December 2024

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
• Fix CSV Serializer in StandaradCSVRunner by @DhanshreeA in #1406

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

Full Changelog: v0.1.36...v0.1.39

November 2024

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
• Performace Improvement on the run CLI(#1299) by @Abellegese in #1353

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
• @Abellegese made their first contribution in #1311
• @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

Full Changelog: v0.1.36...v0.1.38

October 2024

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

Full Changelog: v0.1.36...v0.1.37

August 2024

What's Changed

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

New Contributors

• @dzumii made their first contribution in #1131
• @kartikey-vyas made their first contribution in #1157
• @Malikbadmus made their first contribution in #1132

Full Changelog: v0.1.34...v0.1.36

May 2024 - v0.1.34

What's Changed

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

Full Changelog: v0.1.33...v0.1.34

April 2024 - v0.1.33

What's Changed

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

Full Changelog: v0.1.32...v0.1.33

Docker compatibilty

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

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.

First release of Ersilia

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.