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Merge pull request #332 from mat3ra/chore/latest-dev
update: sync versions with latest WA
2 parents ef30bc3 + 5358f7e commit 8e1a82d

13 files changed

Lines changed: 50 additions & 62 deletions

config.yml

Lines changed: 6 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -29,8 +29,7 @@ notebooks:
2929
- emfs:/drive/packages/pydantic-2.7.1-py3-none-any.whl
3030
- pymatgen-analysis-defects<=2024.4.23
3131
- mat3ra-periodic-table
32-
- mat3ra-esse==2026.4.29.post0
33-
- mat3ra-made>=2025.12.29.post0
32+
- mat3ra-made
3433
# packages below are used when made is installed from GH wheel (made should be installed from below)
3534
# - https://exabyte-io.github.io/made/mat3ra_made-0.1.dev1+ge64d360b8-py3-none-any.whl
3635
# - mat3ra-code
@@ -52,7 +51,7 @@ notebooks:
5251
- emfs:/drive/packages/watchdog-2.3.1-py3-none-any.whl
5352
- name: specific_examples
5453
packages_pyodide:
55-
- mat3ra-standata==2026.5.15.post0
54+
- mat3ra-standata
5655
# - mat3ra-notebooks-utils[utils_standata]
5756
- name: api
5857
packages_pyodide:
@@ -74,13 +73,13 @@ notebooks:
7473
- jinja2
7574
- emfs:/drive/packages/pydantic_core-2.18.2-py3-none-any.whl
7675
- emfs:/drive/packages/pydantic-2.7.1-py3-none-any.whl
77-
- mat3ra-standata==2026.5.15.post0
76+
- mat3ra-standata
7877
- mat3ra-ide
7978
- mat3ra-api-client
8079
- requests
81-
- mat3ra-ade==2026.4.29.post0
82-
- mat3ra-mode==2026.3.4.post0
83-
- mat3ra-wode==2026.5.23.post0
80+
- mat3ra-ade
81+
- mat3ra-mode
82+
- mat3ra-wode
8483
- mat3ra-prode
8584
- name: torch
8685
packages_pyodide:

other/materials_designer/workflows/band_gap.ipynb

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -393,24 +393,24 @@
393393
"\n",
394394
"if RELAXATION_KGRID is not None and ADD_RELAXATION:\n",
395395
" unit = workflow.subworkflows[0].get_unit_by_name(name_regex=\"relax\")\n",
396-
" unit.add_context(PointsGridDataProvider(dimensions=RELAXATION_KGRID, isEdited=True).yield_data())\n",
396+
" unit.add_context(PointsGridDataProvider(dimensions=RELAXATION_KGRID, isEdited=True).get_context_item_data())\n",
397397
" workflow.subworkflows[0].set_unit(unit)\n",
398398
"\n",
399399
"if SCF_KGRID is not None:\n",
400400
" for unit_name in [\"pw_scf\", \"pw_scf_hse\"]:\n",
401401
" unit = bg_subworkflow.get_unit_by_name(name=unit_name)\n",
402402
" if unit:\n",
403-
" unit.add_context(PointsGridDataProvider(dimensions=SCF_KGRID, isEdited=True).yield_data())\n",
403+
" unit.add_context(PointsGridDataProvider(dimensions=SCF_KGRID, isEdited=True).get_context_item_data())\n",
404404
" bg_subworkflow.set_unit(unit)\n",
405405
"\n",
406406
"if NSCF_KGRID is not None:\n",
407407
" unit = bg_subworkflow.get_unit_by_name(name=\"pw_nscf\")\n",
408408
" if unit:\n",
409-
" unit.add_context(PointsGridDataProvider(dimensions=NSCF_KGRID, isEdited=True).yield_data())\n",
409+
" unit.add_context(PointsGridDataProvider(dimensions=NSCF_KGRID, isEdited=True).get_context_item_data())\n",
410410
" bg_subworkflow.set_unit(unit)\n",
411411
"\n",
412412
"if ECUTWFC is not None:\n",
413-
" cutoffs_context = PlanewaveCutoffsContextProvider(wavefunction=ECUTWFC, density=ECUTRHO, isEdited=True).yield_data()\n",
413+
" cutoffs_context = PlanewaveCutoffsContextProvider(wavefunction=ECUTWFC, density=ECUTRHO, isEdited=True).get_context_item_data()\n",
414414
" for unit_name in [\"pw_relax\", \"pw_vc-relax\", \"pw_scf\", \"pw_scf_hse\", \"pw_nscf\"]:\n",
415415
" for swf in workflow.subworkflows:\n",
416416
" unit = swf.get_unit_by_name(name=unit_name)\n",

other/materials_designer/workflows/band_structure.ipynb

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -403,29 +403,29 @@
403403
"\n",
404404
"if RELAXATION_KGRID is not None and ADD_RELAXATION:\n",
405405
" unit = workflow.subworkflows[0].get_unit_by_name(name_regex=\"relax\")\n",
406-
" unit.add_context(PointsGridDataProvider(dimensions=RELAXATION_KGRID, isEdited=True).yield_data())\n",
406+
" unit.add_context(PointsGridDataProvider(dimensions=RELAXATION_KGRID, isEdited=True).get_context_item_data())\n",
407407
" workflow.subworkflows[0].set_unit(unit)\n",
408408
"\n",
409409
"if SCF_KGRID is not None:\n",
410410
" unit = bs_subworkflow.get_unit_by_name(name=\"pw_scf\")\n",
411411
" if unit:\n",
412-
" unit.add_context(PointsGridDataProvider(dimensions=SCF_KGRID, isEdited=True).yield_data())\n",
412+
" unit.add_context(PointsGridDataProvider(dimensions=SCF_KGRID, isEdited=True).get_context_item_data())\n",
413413
" bs_subworkflow.set_unit(unit)\n",
414414
"\n",
415415
"if KPATH is not None:\n",
416416
" unit = bs_subworkflow.get_unit_by_name(name=\"pw_bands\")\n",
417417
" if unit:\n",
418-
" unit.add_context(PointsPathDataProvider(path=KPATH, isEdited=True).yield_data())\n",
418+
" unit.add_context(PointsPathDataProvider(path=KPATH, isEdited=True).get_context_item_data())\n",
419419
" bs_subworkflow.set_unit(unit)\n",
420420
"\n",
421421
"if NSCF_KGRID is not None:\n",
422422
" unit = bs_subworkflow.get_unit_by_name(name=\"pw_nscf\")\n",
423423
" if unit:\n",
424-
" unit.add_context(PointsGridDataProvider(dimensions=NSCF_KGRID, isEdited=True).yield_data())\n",
424+
" unit.add_context(PointsGridDataProvider(dimensions=NSCF_KGRID, isEdited=True).get_context_item_data())\n",
425425
" bs_subworkflow.set_unit(unit)\n",
426426
"\n",
427427
"if ECUTWFC is not None:\n",
428-
" cutoffs_context = PlanewaveCutoffsContextProvider(wavefunction=ECUTWFC, density=ECUTRHO, isEdited=True).yield_data()\n",
428+
" cutoffs_context = PlanewaveCutoffsContextProvider(wavefunction=ECUTWFC, density=ECUTRHO, isEdited=True).get_context_item_data()\n",
429429
" for unit_name in [\"pw_relax\", \"pw_vc-relax\", \"pw_scf\", \"pw_bands\", \"pw_nscf\"]:\n",
430430
" for swf in workflow.subworkflows:\n",
431431
" unit = swf.get_unit_by_name(name=unit_name)\n",

other/materials_designer/workflows/band_structure_hse.ipynb

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -408,29 +408,29 @@
408408
"\n",
409409
"if RELAXATION_KGRID is not None and ADD_RELAXATION:\n",
410410
" unit = workflow.subworkflows[0].get_unit_by_name(name_regex=\"relax\")\n",
411-
" unit.add_context(PointsGridDataProvider(dimensions=RELAXATION_KGRID, isEdited=True).yield_data())\n",
411+
" unit.add_context(PointsGridDataProvider(dimensions=RELAXATION_KGRID, isEdited=True).get_context_item_data())\n",
412412
" workflow.subworkflows[0].set_unit(unit)\n",
413413
"\n",
414414
"if SCF_KGRID is not None:\n",
415415
" unit = preliminary_scf_subworkflow.get_unit_by_name(name=\"pw_scf\")\n",
416416
" if unit:\n",
417-
" unit.add_context(PointsGridDataProvider(dimensions=SCF_KGRID, isEdited=True).yield_data())\n",
417+
" unit.add_context(PointsGridDataProvider(dimensions=SCF_KGRID, isEdited=True).get_context_item_data())\n",
418418
" preliminary_scf_subworkflow.set_unit(unit)\n",
419419
"\n",
420420
" unit = main_hse_subworkflow.get_unit_by_name(name=\"pw_scf_bands_hse\")\n",
421421
" if unit:\n",
422-
" unit.add_context(PointsGridDataProvider(dimensions=SCF_KGRID, isEdited=True).yield_data())\n",
423-
" unit.add_context(PointsGridDataProvider(name=\"qgrid\", dimensions=SCF_KGRID, isEdited=True).yield_data())\n",
422+
" unit.add_context(PointsGridDataProvider(dimensions=SCF_KGRID, isEdited=True).get_context_item_data())\n",
423+
" unit.add_context(PointsGridDataProvider(name=\"qgrid\", dimensions=SCF_KGRID, isEdited=True).get_context_item_data())\n",
424424
" main_hse_subworkflow.set_unit(unit)\n",
425425
"\n",
426426
"if KPATH is not None:\n",
427427
" unit = main_hse_subworkflow.get_unit_by_name(name=\"pw_scf_bands_hse\")\n",
428428
" if unit:\n",
429-
" unit.add_context(PointsPathDataProvider(path=KPATH, isEdited=True).yield_data())\n",
429+
" unit.add_context(PointsPathDataProvider(path=KPATH, isEdited=True).get_context_item_data())\n",
430430
" main_hse_subworkflow.set_unit(unit)\n",
431431
"\n",
432432
"if ECUTWFC is not None:\n",
433-
" cutoffs_context = PlanewaveCutoffsContextProvider(wavefunction=ECUTWFC, density=ECUTRHO, isEdited=True).yield_data()\n",
433+
" cutoffs_context = PlanewaveCutoffsContextProvider(wavefunction=ECUTWFC, density=ECUTRHO, isEdited=True).get_context_item_data()\n",
434434
" for unit_name in [\"pw_relax\", \"pw_vc-relax\", \"pw_scf_bands_hse\"]:\n",
435435
" for swf in workflow.subworkflows:\n",
436436
" unit = swf.get_unit_by_name(name=unit_name)\n",

other/materials_designer/workflows/band_structure_magn.ipynb

Lines changed: 5 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -429,23 +429,23 @@
429429
"\n",
430430
"if RELAXATION_KGRID is not None and ADD_RELAXATION:\n",
431431
" unit = workflow.subworkflows[0].get_unit_by_name(name_regex=\"relax\")\n",
432-
" unit.add_context(PointsGridDataProvider(dimensions=RELAXATION_KGRID, isEdited=True).yield_data())\n",
432+
" unit.add_context(PointsGridDataProvider(dimensions=RELAXATION_KGRID, isEdited=True).get_context_item_data())\n",
433433
" workflow.subworkflows[0].set_unit(unit)\n",
434434
"\n",
435435
"if SCF_KGRID is not None:\n",
436436
" unit = bs_subworkflow.get_unit_by_name(name=\"pw_scf_magn\")\n",
437437
" if unit:\n",
438-
" unit.add_context(PointsGridDataProvider(dimensions=SCF_KGRID, isEdited=True).yield_data())\n",
438+
" unit.add_context(PointsGridDataProvider(dimensions=SCF_KGRID, isEdited=True).get_context_item_data())\n",
439439
" bs_subworkflow.set_unit(unit)\n",
440440
"\n",
441441
"if KPATH is not None:\n",
442442
" unit = bs_subworkflow.get_unit_by_name(name=\"pw_bands_magn\")\n",
443443
" if unit:\n",
444-
" unit.add_context(PointsPathDataProvider(path=KPATH, isEdited=True).yield_data())\n",
444+
" unit.add_context(PointsPathDataProvider(path=KPATH, isEdited=True).get_context_item_data())\n",
445445
" bs_subworkflow.set_unit(unit)\n",
446446
"\n",
447447
"if ECUTWFC is not None:\n",
448-
" cutoffs_context = PlanewaveCutoffsContextProvider(wavefunction=ECUTWFC, density=ECUTRHO, isEdited=True).yield_data()\n",
448+
" cutoffs_context = PlanewaveCutoffsContextProvider(wavefunction=ECUTWFC, density=ECUTRHO, isEdited=True).get_context_item_data()\n",
449449
" for unit_name in [\"pw_relax\", \"pw_vc-relax\", \"pw_scf_magn\", \"pw_bands_magn\"]:\n",
450450
" for swf in workflow.subworkflows:\n",
451451
" unit = swf.get_unit_by_name(name=unit_name)\n",
@@ -586,8 +586,7 @@
586586
" queue=QUEUE_NAME,\n",
587587
" ppn=PPN\n",
588588
")\n",
589-
"print(f\"Using cluster: {compute.cluster.hostname}, queue: {QUEUE_NAME}, ppn: {PPN}\")\n",
590-
"compute.cluster"
589+
"print(f\"Using cluster: {compute.cluster.hostname}, queue: {QUEUE_NAME}, ppn: {PPN}\")"
591590
]
592591
},
593592
{

other/materials_designer/workflows/equation_of_state.ipynb

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -83,7 +83,7 @@
8383
"WORKFLOW_SEARCH_TERM = \"total_energy.json\" # Search term for Workflows Standata\n",
8484
"APPLICATION_NAME = \"espresso\" # Can be switched to another supported application\n",
8585
"# Optional and mainly relevant for workflow/application combinations that expose a relaxation subworkflow.\n",
86-
"ADD_RELAXATION = None\n",
86+
"ADD_RELAXATION = False\n",
8787
"\n",
8888
"# Optional and mainly relevant for periodic plane-wave workflows such as Quantum ESPRESSO.\n",
8989
"RELAXATION_KGRID = None # e.g., [4, 4, 4]\n",
@@ -424,14 +424,14 @@
424424
"from mat3ra.wode.context.providers import PointsGridDataProvider\n",
425425
"\n",
426426
"if RELAXATION_KGRID is not None and ADD_RELAXATION:\n",
427-
" new_context_relax = PointsGridDataProvider(dimensions=RELAXATION_KGRID, isEdited=True).yield_data()\n",
427+
" new_context_relax = PointsGridDataProvider(dimensions=RELAXATION_KGRID, isEdited=True).get_context_item_data()\n",
428428
" relaxation_subworkflow = workflow.subworkflows[0]\n",
429429
" unit_to_modify_relax = relaxation_subworkflow.get_unit_by_name(name_regex=\"relax\")\n",
430430
" unit_to_modify_relax.add_context(new_context_relax)\n",
431431
" relaxation_subworkflow.set_unit(unit_to_modify_relax)\n",
432432
"\n",
433433
"if SCF_KGRID is not None:\n",
434-
" new_context_scf = PointsGridDataProvider(dimensions=SCF_KGRID, isEdited=True).yield_data()\n",
434+
" new_context_scf = PointsGridDataProvider(dimensions=SCF_KGRID, isEdited=True).get_context_item_data()\n",
435435
" total_energy_subworkflow = workflow.subworkflows[1 if ADD_RELAXATION else 0]\n",
436436
" unit_to_modify_scf = total_energy_subworkflow.get_unit_by_name(name=\"pw_scf\")\n",
437437
" unit_to_modify_scf.add_context(new_context_scf)\n",

other/materials_designer/workflows/relaxation.ipynb

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -377,12 +377,12 @@
377377
" for unit_name in relax_unit_names:\n",
378378
" unit = swf.get_unit_by_name(name=unit_name)\n",
379379
" if unit:\n",
380-
" unit.add_context(PointsGridDataProvider(dimensions=KGRID, isEdited=True).yield_data())\n",
380+
" unit.add_context(PointsGridDataProvider(dimensions=KGRID, isEdited=True).get_context_item_data())\n",
381381
" swf.set_unit(unit)\n",
382382
"\n",
383383
"if ECUTWFC is not None:\n",
384384
" cutoffs_context = PlanewaveCutoffsContextProvider(wavefunction=ECUTWFC, density=ECUTRHO,\n",
385-
" isEdited=True).yield_data()\n",
385+
" isEdited=True).get_context_item_data()\n",
386386
" for swf in workflow.subworkflows:\n",
387387
" for unit_name in relax_unit_names:\n",
388388
" unit = swf.get_unit_by_name(name=unit_name)\n",

other/materials_designer/workflows/surface_energy.ipynb

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -400,7 +400,7 @@
400400
"\n",
401401
"def apply_workflow_kgrids(workflow: Workflow, scf_kgrid=None) -> Workflow:\n",
402402
" if scf_kgrid is not None:\n",
403-
" new_context_scf = PointsGridDataProvider(dimensions=scf_kgrid, isEdited=True).yield_data()\n",
403+
" new_context_scf = PointsGridDataProvider(dimensions=scf_kgrid, isEdited=True).get_context_item_data()\n",
404404
" for subworkflow in workflow.subworkflows:\n",
405405
" unit_names = [unit.name for unit in subworkflow.units]\n",
406406
" if \"pw_scf\" not in unit_names:\n",

other/materials_designer/workflows/total_energy.ipynb

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -78,7 +78,7 @@
7878
"# 4. Workflow parameters\n",
7979
"WORKFLOW_SEARCH_TERM = \"total_energy.json\" # Search term for Workflows Standata\n",
8080
"APPLICATION_NAME = \"espresso\" # Specify application name (e.g., \"espresso\", \"vasp\", \"nwchem\")\n",
81-
"ADD_RELAXATION = None # Whether to add relaxation subworkflow as first unit\n",
81+
"ADD_RELAXATION = False # Whether to add relaxation subworkflow as first unit\n",
8282
"\n",
8383
"# set k-grid for relaxation and SCF (if not set, KPPRA is used by default)\n",
8484
"RELAXATION_KGRID = None # e.g., [4, 4, 4]\n",
@@ -378,14 +378,14 @@
378378
"\n",
379379
"if RELAXATION_KGRID is not None and ADD_RELAXATION:\n",
380380
" new_context_relax = PointsGridDataProvider(dimensions=RELAXATION_KGRID,\n",
381-
" isEdited=True).yield_data() if ADD_RELAXATION else None\n",
381+
" isEdited=True).get_context_item_data() if ADD_RELAXATION else None\n",
382382
" relaxation_subworkflow = workflow.subworkflows[0]\n",
383383
" unit_to_modify_relax = relaxation_subworkflow.get_unit_by_name(name_regex=\"relax\")\n",
384384
" unit_to_modify_relax.add_context(new_context_relax)\n",
385385
" relaxation_subworkflow.set_unit(unit_to_modify_relax)\n",
386386
"\n",
387387
"if SCF_KGRID is not None:\n",
388-
" new_context_scf = PointsGridDataProvider(dimensions=SCF_KGRID, isEdited=True).yield_data()\n",
388+
" new_context_scf = PointsGridDataProvider(dimensions=SCF_KGRID, isEdited=True).get_context_item_data()\n",
389389
" band_gap_subworkflow = workflow.subworkflows[1 if ADD_RELAXATION else 0]\n",
390390
" unit_to_modify_scf = band_gap_subworkflow.get_unit_by_name(name=\"pw_scf\")\n",
391391
" unit_to_modify_scf.add_context(new_context_scf)\n",

other/materials_designer/workflows/total_energy_post_processing.ipynb

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -464,12 +464,12 @@
464464
"\n",
465465
"if RELAXATION_KGRID is not None and ADD_RELAXATION:\n",
466466
" unit = workflow.subworkflows[0].get_unit_by_name(name_regex=\"relax\")\n",
467-
" unit.add_context(PointsGridDataProvider(dimensions=RELAXATION_KGRID, isEdited=True).yield_data())\n",
467+
" unit.add_context(PointsGridDataProvider(dimensions=RELAXATION_KGRID, isEdited=True).get_context_item_data())\n",
468468
" workflow.subworkflows[0].set_unit(unit)\n",
469469
"\n",
470470
"if SCF_KGRID is not None:\n",
471471
" unit = pp_subworkflow.get_unit_by_name(name=\"pw_scf\")\n",
472-
" unit.add_context(PointsGridDataProvider(dimensions=SCF_KGRID, isEdited=True).yield_data())\n",
472+
" unit.add_context(PointsGridDataProvider(dimensions=SCF_KGRID, isEdited=True).get_context_item_data())\n",
473473
" pp_subworkflow.set_unit(unit)\n",
474474
"\n",
475475
"visualize_workflow(workflow)"

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