materialsproject/emmet v0.2.3

on GitHub

Version 0.2.3

Commits

• [3634420] Merge pull request #201 from materialsproject/fix-oxidation
• [21df762] fix MPID
• [56dec98] fix tests
• [0f3307d] fix mypy directive outside of function call
• [744fde9] fix mypy issues
• [2ddf348] clean up
• [72daa73] add descriptions and fix types
• [b738071] Use PR labels to generate releases
• [0e57b9b] quote delayed type hint
• [4a1ee8a] fix indent error
• [0a09433] fix docs build
• [c236849] fix class var name clash
• [0071e38] include run_types yaml in distro
• [fa5f834] style clean up
• [1d187e6] Merge pull request #199 from materialsproject/reconcile
• [cb293cd] fix bad structures into oxidation doc test
• [fabbe34] catch warnings from compatability
• [2994cb4] fix counting of chemsys to process
• [03d3512] fix minor conversion bugs
• [8bc1999] add unrecognized task_type
• [ddf6fa1] mark when ismear differs
• [30ce56a] formatting bug
• [b119add] fix misc bugs
• [d7cab8a] update builder names
• [00e4cce] clean up
• [9e47131] compatability will select run_type
• [801f920] add oxidation state builder
• [0791b3b] reraise exception if failure
• [aad5eeb] clean up
• [e74f55f] remove vestige of sandbox
• [d0fc435] jsanitize in process to not bog down main process
• [08db446] add prechunk to thermo and materials
• [870dad4] Add oxidation states to thermo builder
• [8585077] remove deprecation from core since its in builders
• [0210fc2] speed up PD construction
• [97e7fee] Merge branch 'main' into reconcile
• [9082fc4] Merge pull request #198 from materialsproject/oxidation_states
• [4921d69] use defaultdict to average oxidation statees
• [68143e7] udpate name to Doc
• [42bbab2] new oxidation state doc
• [cfc7176] update test since default for use_statics is now True
• [a590c4e] add warnings for kspacing and ismear
• [f929bf9] clean up imports
• [fc8a94c] move use_statics to settings
• [6a5daf4] switch default deprecated tags to setting
• [527c46b] add manual deprecation into validation
• [7bb7485] remove pydash from emmet-core
• [ff57868] add bson to requirements
• [7e85770] remove overlapping requiirements
• [b7f1bf9] remove maggma from emmet-core
• [1fd37d4] make MPID behave more like a string
• [f4e8ec6] fix pydantic type conversion
• [26efbd7] make MPID hashable
• [4f5f85d] Merge pull request #197 from materialsproject/xas
• [03592ab] relax version requirements for now
• [8f3edad] Merge pull request #194 from materialsproject/dependabot/pip/emmet-builders/pydantic-1.8.2
• [9990a50] Merge pull request #193 from materialsproject/dependabot/pip/emmet-core/pydantic-1.8.2
• [f82e423] manually cache since decorated properties not allowed
• [c7e03b9] Bump pydantic from 1.8.1 to 1.8.2 in /emmet-builders
• [c4a0631] Bump pydantic from 1.8.1 to 1.8.2 in /emmet-core
• [1708944] Merge pull request #195 from materialsproject/dependabot/pip/emmet-core/maggma-0.27.0
• [1e301d3] use 3.7 compliant lru_cache
• [3fd4f6b] Merge pull request #196 from materialsproject/dependabot/pip/emmet-core/pymatgen-2022.0.8
• [dcab926] fix some mypy issues
• [df1c926] move XAS logic into doc
• [90d8288] port over XAS generation into document model
• [feea925] Add FEFF Task Doc
• [1263f52] Bump maggma from 0.26.0 to 0.27.0 in /emmet-core
• [51bb0ae] Bump pymatgen from 2022.0.5 to 2022.0.8 in /emmet-core
• [fa66efe] Add Electronic structure and search components (#189)
• [cb97771] switch vasp task_doc to new base
• [88fcc26] add new task doc base
• [2a6b9c3] Merge pull request #186 from materialsproject/dependabot/pip/emmet-core/typing-extensions-3.10.0.0
• [bcbd95f] Bump typing-extensions from 3.7.4.3 to 3.10.0.0 in /emmet-core
• [51704ed] Merge pull request #192 from materialsproject/dependabot/pip/emmet-core/pymongo-3.11.4
• [c51b3c7] action default setup for dependabot
• [08e234c] Bump pymongo from 3.11.3 to 3.11.4 in /emmet-core
• [b9e815a] Merge pull request #191 from materialsproject/dependabot/pip/emmet-core/pymatgen-2022.0.8
• [0a5137a] Bump pymatgen from 2022.0.5 to 2022.0.8 in /emmet-core
• [76bc0e5] test min in a list
• [2c0bcb3] fix dynamic versions
• [f81e6e2] cli: add initial fs_id check (commented out)
• [f5f5913] cli: raise on --task-ids missing
• [14d968b] cli: fix pymatgen root imports
• [56f38b3] Merge pull request #182 from materialsproject/dependabot/github_actions/actions/setup-python-v2.2.2
• [f6fec73] fix mypy
• [3a8ffcb] pycodestyle checks are in flake8 now
• [8b567b6] fix linting
• [76ffb9f] Update MPID
• [15779d3] Fix validation for LDAU
• [cecb131] Fix #183 in jsanitize
• [7f8225f] only consider valid tags
• [3049926] Bump actions/setup-python from v2.2.1 to v2.2.2
• [b67fb41] Merge pull request #180 from materialsproject/dependabot/github_actions/peaceiris/actions-gh-pages-v3.8.0
• [8339d66] Bump peaceiris/actions-gh-pages from v3 to v3.8.0
• [ebcc50b] Merge pull request #178 from jmmshn/elec_dev
• [f2cdc2d] update
• [96d8fbe] deal with nan's
• [03b82b3] update
• [922e93f] updated to be more useful for the API
• [f188b9c] num_steps should be int
• [fb4e0f4] bumped pymatgen
• [28c99cd] bumped pymatgen
• [58b003a] linting
• [1e6d146] typo
• [4ca23cc] allowed sorting by working ion and symmetry.
• [6c891c2] added progress
• [7070bb2] print warning for missing thermo docs
• [402009b] changed default in grouper from -1 back to None
• [2e40a59] changed default in grouper from -1 back to None
• [76ae6a9] fixed typos
• [b60548a] more useful fields
• [c07a7db] num steps int
• [60cfdcd] added elements
• [7dcc4a5] comma
• [d223208] indent
• [d4029e3] working electrode builder
• [b764db4] Merge branch 'elec_dev' of https://github.com/jmmshn/emmet into elec_dev
• [964b05a] fix
• [c0bc566] Merge branch 'elec_dev' of https://github.com/jmmshn/emmet into elec_dev
• [a1edee4] un-mappified builder
• [267e8cf] Merge branch 'elec_dev' of https://github.com/jmmshn/emmet into elec_dev
• [22bdcbf] electrode builder
• [77803b2] update
• [42f05a4] Merge branch 'elec_dev' of https://github.com/jmmshn/emmet into elec_dev
• [3a38e6f] added endpoint ids
• [0549d11] changed group id name
• [bed1f90] Merge branch 'elec_dev' of https://github.com/jmmshn/emmet into elec_dev
• [5f47940] added material ides to the document model
• [2139c36] Merge remote-tracking branch 'origin/main' into elec_dev
• [f2c8a87] fixed query for chemsys
• [30566da] fix linting issues
• [c45f448] use conventional standard structure from VASP
• [ae63060] fix missing test file
• [aaa3942] fix import
• [60cdfdd] Merge pull request #177 from jmmshn/thermo_fixes
• [026bc42] Update emmet-core/emmet/core/vasp/material.py
• [1747828] bug fixes
• [37016f7] Merge pull request #176 from materialsproject/provenance_builder
• [15284a9] fixed get electrode docs back
• [d7c8362] pymatgen 2022
• [35e1669] blk
• [ede2654] blk
• [28e0267] revert
• [30101e6] revert to mp_master
• [6503dcc] Merge branch 'elec_dev' into main
• [b5e2c79] changed pymatgen verion
• [1f74700] Merge branch 'elec_dev' of https://github.com/jmmshn/emmet into elec_dev
• [4f5a0f6] return nothing
• [4acf5cc] fixes
• [13d21b1] updated error message
• [64d3dc8] updated error message
• [aa6692c] updated error message
• [6cee3ff] changed task_id -> material_id
• [d4b4d4e] Merge branch 'main' into elec_dev
• [f72d37f] Merge remote-tracking branch 'jmmshn/main' into main
• [29bb3db] delete spaces
• [7beca8c] wip
• [c23b77b] combined all electrode builders into one file
• [0784751] revert mypy version
• [7dd33fd] working insertion electrode builder
• [9cdf1db] update mypy
• [0df27eb] fix linting
• [1fc3845] revert behavior and change in self-contained PR
• [e3209b9] Fix linting problems
• [5598061] Add provenance builder
• [2783258] Merge branch 'main' into provenance_builder
• [cfd90d7] hot patch for imports
• [618824a] Add provenance settings to build settings
• [f8efbac] clean up
• [637945c] test for provenance from SNLs
• [2be2b1a] Merge pull request #175 from jmmshn/main
• [cea55df] remove stale file
• [528c508] Add method to convert from SNLs
• [c6f415e] add to provenance document
• [bb29757] cli: adjust length of arguments list
• [508c2f7] Merge branch 'main' of https://github.com/jmmshn/emmet into main
• [5f937f3] relaxed enforced typing of input
• [3410530] relaxed enforced typing of input
• [a79b2a4] Add back query to task_validator
• [9a082bc] Merge pull request #174 from materialsproject/settings_update
• [f51232a] linting fixes
• [0bb5b8d] use autoload in builders
• [ee07aaf] hotpatch monty serialization
• [15e5c28] ensure settings can be serialized
• [d15c7c0] remove old metadata
• [23c1d41] add Kspacing to validation
• [ed03f2b] cli: allow restoral of entire blocks
• [1e46dca] cli: remove duplicate tags during parsing
• [3940d01] Bump pymongo from 3.11.2 to 3.11.3 in /emmet-core
• [8392b93] Bump pydantic from 1.7.3 to 1.8.1 in /emmet-core
• [a059d2b] update provenance doc structure
• [c7f8d1d] default bson_compatible types
• [147ab91] clean up
• [af1fb2f] use builder settings
• [7bb81a6] Add builder settings
• [a85acb0] Move more build settings into EmmetBuildSettings
• [07c42a5] use structure_calcs throughout
• [69be808] fix bad import
• [3ed324a] Merge pull request #170 from jmmshn/thermo_fix
• [1b8188f] cli: add snl_metas option for parsing
• [1688542] Merge branch 'master' into thermo_fix
• [c494ba7] cleanup
• [c48bdd7] Merge branch 'thermo_fix'
• [a32f191] serializable builder
• [598cf90] cli: add ntries option for number of jobs
• [18074c0] cli: add reorg flag
• [9c6fe228] cli: also allow res/aflow prefixes
• [89801d1] cli: protect task_type import error
• [b123e8a] fixed validation and setting
• [30142b5] Merge branch 'main' into thermo_fix
• [1128378] Merge branch 'master' into thermo_fix
• [336f269] validator checked
• [9156312] changed electrode back
• [ab3b374] Merge remote-tracking branch 'materialsproject/main' into main
• [28638e4] working Thermo builder, some e_above_hull still look wierd
• [07d34ef] working Thermo builder, some e_above_hull still look wierd
• [fb2f5b5] fixed thermo, changed thermo.entries to ComputedStructureEntry
• [16baf19] Merge remote-tracking branch 'materialsproject/main' into thermo_fix
• [e0f3408] removed sandboxes
• [0704e78] Merge remote-tracking branch 'origin/master'
• [769e51a] post_init
• [ef884a6] fixes
• [5a1a036] Merge pull request #169 from materialsproject/validation-update
• [d4ed351] bad variable name
• [010bfdb] update core settings docs
• [d19b301] update validation builder for manual deprecation
• [24127dc] add builder specific settings
• [99f560e] fix defaults in task doc
• [245bf47] update validator for SCF gradient
• [f6cce6c] use prop not default
• [3242d1c] Add Max SCF Validation
• [953849e] update workflow for branch name change
• [4c03ab7] Merge branch 'main'
• [6f3c994] due to removed stubs
• [ec8ac3d] Merge remote-tracking branch 'materialsproject/main'
• [ef104bd] Merge pull request #162 from jmmshn/master
• [f0689b5] Merge pull request #167 from materialsproject/MPID-type
• [ad657f1] fix MPID
• [6b4af84] test to check ordering of two MPIDs
• [9222ee5] fix mypy issues
• [70e5f1f] lint cleanup
• [7b5e417] update docs to use MPID
• [9b45b56] new MPID type
• [032f783] expected MPID behavior
• [fa2eca1] Bump pymatgen from 2021.2.14 to 2021.2.16 in /emmet-core
• [0ebec4c] Merge remote-tracking branch 'materialsproject/master'
• [c0bb963] Merge pull request #163 from jmmshn/elec_dev
• [d588bd9] Update emmet-builders/emmet/builders/materials/electrodes.py
• [b5c153e] Merge pull request #165 from materialsproject/remove-stubs
• [0f0cd36] install requirements including the right version of monty
• [8e5310f] fix mypy issue
• [c4d0c15] fix composition validators
• [7a4f692] fix imports
• [3121a88] remove stubs
• [d6d9f2c] remove stubs from core
• [a5e2626] remove stubs from docs
• [94dde9a] remove stubs
• [ff263f2] move composition stub to core
• [fecc5a9] move math
• [61db5cc] update monty
• [f08c578] run_stats core fix
• [c17091a] energy for the entries
• [c99993c] typo
• [bd71564] made structure grouper work with material_ids
• [baef399] added support for unrecognized task_type, and try except for materials doc creation with warning
• [2e64c09] Bump pymatgen from 2020.12.31 to 2021.2.14 in /emmet-core
• [7aa5e21] Merge pull request #148 from jmmshn/s_group
• [ddf380d] add query on the material db
• [572a4cb] jsantize
• [93be748] jsantize
• [2012d20] update
• [90d025a] using elecdoc
• [2870c8c] using elecdoc
• [cbb5ae2] using elecdoc
• [8a8a2ec] using elecdoc
• [8cb5dc7] working electrode builder
• [11de9c2] tested structure grouping builder
• [03c9d16] updated update
• [70b1fd4] added working sgroup builder
• [4b98a19] added electrode builder
• [b9c52fd] added electrode builder
• [1fdeaae] cleanup
• [0a30873] cleanup
• [45cef33] cleanup
• [102ca37] cleanup
• [84c33d6] reformat
• [1578ce6] working structure grouping document and tests
• [6207674] Merge remote-tracking branch 'materialsproject/master' into s_group
• [93bcbd9] Merge branch 'electrode_doc' into s_group
• [e30cbf2] Merge pull request #149 from jmmshn/electrode_doc
• [3841e6a] tests cleanup
• [c81d6a0] tests cleanup
• [5e6c9fb] tests cleanup
• [daceb18] tests cleanup
• [783f8f4] Elements
• [efb7b7e] Elements
• [601ff63] Merge remote-tracking branch 'materialsproject/master' into electrode_doc
• [bb644c8] updated prec
• [5c7ae13] Bump maggma from 0.25.0 to 0.26.0 in /emmet-core
• [fb66618] Bump pybtex from 0.23.0 to 0.24.0 in /emmet-core
• [d9141f2] Merge remote-tracking branch 'materialsproject/master' into s_group
• [bc6824b] same typo
• [1a385fc] Merge remote-tracking branch 'materialsproject/master' into electrode_doc
• [987507f] Bump pymatgen from 2020.12.18 to 2020.12.31 in /emmet-core
• [1eff36a] testing
• [0e8a199] testing
• [6fa1c99] Bump pymatgen from 2020.4.29 to 2020.12.18 in /emmet-core
• [40e56e1] Bump actions/setup-python from v2.1.4 to v2.2.1
• [2aa3b7a] copied testfiles over
• [825e3db] copied testfiles over
• [3a4f5fe] length
• [bb9c5c9] length
• [d5d294f] length
• [2a703e4] length
• [e0e6da8] length
• [c43ac89] testfile location
• [8e2180c] moved test
• [989c774] Merge remote-tracking branch 'materialsproject/master' into electrode_doc
• [5a62430] moved test
• [377bba5] mypy
• [f5c74d3] black
• [a5f259b] black
• [2484e5f] pmg version
• [c4918af] pmg version
• [d174c3c] intermediate model to store the result of structure matching
• [d88fa51] fix setuptools_scm
• [9857615] import from init
• [3d15edf] typo
• [0e38b84] added framework and lu
• [9e0da7a] working document model and tests
• [fce294d] working document model and tests
• [56593fe] added electrode document models
• [4c61421] use manual import sorting
• [2bee550] merge composition back into entries stub
• [2dc1e3e] fix validation with import order
• [94fa5ed] better deprecation enum
• [82a4437] fix mypy issues
• [a2c5dee] use ComputedStructureEntries
• [9e9eccd] make computed structure entry stub
• [0d0150e] bare branch
• [e04688a] cleanup
• [5061028] cleanup
• [11b4349] cleanup
• [642e0fe] cleanup
• [1ec5a4c] Merge branch 'master' into s_group
• [c6ea5b7] split electrode builder into two parts
• [62db461] mark thermo test as expected fail because of pymatgen bug
• [89f61e9] remove sandboxes
• [1ddeacb] fix PropertyDoc
• [93658da] fix default generator
• [053ce9b] remove VASP special tags since it's not being used.
• [24e333a] add XRDDoc
• [351f899] fix stub
• [1b08f92] test for XRD docs
• [dbcb4fa] run isort
• [eb1d5fd] add isort to precommit
• [0ef6814] use PyObject to load inputsets
• [9da7d9c] move material property out of material doc
• [a749186] make aspherical a common level tag
• [d69cb52] add stub for XRD pattern
• [6bd779b] Bump pymongo from 3.11.1 to 3.11.2 in /emmet-core
• [dd54664] Bump pydantic from 1.7.2 to 1.7.3 in /emmet-core
• [7e03b3d] Bump maggma from 0.24.2 to 0.25.0 in /emmet-core
• [8fe3af6] updated builder
• [8758cb9] removed sandbox from electrode builder
• [74d2650] removed sandbox from electrode builder
• [97a242f] removed sandbox from electrode builder
• [d1b4265] removed sandbox from electrode builder
• [083a604] Bump pymongo from 3.11.0 to 3.11.1 in /emmet-core
• [5ab5630] Bump pydantic from 1.6.1 to 1.7.2 in /emmet-core
• [285d1a0] Bump maggma from 0.23.3 to 0.24.2 in /emmet-core
• [470df6e] Bump actions/checkout from v2.3.3 to v2.3.4
• [90a31c6] Bump monty from 3.0.2 to 4.0.2 in /emmet-core
• [419d3a0] Merge pull request #141 from materialsproject/static-gen-run_types
• [1b673de] mypy can't get this right so let's surrpress this warning
• [e794814] use try/except rather than search for files
• [903d4df] fix breaks in tests from ValueEnum
• [f25c267] add back utility functions to generate enums
• [e3e3d73] initial commit of static types
• [7b1fde7] generate static enums
• [5ce2ab9] remove old dynamic enums
• [bd28b91] Merge pull request #132 from utf/sanitize-enum
• [564318d] Merge pull request #131 from utf/use-lattice-stub
• [e65daae] cli: improve doc size reduction @utf
• [7284859] added builder to popluate URL data for references
• [9e0a47f] Sanitize Enums
• [3d069e0] store volumetric data @jmmshn @rkingsbury
• [60d9c14] cli: fall back on full task_id distinct
• [c8f4aa4] Use lattice stub
• [27a51a7] cli: absolute path to GARDEN
• [65e54e3] fix create_model usage
• [6c0b262] test document serialization
• [4f93fea] use strings instead of enums in init
• [9f1950d] shouldn't need jsanitize in test anymore
• [7c60ccb] switch to ValueEnum in models
• [e7ba9e2] Add ValueEnum
• [2e1fdbb] add test for materials builder serialization and actually fix it
• [4b375c4] fix materials serialization?
• [cb26342] add update_targets
• [bc6b1fc] Revert "ensure enums saved as values"
• [8749fbf] Merge branch 'master' of github.com:materialsproject/emmet
• [8de0c00] ensure enums saved as values
• [ad3b8d6] remove dangling print
• [1c9dbd8] update materialsbuilder to work with new docs
• [bdb28a5] use structure metadata to get all metadata into task doc
• [61fd349] fix serialization for monty-esque classes such as Composition.
• [6df440f] test for materials builder
• [ae281ee] add parse_chgcar/aeccar flags @jmmshn
• [9e29c0f] Add maggma to core requirements
• [07cb8a4] fix linting issue
• [5ee35fd] test computed entries
• [af9e02c] more sandbox tests
• [0398185] import cleanup
• [9c0c9f8] dynamic sandboxing via tags
• [8702d8c] move vasp tasks and test for sandboxing
• [2e6e7f5] better description for sandbox tags
• [1847bb1] simple test for validation builder
• [4958255] run isort
• [a59b1df] move core task_validation to doc level
• [61d03f0] add hooks for global settings
• [b102c6d] move DocEnum
• [2039f0b] implement validation at doc level
• [663b407] remove new task doc
• [d3b0163] test validation
• [db92748] remove repeat settings
• [4fe29bc] update thermo tests
• [8cbe038] cli: missed a spec_or_dbfile var
• [08a4056] Bump typing-extensions from 3.7.4.2 to 3.7.4.3 in /emmet-core
• [25a909e] Bump pymongo from 3.10.1 to 3.11.0 in /emmet-core
• [8b66381] Bump pybtex from 0.21 to 0.23.0 in /emmet-core
• [c999fe2] Revert "update pymatge"
• [fd26c55] Merge branch 'master' of github.com:materialsproject/emmet
• [ccf2842] update pymatge
• [432ce09] Bump actions/setup-python from v1 to v2.1.4
• [166fbc8] Bump actions/checkout from v1 to v2.3.3
• [70c9348] fix polar mypy issues
• [2645959] move mypy back to testing job
• [d958040] update requirements
• [8173421] auto-merge dependabot updates
• [7c8ed79] fix some mypy issues
• [485b672] move mypy to linting
• [e5407ad] update dependabot
• [63dc354] new pre-commit
• [6924b04] Merge branch 'master' of github.com:materialsproject/emmet
• [3bb81df] more reasonable eneriges
• [9d45967] remove bad import
• [6ef4c8b] use value to make full calc_type
• [4945ac7] enable instantiating partial task doc
• [c7f9a2e] fix property origins
• [149fc44] move calc_type tests
• [5dde4e1] tests for materials doc
• [5f1a5dc] Merge pull request #119 from materialsproject/cli
• [97e5a8b] cli: init VaspCalcDb from db.json @jmmshn
• [6777700] switch to generator method
• [9417961] cli: fix task_types import (closes #121)
• [5766b1b] Merge remote-tracking branch 'origin/master' into cli
• [0a1aaef] Add settings for materials doc building
• [ba879e8] imports cleanup
• [aa9009b] incorporate materials doc building into main model
• [40ce4c4] fix test_dir scope
• [ece4173] move task back to old format and store new format
• [9896e2a] test chemsys_utils
• [6dc87a9] test_dir as fixture
• [4b60abe] remove large bad test files
• [db0dae8] fix mypy issues
• [a0edd5a] check for enums
• [4eca0c1] fix imports
• [e304af3] fix lint and testing issues
• [99459db] add computed entry and remove comment
• [83591d0] remove cyclic import
• [1941c94] fix validation issues
• [8690a9e] test thermo from_entries
• [b0e2f82] fix DocEnum
• [971a446] fix entries type hint
• [25444b7] add test for from_composition
• [aee0e5f] add from_composition
• [6d82383] fix tests
• [903077d] store material_id as entry_id and task_id in data
• [65776de] base process_items
• [1aac88d] properly deal with sandboxing
• [0425132] clean up add generator function
• [348b7ff] Add get_entries
• [d33d7ae] finish get_items
• [f484a2e] helper methods to find docs to update
• [5fc38c3] scaffold thermo
• [335f929] ensure core is possible in sandboxing
• [6f78510] convert tags to sandboxes in builder
• [bce263f] fix imports
• [1740049] include entries in doc
• [c8f7674] store entry in VASP materials builder
• [b3617b2] add entries in to VASP Materials Doc
• [01667df] update ComputedEntry
• [295ab37] conver to CalcType enum
• [8c8a95a] move qual score to settings
• [d9938ea] add chemsys permutations to utils
• [526c1e1] clean old materials in case sandboxes split
• [7fca789] update task_tagger to task_validator
• [d63b2cd] build material per sandbox set
• [215437e] clean up materials doc