# RCSB_EXDB HISTORY
18-Mar-2019 V0.10 Initial version
22-Apr-2019 V0.11 Refining API, separate mock tests fro full cache tests, add taxonomy coverage accessors
23-Apr-2019 V0.12 Consolidated rcsb.exdb.seq into this more general module  (IN PROGRESS)
25-Jun-2019 V0.13 Update development workflows and cleanup
28-Jun-2019 V0.14 Migrating code from py-rcsb_utils_anal module for entity instance extraction
 4-Sep-2019 V0.15 Added tree, chemical reference loader operations and pipeline build tooling
17-Sep-2019 V0.16 Update to latest schemas
30-Sep-2019 V0.17 Updates for chemical reference and tree cli's and update dependencies
15-Oct-2019 V0.18 Refactor, add TaxonomyExtractor(), ReferenceSequenceAssignmentUpdater() and friends.
16-Oct-2019 V0.19 Checkpoint in improving update reference sequences and troubleshooting tree node lists for ATC
17-Oct-2019 V0.20 Checkpoint in refactoring reference sequence update processing.
18-Oct-2019 V0.21 Test version of document-level update of reference sequence assignments
18-Oct-2019 V0.22 Update cache file management
18-Oct-2019 V0.23 Adjust filter behavior, turn off test mode, fix Py27 test parameter.
19-Oct-2019 V0.24 Handle miscellaneous issues in reference sequence processing from Oct 18 full load
20-Oct-2019 V0.25 Handle duplicates from inconsistent struct_ref_* records
 5-Dec-2019 V0.26 Add support for entity typed schema and update dependencies.
 6-Dec-2019 V0.27 Add match index cache recovery.1
11-Dec-2019 V0.28 Adding reference sequence loader and moving pipeline to py38.
15-Dec-2019 V0.29 Added methods to load UniProt features
17-Dec-2019 V0.30 Pre-filter GOIDs and add ExDbWorkflow module with simple wf entry points
20-Dec-2019 V0.31 Adjust package definition
23-Dec-2019 V0.32 Change protocol for supplementing accessions and EC annotations.
04-Jan-2020 V0.33 Add support for rcsb_polymer_entity.rcsb_enzyme_class_combined_depth
09-Jan-2020 V0.34 Add additional cache test criteria for UniProt match cache.
10-Jan-2020 V0.35 Update dependencies for rcsb.utils.go and rcsb.utils.struct
23-Jan-2020 V0.36 Changes to support pre-beta-v1 schema reorganization with the addition of rcsb_polymer_entity_annotation
27-Jan-2020 V0.37 Add annotation extractor modules and adjustments for some missing features.
29-Jan-2020 V0.38 Update dependencies for GO and Drugbank fixes
30-Jan-2020 V0.39 Update dependencies structure domain utilities
 2-Feb-2020 V0.40 Add test fixtures to measure memory usage, streamline some extractions, suppress some diagnostic reporting
 4-Feb-2020 V0.41 Update dependencies to support split configuration
 6-Feb-2020 V0.42 Address issue with duplicated annotations from multiple reference sequences
 8-Feb-2020 V0.43 Adjust the default chunk size in the workflow interface (set the default to 100)
 8-Feb-2020 V0.44 Expose the reference sequence fetch chunk size in the workflow interface
11-Feb-2020 V0.45 Simplify workflow api and update dependencies
13-Feb-2020 V0.46 Added validation tests to troubleshoot UniProt core loading.  Update dependencies.
16-Feb-2020 V0.47 Add alternative cache strategy for reference sequences.
19-Feb-2020 V0.48 Add Pfam and InterPro Providers and associated annotation
20-Feb-2020 V0.49 Combine missing UniProt accessions if available with other reference sequence data.
26-Feb-2020 V0.50 Standardize case for gene names.
 1-Apr-2020 V0.51 Better handling of incomplete primary gene annotations
 5-Apr-2020 V0.52 Suppress diagnostic logging in ReferenceSequenceCacheProvider()
 8-Apr-2020 V0.53 Adjust error handling in ReferenceSequenceCacheProvider()
 5-May-2020 V0.54 Add PubChem loader and workflow extensions
 9-May-2020 V0.55 Adjust cache management for PubChem refresh
 9-May-2020 V0.56 Log formatting adjustments
17-May-2020 V0.57 Revise the index for PubChem search
18-May-2020 V0.58 Cleanup some pipeline and logging issues.
23-May-2020 V0.59 Add PubChem tracking diagnostics
23-May-2020 V0.60 Adjust multiprocessing configuration
28-Jul-2020 V0.61 Added modules PubChemDataCacheProvider() PubChemIndexCacheProvider() PubChemEtlWrapper() and associated tests
28-Jul-2020 V0.62 Relax testing constraints for PubChem lookups and upversion
29-Jul-2020 V0.63 Add module PubChemEtlWorkflow() and associated tests
29-Jul-2020 V0.64 Add an automatic fallback support for stashed data sets.
29-Jul-2020 V0.65 Add stash() method to module PubChemEtlWorkflow()
30-Aug-2020 V0.66 Update dependencies
 8-Dec-2020 V0.67 Add PolymerEntityExtractor() and UniProtExtractor() from rcsb.utils.seqalign, cleanup tests and fixture issues
 9-Dec-2020 V0.68 Simplify API for PolymerEntityExtractor()
18-Jan-2021 V0.69 Update dependencies
25-Feb-2021 V0.70 Update with split out rcsb.utils.dictionary
18-Mar-2021 V0.71 Adjustments in initialization  UniProtExtractor()
13-May-2021 V0.72 Add minSeqLen argument to exportProteinEntityFasta()
24-May-2021 V0.73 Add BranchedEntityExtractor() and associated tests
26-May-2021 V0.74 Add modules GlycanProvider(), GlycanUtils() and associated tests
27-May-2021 V0.75 Implement GlyGen mapping in ReferenceSequenceAnnotationProvider and ReferenceSequenceAnnotationAdapter
28-May-2021 V0.76 Fix idempotent issue in ReferenceSequenceAnnotationAdapter()
30-May-2021 V0.77 Disable Pfam annotation from SIFTS
19-Jun-2021 V0.78 Add ChemRefMappingProvider(), modernize ChemRefExtractor(), and update __docformat__
28-Jun-2021 V0.79 Add LigandNeighborMappingProvider() LigandNeighborMappingExtractor() and associated tests
30-Jun-2021 V0.80 Make GlycanProvider() a subclass of StashableBase(), add GlycanEtlWorkflow() and associated tests
30-Jun-2021 V0.81 Simplify install scripts and update pipeline configuration
26-Jul-2021 V0.82 Replace all explicit use of StashUtil with StashableBase subclasses
26-Jul-2021 V0.83 Add tree node lists for SCOP2 and ECOD
28-Jul-2021 V0.84 Update stash options for GlycanEtlWorkflow and PubChemEtlWrapper
29-Jul-2021 V0.85 Gracefully handle and report missing ligand_comp_id's in LigandNeighborMappingProvider()
 2-Aug-2021 V0.86 Adjust reporting intervals and diagnostic output and update dependencies and configuration
 4-Aug-2021 V0.87 Adjust logging verbosity and dependencies
22-Sep-2021 V0.88 Add modules EntryInfoProvider and EntryInfoEtlWorkflow and associated tests.
23-Sep-2021 V0.89 Update dependencies
 9-Feb-2022 V0.90 Enable http loading of SIFTS data
29-Mar-2022 V0.91 Adjust ReferenceSequenceAnnotationProvider & ReferenceSequenceCacheProvider;
                  Add computed-models to tests & workflow;
                  Fix test case in testObjectExtractor;
                  Switch fixturePdbxLoader to use remote HTTP loading for Azure tests instead of local mock/sandbox paths