Feature/SOF-7766-3 Update: methods implementation for MIN NB to run

.babelrc

@@ -14,4 +14,3 @@
         "@babel/plugin-proposal-class-properties"
     ]
 }
-

.nycrc

@@ -5,4 +5,3 @@
         "src/**/*.jsx"
     ]
 }
-

.pre-commit-config.yaml

@@ -0,0 +1,26 @@
+repos:
+  - repo: https://github.com/Exabyte-io/pre-commit-hooks
+    rev: 2023.6.28
+    hooks:
+      - id: ruff
+        exclude: ^tests/fixtures*|^dist*
+      - id: black
+        exclude: ^tests/fixtures*|^dist*
+      - id: isort
+        exclude: ^tests/fixtures*|^dist*
+      - id: mypy
+        exclude: ^tests/fixtures*|^dist*
+      - id: check-yaml
+        exclude: ^tests/fixtures*|^dist*
+      - id: end-of-file-fixer
+        exclude: ^tests/fixtures*|^dist*
+      - id: trailing-whitespace
+        exclude: ^tests/fixtures*|^dist*
+  - repo: local
+    hooks:
+      - id: lint-staged
+        name: lint-staged
+        language: node
+        entry: npx lint-staged
+        verbose: true
+        pass_filenames: false

.prettierrc

@@ -4,4 +4,3 @@
     "trailingComma": "all",
     "tabWidth": 4
 }
-

00_IMPLEMENTATION_CHECKLIST_MIN.md

@@ -0,0 +1,65 @@
+# MVP Implementation Checklist - Minimal for Notebook
+
+## `src/py/mat3ra/wode/workflows/workflow.py`
+
+### Class: `Workflow`
+
+- `add_subworkflow(subworkflow, head=False, index=-1)`
+- `add_relaxation()`
+- `subworkflows` [property]
+- `create(config)` [classmethod] - Create workflow from standata config
+- `get_unit_by_name(name=None, name_regex=None)` - Search units across all subworkflows
+- `set_unit(unit=None, unit_flowchart_id=None, new_unit=None)` - Replace unit in workflow
+
+## `src/py/mat3ra/wode/subworkflows/subworkflow.py`
+
+### Class: `Subworkflow`
+
+- `units` [property]
+- `get_as_unit()`
+- `get_unit_by_name(name=None, name_regex=None)` - Search units within subworkflow
+- `model` [property with setter] - Ensure model can be set directly
+
+## `src/py/mat3ra/wode/units/unit.py`
+
+### Class: `Unit` (Base)
+
+- `flowchartId` [field]
+- `name` [field] - inherited
+- `context` [field: Dict] - Context data dict
+- `add_context(new_context)` - Update context data
+- `get_context(key, default)` - Get context value
+- `remove_context(key)` - Remove context value
+- `clear_context()` - Clear all context
+
+## `src/py/mat3ra/wode/units/io.py`
+
+### Class: `IOUnit`
+
+- `set_materials(materials)` - Set materials
+- `add_feature(feature)` - Add feature
+- `remove_feature(feature)` - Remove feature
+- `add_target(target)` - Add target
+- `remove_target(target)` - Remove target
+- `has_feature(feature)` - Check feature exists
+- `has_target(target)` - Check target exists
+
+## `src/py/mat3ra/wode/units/map.py`
+
+### Class: `MapUnit`
+
+- `set_workflow_id(id)` - Set workflow ID
+
+## `src/py/mat3ra/wode/units/processing.py`
+
+### Class: `ProcessingUnit`
+
+- `set_operation(op)` - Set operation
+- `set_operation_type(type)` - Set operation type
+- `set_input(input)` - Set input
+
+## `src/py/mat3ra/wode/units/factory.py`
+
+### Class: `UnitFactory`
+
+- `create(config)` [staticmethod] - Factory to instantiate correct unit type based on config["type"]

pyproject.toml

@@ -20,6 +20,11 @@ classifiers = [
 ]
 dependencies = [
     "numpy",
+    "mat3ra-utils",
+    "mat3ra-esse @ git+https://github.com/Exabyte-io/esse.git@5fd47adb825854ac1fc4b0133cc5d0210e18a5bb",
+    "mat3ra-mode",
+    "mat3ra-ade @ git+https://github.com/Exabyte-io/ade.git@7b5bdbae13a1ef87ee64dec7e98ac7fd5661959b",
+    "mat3ra-standata"
 ]
 
 [project.optional-dependencies]
@@ -62,13 +67,15 @@ extend-exclude = '''
     tests\/fixtures*,
     examples\/.*\/.*\.py
   | other\/.*\/.*\.(py|ipynb)
+  | dist\/.*
 )
 '''
 
 [tool.ruff]
 extend-exclude = [
     "src/js",
-    "tests/fixtures"
+    "tests/fixtures",
+    "dist"
 ]
 line-length = 120
 target-version = "py310"
@@ -80,6 +87,7 @@ target-version = "py310"
 profile = "black"
 multi_line_output = 3
 include_trailing_comma = true
+extend_skip_glob = ["dist/*"]
 
 [tool.pytest.ini_options]
 pythonpath = [
@@ -88,4 +96,3 @@ pythonpath = [
 testpaths = [
     "tests/py"
 ]
-

src/py/mat3ra/__init__.py

@@ -1,2 +1 @@
-"""mat3ra namespace package."""
-
+__path__ = __import__("pkgutil").extend_path(__path__, __name__)

src/py/mat3ra/wode/__init__.py

@@ -1,6 +1,36 @@
-import numpy as np
-
-
-def get_length(vec: np.ndarray) -> float:
-    return float(np.linalg.norm(vec))
+from .mixins import FlowchartUnitsManager
+from .subworkflows import Subworkflow
+from .units import (
+    AssertionUnit,
+    AssignmentUnit,
+    ConditionUnit,
+    ExecutionUnit,
+    IOUnit,
+    MapUnit,
+    ProcessingUnit,
+    ReduceUnit,
+    SubworkflowUnit,
+    Unit,
+    UnitFactory,
+)
+from .utils import find_by_name_or_regex, generate_uuid
+from .workflows import Workflow
 
+__all__ = [
+    "Unit",
+    "ExecutionUnit",
+    "AssignmentUnit",
+    "IOUnit",
+    "ConditionUnit",
+    "AssertionUnit",
+    "ProcessingUnit",
+    "MapUnit",
+    "ReduceUnit",
+    "SubworkflowUnit",
+    "Subworkflow",
+    "Workflow",
+    "UnitFactory",
+    "FlowchartUnitsManager",
+    "find_by_name_or_regex",
+    "generate_uuid",
+]

src/py/mat3ra/wode/context/providers/__init__.py

@@ -0,0 +1,3 @@
+from .points_grid_data_provider import PointsGridDataProvider
+
+__all__ = ["PointsGridDataProvider"]

src/py/mat3ra/wode/context/providers/by_application/espresso/qe_pwx_context_provider.py

@@ -0,0 +1,87 @@
+# TODO: We need periodic_table.js equivalent in Python
+# TODO: We need all mixins equivalent in Python
+
+from typing import Any, Dict, List
+
+from ..executable_context_provider import ExecutableContextProvider
+from mat3ra.esse.models.context_providers_directory.by_application.qe_pwx_context_provider import (
+    QEPwxContextProviderSchema,
+)
+
+
+class QEPWXContextProvider(QEPwxContextProviderSchema, ExecutableContextProvider):
+    """
+    Context provider for Quantum ESPRESSO pw.x settings.
+    """
+
+    # self.init_materials_context_mixin()
+    # self.init_method_data_context_mixin()
+    # self.init_workflow_context_mixin()
+    # self.init_job_context_mixin()
+    # self.init_material_context_mixin()
+    _material: Any = None
+    _materials: List[Any] = []
+
+    @staticmethod
+    def atom_symbols(material: Any) -> List[str]:
+        raise NotImplementedError
+
+    @staticmethod
+    def unique_elements_with_labels(material: Any) -> List[str]:
+        raise NotImplementedError
+
+    @staticmethod
+    def atomic_positions_with_constraints(material: Any) -> str:
+        raise NotImplementedError
+
+    @staticmethod
+    def atomic_positions(material: Any) -> str:
+        raise NotImplementedError
+
+    @staticmethod
+    def nat(material: Any) -> int:
+        raise NotImplementedError
+
+    @staticmethod
+    def ntyp(material: Any) -> int:
+        raise NotImplementedError
+
+    @staticmethod
+    def ntyp_with_labels(material: Any) -> int:
+        raise NotImplementedError
+
+    def build_qe_pwx_context(self, material: Any) -> Dict[str, Any]:
+        raise NotImplementedError
+
+    def get_data_per_material(self) -> Dict[str, Any]:
+        raise NotImplementedError
+
+    def get_data(self) -> Dict[str, Any]:
+        raise NotImplementedError
+
+    @property
+    def restart_mode(self) -> str:
+        raise NotImplementedError
+
+    def get_pseudo_by_symbol(self, symbol: str) -> Any:
+        raise NotImplementedError
+
+    def atomic_species(self, material: Any) -> str:
+        raise NotImplementedError
+
+    def atomic_species_with_labels(self, material: Any) -> str:
+        raise NotImplementedError
+
+    @staticmethod
+    def cell_parameters(material: Any) -> str:
+        raise NotImplementedError
+
+    @staticmethod
+    def symbol_to_atomic_specie(symbol: str, pseudo: Any) -> str:
+        raise NotImplementedError
+
+    @staticmethod
+    def element_and_pseudo_to_atomic_specie_with_labels(
+            symbol: str, pseudo: Any, label: str = ""
+    ) -> str:
+        raise NotImplementedError

src/py/mat3ra/wode/context/providers/by_application/executable_context_provider.py

@@ -0,0 +1,8 @@
+from mat3ra.ade.context.context_provider import ContextProvider
+
+
+class ExecutableContextProvider(ContextProvider):
+    """
+    Context provider for executable settings.
+    """
+    domain: str = "executable"

src/py/mat3ra/wode/context/providers/points_grid_data_provider.py

@@ -0,0 +1,55 @@
+from typing import Any, Dict, List
+
+from mat3ra.ade.context.context_provider import ContextProvider
+from mat3ra.esse.models.context_providers_directory.enum import ContextProviderNameEnum
+from mat3ra.esse.models.context_providers_directory.points_grid_data_provider import GridMetricType, \
+    PointsGridDataProviderSchema
+from pydantic import Field
+
+
+# TODO: GlobalSetting for default KPPRA value
+class PointsGridDataProvider(PointsGridDataProviderSchema, ContextProvider):
+    """
+    Context provider for k-point/q-point grid configuration.
+
+    Handles grid dimensions and shifts for reciprocal space sampling.
+    """
+    # TODO: Verify the correctness of the name
+    name: ContextProviderNameEnum = ContextProviderNameEnum.KGridFormDataManager
+    divisor: int = Field(default=1)
+    dimensions: List[int] = Field(default_factory=lambda: [1, 1, 1])
+    shifts: List[float] = Field(default_factory=lambda: [0.0, 0.0, 0.0])
+    grid_metric_type: str = Field(default=GridMetricType.KPPRA)
+
+    # TODO: handle presence of material
+    @property
+    def default_data(self) -> Dict[str, Any]:
+        return {
+            "dimensions": self.dimensions,
+            "shifts": self.shifts,
+            "gridMetricType": self.grid_metric_type,
+            "divisor": self.divisor,
+        }
+
+    # TODO: add a test to verify context and templates are the same as from JS implementation
+    def get_default_grid_metric_value(self, metric: str) -> float:
+        raise NotImplementedError
+
+    def calculate_dimensions(
+            self,
+            grid_metric_type: str,
+            grid_metric_value: float,
+            units: str = "angstrom"
+    ) -> List[int]:
+        raise NotImplementedError
+
+    def calculate_grid_metric(
+            self,
+            grid_metric_type: str,
+            dimensions: List[int],
+            units: str = "angstrom"
+    ) -> float:
+        raise NotImplementedError
+
+    def transform_data(self, data: Dict[str, Any]) -> Dict[str, Any]:
+        raise NotImplementedError

src/py/mat3ra/wode/mixins/__init__.py

@@ -0,0 +1,4 @@
+from .flowchart_units_manager import FlowchartUnitsManager
+
+__all__ = ["FlowchartUnitsManager"]
+