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N.B. This merge has so many commits, many of which experimental, that squashing will be sensible. The Cython branch will be left to preserve the full commit history. * Bare-bones base LMDB store. * Add _open_env method. * Link header files. * Remove pure Python base LMDB store. * Module path adjustments and further base LMDB store enhancements. * Start work on LmdbTriplestore. * WIP init dbi method. * WIP: pxd file. * LmdbTriplestore compiles, links and imports correctly. * Add LMDB libraries. [ci skip] * Separate DBI labels and config; LmdbTriplestore imports and inits. [ci skip] * Simplify error messages; rearrange declarations. [skip ci] * WIP: get methods. [ci skip] * Simplify return code check further; run get_value. [ci skip] * Add put method; properly raise exceptions; pass unsigned char in cpdef. [ci skip] * Basic put & get method working; minimal one-off test script. * Use transaction ctx. * Rearrange and expand txn and cursor management methods. * Add stats. * Start moving functions to PYX file; remove LexicalSequence. * Add _from_key(). * Add low-level lookup methods. [ci skip] * Change _check() format. * Move _triple_keys method. [ci skip] * Inline _to_key(); add _to_triple_key(). [ci skip] * Add logic for all unbound lookup. [ci skip] * _triple_keys() returns tuples. [ci skip] * Add _remove() method; separate Cython and Python triple_keys() methods. * Add key_exists() method. [ci skip] * Make message in _check() optional. * Add _all_terms(). * Add _index_triple(). [ci skip] * Remove methods moved to Cython module from Python module. [ci skip] * Adapt bind() to new framework. [ci skip] * Adapt bind(), namespace(), prefix(), namespaces(), contexts(). [ci skip] * Implement destroy(); minor adjustments. [ci skip] * Remove redundant methods and comment out non-core ones in Python module. [ci skip] * Add destroy definition in pxd file. [ci skip] * Replace all instances of TxnManager with txn_ctx in tests. [ci skip] * Remove redundant Txnmanager class and encode/decode functions. [ci skip] * Adjust store management functions; retype some cpdefs. [ci skip] * Remove TxnManager everywhere. [ci skip] * Add Cython to dev requirements; rename requirements_rtd to _dev. [ci skip] * Some pre-test fixes. [ci skip] * Properly open and close store; avoid double free segfault. [ci skip] * Complete testing environment and transaction lifecycle. [ci skip] * Fix some tests; use default transaction in _cur_open(). [ci skip] * Protect from deadlock in txn context; pass rollback test. [ci skip] * Insert meaningful data. [ci skip] * Replace string assignments with memcpy. [ci skip] * Fix typos. [ci skip] * Rework exception handling. [ci skip] * Use memcmp for array slice comparison. [skip ci] * Add specific exception for overwriting existing key. [ci skip] * Fix lookup_2bound; make memcpy syntax consistent. [ci skip] * Fix segfaults and a number of other issues. [ci skip] * Correct duplicate check. [ci skip] * Align lookup_1bound and lookup_2bound process. [ci skip] * Re-engineer ResultSet. [ci skip] * Fix _get_dup_data. [ci skip] * Fix ResultSet.to_tuple(). [ci skip] * First attempt to fix all-unbound lookup. [ci skip] * Fix all-unbound lookup and broader issues. * Ensure all cursors are closed. * get_dbi() returns a handle. [ci skip] * Fix all-unbound lookup. [ci skip] * Refactor array notation. [ci skip] * _from_key() returns tuple. [ci skip] * Do not truncate terms in _add. [ci skip] * Put index cursor generation in right order. [ci skip] * Catch all KeyNotFoundErrors in lookups. [ci skip] * Fix simple delete test. [ci skip] * Fix namespace methods. [ci skip] * Change a bunch of function signatures to make more sense. [ci skip] * Move add_graph to Cython module. * Pass add_context() and contexts() tests. * Fix several issues with context handling; add a lot of logging. [ci skip] * Add tests: * Adding graph with a RO transaction * Deleting triples for not found graph * Fix adding and deleting context, and ???c lookup. [ci skip] * Fix delete triples without a context. [ci skip] * Fix stats. [ci skip] * Correct txn reference in _append(). All LMDB tests pass locally. * Adapt MetadataStore to BaseLmdbStore; fix test setup. * Various integration fixes. [ci skip] * Fix s p o c lookup. [ci skip] * Fix RDF store setup and teardown. [ci skip] * Fix segfault on remove((s, p, o), c). [ci skip] * Expose txn_id() to Python; add a lot more debugging statements. * Add cleanup tests for LMDB Store; remove `as` in txn_ctx calls. * Fix triples not being completely deleted. All store tests pass. [ci skip] * Enable MetadataStore. * Clear stale readers. [ci skip] * Fix transaction closing that got out of whack somehow. [ci skip] * Fix graph identifiers for contexts in triples(). [ci skip] * Avoid a memcpy() in _from_key(). [ci skip] * Return all contexts for triples() even when filtering by context. [ci skip] * Fix lookup for s p o ?. [ci skip] * Properly clean up context. [ci skip] * More tests. [ci skip] * Recurse into descendants when forgetting resource. [ci skip] * Temp fix for version test; fix get_raw; fix all_terms. [ci skip] * Fix get_inbound_rel()... really. All tests pass locally. [ci skip] * Comment out all debug statements. * Reset metadata store at bootstrap. * Replace RDFlib dataset methods with straight store methods. * Logging adjustments. * Move destroy() method to Cython module. * Start using local transactions. * Test script for concurrent transactions. * Resolve some multiprocessing issues: * Start GUnicorn via shell script * Start one dbenv per process * Move WSGI config to a module * Resolve EAGAIN error with multi-worker server * Add C files. * Travis adjustments: * Bump up Python version (min. 3.6, up to 3.7) * Add Cython dependency * Install LMDB libraries system-wide in Travis * Remove py-lmdb from dev dependencies * Open the metadata store in tests; don't segfault if txn started in a closed store. * Temporary fix for leaked readers on GUnicorn worker restarts. * Remove Cython-generated C sources from VCS. * Align console script naming; some cleanup. * Conftest fixes. * Add three indices but don't use memcpy. 10% write performance penalty. * Save memcpy's. * Move triples() inside Cython module. * Lookup performance improvements: * Use secondary indices * Reduce complexity on lookup_2bound * Parallelize lookup result triple assembly * Avoid duplicate function calls in check_ref_int(); adjust logging. * Replace IMR Graph class with lightweight SimpleGraph and Imr. * Merge performance branch into simple_graph. * Correct errors with SimpleGraph. * Raise error if triple inserted is invalid. * Parallelize data assembly in lookup_2bound. * Fix offsets in lookup_1bound(). * Rename test folder to control execution order (ugly but effective). * Move sandbox. * Fix tests. * Implement custom pickler; re-add C source bundles. * Add term module. * Add TPL header file. * Add TPL header file. * More performance optimizations * Use OpenSSL C SHA1 function * Separate from_key and from_trp_key * Setuptools adjustments; support Python 3.7 in Travis. * Setuptools adjustments; support Python 3.7 in Travis. * Move metadata store out of ldp_rs store. * Setuptools adjustments; support Python 3.7 in Travis. * Fix memory leak in term module. * Fix memory leak in term module. * Comment out or delete code related to RDF hashing. * Some code cleanup. * Remove dependency from Cython for non-developers. * Update documentation. * Subtle rebranding. * Minor cleanup.
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