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Recent Releases of ersilia

ersilia - August 2025

What's Changed

  • Model incorporation debugging by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1672
  • added exceptions for null publication and source code by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1678
  • add exception for contributor, it can be none by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1679
  • update base information with dockerhub by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1680
  • docker architecture escaping and more by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1681
  • build(deps): bump GrantBirki/issue-template-parser from 7.0.3 to 7.0.4 by @dependabot[bot] in https://github.com/ersilia-os/ersilia/pull/1669
  • Deprecating support for string and list input types in Ersilia by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1706
  • remove input shape by @GemmaTuron in https://github.com/ersilia-os/ersilia/pull/1718
  • bugfixes test command by @GemmaTuron in https://github.com/ersilia-os/ersilia/pull/1720
  • Updating links to AirTable and S3 by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1719
  • fix: binray splitting, input missing in output, string wrapper issue by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1717
  • Fix issues by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1723
  • Fix issues with BI class by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1725

Full Changelog: https://github.com/ersilia-os/ersilia/compare/v0.1.45...v0.1.47

- Python
Published by github-actions[bot] 11 months ago

ersilia - July 2025

What's Changed

  • Model incorporation debugging by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1672
  • added exceptions for null publication and source code by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1678
  • add exception for contributor, it can be none by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1679
  • update base information with dockerhub by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1680
  • docker architecture escaping and more by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1681
  • build(deps): bump GrantBirki/issue-template-parser from 7.0.3 to 7.0.4 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1669
  • Deprecating support for string and list input types in Ersilia by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1706
  • Deep command failure, adding failed test breakpoint in playgr… by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1708

Full Changelog: https://github.com/ersilia-os/ersilia/compare/v0.1.45...v0.1.46

- Python
Published by github-actions[bot] 12 months ago

ersilia - June 2025

What's Changed

  • Fix parsing issue and few other fixes in test command by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1636
  • Bump actions/checkout from 3.5.3 to 4.2.2 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1637
  • Bump actions/setup-python from 4 to 5 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1638
  • Bump GrantBirki/json-yaml-validate from 3.2.1 to 3.3.0 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1639
  • Fix precalculation by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1642
  • Implementing deterministic sampling in example command and refactoring deep performance input interval by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1626
  • fix computational performance fields by @GemmaTuron in https://github.com/ersilia-os/ersilia/pull/1643
  • remove pack method from metadata by @GemmaTuron in https://github.com/ersilia-os/ersilia/pull/1645
  • Hotfix/test command by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1646
  • Updates test command by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1658
  • Splunk monitoring including tracking country and use case by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1659
  • Fix caching by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1661

Full Changelog: https://github.com/ersilia-os/ersilia/compare/v0.1.44...v0.1.45

- Python
Published by github-actions[bot] about 1 year ago

ersilia - May 2025

What's Changed

  • Bump abatilo/actions-poetry from 3.0.1 to 4.0.0 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1530
  • Testing Playground Refactor by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1528
  • fix nox config by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1545
  • Bump actions/upload-artifact from 4.5.0 to 4.6.0 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1529
  • Resolve duplication of values in CSV serialization by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1543
  • Test command refactor by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1506
  • remove unnecessary input filtering by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1546
  • Clean up redundant dummy models and circle ci config by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1548
  • Bug fixes h5 by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1547
  • Fix/bug wrong input handling by @OlawumiSalaam in https://github.com/ersilia-os/ersilia/pull/1550
  • Handle BentoML errors & clean up failed models by @OlawumiSalaam in https://github.com/ersilia-os/ersilia/pull/1527
  • hotfix:make airtable conn work by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1554
  • workflow fox by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1557
  • Revert "hotfix:make airtable conn work" by @GemmaTuron in https://github.com/ersilia-os/ersilia/pull/1558
  • Parallel session fix by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1559
  • Fix/incorrect header mapping by @OlawumiSalaam in https://github.com/ersilia-os/ersilia/pull/1556
  • Packing with Ersilia Pack now resolved columns from columns file name, avoiding issues with schema resolution by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1563
  • bentoml used only when necessary by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1565
  • pre commit fixes by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1567
  • test command refactor wip 0 by @GemmaTuron in https://github.com/ersilia-os/ersilia/pull/1568
  • update metadata with newest fields (commented out) by @GemmaTuron in https://github.com/ersilia-os/ersilia/pull/1570
  • fix BI exceptions, Create class to update metadata from airtable, rea… by @GemmaTuron in https://github.com/ersilia-os/ersilia/pull/1572
  • Refactor/v2 test command refactoring by @GemmaTuron in https://github.com/ersilia-os/ersilia/pull/1578
  • Redis cache setup by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1579
  • pack resolver from metadata and docker client setting by @GemmaTuron in https://github.com/ersilia-os/ersilia/pull/1582
  • Fix for arm image endpoint issue by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1591
  • Ultimate arm image error fix by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1593
  • refactoring codes which creates _logs from container by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1585
  • fix date by @GemmaTuron in https://github.com/ersilia-os/ersilia/pull/1594
  • Redis configuration support by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1596
  • resolves issue (#1586): batching and h5, json support in std runner by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1588
  • parsing fix for model output by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1597
  • deprecating isaura by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1599
  • fix: hdf5 proper string parsing by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1603
  • Fix test‑command deep‑flag, H5 string serialization, and adopt log‑scale input sizing for performance by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1606
  • Dimension based empty value filling in hdf5 file by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1607
  • update test workflows for ersilia cli by @GemmaTuron in https://github.com/ersilia-os/ersilia/pull/1613
  • Tracking for splunk by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1616
  • Eliminate input shape requeriment by @GemmaTuron in https://github.com/ersilia-os/ersilia/pull/1621
  • bugfix getting metadata from github by @GemmaTuron in https://github.com/ersilia-os/ersilia/pull/1624
  • Refactor/integrating gdi caching by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1635
  • remove auth command by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1628

Full Changelog: https://github.com/ersilia-os/ersilia/compare/v0.1.41...v0.1.44

- Python
Published by github-actions[bot] about 1 year ago

ersilia - April 2025

What's Changed

  • Bump abatilo/actions-poetry from 3.0.1 to 4.0.0 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1530
  • Testing Playground Refactor by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1528
  • fix nox config by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1545
  • Bump actions/upload-artifact from 4.5.0 to 4.6.0 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1529
  • Resolve duplication of values in CSV serialization by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1543
  • Test command refactor by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1506
  • remove unnecessary input filtering by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1546
  • Clean up redundant dummy models and circle ci config by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1548
  • Bug fixes h5 by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1547
  • Fix/bug wrong input handling by @OlawumiSalaam in https://github.com/ersilia-os/ersilia/pull/1550
  • Handle BentoML errors & clean up failed models by @OlawumiSalaam in https://github.com/ersilia-os/ersilia/pull/1527
  • hotfix:make airtable conn work by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1554
  • workflow fox by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1557
  • Revert "hotfix:make airtable conn work" by @GemmaTuron in https://github.com/ersilia-os/ersilia/pull/1558
  • Parallel session fix by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1559
  • Fix/incorrect header mapping by @OlawumiSalaam in https://github.com/ersilia-os/ersilia/pull/1556
  • Packing with Ersilia Pack now resolved columns from columns file name, avoiding issues with schema resolution by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1563
  • bentoml used only when necessary by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1565
  • pre commit fixes by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1567
  • test command refactor wip 0 by @GemmaTuron in https://github.com/ersilia-os/ersilia/pull/1568
  • update metadata with newest fields (commented out) by @GemmaTuron in https://github.com/ersilia-os/ersilia/pull/1570
  • fix BI exceptions, Create class to update metadata from airtable, rea… by @GemmaTuron in https://github.com/ersilia-os/ersilia/pull/1572
  • Refactor/v2 test command refactoring by @GemmaTuron in https://github.com/ersilia-os/ersilia/pull/1578
  • Redis cache setup by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1579
  • pack resolver from metadata and docker client setting by @GemmaTuron in https://github.com/ersilia-os/ersilia/pull/1582
  • Fix for arm image endpoint issue by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1591
  • Ultimate arm image error fix by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1593
  • refactoring codes which creates _logs from container by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1585
  • fix date by @GemmaTuron in https://github.com/ersilia-os/ersilia/pull/1594
  • Redis configuration support by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1596
  • resolves issue (#1586): batching and h5, json support in std runner by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1588
  • removing rdkit dependencies by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1592

Full Changelog: https://github.com/ersilia-os/ersilia/compare/v0.1.41...v0.1.43

- Python
Published by github-actions[bot] about 1 year ago

ersilia - March 2025

What's Changed

  • Bump abatilo/actions-poetry from 3.0.1 to 4.0.0 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1530
  • Testing Playground Refactor by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1528
  • fix nox config by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1545
  • Bump actions/upload-artifact from 4.5.0 to 4.6.0 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1529
  • Resolve duplication of values in CSV serialization by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1543
  • Test command refactor by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1506
  • remove unnecessary input filtering by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1546
  • Clean up redundant dummy models and circle ci config by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1548
  • Bug fixes h5 by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1547
  • Fix/bug wrong input handling by @OlawumiSalaam in https://github.com/ersilia-os/ersilia/pull/1550
  • Handle BentoML errors & clean up failed models by @OlawumiSalaam in https://github.com/ersilia-os/ersilia/pull/1527
  • hotfix:make airtable conn work by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1554
  • workflow fox by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1557
  • Revert "hotfix:make airtable conn work" by @GemmaTuron in https://github.com/ersilia-os/ersilia/pull/1558
  • Parallel session fix by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1559
  • Fix/incorrect header mapping by @OlawumiSalaam in https://github.com/ersilia-os/ersilia/pull/1556
  • Packing with Ersilia Pack now resolved columns from columns file name, avoiding issues with schema resolution by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1563
  • bentoml used only when necessary by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1565
  • pre commit fixes by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1567
  • test command refactor wip 0 by @GemmaTuron in https://github.com/ersilia-os/ersilia/pull/1568
  • update metadata with newest fields (commented out) by @GemmaTuron in https://github.com/ersilia-os/ersilia/pull/1570

Full Changelog: https://github.com/ersilia-os/ersilia/compare/v0.1.41...v0.1.42

- Python
Published by github-actions[bot] over 1 year ago

ersilia - February 2025

What's Changed

  • Refactor Ersilia test command by @kurysauce in https://github.com/ersilia-os/ersilia/pull/1224
  • Move the model inspection code by @dzumii in https://github.com/ersilia-os/ersilia/pull/1227
  • Bump actions/upload-artifact from 4.3.3 to 4.3.4 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1217
  • Bump GrantBirki/comment from 2.0.10 to 2.1.0 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1218
  • Bump actions/setup-python from 5.1.0 to 5.1.1 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1219
  • Sorting model tags alphabetically by @dzumii in https://github.com/ersilia-os/ersilia/pull/1229
  • Clean up dependencies related to ersilia test module by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1238
  • Remove setup.py in favor of only keeping pyproject.toml by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1239
  • Fix/tracking s3 connection by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1244
  • Make PyAirtable optional by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1245
  • Sorting tags regardless of the case by @dzumii in https://github.com/ersilia-os/ersilia/pull/1240
  • Bump actions/setup-python from 4 to 5 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1252
  • Bump GrantBirki/json-yaml-validate from 3.0.0 to 3.2.1 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1251
  • Bump actions/upload-artifact from 4.3.3 to 4.4.0 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1250
  • Bump GrantBirki/issue-template-parser from 7.0.2 to 7.0.3 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1249
  • Fix 'card' KeyError in ersilia catalog command by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1260
  • Replace metadata.json with metadata.yaml in the update metadata workflow by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1261
  • Ersilia pack dockerization by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1258
  • De-register api command from Ersilia CLI by @adebisi4145 in https://github.com/ersilia-os/ersilia/pull/1289
  • Removing PyAirtable dependency (#1259) by @daud99 in https://github.com/ersilia-os/ersilia/pull/1291
  • Removal of Ersilia current command by @Ajoke23 in https://github.com/ersilia-os/ersilia/pull/1284
  • Merged card command with catalog. #1264 by @teddyCodex in https://github.com/ersilia-os/ersilia/pull/1285
  • Task: Automatically update CodeMeta upon release #1276 by @OlawumiSalaam in https://github.com/ersilia-os/ersilia/pull/1288
  • Removed the api command from the Circleci workflow by @mercybassey in https://github.com/ersilia-os/ersilia/pull/1305
  • Updating Metadata.py file by @Faith-Adegoke in https://github.com/ersilia-os/ersilia/pull/1306
  • Bump rdkit version (#1304) by @daud99 in https://github.com/ersilia-os/ersilia/pull/1308
  • Print ersilia catalog in a table natively by @jubril-adeyi in https://github.com/ersilia-os/ersilia/pull/1292
  • 🐈 Task: Refactor ersilia clear command #1266 by @KimFarida in https://github.com/ersilia-os/ersilia/pull/1301
  • Fix: Update CompoundIdentifier to handle invalid SMILES inputs by @musasizivictoria in https://github.com/ersilia-os/ersilia/pull/1295
  • Fetch CLI decision flow improvement(#1299) by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1311
  • Update approve-trigger.yml by @aderemi1224 in https://github.com/ersilia-os/ersilia/pull/1300
  • Added support for both strings and lists in the information by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1325
  • Update card.py by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1326
  • Add positive unit test for isinputheader in CompoundIdentifier by @musasizivictoria in https://github.com/ersilia-os/ersilia/pull/1320
  • Update release date by @OlawumiSalaam in https://github.com/ersilia-os/ersilia/pull/1322
  • Create DEVELOPMENT.md file by @Ajoke23 in https://github.com/ersilia-os/ersilia/pull/1318
  • Improve CONTRIBUTING.md file by @adebisi4145 in https://github.com/ersilia-os/ersilia/pull/1307
  • Create a positive test for is_key_header by @mercybassey in https://github.com/ersilia-os/ersilia/pull/1324
  • Update inspect.py to include --track flag support for model inspection by @AnushkaShreyam in https://github.com/ersilia-os/ersilia/pull/1327
  • Add negative unit test for iskeyheader in testcompoundidentifier.py by @Ajoke23 in https://github.com/ersilia-os/ersilia/pull/1330
  • Integrate GDI inference store with CLI by @nicholas-kondal in https://github.com/ersilia-os/ersilia/pull/1190
  • Read the JSON file from the S3 interface by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1349
  • Drop Python 3.7 support and update tests by @Darkbeast-glitch in https://github.com/ersilia-os/ersilia/pull/1316
  • Add --all flag to delete all locally available models by @JoyProg in https://github.com/ersilia-os/ersilia/pull/1317
  • Fix control flow by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1378
  • Bump actions/checkout from 3.5.3 to 4.2.2 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1361
  • Bump actions/upload-artifact from 4.4.0 to 4.4.3 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1362
  • Bump abatilo/actions-poetry from 3.0.0 to 3.0.1 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1363
  • Adding table based result output by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1364
  • Singleton implementation and coloring the logging status by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1365
  • Serve time rdkit and other package installation by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1366
  • Make ersilia metadata file agnostic by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1380
  • Bump requests and docker-py by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1150
  • Added CompoundIdentifier class isinputheader negative test by @musasizivictoria in https://github.com/ersilia-os/ersilia/pull/1328
  • Add a positive test unit for issmiles when chem is none in testcompoundidentifier.py by @Ajoke23 in https://github.com/ersilia-os/ersilia/pull/1332
  • Added tests for CatalogTable.aslistof_dicts (#1319) by @daud99 in https://github.com/ersilia-os/ersilia/pull/1331
  • add positive test for the isinchikey method in CompoundIdentifier class by @adebisi4145 in https://github.com/ersilia-os/ersilia/pull/1333
  • Test for guess_type with inchikey in CompoundIdentifier class by @Ajoke23 in https://github.com/ersilia-os/ersilia/pull/1357
  • add negative test for the isinchikey method in CompoundIdentifier class by @adebisi4145 in https://github.com/ersilia-os/ersilia/pull/1334
  • Update test for positive inchikey by @tongyu0924 in https://github.com/ersilia-os/ersilia/pull/1336
  • Make fetch fail if standardrun doesnt work by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1386
  • Bug fixes: inchtokey converter args missing by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1391
  • Add tests for issmiles, isinchikey, and guess_type methods in CompoundIdentifier class by @musasizivictoria in https://github.com/ersilia-os/ersilia/pull/1358
  • Fix dependency vulnerabilities by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1396
  • Remove duplicate flag --repo_path from the fetch command (#1370) by @snufkinwa in https://github.com/ersilia-os/ersilia/pull/1381
  • Logging at realtime from the async subprocess while pulling by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1392
  • Miscellaneous fixes by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1405
  • CLI test integration by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1383
  • Remove setuptools dependency by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1410
  • Remove Airtable dependency completely by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1415
  • Refactor catalog command to show local catalog by default by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1420
  • Copy example files from images built using ersilia pack by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1421
  • Misc CLI clean ups by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1424
  • Update Issue Template to Remove Auto-Assignment by @Malikbadmus in https://github.com/ersilia-os/ersilia/pull/1425
  • Model tester and Inspect command functionality updates by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1416
  • Add detailed docstrings and usage examples to CLI command functions by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1427
  • Refactor Catalog command by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1426
  • Fix/refactor example cmd by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1430
  • Add detailed docstrings and usage examples to Ersilia'a core modules by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1428
  • Add detailed docstrings and usage examples to Ersilia'a hub modules by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1435
  • Add detailed docstrings and usage examples to Ersilia'a db modules and improvement on core and cli module by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1436
  • Add detailed docstrings and usage examples to Ersilia'a io modules by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1440
  • Make ersilia report docker issues better by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1445
  • Clean up workflows by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1446
  • Add detailed docstrings and usage examples to Ersilia'a serve modules by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1439
  • Add detailed docstrings and usage examples to Ersilia'a lake modules by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1438
  • Add detailed docstrings and usage examples to Ersilia'a store modules by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1441
  • Add detailed docstrings and usage examples to Ersilia'a setup modules by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1442
  • Make Ersilia exit when trying to delete a model fetched using docker if Docker is not active by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1447
  • Add detailed docstrings and usage examples to Ersilia'a tool modules by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1444
  • Add detailed docstrings and usage examples to Ersilia'a publish module and few update on the test module by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1443
  • Packaging module not imported error fix by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1457
  • Fixing inspect service skipping few remote checks by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1460
  • Fix thread holding when tracking by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1465
  • Fix For Hard Coded URL In Pytest by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1463
  • add a positive test for pubchemsmilestoinchikey by @olamidepeterojo in https://github.com/ersilia-os/ersilia/pull/1451
  • Update model.py python code to enable rendering in sphinx docs by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1452
  • Legacy bentoml dockerfile python version upgrade by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1469
  • Raise error if model directory doesn't exist by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1471
  • Access the correct index to get model identifier when deleting all local models by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1472
  • Clean up session information for deleted models by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1474
  • Model incorporation with llms by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1475
  • Make python api work by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1476
  • Bump actions/upload-artifact from 4.4.3 to 4.5.0 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1482
  • Bump actions/checkout from 4.1.7 to 4.2.2 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1483
  • Integrating ruff precommit by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1473
  • Support versioning of Dockerized models by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1481
  • Remove models.tsv by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1489
  • Use DataFrame class to serialize h5 and csv by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1490
  • change minimum length for description to 10 by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1485
  • Use marketplace action to setup conda and python by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1499
  • Final CLI Improvements by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1495
  • Bugfix/ python3.12 compatibility issue by @OlawumiSalaam in https://github.com/ersilia-os/ersilia/pull/1498
  • Clean up compound identifier tests by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1502
  • py3.12 incompatibility with scipy and rdkit update by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1500
  • Clean up temp files from model containers by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1512
  • Airtable field update and add unit testing by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1514
  • Fixing tabular output table to support all output types and DS by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1516
  • Refactoring Test Command by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1515
  • Fix: Truncate large debug outputs to prevent terminal clutter and Improve log readability by @OlawumiSalaam in https://github.com/ersilia-os/ersilia/pull/1522
  • upgrade loguru by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1525

New Contributors

  • @adebisi4145 made their first contribution in https://github.com/ersilia-os/ersilia/pull/1289
  • @daud99 made their first contribution in https://github.com/ersilia-os/ersilia/pull/1291
  • @Ajoke23 made their first contribution in https://github.com/ersilia-os/ersilia/pull/1284
  • @teddyCodex made their first contribution in https://github.com/ersilia-os/ersilia/pull/1285
  • @OlawumiSalaam made their first contribution in https://github.com/ersilia-os/ersilia/pull/1288
  • @mercybassey made their first contribution in https://github.com/ersilia-os/ersilia/pull/1305
  • @Faith-Adegoke made their first contribution in https://github.com/ersilia-os/ersilia/pull/1306
  • @jubril-adeyi made their first contribution in https://github.com/ersilia-os/ersilia/pull/1292
  • @KimFarida made their first contribution in https://github.com/ersilia-os/ersilia/pull/1301
  • @musasizivictoria made their first contribution in https://github.com/ersilia-os/ersilia/pull/1295
  • @aderemi1224 made their first contribution in https://github.com/ersilia-os/ersilia/pull/1300
  • @AnushkaShreyam made their first contribution in https://github.com/ersilia-os/ersilia/pull/1327
  • @nicholas-kondal made their first contribution in https://github.com/ersilia-os/ersilia/pull/1190
  • @Darkbeast-glitch made their first contribution in https://github.com/ersilia-os/ersilia/pull/1316
  • @JoyProg made their first contribution in https://github.com/ersilia-os/ersilia/pull/1317
  • @tongyu0924 made their first contribution in https://github.com/ersilia-os/ersilia/pull/1336
  • @snufkinwa made their first contribution in https://github.com/ersilia-os/ersilia/pull/1381
  • @olamidepeterojo made their first contribution in https://github.com/ersilia-os/ersilia/pull/1451

Full Changelog: https://github.com/ersilia-os/ersilia/compare/v0.1.36...v0.1.41

- Python
Published by github-actions[bot] over 1 year ago

ersilia - January 2025

What's Changed

  • Refactor Ersilia test command by @kurysauce in https://github.com/ersilia-os/ersilia/pull/1224
  • Move the model inspection code by @dzumii in https://github.com/ersilia-os/ersilia/pull/1227
  • Bump actions/upload-artifact from 4.3.3 to 4.3.4 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1217
  • Bump GrantBirki/comment from 2.0.10 to 2.1.0 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1218
  • Bump actions/setup-python from 5.1.0 to 5.1.1 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1219
  • Sorting model tags alphabetically by @dzumii in https://github.com/ersilia-os/ersilia/pull/1229
  • Clean up dependencies related to ersilia test module by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1238
  • Remove setup.py in favor of only keeping pyproject.toml by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1239
  • Fix/tracking s3 connection by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1244
  • Make PyAirtable optional by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1245
  • Sorting tags regardless of the case by @dzumii in https://github.com/ersilia-os/ersilia/pull/1240
  • Bump actions/setup-python from 4 to 5 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1252
  • Bump GrantBirki/json-yaml-validate from 3.0.0 to 3.2.1 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1251
  • Bump actions/upload-artifact from 4.3.3 to 4.4.0 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1250
  • Bump GrantBirki/issue-template-parser from 7.0.2 to 7.0.3 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1249
  • Fix 'card' KeyError in ersilia catalog command by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1260
  • Replace metadata.json with metadata.yaml in the update metadata workflow by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1261
  • Ersilia pack dockerization by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1258
  • De-register api command from Ersilia CLI by @adebisi4145 in https://github.com/ersilia-os/ersilia/pull/1289
  • Removing PyAirtable dependency (#1259) by @daud99 in https://github.com/ersilia-os/ersilia/pull/1291
  • Removal of Ersilia current command by @Ajoke23 in https://github.com/ersilia-os/ersilia/pull/1284
  • Merged card command with catalog. #1264 by @teddyCodex in https://github.com/ersilia-os/ersilia/pull/1285
  • Task: Automatically update CodeMeta upon release #1276 by @OlawumiSalaam in https://github.com/ersilia-os/ersilia/pull/1288
  • Removed the api command from the Circleci workflow by @mercybassey in https://github.com/ersilia-os/ersilia/pull/1305
  • Updating Metadata.py file by @Faith-Adegoke in https://github.com/ersilia-os/ersilia/pull/1306
  • Bump rdkit version (#1304) by @daud99 in https://github.com/ersilia-os/ersilia/pull/1308
  • Print ersilia catalog in a table natively by @jubril-adeyi in https://github.com/ersilia-os/ersilia/pull/1292
  • 🐈 Task: Refactor ersilia clear command #1266 by @KimFarida in https://github.com/ersilia-os/ersilia/pull/1301
  • Fix: Update CompoundIdentifier to handle invalid SMILES inputs by @musasizivictoria in https://github.com/ersilia-os/ersilia/pull/1295
  • Fetch CLI decision flow improvement(#1299) by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1311
  • Update approve-trigger.yml by @aderemi1224 in https://github.com/ersilia-os/ersilia/pull/1300
  • Added support for both strings and lists in the information by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1325
  • Update card.py by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1326
  • Add positive unit test for isinputheader in CompoundIdentifier by @musasizivictoria in https://github.com/ersilia-os/ersilia/pull/1320
  • Update release date by @OlawumiSalaam in https://github.com/ersilia-os/ersilia/pull/1322
  • Create DEVELOPMENT.md file by @Ajoke23 in https://github.com/ersilia-os/ersilia/pull/1318
  • Improve CONTRIBUTING.md file by @adebisi4145 in https://github.com/ersilia-os/ersilia/pull/1307
  • Create a positive test for is_key_header by @mercybassey in https://github.com/ersilia-os/ersilia/pull/1324
  • Update inspect.py to include --track flag support for model inspection by @AnushkaShreyam in https://github.com/ersilia-os/ersilia/pull/1327
  • Add negative unit test for iskeyheader in testcompoundidentifier.py by @Ajoke23 in https://github.com/ersilia-os/ersilia/pull/1330
  • Integrate GDI inference store with CLI by @nicholas-kondal in https://github.com/ersilia-os/ersilia/pull/1190
  • Read the JSON file from the S3 interface by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1349
  • Drop Python 3.7 support and update tests by @Darkbeast-glitch in https://github.com/ersilia-os/ersilia/pull/1316
  • Add --all flag to delete all locally available models by @JoyProg in https://github.com/ersilia-os/ersilia/pull/1317
  • Fix control flow by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1378
  • Bump actions/checkout from 3.5.3 to 4.2.2 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1361
  • Bump actions/upload-artifact from 4.4.0 to 4.4.3 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1362
  • Bump abatilo/actions-poetry from 3.0.0 to 3.0.1 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1363
  • Adding table based result output by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1364
  • Singleton implementation and coloring the logging status by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1365
  • Serve time rdkit and other package installation by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1366
  • Make ersilia metadata file agnostic by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1380
  • Bump requests and docker-py by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1150
  • Added CompoundIdentifier class isinputheader negative test by @musasizivictoria in https://github.com/ersilia-os/ersilia/pull/1328
  • Add a positive test unit for issmiles when chem is none in testcompoundidentifier.py by @Ajoke23 in https://github.com/ersilia-os/ersilia/pull/1332
  • Added tests for CatalogTable.aslistof_dicts (#1319) by @daud99 in https://github.com/ersilia-os/ersilia/pull/1331
  • add positive test for the isinchikey method in CompoundIdentifier class by @adebisi4145 in https://github.com/ersilia-os/ersilia/pull/1333
  • Test for guess_type with inchikey in CompoundIdentifier class by @Ajoke23 in https://github.com/ersilia-os/ersilia/pull/1357
  • add negative test for the isinchikey method in CompoundIdentifier class by @adebisi4145 in https://github.com/ersilia-os/ersilia/pull/1334
  • Update test for positive inchikey by @tongyu0924 in https://github.com/ersilia-os/ersilia/pull/1336
  • Make fetch fail if standardrun doesnt work by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1386
  • Bug fixes: inchtokey converter args missing by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1391
  • Add tests for issmiles, isinchikey, and guess_type methods in CompoundIdentifier class by @musasizivictoria in https://github.com/ersilia-os/ersilia/pull/1358
  • Fix dependency vulnerabilities by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1396
  • Remove duplicate flag --repo_path from the fetch command (#1370) by @snufkinwa in https://github.com/ersilia-os/ersilia/pull/1381
  • Logging at realtime from the async subprocess while pulling by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1392
  • Miscellaneous fixes by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1405
  • CLI test integration by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1383
  • Remove setuptools dependency by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1410
  • Remove Airtable dependency completely by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1415
  • Refactor catalog command to show local catalog by default by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1420
  • Copy example files from images built using ersilia pack by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1421
  • Misc CLI clean ups by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1424
  • Update Issue Template to Remove Auto-Assignment by @Malikbadmus in https://github.com/ersilia-os/ersilia/pull/1425
  • Model tester and Inspect command functionality updates by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1416
  • Add detailed docstrings and usage examples to CLI command functions by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1427
  • Refactor Catalog command by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1426
  • Fix/refactor example cmd by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1430
  • Add detailed docstrings and usage examples to Ersilia'a core modules by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1428
  • Add detailed docstrings and usage examples to Ersilia'a hub modules by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1435
  • Add detailed docstrings and usage examples to Ersilia'a db modules and improvement on core and cli module by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1436
  • Add detailed docstrings and usage examples to Ersilia'a io modules by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1440
  • Make ersilia report docker issues better by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1445
  • Clean up workflows by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1446
  • Add detailed docstrings and usage examples to Ersilia'a serve modules by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1439
  • Add detailed docstrings and usage examples to Ersilia'a lake modules by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1438
  • Add detailed docstrings and usage examples to Ersilia'a store modules by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1441
  • Add detailed docstrings and usage examples to Ersilia'a setup modules by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1442
  • Make Ersilia exit when trying to delete a model fetched using docker if Docker is not active by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1447
  • Add detailed docstrings and usage examples to Ersilia'a tool modules by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1444
  • Add detailed docstrings and usage examples to Ersilia'a publish module and few update on the test module by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1443
  • Packaging module not imported error fix by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1457
  • Fixing inspect service skipping few remote checks by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1460
  • Fix thread holding when tracking by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1465
  • Fix For Hard Coded URL In Pytest by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1463
  • add a positive test for pubchemsmilestoinchikey by @olamidepeterojo in https://github.com/ersilia-os/ersilia/pull/1451
  • Update model.py python code to enable rendering in sphinx docs by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1452
  • Legacy bentoml dockerfile python version upgrade by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1469
  • Raise error if model directory doesn't exist by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1471
  • Access the correct index to get model identifier when deleting all local models by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1472
  • Clean up session information for deleted models by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1474
  • Model incorporation with llms by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1475
  • Make python api work by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1476
  • added new categories by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1478

New Contributors

  • @adebisi4145 made their first contribution in https://github.com/ersilia-os/ersilia/pull/1289
  • @daud99 made their first contribution in https://github.com/ersilia-os/ersilia/pull/1291
  • @Ajoke23 made their first contribution in https://github.com/ersilia-os/ersilia/pull/1284
  • @teddyCodex made their first contribution in https://github.com/ersilia-os/ersilia/pull/1285
  • @OlawumiSalaam made their first contribution in https://github.com/ersilia-os/ersilia/pull/1288
  • @mercybassey made their first contribution in https://github.com/ersilia-os/ersilia/pull/1305
  • @Faith-Adegoke made their first contribution in https://github.com/ersilia-os/ersilia/pull/1306
  • @jubril-adeyi made their first contribution in https://github.com/ersilia-os/ersilia/pull/1292
  • @KimFarida made their first contribution in https://github.com/ersilia-os/ersilia/pull/1301
  • @musasizivictoria made their first contribution in https://github.com/ersilia-os/ersilia/pull/1295
  • @aderemi1224 made their first contribution in https://github.com/ersilia-os/ersilia/pull/1300
  • @AnushkaShreyam made their first contribution in https://github.com/ersilia-os/ersilia/pull/1327
  • @nicholas-kondal made their first contribution in https://github.com/ersilia-os/ersilia/pull/1190
  • @Darkbeast-glitch made their first contribution in https://github.com/ersilia-os/ersilia/pull/1316
  • @JoyProg made their first contribution in https://github.com/ersilia-os/ersilia/pull/1317
  • @tongyu0924 made their first contribution in https://github.com/ersilia-os/ersilia/pull/1336
  • @snufkinwa made their first contribution in https://github.com/ersilia-os/ersilia/pull/1381
  • @olamidepeterojo made their first contribution in https://github.com/ersilia-os/ersilia/pull/1451

Full Changelog: https://github.com/ersilia-os/ersilia/compare/v0.1.36...v0.1.40

- Python
Published by github-actions[bot] over 1 year ago

ersilia - December 2024

What's Changed

  • Refactor Ersilia test command by @kurysauce in https://github.com/ersilia-os/ersilia/pull/1224
  • Move the model inspection code by @dzumii in https://github.com/ersilia-os/ersilia/pull/1227
  • Bump actions/upload-artifact from 4.3.3 to 4.3.4 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1217
  • Bump GrantBirki/comment from 2.0.10 to 2.1.0 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1218
  • Bump actions/setup-python from 5.1.0 to 5.1.1 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1219
  • Sorting model tags alphabetically by @dzumii in https://github.com/ersilia-os/ersilia/pull/1229
  • Clean up dependencies related to ersilia test module by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1238
  • Remove setup.py in favor of only keeping pyproject.toml by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1239
  • Fix/tracking s3 connection by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1244
  • Make PyAirtable optional by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1245
  • Sorting tags regardless of the case by @dzumii in https://github.com/ersilia-os/ersilia/pull/1240
  • Bump actions/setup-python from 4 to 5 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1252
  • Bump GrantBirki/json-yaml-validate from 3.0.0 to 3.2.1 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1251
  • Bump actions/upload-artifact from 4.3.3 to 4.4.0 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1250
  • Bump GrantBirki/issue-template-parser from 7.0.2 to 7.0.3 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1249
  • Fix 'card' KeyError in ersilia catalog command by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1260
  • Replace metadata.json with metadata.yaml in the update metadata workflow by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1261
  • Ersilia pack dockerization by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1258
  • De-register api command from Ersilia CLI by @adebisi4145 in https://github.com/ersilia-os/ersilia/pull/1289
  • Removing PyAirtable dependency (#1259) by @daud99 in https://github.com/ersilia-os/ersilia/pull/1291
  • Removal of Ersilia current command by @Ajoke23 in https://github.com/ersilia-os/ersilia/pull/1284
  • Merged card command with catalog. #1264 by @teddyCodex in https://github.com/ersilia-os/ersilia/pull/1285
  • Task: Automatically update CodeMeta upon release #1276 by @OlawumiSalaam in https://github.com/ersilia-os/ersilia/pull/1288
  • Removed the api command from the Circleci workflow by @mercybassey in https://github.com/ersilia-os/ersilia/pull/1305
  • Updating Metadata.py file by @Faith-Adegoke in https://github.com/ersilia-os/ersilia/pull/1306
  • Bump rdkit version (#1304) by @daud99 in https://github.com/ersilia-os/ersilia/pull/1308
  • Print ersilia catalog in a table natively by @jubril-adeyi in https://github.com/ersilia-os/ersilia/pull/1292
  • 🐈 Task: Refactor ersilia clear command #1266 by @KimFarida in https://github.com/ersilia-os/ersilia/pull/1301
  • Fix: Update CompoundIdentifier to handle invalid SMILES inputs by @musasizivictoria in https://github.com/ersilia-os/ersilia/pull/1295
  • Fetch CLI decision flow improvement(#1299) by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1311
  • Update approve-trigger.yml by @aderemi1224 in https://github.com/ersilia-os/ersilia/pull/1300
  • Added support for both strings and lists in the information by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1325
  • Update card.py by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1326
  • Add positive unit test for isinputheader in CompoundIdentifier by @musasizivictoria in https://github.com/ersilia-os/ersilia/pull/1320
  • Update release date by @OlawumiSalaam in https://github.com/ersilia-os/ersilia/pull/1322
  • Create DEVELOPMENT.md file by @Ajoke23 in https://github.com/ersilia-os/ersilia/pull/1318
  • Improve CONTRIBUTING.md file by @adebisi4145 in https://github.com/ersilia-os/ersilia/pull/1307
  • Create a positive test for is_key_header by @mercybassey in https://github.com/ersilia-os/ersilia/pull/1324
  • Update inspect.py to include --track flag support for model inspection by @AnushkaShreyam in https://github.com/ersilia-os/ersilia/pull/1327
  • Add negative unit test for iskeyheader in testcompoundidentifier.py by @Ajoke23 in https://github.com/ersilia-os/ersilia/pull/1330
  • Integrate GDI inference store with CLI by @nicholas-kondal in https://github.com/ersilia-os/ersilia/pull/1190
  • Read the JSON file from the S3 interface by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1349
  • Drop Python 3.7 support and update tests by @Darkbeast-glitch in https://github.com/ersilia-os/ersilia/pull/1316
  • Add --all flag to delete all locally available models by @JoyProg in https://github.com/ersilia-os/ersilia/pull/1317
  • Fix control flow by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1378
  • Bump actions/checkout from 3.5.3 to 4.2.2 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1361
  • Bump actions/upload-artifact from 4.4.0 to 4.4.3 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1362
  • Bump abatilo/actions-poetry from 3.0.0 to 3.0.1 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1363
  • Adding table based result output by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1364
  • Singleton implementation and coloring the logging status by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1365
  • Serve time rdkit and other package installation by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1366
  • Make ersilia metadata file agnostic by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1380
  • Bump requests and docker-py by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1150
  • Added CompoundIdentifier class isinputheader negative test by @musasizivictoria in https://github.com/ersilia-os/ersilia/pull/1328
  • Add a positive test unit for issmiles when chem is none in testcompoundidentifier.py by @Ajoke23 in https://github.com/ersilia-os/ersilia/pull/1332
  • Added tests for CatalogTable.aslistof_dicts (#1319) by @daud99 in https://github.com/ersilia-os/ersilia/pull/1331
  • add positive test for the isinchikey method in CompoundIdentifier class by @adebisi4145 in https://github.com/ersilia-os/ersilia/pull/1333
  • Test for guess_type with inchikey in CompoundIdentifier class by @Ajoke23 in https://github.com/ersilia-os/ersilia/pull/1357
  • add negative test for the isinchikey method in CompoundIdentifier class by @adebisi4145 in https://github.com/ersilia-os/ersilia/pull/1334
  • Update test for positive inchikey by @tongyu0924 in https://github.com/ersilia-os/ersilia/pull/1336
  • Make fetch fail if standardrun doesnt work by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1386
  • Bug fixes: inchtokey converter args missing by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1391
  • Add tests for issmiles, isinchikey, and guess_type methods in CompoundIdentifier class by @musasizivictoria in https://github.com/ersilia-os/ersilia/pull/1358
  • Fix dependency vulnerabilities by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1396
  • Remove duplicate flag --repo_path from the fetch command (#1370) by @snufkinwa in https://github.com/ersilia-os/ersilia/pull/1381
  • Logging at realtime from the async subprocess while pulling by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1392
  • Miscellaneous fixes by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1405
  • Fix CSV Serializer in StandaradCSVRunner by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1406

New Contributors

  • @adebisi4145 made their first contribution in https://github.com/ersilia-os/ersilia/pull/1289
  • @daud99 made their first contribution in https://github.com/ersilia-os/ersilia/pull/1291
  • @Ajoke23 made their first contribution in https://github.com/ersilia-os/ersilia/pull/1284
  • @teddyCodex made their first contribution in https://github.com/ersilia-os/ersilia/pull/1285
  • @OlawumiSalaam made their first contribution in https://github.com/ersilia-os/ersilia/pull/1288
  • @mercybassey made their first contribution in https://github.com/ersilia-os/ersilia/pull/1305
  • @Faith-Adegoke made their first contribution in https://github.com/ersilia-os/ersilia/pull/1306
  • @jubril-adeyi made their first contribution in https://github.com/ersilia-os/ersilia/pull/1292
  • @KimFarida made their first contribution in https://github.com/ersilia-os/ersilia/pull/1301
  • @musasizivictoria made their first contribution in https://github.com/ersilia-os/ersilia/pull/1295
  • @aderemi1224 made their first contribution in https://github.com/ersilia-os/ersilia/pull/1300
  • @AnushkaShreyam made their first contribution in https://github.com/ersilia-os/ersilia/pull/1327
  • @nicholas-kondal made their first contribution in https://github.com/ersilia-os/ersilia/pull/1190
  • @Darkbeast-glitch made their first contribution in https://github.com/ersilia-os/ersilia/pull/1316
  • @JoyProg made their first contribution in https://github.com/ersilia-os/ersilia/pull/1317
  • @tongyu0924 made their first contribution in https://github.com/ersilia-os/ersilia/pull/1336
  • @snufkinwa made their first contribution in https://github.com/ersilia-os/ersilia/pull/1381

Full Changelog: https://github.com/ersilia-os/ersilia/compare/v0.1.36...v0.1.39

- Python
Published by github-actions[bot] over 1 year ago

ersilia - November 2024

What's Changed

  • Refactor Ersilia test command by @kurysauce in https://github.com/ersilia-os/ersilia/pull/1224
  • Move the model inspection code by @dzumii in https://github.com/ersilia-os/ersilia/pull/1227
  • Bump actions/upload-artifact from 4.3.3 to 4.3.4 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1217
  • Bump GrantBirki/comment from 2.0.10 to 2.1.0 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1218
  • Bump actions/setup-python from 5.1.0 to 5.1.1 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1219
  • Sorting model tags alphabetically by @dzumii in https://github.com/ersilia-os/ersilia/pull/1229
  • Clean up dependencies related to ersilia test module by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1238
  • Remove setup.py in favor of only keeping pyproject.toml by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1239
  • Fix/tracking s3 connection by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1244
  • Make PyAirtable optional by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1245
  • Sorting tags regardless of the case by @dzumii in https://github.com/ersilia-os/ersilia/pull/1240
  • Bump actions/setup-python from 4 to 5 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1252
  • Bump GrantBirki/json-yaml-validate from 3.0.0 to 3.2.1 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1251
  • Bump actions/upload-artifact from 4.3.3 to 4.4.0 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1250
  • Bump GrantBirki/issue-template-parser from 7.0.2 to 7.0.3 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1249
  • Fix 'card' KeyError in ersilia catalog command by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1260
  • Replace metadata.json with metadata.yaml in the update metadata workflow by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1261
  • Ersilia pack dockerization by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1258
  • De-register api command from Ersilia CLI by @adebisi4145 in https://github.com/ersilia-os/ersilia/pull/1289
  • Removing PyAirtable dependency (#1259) by @daud99 in https://github.com/ersilia-os/ersilia/pull/1291
  • Removal of Ersilia current command by @Ajoke23 in https://github.com/ersilia-os/ersilia/pull/1284
  • Merged card command with catalog. #1264 by @teddyCodex in https://github.com/ersilia-os/ersilia/pull/1285
  • Task: Automatically update CodeMeta upon release #1276 by @OlawumiSalaam in https://github.com/ersilia-os/ersilia/pull/1288
  • Removed the api command from the Circleci workflow by @mercybassey in https://github.com/ersilia-os/ersilia/pull/1305
  • Updating Metadata.py file by @Faith-Adegoke in https://github.com/ersilia-os/ersilia/pull/1306
  • Bump rdkit version (#1304) by @daud99 in https://github.com/ersilia-os/ersilia/pull/1308
  • Print ersilia catalog in a table natively by @jubril-adeyi in https://github.com/ersilia-os/ersilia/pull/1292
  • 🐈 Task: Refactor ersilia clear command #1266 by @KimFarida in https://github.com/ersilia-os/ersilia/pull/1301
  • Fix: Update CompoundIdentifier to handle invalid SMILES inputs by @musasizivictoria in https://github.com/ersilia-os/ersilia/pull/1295
  • Fetch CLI decision flow improvement(#1299) by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1311
  • Update approve-trigger.yml by @aderemi1224 in https://github.com/ersilia-os/ersilia/pull/1300
  • Added support for both strings and lists in the information by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1325
  • Update card.py by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1326
  • Add positive unit test for isinputheader in CompoundIdentifier by @musasizivictoria in https://github.com/ersilia-os/ersilia/pull/1320
  • Update release date by @OlawumiSalaam in https://github.com/ersilia-os/ersilia/pull/1322
  • Create DEVELOPMENT.md file by @Ajoke23 in https://github.com/ersilia-os/ersilia/pull/1318
  • Improve CONTRIBUTING.md file by @adebisi4145 in https://github.com/ersilia-os/ersilia/pull/1307
  • Create a positive test for is_key_header by @mercybassey in https://github.com/ersilia-os/ersilia/pull/1324
  • Update inspect.py to include --track flag support for model inspection by @AnushkaShreyam in https://github.com/ersilia-os/ersilia/pull/1327
  • Add negative unit test for iskeyheader in testcompoundidentifier.py by @Ajoke23 in https://github.com/ersilia-os/ersilia/pull/1330
  • Integrate GDI inference store with CLI by @nicholas-kondal in https://github.com/ersilia-os/ersilia/pull/1190
  • Read the JSON file from the S3 interface by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1349
  • Drop Python 3.7 support and update tests by @Darkbeast-glitch in https://github.com/ersilia-os/ersilia/pull/1316
  • Performace Improvement on the run CLI(ersilia-os#1299) by @Abellegese in https://github.com/ersilia-os/ersilia/pull/1353

New Contributors

  • @adebisi4145 made their first contribution in https://github.com/ersilia-os/ersilia/pull/1289
  • @daud99 made their first contribution in https://github.com/ersilia-os/ersilia/pull/1291
  • @Ajoke23 made their first contribution in https://github.com/ersilia-os/ersilia/pull/1284
  • @teddyCodex made their first contribution in https://github.com/ersilia-os/ersilia/pull/1285
  • @OlawumiSalaam made their first contribution in https://github.com/ersilia-os/ersilia/pull/1288
  • @mercybassey made their first contribution in https://github.com/ersilia-os/ersilia/pull/1305
  • @Faith-Adegoke made their first contribution in https://github.com/ersilia-os/ersilia/pull/1306
  • @jubril-adeyi made their first contribution in https://github.com/ersilia-os/ersilia/pull/1292
  • @KimFarida made their first contribution in https://github.com/ersilia-os/ersilia/pull/1301
  • @musasizivictoria made their first contribution in https://github.com/ersilia-os/ersilia/pull/1295
  • @Abellegese made their first contribution in https://github.com/ersilia-os/ersilia/pull/1311
  • @aderemi1224 made their first contribution in https://github.com/ersilia-os/ersilia/pull/1300
  • @AnushkaShreyam made their first contribution in https://github.com/ersilia-os/ersilia/pull/1327
  • @nicholas-kondal made their first contribution in https://github.com/ersilia-os/ersilia/pull/1190
  • @Darkbeast-glitch made their first contribution in https://github.com/ersilia-os/ersilia/pull/1316

Full Changelog: https://github.com/ersilia-os/ersilia/compare/v0.1.36...v0.1.38

- Python
Published by github-actions[bot] over 1 year ago

ersilia - October 2024

What's Changed

  • Refactor Ersilia test command by @kurysauce in https://github.com/ersilia-os/ersilia/pull/1224
  • Move the model inspection code by @dzumii in https://github.com/ersilia-os/ersilia/pull/1227
  • Bump actions/upload-artifact from 4.3.3 to 4.3.4 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1217
  • Bump GrantBirki/comment from 2.0.10 to 2.1.0 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1218
  • Bump actions/setup-python from 5.1.0 to 5.1.1 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1219
  • Sorting model tags alphabetically by @dzumii in https://github.com/ersilia-os/ersilia/pull/1229
  • Clean up dependencies related to ersilia test module by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1238
  • Remove setup.py in favor of only keeping pyproject.toml by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1239
  • Fix/tracking s3 connection by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1244
  • Make PyAirtable optional by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1245
  • Sorting tags regardless of the case by @dzumii in https://github.com/ersilia-os/ersilia/pull/1240
  • Bump actions/setup-python from 4 to 5 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1252
  • Bump GrantBirki/json-yaml-validate from 3.0.0 to 3.2.1 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1251
  • Bump actions/upload-artifact from 4.3.3 to 4.4.0 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1250
  • Bump GrantBirki/issue-template-parser from 7.0.2 to 7.0.3 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1249
  • Fix 'card' KeyError in ersilia catalog command by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1260
  • Replace metadata.json with metadata.yaml in the update metadata workflow by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1261
  • Ersilia pack dockerization by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1258

Full Changelog: https://github.com/ersilia-os/ersilia/compare/v0.1.36...v0.1.37

- Python
Published by github-actions[bot] over 1 year ago

ersilia - August 2024

What's Changed

  • Fix table creation while setting setting write api key by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1148
  • Add spdx license identifiers by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1149
  • Use matrix strategy to control build versions in action by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1151
  • Update ersilia-base-image-to-dockerhub.yml by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1152
  • Code Refactor: Remove Pandas as a dependency by using the natively in built csv module instead by @dzumii in https://github.com/ersilia-os/ersilia/pull/1131
  • Update pyproject.toml file by @dzumii in https://github.com/ersilia-os/ersilia/pull/1153
  • fix: relax regex search of docker logs by @kartikey-vyas in https://github.com/ersilia-os/ersilia/pull/1157
  • Resolve duplication between RunLogger in ersilia/core/session.py and RunTracker in ersilia/core/tracking.py by @Malikbadmus in https://github.com/ersilia-os/ersilia/pull/1132
  • Remove multiple and redundant track flags by @dzumii in https://github.com/ersilia-os/ersilia/pull/1160
  • Pin numpy to 1.x.x versions by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1166
  • Removing the stat method from the tracking functionalites by @Malikbadmus in https://github.com/ersilia-os/ersilia/pull/1169
  • Implement the method to log the number of errors and warnings during model run. by @Malikbadmus in https://github.com/ersilia-os/ersilia/pull/1168
  • Rework code calculating memory usage - output and Docker container by @Malikbadmus in https://github.com/ersilia-os/ersilia/pull/1161
  • Fix currentserviceclass method to return "No model served" if ersilia process was interrupted by @Malikbadmus in https://github.com/ersilia-os/ersilia/pull/1172
  • Track without output bug by @dzumii in https://github.com/ersilia-os/ersilia/pull/1170
  • Added the service class method to the modelcard by @Malikbadmus in https://github.com/ersilia-os/ersilia/pull/1173
  • Ersilia Catalog Bug when no models are available by @dzumii in https://github.com/ersilia-os/ersilia/pull/1175
  • Remove annoying debug logs by @Malikbadmus in https://github.com/ersilia-os/ersilia/pull/1177
  • Pull request template by @dzumii in https://github.com/ersilia-os/ersilia/pull/1179
  • Bump actions/checkout from 4.1.6 to 4.1.7 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1182
  • Bump docker/build-push-action from 5 to 6 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1181
  • Modified the time tracking method to accurately track time taken by @Malikbadmus in https://github.com/ersilia-os/ersilia/pull/1176
  • Refactor tracking to support a single SMILES string input by @Malikbadmus in https://github.com/ersilia-os/ersilia/pull/1183
  • Utilise model metadata to resolve model output type and shape by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1184
  • Hotfix: Resotre older licenses for backward compatibility by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1191
  • Fix bug with ersilia fetch from github inside a docker container by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1193
  • Modifying the local Catalog functionality by @Malikbadmus in https://github.com/ersilia-os/ersilia/pull/1195
  • Bump GrantBirki/json-yaml-validate from 2.7.1 to 3.0.0 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1133
  • Fastapi integration by @miquelduranfrigola in https://github.com/ersilia-os/ersilia/pull/1199
  • Specify repo_path while fetching the dummy model by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1200
  • Getting model source value by @Malikbadmus in https://github.com/ersilia-os/ersilia/pull/1202
  • Reflecting correct values in Model information file by @Malikbadmus in https://github.com/ersilia-os/ersilia/pull/1204
  • Fix Airtable to JSON conversion workflow to account for paginated response from Airtable API by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1211
  • Use JsonModelsInterface in ersilia CLI by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1213
  • Make MODELSIZEFILE always go in the model dest directory by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1212
  • Updated catalog local command by @Malikbadmus in https://github.com/ersilia-os/ersilia/pull/1206

New Contributors

  • @dzumii made their first contribution in https://github.com/ersilia-os/ersilia/pull/1131
  • @kartikey-vyas made their first contribution in https://github.com/ersilia-os/ersilia/pull/1157
  • @Malikbadmus made their first contribution in https://github.com/ersilia-os/ersilia/pull/1132

Full Changelog: https://github.com/ersilia-os/ersilia/compare/v0.1.34...v0.1.36

- Python
Published by DhanshreeA almost 2 years ago

ersilia - May 2024 - v0.1.34

What's Changed

  • Use marketplace action to install Conda in ersiila installation test workflow by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1125
  • hotfix: pin requests to a version less than 2.31.x by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1129
  • Clean up issue templates by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1130
  • Bump GrantBirki/comment from 2.0.9 to 2.0.10 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1136
  • Bump actions/upload-artifact from 4.3.1 to 4.3.3 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1135
  • Bump actions/checkout from 4.1.4 to 4.1.6 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1134

Full Changelog: https://github.com/ersilia-os/ersilia/compare/v0.1.33...v0.1.34

- Python
Published by DhanshreeA about 2 years ago

ersilia - April 2024 - v0.1.33

What's Changed

  • Bump GrantBirki/comment from 2.0.8 to 2.0.9 by @dependabot in https://github.com/ersilia-os/ersilia/pull/973
  • Bump GrantBirki/json-yaml-validate from 2.6.0 to 2.6.1 by @dependabot in https://github.com/ersilia-os/ersilia/pull/975
  • Fix failiing docker builds by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1052
  • Bump GrantBirki/issue-template-parser from 7.0.0 to 7.0.1 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1093
  • Bump actions/checkout from 4.1.1 to 4.1.2 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1094
  • Convert Airtable models to a JSON file by @carcablop in https://github.com/ersilia-os/ersilia/pull/1011
  • Patch path to model's python binary by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1099
  • Fix the script to patch model python binary's path by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1101
  • fix a problem with aws access key by @carcablop in https://github.com/ersilia-os/ersilia/pull/1102
  • Add support for model input example.csv in the ersilia example command by @DhanshreeA in https://github.com/ersilia-os/ersilia/pull/1103
  • Bump actions-js/push from 1.4 to 1.5 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1121
  • Bump GrantBirki/json-yaml-validate from 2.6.1 to 2.7.1 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1120
  • Bump actions/checkout from 4.1.1 to 4.1.4 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1119
  • Bump GrantBirki/issue-template-parser from 7.0.1 to 7.0.2 by @dependabot in https://github.com/ersilia-os/ersilia/pull/1118

Full Changelog: https://github.com/ersilia-os/ersilia/compare/v0.1.32...v0.1.33

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ersilia - Docker compatibilty

We now provide compatibility with Docker, which greatly improves the robustness of Ersilia.

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Published by miquelduranfrigola almost 3 years ago

ersilia - First Ersilia Release with a DOI!

This Release contains a stable version of Ersilia's CLI, with bugfixes for predicting large datasets and improved Error notifications for users.

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Published by GemmaTuron over 3 years ago

ersilia - First release of Ersilia with public access to models database

First release of Ersilia with public access to models database

  • Version: 0.1.1

This version includes minor updates with respect to v0.1.0. The major improvement is that the AirTable API Read-Only key is now not hardcoded in the library. It can now be found in the config folder, and it is accessed by the Ersilia CLI online.

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First release of Ersilia!

Version v0.1.0

This is the first release of the Ersilia CLI tool. This version can be used as to fetch, serve and run models available in the Ersilia Model Hub. At the moment, the models available are all chemistry models, meaning the input is one molecule or a set of molecules.

The typical use case is that a model is fetched. At fetching time, a Conda environment is created with the model identifier. This is the environment that is activated when predictions are run.

Disclaimers

Ersilia is still in an experimental phase. If you encounter probles running the tool, please reach out to us and we will resolve your issues promptly.

Next steps

  • Ensure that Ersilia works in Docker containers.
  • Input adapters and output adapters.

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Published by miquelduranfrigola over 3 years ago