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
apicommand 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_headerby @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.pypython 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
- added new categories by @miquelduranfrigola in #1478
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...v0.1.40
Contributors
DhanshreeA, teddyCodex, and 23 other contributors