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| # CHANGELOG | ||
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| ## v1.3.5 (2024-11-21) | ||
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| ## v1.3.4 (2024-11-20) | ||
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| ### Unknown | ||
| ### Refactoring | ||
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| * Merge branch 'master' of https://github.com/EBI-Metabolights/metabolights-utils ([`a473347`](https://github.com/EBI-Metabolights/metabolights-utils/commit/a47334735281040c351d47eda681e82ce17b9979)) | ||
| - Upload submission refactor and create study utility method | ||
| ([`c9ea043`](https://github.com/EBI-Metabolights/metabolights-utils/commit/c9ea043919834d00610d34e8dbe39ea00b8dba53)) | ||
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| ## v1.3.3 (2024-11-20) | ||
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| ### Fixes | ||
| ### Bug Fixes | ||
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| * fix: update search pattern to find new lines in cells ([`bcf703a`](https://github.com/EBI-Metabolights/metabolights-utils/commit/bcf703acad1cbc173e56754aa94dad8742535468)) | ||
| - Update search pattern to find new lines in cells | ||
| ([`bcf703a`](https://github.com/EBI-Metabolights/metabolights-utils/commit/bcf703acad1cbc173e56754aa94dad8742535468)) | ||
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| * fix: ontology source parse errors ([`1d68f25`](https://github.com/EBI-Metabolights/metabolights-utils/commit/1d68f25aa5efc70fda6fa982c3f887b64069b275)) | ||
| - Ontology source parse errors | ||
| ([`1d68f25`](https://github.com/EBI-Metabolights/metabolights-utils/commit/1d68f25aa5efc70fda6fa982c3f887b64069b275)) | ||
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| ## v1.3.2 (2024-11-20) | ||
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| ### Fixes | ||
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| * fix: fix isatable read errors ([`dc61316`](https://github.com/EBI-Metabolights/metabolights-utils/commit/dc6131643c48fb21c1ae97994cbef26d58e34e62)) | ||
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| ### Unknown | ||
| ### Bug Fixes | ||
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| * Merge branch 'master' of https://github.com/EBI-Metabolights/metabolights-utils ([`554f731`](https://github.com/EBI-Metabolights/metabolights-utils/commit/554f731244117c8814171505a5cfb3931dac9be3)) | ||
| - Fix isatable read errors | ||
| ([`dc61316`](https://github.com/EBI-Metabolights/metabolights-utils/commit/dc6131643c48fb21c1ae97994cbef26d58e34e62)) | ||
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| ## v1.3.1 (2024-11-14) | ||
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| ### Fixes | ||
| ### Bug Fixes | ||
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| * fix: isa table parser fix. ([`af9906c`](https://github.com/EBI-Metabolights/metabolights-utils/commit/af9906c5fc7b22cfa5fd00381c7a98f4fe296ca7)) | ||
| - Isa table parser fix. | ||
| ([`af9906c`](https://github.com/EBI-Metabolights/metabolights-utils/commit/af9906c5fc7b22cfa5fd00381c7a98f4fe296ca7)) | ||
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| ### Refactoring | ||
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| * refactor: new local validation endpoint accepts user's api-token ([`4a1c0b8`](https://github.com/EBI-Metabolights/metabolights-utils/commit/4a1c0b8ad25cceae9c48b204648b1f8c5bd24dd0)) | ||
| - New local validation endpoint accepts user's api-token | ||
| ([`4a1c0b8`](https://github.com/EBI-Metabolights/metabolights-utils/commit/4a1c0b8ad25cceae9c48b204648b1f8c5bd24dd0)) | ||
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| ## v1.3.0 (2024-11-14) | ||
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| ### Unknown | ||
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| * Merge branch 'master' of https://github.com/EBI-Metabolights/metabolights-utils ([`94814cf`](https://github.com/EBI-Metabolights/metabolights-utils/commit/94814cf275c6a75d891f146b5235029cc13e9628)) | ||
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| ## v1.2.2 (2024-10-23) | ||
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| ### Features | ||
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| * feat: a new utility method to validate local study with new validation endpoint ([`3db9718`](https://github.com/EBI-Metabolights/metabolights-utils/commit/3db9718af2d90fec6f37476756dbd83a9f4a32d4)) | ||
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| ### Fixes | ||
| ### Bug Fixes | ||
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| * fix: empty line fix ([`abd88aa`](https://github.com/EBI-Metabolights/metabolights-utils/commit/abd88aa3d3d3562aae3d680e04b9ff3a9ee98a1d)) | ||
| - Empty line fix | ||
| ([`abd88aa`](https://github.com/EBI-Metabolights/metabolights-utils/commit/abd88aa3d3d3562aae3d680e04b9ff3a9ee98a1d)) | ||
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| ### Unknown | ||
| ### Features | ||
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| * Merge branch 'master' of https://github.com/EBI-Metabolights/metabolights-utils ([`ae7fcd4`](https://github.com/EBI-Metabolights/metabolights-utils/commit/ae7fcd4d8e4b18e47f0e25848fcf966e406d9f79)) | ||
| - A new utility method to validate local study with new validation endpoint | ||
| ([`3db9718`](https://github.com/EBI-Metabolights/metabolights-utils/commit/3db9718af2d90fec6f37476756dbd83a9f4a32d4)) | ||
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| ## v1.2.1 (2024-10-15) | ||
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| ### Fixes | ||
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| * fix: isa table writer fix ([`e9977ad`](https://github.com/EBI-Metabolights/metabolights-utils/commit/e9977addbe85e27ddc5f521bebf6f002b687f152)) | ||
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| ### Unknown | ||
| ### Bug Fixes | ||
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| * enable remove_empty_rows and remove_new_lines_in_cells parameters ([`2511db3`](https://github.com/EBI-Metabolights/metabolights-utils/commit/2511db3ddfa402aaaf520e9b946063b44e2fc82a)) | ||
| - Isa table writer fix | ||
| ([`e9977ad`](https://github.com/EBI-Metabolights/metabolights-utils/commit/e9977addbe85e27ddc5f521bebf6f002b687f152)) | ||
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| ## v1.2.0 (2024-10-15) | ||
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| ### Features | ||
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| * feat: async metabolights study provider implementation ([`5d670b7`](https://github.com/EBI-Metabolights/metabolights-utils/commit/5d670b7a1e8dafe4e0db16199b84e244737236f1)) | ||
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| ### Unknown | ||
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| * async pytest dependency is added ([`ceac7a5`](https://github.com/EBI-Metabolights/metabolights-utils/commit/ceac7a5cc6ead3c6fa1fb49deb193d14aceabb33)) | ||
| - Async metabolights study provider implementation | ||
| ([`5d670b7`](https://github.com/EBI-Metabolights/metabolights-utils/commit/5d670b7a1e8dafe4e0db16199b84e244737236f1)) | ||
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| ## v1.1.12 (2024-10-14) | ||
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| ### Unknown | ||
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| * Merge branch 'master' of https://github.com/EBI-Metabolights/metabolights-utils ([`fe54fd8`](https://github.com/EBI-Metabolights/metabolights-utils/commit/fe54fd86a195bc30129b8291cd92560e420bfc9a)) | ||
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| ## v1.1.11 (2024-10-12) | ||
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| ### Fixes | ||
| ### Bug Fixes | ||
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| * fix: tsv file read improvement ([`46f81a0`](https://github.com/EBI-Metabolights/metabolights-utils/commit/46f81a0c18da2c8f6f79367658a5025852104fe4)) | ||
| - Tsv file read improvement | ||
| ([`46f81a0`](https://github.com/EBI-Metabolights/metabolights-utils/commit/46f81a0c18da2c8f6f79367658a5025852104fe4)) | ||
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| ### Refactoring | ||
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| * refactor: study metadata data model provider is refactored. added a default fix_new_lines_in_cells parameter to parse isa table file ([`723e757`](https://github.com/EBI-Metabolights/metabolights-utils/commit/723e757f8382c1e3b338776eefb4a575a8502a77)) | ||
| - Study metadata data model provider is refactored. added a default fix_new_lines_in_cells parameter | ||
| to parse isa table file | ||
| ([`723e757`](https://github.com/EBI-Metabolights/metabolights-utils/commit/723e757f8382c1e3b338776eefb4a575a8502a77)) | ||
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| ## v1.1.10 (2024-09-23) | ||
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| ### Testing | ||
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| * test: test data for new parameter to filter empty isa table rows. ([`9c0cab6`](https://github.com/EBI-Metabolights/metabolights-utils/commit/9c0cab60a6d23acd6b13ee142c63ee95fb22e871)) | ||
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| ### Unknown | ||
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| * Merge branch 'master' of https://github.com/EBI-Metabolights/metabolights-utils ([`78b1e1e`](https://github.com/EBI-Metabolights/metabolights-utils/commit/78b1e1e7b116180bd7abbe131a0dcc245c64417d)) | ||
| - Test data for new parameter to filter empty isa table rows. | ||
| ([`9c0cab6`](https://github.com/EBI-Metabolights/metabolights-utils/commit/9c0cab60a6d23acd6b13ee142c63ee95fb22e871)) | ||
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| ## v1.1.9 (2024-09-18) | ||
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| ### Refactoring | ||
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| * refactor: new parameter to filter empty isa table rows. ([`d6aa664`](https://github.com/EBI-Metabolights/metabolights-utils/commit/d6aa6644afc4c9bc805df08a633515f135cd4602)) | ||
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| ### Unknown | ||
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| * Merge branch 'master' of https://github.com/EBI-Metabolights/metabolights-utils ([`2c16d3c`](https://github.com/EBI-Metabolights/metabolights-utils/commit/2c16d3c425c53808d2558eadbdee9acb110b739c)) | ||
| - New parameter to filter empty isa table rows. | ||
| ([`d6aa664`](https://github.com/EBI-Metabolights/metabolights-utils/commit/d6aa6644afc4c9bc805df08a633515f135cd4602)) | ||
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| ## v1.1.8 (2024-09-13) | ||
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| ### Fixes | ||
| ### Bug Fixes | ||
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| * fix: rollback @id field and update investigation tsv file write method ([`ebf17b4`](https://github.com/EBI-Metabolights/metabolights-utils/commit/ebf17b47b70a53d35cc997451ff2ff3b574b9eb8)) | ||
| - Rollback @id field and update investigation tsv file write method | ||
| ([`ebf17b4`](https://github.com/EBI-Metabolights/metabolights-utils/commit/ebf17b47b70a53d35cc997451ff2ff3b574b9eb8)) | ||
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| * fix: investigation file rows fixed ([`b664483`](https://github.com/EBI-Metabolights/metabolights-utils/commit/b664483025d9d1f938984f916d2c9771e41625d4)) | ||
| - Investigation file rows fixed | ||
| ([`b664483`](https://github.com/EBI-Metabolights/metabolights-utils/commit/b664483025d9d1f938984f916d2c9771e41625d4)) | ||
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| * fix: id field is added to base class ([`ef682f4`](https://github.com/EBI-Metabolights/metabolights-utils/commit/ef682f45b9ec8e5a4c26790c339a1d78c87bace3)) | ||
| - Id field is added to base class | ||
| ([`ef682f4`](https://github.com/EBI-Metabolights/metabolights-utils/commit/ef682f45b9ec8e5a4c26790c339a1d78c87bace3)) | ||
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| ### Refactoring | ||
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| * refactor: InvestigationFileWriter write method is now aware of inherited classes of Investigation model ([`1928d04`](https://github.com/EBI-Metabolights/metabolights-utils/commit/1928d04ca64cff1a982174b8f61a8d7c96c46658)) | ||
| - Investigationfilewriter write method is now aware of inherited classes of Investigation model | ||
| ([`1928d04`](https://github.com/EBI-Metabolights/metabolights-utils/commit/1928d04ca64cff1a982174b8f61a8d7c96c46658)) | ||
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| ## v1.1.7 (2024-09-12) | ||
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| ### Unknown | ||
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| * Merge branch 'master' of https://github.com/EBI-Metabolights/metabolights-utils ([`600553d`](https://github.com/EBI-Metabolights/metabolights-utils/commit/600553d5c18be24c882b4b0794d05d7fe3302542)) | ||
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| ## v1.1.6 (2024-08-30) | ||
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| ### Fixes | ||
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| * fix: Comment object accepts str ([`88cecca`](https://github.com/EBI-Metabolights/metabolights-utils/commit/88ceccaa56a77cae773f7c74c6b6956ba062abbd)) | ||
| ### Bug Fixes | ||
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| * fix: validation last update timestamp type is int or float. ([`64c65fa`](https://github.com/EBI-Metabolights/metabolights-utils/commit/64c65faee24fa6b72d0870707d1bce893fb5ac45)) | ||
| - Comment object accepts str | ||
| ([`88cecca`](https://github.com/EBI-Metabolights/metabolights-utils/commit/88ceccaa56a77cae773f7c74c6b6956ba062abbd)) | ||
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| ### Unknown | ||
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| * Merge pull request #2 from nilshoffmann/master | ||
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| Fixed type of last_update_timestamp in validation to float. ([`fe2aba1`](https://github.com/EBI-Metabolights/metabolights-utils/commit/fe2aba188f7401566bffc72f7f9c2261f8eb93b5)) | ||
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| * Fixed type of last_update_timestamp in validation to float. ([`d1fe8f5`](https://github.com/EBI-Metabolights/metabolights-utils/commit/d1fe8f5f09999f39b85a0cd515f3c717fec6f07f)) | ||
| - Validation last update timestamp type is int or float. | ||
| ([`64c65fa`](https://github.com/EBI-Metabolights/metabolights-utils/commit/64c65faee24fa6b72d0870707d1bce893fb5ac45)) | ||
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| ## v1.1.5 (2024-07-22) | ||
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| ### Fixes | ||
| ### Bug Fixes | ||
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| * fix: dependency updates ([`d0217c1`](https://github.com/EBI-Metabolights/metabolights-utils/commit/d0217c12c3a52991f912f1e156e962540a6d633e)) | ||
| - Dependency updates | ||
| ([`d0217c1`](https://github.com/EBI-Metabolights/metabolights-utils/commit/d0217c12c3a52991f912f1e156e962540a6d633e)) | ||
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| ## v1.1.4 (2024-07-22) | ||
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| ### Fixes | ||
| ### Bug Fixes | ||
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| * fix: If there is an undefined characteristics column in sample sheet, set_organism method fails ([`367f919`](https://github.com/EBI-Metabolights/metabolights-utils/commit/367f919ee1731e50283a1e4bedbc26e36488276b)) | ||
| - If there is an undefined characteristics column in sample sheet, set_organism method fails | ||
| ([`367f919`](https://github.com/EBI-Metabolights/metabolights-utils/commit/367f919ee1731e50283a1e4bedbc26e36488276b)) | ||
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| ## v1.1.3 (2024-07-09) | ||
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| ### Fixes | ||
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| * fix: windows path and new line issues ([`e8cf137`](https://github.com/EBI-Metabolights/metabolights-utils/commit/e8cf1371558ee9d0e29cd142a054359b590b18ee)) | ||
| ### Bug Fixes | ||
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| ### Unknown | ||
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| * logs in isatab, provider and utils module files, unit test improvements. ([`2d9850a`](https://github.com/EBI-Metabolights/metabolights-utils/commit/2d9850a1031928c01f0c75b590dbd766ba7e4857)) | ||
| - Windows path and new line issues | ||
| ([`e8cf137`](https://github.com/EBI-Metabolights/metabolights-utils/commit/e8cf1371558ee9d0e29cd142a054359b590b18ee)) | ||
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| ## v1.1.2 (2024-06-23) | ||
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| ### Documentation | ||
| ### Bug Fixes | ||
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| * docs: documentation updates and new log messages ([`50055bc`](https://github.com/EBI-Metabolights/metabolights-utils/commit/50055bca6b030f72a2af54c6a6abb9263a89fca3)) | ||
| - Submitted study download error is fixed. | ||
| ([`ad2cdc8`](https://github.com/EBI-Metabolights/metabolights-utils/commit/ad2cdc883e4bdbed28bc486a16e03a68c6ebb05f)) | ||
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| ### Fixes | ||
| ### Documentation | ||
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| * fix: submitted study download error is fixed. ([`ad2cdc8`](https://github.com/EBI-Metabolights/metabolights-utils/commit/ad2cdc883e4bdbed28bc486a16e03a68c6ebb05f)) | ||
| - Documentation updates and new log messages | ||
| ([`50055bc`](https://github.com/EBI-Metabolights/metabolights-utils/commit/50055bca6b030f72a2af54c6a6abb9263a89fca3)) | ||
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| ## v1.1.1 (2024-06-22) | ||
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| ### Fixes | ||
| ### Bug Fixes | ||
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| * fix: code updates to fix pylint violations. ([`2a7dae0`](https://github.com/EBI-Metabolights/metabolights-utils/commit/2a7dae02d22a22d39a82a45c685207e11529361a)) | ||
| - Code updates to fix pylint violations. | ||
| ([`2a7dae0`](https://github.com/EBI-Metabolights/metabolights-utils/commit/2a7dae02d22a22d39a82a45c685207e11529361a)) | ||
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| ## v1.1.0 (2024-06-20) | ||
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| ### Cli | ||
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| * CLI: submission delete-assay command is added. After deleting assay file, command downloads the latest metadata files from MetaboLights study. ([`f6b1ff5`](https://github.com/EBI-Metabolights/metabolights-utils/commit/f6b1ff580bc29484f392e73128d4985fe8ad3037)) | ||
| - Submission delete-assay command is added. After deleting assay file, command downloads the latest | ||
| metadata files from MetaboLights study. | ||
| ([`f6b1ff5`](https://github.com/EBI-Metabolights/metabolights-utils/commit/f6b1ff580bc29484f392e73128d4985fe8ad3037)) | ||
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| ### Documentation | ||
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| * docs: README document and command message updates. ([`1428f25`](https://github.com/EBI-Metabolights/metabolights-utils/commit/1428f25c652ed0bf9fd70e2b7cb284c2d51f3e31)) | ||
| - Readme document and command message updates. | ||
| ([`1428f25`](https://github.com/EBI-Metabolights/metabolights-utils/commit/1428f25c652ed0bf9fd70e2b7cb284c2d51f3e31)) | ||
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| ## v1.0.1 (2024-06-20) | ||
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| ### Continuous Integration | ||
| ### Bug Fixes | ||
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| * ci: semantic versioning github actions are enabled. ([`cd7e027`](https://github.com/EBI-Metabolights/metabolights-utils/commit/cd7e0272c743db5c55f5a7ca7e972525a2f2848a)) | ||
| - Public describe and submission describe command fixes. | ||
| ([`7effb91`](https://github.com/EBI-Metabolights/metabolights-utils/commit/7effb910417575d83d39c30eacd0edc170db7873)) | ||
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| ### Fixes | ||
| ### Continuous Integration | ||
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| * fix: public describe and submission describe command fixes. ([`7effb91`](https://github.com/EBI-Metabolights/metabolights-utils/commit/7effb910417575d83d39c30eacd0edc170db7873)) | ||
| - Semantic versioning github actions are enabled. | ||
| ([`cd7e027`](https://github.com/EBI-Metabolights/metabolights-utils/commit/cd7e0272c743db5c55f5a7ca7e972525a2f2848a)) | ||
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| ## v1.0.0 (2024-06-20) | ||
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| ### Continuous Integration | ||
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||
| * ci: semantic versioning configuration updates ([`085f5f5`](https://github.com/EBI-Metabolights/metabolights-utils/commit/085f5f5778900ccd6e89d66882bd02cca14d8be6)) | ||
| ### Bug Fixes | ||
|
|
||
| * ci: github actions to run unit tests ([`3529cd7`](https://github.com/EBI-Metabolights/metabolights-utils/commit/3529cd710eec408e5b266e3e638b91ce5bab84e3)) | ||
| - Python3.8 compatibility, new unit tests and lint fixes. ci: sematic release versioning. | ||
| ([`3c6bb6f`](https://github.com/EBI-Metabolights/metabolights-utils/commit/3c6bb6f23698551fcb19527ce4d5578c85414f7e)) | ||
|
|
||
| ### Fixes | ||
|
|
||
| * fix: python3.8 compatibility, new unit tests and lint fixes. ci: sematic release versioning. ([`3c6bb6f`](https://github.com/EBI-Metabolights/metabolights-utils/commit/3c6bb6f23698551fcb19527ce4d5578c85414f7e)) | ||
| ### Continuous Integration | ||
|
|
||
| ### Unknown | ||
| - Semantic versioning configuration updates | ||
| ([`085f5f5`](https://github.com/EBI-Metabolights/metabolights-utils/commit/085f5f5778900ccd6e89d66882bd02cca14d8be6)) | ||
|
|
||
| * feature: Initial commit ([`25c8e5b`](https://github.com/EBI-Metabolights/metabolights-utils/commit/25c8e5b98a3291b137fdbb88113c30263e84ab6c)) | ||
| - Github actions to run unit tests | ||
| ([`3529cd7`](https://github.com/EBI-Metabolights/metabolights-utils/commit/3529cd710eec408e5b266e3e638b91ce5bab84e3)) |
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