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HISTORY.txt
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HISTORY.txt
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# RCSB_UTILS_CHEMREF HISTORY
1-Nov-2018 - V0.10 Created module supporting DrugBank and CCDC model mapping
8-Dec-2018 - V0.11 Add export of loadable DrugBank object.
10-Dec-2018 - V0.12 Adjustments for DrugBank schema compliance
7-Jan-2019 - V0.13 Qualify default section name in config path lookup
25-Jan-2019 - V0.14 DrugBank schema extension
29-Jan-2019. - V0.15 Add context filtering feature in module ChemCompDataPrep
31-Jan-2019 - V0.16 Make copy of all category and attribute lists on remove cycles.
16-Feb-2019 V0.17 add drugbank_container_identifiers.
23-Mar-2019 - V0.18 adjust item name for affected_organisms
10-Apr-2019 - V0.19 add atc_codes
25-Jun-2019 - V0.20 Update development workflows
12-Aug-2019 - V0.21 Refactor DrugBank workflow
14-Aug-2019 - V0.22 Improve cache management
29-Aug-2019 - V0.23 Add DrugBankProvider() and ChemCompModelProvider() modules
9-Sep-2019 - V0.24 Add AtcProvider() module and extract ATC mapping from DrugBank
17-Sep-2019 - V0.25 Schema adjustments to discard private collection keys
16-Oct-2019 - V0.26 Enumerate all ATC parents in tree node list
17-Oct-2019 - V0.27 Ignore root node of the ATC hierarchy and reduce depth by 1.
23-Nov-2019 - V0.28 Add module ChemCompProvider() update to pipeline to py38
14-Dec-2019 - V0.29 Adjust error reporting for DrugBankProvider.testCache()
17-Dec-2019 - V0.30 Prefer http to ftp protocol for default download targets.
24-Jan-2020 - V0.31 Add fallback resource for ATC
29-Jan-2020 - V0.32 Skip escaping non-ascii characters.
3-Feb-2020 - V0.33 Update dependencies
18-Mar-2020 - V0.34 Add ResidProvider() and related modules.
19-Mar-2020 - V0.35 Simplify API and eliminate configuration cache directory items
19-Mar-2020 - V0.36 Add PsiModProvider module
24-Mar-2020 - V0.37 Update dependencies.
1-Apr-2020 - V0.38 New module PubChemUtils()
8-Apr-2020 - V0.39 Extensions for PubChemUtils() with additional tests using namedtuple input
1-May-2020 - V0.40 Extensions for full PubChem data extraction
5-May-2020 - V0.41 PubChemUtils.assemble() api adjustments and object content adjustments
15-May-2020 - V0.42 Reduce DrugBank test memory footprint.
17-May-2020 - V0.43 Extend ChemicalIdentifier
23-May-2020 - V0.44 Update logging
28-May-2020 - V0.45 Hookup alternative URL fetch library.
16-Jul-2020 - V0.46 Extend the API for PubChemUtils.assemble()
20-Jul-2020 - V0.47 Adjust error handling and reporting.
28-Jul-2020 - V0.48 Add PubChemProvider() to manage access to PubChem mapped annotations
28-Jul-2020 - V0.49 Up-version and update dependencies
28-Jul-2020 - V0.50 Tweaking stash configuration options in test cases.
29-Jul-2020 - V0.51 Add public reload() method to PubChemProvider().
30-Jul-2020 - V0.52 Add PharosProvider() module, supporting tests, and ad hoc tools.
30-Jul-2020 - V0.53 Provide bypass for PubChem and PharosProvider testCache() methods.
10-Sep-2020 - V0.54 Disable NCBI pathway tests owing to data availability
10-Sep-2020 - V0.55 Disable further tests for now
19-Sep-2020 - V0.56 Use a version specific Drugbank URL
24-Sep-2020 - V0.57 Use new Drugbank URL
21-Oct-2020 - V0.58 Add brand names to Drugbank mapping file
10-Nov-2020 - V0.59 Add ChEMBLProvider module and tests
11-Nov-2020 - V0.60 Add DrugCentralProvider module and tests
28-Nov-2020 - V0.61 Add CARDProvider module and tests
2-Dec-2020 - V0.62 Add ChEMBL API methods to provide drug, molecule and id mapping data
5-Dec-2020 - V0.63 Require certificates for PubChem lookups, extend timeout
5-Dec-2020 - V0.64 Adjust timeOut argument
9-Dec-2020 - V0.65 Add fallback resource for PSIMOD ontology
4-Feb-2021 - V0.66 Add export of audit details to ChemCompModelProvider()
9-Feb-2021 - V0.67 Add CODProvider() and related tests, add atom count method to ChemCompProvider()
10-Feb-2021 - V0.68 Add RcsbLigandScoreProvider() and related tests
23-Feb-2021 - V0.69 Adjust logging details in RcsbLigandScoreProvider()
28-Apr-2021 - V0.70 Add fallback resource for RESID in ResidProvider()
3-May-2021 - V0.71 Update PIR ftp site URL and path for RESID
1-Jun-2021 - V0.72 Add BirdProvider() module and tests, update __docformat__
5-Jun-2021 - V0.73 Update ATC ontology source and fallback
21-Jun-2021 - V0.74 Add getFeature() method to DrugBankProvider() module.
22-Jun-2021 - V0.75 Add getDrugbankIds() method to DrugBankProvider() module.
24-Jul-2021 - V0.76 Make each provider a subclass of StashableBase, update install and pipeline
25-Jul-2021 - V0.77 Adjust testCache() tests and logging for all providers
27-Jul-2021 - V0.78 Further adjustments to standardize testCache() provider logic
1-Aug-2021 - V0.79 Add release date data and methods to the ChemCompProvider module
16-Oct-2021 - V0.80 Update DrugCentral download url, update base version of ChEMBL data
3-Jan-2022 - V0.81 Update AtcProvider data loading methods to address recent changes in source NCBO ATC files
28-Mar-2022 - V0.82 Fix pylint issue with "Iterated dict modified inside for loop body" in testChemCompProvider
25-Jul-2022 - V0.83 Revert last change to AtcProvider - source NCBO ATC files were updated again to restore previous format
27-Jul-2022 - V0.84 Adapt to multiple possible naming schemes for ATC class IDs
9-Jan-2023 - V0.85 Configuration changes to support tox 4
22-Mar-2023 - V0.86 Update references to py-rcsb_exdb_assets master branch
19-Apr-2023 - V0.87 Update file path in ATCProvider
19-May-2023 - V0.88 Update DNS to PDB archive
5-Jun-2023 - V0.89 Include bond count in ChemCompProvider
20-Sep-2023 - V0.90 Adjust request methods in PubChemUtils; Use HTTPS instead of FTP for ChEMBL data
30-Nov-2023 - V0.91 Add drug product information (approved, country, dates of marketing, etc.)
21-May-2024 - V0.92 Fix pylinting