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Added: Memote example files added to docs Curation and visualization logs are now separated by date in a 'logs' dir Usage of credentials for BioCyc database New structure cobramod.retrieval.Data. It is in charge of parsing into different objects Extra functions in utils Changed: Set object bug fixed [#50] Escher is an optional dependency Pre-hooks uses now ruff instead of flake8 and black. Behaviour to open files if escher is not installed changed to not open browsers Dropped support for python 3.8 and 3.9 Logging format is more human-friendly Dropped support of mypy. Black is replaced with ruff New pyproject.toml Test data updated (19.02.24) Function available_databases replaced by cobramod.retrieval.Databases Structure for retrieval refactored and new parsing sub-packaged created DataVersion moved to parsing package Updated structure of test module Removed multiple "private" methods and functions. Docs files updated to these new changes Test updated to uses new changes Updating functions to not use deprecated pandas functions Removed: Deprecated config files Deprecation warning for SolCyc (Database appears to be shutdown)
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environment: environment.yml | ||
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python: | ||
version: 3.7 | ||
version: 3.10 | ||
install: | ||
- method: pip | ||
path: . |
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# Changelog | ||
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## [Unreleased] | ||
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### Planned | ||
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- Parallelization of downloads and cross-references | ||
- Visualization with other tools than Escher | ||
- Deprecation of SolCyc | ||
- Deprecation of PairDictionary | ||
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## [1.2.0] | ||
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### Added | ||
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- Memote example files added to docs | ||
- Curation and visualization logs are now separated by date in a 'logs' dir | ||
- Usage of credentials for BioCyc database | ||
- New structure `cobramod.retrieval.Data`. It is in charge of parsing into | ||
different objects | ||
- Extra functions in utils | ||
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||
### Changed | ||
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- Set object bug fixed [https://github.com/Toepfer-Lab/cobramod/issues/50] | ||
- Escher is an optional dependency | ||
- Pre-hooks uses now ruff instead of flake8 and black. | ||
- Behaviour to open files if escher is not installed changed to not open browsers | ||
- Dropped support for python 3.8 and 3.9 | ||
- Logging format is more human-friendly | ||
- Dropped support of mypy. Black is replaced with ruff | ||
- New pyproject.toml | ||
- Test data updated (19.02.24) | ||
- Function `available_databases` replaced by `cobramod.retrieval.Databases` | ||
- Structure for retrieval refactored and new parsing sub-packaged created | ||
- DataVersion moved to parsing package | ||
- Updated structure of test module | ||
- Removed multiple "private" methods and functions. | ||
- Docs files updated to these new changes | ||
- Test updated to uses new changes | ||
- Updating functions to not use deprecated pandas functions | ||
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||
### Removed | ||
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- Deprecated config files | ||
- Deprecation warning for SolCyc (Database appears to be shutdown) |
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