v5.0.0

Version 5.0.0

Commits

• [b0b6536] Merge pull request #106 from GENESIS-EFRC/dev
• [f11c27f] upgrade black
• [5dd1c99] upgrade pytest
• [d6b3fcb] linting
• [3544f31] add missing req, update README
• [fd6273e] fix calculate_e_above_hulls bug
• [3f241ff] fix rounding error in cpd
• [3090c98] Add update by key to GridFS
• [32a9a5b] add support for recipes GridFS
• [7a8d593] fix broken task ID problem
• [1652a73] change task_id field to int
• [f4713e3] fix broken counter
• [d563cf4] clean up builder
• [841fbb5] rewrite retrosynthesis builder with new models
• [2638c5b] Update pydantic models, and incorporate into workflows
• [6daf4db] refactoring of drones/models
• [ab0565e] basic support for gridfs (still WIP), added pydantic models
• [5c6cb64] Fix GridFS overwrite
• [8456728] Add missing builder import
• [1fdcfea] add support for GridFS
• [0277719] ignore other NBs
• [7e9db3e] Add simple retrosynthesis builder
• [fc1e445] improve function names
• [97f0550] add more general reaction plotting / DF methods
• [5d63784] change where ray gets initialized
• [8e4d6c3] add missing imports
• [3420caa] add ray to CompetitivenessScoreCalculator
• [3488a41] add print statment for nodes
• [753abdf] remove print
• [f174500] update ray with better initialization and parallelization
• [ccc6ff8] better support for ray clusters
• [0e77dd4] fix tqdm and bug
• [9cd1ad3] update init
• [35f5ecb] ray debugging
• [ca73706] move ray import
• [c365705] add tqdm
• [32259ff] add better threshold for multiprocessing
• [9e61cb1] implement ray for multiprocessing
• [bf6a458] Merge pull request #102 from GENESIS-EFRC/dev
• [8891aa0] fix broken metastable_domains
• [552cae2] Updated CHANGELOG.md

v4.3.0

Version 4.3.0

Commits

• [a321e2a] Merge pull request #100 from GENESIS-EFRC/dev
• [307c7e6] remove error statement
• [12a650c] update release-on-push
• [b1fe2a2] Bump pymdown-extensions from 9.1 to 9.2
• [c136496] Bump pymatgen from 2022.1.24 to 2022.2.10
• [9b852c6] Bump maggma from 0.39.1 to 0.41.0
• [c8560e7] Bump mkdocs-material from 8.1.9 to 8.2.3
• [4edea2c] Bump fireworks from 1.9.8 to 2.0.2
• [5507e0f] Bump numpy from 1.22.1 to 1.22.2
• [d4871d3] Bump mkdocstrings from 0.17.0 to 0.18.0
• [6860000] Merge pull request #90 from GENESIS-EFRC/dev
• [21e7180] fix linting
• [705dae0] fix bug with interpolated entry checking
• [8e08434] linting
• [d2dd348] add missing include_freed_data
• [2875876] Update entry builder task
• [d972ac0] Update NIST JANAF data after fixing bug
• [e3e904a] update broken NB
• [6a508cc] remove elements from metastable_domains
• [a93a66f] linting, add calculate_e_above_hulls flag
• [1983bee] Add method for acquiring e_above_hull from an entry
• [4beef4c] change default e_tol
• [0d277ec] get rid of add_entry
• [6f39cce] Updated CHANGELOG.md

v4.2.0

Version 4.2.0

Commits

• [0a34b8e] Merge pull request #88 from GENESIS-EFRC/dev
• [cf343f8] run black
• [19c0de0] linting
• [a61866b] improve competitiveness score calculator by better filtering
• [e719fdc] add support for chemical potential distance to metastable phases
• [db6db8f] fix metastable domain bug (interior point was wrong)
• [8988340] adding entries to CPDs does not work
• [871900b] Add support for adding entry to existing cpd. Some bugs for domain assgn
• [b1b448b] fix bug in eq for experimental entries
• [a03af78] Add FREEDReferenceEntry, compress existing data,
• [e6f0ff9] add metastable_domains to cpd, add energy_adjustments to expt entry
• [dee3145] parse formula to prevent bug
• [cc471b6] use cached properties for better min entry finding
• [d7e91e7] remove print statemnet
• [8c68259] Add caching for get_min_entry_by_formula, fix speed of minimize enumer
• [996fb8d] Updated CHANGELOG.md

v4.1.0

Version 4.1.0

Commits

• [53bf1a5] Merge pull request #85 from GENESIS-EFRC/dev
• [a6e0d3f] speed up tests considerably
• [7e6aeac] get rid of NO2 entry, test open_elem checking
• [a88c0bf] Fix checking for precursors/targets to speed-up calculations
• [2fc2fb1] Bump mkdocs-material from 8.1.7 to 8.1.9
• [3248c42] Bump pymatgen from 2022.1.20 to 2022.1.24
• [91aabd2] Bump mkdocs-jupyter from 0.19.0 to 0.20.0
• [507e7fb] Bump maggma from 0.38.1 to 0.39.1
• [1787423] unpack metadata in stored results
• [47a6cfe] add cost_function to metadata, fix enumerators metadata bug
• [9a8c3b4] add quiet mode for enumerators
• [8e13987] update bug in EnumeratorFW
• [c579beb] Create CITATION.bib
• [9b11294] Updated CHANGELOG.md

v4.0.2

Version 4.0.2

Commits

v4.0.1

Version 4.0.1

Commits

• [b30eefc] Merge pull request #75 from GENESIS-EFRC/matt-tests
• [f9fcb86] fix github workflows
• [3460d1c] Delete test.md
• [8178bf4] Bump fireworks from 1.9.7 to 1.9.8
• [08794da] Bump numpy from 1.22.0 to 1.22.1
• [d0abccb] Bump pre-commit from 2.15.0 to 2.17.0
• [eef57bb] Bump mkdocs-material from 8.1.3 to 8.1.7
• [78f501e] Bump pymatgen from 2022.01.09 to 2022.1.20

v4.0.0

Version 4.0.0

Commits

• [dd7b22d] Merge pull request #59 from GENESIS-EFRC/matt-tests
• [83c6275] Updating docstrings part 2
• [c047ea2] Updating docstrings part 1
• [dc0eada] fix github action
• [4771827] fix github actions conda problem
• [ea435f7] fix broken tests
• [6dfcd72] add black/pylint to testing requirements
• [c451c8b] pylint
• [69aaddb] flake8 exclude F401
• [592a6f3] linting
• [02ae1a2] fix several mypy issues
• [32d8004] fix broken link for notebooks (had to duplicate)
• [706b31d] update docs and docstrings
• [8c3607c] update docs organization
• [79ed4d3] Fix same numpy bug for lint/docs
• [979a7e9] Ok this might be the one
• [8121ef4] Merge branch 'main' into matt-tests
• [585aecd] bump other reqs, try again for numpy
• [1e0978f] I can't figure out this numpy problem
• [16fa96a] try fixing dependencies again
• [4ec9b26] change GitHub action
• [7bd487b] add numpy to reqs
• [1cfdea3] bump dependencies
• [7a8a99a] docstrings + linting
• [00a092f] move get_entry_task, clean up files
• [984a083] Make enumerator chemsys filtering more robust
• [8c6196d] Fix NIST-JANAF bug with Na2CO3
• [5cd020d] Add fireworks support for calculating c scores
• [096091e] linting and fix reaction competitiveness bug
• [35fdb3e] Add to_dataframe() method for ReactionSet
• [fa8690b] ReactionSet can now regenerate OpenComputedReaction types
• [297c3ae] Add CompetitivenessScoreCalculator
• [a32d29f] fix experimental ref entry bug in network
• [fa05ddc] Fix bug in creating ExperimentalReferenceEntry where comp was wrong
• [a7d4e1c] GibbsEntrySet now only uses minimum experimental entry data
• [39a2e7b] Clean up files
• [05b4a62] fix data bug in ExperimentalReferenceEntry
• [5c37e53] fix broken test
• [2e25462] Test of commit with docstring update
• [f6592c5] fix imports
• [00e62af] clean up files
• [4abf16e] add to git ignore
• [d3b0f26] fix RunNetwork firetask
• [f4900a8] improve RunNetwork firetask
• [2356427] Finish PathwaySet implementation
• [09eda16] Add CalcDb, first part of PathwaySet for saving paths
• [c292704] clean up network firetasks
• [61f3cda] Add supporting firetasks for network generation
• [c54736c] Update network notebook
• [1a615a9] enumerators NB, fix entry_set serialization bug, README update
• [ec71022] Merge remote-tracking branch 'upstream/matt-tests' into matt-tests
• [367510a] NB update part 2
• [603dd44] 1st part of update to example NBs
• [54e7758] fix broken test for entry
• [1181ff8] add barin data warning
• [4b350ab] Generate new NIST-JANAF data
• [858a6ae] fix line length
• [a205041] fix targets bug
• [590ba20] fix bug in enumerator firework
• [92cd517] begin adding firework for network creation
• [6719424] clean up NBs slightly
• [3cd3e5c] major bug fix in pathway solver due to build_indices; added NBs
• [771411b] fix broken test due to added barin data
• [0c44c88] add barin table data, graph saving/loading
• [2bb1cbb] remove entry_set dependency in pymatgen
• [1f10163] add docstrings for linting
• [58fb0e3] Fix bug where open entries were being considered in exclusion
• [f955547] fix enumerator bug, entry_set bug
• [2d3decb] change to exclusive_targets, adjust pathway plotting
• [7e667b6] add pathway plotting, fix testing bug
• [d91b087] add plotting for pathways, fix solver bug
• [ea0cd0e] speed up chempot distance calculation
• [1482ac1] Create CONTRIBUTING.md
• [81754af] Create CODE_OF_CONDUCT.md
• [5a134c8] Bump mkdocstrings from 0.15.2 to 0.16.1
• [691b0f8] Bump pre-commit from 2.14.1 to 2.15.0
• [ff4f98b] Bump mkdocs-minify-plugin from 0.4.0 to 0.4.1
• [19760ed] Updated CHANGELOG.md

v3.0.0

Version 3.0.0

Commits

• [f718861] Merge pull request #45 from GENESIS-EFRC/matt-tests
• [c721e5d] run black
• [e61bf98] fix linting
• [96e5d2b] clean up gh actions
• [a6e0b18] Add more docstrings
• [b2c1b84] fix broken test
• [f913781] finish minimize enumerator tests
• [48d77f3] run black and make BasicOpenEnumerator faster
• [9612ed3] finish major part of enumerator refactor
• [81af4ea] further refactoring of enumerators
• [1e43776] fix linting errors, work on refactor of enumerators
• [f938564] try this order with default
• [f42bd96] fix hyphen
• [4fbd9d1] combine run
• [c7c0c38] try with conda run
• [8070dc5] fix typo
• [bef16ff] and one more one more time
• [d86fb71] one more time with activation
• [3250f2d] try it again with miniconda
• [11b03b4] add test import
• [36eff4b] add print statement
• [176676c] try again
• [e82cc53] trying to fix bug again
• [dbd4773] fix bug in docs
• [eadc9e4] bump python version
• [6a5c0fa] change installation order
• [f4b5495] add graph-tool to docs workflow
• [d80e201] update pymatgen req
• [1ad5c86] fix mkdocs
• [56502bb] fix req
• [df2215a] Merge remote-tracking branch 'upstream/matt-tests' into matt-tests
• [d0d8bf9] Merge branch 'main' into matt-tests
• [6ed37c8] bump reqs
• [1b3f9ce] Add docs files as well
• [725b353] make tests simpler
• [dc33ad8] add basic open enumerator fixtures
• [2e3598a] add enumerator tests, run black
• [f0f9d87] fix circular import
• [95a2dea] fill in missing tests, update README
• [9902291] add balance arrays test
• [bfebbc1] Change pathway solver reaction initialization
• [002874c] clean up enumeration code
• [70f2ea5] clean up attr use
• [bb97950] bug fix for OpenComputedReaction
• [7cfea16] add computed rxn fixture
• [e84ec08] add more tests for entries and reactions
• [2a66a76] add tests for BasicReaction
• [fe374ad] fix core docstrings
• [52a565e] fix calculator kwargs
• [72d60c6] Add test files, clean up test directory, clean class docstrings
• [b84f16b] Bump numba from 0.53.1 to 0.54.0
• [11b1022] Bump pytest from 6.2.1 to 6.2.5
• [f7f754d] Bump graphistry from 0.19.2 to 0.20.1
• [be883b2] Bump pydocstyle from 5.1.1 to 6.1.1
• [bc23886] Bump pytest-cov from 2.11.0 to 2.12.1
• [68f8806] Bump pymatgen from 2022.0.11 to 2022.0.12
• [13695dc] Bump pre-commit from 2.9.3 to 2.14.1
• [22ec0b8] Updated CHANGELOG.md

v2.0.3

Version 2.0.3

Commits

• [e0e6c6e] Merge pull request #34 from GENESIS-EFRC/shyamd-patch-1
• [d23e4ec] Update README.md
• [481af85] Use PAT instead of Github token

v2.0.2

Version 2.0.2

Commits

• [752b218] Merge pull request #33 from GENESIS-EFRC/rxn-bugfix
• [0ede444] fix linting issue
• [f4bce46] bug fix for interdependent rxns
• [eed6c71] Bump mypy from 0.812 to 0.910
• [802baa8] Bump pymatgen from 2021.2.8 to 2022.0.11
• [315fcc4] Merge pull request #32 from GENESIS-EFRC/fix-docs
• [38014af] fix graphistry requirements
• [e4c5569] Remove old references for now
• [e0352d5] Add workflows to test and deploy docs
• [cde0e4f] ignore mypy for now since its a rats nest
• [6082811] ignore another rule incompatible with black
• [29dd635] update python versions
• [6af500a] reference main not master branch
• [58ad278] remove stale files
• [2db22b2] Use regular github token
• [16af355] Merge pull request #23 from GENESIS-EFRC/refactor-networks
• [2faafe0] Merge branch 'main' into refactor-networks
• [3920156] update pre-commit black/isort versions
• [2b7821c] address flake8 issues
• [23aa24c] changes from pre-commit
• [f2174d8] change pre-commit
• [0e5aabf] Add workflow files
• [5a66f96] fix jupyter pin
• [1163893] Add requirements for docs
• [5ce7dd0] Add dependabot config
• [3caaa02] hardpin in requirements.txt
• [59ecc22] Add testing requirements
• [856ad92] clean up some old files, fix README
• [b45534f] fix some imports/reqs
• [0742be6] fix reqs, small bug fix in solver
• [5939f17] update reqs
• [b8e9b7e] add some docstrings, minor fixes
• [b50039c] Add graph-tool cairo visualization
• [9becdc5] cleaning up formatting
• [cc57e66] fixing import order
• [4328171] re-format with black
• [7a4097f] enumerator bug fix for targets
• [99b8578] fix circular imports
• [1fc3091] bug fix for interdependent rxn finder
• [09f1f6e] add implementation of PathwaySolver
• [f3acb18] add PathwaySolver for balancing pathways
• [cf45ce0] reaction reverse() bug fixes
• [c3e5dbf] add more network methods
• [f95f82a] Add basic ReactionNetwork
• [b13dc16] filter warnings
• [dc360b5] remove print statement
• [704c9df] bug fix for deprecated
• [a1d2bca] Adapt for current MP db
• [78fc94d] update building entries from materials DB
• [c39b48a] fix pymatgen imports
• [8831a47] Revert "Add Synthesis and Interface class for MC approach"
• [d810400] Add Synthesis and Interface class for MC approach
• [014edaa] add option of "precursors" to enumerators
• [3de95b3] add conftest better printout
• [75404e8] Move all tests & switch over to pytest
• [f35b4f6] change to tqdm auto and bug fixes
• [398aa5f] add some of the GibbsComputedEntry tests
• [26661a7] implement Shyam's comments (reqs and set_temperature)
• [2cdce29] docstrings for entry and basic enumerators
• [8724082] add docstrings pt2
• [d04a5d9] clean up docstrings more
• [efb520f] Move enumerator staticmethods to utils, clean docstrings, formatting
• [86c731e] add some simple tests, fix reaction copy methods, add reverse method
• [f550568] update reqs and license
• [debc92b] simplify files for release
• [d9d416c] small NB tweak
• [937bf63] update demo with NB with cleaner, simpler example
• [35a153a] update demo NB
• [e4180df] fix environment.yml again!
• [e7a2da9] test environment.yml again
• [cfb12e4] update environment.yml
• [0c08405] change readthedocs environment.yml
• [fff85c9] update doc requirements
• [2cee9db] update mkdocs / readthedocs
• [b4cfc9f] update mkdocs
• [c2af34a] updating docstrings
• [8ab2a84] fix README
• [5e3337e] simplify/clean files for packaging manuscript version
• [6f6512a] update reqs
• [4e8755e] simplify and clean up release
• [848de39] Update README with better instructions
• [3f29c7c] Update README.md with logo
• [d81fa5f] fix bug in creating ReactionSet
• [a5e6ff2] Bug fix in hash of BasicReaction
• [923f1c1] Bug fix in eq of BasicReaction
• [2dbc7c3] add uncertainty to NIST entry, fix bug in RunEnumerators
• [379883b] bug fix for BasicOpenEnumerator
• [b2d2786] add list initialization (bug fix)
• [0ebb61f] add missing Composition import
• [fe5d8e8] one more bug fix in NIST energy method
• [cffc536] change int() to float() in NIST energy method
• [5f120d2] update reqs
• [3ffc0e8] add error catching for unmatched targets
• [9042066] add bug fix for env_chk
• [db06e3b] reaction_set: less memory required for storage
• [45d594c] first attempt to create ReactionSet, better storage
• [cc8289d] fix bug in NIST as_dict(), custom entry DB now working
• [2e3b3a0] fix EnumeratorFW bugs and make Gibbs entry more transparent
• [dbe9c45] Add init files, fix some entry initialization
• [b9d2226] Add some convenient stabilization methods
• [2f5ef41] add input building firetasks and supporting code
• [6e925f8] add first draft of simple firetasks/fireworks
• [552374b] reformatting of entry repr
• [db4d3ff] Add GibbsEntrySet
• [ef4bd1b] simplification of calculators, static-methoding GibbsComputedEntry
• [b50d163] Adding calculator application methodology
• [31b55df] implement calculators into basic enumerators
• [f0d0164] add calculator module
• [be89724] change domains to cached_property
• [fb0a4f1] Add chempot map
• [ae00edc] add chemical potential diagram class
• [0b9e593] small refactoring of reactions/enumerators
• [b5e3bf0] add option for target
• [b726676] run black, fix reaction normalize methods
• [4de40c2] finish simplification of Reaction
• [7510177] simply Reaction to just be two input vectors
• [bd506ac] fix balancing bug pt. 2
• [f4b84f8] normalize rxns and fix repr bug
• [8c468e8] Introduce OpenComputedReaction for calculating changes in grand pot.
• [c0c44cf] finish MinimizeGrandPotentialEnumerator
• [c1b145c] Add is_identity property for filtering reactions
• [2470a6f] add in functions to help with MinimizeGibbsEnumerator
• [5850434] Add first parts of MinimizeGibbsEnumerator
• [b658fb3] write BasicOpenEnumerator, add eq/hash for BasicReaction
• [2043850] write BasicEnumerator, add minimization enumerators
• [2100013] add limited_powerset, add helper methods for enumerators
• [3a3dd49] add utils
• [df03cd7] add enumerators directory/file
• [07161b5] lint cleanup
• [b11714d] initial pathways
• [7be23b8] refactor core into module
• [9592373] remove old entries and reaction
• [2dacde9] bug fix
• [6d3c210] NetworkEntry
• [e651173] more properties for interfaces
• [1023a12] add backwards compatibility with pymatgen to demo NB
• [aaed82b] Merge remote-tracking branch 'upstream/revision'
• [98b5b6b] update demo NB
• [6a323b4] Switch back to pymatgen GibbsComputedStructureEntry
• [59d35b5] update reqs, configure GibbsComputedStructureEntry
• [36639a4] Merge pull request #5 from GENESIS-EFRC/revision
• [9b4acfe] update reqs
• [6f10547] Add json results, update demo NB
• [4df74f7] update reqs, first revision of demo NB
• [2b42a7d] Update README instructions
• [af4276a] supress import order lint error
• [8b3ff45] Add Computed Reaction
• [8a30fbc] Add notes for Matt
• [957855c] update basic reaction for new abstractions
• [306a305] abstract out more properties
• [640c37b] fix init
• [6dccb36] Base reaction implementation
• [01a9135] split entries in two two implemenations
• [71d1b2a] move old core and define new core interfaces
• [420f0d0] fix data loading
• [c30414c] Remove chempot restriction, fix bug with ._structure attribute & data
• [aad1e96] Merge pull request #4 from GENESIS-EFRC/cleanup
• [9e98f73] fix linting errors
• [d1d0b52] automated workflows
• [7eaa926] Add Mkdocs
• [aac33b9] basic lint infrastructure
• [365cd49] switch docs to Markdown
• [34df429] update setup infrastructure
• [39a533e] update license for LBNL
• [e353094] add type hint support
• [a41da83] make data into module
• [c1c569a] make source tree
• [e27238e] total cost now includes more accurate percentage method
• [04d3c42] fix major typo in screening for dummy nodes
• [483aca2] add li2o/na2o data
• [c408502] Change graph creation to dask bag via iterable approach
• [cfffd39] clean up code formatting via black
• [bf27a8a] Add save method (rudimentary) -- also clean up imports
• [1cc583f] batch size tweaks
• [e05b56e] Optimized numba balancing. Much faster
• [dfec16b] New balancing method with numba
• [d5e2f11] Working version of dask delayed, split off entries module
• [7685efc] Move build_path method outside of class
• [80f1fbe] possible memory improvement
• [4297471] simplifying list comprehension
• [5d852bc] Change to filter().map() methodology
• [d01731f] Added to_pd_entry function to reduce memory usage of entry objects
• [3161bca] Speed up ReactionError handling & reduce memory reqs for path arrays
• [4ec110f] temporarily remove client
• [f2bbe74] Switch all parallelization to dask
• [2d2e1b9] more efficient memory handling in pathway enumeration
• [cfd4b89] Revert to using multiprocessing, test of memory reqs
• [3a184ee] working implementation with ray and numba
• [e042196] Better parallelization of path screening/building, add G compound data
• [b6b9d77] finished parallelizing graph network generation
• [9f9f1f5] parallelize reaction edge method, add itertools product support
• [b280820] Add parallelization via pathos
• [e76dfe1] add entry_set filtering
• [d9a7042] add react method
• [eb5aa90] trial feature: intermediate interface reactions
• [700cf2b] Remove trial O2 feature, try composition interpolation
• [7a10df9] Trial feature: Add expanded support for gases in rxns
• [fb8cc56] Interdependent reaction checker works for >2 rxns now
• [091d605] add interdependent rxn filter and chempot cost function filter
• [3f333d0] add back in filtering
• [b466508] change GibbsComputedStructureEntry to pymatgen
• [96850b0] Readthedocs updated yamls
• [7565b0b] fix sphinx build
• [80e4807] fix README
• [89c76ca] Updated docstrings and docs
• [c11fb0c] small README typo
• [58575bc] Updated demo NB and small vertex bug
• [00397aa] Major cleaning pt. 2 and adding more "set" methods
• [36949c0] Major cleaning
• [f88013b] Docstring updates
• [...