just getting data from the repo can already raise IntegrityErrors
in LoggedIO, so we need to catch them also.
see also the code a few lines above where this is done in the same way.
This fixes the problem raised by issue #2314 by requiring that each root
subtree be fully traversed.
The problem occurs when a patterns file excludes a parent directory P later
in the file, but earlier in the file a subdirectory S of P is included.
Because a tree is processed recursively with a depth-first search, P is
processed before S is. Previously, if P was excluded, then S would not even
be considered. Now, it is possible to recurse into P nonetheless, while not
adding P (as a directory entry) to the archive.
With this commit, a `-` in a patterns-file will allow an excluded directory
to be searched for matching descendants. If the old behavior is desired, it
can be achieved by using a `!` in place of the `-`.
The following is a list of specific changes made by this commit:
* renamed InclExclPattern named-tuple -> CmdTuple (with names 'val' and 'cmd'), since it is used more generally for commands, and not only for representing patterns.
* represent commands as IECommand enum types (RootPath, PatternStyle, Include, Exclude, ExcludeNoRecurse)
* archiver: Archiver.build_matcher() paths arg renamed -> include_paths to prevent confusion as to whether the list of paths are to be included or excluded.
* helpers: PatternMatcher has recurse_dir attribute that is used to communicate whether an excluded dir should be recursed (used by Archiver._process())
* archiver: Archiver.build_matcher() now only returns a PatternMatcher instance, and not an include_patterns list -- this list is now created and housed within the PatternMatcher instance, and can be accessed from there.
* moved operation of finding unmatched patterns from Archiver to PatternMatcher.get_unmatched_include_patterns()
* added / modified some documentation of code
* renamed _PATTERN_STYLES -> _PATTERN_CLASSES since "style" is ambiguous and this helps clarify that the set contains classes and not instances.
* have PatternBase subclass instances store whether excluded dirs are to be recursed. Because PatternBase objs are created corresponding to each +, -, ! command it is necessary to differentiate - from ! within these objects.
* add test for '!' exclusion rule (which doesn't recurse)
