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v2.0.2
752b218
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Learn about vigilant mode.

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
  • [64a8abd] Reaction pathways are now balanced using numba
  • [f32f199] Added support for massive phase diagram construction
  • [8503d91] first steps for faster PD constructioon
  • [9b13792] Added structural similarity fingerprint method
  • [c60ea6d] fixed repr
  • [3f43932] check for k error
  • [399a535] rename file
  • [a3576ae] added extend_entries option
  • [dbdbf1d] Preparing for eventual release
  • [1ab3577] Date update
  • [d1315a1] Many more graph-tool updates (+ exp data)
  • [23c5062] Converted entire library to graph-tool
  • [016ff52] Small fixes
  • [a582f94] Add pathway analysis, redox pathway finding
  • [45dfa62] Merge pull request #3 from mattmcdermott/dev
  • [f511b33] Added NIST gas data, StructuralComplexity featurizer, etc.
  • [0b35e59] Added more helpful visualization network
  • [8790300] Successfully balancing combined pathways!
  • [54e1fcb] Merge pull request #2 from mattmcdermott/dev
  • [789ca4d] small bug fix
  • [1e494c1] Gibbs Free Energy SISSO descriptor
  • [ddbec40] Merge pull request #1 from mattmcdermott/dev
  • [142f19d] Added docstrings
  • [9da1a4b] Added requirements.txt (and more refactoring)
  • [89d8936] Small code refactoring part 2
  • [a43014c] Small formatting changes
  • [b93c2bd] Small refactoring
  • [3b07bca] Added support for processing "leftover" reactants
  • [d907c78] Added basic setup.py for local install
  • [780909d] Update README.md
  • [a2f5e5e] Created Reaction Network class and helper classes
  • [e55a689] Initial commit
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