From ac446e40850f54d290e75fe1ce7d39fa5b6982c8 Mon Sep 17 00:00:00 2001
From: Lukas Pielsticker <50139597+lukaspie@users.noreply.github.com>
Date: Tue, 8 Oct 2024 11:10:53 +0200
Subject: [PATCH] regenerate requirements and artifacts
---
gui/tests/artifacts.js | 198 ++++++++++++++++++++++++++-------------
gui/tests/env.js | 10 +-
requirements-dev.txt | 10 +-
requirements-plugins.txt | 2 +-
requirements.txt | 6 +-
5 files changed, 147 insertions(+), 79 deletions(-)
diff --git a/gui/tests/artifacts.js b/gui/tests/artifacts.js
index bda66c0aa5..43db8aed4f 100644
--- a/gui/tests/artifacts.js
+++ b/gui/tests/artifacts.js
@@ -63119,6 +63119,74 @@ window.nomadArtifacts = {
"m_def": "nomad.metainfo.metainfo.Section",
"m_parent_index": 2,
"m_parent_sub_section": "section_definitions",
+ "name": "ShearParameters",
+ "description": "Section containing the parameters pertaining to the shear flow for a molecular dynamics run.",
+ "base_sections": [
+ "/packages/25/section_definitions/0"
+ ],
+ "quantities": [
+ {
+ "m_def": "nomad.metainfo.metainfo.Quantity",
+ "m_parent_index": 0,
+ "m_parent_sub_section": "quantities",
+ "name": "shear_type",
+ "description": "The name of the method used to implement the effect of shear flow within the simulation.\n\nAllowed values are:\n\n| Shear Method | Description |\n\n| ---------------------- | ----------------------------------------- |\n\n| `\"\"` | No thermostat |\n\n| `\"lees_edwards\"` | A.W. Lees and S.F. Edwards,\n[J. Phys. C **5** (1972) 1921](https://doi.org/10.1088/0022-3719/5/15/006)|\n\n| `\"trozzi_ciccotti\"` | A.W. Lees and S.F. Edwards,\n[Phys. Rev. A **29** (1984) 916](https://doi.org/10.1103/PhysRevA.29.916)|\n\n| `\"ashurst_hoover\"` | W. T. Ashurst and W. G. Hoover,\n[Phys. Rev. A **11** (1975) 658](https://doi.org/10.1103/PhysRevA.11.658)|",
+ "type": {
+ "type_kind": "enum",
+ "type_data": [
+ "ashurst_hoover",
+ "lees_edwards",
+ "trozzi_ciccotti"
+ ]
+ },
+ "shape": []
+ },
+ {
+ "m_def": "nomad.metainfo.metainfo.Quantity",
+ "m_parent_index": 1,
+ "m_parent_sub_section": "quantities",
+ "name": "shear_rate",
+ "description": "The external stress tensor include normal (diagonal elements; which are zero in shear simulations)\nand shear stress' rates (off-diagonal elements).\nIts elements are: [[\u03c3_x, \u03c4_yx, \u03c4_zx], [\u03c4_xy, \u03c3_y, \u03c4_zy], [\u03c4_xz, \u03c4_yz, \u03c3_z]],\n where \u03c3 and \u03c4 are the normal and shear stress' rates.\nThe first and second letters in the index correspond to the normal vector to the shear plane and the direction of shearing, respectively.",
+ "type": {
+ "type_kind": "numpy",
+ "type_data": "float64"
+ },
+ "shape": [
+ 3,
+ 3
+ ],
+ "unit": "1 / picosecond"
+ },
+ {
+ "m_def": "nomad.metainfo.metainfo.Quantity",
+ "m_parent_index": 2,
+ "m_parent_sub_section": "quantities",
+ "name": "step_start",
+ "description": "Trajectory step where this shearing starts.",
+ "type": {
+ "type_kind": "python",
+ "type_data": "int"
+ },
+ "shape": []
+ },
+ {
+ "m_def": "nomad.metainfo.metainfo.Quantity",
+ "m_parent_index": 3,
+ "m_parent_sub_section": "quantities",
+ "name": "step_end",
+ "description": "Trajectory step number where this shearing ends.",
+ "type": {
+ "type_kind": "python",
+ "type_data": "int"
+ },
+ "shape": []
+ }
+ ]
+ },
+ {
+ "m_def": "nomad.metainfo.metainfo.Section",
+ "m_parent_index": 3,
+ "m_parent_sub_section": "section_definitions",
"name": "Lambdas",
"description": "Section for storing all lambda parameters for free energy perturbation",
"base_sections": [
@@ -63161,7 +63229,7 @@ window.nomadArtifacts = {
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 3,
+ "m_parent_index": 4,
"m_parent_sub_section": "section_definitions",
"name": "FreeEnergyCalculationParameters",
"description": "Section containing the parameters pertaining to a free energy calculation workflow that interpolates between two system states (defined via the interpolation parameter lambda).\nThe parameters are stored for each molecular dynamics run separately, to be referenced\nby the overarching workflow.",
@@ -63288,14 +63356,14 @@ window.nomadArtifacts = {
"m_parent_sub_section": "sub_sections",
"name": "lambdas",
"description": "Contains the lists of lambda values defined for the interpolation of the system.",
- "sub_section": "/packages/38/section_definitions/2",
+ "sub_section": "/packages/38/section_definitions/3",
"repeats": true
}
]
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 4,
+ "m_parent_index": 5,
"m_parent_sub_section": "section_definitions",
"name": "MolecularDynamicsMethod",
"base_sections": [
@@ -63445,15 +63513,23 @@ window.nomadArtifacts = {
"m_def": "nomad.metainfo.metainfo.SubSection",
"m_parent_index": 2,
"m_parent_sub_section": "sub_sections",
+ "name": "shear_parameters",
+ "sub_section": "/packages/38/section_definitions/2",
+ "repeats": true
+ },
+ {
+ "m_def": "nomad.metainfo.metainfo.SubSection",
+ "m_parent_index": 3,
+ "m_parent_sub_section": "sub_sections",
"name": "free_energy_calculation_parameters",
- "sub_section": "/packages/38/section_definitions/3",
+ "sub_section": "/packages/38/section_definitions/4",
"repeats": true
}
]
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 5,
+ "m_parent_index": 6,
"m_parent_sub_section": "section_definitions",
"name": "Property",
"description": "Generic parent section for all property types.",
@@ -63510,7 +63586,7 @@ window.nomadArtifacts = {
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 6,
+ "m_parent_index": 7,
"m_parent_sub_section": "section_definitions",
"name": "PropertyValues",
"description": "Generic parent section for information regarding the values of a property.",
@@ -63551,12 +63627,12 @@ window.nomadArtifacts = {
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 7,
+ "m_parent_index": 8,
"m_parent_sub_section": "section_definitions",
"name": "EnsemblePropertyValues",
"description": "Generic section containing information regarding the values of an ensemble property.",
"base_sections": [
- "/packages/38/section_definitions/6"
+ "/packages/38/section_definitions/7"
],
"quantities": [
{
@@ -63651,12 +63727,12 @@ window.nomadArtifacts = {
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 8,
+ "m_parent_index": 9,
"m_parent_sub_section": "section_definitions",
"name": "RadialDistributionFunctionValues",
"description": "Section containing information regarding the values of radial distribution functions (rdfs).",
"base_sections": [
- "/packages/38/section_definitions/7"
+ "/packages/38/section_definitions/8"
],
"quantities": [
{
@@ -63692,12 +63768,12 @@ window.nomadArtifacts = {
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 9,
+ "m_parent_index": 10,
"m_parent_sub_section": "section_definitions",
"name": "EnsembleProperty",
"description": "Generic section containing information about a calculation of any static observable from a trajectory (i.e., from an ensemble average).",
"base_sections": [
- "/packages/38/section_definitions/5"
+ "/packages/38/section_definitions/6"
],
"quantities": [
{
@@ -63745,19 +63821,19 @@ window.nomadArtifacts = {
"m_parent_index": 0,
"m_parent_sub_section": "sub_sections",
"name": "ensemble_property_values",
- "sub_section": "/packages/38/section_definitions/7",
+ "sub_section": "/packages/38/section_definitions/8",
"repeats": true
}
]
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 10,
+ "m_parent_index": 11,
"m_parent_sub_section": "section_definitions",
"name": "RadialDistributionFunction",
"description": "Section containing information about the calculation of radial distribution functions (rdfs).",
"base_sections": [
- "/packages/38/section_definitions/9"
+ "/packages/38/section_definitions/10"
],
"sub_sections": [
{
@@ -63765,19 +63841,19 @@ window.nomadArtifacts = {
"m_parent_index": 0,
"m_parent_sub_section": "sub_sections",
"name": "radial_distribution_function_values",
- "sub_section": "/packages/38/section_definitions/8",
+ "sub_section": "/packages/38/section_definitions/9",
"repeats": true
}
]
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 11,
+ "m_parent_index": 12,
"m_parent_sub_section": "section_definitions",
"name": "TrajectoryProperty",
"description": "Generic section containing information about a calculation of any observable defined and stored at each individual frame of a trajectory.",
"base_sections": [
- "/packages/38/section_definitions/5"
+ "/packages/38/section_definitions/6"
],
"quantities": [
{
@@ -63865,12 +63941,12 @@ window.nomadArtifacts = {
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 12,
+ "m_parent_index": 13,
"m_parent_sub_section": "section_definitions",
"name": "RadiusOfGyration",
"description": "Section containing information about the calculation of radius of gyration (Rg).",
"base_sections": [
- "/packages/38/section_definitions/11"
+ "/packages/38/section_definitions/12"
],
"quantities": [
{
@@ -63906,12 +63982,12 @@ window.nomadArtifacts = {
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 13,
+ "m_parent_index": 14,
"m_parent_sub_section": "section_definitions",
"name": "FreeEnergyCalculations",
"description": "Section containing information regarding the instantaneous (i.e., for a single configuration) values of free energies calculated via thermodynamic perturbation.\nThe values stored are actually infinitesimal changes in the free energy, determined as derivatives\nof the Hamiltonian with respect to the coupling parameter (lambda) defining each state for the perturbation.",
"base_sections": [
- "/packages/38/section_definitions/11"
+ "/packages/38/section_definitions/12"
],
"quantities": [
{
@@ -63922,7 +63998,7 @@ window.nomadArtifacts = {
"description": "Links the free energy results with the method parameters.",
"type": {
"type_kind": "reference",
- "type_data": "/packages/38/section_definitions/3"
+ "type_data": "/packages/38/section_definitions/4"
},
"shape": []
},
@@ -63954,29 +64030,18 @@ window.nomadArtifacts = {
"m_def": "nomad.metainfo.metainfo.Quantity",
"m_parent_index": 3,
"m_parent_sub_section": "quantities",
- "name": "value_unit",
- "description": "Unit of the property, using UnitRegistry() notation.\nIn this case, the unit corresponds to all `value` properties stored within this section.",
- "type": {
- "type_kind": "python",
- "type_data": "str"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 4,
- "m_parent_sub_section": "quantities",
"name": "value_total_energy_magnitude",
"description": "Value of the total energy for the present lambda state. The expected dimensions are [\"n_frames\"].\nThis quantity is a reference to the data (file+path), which is stored in an HDF5 file for efficiency.",
"type": {
"type_kind": "custom",
"type_data": "nomad.datamodel.hdf5.HDF5Dataset"
},
- "shape": []
+ "shape": [],
+ "unit": "joule"
},
{
"m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 5,
+ "m_parent_index": 4,
"m_parent_sub_section": "quantities",
"name": "value_PV_energy_magnitude",
"description": "Value of the pressure-volume energy (i.e., P*V) for the present lambda state. The expected dimensions are [\"n_frames\"].\nThis quantity is a reference to the data (file+path), which is stored in an HDF5 file for efficiency.",
@@ -63984,11 +64049,12 @@ window.nomadArtifacts = {
"type_kind": "custom",
"type_data": "nomad.datamodel.hdf5.HDF5Dataset"
},
- "shape": []
+ "shape": [],
+ "unit": "joule"
},
{
"m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 6,
+ "m_parent_index": 5,
"m_parent_sub_section": "quantities",
"name": "value_total_energy_differences_magnitude",
"description": "Values correspond to the difference in total energy between each specified lambda state\nand the reference state, which corresponds to the value of lambda of the current simulation.\nThe expected dimensions are [\"n_frames\", \"n_states\"].\nThis quantity is a reference to the data (file+path), which is stored in an HDF5 file for efficiency.",
@@ -63996,11 +64062,12 @@ window.nomadArtifacts = {
"type_kind": "custom",
"type_data": "nomad.datamodel.hdf5.HDF5Dataset"
},
- "shape": []
+ "shape": [],
+ "unit": "joule"
},
{
"m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 7,
+ "m_parent_index": 6,
"m_parent_sub_section": "quantities",
"name": "value_total_energy_derivative_magnitude",
"description": "Value of the derivative of the total energy with respect to lambda, evaluated for the current\nlambda state. The expected dimensions are [\"n_frames\"].\nThis quantity is a reference to the data (file+path), which is stored in an HDF5 file for efficiency.",
@@ -64008,18 +64075,19 @@ window.nomadArtifacts = {
"type_kind": "custom",
"type_data": "nomad.datamodel.hdf5.HDF5Dataset"
},
- "shape": []
+ "shape": [],
+ "unit": "joule"
}
]
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 14,
+ "m_parent_index": 15,
"m_parent_sub_section": "section_definitions",
"name": "DiffusionConstantValues",
"description": "Section containing information regarding the diffusion constants.",
"base_sections": [
- "/packages/38/section_definitions/6"
+ "/packages/38/section_definitions/7"
],
"quantities": [
{
@@ -64051,12 +64119,12 @@ window.nomadArtifacts = {
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 15,
+ "m_parent_index": 16,
"m_parent_sub_section": "section_definitions",
"name": "CorrelationFunctionValues",
"description": "Generic section containing information regarding the values of a correlation function.",
"base_sections": [
- "/packages/38/section_definitions/6"
+ "/packages/38/section_definitions/7"
],
"quantities": [
{
@@ -64116,12 +64184,12 @@ window.nomadArtifacts = {
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 16,
+ "m_parent_index": 17,
"m_parent_sub_section": "section_definitions",
"name": "MeanSquaredDisplacementValues",
"description": "Section containing information regarding the values of a mean squared displacements (msds).",
"base_sections": [
- "/packages/38/section_definitions/15"
+ "/packages/38/section_definitions/16"
],
"quantities": [
{
@@ -64175,19 +64243,19 @@ window.nomadArtifacts = {
"m_parent_index": 0,
"m_parent_sub_section": "sub_sections",
"name": "diffusion_constant",
- "sub_section": "/packages/38/section_definitions/14",
+ "sub_section": "/packages/38/section_definitions/15",
"repeats": false
}
]
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 17,
+ "m_parent_index": 18,
"m_parent_sub_section": "section_definitions",
"name": "CorrelationFunction",
"description": "Generic section containing information about a calculation of any time correlation function from a trajectory.",
"base_sections": [
- "/packages/38/section_definitions/5"
+ "/packages/38/section_definitions/6"
],
"quantities": [
{
@@ -64217,19 +64285,19 @@ window.nomadArtifacts = {
"m_parent_index": 0,
"m_parent_sub_section": "sub_sections",
"name": "correlation_function_values",
- "sub_section": "/packages/38/section_definitions/15",
+ "sub_section": "/packages/38/section_definitions/16",
"repeats": true
}
]
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 18,
+ "m_parent_index": 19,
"m_parent_sub_section": "section_definitions",
"name": "MeanSquaredDisplacement",
"description": "Section containing information about a calculation of any mean squared displacements (msds).",
"base_sections": [
- "/packages/38/section_definitions/17"
+ "/packages/38/section_definitions/18"
],
"sub_sections": [
{
@@ -64237,14 +64305,14 @@ window.nomadArtifacts = {
"m_parent_index": 0,
"m_parent_sub_section": "sub_sections",
"name": "mean_squared_displacement_values",
- "sub_section": "/packages/38/section_definitions/16",
+ "sub_section": "/packages/38/section_definitions/17",
"repeats": true
}
]
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 19,
+ "m_parent_index": 20,
"m_parent_sub_section": "section_definitions",
"name": "MolecularDynamicsResults",
"base_sections": [
@@ -64296,7 +64364,7 @@ window.nomadArtifacts = {
"m_parent_index": 0,
"m_parent_sub_section": "sub_sections",
"name": "radial_distribution_functions",
- "sub_section": "/packages/38/section_definitions/10",
+ "sub_section": "/packages/38/section_definitions/11",
"repeats": true
},
{
@@ -64304,7 +64372,7 @@ window.nomadArtifacts = {
"m_parent_index": 1,
"m_parent_sub_section": "sub_sections",
"name": "ensemble_properties",
- "sub_section": "/packages/38/section_definitions/9",
+ "sub_section": "/packages/38/section_definitions/10",
"repeats": true
},
{
@@ -64312,7 +64380,7 @@ window.nomadArtifacts = {
"m_parent_index": 2,
"m_parent_sub_section": "sub_sections",
"name": "correlation_functions",
- "sub_section": "/packages/38/section_definitions/17",
+ "sub_section": "/packages/38/section_definitions/18",
"repeats": true
},
{
@@ -64320,7 +64388,7 @@ window.nomadArtifacts = {
"m_parent_index": 3,
"m_parent_sub_section": "sub_sections",
"name": "radius_of_gyration",
- "sub_section": "/packages/38/section_definitions/12",
+ "sub_section": "/packages/38/section_definitions/13",
"repeats": true
},
{
@@ -64328,7 +64396,7 @@ window.nomadArtifacts = {
"m_parent_index": 4,
"m_parent_sub_section": "sub_sections",
"name": "mean_squared_displacements",
- "sub_section": "/packages/38/section_definitions/18",
+ "sub_section": "/packages/38/section_definitions/19",
"repeats": true
},
{
@@ -64336,14 +64404,14 @@ window.nomadArtifacts = {
"m_parent_index": 5,
"m_parent_sub_section": "sub_sections",
"name": "free_energy_calculations",
- "sub_section": "/packages/38/section_definitions/13",
+ "sub_section": "/packages/38/section_definitions/14",
"repeats": true
}
]
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 20,
+ "m_parent_index": 21,
"m_parent_sub_section": "section_definitions",
"name": "MolecularDynamics",
"base_sections": [
@@ -64355,7 +64423,7 @@ window.nomadArtifacts = {
"m_parent_index": 0,
"m_parent_sub_section": "sub_sections",
"name": "method",
- "sub_section": "/packages/38/section_definitions/4"
+ "sub_section": "/packages/38/section_definitions/5"
},
{
"m_def": "nomad.metainfo.metainfo.SubSection",
@@ -64365,7 +64433,7 @@ window.nomadArtifacts = {
"categories": [
"/packages/27/category_definitions/0"
],
- "sub_section": "/packages/38/section_definitions/19"
+ "sub_section": "/packages/38/section_definitions/20"
}
]
}
diff --git a/gui/tests/env.js b/gui/tests/env.js
index 68c0f11004..f5676aee83 100644
--- a/gui/tests/env.js
+++ b/gui/tests/env.js
@@ -4408,7 +4408,7 @@ window.nomadEnv = {
"homepage": "https://github.com/nomad-coe/atomistic-parsers",
"name": "atomisticparsers",
"repository": null,
- "version": "1.0.1"
+ "version": "1.0.2"
},
"bandstructurenormalizer": {
"description": "Band structure normalizer plugin for NOMAD.",
@@ -4504,7 +4504,7 @@ window.nomadEnv = {
"homepage": "https://github.com/nomad-coe/electronic-parsers",
"name": "electronicparsers",
"repository": null,
- "version": "1.0"
+ "version": "1.0.2"
},
"nomad_aitoolkit": {
"description": "Schema and app for AI Toolkit notebooks.",
@@ -4564,7 +4564,7 @@ window.nomadEnv = {
"homepage": "https://github.com/FAIRmat-NFDI/pynxtools",
"name": "pynxtools",
"repository": null,
- "version": "0.5.0"
+ "version": "0.7.0"
},
"runschema": {
"description": "Run schema plugin for NOMAD.",
@@ -4575,7 +4575,7 @@ window.nomadEnv = {
"homepage": "https://github.com/nomad-coe/nomad-schema-plugin-run.git",
"name": "runschema",
"repository": null,
- "version": "1.0.1"
+ "version": "1.0.2"
},
"simulationworkflownormalizer": {
"description": "Simulation workflow nomad plugin for NOMAD.",
@@ -4597,7 +4597,7 @@ window.nomadEnv = {
"homepage": "https://github.com/nomad-coe/nomad-schema-simulation-workflow-plugin",
"name": "simulationworkflowschema",
"repository": null,
- "version": "1.0.1"
+ "version": "1.0.4"
},
"soapnormalizer": {
"description": "SOAP nomad plugin for NOMAD.",
diff --git a/requirements-dev.txt b/requirements-dev.txt
index 458b0a0818..97012eda77 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -76,7 +76,7 @@ imagesize==1.4.1 # via sphinx, -r requirements.txt
importlib-metadata==7.1.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
inflection==0.5.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
iniconfig==2.0.0 # via pytest
-isodate==0.6.1 # via rdflib, -r requirements.txt
+isodate==0.7.0 # via rdflib, -r requirements.txt
isoduration==20.11.0 # via jsonschema, -r requirements.txt
itsdangerous==2.2.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
jinja2==3.1.4 # via jupyterhub, mkdocs, mkdocs-macros-plugin, mkdocs-material, sphinx, -r requirements.txt
@@ -97,7 +97,7 @@ lxml-html-clean==0.2.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
m2r==0.2.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
mako==1.3.5 # via alembic, -r requirements.txt
markdown==3.7 # via mkdocs, mkdocs-click, mkdocs-material, pymdown-extensions
-markupsafe==2.1.5 # via jinja2, mako, mkdocs, -r requirements.txt, nomad-lab (pyproject.toml)
+markupsafe==3.0.0 # via jinja2, mako, mkdocs, -r requirements.txt, nomad-lab (pyproject.toml)
matid==2.1.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
matplotlib==3.9.2 # via ase, pymatgen, -r requirements.txt
mda-xdrlib==0.2.0 # via pyedr, -r requirements.txt
@@ -195,7 +195,7 @@ runstats==2.0.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
scikit-learn==1.5.2 # via matid, -r requirements.txt, nomad-lab (pyproject.toml)
scipy==1.14.1 # via ase, pymatgen, scikit-learn, -r requirements.txt, nomad-lab (pyproject.toml)
sentinels==1.0.0 # via mongomock, -r requirements.txt
-six==1.16.0 # via asttokens, basicauth, elasticsearch-dsl, html5lib, isodate, pybtex, python-dateutil, rdflib, rfc3339-validator, validators, -r requirements.txt
+six==1.16.0 # via asttokens, basicauth, elasticsearch-dsl, html5lib, pybtex, python-dateutil, rdflib, rfc3339-validator, validators, -r requirements.txt
smmap==5.0.1 # via gitdb, -r requirements.txt
sniffio==1.3.1 # via anyio, httpx, -r requirements.txt
snowballstemmer==2.2.0 # via sphinx, -r requirements.txt
@@ -218,7 +218,7 @@ termcolor==2.5.0 # via mkdocs-macros-plugin
texttable==1.7.0 # via nomad-openbis, -r requirements.txt
threadpoolctl==3.5.0 # via scikit-learn, -r requirements.txt
tifffile==2024.9.20 # via h5grove, -r requirements.txt
-tomli==2.0.2 ; python_full_version == '3.11' # via coverage
+tomli==2.0.2 ; python_full_version <= '3.11' # via coverage
toposort==1.10 # via -r requirements.txt, nomad-lab (pyproject.toml)
tornado==6.4.1 # via jupyterhub, -r requirements.txt
tqdm==4.66.5 # via pyedr, pymatgen, -r requirements.txt
@@ -231,7 +231,7 @@ uncertainties==3.2.2 # via pymatgen, -r requirements.txt
unidecode==1.3.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
uri-template==1.3.0 # via jsonschema, -r requirements.txt
urllib3==1.26.20 # via docker, elasticsearch, nomad-openbis, requests, -r requirements.txt
-uv==0.4.18 # via nomad-lab (pyproject.toml)
+uv==0.4.19 # via nomad-lab (pyproject.toml)
uvicorn==0.31.0 # via h5grove, -r requirements.txt, nomad-lab (pyproject.toml)
uvloop==0.20.0 ; platform_python_implementation != 'PyPy' and sys_platform != 'cygwin' and sys_platform != 'win32' # via uvicorn, -r requirements.txt
validators==0.18.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
diff --git a/requirements-plugins.txt b/requirements-plugins.txt
index 471b47c31a..2ed89595b0 100644
--- a/requirements-plugins.txt
+++ b/requirements-plugins.txt
@@ -111,7 +111,7 @@ lmfit==1.3.2 # via pyxem
locket==1.0.0 # via partd
lxml==5.3.0 # via fabio, lxml-html-clean, nomad-lab, nomad-parser-plugins-atomistic, nomad-parser-plugins-electronic, nomad-parser-plugins-workflow, pynxtools, -c requirements-dev.txt
lxml-html-clean==0.2.2 # via nomad-lab, perovskite-solar-cell-database, -c requirements-dev.txt
-markupsafe==2.1.5 # via jinja2, nbconvert, werkzeug, -c requirements-dev.txt
+markupsafe==3.0.0 # via jinja2, nbconvert, werkzeug, -c requirements-dev.txt
matid==2.1.2 # via nomad-lab, nomad-simulations, -c requirements-dev.txt
matplotlib==3.9.2 # via ase, asr, diffsims, hyperspy, kikuchipy, matplotlib-scalebar, mdanalysis, orix, phonopy, pyfai, pymatgen, pyxem, radioactivedecay, -c requirements-dev.txt
matplotlib-inline==0.1.7 # via ipykernel, ipython
diff --git a/requirements.txt b/requirements.txt
index d3af134712..a4fd464be5 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -65,7 +65,7 @@ idna==3.10 # via anyio, email-validator, httpx, jsonschema, reque
imagesize==1.4.1 # via sphinx
importlib-metadata==7.1.0 # via nomad-lab (pyproject.toml)
inflection==0.5.1 # via nomad-lab (pyproject.toml)
-isodate==0.6.1 # via rdflib
+isodate==0.7.0 # via rdflib
isoduration==20.11.0 # via jsonschema
itsdangerous==2.2.0 # via nomad-lab (pyproject.toml)
jinja2==3.1.4 # via jupyterhub, sphinx
@@ -85,7 +85,7 @@ lxml==5.3.0 # via lxml-html-clean, nomad-lab (pyproject.toml)
lxml-html-clean==0.2.2 # via nomad-lab (pyproject.toml)
m2r==0.2.1 # via nomad-lab (pyproject.toml)
mako==1.3.5 # via alembic
-markupsafe==2.1.5 # via jinja2, mako
+markupsafe==3.0.0 # via jinja2, mako
matid==2.1.2 # via nomad-lab (pyproject.toml)
matplotlib==3.9.2 # via ase, pymatgen
mda-xdrlib==0.2.0 # via pyedr
@@ -154,7 +154,7 @@ runstats==2.0.0 # via nomad-lab (pyproject.toml)
scikit-learn==1.5.2 # via matid, nomad-lab (pyproject.toml)
scipy==1.14.1 # via ase, pymatgen, scikit-learn, nomad-lab (pyproject.toml)
sentinels==1.0.0 # via mongomock
-six==1.16.0 # via basicauth, elasticsearch-dsl, html5lib, isodate, pybtex, python-dateutil, rdflib, rfc3339-validator, validators
+six==1.16.0 # via basicauth, elasticsearch-dsl, html5lib, pybtex, python-dateutil, rdflib, rfc3339-validator, validators
smmap==5.0.1 # via gitdb
sniffio==1.3.1 # via anyio, httpx
snowballstemmer==2.2.0 # via sphinx
--
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