reaction-network - v8.5.1

Version 8.5.1

Commits

• [e0a93e46] Merge pull request #294 from materialsproject/update
• [16126d66] fix schema typing issue
• [d3d614f1] amend missing code update
• [a0d4cd76] fix broken README
• [6fb724bf] fix missing section from release

- Python
Published by mattmcdermott about 1 year ago

reaction-network - v8.5.0

Version 8.5.0

Commits

- Python
Published by mattmcdermott about 1 year ago

reaction-network - v8.4.0

Version 8.4.0

Commits

• [b74434cc] Merge pull request #293 from materialsproject/update
• [15f0f1df] upgrade setup-python github action version
• [6454cf3f] ruff ignore PLC0206
• [49487f67] update ruff py310
• [55bb746f] deprecate python=3.9
• [834d2d02] lint and update dependencies
• [23044c58] pin pymongo version due to kwarg bug
• [77870b69] add grand potential phase diagrams to expand_pd (fixes bug in cpd)

- Python
Published by mattmcdermott about 1 year ago

reaction-network - v8.3.4

Version 8.3.4

Commits

• [5b820155] Merge pull request #291 from materialsproject/update
• [e6d0cd0a] trigger release

- Python
Published by mattmcdermott over 1 year ago

reaction-network - v8.3.3

Version 8.3.3

Commits

• [8aff456b] Merge pull request #290 from materialsproject/update
• [f723c456] final ruff fixes
• [7d2785a1] add back missing ruff ignore
• [055403bc] move ruff check
• [5326b7e4] fix broken linting
• [be697d22] exclude ipynb from linting
• [6e74c9f5] further cleanup
• [59b1c245] lint
• [aeac1b17] clean up

- Python
Published by mattmcdermott over 1 year ago

reaction-network - v8.3.2

Version 8.3.2

Commits

• [3c06dbdd] Merge pull request #289 from materialsproject/update
• [35668702] downgrade numpy<2
• [e9161d22] update reqs
• [5b0ef21b] ruff fixes
• [fa1aa1bb] fix getnewtemperature() to include energy adjustments
• [9f62eef4] change default entry db function
• [fcca453d] add better custom entry db retrieval

- Python
Published by mattmcdermott over 1 year ago

reaction-network - v8.3.1

Version 8.3.1

Commits

• [fbfe2692] Merge pull request #288 from materialsproject/ci_update
• [b536ff35] fix last remaining broken workflows
• [6f0197ca] fix test
• [b78a0c4c] add missing venv line
• [5a37fa77] get consistent venv activation
• [1f8d938e] activate venv
• [5dac49a1] add uv venv
• [26315853] change CI to include uv installation
• [56e65b85] Updated CHANGELOG.md

- Python
Published by mattmcdermott almost 2 years ago

reaction-network - v8.3.0

Version 8.3.0

Commits

• [78684bc8] Merge pull request #287 from materialsproject/new_rlease
• [39205b16] linting with ruff 3
• [321d4ea7] change ruff settings for 3.0
• [aaf9996b] Get ready for new release
• [eb997c2c] Merge pull request #286 from materialsproject/dep-fix
• [29095803] add test for energy adjustment comparison
• [96c9380a] Fix bug in ExperimentalReferenceEntry; was not comparing equality
• [a5949a74] fix typing of last_updated
• [b27f423e] Updated CHANGELOG.md

- Python
Published by mattmcdermott almost 2 years ago

reaction-network - v8.2.1

Version 8.2.1

Commits

• [c4565820] Merge pull request #284 from materialsproject/dep-fix
• [6bb6b256] Add missing factor of 1/3 to CO2 correction
• [b91033f6] Merge pull request #283 from materialsproject/dep-fix
• [0a20a88c] add CO2 atmospheric correction (model pCO2)
• [27211199] Updated CHANGELOG.md

- Python
Published by mattmcdermott about 2 years ago

reaction-network - v8.2.0

Version 8.2.0

Commits

• [46c8ce03] Merge pull request #282 from materialsproject/dep-fix
• [b294d9c6] fix interpolated entry get new temperature bug
• [0e832752] fix dependency bug
• [2663cd1f] add Deprecated entry checking, update dependencies
• [39d855c2] Add common gases, get rid of NaCO3 (how did this end up in NIST?)
• [f2fa8586] fix broken network repr
• [b08dcf47] fix ruffs broken docstrings :(
• [eac4e3e2] Updated CHANGELOG.md

- Python
Published by mattmcdermott about 2 years ago

reaction-network - v8.1.0

Version 8.1.0

Commits

• [ae321f40] Merge pull request #279 from materialsproject/pydantic2
• [5d70c674] linting correction
• [04f4c4ec] fix broken test
• [5bd90f0d] clean-up docs
• [54c6704d] enforce pydantic<2.5
• [2b2c5ff8] rerun tests
• [ab0b326c] patch for github workflow while mp-api broken
• [80fbb501] fix broken entry job
• [280f46f8] attempt to fix typing problem
• [25289471] fix broken tests
• [41344f6a] Update CITATION.bib with new paper
• [87957398] more linting (mypy)
• [7b93a61e] linting
• [1ac4f910] implement ruff pt 2
• [53df69ef] Implement ruff
• [cc427947] add DB access script
• [ed295a24] python=3.8 dropped (not ready for python=3.12 yet)
• [21065dcf] Drop support for python=3.8 due to dependencies (i.e., pymatgen)
• [7505cef7] fix broken pathway plotting
• [2b8b0f25] add Optional
• [7d661292] update deps
• [af769d8e] Merge pull request #278 from materialsproject/update_notebooks
• [10e00361] Update networks NB
• [85217720] Updated CHANGELOG.md

- Python
Published by mattmcdermott over 2 years ago

reaction-network - v8.0.4

Version 8.0.4

Commits

• [8b72e0d8] Merge pull request #277 from materialsproject/entry_id-bug-fix
• [211f5ed5] Merge pull request #276 from materialsproject/comp-bug-fix
• [32c3e3bc] Add default entry_id creation and better docs
• [0daf280f] fix Gibbs entry bug when initializing with Species
• [bb93f397] Updated CHANGELOG.md

- Python
Published by mattmcdermott over 2 years ago

reaction-network - v8.0.3

Version 8.0.3

Commits

• [4be8a4c5] Merge pull request #273 from materialsproject/dev
• [b3f0b0f8] fix broken doc release
• [e790580b] get rid of changelog in action
• [33527ddd] fix broken symlink

- Python
Published by mattmcdermott over 2 years ago

reaction-network - v8.0.2

Version 8.0.2

Commits

- Python
Published by mattmcdermott over 2 years ago

reaction-network - v8.0.1

Version 8.0.1

Commits

• [fcc5cd96] Merge pull request #272 from materialsproject/dev
• [957a78d7] fix docs
• [24820e68] fix broken badge
• [05472a23] Update README.md

- Python
Published by mattmcdermott over 2 years ago

reaction-network - v8.0.0

Version 8.0.0

Commits

• [8b79b4fb] Merge pull request #271 from materialsproject/dev
• [91ae7ea9] fix release
• [e0aebaa3] Merge remote-tracking branch 'origin/main' into dev
• [b32133ce] fix token problem
• [11961d5f] Update README.md
• [a15cc286] Merge pull request #270 from materialsproject/dev
• [5a008360] fix broken notebooks sphinx
• [cb99ebc0] possible pydantic issue fix
• [f9f45f3f] update python ver
• [08cbff49] update github actions for docs
• [ec2d2fa7] switch to sphinx for docs
• [ef29b05e] upgrade python version
• [d5ba7421] linting
• [5ab13876] fix jobflow dependency
• [ff747915] fix merge
• [e55584ab] Merge remote-tracking branch 'origin/main' into dev
• [0b756a08] clean up tests
• [adf5f712] update README and dependencies
• [1032dd0b] Update network NB
• [34be2ca2] update demo NB 1
• [686c5b8e] add some tests, improve coverage profiling
• [498cb22c] fix broken tests
• [346e543a] fix strange typing bug with inheritance
• [9ada46c5] clean up enumerator method signatures
• [f3770e0d] Fix enumerator docstrings
• [5a407745] clean up docs yaml
• [7d26abe9] cleaning up docs and typing pt 4 (network, flows, jobs)
• [c342b462] cleaning up docs and typing pt 3 (mostly pathways, network)
• [fc050ffd] cleaning up docs and typing pt 2 (mostly enum, reactions, thermo)
• [01b3b71f] cleaning up docs and typing pt 1
• [fd1f91d2] update docs
• [8c050c82] lots of cleanup, parallel testing, fix math.isclose bug, old tests
• [5f68d3da] updating docstrings pt1
• [9329e53b] finish cleaning base/core
• [a7d671f3] move base classes into base files
• [09be500e] remove builders (they were unused)
• [234b8e61] Merge remote-tracking branch 'origin/dev' into dev
• [0efcfca2] add option for custom entries
• [d3f6098a] Update README.md for new org
• [6e7b7965] Update README.md for new org
• [5fa9f5ba] Delete dependabot.yml
• [f17cb1f7] Delete dependabot.yml
• [89ca65c5] Change name of synthesis planning flow
• [308840df] improve some broken tests
• [28a49a79] shift code around, update dependencies
• [473c0fb9] Merge pull request #254 from GENESIS-EFRC/improv/change-rxn-set
• [e66ad69d] add tests for new reaction set methods
• [42378335] Add methods for setting open element and temp on reaction set
• [736acc3d] default include nist data True
• [b034947e] test commit

- Python
Published by mattmcdermott over 2 years ago

reaction-network - v7.0.1

Version 7.0.1

Commits

• [49687285] Merge pull request #221 from GENESIS-EFRC/fix_release
• [603c2918] dummy commit
• [714d1d57] Merge remote-tracking branch 'upstream/main' into fix_release
• [f20624e6] Merge pull request #220 from GENESIS-EFRC/fix_release
• [2230d368] Fix broken badge on README.md
• [1bf3f0c4] fix bug with prospector downgrading
• [adab94c4] change order of installation prospector, fix typing bug
• [0c05125b] fix no implicit optional (new mypy bug)
• [b26ddfa4] run black
• [e48b9507] fix broken linting
• [be76016d] Merge pull request #218 from R1j1t/bug/missingDataFile
• [3d577174] fixed the file path
• [296eab7b] added data file in pip package
• [c74d28bb] update reqs and fix broken python-requires option
• [85e72b84] Merge pull request #189 from GENESIS-EFRC/dependabot/pip/mkdocs-1.4.2
• [1d79629a] Merge pull request #187 from GENESIS-EFRC/dependabot/pip/pymatgen-2022.11.1
• [85682385] Bump mkdocs from 1.4.0 to 1.4.2
• [bba6de78] Bump pymatgen from 2022.10.22 to 2022.11.1
• [afce1fdc] Merge pull request #184 from GENESIS-EFRC/dependabot/pip/pymatgen-2022.10.22
• [fceb2044] Bump pymatgen from 2022.09.21 to 2022.10.22
• [934cc109] Updated CHANGELOG.md

- Python
Published by mattmcdermott about 3 years ago

reaction-network - v7.0.0

Version 7.0.0

Commits

• [e64a82b5] Merge pull request #176 from GENESIS-EFRC/nci-hackathon
• [d334e004] update README to reflect new rustworkx
• [8c94544e] update docs for rx
• [ae538709] update demo NBs
• [7406aec0] Fix serialization of reaction network
• [21df4a4c] first attempt at fixing problems with serialization
• [6fbda684] remove pytest xvfb
• [483b22aa] implement gh caching for other workflows
• [04528060] fix warning and try caching
• [5f4c53e8] fix broken github action for caching and python version
• [2033864f] fix broken docs from gt removal
• [82261f08] add caching to github action
• [f59300bc] Merge remote-tracking branch 'upstream/nci-hackathon' into nci-hackathon
• [1895bc83] fix typing errors
• [b77e202d] Merge branch 'main' into nci-hackathon
• [2cd40183] Merge pull request #175 from GENESIS-EFRC/rustworkx
• [c41d417f] linting
• [26d295f3] adjust reqs and github actions
• [3593131e] Add serialization support for ReactionNetwork
• [79288a05] fix network visualization for rustworkx
• [8ebdae21] fix yen's algorithm problem
• [b026a370] finish implementation of rustworkx
• [da80136c] add precursors/target support for rustworkx
• [fe57f82e] Updated CHANGELOG.md

- Python
Published by mattmcdermott over 3 years ago

reaction-network - v6.1.1

Version 6.1.1

Commits

• [76980c6f] Merge pull request #174 from GENESIS-EFRC/new_version
• [c38bccf2] fix broken docs github workflow
• [a69f73e3] Updated CHANGELOG.md

- Python
Published by mattmcdermott over 3 years ago

reaction-network - v6.1.0

Version 6.1.0

Commits

• [d2b1246b] Merge pull request #173 from GENESIS-EFRC/new_version
• [65682b95] hopefully fix broken release workflow

- Python
Published by mattmcdermott over 3 years ago

reaction-network - v6.0.1

Version 6.0.1

Commits

• [0827a9b6] Merge pull request #172 from GENESIS-EFRC/new_version
• [4a2f36d2] trigger new version release

- Python
Published by mattmcdermott over 3 years ago

reaction-network - v6.0.0

Version 6.0.0

Commits

• [427b5c8c] Merge pull request #171 from GENESIS-EFRC/new_version
• [db11796d] test commit for new release
• [0342aad4] test commit for new release
• [b78e88d4] clean up post-process
• [665026e2] fix github pypi release workflow
• [b4a61105] fix docstring
• [9baca901] Merge pull request #170 from GENESIS-EFRC/mattmcdermott-patch-1
• [26fd14e4] Update README with better description
• [39925207] Update README shields
• [f961789e] Merge pull request #169 from GENESIS-EFRC/version_update
• [0e3bf315] cleanup for release pt2
• [5f404a2e] cleanup pt 1
• [2e123087] fix broken pathway solver test
• [36877e5d] add support for network store
• [842572be] make sure formulas are included in network flow
• [3f0ae1bd] linting, fix broken test
• [3782ec16] update network NB, fix bug in pathway solver
• [906745fd] update enumerators NB
• [aa1a2351] move files
• [8648b0f0] fix broken tests
• [fa10bf4d] run black
• [07f45ea5] change name of GibbsEntrySet.fromcomputedentries
• [4a319f91] switch to tol per atom
• [5502c545] change default interpolated entry tolerance
• [46b6cccd] adjust interpolated entry repr
• [2e954f9b] add hash for interpolated entry
• [9493811c] improve eq methods
• [9e8f2b6f] better error handling for cpd
• [4405297e] fix bug in test
• [96f45a5f] fix bug in interpolated entry init
• [edf77345] add back in tqdm disable
• [8a67c8ae] clean up conftest
• [878fe73a] change logging to debug
• [1c423908] add further secondary selectivity calcs
• [e76b21e4] run black
• [279f2c62] improve chunking / batch sizes
• [e368f52a] add type for metastable domains
• [ab611916] deleting whitespace
• [be9d3d18] fix strange problem in applying carbonate corrections
• [35c81be1] add simple builder schema tests
• [93d57c57] fix linting bugs
• [e7bb2a62] run black
• [3100ec0b] fix typo in plotly express
• [cb561fe6] fix linting
• [b71e8989] update README badges and add support for gtk during tests
• [d9ba7236] add MP API key secret
• [265cc043] update docs with refactor of code
• [e4112cd3] update reqs for docs
• [18fb48fe] format with black
• [75c94559] test new github workflow scheme

- Python
Published by mattmcdermott over 3 years ago

reaction-network - v5.1.0

Version 5.1.0

Commits

• [f85a827f] Merge pull request #133 from GENESIS-EFRC/dev
• [7c6b0454] fix setup
• [08c18725] fix broken github action
• [a5b3f58c] update docs
• [bcfec1b4] linting
• [34ed235f] update reqs and README
• [bec2bd0d] add support for turning off enumeration parallelization
• [4d77ca04] update reqs (still waiting on the new numba)
• [79e2a032] fix broken monty for new carbonate correction & change default limit
• [28d95fcf] update carbonate jupyter NB
• [883ed662] Add carbonate correction and jupyter NB with fitting function
• [5a6c8440] add getnewtemperature to reaction
• [6d7a008b] update competition name, thermodynamic data README
• [c7c8ca49] Merge remote-tracking branch 'upstream/main' into dev
• [ba0c969e] better dataframe handling, adjusted default c_score scale
• [56a9d3db] Bump mkdocs-material from 8.2.8 to 8.2.12
• [df66d9d3] Bump pymdown-extensions from 9.3 to 9.4
• [699ecb39] fix interpolated entry hashing bug
• [a6fb4dbc] add support for target formulas in competition score
• [bf58b2d7] Bump numpy from 1.22.2 to 1.22.3
• [7d662941] Bump mkdocstrings from 0.18.0 to 0.18.1
• [72821b2e] Bump mkdocs-material from 8.2.3 to 8.2.8
• [31729e31] Bump pymdown-extensions from 9.2 to 9.3
• [b7de74d9] Bump mypy from 0.931 to 0.942
• [2def7e3e] Bump maggma from 0.41.0 to 0.44.1
• [632bf414] Bump mkdocs-autorefs from 0.3.1 to 0.4.1
• [9c6c3cbb] Bump mkdocs-jupyter from 0.20.0 to 0.20.1
• [1562be13] Bump mkdocs-section-index from 0.3.3 to 0.3.4
• [548361d2] Bump pymatgen from 2022.2.10 to 2022.3.29
• [2abf372d] Updated CHANGELOG.md
• [f90d10b2] Bump pytest from 7.0.1 to 7.1.1

- Python
Published by mattmcdermott over 3 years ago

reaction-network - v5.0.0

Version 5.0.0

Commits

• [b0b65369] Merge pull request #106 from GENESIS-EFRC/dev
• [f11c27fb] upgrade black
• [5dd1c99b] upgrade pytest
• [d6b3fcbb] linting
• [3544f313] add missing req, update README
• [fd6273e4] fix calculateeabove_hulls bug
• [3f241ffc] fix rounding error in cpd
• [3090c98a] Add update by key to GridFS
• [32a9a5b5] add support for recipes GridFS
• [7a8d5933] fix broken task ID problem
• [1652a738] change task_id field to int
• [f4713e38] fix broken counter
• [d563cf42] clean up builder
• [841fbb52] rewrite retrosynthesis builder with new models
• [2638c5ba] Update pydantic models, and incorporate into workflows
• [6daf4db0] refactoring of drones/models
• [ab0565e0] basic support for gridfs (still WIP), added pydantic models
• [5c6cb64b] Fix GridFS overwrite
• [84567286] Add missing builder import
• [1fdcfeac] add support for GridFS
• [0277719c] ignore other NBs
• [7e9db3e6] Add simple retrosynthesis builder
• [fc1e445a] improve function names
• [97f0550b] add more general reaction plotting / DF methods
• [5d63784e] change where ray gets initialized
• [8e4d6c34] add missing imports
• [3420caa7] add ray to CompetitivenessScoreCalculator
• [3488a41e] add print statment for nodes
• [753abdf7] remove print
• [f174500c] update ray with better initialization and parallelization
• [ccc6ff8d] better support for ray clusters
• [0e77dd4f] fix tqdm and bug
• [9cd1ad36] update init
• [35f5ecbe] ray debugging
• [ca737061] move ray import
• [c365705a] add tqdm
• [32259ff6] add better threshold for multiprocessing
• [9e61cb1d] implement ray for multiprocessing
• [bf6a4589] Merge pull request #102 from GENESIS-EFRC/dev
• [8891aa0d] fix broken metastable_domains
• [552cae26] Updated CHANGELOG.md

- Python
Published by mattmcdermott almost 4 years ago

reaction-network - v4.3.0

Version 4.3.0

Commits

• [a321e2a4] Merge pull request #100 from GENESIS-EFRC/dev
• [307c7e69] remove error statement
• [12a650cb] update release-on-push
• [b1fe2a21] Bump pymdown-extensions from 9.1 to 9.2
• [c1364961] Bump pymatgen from 2022.1.24 to 2022.2.10
• [9b852c6d] Bump maggma from 0.39.1 to 0.41.0
• [c8560e7b] Bump mkdocs-material from 8.1.9 to 8.2.3
• [4edea2cf] Bump fireworks from 1.9.8 to 2.0.2
• [5507e0f9] Bump numpy from 1.22.1 to 1.22.2
• [d4871d37] Bump mkdocstrings from 0.17.0 to 0.18.0
• [68600000] Merge pull request #90 from GENESIS-EFRC/dev
• [21e7180d] fix linting
• [705dae0e] fix bug with interpolated entry checking
• [8e08434b] linting
• [d2dd3488] add missing includefreeddata
• [2875876c] Update entry builder task
• [d972ac0d] Update NIST JANAF data after fixing bug
• [e3e904a7] update broken NB
• [6a508cc2] remove elements from metastable_domains
• [a93a66f9] linting, add calculateeabove_hulls flag
• [1983bee5] Add method for acquiring eabovehull from an entry
• [4beef4c7] change default e_tol
• [0d277ec4] get rid of add_entry
• [6f39cced] Updated CHANGELOG.md

- Python
Published by mattmcdermott almost 4 years ago

reaction-network - v4.2.0

Version 4.2.0

Commits

• [0a34b8ee] Merge pull request #88 from GENESIS-EFRC/dev
• [cf343f83] run black
• [19c0de09] linting
• [a61866bb] improve competitiveness score calculator by better filtering
• [e719fdc5] add support for chemical potential distance to metastable phases
• [db6db8f6] fix metastable domain bug (interior point was wrong)
• [8988340d] adding entries to CPDs does not work
• [871900be] Add support for adding entry to existing cpd. Some bugs for domain assgn
• [b1b448b3] fix bug in eq for experimental entries
• [a03af788] Add FREEDReferenceEntry, compress existing data,
• [e6f0ff9c] add metastabledomains to cpd, add energyadjustments to expt entry
• [dee31458] parse formula to prevent bug
• [cc471b60] use cached properties for better min entry finding
• [d7e91e7f] remove print statemnet
• [8c682593] Add caching for getminentrybyformula, fix speed of minimize enumer
• [996fb8df] Updated CHANGELOG.md

- Python
Published by mattmcdermott about 4 years ago

reaction-network - v4.1.0

Version 4.1.0

Commits

• [53bf1a52] Merge pull request #85 from GENESIS-EFRC/dev
• [a6e0d3ff] speed up tests considerably
• [7e6aeac0] get rid of NO2 entry, test open_elem checking
• [a88c0bfd] Fix checking for precursors/targets to speed-up calculations
• [2fc2fb17] Bump mkdocs-material from 8.1.7 to 8.1.9
• [3248c428] Bump pymatgen from 2022.1.20 to 2022.1.24
• [91aabd2b] Bump mkdocs-jupyter from 0.19.0 to 0.20.0
• [507e7fba] Bump maggma from 0.38.1 to 0.39.1
• [1787423f] unpack metadata in stored results
• [47a6cfe5] add cost_function to metadata, fix enumerators metadata bug
• [9a8c3b4c] add quiet mode for enumerators
• [8e139874] update bug in EnumeratorFW
• [c579bebb] Create CITATION.bib
• [9b112944] Updated CHANGELOG.md

- Python
Published by mattmcdermott about 4 years ago

reaction-network - v4.0.2

Version 4.0.2

Commits

- Python
Published by mattmcdermott about 4 years ago

reaction-network - v4.0.1

Version 4.0.1

Commits

• [b30eefcb] Merge pull request #75 from GENESIS-EFRC/matt-tests
• [f9fcb867] fix github workflows
• [3460d1cd] Delete test.md
• [8178bf44] Bump fireworks from 1.9.7 to 1.9.8
• [08794dad] Bump numpy from 1.22.0 to 1.22.1
• [d0abccbf] Bump pre-commit from 2.15.0 to 2.17.0
• [eef57bbd] Bump mkdocs-material from 8.1.3 to 8.1.7
• [78f501ee] Bump pymatgen from 2022.01.09 to 2022.1.20

- Python
Published by mattmcdermott about 4 years ago

reaction-network - v4.0.0

Version 4.0.0

Commits

• [dd7b22d0] Merge pull request #59 from GENESIS-EFRC/matt-tests
• [83c6275c] Updating docstrings part 2
• [c047ea27] Updating docstrings part 1
• [dc0eadab] fix github action
• [47718277] fix github actions conda problem
• [ea435f7c] fix broken tests
• [6dfcd722] add black/pylint to testing requirements
• [c451c8bb] pylint
• [69aaddbc] flake8 exclude F401
• [592a6f32] linting
• [02ae1a22] fix several mypy issues
• [32d8004a] fix broken link for notebooks (had to duplicate)
• [706b31db] update docs and docstrings
• [8c3607cb] update docs organization
• [79ed4d38] Fix same numpy bug for lint/docs
• [979a7e95] Ok this might be the one
• [8121ef45] Merge branch 'main' into matt-tests
• [585aecd6] bump other reqs, try again for numpy
• [1e0978f0] I can't figure out this numpy problem
• [16fa96a3] try fixing dependencies again
• [4ec9b26c] change GitHub action
• [7bd487bb] add numpy to reqs
• [1cfdea3a] bump dependencies
• [7a8a99af] docstrings + linting
• [00a092f3] move getentrytask, clean up files
• [984a0837] Make enumerator chemsys filtering more robust
• [8c6196df] Fix NIST-JANAF bug with Na2CO3
• [5cd020dc] Add fireworks support for calculating c scores
• [096091ef] linting and fix reaction competitiveness bug
• [35fdb3ef] Add to_dataframe() method for ReactionSet
• [fa8690b7] ReactionSet can now regenerate OpenComputedReaction types
• [297c3ae7] Add CompetitivenessScoreCalculator
• [a32d29f8] fix experimental ref entry bug in network
• [fa05ddc1] Fix bug in creating ExperimentalReferenceEntry where comp was wrong
• [a7d4e1c8] GibbsEntrySet now only uses minimum experimental entry data
• [39a2e7b5] Clean up files
• [05b4a626] fix data bug in ExperimentalReferenceEntry
• [5c37e531] fix broken test
• [2e254625] Test of commit with docstring update
• [f6592c57] fix imports
• [00e62af0] clean up files
• [4abf16e4] add to git ignore
• [d3b0f267] fix RunNetwork firetask
• [f4900a8e] improve RunNetwork firetask
• [23564277] Finish PathwaySet implementation
• [09eda16f] Add CalcDb, first part of PathwaySet for saving paths
• [c2927044] clean up network firetasks
• [61f3cdab] Add supporting firetasks for network generation
• [c54736c7] Update network notebook
• [1a615a98] enumerators NB, fix entry_set serialization bug, README update
• [ec710222] Merge remote-tracking branch 'upstream/matt-tests' into matt-tests
• [367510a4] NB update part 2
• [603dd440] 1st part of update to example NBs
• [54e77584] fix broken test for entry
• [1181ff8f] add barin data warning
• [4b350abd] Generate new NIST-JANAF data
• [858a6ae7] fix line length
• [a2050413] fix targets bug
• [590ba20c] fix bug in enumerator firework
• [92cd517e] begin adding firework for network creation
• [6719424e] clean up NBs slightly
• [3cd3e5c5] major bug fix in pathway solver due to build_indices; added NBs
• [771411b0] fix broken test due to added barin data
• [0c44c886] add barin table data, graph saving/loading
• [2bb1cbb1] remove entry_set dependency in pymatgen
• [1f101631] add docstrings for linting
• [58fb0e33] Fix bug where open entries were being considered in exclusion
• [f9555472] fix enumerator bug, entry_set bug
• [2d3decb5] change to exclusive_targets, adjust pathway plotting
• [7e667b65] add pathway plotting, fix testing bug
• [d91b0871] add plotting for pathways, fix solver bug
• [ea0cd0e6] speed up chempot distance calculation
• [1482ac1b] Create CONTRIBUTING.md
• [81754af8] Create CODEOFCONDUCT.md
• [5a134c8b] Bump mkdocstrings from 0.15.2 to 0.16.1
• [691b0f8a] Bump pre-commit from 2.14.1 to 2.15.0
• [ff4f98b3] Bump mkdocs-minify-plugin from 0.4.0 to 0.4.1
• [19760ed8] Updated CHANGELOG.md

- Python
Published by mattmcdermott about 4 years ago

reaction-network - v3.0.0

Version 3.0.0

Commits

• [f7188610] Merge pull request #45 from GENESIS-EFRC/matt-tests
• [c721e5d2] run black
• [e61bf983] fix linting
• [96e5d2b7] clean up gh actions
• [a6e0b187] Add more docstrings
• [b2c1b84a] fix broken test
• [f913781d] finish minimize enumerator tests
• [48d77f3e] run black and make BasicOpenEnumerator faster
• [9612ed33] finish major part of enumerator refactor
• [81af4eac] further refactoring of enumerators
• [1e43776e] fix linting errors, work on refactor of enumerators
• [f938564b] try this order with default
• [f42bd968] fix hyphen
• [4fbd9d1d] combine run
• [c7c0c380] try with conda run
• [8070dc5f] fix typo
• [bef16ff3] and one more one more time
• [d86fb717] one more time with activation
• [3250f2d3] try it again with miniconda
• [11b03b45] add test import
• [36eff4b5] add print statement
• [176676c2] try again
• [e82cc53e] trying to fix bug again
• [dbd4773f] fix bug in docs
• [eadc9e45] bump python version
• [6a5c0fa4] change installation order
• [f4b5495d] add graph-tool to docs workflow
• [d80e201a] update pymatgen req
• [1ad5c860] fix mkdocs
• [56502bb2] fix req
• [df2215a9] Merge remote-tracking branch 'upstream/matt-tests' into matt-tests
• [d0d8bf91] Merge branch 'main' into matt-tests
• [6ed37c83] bump reqs
• [1b3f9ce6] Add docs files as well
• [725b3538] make tests simpler
• [dc33ad81] add basic open enumerator fixtures
• [2e3598ad] add enumerator tests, run black
• [f0f9d87c] fix circular import
• [95a2dea2] fill in missing tests, update README
• [9902291b] add balance arrays test
• [bfebbc1e] Change pathway solver reaction initialization
• [002874cf] clean up enumeration code
• [70f2ea5c] clean up attr use
• [bb97950a] bug fix for OpenComputedReaction
• [7cfea161] add computed rxn fixture
• [e84ec08b] add more tests for entries and reactions
• [2a66a760] add tests for BasicReaction
• [fe374ad8] fix core docstrings
• [52a565e4] fix calculator kwargs
• [72d60c62] Add test files, clean up test directory, clean class docstrings
• [b84f16b7] Bump numba from 0.53.1 to 0.54.0
• [11b1022c] Bump pytest from 6.2.1 to 6.2.5
• [f7f754d5] Bump graphistry from 0.19.2 to 0.20.1
• [be883b2e] Bump pydocstyle from 5.1.1 to 6.1.1
• [bc23886c] Bump pytest-cov from 2.11.0 to 2.12.1
• [68f88061] Bump pymatgen from 2022.0.11 to 2022.0.12
• [13695dc8] Bump pre-commit from 2.9.3 to 2.14.1
• [22ec0b84] Updated CHANGELOG.md

- Python
Published by mattmcdermott over 4 years ago

reaction-network - v2.0.3

Version 2.0.3

Commits

• [e0e6c6eb] Merge pull request #34 from GENESIS-EFRC/shyamd-patch-1
• [d23e4ec6] Update README.md
• [481af850] Use PAT instead of Github token

- Python
Published by mattmcdermott over 4 years ago

reaction-network - v2.0.2

Version 2.0.2

Commits

• [752b2184] Merge pull request #33 from GENESIS-EFRC/rxn-bugfix
• [0ede4449] fix linting issue
• [f4bce464] bug fix for interdependent rxns
• [eed6c715] Bump mypy from 0.812 to 0.910
• [802baa8e] Bump pymatgen from 2021.2.8 to 2022.0.11
• [315fcc47] Merge pull request #32 from GENESIS-EFRC/fix-docs
• [38014af4] fix graphistry requirements
• [e4c55697] Remove old references for now
• [e0352d51] Add workflows to test and deploy docs
• [cde0e4f4] ignore mypy for now since its a rats nest
• [6082811c] ignore another rule incompatible with black
• [29dd635f] update python versions
• [6af500ac] reference main not master branch
• [58ad2788] remove stale files
• [2db22b2d] Use regular github token
• [16af3556] Merge pull request #23 from GENESIS-EFRC/refactor-networks
• [2faafe04] Merge branch 'main' into refactor-networks
• [39201563] update pre-commit black/isort versions
• [2b7821c0] address flake8 issues
• [23aa24c1] changes from pre-commit
• [f2174d87] change pre-commit
• [0e5aabf9] Add workflow files
• [5a66f964] fix jupyter pin
• [11638939] Add requirements for docs
• [5ce7dd0d] Add dependabot config
• [3caaa025] hardpin in requirements.txt
• [59ecc22b] Add testing requirements
• [856ad92d] clean up some old files, fix README
• [b45534f6] fix some imports/reqs
• [0742be69] fix reqs, small bug fix in solver
• [5939f17c] update reqs
• [b8e9b7e9] add some docstrings, minor fixes
• [b50039c0] Add graph-tool cairo visualization
• [9becdc5e] cleaning up formatting
• [cc57e662] fixing import order
• [4328171a] re-format with black
• [7a4097f9] enumerator bug fix for targets
• [99b8578f] fix circular imports
• [1fc30916] bug fix for interdependent rxn finder
• [09f1f6ee] add implementation of PathwaySolver
• [f3acb189] add PathwaySolver for balancing pathways
• [cf45ce0f] reaction reverse() bug fixes
• [c3e5dbfb] add more network methods
• [f95f82a8] Add basic ReactionNetwork
• [b13dc16a] filter warnings
• [dc360b52] remove print statement
• [704c9df2] bug fix for deprecated
• [a1d2bca1] Adapt for current MP db
• [78fc94dc] update building entries from materials DB
• [c39b48ab] fix pymatgen imports
• [8831a47a] Revert "Add Synthesis and Interface class for MC approach"
• [d8104000] Add Synthesis and Interface class for MC approach
• [014edaaa] add option of "precursors" to enumerators
• [3de95b3a] add conftest better printout
• [75404e8d] Move all tests & switch over to pytest
• [f35b4f66] change to tqdm auto and bug fixes
• [398aa5fb] add some of the GibbsComputedEntry tests
• [26661a7a] implement Shyam's comments (reqs and set_temperature)
• [2cdce294] docstrings for entry and basic enumerators
• [8724082a] add docstrings pt2
• [d04a5d94] clean up docstrings more
• [efb520f9] Move enumerator staticmethods to utils, clean docstrings, formatting
• [86c731e4] add some simple tests, fix reaction copy methods, add reverse method
• [f550568e] update reqs and license
• [debc92b1] simplify files for release
• [d9d416ce] small NB tweak
• [937bf63a] update demo with NB with cleaner, simpler example
• [35a153a5] update demo NB
• [e4180df3] fix environment.yml again!
• [e7a2da93] test environment.yml again
• [cfb12e4c] update environment.yml
• [0c084051] change readthedocs environment.yml
• [fff85c97] update doc requirements
• [2cee9dba] update mkdocs / readthedocs
• [b4cfc9fa] update mkdocs
• [c2af34a7] updating docstrings
• [8ab2a845] fix README
• [5e3337ed] simplify/clean files for packaging manuscript version
• [6f6512a5] update reqs
• [4e8755ed] simplify and clean up release
• [848de399] Update README with better instructions
• [3f29c7c0] Update README.md with logo
• [d81fa5f6] fix bug in creating ReactionSet
• [a5e6ff2e] Bug fix in hash of BasicReaction
• [923f1c11] Bug fix in eq of BasicReaction
• [2dbc7c37] add uncertainty to NIST entry, fix bug in RunEnumerators
• [379883bd] bug fix for BasicOpenEnumerator
• [b2d2786f] add list initialization (bug fix)
• [0ebb61fd] add missing Composition import
• [fe5d8e8d] one more bug fix in NIST energy method
• [cffc536d] change int() to float() in NIST energy method
• [5f120d2a] update reqs
• [3ffc0e8b] add error catching for unmatched targets
• [90420666] add bug fix for env_chk
• [db06e3b6] reaction_set: less memory required for storage
• [45d594c6] first attempt to create ReactionSet, better storage
• [cc8289da] fix bug in NIST as_dict(), custom entry DB now working
• [2e3b3a03] fix EnumeratorFW bugs and make Gibbs entry more transparent
• [dbe9c452] Add init files, fix some entry initialization
• [b9d2226b] Add some convenient stabilization methods
• [2f5ef41b] add input building firetasks and supporting code
• [6e925f81] add first draft of simple firetasks/fireworks
• [552374b0] reformatting of entry repr
• [db4d3ffa] Add GibbsEntrySet
• [ef4bd1b3] simplification of calculators, static-methoding GibbsComputedEntry
• [b50d1635] Adding calculator application methodology
• [31b55dfc] implement calculators into basic enumerators
• [f0d01647] add calculator module
• [be89724c] change domains to cached_property
• [fb0a4f10] Add chempot map
• [ae00edc9] add chemical potential diagram class
• [0b9e593f] small refactoring of reactions/enumerators
• [b5e3bf05] add option for target
• [b7266769] run black, fix reaction normalize methods
• [4de40c2e] finish simplification of Reaction
• [75101779] simply Reaction to just be two input vectors
• [bd506aca] fix balancing bug pt. 2
• [f4b84f8b] normalize rxns and fix repr bug
• [8c468e8d] Introduce OpenComputedReaction for calculating changes in grand pot.
• [c0c44cf3] finish MinimizeGrandPotentialEnumerator
• [c1b145ca] Add is_identity property for filtering reactions
• [2470a6ff] add in functions to help with MinimizeGibbsEnumerator
• [58504349] Add first parts of MinimizeGibbsEnumerator
• [b658fb35] write BasicOpenEnumerator, add eq/hash for BasicReaction
• [20438501] write BasicEnumerator, add minimization enumerators
• [2100013f] add limited_powerset, add helper methods for enumerators
• [3a3dd491] add utils
• [df03cd77] add enumerators directory/file
• [07161b5d] lint cleanup
• [b11714df] initial pathways
• [7be23b8f] refactor core into module
• [95923733] remove old entries and reaction
• [2dacde9d] bug fix
• [6d3c2102] NetworkEntry
• [e651173f] more properties for interfaces
• [1023a121] add backwards compatibility with pymatgen to demo NB
• [aaed82bb] Merge remote-tracking branch 'upstream/revision'
• [98b5b6b1] update demo NB
• [6a323b4e] Switch back to pymatgen GibbsComputedStructureEntry
• [59d35b53] update reqs, configure GibbsComputedStructureEntry
• [36639a49] Merge pull request #5 from GENESIS-EFRC/revision
• [9b4acfed] update reqs
• [6f105473] Add json results, update demo NB
• [4df74f71] update reqs, first revision of demo NB
• [2b42a7dd] Update README instructions
• [af4276a6] supress import order lint error
• [8b3ff45e] Add Computed Reaction
• [8a30fbcc] Add notes for Matt
• [957855c7] update basic reaction for new abstractions
• [306a3057] abstract out more properties
• [640c37ba] fix init
• [6dccb364] Base reaction implementation
• [01a9135d] split entries in two two implemenations
• [71d1b2a7] move old core and define new core interfaces
• [420f0d07] fix data loading
• [c30414cc] Remove chempot restriction, fix bug with ._structure attribute & data
• [aad1e969] Merge pull request #4 from GENESIS-EFRC/cleanup
• [9e98f735] fix linting errors
• [d1d0b522] automated workflows
• [7eaa9265] Add Mkdocs
• [aac33b9a] basic lint infrastructure
• [365cd492] switch docs to Markdown
• [34df4298] update setup infrastructure
• [39a533ee] update license for LBNL
• [e3530945] add type hint support
• [a41da83f] make data into module
• [c1c569ab] make source tree
• [e27238ef] total cost now includes more accurate percentage method
• [04d3c428] fix major typo in screening for dummy nodes
• [483aca25] add li2o/na2o data
• [c408502f] Change graph creation to dask bag via iterable approach
• [cfffd393] clean up code formatting via black
• [bf27a8a8] Add save method (rudimentary) -- also clean up imports
• [1cc583f3] batch size tweaks
• [e05b56e9] Optimized numba balancing. Much faster
• [dfec16ba] New balancing method with numba
• [d5e2f112] Working version of dask delayed, split off entries module
• [7685efcd] Move build_path method outside of class
• [80f1fbe5] possible memory improvement
• [4297471c] simplifying list comprehension
• [5d852bc4] Change to filter().map() methodology
• [d01731f5] Added topdentry function to reduce memory usage of entry objects
• [3161bcab] Speed up ReactionError handling & reduce memory reqs for path arrays
• [4ec110ff] temporarily remove client
• [f2bbe742] Switch all parallelization to dask
• [2d2e1b90] more efficient memory handling in pathway enumeration
• [cfd4b89c] Revert to using multiprocessing, test of memory reqs
• [3a184ee7] working implementation with ray and numba
• [e0421965] Better parallelization of path screening/building, add G compound data
• [b6b9d77f] finished parallelizing graph network generation
• [9f9f1f50] parallelize reaction edge method, add itertools product support
• [b280820b] Add parallelization via pathos
• [e76dfe13] add entry_set filtering
• [d9a70427] add react method
• [eb5aa90b] trial feature: intermediate interface reactions
• [700cf2be] Remove trial O2 feature, try composition interpolation
• [7a10df9e] Trial feature: Add expanded support for gases in rxns
• [fb8cc563] Interdependent reaction checker works for >2 rxns now
• [091d6059] add interdependent rxn filter and chempot cost function filter
• [3f333d0c] add back in filtering
• [b4665080] change GibbsComputedStructureEntry to pymatgen
• [96850b01] Readthedocs updated yamls
• [7565b0b0] fix sphinx build
• [80e48071] fix README
• [89c76ca9] Updated docstrings and docs
• [c11fb0c1] small README typo
• [58575bce] Updated demo NB and small vertex bug
• [00397aa2] Major cleaning pt. 2 and adding more "set" methods
• [36949c05] Major cleaning
• [f88013be] Docstring updates
• [64a8abd4] Reaction pathways are now balanced using numba
• [f32f1992] Added support for massive phase diagram construction
• [8503d911] first steps for faster PD constructioon
• [9b13792a] Added structural similarity fingerprint method
• [c60ea6da] fixed repr
• [3f439323] check for k error
• [399a5359] rename file
• [a3576ae9] added extend_entries option
• [dbdbf1d5] Preparing for eventual release
• [1ab35776] Date update
• [d1315a1f] Many more graph-tool updates (+ exp data)
• [23c5062f] Converted entire library to graph-tool
• [016ff523] Small fixes
• [a582f94b] Add pathway analysis, redox pathway finding
• [45dfa627] Merge pull request #3 from mattmcdermott/dev
• [f511b339] Added NIST gas data, StructuralComplexity featurizer, etc.
• [0b35e59f] Added more helpful visualization network
• [8790300d] Successfully balancing combined pathways!
• [54e1fcb6] Merge pull request #2 from mattmcdermott/dev
• [789ca4d2] small bug fix
• [1e494c17] Gibbs Free Energy SISSO descriptor
• [ddbec40b] Merge pull request #1 from mattmcdermott/dev
• [142f19d5] Added docstrings
• [9da1a4b3] Added requirements.txt (and more refactoring)
• [89d89363] Small code refactoring part 2
• [a43014c8] Small formatting changes
• [b93c2bd1] Small refactoring
• [3b07bca2] Added support for processing "leftover" reactants
• [d907c78b] Added basic setup.py for local install
• [780909db] Update README.md
• [a2f5e5ee] Created Reaction Network class and helper classes
• [e55a689a] Initial commit

- Python
Published by github-actions[bot] over 4 years ago

reaction-network - Manual Release to establish baseline for auto-release

- Python
Published by shyamd over 4 years ago

reaction-network - Version 1.1 (paper)

This release accompanies the final revision(s) of the accompanying manuscript, which is under review at Nature Communications:

McDermott, M.J., Dwaraknath, S.S., and Persson, K.A. (2021). A graph-based network for predicting chemical reaction pathways in solid-state materials synthesis.

The repository includes the results from the manuscript and a demo notebook for recreating the results/analysis.

- Python
Published by mattmcdermott almost 5 years ago

reaction-network - Version 1.0 -- Preprint

This is the first release of the reaction-network code, as it was when originally submitted to Nature Comm. (before reviews).

- Python
Published by mattmcdermott over 5 years ago