February 2025

What's Changed

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

New Contributors

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

Full Changelog: v0.1.36...v0.1.41