{"action":"opened","number":5,"pull_request":{"url":"https://api.github.com/repos/ncgr/aakbar/pulls/5","id":222972255,"node_id":"MDExOlB1bGxSZXF1ZXN0MjIyOTcyMjU1","html_url":"https://github.com/ncgr/aakbar/pull/5","diff_url":"https://github.com/ncgr/aakbar/pull/5.diff","patch_url":"https://github.com/ncgr/aakbar/pull/5.patch","issue_url":"https://api.github.com/repos/ncgr/aakbar/issues/5","number":5,"state":"open","locked":false,"title":"Scheduled weekly dependency update for week 41","user":{"login":"pyup-bot","id":16239342,"node_id":"MDQ6VXNlcjE2MjM5MzQy","avatar_url":"https://avatars0.githubusercontent.com/u/16239342?v=4","gravatar_id":"","url":"https://api.github.com/users/pyup-bot","html_url":"https://github.com/pyup-bot","followers_url":"https://api.github.com/users/pyup-bot/followers","following_url":"https://api.github.com/users/pyup-bot/following{/other_user}","gists_url":"https://api.github.com/users/pyup-bot/gists{/gist_id}","starred_url":"https://api.github.com/users/pyup-bot/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pyup-bot/subscriptions","organizations_url":"https://api.github.com/users/pyup-bot/orgs","repos_url":"https://api.github.com/users/pyup-bot/repos","events_url":"https://api.github.com/users/pyup-bot/events{/privacy}","received_events_url":"https://api.github.com/users/pyup-bot/received_events","type":"User","site_admin":false},"body":"\n\n\n\n\n### Update [click-plugins](https://pypi.org/project/click-plugins) from **1.0.3** to **1.0.4**.\n\n\n<details>\n  <summary>Changelog</summary>\n  \n  \n   ### 1.0.4\n   ```\n   ------------------\n\n- Preemptive fix for a breaking change in Click v7.  CLI command names generated from functions with underscores will have dashes instead of underscores.  See https://github.com/click-contrib/click-plugins/issues/19.\n   ```\n   \n  \n</details>\n\n\n \n\n<details>\n  <summary>Links</summary>\n  \n  - PyPI: https://pypi.org/project/click-plugins\n  - Changelog: https://pyup.io/changelogs/click-plugins/\n  - Repo: https://github.com/click-contrib/click-plugins\n</details>\n\n\n\n\n\n### Update [click](https://pypi.org/project/click) from **6.7** to **7.0**.\n\n\n<details>\n  <summary>Changelog</summary>\n  \n  \n   ### 7.0\n   ```\n   -----------\n\nReleased 2018-09-25\n\n-   Drop support for Python 2.6 and 3.3. (`967`_, `976`_)\n-   Wrap ``click.Choice``&#39;s missing message. (`202`_, `1000`_)\n-   Add native ZSH autocompletion support. (`323`_, `865`_)\n-   Document that ANSI color info isn&#39;t parsed from bytearrays in\n    Python 2. (`334`_)\n-   Document byte-stripping behavior of ``CliRunner``. (`334`_,\n    `1010`_)\n-   Usage errors now hint at the ``--help`` option. (`393`_, `557`_)\n-   Implement streaming pager. (`409`_, `889`_)\n-   Extract bar formatting to its own method. (`414`_)\n-   Add ``DateTime`` type for converting input in given date time\n    formats. (`423`_)\n-   ``secho``&#39;s first argument can now be ``None``, like in ``echo``.\n    (`424`_)\n-   Fixes a ``ZeroDivisionError`` in ``ProgressBar.make_step``, when the\n    arg passed to the first call of ``ProgressBar.update`` is 0.\n    (`447`_, `1012`_)\n-   Show progressbar only if total execution time is visible. (`487`_)\n-   Added the ability to hide commands and options from help. (`500`_)\n-   Document that options can be ``required=True``. (`514`_, `1022`_)\n-   Non-standalone calls to ``Context.exit`` return the exit code,\n    rather than calling ``sys.exit``. (`533`_, `667`_, `1098`_)\n-   ``click.getchar()`` returns Unicode in Python 3 on Windows,\n    consistent with other platforms. (`537`_, `821`_, `822`_,\n    `1088`_, `1108`_)\n-   Added ``FloatRange`` type. (`538`_, `553`_)\n-   Added support for bash completion of ``type=click.Choice`` for\n    ``Options`` and ``Arguments``. (`535`_, `681`_)\n-   Only allow one positional arg for ``Argument`` parameter\n    declaration. (`568`_, `574`_, `1014`_)\n-   Add ``case_sensitive=False`` as an option to Choice. (`569`_)\n-   ``click.getchar()`` correctly raises ``KeyboardInterrupt`` on &quot;^C&quot;\n    and ``EOFError`` on &quot;^D&quot; on Linux. (`583`_, `1115`_)\n-   Fix encoding issue with ``click.getchar(echo=True)`` on Linux.\n    (`1115`_)\n-   ``param_hint`` in errors now derived from param itself. (`598`_,\n    `704`_, `709`_)\n-   Add a test that ensures that when an argument is formatted into a\n    usage error, its metavar is used, not its name. (`612`_)\n-   Allow setting ``prog_name`` as extra in ``CliRunner.invoke``.\n    (`616`_, `999`_)\n-   Help text taken from docstrings truncates at the ``\\f`` form feed\n    character, useful for hiding Sphinx-style parameter documentation.\n    (`629`_, `1091`_)\n-   ``launch`` now works properly under Cygwin. (`650`_)\n-   Update progress after iteration. (`651`_, `706`_)\n-   ``CliRunner.invoke`` now may receive ``args`` as a string\n    representing a Unix shell command. (`664`_)\n-   Make ``Argument.make_metavar()`` default to type metavar. (`675`_)\n-   Add documentation for ``ignore_unknown_options``. (`684`_)\n-   Add bright colors support for ``click.style`` and fix the reset\n    option for parameters ``fg`` and ``bg``. (`703`_, `809`_)\n-   Add ``show_envvar`` for showing environment variables in help.\n    (`710`_)\n-   Avoid ``BrokenPipeError`` during interpreter shutdown when stdout or\n    stderr is a closed pipe. (`712`_, `1106`_)\n-   Document customizing option names. (`725`_, `1016`_)\n-   Disable ``sys._getframes()`` on Python interpreters that don&#39;t\n    support it. (`728`_)\n-   Fix bug in test runner when calling ``sys.exit`` with ``None``.\n    (`739`_)\n-   Clarify documentation on command line options. (`741`_, `1003`_)\n-   Fix crash on Windows console. (`744`_)\n-   Fix bug that caused bash completion to give improper completions on\n    chained commands. (`754`_, `774`_)\n-   Added support for dynamic bash completion from a user-supplied\n    callback. (`755`_)\n-   Added support for bash completions containing spaces. (`773`_)\n-   Allow autocompletion function to determine whether or not to return\n    completions that start with the incomplete argument. (`790`_,\n    `806`_)\n-   Fix option naming routine to match documentation and be\n    deterministic. (`793`_, `794`_)\n-   Fix path validation bug. (`795`_, `1020`_)\n-   Add test and documentation for ``Option`` naming: functionality.\n    (`799`_)\n-   Update doc to match arg name for ``path_type``. (`801`_)\n-   Raw strings added so correct escaping occurs. (`807`_)\n-   Fix 16k character limit of ``click.echo`` on Windows. (`816`_,\n    `819`_)\n-   Overcome 64k character limit when writing to binary stream on\n    Windows 7. (`825`_, `830`_)\n-   Add bool conversion for &quot;t&quot; and &quot;f&quot;. (`842`_)\n-   ``NoSuchOption`` errors take ``ctx`` so that ``--help`` hint gets\n    printed in error output. (`860`_)\n-   Fixed the behavior of Click error messages with regards to Unicode\n    on 2.x and 3.x. Message is now always Unicode and the str and\n    Unicode special methods work as you expect on that platform.\n    (`862`_)\n-   Progress bar now uses stderr by default. (`863`_)\n-   Add support for auto-completion documentation. (`866`_, `869`_)\n-   Allow ``CliRunner`` to separate stdout and stderr. (`868`_)\n-   Fix variable precedence. (`873`_, `874`_)\n-   Fix invalid escape sequences. (`877`_)\n-   Fix ``ResourceWarning`` that occurs during some tests. (`878`_)\n-   When detecting a misconfigured locale, don&#39;t fail if the ``locale``\n    command fails. (`880`_)\n-   Add ``case_sensitive=False`` as an option to ``Choice`` types.\n    (`887`_)\n-   Force stdout/stderr writable. This works around issues with badly\n    patched standard streams like those from Jupyter. (`918`_)\n-   Fix completion of subcommand options after last argument (`919`_,\n    `930`_)\n-   ``_AtomicFile`` now uses the ``realpath`` of the original filename\n    so that changing the working directory does not affect it.\n    (`920`_)\n-   Fix incorrect completions when defaults are present (`925`_,\n    `930`_)\n-   Add copy option attrs so that custom classes can be re-used.\n    (`926`_, `994`_)\n-   &quot;x&quot; and &quot;a&quot; file modes now use stdout when file is ``&quot;-&quot;``.\n    (`929`_)\n-   Fix missing comma in ``__all__`` list. (`935`_)\n-   Clarify how parameters are named. (`949`_, `1009`_)\n-   Stdout is now automatically set to non blocking. (`954`_)\n-   Do not set options twice. (`962`_)\n-   Move ``fcntl`` import. (`965`_)\n-   Fix Google App Engine ``ImportError``. (`995`_)\n-   Better handling of help text for dynamic default option values.\n    (`996`_)\n-   Fix ``get_winter_size()`` so it correctly returns ``(0,0)``.\n    (`997`_)\n-   Add test case checking for custom param type. (`1001`_)\n-   Allow short width to address cmd formatting. (`1002`_)\n-   Add details about Python version support. (`1004`_)\n-   Added deprecation flag to commands. (`1005`_)\n-   Fixed issues where ``fd`` was undefined. (`1007`_)\n-   Fix formatting for short help. (`1008`_)\n-   Document how ``auto_envvar_prefix`` works with command groups.\n    (`1011`_)\n-   Don&#39;t add newlines by default for progress bars. (`1013`_)\n-   Use Python sorting order for ZSH completions. (`1047`_, `1059`_)\n-   Document that parameter names are converted to lowercase by default.\n    (`1055`_)\n-   Subcommands that are named by the function now automatically have\n    the underscore replaced with a dash. If you register a function\n    named ``my_command`` it becomes ``my-command`` in the command line\n    interface.\n-   Hide hidden commands and options from completion. (`1058`_,\n    `1061`_)\n-   Fix absolute import blocking Click from being vendored into a\n    project on Windows. (`1068`_, `1069`_)\n-   Fix issue where a lowercase ``auto_envvar_prefix`` would not be\n    converted to uppercase. (`1105`_)\n\n.. _202: https://github.com/pallets/click/issues/202\n.. _323: https://github.com/pallets/click/issues/323\n.. _334: https://github.com/pallets/click/issues/334\n.. _393: https://github.com/pallets/click/issues/393\n.. _409: https://github.com/pallets/click/issues/409\n.. _414: https://github.com/pallets/click/pull/414\n.. _423: https://github.com/pallets/click/pull/423\n.. _424: https://github.com/pallets/click/pull/424\n.. _447: https://github.com/pallets/click/issues/447\n.. _487: https://github.com/pallets/click/pull/487\n.. _500: https://github.com/pallets/click/pull/500\n.. _514: https://github.com/pallets/click/issues/514\n.. _533: https://github.com/pallets/click/pull/533\n.. _535: https://github.com/pallets/click/issues/535\n.. _537: https://github.com/pallets/click/issues/537\n.. _538: https://github.com/pallets/click/pull/538\n.. _553: https://github.com/pallets/click/pull/553\n.. _557: https://github.com/pallets/click/pull/557\n.. _568: https://github.com/pallets/click/issues/568\n.. _569: https://github.com/pallets/click/issues/569\n.. _574: https://github.com/pallets/click/issues/574\n.. _583: https://github.com/pallets/click/issues/583\n.. _598: https://github.com/pallets/click/issues/598\n.. _612: https://github.com/pallets/click/pull/612\n.. _616: https://github.com/pallets/click/issues/616\n.. _629: https://github.com/pallets/click/pull/629\n.. _650: https://github.com/pallets/click/pull/650\n.. _651: https://github.com/pallets/click/issues/651\n.. _664: https://github.com/pallets/click/pull/664\n.. _667: https://github.com/pallets/click/issues/667\n.. _675: https://github.com/pallets/click/pull/675\n.. _681: https://github.com/pallets/click/pull/681\n.. _684: https://github.com/pallets/click/pull/684\n.. _703: https://github.com/pallets/click/issues/703\n.. _704: https://github.com/pallets/click/issues/704\n.. _706: https://github.com/pallets/click/pull/706\n.. _709: https://github.com/pallets/click/pull/709\n.. _710: https://github.com/pallets/click/pull/710\n.. _712: https://github.com/pallets/click/pull/712\n.. _719: https://github.com/pallets/click/issues/719\n.. _725: https://github.com/pallets/click/issues/725\n.. _728: https://github.com/pallets/click/pull/728\n.. _739: https://github.com/pallets/click/pull/739\n.. _741: https://github.com/pallets/click/issues/741\n.. _744: https://github.com/pallets/click/issues/744\n.. _754: https://github.com/pallets/click/issues/754\n.. _755: https://github.com/pallets/click/pull/755\n.. _773: https://github.com/pallets/click/pull/773\n.. _774: https://github.com/pallets/click/pull/774\n.. _790: https://github.com/pallets/click/issues/790\n.. _793: https://github.com/pallets/click/issues/793\n.. _794: https://github.com/pallets/click/pull/794\n.. _795: https://github.com/pallets/click/issues/795\n.. _799: https://github.com/pallets/click/pull/799\n.. _801: https://github.com/pallets/click/pull/801\n.. _806: https://github.com/pallets/click/pull/806\n.. _807: https://github.com/pallets/click/pull/807\n.. _809: https://github.com/pallets/click/pull/809\n.. _816: https://github.com/pallets/click/pull/816\n.. _819: https://github.com/pallets/click/pull/819\n.. _821: https://github.com/pallets/click/issues/821\n.. _822: https://github.com/pallets/click/issues/822\n.. _825: https://github.com/pallets/click/issues/825\n.. _830: https://github.com/pallets/click/pull/830\n.. _842: https://github.com/pallets/click/pull/842\n.. _860: https://github.com/pallets/click/issues/860\n.. _862: https://github.com/pallets/click/issues/862\n.. _863: https://github.com/pallets/click/pull/863\n.. _865: https://github.com/pallets/click/pull/865\n.. _866: https://github.com/pallets/click/issues/866\n.. _868: https://github.com/pallets/click/pull/868\n.. _869: https://github.com/pallets/click/pull/869\n.. _873: https://github.com/pallets/click/issues/873\n.. _874: https://github.com/pallets/click/pull/874\n.. _877: https://github.com/pallets/click/pull/877\n.. _878: https://github.com/pallets/click/pull/878\n.. _880: https://github.com/pallets/click/pull/880\n.. _883: https://github.com/pallets/click/pull/883\n.. _887: https://github.com/pallets/click/pull/887\n.. _889: https://github.com/pallets/click/pull/889\n.. _918: https://github.com/pallets/click/pull/918\n.. _919: https://github.com/pallets/click/issues/919\n.. _920: https://github.com/pallets/click/pull/920\n.. _925: https://github.com/pallets/click/issues/925\n.. _926: https://github.com/pallets/click/issues/926\n.. _929: https://github.com/pallets/click/pull/929\n.. _930: https://github.com/pallets/click/pull/930\n.. _935: https://github.com/pallets/click/pull/935\n.. _949: https://github.com/pallets/click/issues/949\n.. _954: https://github.com/pallets/click/pull/954\n.. _962: https://github.com/pallets/click/pull/962\n.. _965: https://github.com/pallets/click/pull/965\n.. _967: https://github.com/pallets/click/pull/967\n.. _976: https://github.com/pallets/click/pull/976\n.. _990: https://github.com/pallets/click/pull/990\n.. _991: https://github.com/pallets/click/pull/991\n.. _993: https://github.com/pallets/click/pull/993\n.. _994: https://github.com/pallets/click/pull/994\n.. _995: https://github.com/pallets/click/pull/995\n.. _996: https://github.com/pallets/click/pull/996\n.. _997: https://github.com/pallets/click/pull/997\n.. _999: https://github.com/pallets/click/pull/999\n.. _1000: https://github.com/pallets/click/pull/1000\n.. _1001: https://github.com/pallets/click/pull/1001\n.. _1002: https://github.com/pallets/click/pull/1002\n.. _1003: https://github.com/pallets/click/pull/1003\n.. _1004: https://github.com/pallets/click/pull/1004\n.. _1005: https://github.com/pallets/click/pull/1005\n.. _1007: https://github.com/pallets/click/pull/1007\n.. _1008: https://github.com/pallets/click/pull/1008\n.. _1009: https://github.com/pallets/click/pull/1009\n.. _1010: https://github.com/pallets/click/pull/1010\n.. _1011: https://github.com/pallets/click/pull/1011\n.. _1012: https://github.com/pallets/click/pull/1012\n.. _1013: https://github.com/pallets/click/pull/1013\n.. _1014: https://github.com/pallets/click/pull/1014\n.. _1016: https://github.com/pallets/click/pull/1016\n.. _1020: https://github.com/pallets/click/pull/1020\n.. _1022: https://github.com/pallets/click/pull/1022\n.. _1027: https://github.com/pallets/click/pull/1027\n.. _1047: https://github.com/pallets/click/pull/1047\n.. _1055: https://github.com/pallets/click/pull/1055\n.. _1058: https://github.com/pallets/click/pull/1058\n.. _1059: https://github.com/pallets/click/pull/1059\n.. _1061: https://github.com/pallets/click/pull/1061\n.. _1068: https://github.com/pallets/click/issues/1068\n.. _1069: https://github.com/pallets/click/pull/1069\n.. _1088: https://github.com/pallets/click/issues/1088\n.. _1091: https://github.com/pallets/click/pull/1091\n.. _1098: https://github.com/pallets/click/pull/1098\n.. _1105: https://github.com/pallets/click/pull/1105\n.. _1106: https://github.com/pallets/click/pull/1106\n.. _1108: https://github.com/pallets/click/pull/1108\n.. _1115: https://github.com/pallets/click/pull/1115\n   ```\n   \n  \n</details>\n\n\n \n\n<details>\n  <summary>Links</summary>\n  \n  - PyPI: https://pypi.org/project/click\n  - Changelog: https://pyup.io/changelogs/click/\n  - Homepage: https://palletsprojects.com/p/click/\n</details>\n\n\n\n\n\n### Update [pyfaidx](https://pypi.org/project/pyfaidx) from **0.5.4.2** to **0.5.5**.\n\n\n<details>\n  <summary>Changelog</summary>\n  \n  \n   ### 0.5.5\n   ```\n   - Added proper BGZF support, fixing 131. Note: this fix requires code present in Biopython 1.73, which is not yet released. If you need this functionality in the mean time, install the biopython development version\n- Enhancement to `faidx` script: allow -v to be specified alongside -g (142). Thanks daler!\n   ```\n   \n  \n</details>\n\n\n \n\n<details>\n  <summary>Links</summary>\n  \n  - PyPI: https://pypi.org/project/pyfaidx\n  - Changelog: https://pyup.io/changelogs/pyfaidx/\n  - Homepage: http://mattshirley.com\n  - Docs: https://pythonhosted.org/pyfaidx/\n</details>\n\n\n\n\n\n### Update [pyparsing](https://pypi.org/project/pyparsing) from **2.2.1** to **2.2.2**.\n\n\n<details>\n  <summary>Changelog</summary>\n  \n  \n   ### 2.2.2\n   ```\n   -------------------------------\n- Fixed bug in SkipTo, if a SkipTo expression that was skipping to\n  an expression that returned a list (such as an And), and the \n  SkipTo was saved as a named result, the named result could be \n  saved as a ParseResults - should always be saved as a string.\n  Issue 28, reported by seron.\n\n- Added simple_unit_tests.py, as a collection of easy-to-follow unit \n  tests for various classes and features of the pyparsing library. \n  Primary intent is more to be instructional than actually rigorous \n  testing. Complex tests can still be added in the unitTests.py file.\n\n- New features added to the Regex class:\n  - optional asGroupList parameter, returns all the capture groups as\n    a list\n  - optional asMatch parameter, returns the raw re.match result\n  - new sub(repl) method, which adds a parse action calling\n    re.sub(pattern, repl, parsed_result). Simplifies creating \n    Regex expressions to be used with transformString. Like re.sub,\n    repl may be an ordinary string (similar to using pyparsing&#39;s \n    replaceWith), or may contain references to capture groups by group \n    number, or may be a callable that takes an re match group and \n    returns a string.\n    \n    For instance:\n        expr = pp.Regex(r&quot;([Hh]\\d):\\s*(.*)&quot;).sub(r&quot;&lt;\\1&gt;\\2&lt;/\\1&gt;&quot;)\n        expr.transformString(&quot;h1: This is the title&quot;)\n\n    will return\n        &lt;h1&gt;This is the title&lt;/h1&gt;\n\n- Fixed omission of LICENSE file in source tarball, also added \n  CODE_OF_CONDUCT.md per GitHub community standards.\n   ```\n   \n  \n</details>\n\n\n \n\n<details>\n  <summary>Links</summary>\n  \n  - PyPI: https://pypi.org/project/pyparsing\n  - Changelog: https://pyup.io/changelogs/pyparsing/\n  - Repo: https://github.com/pyparsing/pyparsing/\n  - Docs: https://pythonhosted.org/pyparsing/\n</details>\n\n\n\n\n\n### Update [biopython](https://pypi.org/project/biopython) from **1.72** to **1.72**.\n\n\n<details>\n  <summary>Changelog</summary>\n  \n  \n   ### 1.51\n   ```\n   the OBF mailing lists with EMBOSS, BioPerl, BioJava and BioRuby for inter-\nconversion and the valid score range for each FASTQ variant. This means\nSolexa FASTQ scores can be from -5 to 62 (format name &quot;fastq-solexa&quot; in\nBio.SeqIO), Illumina 1.3+ FASTQ files have PHRED scores from 0 to 62 (format\nname &quot;fastq-illumina&quot;), and Sanger FASTQ files have PHRED scores from 0 to\n93 (format name &quot;fastq&quot; or &quot;fastq-sanger&quot;).\n\nBio.Sequencing.Phd has been updated, for example to cope with missing peak\npositions. The &quot;phd&quot; support in Bio.SeqIO has also been updated to record\nthe PHRED qualities (and peak positions) in the SeqRecord&#39;s per-letter\nannotation. This allows conversion of PHD files into FASTQ or QUAL which may\nbe useful for meta-assembly.\n\nSee the notes below for the Biopython 1.50 beta release for changes since\nBiopython 1.49 was released. This includes dropping support for Python 2.3,\nremoving our deprecated parsing infrastructure (Martel and Bio.Mindy), and\nhence removing any dependence on mxTextTools.\n\nAdditionally, since the beta, a number of small bugs have been fixed, and\nthere have been further additions to the test suite and documentation.\n\n\nJune 23, 2009: Biopython 1.51 beta released.\n============================================\n\nBiopython no longer supports Python 2.3.  Currently we support Python 2.4,\n2.5 and 2.6.\n\nOur deprecated parsing infrastructure (Martel and Bio.Mindy) has been\nremoved.  This means Biopython no longer has any dependence on mxTextTools.\n\nA few cosmetic issues in GenomeDiagram with arrow sigils and labels on\ncircular diagrams have been fixed.\n\nBio.SeqIO will now write GenBank files with the feature table (previously\nomitted), and a couple of obscure errors parsing ambiguous locations have\nbeen fixed.\n\nBio.SeqIO can now read and write Illumina 1.3+ style FASTQ files (which use\nPHRED quality scores with an ASCII offset of 64) under the format name\n&quot;fastq-illumina&quot;. Biopython 1.50 supported just &quot;fastq&quot; (the original Sanger\nstyle FASTQ files using PHRED scores with an ASCII offset of 33), and\n&quot;fastq-solexa&quot; (the original Solexa/Illumina FASTQ format variant holding\nSolexa scores with an ASCII offset of 64) .\n\nFor parsing the &quot;swiss&quot; format, Bio.SeqIO now uses the new Bio.SwissProt\nparser, making it about twice as fast as in Biopython 1.50, where the older\nnow deprecated Bio.SwissProt.SProt was used. There should be no functional\ndifferences as a result of this change.\n\nOur command line wrapper objects have been updated to support accessing\nparameters via python properties, and setting of parameters at initiation\nwith keyword arguments.  Additionally Cymon Cox has contributed several new\nmultiple alignment wrappers under Bio.Align.Applications.\n\nA few more issues with Biopython&#39;s BioSQL support have been fixed (mostly by\nCymon Cox). In particular, the default PostgreSQL schema includes some rules\nintended for BioPerl support only, which were causing problems in Biopython\n(see BioSQL bug 2839).\n\nThere have also been additions to the tutorial, such as the new alignment\nwrappers, with a whole chapter for the SeqRecord object. We have also added\nto the unit test coverage.\n\n\nApril 20, 2009: Biopython 1.50 released.\n========================================\n\nSee the notes below for the Biopython 1.50 beta release for more details,\nbut the highlights are:\n\n* The SeqRecord supports slicing and per-letter-annotation\n* Bio.SeqIO can read and write FASTQ and QUAL files\n* Bio.Seq now has an UnknownSeq object\n* GenomeDiagram has been integrated into Biopython\n* New module Bio.Motif will later replace Bio.AlignAce and Bio.MEME\n* This will be the final release to support Python 2.3\n* This will be the final release with Martel and Bio.Mindy\n\nSince the 1.50 beta release:\n\n* The NCBI&#39;s Entrez EFetch no longer supports rettype=&quot;genbank&quot;\n  and &quot;gb&quot; (or &quot;gp&quot;) should be used instead.\n* Bio.SeqIO now supports &quot;gb&quot; as an alias for &quot;genbank&quot;.\n* The Seq object now has string-like startswith and endswith methods\n* Bio.Blast.NCBIXML now has a read function for single record files\n* A few more unit tests were added\n* More documentation\n\n\nApril 3, 2009: Biopython 1.50 beta released.\n============================================\n\nThe SeqRecord object has a new dictionary attribute, letter_annotations,\nwhich is for holding per-letter-annotation information like sequence\nquality scores or secondary structure predictions.  As part of this work,\nthe SeqRecord object can now be sliced to give a new SeqRecord covering\njust part of the sequence.  This will slice the per-letter-annotation to\nmatch, and will also include any SeqFeature objects as appropriate.\n\nBio.SeqIO can now read and write FASTQ and QUAL quality files using PHRED\nquality scores (Sanger style, also used for Roche 454 sequencing), and FASTQ\nfiles using Solexa/Illumina quality scores.\n\nThe Bio.Seq module now has an UnknownSeq object, used for when we have a\nsequence of known length, but unknown content.  This is used in parsing\nGenBank and EMBL files where the sequence may not be present (e.g. for a\ncontig record) and when parsing QUAL files (which don&#39;t have the sequence)\n\nGenomeDiagram by Leighton Pritchard has been integrated into Biopython as\nthe Bio.Graphics.GenomeDiagram module  If you use this code, please cite the\npublication Pritchard et al. (2006), Bioinformatics 22 616-617.  Note that\nlike Bio.Graphics, this requires the ReportLab python library.\n\nA new module Bio.Motif has been added, which is intended to replace the\nexisting Bio.AlignAce and Bio.MEME modules.\n\nThe set of NCBI DTD files included with Bio.Entrez has been updated with the\nrevised files the NCBI introduced on 1 Jan 2009.\n\nMinor fix to BioSQL for retrieving references and comments.\n\nBio.SwissProt has a new faster parser which will be replacing the older\nslower code in Bio.SwissProt.SProt (which we expect to deprecate in the next\nrelease).\n\nWe&#39;ve also made some changes to our test framework, which is now given a\nwhole chapter in the tutorial.  This intended to help new developers or\ncontributors wanting to improve our unit test coverage.\n\n\nNovember 21, 2008: Biopython 1.49 released.\n===========================================\n\nSee the notes below for the Biopython 1.49 beta release for more details,\nbut the highlights are:\n\n* Biopython has transitioned from Numeric to NumPy\n* Martel and Bio.Mindy are now deprecated\n\nSince the 1.49 beta release:\n\n* A couple of NumPy issues have been resolved\n* Further small improvements to BioSQL\n* Bio.PopGen.SimCoal should now work on Windows\n* A few more unit tests were added\n\n\nNovember 7, 2008: Biopython 1.49 beta released.\n===============================================\n\nBiopython has transitioned from Numeric to NumPy.  Please move to NumPy.\n\nA number of small changes have been made to support Python 2.6 (mostly\navoiding deprecated functionality), and further small changes have been\nmade for better compatibility with Python 3 (this work is still ongoing).\nHowever, we intend to support Python 2.3 for only a couple more releases.\n\nAs part of the Numeric to NumPy migration, Bio.KDTree has been rewritten in\nC instead of C++ which therefore simplifies building Biopython from source.\n\nMartel and Bio.Mindy are now considered to be deprecated, meaning mxTextTools\nis no longer required to use Biopython.  See the DEPRECATED file for details\nof other deprecations.\n\nThe Seq object now supports more string like methods (gaining find, rfind,\nsplit, rsplit, strip, lstrip and rstrip in addition to previously supported\nmethods like count).  Also, biological methods transcribe, back_transcribe\nand translate have been added, joining the pre-existing reverse_complement\nand complement methods.  Together these changes allow a more object\norientated programming style using the Seq object.\n\nThe behaviour of the Bio.Seq module&#39;s translate function has changed so that\nambiguous codons which could be a stop codon like &quot;TAN&quot; or &quot;NNN&quot; are now\ntranslated as &quot;X&quot; (consistent with EMBOSS and BioPerl - Biopython previously\nraised an exception), and a bug was fixed so that invalid codons (like &quot;A-T&quot;)\nnow raise an exception (previously these were translated as stop codons).\n\nBioSQL had a few bugs fixed, and can now optionally fetch the NCBI taxonomy\non demand when loading sequences (via Bio.Entrez) allowing you to populate\nthe taxon/taxon_name tables gradually.  This has been tested in combination\nwith the BioSQL load_ncbi_taxonomy.pl script used to populate or update the\ntaxon/taxon_name tables.  BioSQL should also now work with the psycopg2\ndriver for PostgreSQL as well as the older psycopg driver.\n\nThe PDB and PopGen sections of the Tutorial have been promoted to full\nchapters, and a new chapter has been added on supervised learning methods\nlike logistic regression.  The &quot;Cookbook&quot; section now has a few graphical\nexamples using Biopython to calculate sequence properties, and matplotlib\n(pylab) to plot them.\n\nThe input functions in Bio.SeqIO and Bio.AlignIO now accept an optional\nargument to specify the expected sequence alphabet.\n\nThe somewhat quirky unit test GUI has been removed, the unit tests are now\nrun via the command line by default.\n\n\nSeptember 8, 2008: Biopython 1.48 released.\n===========================================\n\nThe SeqRecord and Alignment objects have a new method to format the object as\na string in a requested file format (handled via Bio.SeqIO and Bio.AlignIO).\n\nAdditional file formats supported in Bio.SeqIO and Bio.AlignIO:\n\n- reading and writing &quot;tab&quot; format (simple tab separated)\n- writing &quot;nexus&quot; files.\n- reading &quot;pir&quot; files (NBRF/PIR)\n- basic support for writing &quot;genbank&quot; files (GenBank plain text)\n\nFixed some problems reading Clustal alignments (introduced in Biopython 1.46\nwhen consolidating Bio.AlignIO and Bio.Clustalw).\n\nUpdates to the Bio.Sequencing parsers.\n\nBio.PubMed and the online code in Bio.GenBank are now considered obsolete,\nand we intend to deprecate them after the next release. For accessing PubMed\nand GenBank, please use Bio.Entrez instead.\n\nBio.Fasta is now considered to be obsolete, please use Bio.SeqIO instead. We\ndo intend to deprecate this module eventually, however, for several years\nthis was the primary FASTA parsing module in Biopython and is likely to be in\nuse in many existing scripts.\n\nMartel and Bio.Mindy are now considered to be obsolete, and are likely to be\ndeprecated and removed in a future release.\n\nIn addition a number of other modules have been deprecated, including:\nBio.MetaTool, Bio.EUtils, Bio.Saf, Bio.NBRF, and Bio.IntelliGenetics\nSee the DEPRECATED file for full details.\n\n\nJuly 5, 2008: Biopython 1.47 released.\n======================================\n\nImproved handling of ambiguous nucleotides in Bio.Seq.Translate().\nBetter handling of stop codons in the alphabet from a translation.\nFixed some codon tables (problem introduced in Biopython 1.46).\n\nUpdated Nexus file handling.\n\nFixed a bug in Bio.Cluster potentially causing segfaults in the\nsingle-linkage hierarchical clustering library.\n\nAdded some DTDs to be able to parse EFetch results from the\nnucleotide database.\n\nAdded IntelliGenetics/MASE parsing to Bio.SeqIO (as the &quot;ig&quot; format).\n\n\nJune 29, 2008: Biopython 1.46 released.\n=======================================\n\nBio.Entrez now has several Entrez format XML parsers, and a chapter\nin the tutorial.\n\nAddition of new Bio.AlignIO module for working with sequence alignments\nin the style introduced with Bio.SeqIO in recent releases, with a whole\nchapter in the tutorial.\n\nA problem parsing certain EMBL files was fixed.\n\nSeveral minor fixes were made to the NCBI BLAST XML parser, including\nsupport for the online version 2.2.18+ introduced in May 2008.\n\nThe NCBIWWW.qblast() function now allows other programs (blastx, tblastn,\ntblastx) in addition to just blastn and blastp.\n\nBio.EUtils has been updated to explicitly enforce the NCBI&#39;s rule of at\nmost one query every 3 seconds, rather than assuming the user would obey\nthis.\n\nIterators in Bio.Medline, Bio.SCOP, Bio.Prosite, Bio.Prosite.Prodoc,\nBio.SwissProt, and others to make them more generally usable.\n\nPhylip export added to Bio.Nexus.\n\nImproved handling of ambiguous nucleotides and stop codons in\nBio.Seq.Translate (plus introduced a regression fixed in Biopython 1.47).\n\n\nMarch 22, 2008: Biopython 1.45 released.\n========================================\n\nThe Seq and MutableSeq objects act more like python strings, in particular\nstr(object) now returns the full sequence as a plain string.  The existing\ntostring() method is preserved for backwards compatibility.\n\nBioSQL has had some bugs fixed, and has an additional unit test which loads\nrecords into a database using Bio.SeqIO and then checks the records can be\nretrieved correctly.  The DBSeq and DBSeqRecord classes now subclass the\nSeq and SeqRecord classes, which provides more functionality.\n\nThe modules under Bio.WWW are being deprecated.\nFunctionality in Bio.WWW.NCBI, Bio.WWW.SCOP, Bio.WWW.InterPro and\nBio.WWW.ExPASy is now available from Bio.Entrez, Bio.SCOP, Bio.InterPro and\nBio.ExPASy instead. Bio.Entrez was used to fix a nasty bug in Bio.GenBank.\n\nTiago Antao has included more functionality in the Population Genetics\nmodule, Bio.PopGen.\n\nThe Bio.Cluster module has been updated to be more consistent with other\nBiopython code.\n\nThe tutorial has been updated, including devoting a whole chapter to\nSwiss-Prot, Prosite, Prodoc, and ExPASy. There is also a new chapter on\nBio.Entrez.\n\nBio.biblio was deprecated.\n\n\nOctober 28, 2007: Biopython 1.44 released.\n==========================================\n\nNOTE: This release includes some rather drastic code changes, which were\nnecessary to get Biopython to work with the new release of mxTextTools.\n\nThe (reverse)complement functions in Bio.Seq support ambiguous nucleotides.\n\nBio.Kabat, which was previously deprecated, is now removed from Biopython.\n\nBio.MarkupEditor was deprecated, as it does not appear to have any users.\n\nBio.Blast.NCBI.qblast() updated with more URL options, thanks to a patch\nfrom Chang Soon Ong.\n\nSeveral fixes to the Blast parser.\n\nThe deprecated Bio.Blast.NCBIWWW functions blast and blasturl were removed.\n\nThe standalone Blast functions blastall, blastpgp now create XML output by\ndefault.\n\nBio.SeqIO.FASTA and Bio.SeqIO.generic have been deprecated in favour of\nthe new Bio.SeqIO module.\n\nBio.FormatIO has been removed (a gradual deprecation was not possible).\nPlease look at Bio.SeqIO for sequence input/output instead.\n\nFix for a bug in Bio.Cluster, which caused kcluster() to hang on some platforms.\n\nBio.expressions has been deprecated.\n\nBio.SeqUtils.CheckSum created, including new methods from Sebastian Bassi,\nand functions crc32 and crc64 which were moved from Bio/crc.py.\nBio.crc is now deprecated. Bio.lcc was updated and moved to Bio.SeqUtils.lcc.\n\nBio.SwissProt parser updated to cope with recent file format updates.\n\nBio.Fasta, Bio.KEGG and Bio.Geo updated to pure python parsers which\ndon&#39;t rely on Martel.\n\nNumerous fixes in the Genbank parser.\n\nSeveral fixes in Bio.Nexus.\n\nBio.MultiProc and Bio.Medline.NLMMedlineXML were deprecating, as they failed\non some platforms, and seemed to have no users. Deprecated concurrent\nbehavior in Bio.config.DBRegistry and timeouts in Bio.dbdefs.swissprot,\nwhich relies on Bio.MultiProc.\n\nTiago Antao has started work on a Population Genetics module, Bio.PopGen\n\nUpdates to the tutorial, including giving Bio.Seq and Bio.SeqIO a whole\nchapter each.\n\n\nMarch 17, 2007: Biopython 1.43 released.\n========================================\n\nNew Bio.SeqIO module for reading and writing biological sequence files\nin various formats, based on SeqRecord objects.  This includes a new fasta\nparser which is much faster than Bio.Fasta, particularly for larger files.\nEasier to use, too.\n\nVarious improvements in Bio.SeqRecord.\n\nRunning Blast using Bio.Blast.NCBIStandalone now generates output in XML\nformat by default.\nThe new function Bio.Blast.NCBIXML.parse can parse multiple Blast records\nin XML format.\n\nBio.Cluster no longer uses ranlib, but uses its own random number generator\ninstead. Some modifications to make Bio.Cluster more compatible with the new\nNumPy (we&#39;re not quite there yet though).\n\nNew Bio.UniGene parser.\n\nNumerous improvements in Bio.PDB.\n\nBug fixes in Bio.SwissProt, BioSQL, Bio.Nexus, and other modules.\n\nFaster parsing of large GenBank files.\n\nNew EMBL parser under Bio.GenBank and also integrated into (new) Bio.SeqIO\n\nCompilation of KDTree (C++ code) is optional (setup.py asks the user if it\nshould be compiled). For the Windows installer, C++ code is now included.\n\nNominating Bio.Kabat for removal.\n\nBelieve it or not, even the documentation was updated.\n\n\nJuly 16, 2006: Biopython 1.42 released.\n=======================================\n\nBio.GenBank: New parser by Peter, which doesn&#39;t rely on Martel.\n\nNumerous updates in Bio.Nexus and Bio.Geo.\n\nBio.Cluster became (somewhat) object-oriented.\n\nLots of bug fixes, and updates to the documentation.\n\n\nOctober 28, 2005: Biopython 1.41 released.\n==========================================\n\nMajor changes:\n\nNEW: Bio.MEME -- thanks to Jason Hackney\n\nAdded transcribe, translate, and reverse_complement functions to Bio.Seq that\nwork both on Seq objects and plain strings.\n\nMajor code optimization in cpairwise2module.\n\nCompareACE support added to AlignAce.\n\nUpdates to Blast parsers in Bio.Blast, in particular use of the XML parser\nin NCBIXML contributed by Bertrand Frottier, and the BLAT parser by Yair\nBenita.\n\nPairwise single-linkage hierarchical clustering in Bio.Cluster became much\nfaster and memory-efficient, allowing clustering of large data sets.\n\nBio.Emboss: Added command lines for einverted and palindrome.\n\nBio.Nexus: Added support for StringIO objects.\n\nNumerous updates in Bio.PDB.\n\nLots of fixes in the documentation.\n\nMarch 29, 2005: MEME parser added. Thanks to Jason Hackney\n\n\nFeb 18, 2005: Biopython 1.40 beta\n=================================\nMajor Changes since v1.30. For a full list of changes please see the CVS\n\nIMPORTANT: Biopython now works with Python version &gt;= 2.3\n\nNEW: Bio.Nexus -- thanks to Frank Kauff\nBio.Nexus is a Nexus file parser. Nexus is a common format for phylogenetic trees.\n\nNEW: CAPS module -- Thanks to Jonathan Taylor.\n\nNEW: Restriction enzyme package contributed by Frederic Sohm. This includes classes for\nmanipulating enzymes, updating from Rebase, as well as documentation and Tests.\n\nCHANGED: Bio.PDB -- thanks to Thomas Hamelryck.\n\n- Added atom serial number.\n- Epydoc style documentation.\n- Added secondary structure support (through DSSP).\n- Added Accessible Surface Area support (through DSSP).\n- Added Residue Depth support (through MSMS).\n- Added Half Sphere Exposure.\n- Added Fragment classification of the protein backbone (see Kolodny et al.,\n- JMB, 2002).\n- Corrected problem on Windows with PDBList (thanks to Matt Dimmic)\n- Added StructureAlignment module to superimpose structures based on a FASTA\n  sequence alignment.\n- Various additions to Polypeptide.\n- Various bug corrections in Vector.\n- Lots of smaller bug corrections and additional features\n\nCHANGED: MutableSeq -- thanks to Michiel De Hoon\nAdded the functions &#39;complement&#39; and &#39;reverse_complement&#39; to Bio.Seq&#39;s Seq and\nMutableSeq objects. Similar functions previously existed in various locations\nin BioPython:\n\n- forward_complement, reverse_complement in Bio.GFF.easy\n- complement, antiparallel in Bio.SeqUtils\n\nThese functions have now been deprecated, and will generate a DeprecationWarning\nwhen used.\nThe functions complement and reverse_complement, when applied to a Seq object,\nwill return a new Seq object. The same function applied to a MutableSeq object\nwill modify the MutableSeq object itself, and don&#39;t return anything.\n\n\n\nMay 14, 2004: Biopython 1.30\n============================\n\n- Affy package added for dealing with Affymetrix cel files -- thanks to Harry\n  Zuzan.\n- Added code for parsing Blast XML output -- thanks to Bertrand Frottier.\n- Added code for parsing Compass output -- thanks to James Casbon.\n- New melting temperature calculation module -- thanks to Sebastian Bassi.\n- Added lowess function for non-parameteric regression -- thanks to Michiel.\n- Reduced protein alphabet supported added -- thanks to Iddo.\n\n- Added documentation for Logistic Regression and Bio.PDB -- thanks to Michiel\n  and Thomas.\n- Documentation added for converting between file formats.\n- Updates to install documentation for non-root users -- thanks to Jakob\n  Fredslund.\n- epydoc now used for automatic generation of documentation.\n\n- Fasta parser updated to use Martel for parsing and indexing, allowing better\n  speed and dealing with large data files.\n- Updated to Registry code. Now &#39;from Bio import db&#39; gives you a number of new\n  retrieval options, including embl, fasta, genbak, interpro, prodoc and swissprot.\n- GenBank parser uses new Martel format. GenBank retrieval now uses EUtils instead\n  of the old non-working entrez scripts. GenBank indexing uses standard Mindy\n  indexing. Fix for valueless qualifiers in feature keys -- thanks to Leighton\n  Pritchard.\n- Numerous updated to Bio.PDB modules -- thanks to Thomas. PDB can now parse headers\n  -- thanks to Kristian Rother.\n- Updates to the Ace parser -- thanks to Frank Kauff and Leighton Pritchard.\n\n- Added pgdb (PyGreSQL) support to BioSQL -- thanks to Marc Colosimo.\n- Fix problems with using py2exe and Biopython -- thanks to Michael Cariaso.\n- PSIBlast parser fixes -- thanks to Jer-Yee John Chuang and James Casbon.\n- Fix to NCBIWWW retrieval so that HTML results are returned correctly.\n- Fix to Clustalw to handle question marks in title names -- thanks to Ashleigh\n  Smythe.\n- Fix to NBRF parsing to it accepts files produced by Clustalw -- thanks to\n  Ashleigh Smythe.\n- Fixes to the Enyzme module -- thanks to Marc Colosimo.\n- Fix for bugs in SeqUtils -- thanks to Frank Kauff.\n- Fix for optional hsps in ncbiblast Martel format -- thanks to Heiko.\n- Fix to Fasta parsing to allow  comment lines -- thanks to Karl Diedrich.\n- Updates to the C clustering library -- thanks to Michiel.\n- Fixes for breakage in the SCOP module and addition of regression tests to\n  framework -- thanks to Gavin.\n- Various fixes to Bio.Wise -- thanks to Michael.\n- Fix for bug in FastaReader -- thanks to Micheal.\n- Fix EUtils bug where efetch would only return 500 sequences.\n- Updates for Emboss commandlines, water and tranalign.\n- Fixes to the FormatIO system of file conversion.\n\n- C++ code (KDTree, Affy) now compiled by default on most platforms -- thanks to\n  Michael for some nice distutils hacks and many people for testing.\n- Deprecated Bio.sequtils -- use Bio.SeqUtils instead.\n- Deprecated Bio.SVM -- use libsvm instead.\n- Deprecated Bio.kMeans and Bio.xkMeans -- use Bio.cluster instead.\n- Deprecated RecordFile -- doesn&#39;t appear to be finished code.\n\n\nFeb 16, 2004: Biopython 1.24\n============================\n\n- New parsers for Phred and Ace format files -- thanks to Frank Kauff\n- New Code for dealing with NMR data -- thanks to Bob Bussell\n- New SeqUtils modules for codon usage, isoelectric points and other\n  protein properties -- thanks to Yair Benita\n- New code for dealing with Wise contributed by Michael\n- EZ-Retrieve sequence retrieval now supported thanks to Jeff\n- Bio.Cluster updated along with documentation by Michiel\n- BioSQL fixed so it now works with the current SQL schema -- thanks to Yves\n  Bastide for patches\n- Patches to Bio/__init__ to make it compatible with py2exe -- thanks to\n  Leighton Pritchard\n- Added __iter__ to all Biopython Iterators to make them Python 2.2 compatible\n- Fixes to NCBIWWW for retrieving from NCBI -- thanks to Chris Wroe\n- Retrieval of multiple alignment objects from BLAST records -- thanks to\n  James Casbon\n- Fixes to GenBank format for new tags by Peter\n- Parsing fixes in clustalw parsed -- thanks to Greg Singer and Iddo\n- Fasta Indexes can have a specified filename -- thanks to Chunlei Wu\n- Fix to Prosite parser -- thanks to Mike Liang\n- Fix in GenBank parsing -- mRNAs now get strand information\n\n\nOct 18, 2003: Biopython 1.23\n============================\n\n- Fixed distribution of files in Bio/Cluster\n- Now distributing Bio/KDTree/_KDTree.swig.C\n- minor updates in installation code\n- added mmCIF support for PDB files\n\n\nOct 9, 2003: Biopython 1.22\n===========================\n\n- Added Peter Slicker&#39;s patches for speeding up modules under Python 2.3\n- Fixed Martel installation.\n- Does not install Bio.Cluster without Numeric.\n- Distribute EUtils DTDs.\n- Yves Bastide patched NCBIStandalone.Iterator to be Python 2.0 iterator\n- Ashleigh&#39;s string coersion fixes in Clustalw.\n- Yair Benita added precision to the protein molecular weights.\n- Bartek updated AlignAce.Parser and added Motif.sim method\n- bug fixes in Michiel De Hoon&#39;s clustering library\n- Iddo&#39;s bug fixes to Bio.Enzyme and new RecordConsumer\n- Guido Draheim added patches for fixing import path to xbb scripts\n- regression tests updated to be Python 2.3 compatible\n- GenBank.NCBIDictionary is smarter about guessing the format\n\n\nJul 28, 2003: Biopython 1.21\n============================\n\n- Martel added back into the released package\n- new AlignACE module by Bartek Wilczynski\n- Andreas Kuntzagk fix for GenBank Iterator on empty files\n\n\nJul 27, 2003: Biopython 1.20\n============================\n\n- added Andrew Dalke&#39;s EUtils library\n- added Michiel de Hoon&#39;s gene expression analysis package\n- updates to setup code, now smarter about dependencies\n- updates to test suite, now smarter about code that is imported\n- Michael Hoffman&#39;s fixes to DocSQL\n- syntax fixes in triemodule.c to compile on SGI, Python 2.1 compatible\n- updates in NCBIStandalone, short query error\n- Sebastian Bassi submitted code to calculate LCC complexity\n- Greg Kettler&#39;s NCBIStandalone fix for long query lengths\n- slew of miscellaneous fixes from George Paci\n- miscellaneous cleanups and updates from Andreas Kuntzagk\n- Peter Bienstman&#39;s fixes to Genbank code -- now parses whole database\n- Kayte Lindner&#39;s LocusLink package\n- miscellaneous speedups and code cleanup in ParserSupport by Brad Chapman\n- miscellaneous BLAST fixes and updates\n- Iddo added new code to parse BLAST table output format\n- Karl Diedrich&#39;s patch to read T_Coffee files\n- Larry Heisler&#39;s fix for primer3 output\n- Bio.Medline now uses proper iterator objects\n- copen now handles SIGTERM correctly\n- small bugfixes and updates in Thomas Hamelryck&#39;s PDB package\n- bugfixes and updates to SeqIO.FASTA reader\n- updates to Registry system, conforms to 2003 hackathon OBDA spec\n- Yu Huang patch to support tblastn in wublast expression\n\n\nDec 17, 2002: Biopython 1.10\n============================\n\n- Python requirement bumped up to 2.2\n- hierarchy reorg, many things moved upwards into Bio namespace\n- pairwise2 replaces fastpairwise and pairwise\n- removed deprecated Sequence.py package\n- minor bug fix in File.SGMLStripper\n- added Scripts/debug/debug_blast_parser.py to diagnose blast parsing errors\n- IPI supported by SwissProt/SProt.py parser\n- large speedup for kmeans\n- new registry framework for generic access to databases and parsers\n- small bug fix in stringfns.split\n- scripts that access NCBI moved over to new EUtils system\n- new crc module\n- biblio.py supports the EBI Bibliographic database\n- new CDD parser\n- new Ndb parser\n- new ECell parser\n- new Geo parser\n- access to GFF databases\n- new KDTree data structure\n- new LocusLink parser\n- new MarkovModel algorithm\n- new Saf parser\n- miscellaneous sequence handling functions in sequtils\n- new SVDSuperimpose algorithm\n   ```\n   \n  \n  \n   ### 1.00a4\n   ```\n   =============================\n\n- minor bug fix in NCBIStandalone.blastall\n- optimization in dynamic programming code\n- new modules for logistic regression and maximum entropy\n- minor bug fix in ParserSupport\n- minor bug fixes in SCOP package\n- minor updates in the kMeans cluster selection code\n- minor bug fixes in SubsMat code\n- support for XML-formatted MEDLINE files\n- added MultiProc.run to simplify splitting code across processors\n- listfns.items now supports lists with unhashable items\n- new data type for pathways\n- new support for intelligenetics format\n- new support for metatool format\n- new support for NBRF format\n- new support for generalized launching of applications\n- new support for genetic algorithms\n- minor bug fixes in GenBank parsing\n- new support for Primer in the Emboss package\n- new support for chromosome graphics\n- new support for HMMs\n- new support for NeuralNetwork\n- slew of Martel fixes (see Martel docs)\n   ```\n   \n  \n  \n   ### 1.00a3\n   ```\n   =============================\n\n- added package to support KEGG\n- added sequtils module for computations on sequences\n- added pairwise sequence alignment algorithm\n- major bug fixes in UndoHandle\n- format updates in PubMed\n- Tk interface to kMeans clustering\n   ```\n   \n  \n  \n   ### 1.00a2\n   ```\n   =============================\n\n- deprecated old regression testing frameworks\n- deprecated Sequence.py\n- Swiss-Prot parser bug fixes\n- GenBank parser bug fixes\n- Can now output GenBank format\n- can now download many sequences at a time from GenBank\n- kMeans clustering algorithm\n- Kabat format now supported\n- FSSP format now supported\n- more functionality for alignment code\n- SubsMat bug fixes and updates\n- fixed memory leak in listfns bug fixes\n- Martel bundled and part of the install procedure\n- Medline.Parser bug fixes\n- PubMed.download_many handles broken IDs better\n\n\nMar 3, 2001: Biopython 1.00a1\n=============================\n\n- Refactoring of modules.  X/X.py moved to X/__init__.py.\n- Can search sequences for Prosite patterns at ExPASy\n- Can do BLAST searches against stable URL at NCBI\n- Prosite Pattern bug fixes\n- GenBank parser\n- Complete Seq and SeqFeatures framework\n- distutils cleanup\n- compile warning cleanups\n- support for UniGene\n- code for working with substitution matrices\n- Tools.MultiProc package for rudimentary multiprocessing stuff\n\n\nNov 10, 2000: Biopython 0.90d04\n===============================\n\n- Added support for multiple alignments, ClustalW\n- BLAST updates, bug fixes, and BlastErrorParser\n- Fixes for PSI-BLAST in master-slave mode\n- Minor update in stringfns, split separators can be negated\n- Added download_many function to PubMed\n- xbbtools updates\n- Prodoc parser now accepts a copyright at the end of a record\n- Swiss-Prot parser now handles taxonomy ID tag\n\n\nSept 6, 2000: Biopython 0.90d03\n===============================\n\n- Blast updates:\n\n  - bug fixes in NCBIStandalone, NCBIWWW\n  - some __str__ methods in Record.py implemented (incomplete)\n\n- Tests:\n\n  - new BLAST regression tests\n  - prosite tests fixed\n\n- New parsers for Rebase, Gobase\n- pure python implementation of C-based tools\n- Thomas Sicheritz-Ponten&#39;s xbbtools\n- can now generate documentation from docstrings using HappyDoc\n\n\nAug17-18, 2000: Bioinformatics Open Source Conference 2000\n==========================================================\n\nWe had a very good Birds-of-a-Feather meeting:\nhttp://www.biopython.org/pipermail/biopython/2000-August/000360.html\n\n\nAug 2, 2000: Biopython 0.90d02 is released.\n===========================================\n\n- Blast updates:\n  - now works with v2.0.14\n  - HSP.identities and HSP.positives now tuples\n  - HSP.gaps added\n- SCOP updates:\n  - Lin.Iterator now works with release 50\n- Starting a tutorial\n- New regression tests for Prodoc\n\n\nJuly 6, 2000: Biopython 0.90d01 is released.\n============================================\n\n\nFebruary 8, 2000: Anonymous CVS made available.\n===============================================\n\n\nAugust 1999: Biopython project founded.\n=======================================\n\nCall for Participation sent out to relevant mailing lists, news\ngroups.\n\nThe Biopython Project (http://www.biopython.org/) is a new open\ncollaborative effort to develop freely available Python libraries and\napplications that address the needs of current and future work in\nbioinformatics, including sequence analysis, structural biology,\npathways, expression data, etc.  When available, the source code will\nbe released as open source (http://www.biopython.org/License.shtml)\nunder terms similar to Python.\n\nThis is a Call for Participation for interested people to join the\nproject.  We are hoping to attract people from a diverse set of\nbackgrounds to help with code development, site maintenance,\nscientific discussion, etc.  This project is open to everyone.  If\nyou&#39;re interested, please visit the web page, join the biopython\nmailing list, and let us know what you think!\n\nJeffrey Chang &lt;jchangsmi.stanford.edu&gt;\nAndrew Dalke &lt;dalkebioreason.com&gt;\n   ```\n   \n  \n</details>\n\n\n \n\n<details>\n  <summary>Links</summary>\n  \n  - PyPI: https://pypi.org/project/biopython\n  - Changelog: https://pyup.io/changelogs/biopython/\n  - Homepage: https://biopython.org/\n</details>\n\n\n\n\n\n### Update [click_plugins](https://pypi.org/project/click_plugins) from **1.0.4** to **1.0.4**.\n\n\n<details>\n  <summary>Changelog</summary>\n  \n  \n   ### 1.0.4\n   ```\n   ------------------\n\n- Preemptive fix for a breaking change in Click v7.  CLI command names generated from functions with underscores will have dashes instead of underscores.  See https://github.com/click-contrib/click-plugins/issues/19.\n   ```\n   \n  \n  \n   ### 1.0.3\n   ```\n   ------------------\n\n- Include tests in MANIFEST.in - See further discussion in 8\n   ```\n   \n  \n  \n   ### 1.0.2\n   ```\n   ------------------\n\n- General packaging and Travis-CI improvements.\n- Don&#39;t include tests in MANIFEST.in - 8\n   ```\n   \n  \n  \n   ### 1.0.1\n   ```\n   ------------------\n\n- Fixed a typo in an error message - 5\n   ```\n   \n  \n  \n   ### 1.0\n   ```\n   ----------------\n\n- Initial release.\n   ```\n   \n  \n</details>\n\n\n \n\n<details>\n  <summary>Links</summary>\n  \n  - PyPI: https://pypi.org/project/click-plugins\n  - Changelog: https://pyup.io/changelogs/click-plugins/\n  - Repo: https://github.com/click-contrib/click-plugins\n</details>\n\n\n\n\n\n### Update [coverage](https://pypi.org/project/coverage) from **4.5.1** to **4.5.1**.\n\n\n<details>\n  <summary>Changelog</summary>\n  \n  \n   ### 4.5.1\n   ```\n   ----------------------------\n\n- Now that 4.5 properly separated the ``[run] omit`` and ``[report] omit``\n  settings, an old bug has become apparent.  If you specified a package name\n  for ``[run] source``, then omit patterns weren&#39;t matched inside that package.\n  This bug (`issue 638`_) is now fixed.\n\n- On Python 3.7, reporting about a decorated function with no body other than a\n  docstring would crash coverage.py with an IndexError (`issue 640`_).  This is\n  now fixed.\n\n- Configurer plugins are now reported in the output of ``--debug=sys``.\n\n.. _issue 638: https://bitbucket.org/ned/coveragepy/issues/638/run-omit-is-ignored-since-45\n.. _issue 640: https://bitbucket.org/ned/coveragepy/issues/640/indexerror-reporting-on-an-empty-decorated\n\n\n.. _changes_45:\n   ```\n   \n  \n  \n   ### 4.5\n   ```\n   --------------------------\n\n- A new kind of plugin is supported: configurators are invoked at start-up to\n  allow more complex configuration than the .coveragerc file can easily do.\n  See :ref:`api_plugin` for details.  This solves the complex configuration\n  problem described in `issue 563`_.\n\n- The ``fail_under`` option can now be a float.  Note that you must specify the\n  ``[report] precision`` configuration option for the fractional part to be\n  used.  Thanks to Lars Hupfeldt Nielsen for help with the implementation.\n  Fixes `issue 631`_.\n\n- The ``include`` and ``omit`` options can be specified for both the ``[run]``\n  and ``[report]`` phases of execution.  4.4.2 introduced some incorrect\n  interactions between those phases, where the options for one were confused\n  for the other.  This is now corrected, fixing `issue 621`_ and `issue 622`_.\n  Thanks to Daniel Hahler for seeing more clearly than I could.\n\n- The ``coverage combine`` command used to always overwrite the data file, even\n  when no data had been read from apparently combinable files.  Now, an error\n  is raised if we thought there were files to combine, but in fact none of them\n  could be used.  Fixes `issue 629`_.\n\n- The ``coverage combine`` command could get confused about path separators\n  when combining data collected on Windows with data collected on Linux, as\n  described in `issue 618`_.  This is now fixed: the result path always uses\n  the path separator specified in the ``[paths]`` result.\n\n- On Windows, the HTML report could fail when source trees are deeply nested,\n  due to attempting to create HTML filenames longer than the 250-character\n  maximum.  Now filenames will never get much larger than 200 characters,\n  fixing `issue 627`_.  Thanks to Alex Sandro for helping with the fix.\n\n.. _issue 563: https://bitbucket.org/ned/coveragepy/issues/563/platform-specific-configuration\n.. _issue 618: https://bitbucket.org/ned/coveragepy/issues/618/problem-when-combining-windows-generated\n.. _issue 621: https://bitbucket.org/ned/coveragepy/issues/621/include-ignored-warning-when-using\n.. _issue 622: https://bitbucket.org/ned/coveragepy/issues/622/report-omit-overwrites-run-omit\n.. _issue 627: https://bitbucket.org/ned/coveragepy/issues/627/failure-generating-html-reports-when-the\n.. _issue 629: https://bitbucket.org/ned/coveragepy/issues/629/multiple-use-of-combine-leads-to-empty\n.. _issue 631: https://bitbucket.org/ned/coveragepy/issues/631/precise-coverage-percentage-value\n\n\n.. _changes_442:\n   ```\n   \n  \n  \n   ### 4.4.2\n   ```\n   ----------------------------\n\n- Support for Python 3.7.  In some cases, class and module docstrings are no\n  longer counted in statement totals, which could slightly change your total\n  results.\n\n- Specifying both ``--source`` and ``--include`` no longer silently ignores the\n  include setting, instead it displays a warning. Thanks, Loïc Dachary.  Closes\n  `issue 265`_ and `issue 101`_.\n\n- Fixed a race condition when saving data and multiple threads are tracing\n  (`issue 581`_). It could produce a &quot;dictionary changed size during iteration&quot;\n  RuntimeError.  I believe this mostly but not entirely fixes the race\n  condition.  A true fix would likely be too expensive.  Thanks, Peter Baughman\n  for the debugging, and Olivier Grisel for the fix with tests.\n\n- Configuration values which are file paths will now apply tilde-expansion,\n  closing `issue 589`_.\n\n- Now secondary config files like tox.ini and setup.cfg can be specified\n  explicitly, and prefixed sections like `[coverage:run]` will be read. Fixes\n  `issue 588`_.\n\n- Be more flexible about the command name displayed by help, fixing\n  `issue 600`_. Thanks, Ben Finney.\n\n.. _issue 101: https://bitbucket.org/ned/coveragepy/issues/101/settings-under-report-affect-running\n.. _issue 581: https://bitbucket.org/ned/coveragepy/issues/581/race-condition-when-saving-data-under\n.. _issue 588: https://bitbucket.org/ned/coveragepy/issues/588/using-rcfile-path-to-toxini-uses-run\n.. _issue 589: https://bitbucket.org/ned/coveragepy/issues/589/allow-expansion-in-coveragerc\n.. _issue 600: https://bitbucket.org/ned/coveragepy/issues/600/get-program-name-from-command-line-when\n\n\n.. _changes_441:\n   ```\n   \n  \n  \n   ### 4.4.1\n   ```\n   ----------------------------\n\n- No code changes: just corrected packaging for Python 2.7 Linux wheels.\n\n\n.. _changes_44:\n   ```\n   \n  \n  \n   ### 4.4\n   ```\n   --------------------------\n\n- Reports could produce the wrong file names for packages, reporting ``pkg.py``\n  instead of the correct ``pkg/__init__.py``.  This is now fixed.  Thanks, Dirk\n  Thomas.\n\n- XML reports could produce ``&lt;source&gt;`` and ``&lt;class&gt;`` lines that together\n  didn&#39;t specify a valid source file path.  This is now fixed. (`issue 526`_)\n\n- Namespace packages are no longer warned as having no code. (`issue 572`_)\n\n- Code that uses ``sys.settrace(sys.gettrace())`` in a file that wasn&#39;t being\n  coverage-measured would prevent correct coverage measurement in following\n  code. An example of this was running doctests programmatically. This is now\n  fixed. (`issue 575`_)\n\n- Errors printed by the ``coverage`` command now go to stderr instead of\n  stdout.\n\n- Running ``coverage xml`` in a directory named with non-ASCII characters would\n  fail under Python 2. This is now fixed. (`issue 573`_)\n\n.. _issue 526: https://bitbucket.org/ned/coveragepy/issues/526/generated-xml-invalid-paths-for-cobertura\n.. _issue 572: https://bitbucket.org/ned/coveragepy/issues/572/no-python-source-warning-for-namespace\n.. _issue 573: https://bitbucket.org/ned/coveragepy/issues/573/cant-generate-xml-report-if-some-source\n.. _issue 575: https://bitbucket.org/ned/coveragepy/issues/575/running-doctest-prevents-complete-coverage\n   ```\n   \n  \n  \n   ### 4.4b1\n   ```\n   ----------------------------\n\n- Some warnings can now be individually disabled.  Warnings that can be\n  disabled have a short name appended.  The ``[run] disable_warnings`` setting\n  takes a list of these warning names to disable. Closes both `issue 96`_ and\n  `issue 355`_.\n\n- The XML report now includes attributes from version 4 of the Cobertura XML\n  format, fixing `issue 570`_.\n\n- In previous versions, calling a method that used collected data would prevent\n  further collection.  For example, `save()`, `report()`, `html_report()`, and\n  others would all stop collection.  An explicit `start()` was needed to get it\n  going again.  This is no longer true.  Now you can use the collected data and\n  also continue measurement. Both `issue 79`_ and `issue 448`_ described this\n  problem, and have been fixed.\n\n- Plugins can now find unexecuted files if they choose, by implementing the\n  `find_executable_files` method.  Thanks, Emil Madsen.\n\n- Minimal IronPython support. You should be able to run IronPython programs\n  under ``coverage run``, though you will still have to do the reporting phase\n  with CPython.\n\n- Coverage.py has long had a special hack to support CPython&#39;s need to measure\n  the coverage of the standard library tests. This code was not installed by\n  kitted versions of coverage.py.  Now it is.\n\n.. _issue 79: https://bitbucket.org/ned/coveragepy/issues/79/save-prevents-harvesting-on-stop\n.. _issue 96: https://bitbucket.org/ned/coveragepy/issues/96/unhelpful-warnings-produced-when-using\n.. _issue 355: https://bitbucket.org/ned/coveragepy/issues/355/warnings-should-be-suppressable\n.. _issue 448: https://bitbucket.org/ned/coveragepy/issues/448/save-and-html_report-prevent-further\n.. _issue 570: https://bitbucket.org/ned/coveragepy/issues/570/cobertura-coverage-04dtd-support\n\n\n.. _changes_434:\n   ```\n   \n  \n  \n   ### 4.3.4\n   ```\n   ----------------------------\n\n- Fixing 2.6 in version 4.3.3 broke other things, because the too-tricky\n  exception wasn&#39;t properly derived from Exception, described in `issue 556`_.\n  A newb mistake; it hasn&#39;t been a good few days.\n\n.. _issue 556: https://bitbucket.org/ned/coveragepy/issues/556/43-fails-if-there-are-html-files-in-the\n\n\n.. _changes_433:\n   ```\n   \n  \n  \n   ### 4.3.3\n   ```\n   ----------------------------\n\n- Python 2.6 support was broken due to a testing exception imported for the\n  benefit of the coverage.py test suite.  Properly conditionalizing it fixed\n  `issue 554`_ so that Python 2.6 works again.\n\n.. _issue 554: https://bitbucket.org/ned/coveragepy/issues/554/traceback-on-python-26-starting-with-432\n\n\n.. _changes_432:\n   ```\n   \n  \n  \n   ### 4.3.2\n   ```\n   ----------------------------\n\n- Using the ``--skip-covered`` option on an HTML report with 100% coverage\n  would cause a &quot;No data to report&quot; error, as reported in `issue 549`_. This is\n  now fixed; thanks, Loïc Dachary.\n\n- If-statements can be optimized away during compilation, for example, `if 0:`\n  or `if __debug__:`.  Coverage.py had problems properly understanding these\n  statements which existed in the source, but not in the compiled bytecode.\n  This problem, reported in `issue 522`_, is now fixed.\n\n- If you specified ``--source`` as a directory, then coverage.py would look for\n  importable Python files in that directory, and could identify ones that had\n  never been executed at all.  But if you specified it as a package name, that\n  detection wasn&#39;t performed.  Now it is, closing `issue 426`_. Thanks to Loïc\n  Dachary for the fix.\n\n- If you started and stopped coverage measurement thousands of times in your\n  process, you could crash Python with a &quot;Fatal Python error: deallocating\n  None&quot; error.  This is now fixed.  Thanks to Alex Groce for the bug report.\n\n- On PyPy, measuring coverage in subprocesses could produce a warning: &quot;Trace\n  function changed, measurement is likely wrong: None&quot;.  This was spurious, and\n  has been suppressed.\n\n- Previously, coverage.py couldn&#39;t start on Jython, due to that implementation\n  missing the multiprocessing module (`issue 551`_). This problem has now been\n  fixed. Also, `issue 322`_ about not being able to invoke coverage\n  conveniently, seems much better: ``jython -m coverage run myprog.py`` works\n  properly.\n\n- Let&#39;s say you ran the HTML report over and over again in the same output\n  directory, with ``--skip-covered``. And imagine due to your heroic\n  test-writing efforts, a file just achieved the goal of 100% coverage. With\n  coverage.py 4.3, the old HTML file with the less-than-100% coverage would be\n  left behind.  This file is now properly deleted.\n\n.. _issue 322: https://bitbucket.org/ned/coveragepy/issues/322/cannot-use-coverage-with-jython\n.. _issue 426: https://bitbucket.org/ned/coveragepy/issues/426/difference-between-coverage-results-with\n.. _issue 522: https://bitbucket.org/ned/coveragepy/issues/522/incorrect-branch-reporting-with-__debug__\n.. _issue 549: https://bitbucket.org/ned/coveragepy/issues/549/skip-covered-with-100-coverage-throws-a-no\n.. _issue 551: https://bitbucket.org/ned/coveragepy/issues/551/coveragepy-cannot-be-imported-in-jython27\n\n\n.. _changes_431:\n   ```\n   \n  \n  \n   ### 4.3.1\n   ```\n   ----------------------------\n\n- Some environments couldn&#39;t install 4.3, as described in `issue 540`_. This is\n  now fixed.\n\n- The check for conflicting ``--source`` and ``--include`` was too simple in a\n  few different ways, breaking a few perfectly reasonable use cases, described\n  in `issue 541`_.  The check has been reverted while we re-think the fix for\n  `issue 265`_.\n\n.. _issue 540: https://bitbucket.org/ned/coveragepy/issues/540/cant-install-coverage-v43-into-under\n.. _issue 541: https://bitbucket.org/ned/coveragepy/issues/541/coverage-43-breaks-nosetest-with-coverage\n\n\n.. _changes_43:\n   ```\n   \n  \n  \n   ### 4.3\n   ```\n   --------------------------\n\nSpecial thanks to **Loïc Dachary**, who took an extraordinary interest in\ncoverage.py and contributed a number of improvements in this release.\n\n- Subprocesses that are measured w","created_at":"2018-10-15T16:45:26Z","updated_at":"2018-10-15T16:45:26Z","closed_at":null,"merged_at":null,"merge_commit_sha":null,"assignee":null,"assignees":[],"requested_reviewers":[],"requested_teams":[],"labels":[],"milestone":null,"commits_url":"https://api.github.com/repos/ncgr/aakbar/pulls/5/commits","review_comments_url":"https://api.github.com/repos/ncgr/aakbar/pulls/5/comments","review_comment_url":"https://api.github.com/repos/ncgr/aakbar/pulls/comments{/number}","comments_url":"https://api.github.com/repos/ncgr/aakbar/issues/5/comments","statuses_url":"https://api.github.com/repos/ncgr/aakbar/statuses/26a804498b1270d0c440228dd36a9f556ca699a3","head":{"label":"ncgr:pyup-scheduled-update-2018-10-15","ref":"pyup-scheduled-update-2018-10-15","sha":"26a804498b1270d0c440228dd36a9f556ca699a3","user":{"login":"ncgr","id":1108054,"node_id":"MDEyOk9yZ2FuaXphdGlvbjExMDgwNTQ=","avatar_url":"https://avatars3.githubusercontent.com/u/1108054?v=4","gravatar_id":"","url":"https://api.github.com/users/ncgr","html_url":"https://github.com/ncgr","followers_url":"https://api.github.com/users/ncgr/followers","following_url":"https://api.github.com/users/ncgr/following{/other_user}","gists_url":"https://api.github.com/users/ncgr/gists{/gist_id}","starred_url":"https://api.github.com/users/ncgr/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ncgr/subscriptions","organizations_url":"https://api.github.com/users/ncgr/orgs","repos_url":"https://api.github.com/users/ncgr/repos","events_url":"https://api.github.com/users/ncgr/events{/privacy}","received_events_url":"https://api.github.com/users/ncgr/received_events","type":"Organization","site_admin":false},"repo":{"id":48630915,"node_id":"MDEwOlJlcG9zaXRvcnk0ODYzMDkxNQ==","name":"aakbar","full_name":"ncgr/aakbar","private":false,"owner":{"login":"ncgr","id":1108054,"node_id":"MDEyOk9yZ2FuaXphdGlvbjExMDgwNTQ=","avatar_url":"https://avatars3.githubusercontent.com/u/1108054?v=4","gravatar_id":"","url":"https://api.github.com/users/ncgr","html_url":"https://github.com/ncgr","followers_url":"https://api.github.com/users/ncgr/followers","following_url":"https://api.github.com/users/ncgr/following{/other_user}","gists_url":"https://api.github.com/users/ncgr/gists{/gist_id}","starred_url":"https://api.github.com/users/ncgr/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ncgr/subscriptions","organizations_url":"https://api.github.com/users/ncgr/orgs","repos_url":"https://api.github.com/users/ncgr/repos","events_url":"https://api.github.com/users/ncgr/events{/privacy}","received_events_url":"https://api.github.com/users/ncgr/received_events","type":"Organization","site_admin":false},"html_url":"https://github.com/ncgr/aakbar","description":"Amino-Acid k-mer Tool","fork":false,"url":"https://api.github.com/repos/ncgr/aakbar","forks_url":"https://api.github.com/repos/ncgr/aakbar/forks","keys_url":"https://api.github.com/repos/ncgr/aakbar/keys{/key_id}","collaborators_url":"https://api.github.com/repos/ncgr/aakbar/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/ncgr/aakbar/teams","hooks_url":"https://api.github.com/repos/ncgr/aakbar/hooks","issue_events_url":"https://api.github.com/repos/ncgr/aakbar/issues/events{/number}","events_url":"https://api.github.com/repos/ncgr/aakbar/events","assignees_url":"https://api.github.com/repos/ncgr/aakbar/assignees{/user}","branches_url":"https://api.github.com/repos/ncgr/aakbar/branches{/branch}","tags_url":"https://api.github.com/repos/ncgr/aakbar/tags","blobs_url":"https://api.github.com/repos/ncgr/aakbar/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/ncgr/aakbar/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/ncgr/aakbar/git/refs{/sha}","trees_url":"https://api.github.com/repos/ncgr/aakbar/git/trees{/sha}","statuses_url":"https://api.github.com/repos/ncgr/aakbar/statuses/{sha}","languages_url":"https://api.github.com/repos/ncgr/aakbar/languages","stargazers_url":"https://api.github.com/repos/ncgr/aakbar/stargazers","contributors_url":"https://api.github.com/repos/ncgr/aakbar/contributors","subscribers_url":"https://api.github.com/repos/ncgr/aakbar/subscribers","subscription_url":"https://api.github.com/repos/ncgr/aakbar/subscription","commits_url":"https://api.github.com/repos/ncgr/aakbar/commits{/sha}","git_commits_url":"https://api.github.com/repos/ncgr/aakbar/git/commits{/sha}","comments_url":"https://api.github.com/repos/ncgr/aakbar/comments{/number}","issue_comment_url":"https://api.github.com/repos/ncgr/aakbar/issues/comments{/number}","contents_url":"https://api.github.com/repos/ncgr/aakbar/contents/{+path}","compare_url":"https://api.github.com/repos/ncgr/aakbar/compare/{base}...{head}","merges_url":"https://api.github.com/repos/ncgr/aakbar/merges","archive_url":"https://api.github.com/repos/ncgr/aakbar/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/ncgr/aakbar/downloads","issues_url":"https://api.github.com/repos/ncgr/aakbar/issues{/number}","pulls_url":"https://api.github.com/repos/ncgr/aakbar/pulls{/number}","milestones_url":"https://api.github.com/repos/ncgr/aakbar/milestones{/number}","notifications_url":"https://api.github.com/repos/ncgr/aakbar/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/ncgr/aakbar/labels{/name}","releases_url":"https://api.github.com/repos/ncgr/aakbar/releases{/id}","deployments_url":"https://api.github.com/repos/ncgr/aakbar/deployments","created_at":"2015-12-27T03:07:57Z","updated_at":"2018-09-25T20:37:50Z","pushed_at":"2018-10-15T16:45:25Z","git_url":"git://github.com/ncgr/aakbar.git","ssh_url":"git@github.com:ncgr/aakbar.git","clone_url":"https://github.com/ncgr/aakbar.git","svn_url":"https://github.com/ncgr/aakbar","homepage":null,"size":860,"stargazers_count":0,"watchers_count":0,"language":"Python","has_issues":true,"has_projects":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":1,"mirror_url":null,"archived":false,"open_issues_count":2,"license":{"key":"other","name":"Other","spdx_id":"NOASSERTION","url":null,"node_id":"MDc6TGljZW5zZTA="},"forks":1,"open_issues":2,"watchers":0,"default_branch":"master"}},"base":{"label":"ncgr:master","ref":"master","sha":"ab0c0f7df672eaae7fc5267341f2edf6f8389b99","user":{"login":"ncgr","id":1108054,"node_id":"MDEyOk9yZ2FuaXphdGlvbjExMDgwNTQ=","avatar_url":"https://avatars3.githubusercontent.com/u/1108054?v=4","gravatar_id":"","url":"https://api.github.com/users/ncgr","html_url":"https://github.com/ncgr","followers_url":"https://api.github.com/users/ncgr/followers","following_url":"https://api.github.com/users/ncgr/following{/other_user}","gists_url":"https://api.github.com/users/ncgr/gists{/gist_id}","starred_url":"https://api.github.com/users/ncgr/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ncgr/subscriptions","organizations_url":"https://api.github.com/users/ncgr/orgs","repos_url":"https://api.github.com/users/ncgr/repos","events_url":"https://api.github.com/users/ncgr/events{/privacy}","received_events_url":"https://api.github.com/users/ncgr/received_events","type":"Organization","site_admin":false},"repo":{"id":48630915,"node_id":"MDEwOlJlcG9zaXRvcnk0ODYzMDkxNQ==","name":"aakbar","full_name":"ncgr/aakbar","private":false,"owner":{"login":"ncgr","id":1108054,"node_id":"MDEyOk9yZ2FuaXphdGlvbjExMDgwNTQ=","avatar_url":"https://avatars3.githubusercontent.com/u/1108054?v=4","gravatar_id":"","url":"https://api.github.com/users/ncgr","html_url":"https://github.com/ncgr","followers_url":"https://api.github.com/users/ncgr/followers","following_url":"https://api.github.com/users/ncgr/following{/other_user}","gists_url":"https://api.github.com/users/ncgr/gists{/gist_id}","starred_url":"https://api.github.com/users/ncgr/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ncgr/subscriptions","organizations_url":"https://api.github.com/users/ncgr/orgs","repos_url":"https://api.github.com/users/ncgr/repos","events_url":"https://api.github.com/users/ncgr/events{/privacy}","received_events_url":"https://api.github.com/users/ncgr/received_events","type":"Organization","site_admin":false},"html_url":"https://github.com/ncgr/aakbar","description":"Amino-Acid k-mer Tool","fork":false,"url":"https://api.github.com/repos/ncgr/aakbar","forks_url":"https://api.github.com/repos/ncgr/aakbar/forks","keys_url":"https://api.github.com/repos/ncgr/aakbar/keys{/key_id}","collaborators_url":"https://api.github.com/repos/ncgr/aakbar/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/ncgr/aakbar/teams","hooks_url":"https://api.github.com/repos/ncgr/aakbar/hooks","issue_events_url":"https://api.github.com/repos/ncgr/aakbar/issues/events{/number}","events_url":"https://api.github.com/repos/ncgr/aakbar/events","assignees_url":"https://api.github.com/repos/ncgr/aakbar/assignees{/user}","branches_url":"https://api.github.com/repos/ncgr/aakbar/branches{/branch}","tags_url":"https://api.github.com/repos/ncgr/aakbar/tags","blobs_url":"https://api.github.com/repos/ncgr/aakbar/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/ncgr/aakbar/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/ncgr/aakbar/git/refs{/sha}","trees_url":"https://api.github.com/repos/ncgr/aakbar/git/trees{/sha}","statuses_url":"https://api.github.com/repos/ncgr/aakbar/statuses/{sha}","languages_url":"https://api.github.com/repos/ncgr/aakbar/languages","stargazers_url":"https://api.github.com/repos/ncgr/aakbar/stargazers","contributors_url":"https://api.github.com/repos/ncgr/aakbar/contributors","subscribers_url":"https://api.github.com/repos/ncgr/aakbar/subscribers","subscription_url":"https://api.github.com/repos/ncgr/aakbar/subscription","commits_url":"https://api.github.com/repos/ncgr/aakbar/commits{/sha}","git_commits_url":"https://api.github.com/repos/ncgr/aakbar/git/commits{/sha}","comments_url":"https://api.github.com/repos/ncgr/aakbar/comments{/number}","issue_comment_url":"https://api.github.com/repos/ncgr/aakbar/issues/comments{/number}","contents_url":"https://api.github.com/repos/ncgr/aakbar/contents/{+path}","compare_url":"https://api.github.com/repos/ncgr/aakbar/compare/{base}...{head}","merges_url":"https://api.github.com/repos/ncgr/aakbar/merges","archive_url":"https://api.github.com/repos/ncgr/aakbar/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/ncgr/aakbar/downloads","issues_url":"https://api.github.com/repos/ncgr/aakbar/issues{/number}","pulls_url":"https://api.github.com/repos/ncgr/aakbar/pulls{/number}","milestones_url":"https://api.github.com/repos/ncgr/aakbar/milestones{/number}","notifications_url":"https://api.github.com/repos/ncgr/aakbar/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/ncgr/aakbar/labels{/name}","releases_url":"https://api.github.com/repos/ncgr/aakbar/releases{/id}","deployments_url":"https://api.github.com/repos/ncgr/aakbar/deployments","created_at":"2015-12-27T03:07:57Z","updated_at":"2018-09-25T20:37:50Z","pushed_at":"2018-10-15T16:45:25Z","git_url":"git://github.com/ncgr/aakbar.git","ssh_url":"git@github.com:ncgr/aakbar.git","clone_url":"https://github.com/ncgr/aakbar.git","svn_url":"https://github.com/ncgr/aakbar","homepage":null,"size":860,"stargazers_count":0,"watchers_count":0,"language":"Python","has_issues":true,"has_projects":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":1,"mirror_url":null,"archived":false,"open_issues_count":2,"license":{"key":"other","name":"Other","spdx_id":"NOASSERTION","url":null,"node_id":"MDc6TGljZW5zZTA="},"forks":1,"open_issues":2,"watchers":0,"default_branch":"master"}},"_links":{"self":{"href":"https://api.github.com/repos/ncgr/aakbar/pulls/5"},"html":{"href":"https://github.com/ncgr/aakbar/pull/5"},"issue":{"href":"https://api.github.com/repos/ncgr/aakbar/issues/5"},"comments":{"href":"https://api.github.com/repos/ncgr/aakbar/issues/5/comments"},"review_comments":{"href":"https://api.github.com/repos/ncgr/aakbar/pulls/5/comments"},"review_comment":{"href":"https://api.github.com/repos/ncgr/aakbar/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/ncgr/aakbar/pulls/5/commits"},"statuses":{"href":"https://api.github.com/repos/ncgr/aakbar/statuses/26a804498b1270d0c440228dd36a9f556ca699a3"}},"author_association":"NONE","merged":false,"mergeable":null,"rebaseable":null,"mergeable_state":"unknown","merged_by":null,"comments":0,"review_comments":0,"maintainer_can_modify":false,"commits":12,"additions":12,"deletions":12,"changed_files":2}}
{"actor":{"display_login":"pyup-bot"}}