Code

Onto codevelopment#162

Code

Merged

liamhuber merged 109 commits intomainpyiron/ironflow:mainfrom onto_codevelopmentpyiron/ironflow:onto_codevelopmentCopy head branch name to clipboardMar 17, 2023

+2,128-77

Commits

Commits on Jan 24, 2023

• Introduce an ontological type to ports

  liamhuber

  committed
  fb7210e

  Copy full SHA for fb7210e

• Make node for selecting material properties from the ontology

  Show description for feb0a23
  liamhuber

  committed
  feb0a23

  Copy full SHA for feb0a23

• Add available onto types to the Murnaghan node

  liamhuber

  committed
  a6e5459

  Copy full SHA for a6e5459

• Fix string formatting

  Show description for 0f0acf8
  liamhuber

  committed
  0f0acf8

  Copy full SHA for 0f0acf8

Commits on Jan 25, 2023

• Remove print

  liamhuber

  committed
  90e4a52

  Copy full SHA for 90e4a52

• Handle (de)serialization of the otype

  Show description for e23e5cc
  liamhuber

  committed
  e23e5cc

  Copy full SHA for e23e5cc

• Add scaffolding for ontological validity checks

  Show description for 97822a7
  liamhuber

  committed
  97822a7

  Copy full SHA for 97822a7

• Fix typo

  liamhuber

  committed
  24d9fb5

  Copy full SHA for 24d9fb5

• 🐛 refactor to make sure the other type checks get used in all cases

  liamhuber

  committed
  45f8e6d

  Copy full SHA for 45f8e6d

• 🐛 add parent class to get the MRO working right

  liamhuber

  committed
  c4d70c9

  Copy full SHA for c4d70c9

• Only invalidate input based on otype connections

  Show description for 2349d78
  liamhuber

  committed
  2349d78

  Copy full SHA for 2349d78

• Leverage new ontology tool

  Show description for 95ffa56
  liamhuber

  committed
  95ffa56

  Copy full SHA for 95ffa56

• Draft method for walking the graph and scraping conditions

  Show description for 253ccf8
  liamhuber

  committed
  253ccf8

  Copy full SHA for 253ccf8

• Add available otypes to Lammps and BulkStructure nodes

  liamhuber

  committed
  d27e503

  Copy full SHA for d27e503

Commits on Jan 26, 2023

• No type hinting is better than wrong type hinting

  Show description for 049fd37
  liamhuber

  committed
  049fd37

  Copy full SHA for 049fd37

• Update import pattern

  liamhuber

  committed
  ae68e3b

  Copy full SHA for ae68e3b

• Don't iterate over connection, just pull out the input

  liamhuber

  committed
  44d587c

  Copy full SHA for 44d587c

• Use new condition getter that filters correctly with transitive options

  liamhuber

  committed
  670f9ae

  Copy full SHA for 670f9ae

• Add requirements

  Show description for 0ac1a45
  liamhuber

  committed
  0ac1a45

  Copy full SHA for 0ac1a45

• Update env file

  pyiron-runner

  committed
  1e5195c

  Copy full SHA for 1e5195c

• Give canvas widgets direct access to the model

  liamhuber

  committed
  d426d0f

  Copy full SHA for d426d0f

• Fix example

  Show description for 2a898cb
  liamhuber

  committed
  2a898cb

  Copy full SHA for 2a898cb

• Create space for the recommender

  liamhuber

  committed
  aa694ff

  Copy full SHA for aa694ff

• Give correct type hint

  liamhuber

  committed
  f5de98e

  Copy full SHA for f5de98e

• Make sure the GUI is available to all canvas widgets

  liamhuber

  committed
  165526a

  Copy full SHA for 165526a

• Use the term GUI throughout where the gui is

  Show description for 97cb29a
  liamhuber

  committed
  97cb29a

  Copy full SHA for 97cb29a

• Change calling path for ontological recommendations

  liamhuber

  committed
  cb445a8

  Copy full SHA for cb445a8

• 🐛 sync onto access with pyiron_ontology

  liamhuber

  committed
  192e08f

  Copy full SHA for 192e08f

• Create space for recommended nodes

  liamhuber

  committed
  0a590a9

  Copy full SHA for 0a590a9

• Recommend nodes for input

  liamhuber

  committed
  69ca3e9

  Copy full SHA for 69ca3e9

• Make sure the GUI for the list gets updated live

  liamhuber

  committed
  f9d1513

  Copy full SHA for f9d1513

• Actually recommend some nodes

  liamhuber

  committed
  0ee3e24

  Copy full SHA for 0ee3e24

Commits on Jan 27, 2023

• Refactor: rename and make public

  liamhuber

  committed
  85c7052

  Copy full SHA for 85c7052

• Add highlighting field for port widgets

  Show description for 08d06a1
  liamhuber

  committed
  08d06a1

  Copy full SHA for 08d06a1

• Have the canvas highlight ports ontologically

  Show description for 435a405
  liamhuber

  committed
  435a405

  Copy full SHA for 435a405

• Refactor: change signature

  liamhuber

  committed
  ecedc5c

  Copy full SHA for ecedc5c

• Refactor: rename

  liamhuber

  committed
  a4aaad0

  Copy full SHA for a4aaad0

• Format black

  pyiron-runner

  committed
  ff6fd79

  Copy full SHA for ff6fd79

Commits on Jan 30, 2023

• Rename node

  liamhuber

  committed
  d6f8a0c

  Copy full SHA for d6f8a0c

• Initialize to None

  Show description for 860d9da
  liamhuber

  committed
  860d9da

  Copy full SHA for 860d9da

• Start with space for recommendations

  liamhuber

  committed
  8cba54d

  Copy full SHA for 8cba54d

• Don't depopulate the recommendation list

  Show description for 6492934
  liamhuber

  committed
  6492934

  Copy full SHA for 6492934

• 🐛 only highlight stuff for ontological ports

  liamhuber

  committed
  3bb716b

  Copy full SHA for 3bb716b

• Add example notebook

  liamhuber

  committed
  346ddb8

  Copy full SHA for 346ddb8

• Make ontology dependence strict

  liamhuber

  committed
  1b5f465

  Copy full SHA for 1b5f465

• Add project as ontological input

  liamhuber

  committed
  df6c624

  Copy full SHA for df6c624

• Add slab structure

  liamhuber

  committed
  748a409

  Copy full SHA for 748a409

Commits on Feb 18, 2023

• Format black

  pyiron-runner

  committed
  f35a356

  Copy full SHA for f35a356

Commits on Mar 9, 2023

• Update onto access

  liamhuber

  committed
  771a69c

  Copy full SHA for 771a69c

• Refactor rename

  Show description for 1a21086
  liamhuber

  committed
  1a21086

  Copy full SHA for 1a21086

• Merge branch 'main' into onto_codevelopment

  liamhuber

  committed
  00266fc

  Copy full SHA for 00266fc

• Refactor type checking

  liamhuber

  committed
  281deed

  Copy full SHA for 281deed

Commits on Mar 10, 2023

• Match public loader name to ontology namespace

  liamhuber

  committed
  36e2506

  Copy full SHA for 36e2506

• Only follow downstream requirement paths where _both_ IO are typed

  liamhuber

  committed
  fd3e041

  Copy full SHA for fd3e041

• Update nodes onto new individuals-based setup

  liamhuber

  committed
  a124169

  Copy full SHA for a124169

• Pin the ontology version

  liamhuber

  committed
  6c74cff

  Copy full SHA for 6c74cff

• Update env file

  pyiron-runner

  committed
  f12cdf4

  Copy full SHA for f12cdf4

• Format black

  pyiron-runner

  committed
  bf073ec

  Copy full SHA for bf073ec

• Merge branch 'onto_codevelopment' into port_recommender

  Show description for 94a10ed
  liamhuber

  committed
  94a10ed

  Copy full SHA for 94a10ed

• Use correct method name

  liamhuber

  committed
  3321ee1

  Copy full SHA for 3321ee1

• Refactor: rename

  liamhuber

  committed
  377eea8

  Copy full SHA for 377eea8

• Merge branch 'onto_codevelopment' into node_recommender

  Show description for be46f4e
  liamhuber

  committed
  be46f4e

  Copy full SHA for be46f4e

• Use correct method

  liamhuber

  committed
  dbc0528

  Copy full SHA for dbc0528

• Refactor: rename

  liamhuber

  committed
  37200ee

  Copy full SHA for 37200ee

• Merge branch 'node_recommender' into port_recommender

  liamhuber

  committed
  9e13f4b

  Copy full SHA for 9e13f4b

• Expose otype acceptance check for input ports

  liamhuber

  committed
  bcbb00e

  Copy full SHA for bcbb00e

• Merge branch 'port_recommender' into example_bulk_modulus

  Show description for 830ed44
  liamhuber

  committed
  830ed44

  Copy full SHA for 830ed44

• Merge branch 'example_bulk_modulus' into extend_ontology

  liamhuber

  committed
  0b7003c

  Copy full SHA for 0b7003c

• Update to new ontology

  liamhuber

  committed
  c0c1927

  Copy full SHA for c0c1927

• Update notebook instructions

  liamhuber

  committed
  a708ea9

  Copy full SHA for a708ea9

• Merge pull request #166 from pyiron/extend_ontology

  Show description for 9351c36
  liamhuber

  authored
  9351c36

  Copy full SHA for 9351c36

• Update bulk modulus example

  liamhuber

  committed
  47bea65

  Copy full SHA for 47bea65

• Merge pull request #165 from pyiron/example_bulk_modulus

  Show description for 353c7c7
  liamhuber

  authored
  353c7c7

  Copy full SHA for 353c7c7

• Merge pull request #164 from pyiron/port_recommender

  Show description for e5a97dd
  liamhuber

  authored
  e5a97dd

  Copy full SHA for e5a97dd

• Merge pull request #163 from pyiron/node_recommender

  Show description for 35da876
  liamhuber

  authored
  35da876

  Copy full SHA for 35da876

• Make notebook CI-compliant

  liamhuber

  committed
  997601f

  Copy full SHA for 997601f

• Merge pull request #168 from pyiron/example_bulk_modulus

  Show description for 5ead446
  liamhuber

  authored
  5ead446

  Copy full SHA for 5ead446

• Don't offer mx2

  Show description for e91b1ef
  liamhuber

  committed
  e91b1ef

  Copy full SHA for e91b1ef

• Break apart the size arg

  Show description for 54d4ae1
  liamhuber

  committed
  54d4ae1

  Copy full SHA for 54d4ae1

• Increase default vacuum

  liamhuber

  committed
  7e6f71c

  Copy full SHA for 7e6f71c

• Return only the final frame

  liamhuber

  committed
  cd8947a

  Copy full SHA for cd8947a

• Add ontological typing to atomistic job taker nodes

  liamhuber

  committed
  fff7707

  Copy full SHA for fff7707

• Add surface energy node

  liamhuber

  committed
  40b1718

  Copy full SHA for 40b1718

Commits on Mar 13, 2023

• Refactor: extract methods

  liamhuber

  committed
  5207fed

  Copy full SHA for 5207fed

• Refactor: change signature and name

  Show description for 8bcd54e
  liamhuber

  committed
  8bcd54e

  Copy full SHA for 8bcd54e

• Recursively make sure all the other connections are ok

  Show description for 2190b1f
  liamhuber

  committed
  2190b1f

  Copy full SHA for 2190b1f

• Add otype validation for outputs

  liamhuber

  committed
  3fb4bf0

  Copy full SHA for 3fb4bf0

Commits on Mar 14, 2023

• Do port recommendations by comparing an actual graph to the tree

  liamhuber

  committed
  309ac48

  Copy full SHA for 309ac48

• Only calculate the tree once when selecting an input node

  liamhuber

  committed
  5074573

  Copy full SHA for 5074573

• Fix typo

  Show description for ff17973
  liamhuber

  committed
  ff17973

  Copy full SHA for ff17973

• Progressively filter inputs when looking for valid spots for an output

  Show description for aa403a3
  liamhuber

  committed
  aa403a3

  Copy full SHA for aa403a3

• Use the same tricks for the value check

  liamhuber

  committed
  dd20c14

  Copy full SHA for dd20c14

• Remove unused code

  liamhuber

  committed
  31b77f6

  Copy full SHA for 31b77f6

Commits on Mar 15, 2023

• Exploit early stopping

  Show description for cd2262c
  liamhuber

  committed
  cd2262c

  Copy full SHA for cd2262c

• Don't use ryvencore's NodeInputBP, use our override

  liamhuber

  committed
  442620a

  Copy full SHA for 442620a

Commits on Mar 16, 2023

• Merge pull request #172 from pyiron/port_recommendation_performance

  Show description for 9d199c9
  liamhuber

  authored
  9d199c9

  Copy full SHA for 9d199c9

• Merge pull request #170 from pyiron/fix_port_recommendation

  Show description for 75df989
  liamhuber

  authored
  75df989

  Copy full SHA for 75df989

• Tweak language in bulk modulus example

  liamhuber

  committed
  e68814f

  Copy full SHA for e68814f

• Add surface energy example

  liamhuber

  committed
  ce712b8

  Copy full SHA for ce712b8

• Merge pull request #169 from pyiron/surface_energy

  Show description for 13a02fb
  liamhuber

  authored
  13a02fb

  Copy full SHA for 13a02fb

Commits on Mar 17, 2023

• Update ironflow dependency

  liamhuber

  committed
  8622971

  Copy full SHA for 8622971

• Update env file

  pyiron-runner

  committed
  1a953d4

  Copy full SHA for 1a953d4

• Update stored graph for bulk modulus example

  liamhuber

  committed
  79c604a

  Copy full SHA for 79c604a

• Be upfront about performance issues

  Show description for a78702c
  liamhuber

  committed
  a78702c

  Copy full SHA for a78702c

• Add otyping to the readme

  liamhuber

  committed
  4631111

  Copy full SHA for 4631111

• Merge remote-tracking branch 'origin/onto_codevelopment' into onto_codevelopment

  liamhuber

  committed
  da30138

  Copy full SHA for da30138

• Try with local path to video

  liamhuber

  committed
  31f5b37

  Copy full SHA for 31f5b37

• Refactor: slide text

  liamhuber

  committed
  f7bf498

  Copy full SHA for f7bf498

• Format black

  pyiron-runner

  committed
  469646a

  Copy full SHA for 469646a