- Drop support for
Python 3.7. - Test support for
Python 3.10(condanumpyisn't ready). - Implement
strenconding changes that accomdate all versions ofbiopython(>=1.74). - Consolidate
pytestandpycovcommand totest/test.py. BuildandExampleworkflow include more comprehensive tests forconda.- Create a fallback conda environment for installation (
environment.yaml). - Applied a hotfix for problematic packaging of
lxmlinconda.
a3bb443cupdate pre-commit dependenciese5d6420bchange v0.8.3dev to v0.8.31d45f5bbupdate recent projects in READMEb0fab147update paths to docs22d7f0f7update notes for v0.8.330bc84e3add lxml hotfix to build3d1e7040restore gcc to environment6f4b3f9cupdate install documentation560b8175add auto yes to pip uninstall9087056eremove python 3.10, try lxml hotfixf892e9b9fix missing activatec003f02aupdate development docs9b5c819ecreate named conda environmentde731feffix missing conda activate6d3e91fctry to run example from conda using different python versions636931ddtry to install from conda using different python versions2c9e2c62restrict workflows py 3.10 version to 3.10.1b970d73asimplify calls to pytest and pycovececd98cimplement functionality for different biopython versions88061b34specify python 3.10.1 is supported0acf7a5frelax biopython dependencies to allow most recent package1abff891delete old annotate replace file42907aa9lint test files801614dftry putting 3.10 in quotes709a8817add a full environment for conda install11024c4cdrop 3.6 add 3.10 in CI47dd5849add a stock environment for dev0828d35erelax dependenciesd93afb2benable debugging modeb9f0afdbupdate sars-cov-2 search term8ff08d70update README with v0.8.2 project as releasedf81e8184note conda install issue
- Add quiet mode with
--quiet. - Create
NCBImetaAnnotatethat consolidatesNCBImetaAnnotateReplaceandNCBImetaAnnotateConcatenate. - Add configs
yersinia_pestis,mammuthus,hmp_oral,ncov_canada. - Remove
sphinxrelated dev dependencies.
089858eeinclude notes in CHANGELOGc1a4b2a1update notesaed461b8update CHANGELOGd040d1ceupdate README and CHANGELOG79a35353re add autolots as submodulee1712b86remove autologs372589b2change config outputs to database dir38869cbcadd bioproject and sra to ncov_canadac29cab00update help documentation653fe168add quiet modeb11ed919add execute permissions to new annotate script72d4b870add ncov canada configf2b54b21adjust test workflow for renamed annotatef4a9bd65fix code block in README741185b1new configs for hmp_oral and yersinia_pestise4efa58fremove wheel and sphinx related from setupbdd193f3remove wheel and sphinx related dependencies58c162b5adjust wheel pos in requirements14fedacdtry adding wheel to requirements07f4bb2cadjust workflows for new example and annotation2e24ec28consolidate the annotation tool to a single filebe0d6036update install channels in build31ce01acupdate install instructionsae039b34add png versions of paper figures2706b1a8relax dependencies07bde416try to limit codecov to os and python55ec78d0remove the executable suffix in pypi testing
- Add Python 3.9 Support.
- Bugfix the test export workflow.
- Update dependncies: lxml, PyYAML, NumPy
- Disable example workflow.
pull/22Add Python 3.9 Support
f0ebe0a0remove dev suffix from version8a7e17f7update docs45baf436update autologs with standardized hashdab96e71Merge pull request #22 from ktmeaton/devdcaca613add python 3.9 to the install job of build038d4f3bdocument example workflow disabled6d491ac5relocate codecov config2c798bcaadd config file for codecove0d7920fupdate docs before PR3d79271ctest numpy-1.19.53bbbe596bugfix in example workflow trigger05d19602remove print statementd3028113update dependencies lxml pyaml and numpyd5eaf85bfix bug in test_export biosample date4a1d4a7badd python 3.9 to the testing matrix31bfcafeupdate ver number to v0.8.14272d9edupdate changelog for v0.8.0
- Start new dev branch.
- Update miniconda actions and use mamba.
- Update lxml for security vulnerability.
- Add autologs as a submodule.
- Create CHANGELOG with autologs.
- Simplify test config with less fields to check.
- Remove .py extension from executable scripts.
pull/19Security fix for lxml, autologs, and workflow overhaul
3b3d630fupdate autologs for branch and tag linkb5ee965aupdate submodules for release2290cfcerestrict testing workflows to master and dev3efed457Merge pull request #19 from ktmeaton/devb325be9edisable fail fast and restrict codecov upload5cb358ebworkflow overhaulcc99998erestrict python versions to >=3.6,<3.94eaa9bc6overhaul test workflowc174036foverhaul build workflowcb0ba1f5add execute permissions to the newly renamed files0a519e0breplace .py extensions for Utilities scriptbf4f608bupdate autologsdb06fd2fupdate to v0.8.06b858776Remove .py extension from executable scriptsc73cb41bUpdate dev changelog7c221988simplify database columns for export9aacd232add autolog notes for v0.7.034ba5495update lxml for security fixes2e203c12update miniconda action and use mamba for macos78b42297lint new mammuthus config6dd43d81update miniconda action and use mambad275545bstart new dev branch for v0.7.1c96c186fresolve merges before v0.7.142239bc3add mammuthus config97fcd956add new logo to READMEe466196fadd new logo
- Allow config parameters to be specified at run-time.
- Restrict biopython to >=1.74,<1.77 because of Issue #13
- Specify versions for all user and dev dependencies.
- Updated and moved PR template.
- Updated Contributor's Guideline
- Remove Python 3.5 support because of incompatibility with black.
- Remove user email and API key from stdout.
18bf0c8dremove dev suffix from version numberfc0a25d4Merge pull request #16 from ktmeaton/cli-params1592e45eupdate help output28233181add tests for cli param and bad api key2710af1ccli parameters for NCBI apib5d48112reorganize community and additional contributors34cf2259update docs with final changes from typeerroradb51d7fMerge pull request #14 from ktmeaton/typeerror2baf5ba0update the PR checklist1faf1bc6change ver to 0.7.0dev and restrict all ver894f428frestrict pytest and cov ver8c490bcdfix lint workflow desc6dd00337remove python 3.5 supportd3a5a060update changelog for v0.6.7deve9ce2d09fix build ver broken linkffe033b4merge pr changes for lint workflow4146f54fMerge branch 'dev' into typeerror5e69d662change PR templatebf2e903crestrict pre-commit to <= 2.6.06da67ac9reformat workflows and use pip dev installfa35c1e7restrict biopython ver to <1.77b6379306update to 0.6.7devdca6bb2dremove outdated project ver numberf7d748fcadd python support and black lintingaa1f84c1update test table assembly valuesb7094501add black and flake8 to dev dependencies41290068fix list numbering indentationf302cce8add logo asset attribution5acd4b78add draft logod9ce0451add logo draft2723e189add url link for ncbi ref86776275note add contributorsd9b47239conda link
e931c8betest post suffix againc4b682b5update to a1 ver5aafdbc0run example workflow when src py is changedffe86dd9just increment the minor ver for bug fixd4e906b2commit to post suffix after test5be6eb63update ver use the post suffix7103b41bremove tag hook causes problems for pypi dup32dcb8adupdate vercb2997e4delete bad position tags047e96b6move tag hook under push action93d6b819also run workflows on tags72c05853update to ver v0.6.7a43747be1update pip and setuptools6116cdb1remove mention of setuptools install792e28c5mark project v0.6.6 as RELEASED9582d78cmake pypi install plain no ver
pull/12Contributors Guide Test
739cad3dswitch release trigger to publishedc68e5404run all workflows on releaseceb5b369fix github linksb5681abdMerge pull request #12 from ktmeaton/dev1d40f9a9change ver back to v0.6.66d99f145update links1d939decupdate pypi workflows6f383e32update version numbers with dev suffix1c30f04cchange version to v0.6.6dev74dffef0remove test dir from package89875fa0tidy up pull request templateebceb166tidy up pull request templatec0cc2e2eforce linters to wait for pre-commitdcf8bf8echange flake8 py find file94762f74trial yaml lint90e10878contributors guide file update6add9ae9contributors guide file updatef11e68f4install notes and project update5a515e4eseparate install and run for flake8764cbac0add back in flake869d8a7cdadd back in python lintingd96c0d05remove python linting4ad65ae9remove python linting445c69aaremove python linting8f51169cjust test flake8 install66376349temp remove pr hook and test flake8522e1243add macos conda install test56b3ec1dadd macos build workflow2750e066use conda setup action36b88dadcomment out PyPI repo install for now48b15d51remove setuptools installd44db942MAJOR bug fix for build workflow86c90653try to force build workflow with python3d7c1f9f2test lint workflow no req9870d239update markdownlint-cli to ignore paper dir062928c4lint setupc684f97clint bug_reportf7a62b57new pull request template9cdc4ce6more detailed contibute guide0c1fcd16more paths to lint12078ef7lint conftest4976309alint schema READMEcd724f9elint config README93035ff7update linting workflowaab8b906lint conftest max 803c4f9a8blint conftest max 807d6217dblint test_ncbimeta max 80f8952f59lint test_ncbimeta max 80267b401dlint test_xml max 80534f3971lint test_utilities max 805cc8065flint test_utilities max 80499c75f3lint test_join max 801dd3536flint test_annotate max 8006938061lint test_export max 80c8c67ccalint test_errorsdb12ca1flint NCBImetaAnnotate max 80b8030efblint NCBImetaJoin max 806b78c19clint NCBImetaJoin max 8049a4e918lint NCBImetaErrors max 808e511183lint NCBImetaErrors max 801c909129redo py linting max 803a912e59lint NCBImetaUtilities max 8069abba67lint NCBImetaUtilities max 80c635f83flint NCBImetaUtilities max 80f0818fd5lint NCBImetaUtilities max 804997e76flint NCBImetaUtilities max 80d2c2f6d6lint NCBImetaExport max 806cc3f06dlint NCBImetaExport max 808f3f898dupdate badges and requirements54327273more informative names for build jobs229fc561lint CHANGELOG with line len35a6482aupdate build badge to gh actions64f51457simplify workflow names96259597simplify workflow names8bf6dbealint CHANGELOG3158f783add markdownlint-cli to pre-commit lint863aaf23ncbimeta adhere to B950 max 80f6e58b2fignore B950 in conftesta609a1e7fix i var in loop212fd6e4revert to len 80eb1b9f0frevert to len 80a3c2b937lint ncbimeta with bugbearabdb2eb5lint ncbimeta with bugbearb223578blint ncbimeta with bugbearf60b4258lint ncbimeta with bugbearec29ac9dlint ncbimeta with bugbear0e1b5198lint ncbimetaa790dd61attempte bugbear for flake83e93d0f4more str format for black37beb315reformat str to make black happycaf0312clint with new rules15b5e41flint with new rulesa7a8e327lint with new rulese63ddc95lint with new rules048855c4lint with new rulesf69c9bfdlint with new rules9ccea9c9fix test module import55da36c0lint confteste41452e7test file specific rule excludecad97a45change E501 exclude to conftest294bc50bflake8 config in setup.cfgab237975test flake8 ignore conftest4563f59alint test_ncbimeta9fa14aa5lint test_ncbimetab22f4915lint test_utilities2be38960lint test_utilities082f9156lint test_joinb5742fd9lint test_export7d4f29c1lint test_joinefa7c750lint test_export93cffa9flint test_errorsc25df97flint test_errorscde103fefix comment spacing5d574303fix comment spacing25ee239alint test_xml000d9060lint test_xml810a70cclint test_annotateconcatenatec76738a5lint test_annotateconcatenate04dd0992lint test_annotatereplacece0f9e0dlint test_annotatereplacea6acbc0alint test_annotatereplacef039442clint NCBImeta489fc1b5lint NCBImetacf980d10lint NCBImetaAnnotate2829ebfelint NCBImetaAnnotate8388eb77lint NCBImetaAnnotateReplace4ccfc225lint NCBImetaExportc2aab367lint NCBImetaExportb00abcd0add lint checklist for py filescc8243dflint NCBImetaJoin7614502dlint single quotes3fe54360pull request template6d2c1b7bremove old dev require file58b0669cdraft contributors guide6fdf6f2eupdate build comments348dd6dflinting and dev depend update854a4371remove old contributor notesce36f022remove poetry tomldb9889b6update Lat and Lon for BioSample schema yamle3259858notes on replacing old schemaebaf5eb2dev testing toml filee83d45c9formatting notes4c9de0a2fix line wrapff0bb82eadd python file triggercb07360ablack and flake8 format1b1454f5poetry experiment3f1e9117force python 3.7dc9da600rename dev requirements323627eabasic deploy workflow for pypib9d387a0fix indendation506d2c30create deploy.yaml22652e0aline endings fixb0729285developer dependencies install guidea35875fefix mixed line endings5b32ea92pre-commit configuration52e9e799remove trailing whitespace and file endings094ff71fgh actions and linting1cc59eadfix indentation5bdb96eecorrect lint extension0dc356f9restrict paths and add more workflow6a5590c6remove codecov command58d10a9cupdate all namese6485616path in quotes8abaea04linting yaml with markdownd1a446a2add workflow to pathfce336dfwildcard paths in quotese5332c86all branches restrict pathsff2e1c62restrict paths remove example76d1a77bchange repo name to actionba746033remove version numberc2d46a19change repo tarball ver906fc27aquick start examplee5e516c1codecov upload01b938f2fix indentationc65775fbensure unique namese49c4b11formatting and new test49a80089rename to build07f4bc79add main installation744a0d4cuse the pip tutorial gh actionsd6c38cd1sudo for pip installsb31a524ctry sudo instead3bec2315remember to activated37982a8try in conda enveb7ea002Try github actions16799dcbtest out github actions3cc15721fix line ending0e901059MANIFEST for pypi packaging228c3698update v0.6.5 to v0.6.67f92720fminor update77403356config for manifest5c4479bfdocument dev dependencies42ba5eacignore fusion table3c9abf3bConvert BioProjectTitle to XPath querya150cd64SQL Update fix for char escape and securitybb52506afix slack PR notification boole55544e3temp pip instructions3a88be83pypi install note
pull/9Add ability to use XPath queries from within the .yaml config
ccfabe3aMerge branch 'master' into dev4531fdf6update dates, ver, community guidelinesa455008cMove XPath query explanation to README_schema docb61f931dupdate version number to v0.6.5138cc5f7Merge pull request #9 from hellothisisMatt/feature/add-xpath-supporta7415066Update all other issues template [skip ci]7d375742Update feature request template86ccf013Update bug report templates66dfb737remove branch pr9 from travis testingfd166157update unittests to include new values retrieved with advanced Xpath564c18fbtest implementation and error class when Xpath query is empty and unspecified9b0b11fddefine an error class for when the Xpath query is empty and unspecifiedade807c0check if the Xpath query was left empty and unspecified2c5e9a20add XPath queries to match the example config35b7b950Merge pull request #1 from ktmeaton/pr9659238aeupdate changelog with error classes, run CIc8b6584fNew error classes that can be raised in adv_xml_searchc04e981drevise adv_xml_search to check type of result1817705cremove outdated test xpath commandsa5c2fff6fix non-specific BioSampleBioProjectAccessionc390ff66refine xpath search for attr value84180028Enable attribute returns and error checkinga9b80573enable dev and py9 for CIddc6a065correct NucleotideBioSampleAccession xpath query8f0e2eadsimplified test example for tip search0a5fb699add contrib infobffe8294XPATH use, remove nonspecific NucleotideAssemblyAccession16451e7dclarify comma separated with space6e972c212 tests of adv_xml_search starting from root or starting from tip51584860xpath param of adv_xml_search as preformatted xmlc22c8596document the space and comma65353dcaMerge upstream dev changes into pr955859648Add XPATH Information to config readme56e0b3c5Add ability to use full XPath for XML searching3206959anew to do fixes62ab0e7cSRABioProjectAccession edge cases0cadcec0SRABioSampleAccession typo5232f359update SRABioProjectAccession24bdfe01v0.6.5 init changescd5efb4dupdate BioSample schema and example for SRABioSampleAccessionfb579507badge update and rearrange [skip ci]
33cdca3fswitch travis back to master only03481fe5expand issues section [skip ci]1b94dfebupcoming features section [skip ci]a55df18fdoc update [skip ci]80889436test multi match7e5cabd9update nucleotide data575b153cswitch travis to dev branch9e56cec6small progress on nucleotide dataa81357e4v0.6.4 notesc7dd8faaignore some example and test filesd3fa6ccdver updatea4a3d9eecommit to encode removald3abba52working on nucleotide export300055a7encode decode purgecdf506f8uncomment encode decode calls33192fafSQL parameter and table col check31f92037Extra param checking Issue #7585a200atable and column name catching5b46aaa0SQL parameter completeb11f401bsanitize output format again4eca45d9sanitize output format69b1f769test for table and column name format8104b940SQL table name add73af61a4before more sql select changee4c17c70slack travis-ci integration
77e6fe17enable master branch CI8850b76bcodecov spacing syntax error523687beallow dev CI16a4f56fbioconda autobump bot rely4446f94fremove bioconda scriptsb92681f4autobump script update49e4bab7hidden script names and autobump script [skip ci]502338b1resume full testinga76ff011use the bioconda recommended install code [skip ci]052a82c5solved mystery of branch bc-tbd [skip ci]324b668eautomate ver number update [skip ci]41ed42edswitch zenodo citation to the all ver DOI [skip ci]c00f4784remove unnecessary tag condition2d5dda85if statement spacingf139b226simplify commit message [skip ci]d6c3c027travis tag match v553124d1tag checkfb349cadfile format linux086851a2executable mode4053814amove conda update commands to script23292884set branch upstream origin6b3d224fadd, commit, push recipe20b58f61enforce semicolon98609ac1split up branch creation and check outc9ac4a55no tag enforcement yet03b675eeforgotten symbols5d742c2esed replacement checkd6268fe0src sha256 refine4c11045cpath and url fixd8fc06b9conda var first pass5f6d8ca5hide user ref [skip ci]e48c1e67remove dir checks87266f3cremove comments4e1606b1travis-ci test post local verify4554da93fix incorrect slug usagea0fa57eeshow git config664a2aa6directory checking3d711f34config param fixa1a9fa07bioconda update attempt 2dfbd7e38bioconda update attempt8f0c064emore pwd checks95801e52pwd testb6b0856dcondition testingcb497125Document the bioconda repo master branch switch
pull/5Adding Bioconda as an installation option
3f8fac57PR and Issue linking4c942075branch match ver release name [skip ci]d421128ddate update v0.6.2 [skip ci]7dc34dd5automate pypi deploy [skip ci]e636c6a0CI branch on master37aedb52Merge branch 'dev'71ab0e87merge dev into master3de43a83Merge branch 'dev' of https://github.com/ktmeaton/NCBImeta into dev7a2a3f3aversion updatea9605de3version update [skip ci]2dc59202ver update to 0.6.2 [skip ci]92d810d1Ouput dir is created instead of raising error [skip ci]bd10fbd7remove slash [skip ci]f8200686bioconda installation and media as raw links [skip ci]f994d973Merge branch 'dev' of https://github.com/ktmeaton/NCBImeta into devf89ccc53CI on dev5be403b9v0.6.2 bioconda and output dir619e1dbav0.6.2 bioconda and output dirc6409285Remove the output dir error class [skip ci]a68d17adMake output dir instead of raising errora99a4bf4Test if output dir is created [skip ci]c0c1019dMerge pull request #5 from druvus/patch-1c3fc9a43Paper remove unnecessary reference ncbi website [skip ci]55e8bf7dAdding Bioconda as an installation option17d6ba13Zenodo citation and badge [skip ci]
0ab131a5update schema doc for new xml parsing [skip ci]680ddb26ref and capitalization [skip ci]edaa3b00python 3 spacing [skip ci]49132f98re-enable master CIfb3a01cfaeruginosa text db7dd98044aeruginosa paper dbc50677f2add release namesa93d1a11Name for upcoming v0.6.1a24a82f6release to development32d162baprematurely add v0.6.1 links88d6d0c1format and typos5ccd379aconceptual rearrangebe940044Initial commit desc37068fc7complicated compare8637310flink fix900c6a55test commit compare8efd0815hyperlink exp3b17a514aeruginosa config filefdc4672blist format tables4bbeb109renamef7f53111remove old gif27d1a2debiosample gife5716aa2gif larger79b82f1egif rename867775afimage swap37dd9c90gif full path, reformat print107fa144State CLI Application69f17655specify CLI application8a72fc83asciicast7d0a4cccdependency reference to filee2674d74JOSS file additionsbec9abe9update record number08b5e589uncomment xml print084f2006jpg renamed1bd7ae9doc xml printing, disable master cibd92205bdoc update API optional [skip ci]2c72df89doc update node parse [skip ci]c7a77e46new prettyprint func [skip ci]c78b8c25update version [skip ci]ec6ebf8fedit description [skip ci]daa228b4JOSS Paper82b7b4f3Reformat headings [skip ci]7cbabc9aconfig file name update [skip ci]9808a6bdClarify and formatting [skip ci]
44805c70remove exp code717431a8license badge update [skip ci]05b3aeaaMerge branch 'dev'cb575aeaconflict resolveb489ca62v0.6.0 updates [skip ci]778ab45fignore test database and log files [skip ci]b3a310c5Single quote sql query fix0e0be9cbXML overhaul test updateb0dc3bccsuccessful run848cb532quotation fixe03597afbugfixes for xml_searche0ff551aremove old search and flatten functions546c368eBefore function move9d97bbe0efetch part functional for sraab88a2c4before nucleotide switch to efetch393466d3bioproject with efetchbe00272befetch switchee6cf173lxml overhaul31de27e9before efetch switch1b720a82xml in xml parsingd33d58e5cdata testing940ba360lxml experiment88b7c0deConfig and Schema README as full path [skip ci]0b1030ddignore build dir [skip ci]e4be83d4change codecov to branch master [skip ci]f3b30de3v0.5.0 version update [skip ci]
046f68betravis-ci only mastercecb1aaeMerge branch 'dev'0d844574v0.5.0 updates [skip ci]849f7335Explain default slow download [skip ci]b810c2adFix codecov badge link [skip ci]5d4c83bcSwitch release badge to PyPI [skip ci]4112027bcodecov url fix [skip ci]29a80f52try codecov badge with dev [skip ci]1488da73Clear debugging output199559b5formatting [skip ci]e6bd3b70document column_index bugfix [skip ci]f560dfe5Correct bioproject accession10e1d2aecolumn_index reposition75edf10ehttp error catching for esearch1bc53175strpath for tmpdir [skip ci]fd509f42Fix sys path and list comparison3eb83673Remove Python 3.4 linux build [skip ci]6bd4d8d8require time module8df42459test db path fix [skip ci]1488745aPython 3.5+ required (no more 3.4) [skip ci]d5624e19travis troubleshooting763c54f8bash uploader for codecovb807bb02example config reset595959b9Merge branch 'dev' of https://github.com/ktmeaton/NCBImeta into dev4c9b15bcfull travis-ci test build8f5f38b2full travis-ci test builde2ede2c0pytest for non-flat mode7d4ec415prototype master table checkea642b8cMove the HTTPErrorCatch method to utilities [skip ci]dd55698epytest db verify SRA8de4febdpytesting and db verification [skip ci]bc7f6b29Update test biosample metadata6771d87aExclude temporary test files [skip ci]b2df525dpytest pubmed [skip ci]a88ba92dpytest export nucleotide table valuesa21df9ebpytest conftest assembly and bioprojectfe28e8b3pytest export assembly and bioproject918f1e3cremove annot file [skip ci]26b8d15fpytest join87ca364aComment clarification [skip ci]e84af09bpytest annotatereplace90da7506annotateconcat 90% cov34725c9efix indentation4eea6b32annotation file for pytest [skip ci]1a4f0682specify pytest files in order98a4221fmodule import in test dir [skip ci]88279923sra table metadata re-fix [skip ci]debd22abdebug help points [skip ci]7150dc32generic test db name [skip ci]cac8a129pytest annotateconcatenate [skip ci]e16d6e8cformatting [skip ci]469bb6a6proper support for SRA [skip ci]b5e57539codecov badge [skip ci]26221240remove extra script081a76e3execute permissions [skip ci]ef5b084cremove the test1 ref14133ba0update execute permissions again90d9bfbctest for output dir9a1533e3config data yaml test [skip ci]12b67361old cov [skip ci]14ce1bf7remove extraneous [skip ci]7d8037b6simplify name [skip ci]f7b4502eyaml file error test [skip ci]727e547bmain test [skip ci]1efd2793give unique names [skip ci]dac651b8print config file path [skip ci]e2de1968yaml file test [skip ci]0eb16810yaml files for testing [skip ci]805efa69super simple config [skip ci]de49481aProper os join7a9be44cpytest Errors complete8afd1ce9pytest errorsebfc8af1duplicate column debugging [skip ci]b663a974str repr of errors proper return [skip ci]c51cd55bcheck for duplicate column names1725bc6bpytest and coverage [skip ci]35ffd83bcleanup docstring [skip ci]640ed49euse tmp dir and files13b0edb6remove unnecessary code [skip ci]fb3bff1dRe-enable full travis-ci [skip ci]ac82f6b3remove unnecessary type checking1a801bc2codecov take 2e6b8977fcodecov coverage test upload [skip ci]40a601f1remove testing modules to travis requirements60213802codecov require and testa35e2513pytest-cov requirementef914477pytest troubleshooting34850960--cov-report= proper parameter2bbd4258pytest and codecovba90d3f2Longer description [skip ci]971a6335Comment out debugging [skip ci]eb75e654v0.4.3 changelog updates [skip ci]3fd7cec2Remove unicode refe9086255Remove XmlXXXConfig Functions120cfa5eExtended description, remove troubleshooting printout [skip ci]a462b23dNamespace clarify6bde5f20Expanded type checking1c7bd73aStringElement items troubleshooting62aceba4Extra type checking30423509Fix internal recursion function name5b4de6b2Correct and document flatten_dict implementation4bdedf32More testingefb3b86fUtilities testing269ca821Recode unicode and remove sysa20daf6aDescription in header [skip ci]05f693ecRemove sys module and flushprint [skip ci]e9efc279cleanup [skip ci]d92dc091NCBImetaErrors namespacefc983047Remove io module78032d93Remove sys module [skip ci]f76c6dc1Error classes documented45ddc1bbDescription in header [skip ci]1f86ec3dRemove sys module and flushprintb1b668a0Remove sys module8400f5f2Code doc first pass [skip ci]b681b08dReduce code redundancy86be6028Document UpdateDB [skip CI]d7a22f2eForce unicode str recode691111abCleanup, document HTTPErrorCatch778817bfimport slim down470e3422flush print true case sensitive4addaaa3Travis CI for dev5ae1c7afReplace flushprint method python390bedfbaMerge branch 'master' into dev5f3548e1Header change12722915Gif reupload and typo fix359b0ee6Nucleotidet typo fix5e56fee8gif reupload6f6d74c5Delete broken DB gif4e53ed01Delete broken CLI gif546edd68Move requirements higher [skip ci]
37adf6ecv0.4.2 finish296f34faRequire cloning github [skip ci]2847a272section break [skip ci]b1cb2ce3Remove test warning [skip ci]994f4b1eWeb portal links, src dir fix [skip ci]359f572fExtra quotes remove [skip ci]8edd0a2aFix module import and author credit01f45929fix quoteb477b425missing comma02f81dcfpip install match PyPI Repo [skip ci]2c856e20Remove underscoresc6cd147bRemove src dir links [skip ci]6c5ba1e4Install update [skip ci]473ca4c1Home url and markdown desc [skip ci]b8b71bd9Short description [skip CI]82a05e65pip install included05cb9a0ebranch restrict rearrangef3510328travis troubleshooting part 2d9f58431travis troubleshootingf574720drequirements notea411aea1v0.4.2 starts, PyPIbc572124Merge branch 'dev'9909a130PyPI Preparation27568510setup.py install works!b549268dRename src dir to ncbimetad25112a9More setup.py config4236cecarequirements.txt control for setup0978441eAdded setup.pyff158f0eRemove underscores in programf074685bMerge branch 'master' into dev0f33450fRun Travis CI only on mastera7d90383v0.4.1 version update
69941adav0.4.1 releaseabf1e032Rearrange and simplify [skip ci]92c7b601Update CLI gif to v0.4.0 [skip ci]86b5eb58relative path change gif [skip ci]1479a5acMerge branch 'dev'f8112bd1url update [skip ci]770f7e5bgh pages url [skip ci]00c72f40Merge branch 'master' into dev46931e02Dependency clarification83ceb7fbMerge branch 'dev'ac09f722Multi-python linux6731c998Remove accessory program section [skip ci]50121e98Spacing [skip ci]409dfcc9Describe OS support [skip ci]6defc7b7Description simplify [skip ci]790dd776Links and issues doc9c2de04eUpdate program descriptionda2c18c3Simple Linux and MacOS Build04151edbRemove URL Error code printc67c9d5fTravis-CI MacOS Supported!f22cedcbesearch cmd rearrangec3b34440kwargs typodf09ab4bTypo http_metthod4e38e926Try to catch URL Errore8b43d98Retry macos testingfb9c1e77Macos test first20762ef8Pip3 change and multi-python test19eb7e98Bugfix plus exclude windwos from travis8571960eTest with python3 prefixd4a1b519Windows travis-ci test5e8e305cPy 3.7.4 multi-dist test65be703bAdd Travis-CI Badge [skip ci]0f8c65f3Just test python 3.6 on devbe9fc9b0v0.4.1 preparation [skip ci]53006214Annotation script bugfixes [skip ci]c0218440Updated biopython requirement to 1.74 [skip ci]535aa7fcAdd numpy to requirements although packaged with biopythonb837b59fOnly dev branches for travis-ci56105f96Add execute permissions to scriptsd4f8c295Remove --user flag from travis-ci pip9a436e42Travis CI Integrationdf2ddfd0Merge branch 'master' into dev3b6276d7Simplify dependency written desc
c7b320dfv0.4.0 release changes5a4a799cMerge branch 'dev'17527168Variable formatting3a910cb9Formatting test70ee5cb3Improved parameter description882140afannot file updates3c257cd6Fixed program description.92bee130Improved description6471de76Additional explanation for join and export9a0e1957Section rearrange0ccfe8a9Fix incorrect release version links8ae3a9c5more typosd1df6f8cTypos etc87802934Release links82eacccbMain README simplify28c28d74Force metadata concatenation even if same valueacb33f82Simply annotation file name32de6625Print msg upon successful matchedca4c0dRmv records outside time boundaryf42d0a61Rmv annot file outside time boundary792d683bOutput msg for succesful match047124b1Schema updatesa33cc251Removed scripts folder with R code930f2e52Clarify whitespace importancebb86c43dRemove unsupported schema txt files5e2a608aDoc formatting7008c663Doc formatting and spacinga1c5bed5Schema documentation update for yamlb7edcea2schema files in yaml format4762bb94Added comment field to Pubmed tablee431a2b0badge typo and gif to be updated52ad0019Sanity commit23005247update, MWE back to plague0014b8c5MWE organism change and direct execution without python3 call4ebc22b9Shebang updates for source filese81f17e0Annotation file renamea883af4fSwitch MWE back to plague for shorter time7dc0cb4aRemove old py config file5320f671Slowdown fetch as defaultc8973be6Shebang typo58829cceImplement read handle error checking035d0fdbError class for read errors1df91ae4add db name25aff7c9Switch example config file to P. aeruginosa to match paperd50e012dv0.4.0 update rename91b3d626HTTP 429 error checking for efetch906b10ceExample command now references config.yaml99ed046bUpdates for v0.3.4 and v0.3.5d6483289Implement hiearchical fields36639a2dUpdate hierarchical docs66ab5c06comma space sep hierarchical fields6da14858Removed extra config filese4f36d3dAdd requirements filed772064eImplement config file as yaml91cd02daError for incorrect config parametersb6966d80config file in yaml formata16f9699Merge branch 'master' into dev
da80053dUpdatef53bdac5Merge branch 'dev'297f12feDocument AnnotateReplace and AnnotateConcatenate18cf30abDocument FORCE_PAUSE_SECONDS parameter8bf17376Include all 6 tables in config files424e4a63Create a parameter to allow force pausing in seconds09425f43Implemented NCBI API key acceptance9927043aAdd P. aeruginosa config file3bc04b38Added error when max fetch records is exceeded5464bc40Bugfix for HTTPError 429 checking8bb603e9HTTP Error catching for Entrez esummaryaad5f391shebang change to python33ebd8e0cSet theme jekyll-theme-slate578e473bSet theme jekyll-theme-minimalb1981633Goal: Config file as yaml format.
2c8f1d5ev0.3.3 Releaseb792547bMerge branch 'dev'27974444README update3c557c6dForce python3 command5e10baa8Changelog includes Pubmed support7e2196cdPubmed add and successful example testf12a9201Schema update and Pubmed addition83e321e6Pubmed Table functionality addedea5e6768Added a str conversion to xml parsing step for Pubmed tabled08dc500v0.3.3 development begins
f800a8a3Changelog update39ab0e2bDelete my_organism_annot.txt86abec38New annotation files for exampel8eeb4be8NCBImeta_Export converted to python36ec68501Missing DB Error added315a3889Last commit before v0.3.363141bd9Nucleotide annotations fully fixed0d3db343Nucleotide schema CDSs pluralize65b03ee5Nucleotide Table accession fix1fe7dc10Fix Nucleotide annotations for py336027f7dRemove utf encode for py3 functionalityc3923ca4Unicode decoding for Python3359a2f7ddict_items error fix7c10cc81dev branch reinstatedd7603d54Add XPath and XLST to wishlistc2838e84Update README.mdd21c83efUpdated instructions to reflect no dev branch yet4f37c238Update development branch names to dev0472be92Update README.md689a5452First successful completion of the master join tablea21171daJoin script beginning functional28f47249Major fix in Nucleotide metadata retrieval, properly recovering annotations22aa44d7Little things in README8d2f0cf9example update1a852f1eRename default column names so that they are all uniquee53deb13Metadata annotation scripts now allow concatenation5cdd9bb5Change annotation script to 2 options, replace or concatenate6f9247c8Use harmonized_name attribute for BioSample fieldsbffefeefRemove excess config files and example outputc45fc56cSlow down NCBI fetch requests to 1 per seconda0459535Update README.mdc90c644fUpdate README.mdb7315650Update README.md5993154bGIFsb21cbfdeAdd files via upload8cd4cbe7Encode rather than unicode, experiment
pull/11.1
cd8fda64Update README.mde6da6252Update README_schema.md2d96701bUpdate README_schema.md57ff5348Update README_schema.md38e48611Update README_schema.md13d25e7bUpdate README_schema.md93b830daUpdate and rename README_schema.txt to README_schema.md4b806836Update README_config.mddc775f57Update README_config.md766c815bUpdate README_config.mdfd2a4f4eUpdate README_config.md328a571bUpdate README_config.mdee9eedc4Update and rename README_config.txt to README_config.mdb6d4bac2Update README.md047b0afaMove imagese5c3f027Moved images87a24a72Update README.md77148b58Update README.md104ef14aUpdate README.md57349436Update README.md09ec0dc4Update README.md40858177Update README.md69347c18Update README.mdc3488df1Update README.mde3ac31c6Update README.md3551c725Add files via upload3963afcaUpdate README.mdd49de82aUpdate README.md25bf63e1Add files via uploadac30fd21Delete NCBImeta_screenshot.pngf3afa94eUpdate README.md3a393d08higher5349f1a1mergee2a132bbhigher resd65ee345Delete NCBImeta_snapshot.jpg82a1350eDelete NCBImeta_screenshot.pnga15b8041Update README.md693012caUpdate README.mdf9b1169cUpdate README.md97e58579Update README.md489bd94bUpdate README.md01670d9dUpdate README.md7118d274Update README.md58dce4cdUpdate README.mddd7c5a0dUpdate README.mdddd78577Update README.mddf34ed8aUpdate README.md94d1827eUpdate README.md3bd6f24cUpdate README.mdc84af731Update README.md037833f4Update README.md24a010b8Update README.md830ca965Image adde906acc4Update README.md719e986bUpdate README.md1f590d11Update README.md35eb86ecUpdate README.md331489acUpdate README.mda6485891Update README.mda6be4056Update README.md18cb81a8Update README.md0ca9547aUpdate README.md65b290f7Update README.md00817806Update README.mdede0ebe4example dir, more unicode testing13b657b1Bug fixing more unicodede6e9bbaUpdate NCBImeta.pyc4051788Update README.md7c136555Update README.mdaa71c05cUpdate README.md4df6f8f3Update README.md46041edcUpdate README.mdfdc00290Update README.md9ffcf42aUpdate README.mdcf734b6fUpdate README.mde2937a41Update README.md95228b11Update README.md39217244Update README.mde74a81a1Update README.md3fc5925aUpdate README.md88dd3d8aUpdate README.mdc4064540Update README.md611501b9Update README.md06193bf2Update README.md65594c59Update README.mda33ef410Update README.mdee70c20cUpdate README.mdc0ba54c0Update README.mdb9563742Update README.mdf8bd00d9Update README.md5d504ec8Update README.mda4a7a42dUpdate README.md576f7df7Update README.md6c3c5f6bUpdate README.md4716032eUpdate README.md5360f6dbBadge Testingc268d121Update geocode.R21dcccdaUpdate CHANGELOG.md995b7027Update CHANGELOG.md7cdae9c5Update CHANGELOG.mde2d363deMerge branch 'master' of https://github.com/ktmeaton/NCBImeta2b24140cRemove R tmpd98765f8Delete .Rhistory97df6dc6Ignore .pycb759f156Cleanupab545b4bcleanup .pyc7a133696License and setup7118d109Set theme jekyll-theme-slateb946a249Delete _config.yml17af0aceUpdate _config.ymlc9c73316Set theme jekyll-theme-architecteb87a53cUpdate5fa31d50Update _config.yml09b4b07eUpdate _config.yml2471e051Update _config.yml63caeaaaUpdate _config.yml50b00455Initial config3dd8ba90GH Pages0d15ea95Set theme jekyll-theme-architect7aa3cf5dSet theme jekyll-theme-architect02115ff9Python 2/3 compatability fix for unicodee3faf17cUpdate README.md42d82a16Update requirementsaed30d83v0.3.2 Begins0eb820cbMerge branch 'v0.3.1'7a23c244Ignore pycache directoriesd5701128Ignore4e90e7f7Cleanupa606819cCleanupc541c9bbREADMEs, bug fix on error raising6bddcdefremove kits9d21d465v0.3.1 begins1c97b6b4Merge branch 'v0.3.0'd78b88bfmerge with mastered269111Final commit of v0.3.0df8cedbaFixed node-attribute conflictionc57bafafCleanup old source filesb069d4fbProper unicode re-encoding5f673b7bFunction Assembly, Biosample, BioProject, SRAe49648e2Functional state SRAace7c457Temp save5693e3efFunctional automation of Assembly and BioSample7790c658Remove some files700bded3Rename and reorganize3bf8e94cDynamic playf39e9c6cAnnotate update2ff7b251Annotations8cdc64c7Duplicate removal7edfbc17XML frustration26b50189On the fly, database creation27eb8a32v0.3.0 rewrite main scriptefa56ceev0.3.0 Development Beings - Automated00b6f1bav0.3.0 Development Begins - Automated7e77ac20Merge branch 'v0.2.1'9383f6c5More annotations97f6419cMore annotation49654725Massive annotationa09d4012CURATED annotation files5df0f48ebioproject addition to annotate4b3a27f3Check multiple matches in annotation, removed BioSample columns82661a4bConsensus file after plotting710d6b57First pass at plotting geographic distribution, Pandemic, PubUsed851f704Plottingfc2a0712Plotting1248978bConsensus lat,long,pandemic,established2716c6baGeocoding switched to Doogald8161aeegeocoding9a59fd28Yp database for plottinge5036c05More annotations69a3865aAnnotation files1f095613Dare I say.. functional v0.2?2d4399d1Heuristisc approach to mergefcce7556Biosample improve4450cd1aREADME Title Fix665b47c3v0.2.1 README Update64467aeeAssembly, SRA, Bioproject functionald33fc246Update CHANGELOG.md38be909ev0.2.0 In Development Begins, Rename NCBInfectb0103143v0.2.0 Begins Development9dfe4d7eMerge branch 'v0.1.2'594b4bc4Sanity commit, Jan 20180d6b9312Update CHANGELOG.mdae8d3b31Update CHANGELOG.mdee485710Update CHANGELOG.md0e3e2f33v0.1.2 changes973d416fUpdate README.mdb7326d9aUpdate README.md6e1a7000Create CHANGELOG.md08053019Moved annotate file54f194f7Merge branch 'master' of https://github.com/ktmeaton/GenomeCollectorb8af9498Big Changes43c68690Annotate File3e0e006epython3 version fixe8e40418python3 print statement fixa80db3fdAdded extra fields in SRA table5453c8dcVersion 2.0 fully functional2a1c06e0SRA functionality as separate module7280508aPartially working version of SRA Table5c8f3e98Added SRA function85654bcfAdded more to do in README.md2e859b11Added genomeannotator log file writingc6ecaf04Added the GenomeAnnotator tool5de9f53fRemoved tmp file writing for record_dict testingfdbe0768Changed biosample Entrez parsing to validate=falsebac6eb7aField AsmReleaseDate replaced with SubmissionDate642c2a2aUpdated README.md to version 2.0506b9768Merge pull request #1 from ktmeaton/1.1fdc45fb2Update README.mdcde62fabUpdate README.mda521f23fUpdate README.mdfc5bea46Update genomecollector.pyc433ef22Update genomecollector.py7736c0eaAdd files via uploaddfff42c1Delete genomeconcatenate.pyac643db0Add files via upload