Modified files to pass mypy checks, adding classes/functions to serialise objects.

.azure-pipelines/ci.yml

@@ -31,6 +31,11 @@ steps:
   displayName: Run tests
   workingDirectory: $(Pipeline.Workspace)/src
 
+- script: |
+    PYTHONDEVMODE=1 mypy src tests
+  displayName: Mypy
+  workingDirectory: $(Pipeline.Workspace)
+
 - bash: bash <(curl -s https://codecov.io/bash) -n "Python $(PYTHON_VERSION) $(Agent.OS)"
   env:
     CODECOV_TOKEN: $(CODECOV_TOKEN)

.devcontainer/Dockerfile

@@ -0,0 +1,21 @@
+# See here for image contents: https://github.com/microsoft/vscode-dev-containers/tree/v0.241.1/containers/python-3/.devcontainer/base.Dockerfile
+
+# [Choice] Python version (use -bullseye variants on local arm64/Apple Silicon): 3, 3.10, 3.9, 3.8, 3.7, 3.6, 3-bullseye, 3.10-bullseye, 3.9-bullseye, 3.8-bullseye, 3.7-bullseye, 3.6-bullseye, 3-buster, 3.10-buster, 3.9-buster, 3.8-buster, 3.7-buster, 3.6-buster
+ARG VARIANT="3.10-bullseye"
+FROM mcr.microsoft.com/vscode/devcontainers/python:0-${VARIANT}
+
+# [Choice] Node.js version: none, lts/*, 16, 14, 12, 10
+ARG NODE_VERSION="none"
+RUN if [ "${NODE_VERSION}" != "none" ]; then su vscode -c "umask 0002 && . /usr/local/share/nvm/nvm.sh && nvm install ${NODE_VERSION} 2>&1"; fi
+
+# [Optional] If your pip requirements rarely change, uncomment this section to add them to the image.
+# COPY requirements.txt /tmp/pip-tmp/
+# RUN pip3 --disable-pip-version-check --no-cache-dir install -r /tmp/pip-tmp/requirements.txt \
+#    && rm -rf /tmp/pip-tmp
+
+# [Optional] Uncomment this section to install additional OS packages.
+# RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
+#     && apt-get -y install --no-install-recommends <your-package-list-here>
+
+# [Optional] Uncomment this line to install global node packages.
+# RUN su vscode -c "source /usr/local/share/nvm/nvm.sh && npm install -g <your-package-here>" 2>&1

.devcontainer/devcontainer.json

@@ -0,0 +1,54 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
+// https://github.com/microsoft/vscode-dev-containers/tree/v0.241.1/containers/python-3
+{
+	"name": "Python 3",
+	"build": {
+		"dockerfile": "Dockerfile",
+		"context": "..",
+		"args": { 
+			// Update 'VARIANT' to pick a Python version: 3, 3.10, 3.9, 3.8, 3.7, 3.6
+			// Append -bullseye or -buster to pin to an OS version.
+			// Use -bullseye variants on local on arm64/Apple Silicon.
+			"VARIANT": "3.8",
+			// Options
+			"NODE_VERSION": "none"
+		}
+	},
+
+	// Configure tool-specific properties.
+	"customizations": {
+		// Configure properties specific to VS Code.
+		"vscode": {
+			// Set *default* container specific settings.json values on container create.
+			"settings": { 
+				"python.defaultInterpreterPath": "/usr/local/bin/python",
+				"python.linting.enabled": true,
+				"python.linting.pylintEnabled": true,
+				"python.formatting.autopep8Path": "/usr/local/py-utils/bin/autopep8",
+				"python.formatting.blackPath": "/usr/local/py-utils/bin/black",
+				"python.formatting.yapfPath": "/usr/local/py-utils/bin/yapf",
+				"python.linting.banditPath": "/usr/local/py-utils/bin/bandit",
+				"python.linting.flake8Path": "/usr/local/py-utils/bin/flake8",
+				"python.linting.mypyPath": "/usr/local/py-utils/bin/mypy",
+				"python.linting.pycodestylePath": "/usr/local/py-utils/bin/pycodestyle",
+				"python.linting.pydocstylePath": "/usr/local/py-utils/bin/pydocstyle",
+				"python.linting.pylintPath": "/usr/local/py-utils/bin/pylint"
+			},
+
+			// Add the IDs of extensions you want installed when the container is created.
+			"extensions": [
+				"ms-python.python",
+				"ms-python.vscode-pylance"
+			]
+		}
+	},
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Use 'postCreateCommand' to run commands after the container is created.
+	// "postCreateCommand": "pip3 install --user -r requirements.txt",
+
+	// Comment out to connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
+	// "remoteUser": "vscode"
+}

src/diffcalc/hkl/calc.py

@@ -6,9 +6,10 @@
 from copy import copy
 from itertools import product
 from math import acos, asin, atan, atan2, cos, degrees, isnan, pi, sin, sqrt, tan
-from typing import Dict, Iterator, List, Optional, Tuple
+from typing import Any, Dict, Iterator, List, Optional, Tuple
 
 import numpy as np
+from diffcalc.hkl.constraints import Constraints
 from diffcalc.hkl.geometry import (
     Position,
     get_rotation_matrices,
@@ -18,6 +19,7 @@
     rot_PHI,
 )
 from diffcalc.log import logging
+from diffcalc.ub.calc import UBCalculation
 from diffcalc.util import (
     SMALL,
     DiffcalcException,
@@ -508,8 +510,8 @@ def _calc_psi(
             else:
                 sin_psi = cos(alpha) * sin(qaz - naz)
                 sgn = sign(sin_tau)
-                eps = sin_psi ** 2 + cos_psi ** 2
-                sigma_ = eps / sin_tau ** 2 - 1
+                eps = sin_psi**2 + cos_psi**2
+                sigma_ = eps / sin_tau**2 - 1
                 if not is_small(sigma_):
                     print(
                         "WARNING: Diffcalc could not calculate a unique azimuth "
@@ -937,7 +939,7 @@ def __get_last_sample_angle(A: float, B: float, C: float) -> List[float]:
                     "Sample orientation cannot be chosen uniquely. Please choose a different set of constraints."
                 )
             ks = atan2(A, B)
-            acos_alp = acos(bound(C / sqrt(A ** 2 + B ** 2)))
+            acos_alp = acos(bound(C / sqrt(A**2 + B**2)))
             if is_small(acos_alp):
                 alp_list = [
                     ks,
@@ -1513,7 +1515,7 @@ def _calc_sample_angles_given_two_sample_and_detector(
                 acos_phi = acos(
                     bound(
                         (N_phi[2, 0] * cos(chi) - V20)
-                        / (sin(chi) * sqrt(A ** 2 + B ** 2))
+                        / (sin(chi) * sqrt(A**2 + B**2))
                     )
                 )
             except AssertionError:
@@ -1562,7 +1564,7 @@ def _calc_sample_angles_given_two_sample_and_detector(
             try:
                 acos_rhs = acos(
                     bound(
-                        (sin(qaz) * cos(theta) / cos(eta) - V) / sqrt(X ** 2 + Y ** 2)
+                        (sin(qaz) * cos(theta) / cos(eta) - V) / sqrt(X**2 + Y**2)
                     )
                 )
             except AssertionError:
@@ -1605,7 +1607,7 @@ def _calc_sample_angles_given_two_sample_and_detector(
                 acos_V00 = acos(
                     bound(
                         (cos(theta) * sin(qaz) - N_phi[2, 0] * cos(eta) * sin(chi))
-                        / sqrt(A ** 2 + B ** 2)
+                        / sqrt(A**2 + B**2)
                     )
                 )
             except AssertionError:
@@ -1785,3 +1787,16 @@ def _verify_virtual_angles(
                         "anglesToVirtualAngles of %f" % virtual_angles_readback[key]
                     )
                     raise DiffcalcException(s)
+
+    @property
+    def asdict(self) -> Dict[str, Any]:
+        return {"ubcalc": self.ubcalc.asdict, "constraints": self.constraints.asdict}
+
+    @classmethod
+    def fromdict(cls, data: Dict[str, Any]) -> "HklCalculation":
+        constraint_data = data["constraints"]
+        indegrees = constraint_data.pop("indegrees")
+        return HklCalculation(
+            UBCalculation.fromdict(data["ubcalc"]),
+            Constraints(constraint_data, indegrees),
+        )

src/diffcalc/hkl/constraints.py

@@ -20,6 +20,7 @@ class _Constraint:
 
     @property
     def active(self) -> bool:
+        # in the below statement, how can self.value ever be False?
         return self.value is not False and self.value is not None
 
 
@@ -184,7 +185,11 @@ def asdict(self) -> Dict[str, Union[float, bool]]:
         Dict[str, Union[float, bool]]
             Dictionary with all constrained angle names and values.
         """
-        return {con.name: getattr(self, con.name) for con in self._all if con.active}
+        con_dict = {
+            con.name: getattr(self, con.name) for con in self._all if con.active
+        }
+        con_dict["indegrees"] = self.indegrees
+        return con_dict
 
     @asdict.setter
     def asdict(self, constraints):