Merge pull request #70 from LemurPwned/hotfix/submodules

Hotfix/submodules

.dockerignore

@@ -0,0 +1,19 @@
+*.jpg
+*.png
+deprecated/
+build/
+scratch/
+*.egg-info/
+__pycache__/
+*.pyc
+*.pyo
+*.pyd
+*.so
+.eggs/
+.ipynb_checkpoints/
+.vscode/
+.idea/
+assets/
+articles/
+examples/
+docs/

MANIFEST.in

@@ -0,0 +1,2 @@
+include cmtj/__init__.pyi
+include cmtj/py.typed

README.md

@@ -62,7 +62,7 @@ python3 -m pip install cmtj
 3. Straight from source:
 
 ```bash
-python3 -m pip install https://github.com/LemurPwned/cmtj.git
+python3 -m pip install git+https://github.com/LemurPwned/cmtj.git
 ```
 
 4. Clone the repository:
@@ -84,7 +84,7 @@ The package requires (if `utils` subpackage is used):
 
 ## Documentation and examples
 
-Documentation: [https://lemurpwned.github.io/cmtj](https://lemurpwned.github.io/cmtj)
+Documentation: [https://lemurpwned.github.io/cmtj](https://lemurpwned.github.io/cmtj).
 There are many examples available, check out the [examples section in the docs](https://lemurpwned.github.io/cmtj/experimental-methods/introduction/)
 
 ## Extensions

cmtj/__init__.pyi

@@ -216,20 +216,17 @@ class Junction:
         :param SMR_Y: Spin magnetoresistance transverse
         :param AHE: Anomalous Hall effect resistance offset (transverse only)
         """
+        ...
 
     @overload
     def __init__(*args, **kwargs) -> Any: ...
     def clearLog(self) -> Dict[str, Any]:
-        """
-        Reset current simulation state`
-        """
+        """Reset current simulation state."""
         ...
 
     def getLayerMagnetisation(self, layer_id: str) -> CVector: ...
     def getLog(self) -> Dict[str, List[float]]:
-        """
-        Retrieve the simulation log [data].
-        """
+        """Retrieve the simulation log [data]."""
         ...
 
     def getMagnetoresistance(self) -> List[float]: ...
@@ -329,7 +326,7 @@ class Layer:
         demagTensor: List[CVector],
         temperature: float = ...,
         damping: float = ...,
-    ) -> None:
+    ) -> Layer:
         """
         The basic structure is a magnetic layer.
         Its parameters are defined by the constructor and may be altered
@@ -342,7 +339,6 @@ class Layer:
         :param Ms: magnetisation saturation. Unit: Tesla [T].
         :param thickness: thickness of the layer. Unit: meter [m].
         :param cellSurface: surface of the layer, for volume calculation. Unit: meter^2 [m^2].
-        :param dipoleTensor: dipole tensor of the layer.
         :param damping: often marked as alpha in the LLG equation. Damping of the layer. Default 0.011. Dimensionless
         """
         ...
@@ -359,7 +355,7 @@ class Layer:
         damping: float = 0.11,
         fieldLikeTorque: float = 0,
         dampingLikeTorque: float = 0,
-    ) -> "Layer":
+    ) -> Layer:
         """
         Create SOT layer -- including damping and field-like torques that are
         calculated based on the effective Spin Hall angles.
@@ -369,7 +365,6 @@ class Layer:
         :param Ms: magnetisation saturation. Unit: Tesla [T].
         :param thickness: thickness of the layer. Unit: meter [m].
         :param cellSurface: surface of the layer, for volume calculation. Unit: meter^2 [m^2].
-        :param dipoleTensor: dipole tensor of the layer.
         :param temperature: resting temperature of the layer. Unit: Kelvin [K].
         :param damping: often marked as alpha in the LLG equation. Damping of the layer. Default 0.011. Dimensionless.
         """
@@ -388,7 +383,7 @@ class Layer:
         SlonczewskiSpacerLayerParameter: float = 1.0,
         beta: float = 0.0,
         spinPolarisation: float = 0.0,
-    ) -> "Layer":
+    ) -> Layer:
         """
         Create STT layer -- with the standard Slomczewski formulation.
         :param id: identifiable name for a layer -- e.g. "bottom" or "free".
@@ -397,7 +392,6 @@ class Layer:
         :param Ms: magnetisation saturation. Unit: Tesla [T].
         :param thickness: thickness of the layer. Unit: meter [m].
         :param cellSurface: surface of the layer, for volume calculation. Unit: meter^2 [m^2].
-        :param dipoleTensor: dipole tensor of the layer.
         :param damping: often marked as alpha in the LLG equation. Damping of the layer. Default 0.011. Dimensionless.
         :param SlonczewskiSpacerLayerParameter: Slomczewski parameter. Often marked as lambda.
         :param beta: beta parameter that scales FL/DL ratio.
@@ -469,7 +463,6 @@ class ScalarDriver:
         """
         Constant driver produces a constant signal of a fixed amplitude.
         :param constantValue: constant value of the driver (constant offset/amplitude)
-
         """
         ...
 
@@ -497,7 +490,6 @@ class ScalarDriver:
         :param amplitude: amplitude of the sine wave
         :param frequency: frequency of the sine
         :param phase: phase of the sine in radians.
-
         """
         ...
 

cmtj/llgb/__init__.pyi

@@ -0,0 +1,51 @@
+from typing import Dict, List, Tuple
+
+import cmtj
+
+class LLGBJunction:
+    def __init__(self, layers: List[LLGBLayer]) -> None: ...
+    def clearLog(self) -> None: ...
+    def getLog(self) -> Dict[str, List[float]]: ...
+    def runSimulation(
+        self,
+        totalTime: float,
+        timeStep: float = ...,
+        writeFrequency: float = ...,
+        log: bool = ...,
+        solverMode: cmtj.SolverMode = ...,
+    ) -> None: ...
+    def saveLogs(self, arg0: str) -> None: ...
+    def setLayerExternalFieldDriver(
+        self, arg0: str, arg1: cmtj.AxialDriver
+    ) -> None: ...
+    def setLayerTemperatureDriver(self, arg0: str, arg1: cmtj.ScalarDriver) -> None: ...
+
+class LLGBLayer:
+    def __init__(
+        self,
+        id: str,
+        mag: cmtj.CVector,
+        anis: cmtj.CVector,
+        Ms: float,
+        thickness: float,
+        cellSurface: float,
+        demagTensor: List[cmtj.CVector],
+        damping: float,
+        Tc: float,
+        susceptibility: float,
+        me: float,
+    ) -> None: ...
+    def setAnisotropyDriver(self, arg0: cmtj.ScalarDriver) -> None: ...
+    def setExternalFieldDriver(self, arg0: cmtj.AxialDriver) -> None: ...
+    def setTemperatureDriver(self, arg0: cmtj.ScalarDriver) -> None: ...
+
+def MFAWeissCurie(
+    me: float,
+    T: float,
+    J0: float,
+    relax: float = ...,
+    tolerance: float = ...,
+    maxIter: int = ...,
+) -> Tuple[float, float]: ...
+def langevin(arg0: float) -> float: ...
+def langevinDerivative(arg0: float) -> float: ...

cmtj/utils/general.py

@@ -16,6 +16,7 @@ class VectorObj:
     :param phi: positive x-axis (in xy plane) angle in radians
     :param mag: magnitude of the vector, if not set defaults to 1 *unit vector*
     """
+
     theta: float  # in radians
     phi: float  # rad
     mag: float = 1
@@ -41,7 +42,8 @@ def __hash__(self) -> int:
         return hash(str(self))
 
     def __eq__(self, __value: "VectorObj") -> bool:
-        return self.theta == __value.theta and self.phi == __value.phi and self.mag == __value.mag
+        return (self.theta == __value.theta and self.phi == __value.phi
+                and self.mag == __value.mag)
 
     def _componentwise_mul(self, other):
         coors = self.get_cartesian()
@@ -61,13 +63,16 @@ def from_spherical(theta, phi, mag=1):
         """Creates a Cartesian vector from spherical components"""
         return [
             mag * math.sin(theta) * math.cos(phi),
-            mag * math.sin(theta) * math.sin(phi), mag * math.cos(theta)
+            mag * math.sin(theta) * math.sin(phi),
+            mag * math.cos(theta),
         ]
 
     @staticmethod
     def from_cartesian(x: float, y: float, z: float):
         """Creates a spherical vector from Cartesian components"""
         mag = math.sqrt(x**2 + y**2 + z**2)
+        if mag == 0:
+            return VectorObj(0, 0, 0)
         theta = math.acos(z / mag)
         phi = math.atan2(y, x)
         return VectorObj(theta, phi, mag)
@@ -76,6 +81,8 @@ def from_cartesian(x: float, y: float, z: float):
     def from_cvector(cvector: CVector):
         """Creates a spherical vector from Cartesian components"""
         mag = cvector.length()
+        if mag == 0:
+            return VectorObj(0, 0, 0)
         theta = math.acos(cvector.z / mag)
         phi = math.atan2(cvector.y, cvector.x)
         return VectorObj(theta, phi, mag)

docker/Dockerfile.wheel

@@ -0,0 +1,22 @@
+FROM python:3.9
+
+# let's copy all the necessary files
+# we install our only 2 dependencies :) and vim for nice workflow
+RUN apt-get update && \
+    apt-get install -y build-essential libfftw3-dev git python3 python3-pip vim
+RUN python3 -m pip install --upgrade pip
+WORKDIR /scratch
+
+COPY setup.py /scratch
+COPY setup.cfg /scratch
+COPY python /scratch/python
+COPY core /scratch/core
+COPY third_party /scratch/third_party
+COPY cmtj /scratch/cmtj
+
+RUN python3 -m setup bdist_wheel && \
+    python3 -m pip install dist/*.whl numpy scipy tqdm
+
+WORKDIR /app
+RUN python3 -c "import cmtj; from cmtj.utils import FieldScan" && \
+    python3 -c "import cmtj; from cmtj import Layer"

docs/docgen.py

@@ -1,12 +1,17 @@
 import glob
+import logging
 import os
 import re
 from dataclasses import dataclass
 
+log = logging.getLogger("mkdocs")
+
 py_signature = r"(def (.+?) -> ([\'\[\]\,\sA-z]+)\:)"
 c_py_signature = re.compile(py_signature)
 
-joint_py = r"(?s)(def (.+?) -> ([\'\[\]\,\sA-z]+)\:)\n{0,}\s{8}(\"{3}(.+?)\"{3})"
+# old regex that does not allow for optional docstrings and quoted rtype
+# joint_py = r"(?s)(def (.+?) -> ([\"\'\[\]\,\sA-z]+)\:)\n{0,}\s{8}(\"{3}(.+?)\"{3})"
+joint_py = r"(?s)(def (.+?) -> ([\"\'\[\]\,\sA-z]+)\:)(?:\n\s*(\"{3}(.+?)\"{3}))?"
 c_joint_py = re.compile(joint_py)
 
 pydoc_regex = r"(?s)(\"{3}(.+?)\"{3})"
@@ -81,6 +86,7 @@ def py_signature_to_markdown(self):
 
 def extract_python_docs(file_text):
     for captured in c_joint_py.findall(file_text):
+        print(captured)
         if captured:
             yield PythonDocstring(
                 signature=captured[1].strip().replace("\n", ""),
@@ -109,10 +115,16 @@ def create_api_markdown_file(src_filename):
 
         class_docs = ftext.split("class")[1:]
         for i, doc_ in enumerate(class_docs):
+            doc_ = (
+                doc_.strip()
+                .replace("@staticmethod", "")
+                .replace("@classmethod", "")
+                .replace("@overload", "")
+            )
             class_name = doc_.partition("\n")[0].replace(":", "").strip()
             print(i, class_name)
             md_fn += f"## `{class_name}`"
-            for g in extract_python_docs(doc_):
+            for g in extract_python_docs(doc_.replace("...", "...\n")):
                 sig = g.py_signature_to_markdown()
                 md_fn += f"\n{sig}\n"
             md_fn += "  \n"
@@ -123,10 +135,14 @@ def create_api_markdown_file(src_filename):
         f.write(md_fn)
 
 
-if __name__ == "__main__":
+def on_startup(command, dirty, **kwargs):
     fn_lists = [
         *glob.glob(os.path.join(os.path.dirname(__file__), "..", "cmtj/*/*.pyi")),
         *glob.glob(os.path.join(os.path.dirname(__file__), "..", "cmtj/*.pyi")),
     ]
     for fn in fn_lists:
         create_api_markdown_file(fn)
+
+
+if __name__ == "__main__":
+    on_startup()