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Created with Raphaël 2.2.010Feb765329Jan171413107230Dec201918171698653229Nov2827262523212015141323Oct144330Sep2523328Aug12510Jul942124Jun191817141312331May29272423222016151413924Apr179320Mar1514625Feb2019171411765432130Jan24221615141311109818Dec13328Nov222120923Oct326Sep2413106514Aug13109731Jul201918106229Jun115425May2327Apr2625242320191816131211105431Mar29282723222120181615141352128Feb27262322212015931Dec301328Nov6220Oct27Sep212030Aug292423221817161028Jul27262521201312111076521Jun14SCHWED-4612: Reduce Numpy compilation warningsMerge branch 'python3_port' into hmm_scoreslightly relax dcd io unit testremove openmm density plugin which has always been experimental and was never thoroughly testedSCHWED-4612: Update CMake call for CI.SCHWED-4612: Dealing with the NumPy deprecation compiler warning.Python export for HMM algorithmhook up hmm algorithms in build systemalgorithm that calculates an HMM-HMM alignment score the hhblits wayAlgorithms to add pseudo counts to ProfileHandle objects which contain HMM informationadd support for hmm related data in ProfileHandleSCHWED-4612: Ignore warning about unused functions by GCC, while the functions are used by unit tests.SCHWED-4612: Fix warning on unused (static) function.SCHWED-4612: Remove use of deprecated function.SCHWED-4612: Get rid of '-Wmaybe-uninitialized' from Vec3Try to force C++11 for older compilers.doc: fix indexing of ost.bindingsdoc: document filtering of chains by qsscoringReplace all subprocess wait with runSubprocess wait in deadlock avertedMerge branch 'master' into developMerge branch 'release-1.11.0'1.11.01.11.0SCHWED-4556: ensure six is available in venvUpdate version to 1.11.0SCHWED-4554: updated CHANGELOG with note on py2.SCHWED-4554: updated CHANGELOG.SCHWED-4553: doc (c) moved to 2020.keep this as bytes Wrote abstract state sequence toRead as binary in exec compile opendecode subprocess soutdecode subprocess soutreplace deprecated importUse sphinx.application.Sphinx instead of a main function.Revert "Attempt to restore compatibility with older versions of Sphinx"Attempt to restore compatibility with older versions of SphinxDecode output of Blast to return a string with outfmt=1.Update call to sphinx to build documentation.add note on Python 2 support in install instructionsTemporary error to remind for careful checks in versions etc. in first Python 3 releaseuse buffered stdout in compare-structures