Commits for mmaddren

v257_preview2 to v257_base (2011-09-13 to 2011-09-19) v257

• Willys changes to add geo accession numbers to Sydh submissions
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra - lines changed 109, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 19, context: html, text, full: html, text
• large-scale renaming change to allow python to be built into cluster/bin, also mkGeoPkg now renames files
  • python/lib/ucscgenomics/bed.py - lines changed 49, context: html, text, full: html, text
  • python/lib/ucscgenomics/compositetrack/CompositeTrack.py - lines changed 228, context: html, text, full: html, text
  • python/lib/ucscgenomics/cv.py - lines changed 507, context: html, text, full: html, text
  • python/lib/ucscgenomics/cvfile/CvFile.py - lines changed 504, context: html, text, full: html, text
  • python/lib/ucscgenomics/cvfile/unittest/input/Antibody/BlankKey.ra - lines changed 25, context: html, text, full: html, text
  • python/lib/ucscgenomics/cvfile/unittest/input/Antibody/ExtraKey.ra - lines changed 26, context: html, text, full: html, text
  • python/lib/ucscgenomics/cvfile/unittest/input/Antibody/MissingKey.ra - lines changed 24, context: html, text, full: html, text
  • python/lib/ucscgenomics/cvfile/unittest/input/Antibody/NonmatchKey.ra - lines changed 25, context: html, text, full: html, text
  • python/lib/ucscgenomics/cvfile/unittest/input/Antibody/ValidStanza.ra - lines changed 36, context: html, text, full: html, text
  • python/lib/ucscgenomics/cvfile/unittest/input/CellLine/BlankKey.ra - lines changed 34, context: html, text, full: html, text
  • python/lib/ucscgenomics/cvfile/unittest/input/CellLine/ExtraKey.ra - lines changed 35, context: html, text, full: html, text
  • python/lib/ucscgenomics/cvfile/unittest/input/CellLine/MissingKey.ra - lines changed 33, context: html, text, full: html, text
  • python/lib/ucscgenomics/cvfile/unittest/input/CellLine/NonmatchKey.ra - lines changed 34, context: html, text, full: html, text
  • python/lib/ucscgenomics/cvfile/unittest/input/CellLine/ValidStanza.ra - lines changed 33, context: html, text, full: html, text
  • python/lib/ucscgenomics/cvfile/unittest/input/Mouse/BlankKey.ra - lines changed 37, context: html, text, full: html, text
  • python/lib/ucscgenomics/cvfile/unittest/input/Mouse/ExtraKey.ra - lines changed 38, context: html, text, full: html, text
  • python/lib/ucscgenomics/cvfile/unittest/input/Mouse/MissingKey.ra - lines changed 36, context: html, text, full: html, text
  • python/lib/ucscgenomics/cvfile/unittest/input/Mouse/NonmatchKey.ra - lines changed 37, context: html, text, full: html, text
  • python/lib/ucscgenomics/cvfile/unittest/input/Mouse/ValidStanza.ra - lines changed 37, context: html, text, full: html, text
  • python/lib/ucscgenomics/cvfile/unittest/testCvFile - lines changed 95, context: html, text, full: html, text
  • python/lib/ucscgenomics/ordereddict.py - lines changed 58, context: html, text, full: html, text
  • python/lib/ucscgenomics/ordereddict/OrderedDict.py - lines changed 58, context: html, text, full: html, text
  • python/lib/ucscgenomics/ra.py - lines changed 214, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/RaFile.py - lines changed 214, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/testRaFile.py - lines changed 205, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/testoutput/BasicDiff.out - lines changed 27, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/testoutput/CommentsDiff.out - lines changed 31, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/testoutput/DeleteItem.out - lines changed 39, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/testoutput/ExtraneousWhitespace.out - lines changed 70, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/testoutput/GetItem.out - lines changed 13, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/testoutput/InlineCommentsDiff.out - lines changed 27, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/testoutput/IterEntryItems.out - lines changed 27, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/testoutput/IterEntryKeys.out - lines changed 27, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/testoutput/IterEntryValues.out - lines changed 27, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/testoutput/IterItems.out - lines changed 19, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/testoutput/IterKeys.out - lines changed 11, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/testoutput/IterValues.out - lines changed 41, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/tests/BasicDiff.ra - lines changed 12, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/tests/CommentsDiff.ra - lines changed 14, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/tests/DeleteItem.ra - lines changed 18, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/tests/DuplicateKeys.ra - lines changed 8, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/tests/FunctionalityCheck.ra - lines changed 23, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/tests/GetItem.ra - lines changed 5, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/tests/InlineCommentsDiff.ra - lines changed 12, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/tests/IterEntryItems.ra - lines changed 12, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/tests/IterEntryKeys.ra - lines changed 12, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/tests/IterEntryValues.ra - lines changed 12, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/tests/IterItems.ra - lines changed 8, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/tests/IterKeys.ra - lines changed 4, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/tests/IterValues.ra - lines changed 19, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/tests/MisplacedKeys.ra - lines changed 8, context: html, text, full: html, text
  • python/lib/ucscgenomics/rafile/unittest/tests/NonNewlineFile.ra - lines changed 5, context: html, text, full: html, text
  • python/lib/ucscgenomics/soft.py - lines changed 392, context: html, text, full: html, text
  • python/lib/ucscgenomics/softfile/SoftFile.py - lines changed 392, context: html, text, full: html, text
  • python/lib/ucscgenomics/softfile/unittest/testSoft - lines changed 10, context: html, text, full: html, text
  • python/lib/ucscgenomics/styles.py - lines changed 38, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_cv - lines changed 95, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_cv_input/Antibody/BlankKey.ra - lines changed 25, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_cv_input/Antibody/ExtraKey.ra - lines changed 26, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_cv_input/Antibody/MissingKey.ra - lines changed 24, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_cv_input/Antibody/NonmatchKey.ra - lines changed 25, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_cv_input/Antibody/ValidStanza.ra - lines changed 36, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_cv_input/CellLine/BlankKey.ra - lines changed 34, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_cv_input/CellLine/ExtraKey.ra - lines changed 35, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_cv_input/CellLine/MissingKey.ra - lines changed 33, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_cv_input/CellLine/NonmatchKey.ra - lines changed 34, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_cv_input/CellLine/ValidStanza.ra - lines changed 33, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_cv_input/Mouse/BlankKey.ra - lines changed 37, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_cv_input/Mouse/ExtraKey.ra - lines changed 38, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_cv_input/Mouse/MissingKey.ra - lines changed 36, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_cv_input/Mouse/NonmatchKey.ra - lines changed 37, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_cv_input/Mouse/ValidStanza.ra - lines changed 37, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_ra - lines changed 206, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_ra_file/testoutput/BasicDiff.out - lines changed 27, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_ra_file/testoutput/CommentsDiff.out - lines changed 31, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_ra_file/testoutput/DeleteItem.out - lines changed 39, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_ra_file/testoutput/ExtraneousWhitespace.out - lines changed 70, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_ra_file/testoutput/GetItem.out - lines changed 13, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_ra_file/testoutput/InlineCommentsDiff.out - lines changed 27, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_ra_file/testoutput/IterEntryItems.out - lines changed 27, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_ra_file/testoutput/IterEntryKeys.out - lines changed 27, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_ra_file/testoutput/IterEntryValues.out - lines changed 27, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_ra_file/testoutput/IterItems.out - lines changed 19, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_ra_file/testoutput/IterKeys.out - lines changed 11, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_ra_file/testoutput/IterValues.out - lines changed 41, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_ra_input/BasicDiff.ra - lines changed 12, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_ra_input/CommentsDiff.ra - lines changed 14, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_ra_input/DeleteItem.ra - lines changed 18, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_ra_input/DuplicateKeys.ra - lines changed 8, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_ra_input/FunctionalityCheck.ra - lines changed 23, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_ra_input/GetItem.ra - lines changed 5, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_ra_input/InlineCommentsDiff.ra - lines changed 12, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_ra_input/IterEntryItems.ra - lines changed 12, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_ra_input/IterEntryKeys.ra - lines changed 12, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_ra_input/IterEntryValues.ra - lines changed 12, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_ra_input/IterItems.ra - lines changed 8, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_ra_input/IterKeys.ra - lines changed 4, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_ra_input/IterValues.ra - lines changed 19, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_ra_input/MisplacedKeys.ra - lines changed 8, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_ra_input/NonNewlineFile.ra - lines changed 5, context: html, text, full: html, text
  • python/lib/ucscgenomics/test/test_soft - lines changed 10, context: html, text, full: html, text
  • python/lib/ucscgenomics/textstyle.py - lines changed 40, context: html, text, full: html, text
  • python/lib/ucscgenomics/textstyle/TextStyle.py - lines changed 40, context: html, text, full: html, text
  • python/lib/ucscgenomics/track.py - lines changed 234, context: html, text, full: html, text
  • python/programs/cvValidate/cvValidate - lines changed 2, context: html, text, full: html, text
  • python/programs/mkChangeNotes/mkChangeNotes - lines changed 123, context: html, text, full: html, text
  • python/programs/mkGeoPkg/mkGeoPkg - lines changed 94, context: html, text, full: html, text
  • python/programs/mkGeoPkg/trackInfo - lines changed 183, context: html, text, full: html, text
  • python/programs/trackInfo/trackInfo - lines changed 179, context: html, text, full: html, text
• ra file updated
  • python/lib/ucscgenomics/ra.py - lines changed 5, context: html, text, full: html, text
• Merge branch 'master' into mmaddren_pythondev
• removed extraneous files
  • python/lib/ucscgenomics/cvfile/__init__.py - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • python/lib/ucscgenomics/rafile/__init__.py - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • python/lib/ucscgenomics/softfile/__init__.py - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• removed additional extra files
  • python/lib/ucscgenomics/compositetrack/__init__.py - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • python/lib/ucscgenomics/ordereddict/__init__.py - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • python/lib/ucscgenomics/textstyle/__init__.py - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• Merge branch 'master' into mmaddren_pythondev
• Merge branch 'mmaddren_pythondev'