This is the monolithic changelog for the 0.0, 0.1, 0.2, and 0.3 series of hgvs releases. Beginning with 0.4, changes will be recorded in release-specific files; see Change Log.
0.3 Series¶
0.3.7 (2015-06-23)¶
Client Changes¶
- #233: Expose UTA’s notions of transcript similarity via the UTA data provider. See get_similar_transcripts().
- #236: Added seqfetcher.SeqFetcher to fetch sequences from NCBI & Ensembl
- #199: Improved installation documentation re: PostgreSQL dependency
- #232: Migrated to major.minor versions for schemas and schema provider-client compatibility; “compatible” := (provided x == required x) ^ (provided y >= required y)
- misc/experimental/vcf-add-hgvs: optionally generate coding variants
- numerous doc updates
Internal and Developer Changes¶
- add missing requests library to setup.py (only affected developers)
- updated bioutils version in setup.py
0.3.6 (2015-06-02)¶
0.3.5 (2015-05-19)¶
0.3.4 (unreleased)¶
0.3.3 (2014-08-28)¶
- #194: fix bug when reverse complementing nucleotides parsed from unicode
- #197: use utf-8 coding, unicode, and all py3k __future__ features in all source
- #198: documentation improvements
- #202: implement mutalyzer comparisons
- #203: return HGVSParseError instead of ometa.runtime.ParseError for parsing errors
- #205: fix “base” bias for the exact middle of an odd-length intron
- #206: make get_tx_for_region return only transcripts with alignment data
- added flake8 configuration
- added regression test framework (tests/data/gcp/regression.tsv)
0.3.1 (2014-07-12)¶
0.3.0 (2014-06-19)¶
- #103: significantly updated documentation
- #162: provide simplified mapping interface, EasyVariantMapper
- #171: integrate the data provider interface into hgvs, obsoleting bdi. See hgvs.dataproviders.*
- #177: rename mapping functions to x_to_y (dropping “hgvs” prefix)
- #180: made set_uncertain an internal method (_set_uncertain)
- #181: renamed hgvs.hgvsmapper.HGVSMapper to hgvs.variantmapper.VariantMapper
- #184: rename HGVSPosition.seqref to ac
- #185: enable validator to use HDPI to fetch sequence data; mfdb now required only for genomic sequences
- Makefile: print machine info during testing to calibrate/debug timing probs
- moved hgvs/data to hgvs/_data to emphasize it is internal and avoid tab completion on it
- remove unused args from VariantMapper.c_to_p()
- replace u1/uta1 references with hdp; update docs
- replaced bdi with hdp when referencing the data provider; tests pass
- setup.py: removed nose-timer (appeared to cause problems with pip install)
- standardize exception names with “HGVS” prefix
- updated examples/manuscript-example; other minor changes
0.2 Series¶
0.2.2 (2014-06-12)¶
- #103: significantly updated documentation
- #142: added BIC test cases
- #167: disable the any_variant rule because it is confusing
- #179: added quick and extra tags to tests; updated Makefile to support make test, test-quick, test-extra; removed test_hgvs_parser_real (but kept gcp version)
- added support for testing models (“models” attr and test-models)
0.2.1 (2014-06-11)¶
- #157: don’t reverse complement numeric “sequences” (as in del26)
- #159: Update comment in tests/data/ADRA2B-dbSNP.tsv
- #161: transform examples to sphinx doc (+upload)
- #167: disable the any_variant rule because it is confusing
- #175: added type to NADupN and Copy edit classes
- Added Important Notes section in README.rst
- Makefile: “test” target should depend on “setup” after all
- added example for stringification to README.rst
- added examples/Manuscript Example.ipynb
- added installation status (from hgvs-integration-test at travis-ci) and build status (from drone.io)
- hgvsmapper: use deepcopy when converting edits
- removed unused sphinx_pypi_upload.py
- updated examples to use uta1
0.2.0 (2014-03-09)¶
- updated README.rst example to use uta1; added .rst files to nosetest testing
- added ci-test-ve; switched to hgtools 5.0 use_vcs_version in setup.py
- take 1 on reconcililing test differences between internal jenkins and drone.io
- removed accidental tag (!); added sphinxcontrib-fulltoc to setup.py
0.1 Series¶
0.1.11 (2014-03-05)¶
- removed accidental tag (!); added sphinxcontrib-fulltoc to setup.py
- updated package metadata; removed requirements.txt; tests pass
0.1.9 (2014-03-05)¶
- #40: added additional tests
- #114: add test that checks that all rules have been tested - and add tests for rules that were missed!
- #135: add more tests; fixed and enabled tests previously commented out
- #147: update tests to use updated sqlite test DB
- Added U14680.1 (BIC tx) to grammar test
- ExtrinsicValidator should not guess about bdi and mfdb sources; instead require caller to specify
- Fixed an un-handled case for parsing AA frameshifts - short form, e.g. “Ala97fs” (no alt AA). Added tests.
- Makefile, setup,py, setup.cfg sync with sibling projects
- Merged hgvs_using_uta1 into default
- Merged in extrinsic_validation (pull request #5)
- Remove redundant test
- added Validator class that wraps instrinsic and extrinsic validation
- added bdi accession testing
- added codeship status badge to README.rst, for testing
- added creating-a-variant example
- added sbin/get-dbsnp-tests-for-gene
- added tests from dbSNP for 6 new gene; fixed probs with uncertainty and Terd+ in existing tests
- bug fixes for uta1 integration; all tests pass except for sqlite db test
- checking cigar ref tgt orientation
- cigar intron count fix
- cut DNAH11 tests to representative set (apx 80% cut)
- finished integrating uta1 into hgvs and started updating tests
- fixed DNAH11-dbSNP tests
- fixed bug when falling off transcripts
- hgvsmapper is updated with uta1 requirements. testing modifications using hgvs-shell
- removed accession test from extrinsic validator (sequence lookup covers accession lookup)
- removed codeship badge
- renamed ~Validation to ~Validator to keep with class-as-actor naming scheme
- starting external validation with bdi
- testing
- trivial change to tickle codeship build
- updated edit type and tests to include identity for sub e.g., T>T
- updated external validation using bdi; added identity edit type for sub T>T; added HGVSValidationException class; added sample tests for mfdb
- updated package metadata; removed requirements.txt; tests pass
- upped bdi min version to >=0.1.0 (interface1)
- use pip installation status as build status since that’s what users will experience
- working through updating TM and IM. HM g_to_c appears to work
0.1.8 (2014-01-22)¶
- updated README.rst example for bdi connect()
0.1.7 (2014-01-22)¶
- #106, #108: parse uncertain hgvsp/hgvsr; converter produces uncertain hgvsp.
- #110, #111: handle cases of entire gene deletion (p.0?) and stop codon in frame (p.?). Updated tests.
- #65, #89: can now parse Met1? and ext*N; removed extra fs parsing from delins.
- #65: cleanup; AASub can go back to being a subclass of AARefAlt
- #65: def_p_pos needs to accept term13 as well as aa13 for ext; tests updated.
- #65: fixed an ordering bug; added tests.
- #65: fs/ext are now their own pro_edit types; they correspond to their own class objects. 5’ extensions and 3’ extensions can be parsed. Tests updated.
- #65: should be stringifying * as Ter; fixed code in 2 lines & tests in many.
- #65: tighten ext rules; require a number for new start positions.
- #90: added dup in hgvsmapper; allowed rev complement util to handle None (was triggering exceptions); added tests for dup.
- #91: add extension support for parsing copyN and DupN
- #91: make adding default totally extendable by allowing additional imports for the base grammar (default empty list)
- #91: simplest implementation of parsing copyN, dupN - added directly to grammar (no extension)
- #99: fix aa13t parsing
- #99: fix aa13t parsing, take 2; tests pass (including G* test)
- #99: re-enable tests related to this issue.
- Fixed a bug where del5insT was getting stringified as “5>T”
- added datum to range checking
- added datum to range checking
- added edit type as a property to the edit object; updated tests; added examples to hgvs-shell
- added edit type as a property to the edit object; updated tests; added examples to hgvs-shell
- close anonymous branch
- closed experimental dev branch
- closed hgvsvalidator feature branch on wrong default branch (grafted to default)
- doc updates and Makefile fix after fouled merge
- fixed minor doc typos
- hgvsc_to_hgvsp - ac defaults to None; seems better than forcing the user to pass ‘None’ as a param if they want the protein accession looked up.
- iv grammar branch
- make doc is broken & not used; removing it from make ci-test for now.
- merged in validator (pull request #4)
- minor change to rebase
- removed links section from README
- renamed hgvsvalidator to validator and corresponding test; corrected start-end check added tests
- revised intrinsic validator and tests; deleted requests from setup.py
- updated README.rst example for bdi connect()
- updated docs to point back to pythonhosted
- updated installation.rst
- updated ipython notebook examples
- updated railroad building
- updated railroad in docs
- updated the fragile railroad building again
0.1.6 (2014-01-11)¶
- updated docs to point back to pythonhosted
- added setuptools to requirements.txt
- updated requirements.txt
- fixed bug in setup.py re: classifiers
0.1.5 (2014-01-11)¶
- fixed bug in setup.py re: classifiers
0.1.3 (2014-01-11)¶
- #60: 1st stab at grammar tests from the bottom-up (through locations/definite positions). (See header in test_hgvs_grammar_full.py for details.) Also added a few error checking tests.
- #60: drop None from SequenceVariant (use case - only parsing an edit); grammar update for offset
- #60: implement cleanup; distributed remaining items to separate issues.
- #73: migrate hgvs to bdi-based protein accession lookup
- #90: fixed typo for delins and ins for parsing hgvsp
- #92: add a subclass of AARefAlt (AASub) which overrides __str__ to get the representation right; grammar update
- #92: fix error in NARefAlt
- #93: added variant liftover for HGVS projector, with tests
- #93: implemented HGVS projector for interval liftover
- #96: cleanup and test update
- #96: deleting tests/data
- #96: fix file
- #96: name cleanup
- #96: removed nightly test target
- #96: short set of real data for gcp parsing
- #97: a bagillion doc updates; branch closed
- #97: major doc restructuring, cleanup, additions
- A few more basic tests
- Add parser test which just tries to parse all the cvids (g, c and p) - currently skips unsupported forms. Also tweaked the r variants in the all cvid file (T should be U).
- Add some basic intervalmapper tests based on the coverage results
- Fill in more protein edit tests
- Fixed a bug breaking n_edit and m_edit; updated tests.
- Make documentation more Sphinx-friendly
- More grammar tests; simplified dup check for hgvsc to p conversion
- Tweak HGVSp expected so an edit creating a stop codon is represented by Ter instead of * (to match hgvs string code)
- add alternative UTA_DB_URL options to Makefile; cleanup eggs in cleanest (not cleaner) and bdist et al. in cleaner (not cleanest)
- added .travis.yml
- added a projector example
- added classifiers and keywords to setup.py
- added license to docs
- added railroad diagram to docs
- additional grammar tests - HGVS edits are failing commented out for now
- bug fix: make test was running nightly tests
- build reST doc for railroad grammar
- code cleanup
- commenting out test until I am in a place where I can run it
- doc updates
- eliminated most sphinx warnings
- lots of doc restructuring and consolidation
- minor cleanup
- more grammar tests
- removed reST examples
- sync default into branch
- sync default into dev
- updated README with pypi info
- updated installation
- updated misc/hgvs-shell for new bdi.uta0.connect()
- updated railroad diagram to include version number
- updated sphinx doc/source/conf.py
- yet more doc changes
0.1.2 (2014-01-05)¶
- #85: adapted hgvs to bdi with runtime-selectable UTA connections
- updated README with pypi info
- doc updates
- now depend on uta and bdi from PyPI (not dependency_links); sync’d Makefile and setup.py with uta; updated test and docs targets
0.1.1 (2014-01-03)¶
- #64: handle the following: (1) indel crosses stop codon; (2) indel crosses start codon; need to retest on full suite
- #64: update 4 tests to reflect p.Met1? behavior for deletions crossing from 5’utr to cds:
- #83: cleanup fs* cases where mutalyzer assigns fs*N where N = end of transcript instead of an actual stop codon (expected result is now fs*?)
- #83: comment out tests that need review/cleanup (and added comment); fixed tests where expected result was incorrect (still need to check tests w/ no expected result)
- #83: fill in intronic variants with expected hgvsp results (p.?) per curators
- #84: ext with no stop codons are represented as ext*? - updated tests accordingly
- #84: fix expected result
- Turn off dbg
- Turn off more dbg
- added lots of documentation
- added Apache license and code boilerplate to all source files and scripts
- doc updates
- fix coverage by calling tests via python setup.py nosetest; fix test name
- logo: rotated, moved to subdir, created favicon
- made png and ico logos transparent
- moved sphinx sources to doc/source and updated configs
- now depend on uta and bdi from PyPI (not dependency_links); sync’d Makefile and setup.py with uta; updated test and docs targets
- removed test-setup-coverage from Makefile dependencies (put in setup.py instead)
- s/locusdevelopment/invitae/
- updated doc static images
- updated hgvs-logo.png per Makefile
- updated setup.py “license” attribute
- vastly improved sphinx documentation. More to do
0.1.0 (2013-12-30)¶
- #52: generate syntax/railroad diagrams (in misc/railroad/)
- #56: updated tests; fixed fs*N (only one still broken)
- #62: synchronized setup files among UTA program components
- #66: added support for p.0, p.=, p.?, p.(=), p.(?), with tests
- #66: updated grammar for p.0, p.=, p.?, p.(=), p.(?) to reject invalid p.(0), etc.
- #72: update hgvs to use bdi (no direct connections to uta anymore)
- Close branch jenkins.
- Convert test input and consumer to use 4-column format
- Fix extension for frameshift case; update test to get around dupN (trim the N)
- Fix tag
- Last cleanup before merge
- README.rst: fixed preformatted text (that wasn’t)
- Refactored cp tests to work from a common base which more closely resembles the gcp test. All-CVID test input file is in 4-column format (lots of missing data, though)
- Revamp of c to p based on tests results; checkpoint. Sanity & EH tests all run.
- Update makefile to include a mechanism for generating code coverage during tests
- Updated Makefile test task to skip tests prefixed with test_nightly; added task to run all; enabled all cvid test to check this
- add missing files to package_data
- added Apache license and code boilerplate to all source files and scripts
- added architecture & dependency info to README.rst
- added comments to failed and broken tests
- added examples directory
- added sbin/test-runner (see script header for example)
- added setuptools>2.0 to setup.py (testing); updated README.rst
- close branch
- corrected minor README typo
- fix test
- fixed bug in reported AA edit for extensions
- fixed bug introduced in 63e0baf7c986; removed unnecessary and obsolete edti.interface import in tests/framework/mock_input_source.py
- fixed bug that caused protein accession to be not looked up when not specified
- fixed bug with unqualified class names in hgvs.pymeta
- hgvsc to hgvsp bug fixes/updates: changed del/dups to represent the c-terminal end; variants in utr, intron & 1st AA are treated as p.? (subject to review). Cleaned up test data. Tweaked seguid data so the tests pick up the correct NP in a case where there’s more than one match - mainly just to get the tests to pass.
- hgvsc to p takes an accession
- make the nightly start from make cleanest (tougher)
- merge into default
- more README and setup.py updates
- move edti bits to bdi
- moved misc/hgvs-shell to sbin
- setup.py: testing yet another dependency_links format
- updated README.rst
- updated bdi and tests to use external UTA instance
- updated examples dir
- updated logo and README
0.0 Series¶
0.0.9 (2013-12-16)¶
- added comments to failed and broken tests
- renamed grammars to .pymeta
- consolidated g-c-p testing into a single test file; commented out putatively broken tests; DNAH11 works!
- add forgotten sbin/fasta-seguid for commit -2 (0d29d0ea2d42)
- fixed minor grammar bugs re: AA term and frameshift
- added accession lookup for all of RefSeq protein
- got ‘make jenkins’ target working
- harmonized with UTA Makefile and setup.py to try to get tests working
- added biopython to setup.py
- fixed pro_eq grammar bug mentioned in #42
- Updated DNAH11 and NEFL tests. They run, so I’ll mark as complete, but there are errors associated with the proteins
- hgvsc_to_hgvsp: Fixed a delins bug
- hgvsc_to_hgvsp: Fixed bug in insertion indexing; improved exception handing
- added misc/hgvs-shell to simplify manual testing
- hgvs tests for DNAH11 and NEFL -> note protein not currently working just change if statement
- initial checkin for jenkins branch; want to test this in the build context
- Close branch c_to_p
- Merged in c_to_p (pull request #3)
- Incorporate AASpecial; tests pass.
- merge from default
- merged default into c_to_p
- added AASpecial to handle p.=, p.?, p.0 (and parenthesized versions)
- fixed setup.py issue that caused omission of hgvs.utils on install
- Forgot to add a test file to mercurial
- Merged from default; fixed a test.
- Make test file name more consistent
- SImplified comparison in the event of a simple substitution; updated tests so the failed tests are commented out.
- Reformatted Emily’s test data to make it more consumer-friendly; continuous test tweaking - latest checkpoint.
- Another couple of fixes based on EH tests; checking in working version of the tests.
- updated hgvsmapper with all g<->r<->c transformations
- remove explicit class references from makeGrammar invocation, require fully-qualified class name in hgvs.ometa
- close uncertainty branch
- added chr_to_NC in utils, added c_to_g in hgvsmapper
- Name cleanup for tests
- Tests now play nicely with both real data and the mock data.
- Add call to get_tx_seq()
- Missed a rename in the tests.
- Rename test classes to be a bit more consistent with their use.
- Inserted hgvsc_to_hgvsp into hgvsmapper.
- merge from default
- align with developer.rst conventions on naming hgvs variants vs. strings
- Fix tests to run in makefile context; some more documentation
- revamped hgvs_c_to_p so its interface matches hgvsmapper; should make incorporation a simple matter of copying the hgvsc_to_hgvsp method in. Updated tests accordingly. Moved tests to top-level.
- Merge from default
- Re-arranging code for utils/staging for hgvs mapper.
- Purged debug code
- Ack - last checkin broke the tests; fixed accession setup
- format cleanup
- Incorporate stopgap for protein accession; refactor so interface consumes data in the current UTA format; refactor tests to mimic UTA input; getting actual seq is still a placeholder.
- merging default into c_to_p
- added location uncertainty (parsing, representation, formatting, testing)
- added multifastadb code and tests
- [mq]: hgvsmapper-work
- imported patch hgvs-utils-dir
- added multifastadb tool and tests
- added Rudy’s AA p.= rule
- [mq]: grammar-relo
- added hgvs.stopgap
- Close branch transcriptmapper
- Merged in transcriptmapper (pull request #2)
- added TODO for tracking, prior to merging pull request
- Basic handling of variants in non-coding regions; will return p.= in all cases; this does not handle the case where a 5’utr variant results in the creation of an upstream Met.
- merged with default, TM bug fixes and more tests
- cleanup names (or at least make them a little more descriptive)
- added tm.cds_start_i in place of hard coding cds
- refactoring
- Roll back exon-specific changes and assume input is entire transcript concatenated together; retain the transcript data as recordtype
- fix test for AA in 2nd exon
- Convert transcript data object to recordtype; add tests for multi-exon (in progress)
- more tests
- additional TM fixes and more tests with multiple exons and strands
- Account for transcripts w/ more than 1 exon (test input assumed one)
- added some 1-exon tests
- Incorporate aa util and extend interval class (for test data); convert code to produce SequenceVariant objects for hgvs c to p. Also hacked in a way to handle p.= into the grammar (should be reviewed before merge).
- bug fixes
- Merged default into c_to_p
- added enum to transcriptmapper tests
- Last cleanup before merging default into here
- all input/output is hgvs-based. updated tests accordingly
- Close branch protein-variants
- Merged in protein-variants (pull request #1)
- hgvs.edit: fixed and improved fs handling, and added mediocre tests
- hgvs.utils: added Xaa=X, Ter=*, Sec=U for aa1-to-aa3 & aa3-to-aa1 translation
- code cleaning
- finished tests for transcriptmapper
- finished all the g,r,c conversions adding more tests
- More cleanup; simplify variant inserter code
- updated transcriptmapper to support g->r, r->g, r->c and appropriate tests
- minor cleanup
- variant insert tests
- merged edti-uta0 branch
- closing branch prior to merge
- edti: added __metaclass__ to edti.interface; added fetch_gene_info to uta0
- hgvs.edti: EDTI base interface and UTA0 implementation milestone
- hgvs.parser: add function attributes for every rule to enable, e.g., Parser.parse_c_interval(…)
- implemented p. parsing and formatting, with tests
- hgvs.utils: handle case when aa string is None
- hgvs.utils: added aa_to_aa{1,3} functions to coerce to 1- or 3-letter amino acids
- hgvs.utils: added protein 1-letter and 3-letter conversion
- Checkpoint for new branch (hgvs c to p)
- branched transcriptmapper
- improved parsing of hgvs_position rules (i.e., without edits) to handle g,m,n,r,c,p types distinctly
- added {gmn,c,r,p}_edit rule to parse variants without accesssions (e.g., c.76A>T)
- renamed DelIns class to RefAlt
- renamed Variant to SequenceVariant, and instance variant seqref to ac
- closed abandoned protein-support branch
- updated parser tests to include aspirational and “reject” tests
- [mq]: import-location-changes
- [mq]: import
- hgvs.location: renamed location classes; added BaseOffset position for r. and c.; removed predicate methods (is_exonic, etc);
- incomplete, buggy milestone
- setup.py: use full path for doc/description.rst
- updated CDSPosition to include datum and added tests
- use get_distribution() rather than require() to fetch version
- Fix for pathing to grammar.txt from within hgvs.parser.Parser
- modified setup.py to zipsafe false
- TODO edited online with Bitbucket
- Making setup.py file pathing absolute
- Fix for setup.py
- updated Makefile and setup.py
- revert directory to current after upload
- fixed bug in HGVSPosition.__str__ and added HGVSPosition test
0.0.7 (2013-10-11)¶
- fixed bug in HGVSPosition.__str__ and added HGVSPosition test
- collapsed grammar cases for c_pos; fixed variant test case typo
0.0.6 (2013-10-11)¶
- collapsed grammar cases for c_pos; fixed variant test case typo
- updated docs; fixed typo in variant
0.0.5 (2013-10-11)¶
- updated docs; fixed typo in variant
- added HGVSPosition (aka HGVS Lite)
0.0.4 (2013-10-11)¶
- added HGVSPosition (aka HGVS Lite)
- “simple” (single site) variants now pass tests
- update hgvs.__init__ and sphinx to use version from hgtools
0.0.3 (2013-10-10)¶
- update hgvs.__init__ and sphinx to use version from hgtools
- removed home-grown hg versioning in favor of hgtools
- removed virtualenv support and cleaned up Makefile
- milestone sync; c, gmn, and r types mostly work; some tests broken
- updated variant and added test
- updated grammar (more to do) and tests
- added hgvs.posedit and tests
- updated hgvs.edit
- removed CDSInterval (will use Interval for all intervals)
- fixed typo
- update hgvs.location and tests
- minor setup.py changes
0.0.2 (2013-09-20)¶
- minor setup.py changes
- grammar simplification; added Laros grammar, examples, comments
- Reverted Lawrence’s changes to edit.py (after discussing with him).
- Adding some convenience properties to be used in Geneticus.
- updated grammar; added README.rst
- added missing deps to setup.py; switched to plain ole distutils
- added developer notes, logo, sphinx config
0.0.1 (2014-08-01)¶
- initial commit