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| Original file line number | Diff line number | Diff line change |
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| ### Changelog | ||
| # Changelog | ||
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| All notable changes to this project will be documented in this file. Dates are displayed in UTC. | ||
| ## v8.2.0 (2023-12-21) | ||
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| Generated by [`auto-changelog`](https://github.com/CookPete/auto-changelog). | ||
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| #### [8.1.0](https://github.com/GENESIS-EFRC/reaction-network/compare/v8.0.4...v8.1.0) | ||
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| - Update networks notebook [`#278`](https://github.com/GENESIS-EFRC/reaction-network/pull/278) | ||
| - implement ruff pt 2 [`1ac4f91`](https://github.com/GENESIS-EFRC/reaction-network/commit/1ac4f910343326e3447a88c6cc8ea5682400d004) | ||
| - Implement ruff [`53df69e`](https://github.com/GENESIS-EFRC/reaction-network/commit/53df69efaf7249b57ab41447775d9e124fe415d9) | ||
| - linting [`7b93a61`](https://github.com/GENESIS-EFRC/reaction-network/commit/7b93a61e5daef90742c9c57a0da5b4d83ac669c2) | ||
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| #### [v8.0.4](https://github.com/GENESIS-EFRC/reaction-network/compare/v8.0.3...v8.0.4) | ||
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| > 11 October 2023 | ||
| - Add default entry_id creation and better docs [`#277`](https://github.com/GENESIS-EFRC/reaction-network/pull/277) | ||
| - Fix Gibbs entry bug when initializing with Species [`#276`](https://github.com/GENESIS-EFRC/reaction-network/pull/276) | ||
| - Updated CHANGELOG.md [`bb93f39`](https://github.com/GENESIS-EFRC/reaction-network/commit/bb93f397c486217d0eebd075c2c735ee747abd3a) | ||
| - fix Gibbs entry bug when initializing with Species [`0daf280`](https://github.com/GENESIS-EFRC/reaction-network/commit/0daf280ff94ec513e8551f7f2d888c37601bfe4b) | ||
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| #### [v8.0.3](https://github.com/GENESIS-EFRC/reaction-network/compare/v8.0.2...v8.0.3) | ||
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| > 1 September 2023 | ||
| - Fix broken doc release / changelog [`#273`](https://github.com/GENESIS-EFRC/reaction-network/pull/273) | ||
| - fix broken doc release [`b3f0b0f`](https://github.com/GENESIS-EFRC/reaction-network/commit/b3f0b0f8aa733c3a54bf991d4f2fb39b00762984) | ||
| - get rid of changelog in action [`e790580`](https://github.com/GENESIS-EFRC/reaction-network/commit/e790580b53fdf19eb78f2d9e8ee3137e75c46cef) | ||
| - fix broken symlink [`33527dd`](https://github.com/GENESIS-EFRC/reaction-network/commit/33527ddd86f1c336efa807a667d4740a8bd12a0e) | ||
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| #### [v8.0.2](https://github.com/GENESIS-EFRC/reaction-network/compare/v8.0.1...v8.0.2) | ||
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| > 1 September 2023 | ||
| #### [v8.0.1](https://github.com/GENESIS-EFRC/reaction-network/compare/v8.0.0...v8.0.1) | ||
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| > 1 September 2023 | ||
| - Fix docs [`#272`](https://github.com/GENESIS-EFRC/reaction-network/pull/272) | ||
| - fix docs [`957a78d`](https://github.com/GENESIS-EFRC/reaction-network/commit/957a78d7de5cdbf318e4134c9277e28afcd1cc61) | ||
| - fix broken badge [`24820e6`](https://github.com/GENESIS-EFRC/reaction-network/commit/24820e682f9d35c166380b071d9e9738c0fad5b9) | ||
| - Update README.md [`05472a2`](https://github.com/GENESIS-EFRC/reaction-network/commit/05472a231b1d898b07af498f709b235832205567) | ||
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| ### [v8.0.0](https://github.com/GENESIS-EFRC/reaction-network/compare/v7.0.1...v8.0.0) | ||
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| > 31 August 2023 | ||
| - Fix release [`#271`](https://github.com/GENESIS-EFRC/reaction-network/pull/271) | ||
| - Add synthesis planning code: interface reaction hulls, jobs/flows, and more [`#270`](https://github.com/GENESIS-EFRC/reaction-network/pull/270) | ||
| - Add methods for setting open element and temperature to reaction set [`#254`](https://github.com/GENESIS-EFRC/reaction-network/pull/254) | ||
| - GPU pathway solver updates [`#190`](https://github.com/GENESIS-EFRC/reaction-network/pull/190) | ||
| - Update for NCI hackathon [`#186`](https://github.com/GENESIS-EFRC/reaction-network/pull/186) | ||
| - add r2scan carbonate correction NB [`5e24e06`](https://github.com/GENESIS-EFRC/reaction-network/commit/5e24e0647b25c43e34062080f97cf3966f8f9b7d) | ||
| - remove unnecessary nb [`a32a2f0`](https://github.com/GENESIS-EFRC/reaction-network/commit/a32a2f0ba5e38927d71b4452079cdf4865b0ab2f) | ||
| - add weighted sum cf, fix secondary formula, update carbonate correction [`2c8b66e`](https://github.com/GENESIS-EFRC/reaction-network/commit/2c8b66e43e5fbc591468c3866283fa45e1f3b340) | ||
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| #### [v7.0.1](https://github.com/GENESIS-EFRC/reaction-network/compare/v7.0.0...v7.0.1) | ||
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| > 7 February 2023 | ||
| - Patch release [`#221`](https://github.com/GENESIS-EFRC/reaction-network/pull/221) | ||
| - Fix broken testing for next patch release [`#220`](https://github.com/GENESIS-EFRC/reaction-network/pull/220) | ||
| - added data file in pip package [`#218`](https://github.com/GENESIS-EFRC/reaction-network/pull/218) | ||
| - Bump mkdocs from 1.4.0 to 1.4.2 [`#189`](https://github.com/GENESIS-EFRC/reaction-network/pull/189) | ||
| - Bump pymatgen from 2022.10.22 to 2022.11.1 [`#187`](https://github.com/GENESIS-EFRC/reaction-network/pull/187) | ||
| - Bump pymatgen from 2022.09.21 to 2022.10.22 [`#184`](https://github.com/GENESIS-EFRC/reaction-network/pull/184) | ||
| - fix broken linting [`e48b950`](https://github.com/GENESIS-EFRC/reaction-network/commit/e48b95075fb6d84aba024fcf0c2c0895598a98c7) | ||
| - Updated CHANGELOG.md [`934cc10`](https://github.com/GENESIS-EFRC/reaction-network/commit/934cc109aa2bca5195ff2b589db63720d48e2fac) | ||
| - fix no implicit optional (new mypy bug) [`0c05125`](https://github.com/GENESIS-EFRC/reaction-network/commit/0c05125bee499541719c6159c61c9dec0429557d) | ||
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| ### [v7.0.0](https://github.com/GENESIS-EFRC/reaction-network/compare/v6.1.1...v7.0.0) | ||
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| > 27 October 2022 | ||
| - Implement support for rustworkx, drop graph-tool [`#176`](https://github.com/GENESIS-EFRC/reaction-network/pull/176) | ||
| - Swap graph-tool for rustworkx [`#175`](https://github.com/GENESIS-EFRC/reaction-network/pull/175) | ||
| - Fix serialization of reaction network [`7406aec`](https://github.com/GENESIS-EFRC/reaction-network/commit/7406aec023a98aa917a1027dc84d73958e57b8a3) | ||
| - first attempt at fixing problems with serialization [`21df4a4`](https://github.com/GENESIS-EFRC/reaction-network/commit/21df4a4ce07af836b9fd6825f116952bc582af00) | ||
| - fix broken docs from gt removal [`2033864`](https://github.com/GENESIS-EFRC/reaction-network/commit/2033864f1da6e66dfe4ab7e0dcb416ada60fd54e) | ||
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| #### [v6.1.1](https://github.com/GENESIS-EFRC/reaction-network/compare/v6.1.0...v6.1.1) | ||
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| > 25 October 2022 | ||
| - fix broken docs github workflow [`#174`](https://github.com/GENESIS-EFRC/reaction-network/pull/174) | ||
| - Updated CHANGELOG.md [`a69f73e`](https://github.com/GENESIS-EFRC/reaction-network/commit/a69f73e31ce2871e8ac4e13a113801a92e8956ec) | ||
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| #### [v6.1.0](https://github.com/GENESIS-EFRC/reaction-network/compare/v6.0.2...v6.1.0) | ||
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| > 25 October 2022 | ||
| - hopefully fix broken release workflow [`#173`](https://github.com/GENESIS-EFRC/reaction-network/pull/173) | ||
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| #### [v6.0.2](https://github.com/GENESIS-EFRC/reaction-network/compare/v6.0.1...v6.0.2) | ||
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| > 25 October 2022 | ||
| #### [v6.0.1](https://github.com/GENESIS-EFRC/reaction-network/compare/v6.0.0...v6.0.1) | ||
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| > 25 October 2022 | ||
| - trigger new version release [`#172`](https://github.com/GENESIS-EFRC/reaction-network/pull/172) | ||
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| ### [v6.0.0](https://github.com/GENESIS-EFRC/reaction-network/compare/v5.1.0...v6.0.0) | ||
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| > 25 October 2022 | ||
| - Release new version to PyPI [`#171`](https://github.com/GENESIS-EFRC/reaction-network/pull/171) | ||
| - Update README with better description, new patch release 6.0.1 [`#170`](https://github.com/GENESIS-EFRC/reaction-network/pull/170) | ||
| - Major update of reaction-network [`#169`](https://github.com/GENESIS-EFRC/reaction-network/pull/169) | ||
| - update enumerators NB [`906745f`](https://github.com/GENESIS-EFRC/reaction-network/commit/906745fd20bb599061cab7c89e9233111a83e2ca) | ||
| - Fix bugs in network job/flow [`b62832d`](https://github.com/GENESIS-EFRC/reaction-network/commit/b62832d0a9434ce3c65b60b4e1394d7c5b43be68) | ||
| - remove fireworks support, better dataframe handling, network flow, bug [`90284a2`](https://github.com/GENESIS-EFRC/reaction-network/commit/90284a296fff2dd4bdea136d7683d787b4dcedd8) | ||
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| #### [v5.1.0](https://github.com/GENESIS-EFRC/reaction-network/compare/v5.0.0...v5.1.0) | ||
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| > 26 May 2022 | ||
| - Add carbonate correction, ability to turn off enumeration parallelization, minor bug fixes, new numba [`#133`](https://github.com/GENESIS-EFRC/reaction-network/pull/133) | ||
| - Add carbonate correction and jupyter NB with fitting function [`883ed66`](https://github.com/GENESIS-EFRC/reaction-network/commit/883ed662193c3520ad30b1a332bd10863f419e72) | ||
| - fix broken monty for new carbonate correction & change default limit [`79e2a03`](https://github.com/GENESIS-EFRC/reaction-network/commit/79e2a032f8cce459339609e884343688a826f159) | ||
| - update carbonate jupyter NB [`28d95fc`](https://github.com/GENESIS-EFRC/reaction-network/commit/28d95fcf59b25564b111d48f372e947ee0073fa4) | ||
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| ### [v5.0.0](https://github.com/GENESIS-EFRC/reaction-network/compare/v4.3.0...v5.0.0) | ||
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| > 31 March 2022 | ||
| - Add support for multiprocessing via ray, add builders and pydantic models, bug fixes [`#106`](https://github.com/GENESIS-EFRC/reaction-network/pull/106) | ||
| - Fix broken metastable_domains in chemical potential diagram [`#102`](https://github.com/GENESIS-EFRC/reaction-network/pull/102) | ||
| - Add simple retrosynthesis builder [`7e9db3e`](https://github.com/GENESIS-EFRC/reaction-network/commit/7e9db3e68ac9c7c8122e63ec9a111301a315f2b5) | ||
| - update ray with better initialization and parallelization [`f174500`](https://github.com/GENESIS-EFRC/reaction-network/commit/f174500cc5e86fdc7a03c26397705fec103fc230) | ||
| - add better threshold for multiprocessing [`32259ff`](https://github.com/GENESIS-EFRC/reaction-network/commit/32259ff62fe3d20c5b3af4d2f9b8407c9c89e576) | ||
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| #### [v4.3.0](https://github.com/GENESIS-EFRC/reaction-network/compare/v4.2.0...v4.3.0) | ||
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| > 1 March 2022 | ||
| - Update Github action for release [`#100`](https://github.com/GENESIS-EFRC/reaction-network/pull/100) | ||
| - Fix for broken NIST data and small speedups for e_above_hull calculations [`#90`](https://github.com/GENESIS-EFRC/reaction-network/pull/90) | ||
| - update broken NB [`e3e904a`](https://github.com/GENESIS-EFRC/reaction-network/commit/e3e904a70fbacae35c6d034939ff6df92a27fe1e) | ||
| - Add method for acquiring e_above_hull from an entry [`1983bee`](https://github.com/GENESIS-EFRC/reaction-network/commit/1983bee52d740b11b87ea62555a386a2169b7b65) | ||
| - linting, add calculate_e_above_hulls flag [`a93a66f`](https://github.com/GENESIS-EFRC/reaction-network/commit/a93a66f9cb1a1174b179c0f9fdff6a6c0ff73375) | ||
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| #### [v4.2.0](https://github.com/GENESIS-EFRC/reaction-network/compare/v4.1.0...v4.2.0) | ||
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| > 10 February 2022 | ||
| - Address several performance issues, add FREED data, support for metastable CPDs [`#88`](https://github.com/GENESIS-EFRC/reaction-network/pull/88) | ||
| - Add FREEDReferenceEntry, compress existing data, [`a03af78`](https://github.com/GENESIS-EFRC/reaction-network/commit/a03af788e309b871287ef1a76a78956351cd1c9b) | ||
| - Add caching for get_min_entry_by_formula, fix speed of minimize enumer [`8c68259`](https://github.com/GENESIS-EFRC/reaction-network/commit/8c6825937ded9d5ab1dd05810452b9c9b116d66c) | ||
| - Add support for adding entry to existing cpd. Some bugs for domain assgn [`871900b`](https://github.com/GENESIS-EFRC/reaction-network/commit/871900bee47eca4baf7ae1c4729de41d0f228bdd) | ||
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| #### [v4.1.0](https://github.com/GENESIS-EFRC/reaction-network/compare/v4.0.2...v4.1.0) | ||
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| > 1 February 2022 | ||
| - Speed up enumerators and tests [`#85`](https://github.com/GENESIS-EFRC/reaction-network/pull/85) | ||
| - speed up tests considerably [`a6e0d3f`](https://github.com/GENESIS-EFRC/reaction-network/commit/a6e0d3ffc3d34b0c254f6e161a9f7b18c9e1d492) | ||
| - Updated CHANGELOG.md [`9b11294`](https://github.com/GENESIS-EFRC/reaction-network/commit/9b112944d7c071d0b8d660f2444398d855c2df6d) | ||
| - get rid of NO2 entry, test open_elem checking [`7e6aeac`](https://github.com/GENESIS-EFRC/reaction-network/commit/7e6aeac08e3a1da1206a1699ec73493541aeeb90) | ||
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| #### [v4.0.2](https://github.com/GENESIS-EFRC/reaction-network/compare/v4.0.1...v4.0.2) | ||
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| > 21 January 2022 | ||
| #### [v4.0.1](https://github.com/GENESIS-EFRC/reaction-network/compare/v4.0.0...v4.0.1) | ||
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| > 21 January 2022 | ||
| - Fix github workflows [`#75`](https://github.com/GENESIS-EFRC/reaction-network/pull/75) | ||
| - fix github workflows [`f9fcb86`](https://github.com/GENESIS-EFRC/reaction-network/commit/f9fcb867834e44011ba3193b01a727dab0509469) | ||
| - Bump fireworks from 1.9.7 to 1.9.8 [`8178bf4`](https://github.com/GENESIS-EFRC/reaction-network/commit/8178bf441ec26d6a25d4a9e49a804edecc245a81) | ||
| - Bump numpy from 1.22.0 to 1.22.1 [`08794da`](https://github.com/GENESIS-EFRC/reaction-network/commit/08794dad955199c18ecb4edfb62bb3658f6a4a67) | ||
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| ### [v4.0.0](https://github.com/GENESIS-EFRC/reaction-network/compare/v3.0.0...v4.0.0) | ||
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| > 21 January 2022 | ||
| - New NetworkFW, competitiveness scores, updates to enumerators, and bug fixes + speed-ups [`#59`](https://github.com/GENESIS-EFRC/reaction-network/pull/59) | ||
| - add barin table data, graph saving/loading [`0c44c88`](https://github.com/GENESIS-EFRC/reaction-network/commit/0c44c88672246c4e41136260f7ab7b5a1c2b4c5d) | ||
| - Generate new NIST-JANAF data [`4b350ab`](https://github.com/GENESIS-EFRC/reaction-network/commit/4b350abd83147ab8d902b2ab631bae70c948d2bb) | ||
| - update docs and docstrings [`706b31d`](https://github.com/GENESIS-EFRC/reaction-network/commit/706b31db757bf6b2c28092297c878b3e2bd36f68) | ||
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| ### [v3.0.0](https://github.com/GENESIS-EFRC/reaction-network/compare/v2.0.3...v3.0.0) | ||
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| > 30 September 2021 | ||
| - [WIP] Add much-needed tests [`#45`](https://github.com/GENESIS-EFRC/reaction-network/pull/45) | ||
| - Add docs files as well [`1b3f9ce`](https://github.com/GENESIS-EFRC/reaction-network/commit/1b3f9ce68e6f8fe6a1082f8ad035b53fc732e0d7) | ||
| - add more tests for entries and reactions [`e84ec08`](https://github.com/GENESIS-EFRC/reaction-network/commit/e84ec08b0acc9be5e9dba93a41aa8e7326ca5030) | ||
| - Add test files, clean up test directory, clean class docstrings [`72d60c6`](https://github.com/GENESIS-EFRC/reaction-network/commit/72d60c62ef4f123001ee11c2e90d7679189e2641) | ||
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| #### [v2.0.3](https://github.com/GENESIS-EFRC/reaction-network/compare/v2.0.2...v2.0.3) | ||
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| > 5 August 2021 | ||
| - Update README and trigger release [`#34`](https://github.com/GENESIS-EFRC/reaction-network/pull/34) | ||
| - Update README.md [`d23e4ec`](https://github.com/GENESIS-EFRC/reaction-network/commit/d23e4ec6d5c2b03f9cbb85486f5839306dc7076c) | ||
| - Use PAT instead of Github token [`481af85`](https://github.com/GENESIS-EFRC/reaction-network/commit/481af8506c56f04c068556bedc447be05bef7082) | ||
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| #### [v2.0.2](https://github.com/GENESIS-EFRC/reaction-network/compare/v2.0.1...v2.0.2) | ||
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| > 5 August 2021 | ||
| - Bug fix for interdependent reactions [`#33`](https://github.com/GENESIS-EFRC/reaction-network/pull/33) | ||
| - bug fix for interdependent rxns [`f4bce46`](https://github.com/GENESIS-EFRC/reaction-network/commit/f4bce4641f5c92800699d735d14da64cf9f18eb0) | ||
| - fix linting issue [`0ede444`](https://github.com/GENESIS-EFRC/reaction-network/commit/0ede44496f4da3e6f1daa73c7e207915d92571d7) | ||
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| #### [v2.0.1](https://github.com/GENESIS-EFRC/reaction-network/compare/v2.0.0...v2.0.1) | ||
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| > 5 August 2021 | ||
| - Fix and deploy docs [`#32`](https://github.com/GENESIS-EFRC/reaction-network/pull/32) | ||
| - Add workflows to test and deploy docs [`e0352d5`](https://github.com/GENESIS-EFRC/reaction-network/commit/e0352d5111cf7cfccbb3a0009804dbb8e76e403e) | ||
| - Remove old references for now [`e4c5569`](https://github.com/GENESIS-EFRC/reaction-network/commit/e4c55697d29c53d482be3da013b3440b104bf425) | ||
| - update python versions [`29dd635`](https://github.com/GENESIS-EFRC/reaction-network/commit/29dd635f2f07c376e66b7376435a0627709b2a8e) | ||
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| ### [v2.0.0](https://github.com/GENESIS-EFRC/reaction-network/compare/v1.0...v2.0.0) | ||
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| > 5 August 2021 | ||
| - Major refactor of entire reaction-network package [`#23`](https://github.com/GENESIS-EFRC/reaction-network/pull/23) | ||
| - Merging of major revision reaction-network code [`#5`](https://github.com/GENESIS-EFRC/reaction-network/pull/5) | ||
| - Repo Cleanup [`#4`](https://github.com/GENESIS-EFRC/reaction-network/pull/4) | ||
| - switch docs to Markdown [`365cd49`](https://github.com/GENESIS-EFRC/reaction-network/commit/365cd49215344ac3c48e8c1024bcedcd8b70ebd7) | ||
| - update demo NB [`35a153a`](https://github.com/GENESIS-EFRC/reaction-network/commit/35a153a573389acb4c1f3476c6c341c09e5d9972) | ||
| - fix environment.yml again! [`e4180df`](https://github.com/GENESIS-EFRC/reaction-network/commit/e4180df37aef5966db726136fc7ec79329f25d96) | ||
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| #### v1.0 | ||
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| > 21 July 2020 | ||
| - Added pathway balancing, NIST gas data, StructuralComplexity cost metric, and more. [`#3`](https://github.com/GENESIS-EFRC/reaction-network/pull/3) | ||
| - Implemented Gibbs Free Energy SISSO descriptor [`#2`](https://github.com/GENESIS-EFRC/reaction-network/pull/2) | ||
| - Added refactoring and documentation [`#1`](https://github.com/GENESIS-EFRC/reaction-network/pull/1) | ||
| - Major cleaning [`36949c0`](https://github.com/GENESIS-EFRC/reaction-network/commit/36949c0563bf61d493be2aaa16f8d48f62312ef6) | ||
| - Many more graph-tool updates (+ exp data) [`d1315a1`](https://github.com/GENESIS-EFRC/reaction-network/commit/d1315a1f3e17bd036df2fe156299b91b7a74756c) | ||
| - Updated docstrings and docs [`89c76ca`](https://github.com/GENESIS-EFRC/reaction-network/commit/89c76ca9ddeaea496c62ab4ac4cac49bd0440b31) |