GitLab

Flexiable recorder/parser functions added to SmartParser, Stream RTF, PAR, CRD, COOR readers and force field parameters with ParmEd support added to MDDataAccess, resetting support added to MetaInfoStorage.

3dbeda49095faf438840110e9b6e3fccd06a1aef -- Allowed the usage of schemes other than nmd:// in the JSON files. This allows testing with files generated on a local machine.
f689e878a4775b1c4a06a70e5aabbaf2d42be25c -- return code-specific section (named '^x_.*_section.*') as ArchiveSectionJSON
e24727f9a67462d59c5a580888edbc73ac131aeb -- comment on code-specific x_*_section
be56a3083cf035ea0d7d53946581ee1ac4c9e0b4 -- fix repeating-values issue in archive.py (instead of N actual values, N times the first value was returned when looking up indices)
ae7880e302553768a40fa16cef06b848ca33359d -- moved reading mainfile_uri to archiveiterator
75f571c6c99c5377da46b6f56e276689327dfa6e -- Added pid to mongodb. Fixed tests for db changes. Fixed schema and postprocessor for empty pids and repository download uris.

Removed stdout.flush() at backend. Borken Pipe Error seams to exist when stderr is closed in Python3 not relevant with parsing.

json.dump fails for python3 with Broken Pipe Error for IO buffer due to . Trying to fix it with stdout.flush().

Add test/store to MetaInfoStorage, update table_reader in SmartParser and topology extracter of Pymolfile in MDDataAccess