# File: HISTORY.txt
#
 5-Nov-2019 - V0.11 Created module with preliminary dependency cache management
18-Jan-2020 - V0.12 Preliminary APIs for OpenEye TK, RDKIT, OpenBabel/Pybel, and CACTVS.
25-Jan-2020 - V0.13 Add CactvsMoleculeFactory() and test methods.
 7-Mar-2020 - V0.14 Add OeSearchMoleculeProvider(), ChemCompSearchIndexProvider()
10-Mar-2020 - V0.15 Add CI pipeline configuration.
11-Mar-2020 - V0.16 Update documentation and path defaults for concatenated component dictionaries
12-Mar-2020 - V0.17 Add ChemCompSearchWrapper() and associated tests
13-Mar-2020 - V0.18 Add formula matching method in ChemCompSearchIndexProvider()
13-Mar-2020 - V0.19 Make formula result MatchResults()
14-Mar-2020 - V0.20 Add formula parser in module MolecularFormula()
16-Mar-2020 - V0.21 Adjust formula range search filter.
16-Mar-2020 - V0.22 Simplify joint fingerprint and ssSearch -
16-Mar-2020 - V0.23 Suppress logging of formula results
27-Mar-2020 - V0.24 Adjust atom and bond stereo depiction avoid display undefined features
 2-Apr-2020 - V0.25 Adjustments to improve labeling of large structures and include W/H stereo
10-Apr-2020 - V0.26 Adjustments for default substructure search constraints and build defaults
16-Apr-2020 - V0.27 Return screening fpScores with substructure search results - adjustments in depiction resolution
16-May-2020 - V0.28 Revise search index unique identifiers, adjustments for refine aligned depictions, add ChemCompDepictWrapper()
16-May-2020 - V0.29 Asign substructure name in mol2* files
17-May-2020 - V0.30 Adjust labeling in search index.
 3-Jun-2020 - V0.31 Add getIndexFilePath() methods to each index provider class.
 9-Jun-2020 - V0.32 Additional ChemCompSearchWrapper() methods to manage dependencies
10-Jun-2020 - V0.33 Allow file name adjustments to stash and recover methods and further suppress logging in quietMode
11-Jun-2020 - V0.34 Maintain the consistent cache behavior
11-Jun-2020 - V0.35 Allow cache reuse when rebuilding dependencies
27-Jun-2020 - V0.36 Unify cache management in search and depict wrapper classes
28-Jun-2020 - V0.37 Adding a fallback for missing depict config file
 1-Jul-2020 - V0.38 Adjust match option names.
 1-Jul-2020 - V0.39 Avoid exhaustive ss search for negative pre-filter results
20-Aug-2020 - V0.40 Update dependencies
29-Sep-2020 - V0.41 Update dependencies
21-Oct-2020 - V0.42 Separate substructure search in a new module, adjustments for latest black formatting
23-Oct-2020 - V0.43 Integrate new substructure search with ChemCompSearchWrapper()
10-Dec-2020 - V0.45 In progress update to py39, add toMolFile() to ChemCompDepictWrapper(), upversion
15-Dec-2020 - V0.47 Make the build type options adjustable in OeMoleculeFactory.buildRelated(), add tests, upversion
18-Dec-2020 - V0.48 Corrections in fileToMols() and stringToMols(), and add OeMcssSearchUtils() and tests
18-Jan-2021 - V0.49 Add module OeChemCompUtils() and tests, and update dependencies
18-Jan-2021 - V0.50 Reorder chem_comp_atom data items in OeChemCompUtils()
26-Jan-2021 - V0.51 Add module ChemCompAlignUtils() and update dependencies
27-Jan-2021 - V0.52 Adjustments to error handling in OeSearchMoleculeProvider()
31-Jan-2021 - V0.53 API adjustments in OeAlignUtils() to export feature coordinates/formal charge for cif/OE molecules
 1-Feb-2021 - V0.54 Fix initialization for missing coordinates OeMoleculeFactory.getAtomDetails()
 1-Feb-2021 - V0.55 Adjust reporting of undefined CIP stereochemistry for non-carbon atoms.
 2-Feb-2021 - V0.56 Make OE warnings optional in OeAlignUtils().
 2-Feb-2021 - V0.57 Add working path to OeAlignUtils().
 3-Feb-2021 - V0.58 Add search criteria relaxed-stereo-sdeq and relaxed-sdeq
 4-Feb-2021 - V0.59 Increase timeout in OeAlignUtils() and add return atom counts for molecule setters.
 4-Feb-2021 - V0.60 Add working path for MarshalUtil() in OeAlignUtils()
 4-Feb-2021 - V0.61 Reduce timeout to 120s in OeAlignUtils()
 2-Mar-2021 - V0.62 Updating a search criteria, adding multipage substructure alignment depiction,
                    and new comparison searchtests with depiction.
 5-Mar-2021 - V0.63 Add BatchChemSearch() module and associated tests
 8-Mar-2021 - V0.64 Add option (largestPart) to read/process the largest connected part in fileToMols()/OeMoleculeFactory()
 9-Mar-2021 - V0.65 Add methods to import oeMol directly into OeAlignUtils(), add method to get CIF container object from OeChemCompUtils()
11-Mar-2021 - V0.66 Add option to skip annotations in OeChemCompUtils()
11-Mar-2021 - V0.67 Add timeout decorator to method addOeMol() OeChemCompUtils()
12-Mar-2021 - V0.68 Add constraint on the maximum number of matches for OESubSearch() in OeAlignUtils.
12-Mar-2021 - V0.69 Add constraint on the maximum number of substructure matches for OeDepictAlign().
13-Mar-2021 - V0.70 Change to multi-process timeout decorator with variable timeout settings.
 5-May-2021 - V0.71 Update dependencies
 9-Jun-2021 - V0.72 Update installation tools and add diagnostic output for fingerprint score results
 9-Jun-2021 - V0.73 Update manifest files
22-Aug-2021 - V0.74 Add ChemAxonDescriptorProvider and associated tests.  Add ChemAxon smiles to search index build.
26-Aug-2021 - V0.75 Add filter for obsolete definitions in ChemCompMoleculeProvider and ChemCompSearchIndexProvider modules
23-Sep-2021 - V0.76 Set default for skipObsolete to True
 9-Jan-2023 - V0.77 Configuration changes to support tox 4
19-May-2023 - V0.78 Update DNS to PDB archive
 6-Feb-2024 - V0.79 Update Azure testing pipelines to use MacOS 13;
                    Suppress errors logged for UNL (UNknown Ligand) chemical component
21-May-2024 - V0.80 Fix pylinting
11-Feb-2025 - V0.81 Update requirements and update CI/CD to python 3.10
26-Feb-2025 - V0.82 Adjust ChemAxon API request for SMILES standardization (following changes to their converter API)
31-Jul-2025 - V0.83 Loosen OpenEye requirement from `>= 2024.1.1` to `>= 2022.1`
18-Aug-2025 - V0.84 Update OpenEye requirement to be `>= 2022.1.0` (`2022.1` doesn't exist)
 2-Dec-2025 - V0.85 Switch from setuptools to hatch build system;
                    Update pipelines to use python 3.12 (note that latest OpenEye (2025.1.1) only supports up to 3.12)
16-Feb-2026 - V0.86 Update CactvsMoleculeFactory imports
