14 Luiz Irber <khmer@luizirber.org>
* lib/subset.cc: check iterator before decrementing in
repartition_largest_partition
2015-10-25 Titus Brown <titus@idyll.org>
* scripts/normalize-by-median.py,tests/test_normalize_by_median.py: test
and fix for close of --output file after first input file.
2015-10-19 Michael R. Crusoe <crusoe@ucdavis.edu>
* versioneer.py,khmer/_version.py,setup.py,setup.cfg: upgrade Versioneer to
version 0.15+dev, Mon Jun 29 2015 99d5d9341830945f7080537ddd3bbd79c4aa1732
* doc/conf.py, lib/Makefile: update method of retrieving current version
* lib/get_version.py: no longer needed, removed
2015-10-05 Michael R. Crusoe <crusoe@ucdavis.edu>
* lib/magic: add file extensions, one media type, and a better comment
* khmer/__init__.py: Replace an errant 'Presence table' with 'node graph'
2015-09-28 Lisa Cohen <ljcohen@ucdavis.edu>
* tests/test_read_handling.py: created new file with interleave-reads,
split-paired-reads, and extract-paired-reads functions
* tests/test_scripts.py: removed functions mentioned above
2015-09-19 Titus Brown <titus@idyll.org>
* scripts/filter-abund.py: fixed bug with -o and --gzip used together.
* tests/test_scripts.py: added test for fixed bug.
* sandbox/count-kmers.py: added executable bit.
2015-09-17 Camille Scott <camille.scott.w@gmail.com>
* scripts/interleave-reads.py: Added --no-reformat flag
to disable format checking and renaming of headers
* tests/{test_scripts.py, test-data/paired.malformat*}: Tests
and test data for --no-reformat flag.
2015-09-11 Russell Y. Neches <ryneches@ucdavis.edu>
* lib/hashbits.hh: added get_raw_tables to Hashbits
* khmer/_khmer.cc: added get_raw_tables to Hashbits
* tests/test_nodegraph.py: added test for Nodegraph.get_raw_tables
2015-09-11 Camille Scott <camille.scott.w@gmail.com>
* lib/hashbits.cc: Make hasbits::update_from() correctly update
_occupied_bins.
* lib/test_nodegraph.py: Test Nodegraph.n_occupied() after update.
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.
2015-08-13 Jacob Fenton <bocajnotnef@gmail.com>
* scripts/extract-partitions.py: refactored much of the processing into
generators
* tests/test_scripts.py: added test
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>