Merge pull request #15 from JR-1991/main

Added testing CI and compliance to Python >=3.7

.github/workflows/build.yml

@@ -0,0 +1,26 @@
+name: Build and Test
+
+on: [push]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 4
+      matrix:
+        python-version: ['3.7', '3.8', '3.9', '3.10']
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v1
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python3 -m pip install --upgrade pip
+          pip3 install -e .
+      - name: Test with pytest
+        run: |
+          python3 -m pytest

pyproject.toml

@@ -7,7 +7,7 @@ name = "SAS-tools"
 version = "0.0"
 description = "SAS-tools contains useful functions and classes for working with SAS data."
 readme = "README.md"
-requires-python = ">=3.10"
+requires-python = ">=3.7"
 license = {file = "LICENSE"}
 authors = [
     {name = "Torsten Giess", email = "[email protected]"},
@@ -32,9 +32,10 @@ dependencies = [
     "matplotlib",
     "numpy",
     "pandas",
-    "pyaniml",
+    "pyAnIML==1.0.2",
     "seaborn",
     "scipy",
+    "pytest>=7.2.0"
 ]
 
 [project.urls]

sastools/analyzer/curvefitting.py

@@ -6,6 +6,7 @@
 import random
 
 from pathlib import Path
+from typing import Tuple, Dict, Optional
 
 import numpy as np
 import pandas as pd
@@ -37,14 +38,15 @@ def __init__(
             path_plots (Path): Path to where plots are to be saved.
             path_fitting_data (Path): Path to where fitting data is to be saved.
         """
+
         self.exp_data = experimental_data
         self.x = self.exp_data.iloc[:, 0].values.tolist()
         self.y = self.exp_data.iloc[:, 1].values.tolist()
         self.file_name = file_name
         self.path_plots = path_plots
         self.path_fitting_data = path_fitting_data
 
-    def _pack_data_into_dict(self) -> dict:
+    def _pack_data_into_dict(self) -> Dict:
         # Stores the data in a dictionary
         data_dict = {"data": {"x": self.x, "y": self.y}}
         return data_dict
@@ -63,7 +65,7 @@ def plot_raw_data(self) -> None:
         )
 
     def find_peaks_cwt(
-        self, peak_widths: tuple = (20,), cutoff_amplitude: float = None
+        self, peak_widths: Tuple = (20,), cutoff_amplitude: Optional[float] = None
     ) -> None:
         """Find peaks using the `find_peaks_cwt` method from signal.
         Prints number of found peaks. Figure with positions of found
@@ -108,7 +110,7 @@ def plot_found_peak(self) -> None:
         )
 
     def set_specifications_manually(
-        self, number_of_models: int, model_specifications: dict
+        self, number_of_models: int, model_specifications: Dict
     ) -> None:
         """Manually sets the specifications for the individual model
         used for the fitting procedure. Stores the generated
@@ -176,7 +178,7 @@ def set_specifications_automatically(
         ) as outfile:
             outfile.write(json_models_dict)
 
-    def generate_model(self, speci: dict) -> tuple:
+    def generate_model(self, speci: Dict) -> tuple:
         """Generates a composite model and corresponding parameters
         based on the provided specifications using the `model` class
         of the python library `lmfit`.

sastools/analyzer/llcphase.py

@@ -1,6 +1,7 @@
 """ABC defining properties of different LLC phases."""
 
 from abc import ABC, abstractmethod
+from typing import List, Tuple, Dict
 
 from sastools.analyzer.enums import LLCPhases, LLCSpaceGroups
 
@@ -9,7 +10,7 @@ class LLCPhase(ABC):
     """ABC defining the properties of an LLC Phase."""
 
     @abstractmethod
-    def calculate_lattice_parameters(self, d_meas: list[float]):
+    def calculate_lattice_parameters(self, d_meas: List[float]):
         ...
 
     @property
@@ -24,15 +25,15 @@ def space_group(self) -> LLCSpaceGroups:
 
     @property
     @abstractmethod
-    def miller_indices(self) -> tuple[list[int], list[int], list[int]]:
+    def miller_indices(self) -> Tuple[List[int], List[int], List[int]]:
         ...
 
     @property
     @abstractmethod
-    def lattice_parameters(self) -> list[float]:
+    def lattice_parameters(self) -> List[float]:
         ...
 
     @property
     @abstractmethod
-    def phase_information(self) -> dict:
+    def phase_information(self) -> Dict:
         ...

sastools/analyzer/llcphases.py

@@ -2,6 +2,8 @@
 
 import numpy as np
 
+from typing import List, Tuple, Dict
+
 from sastools.analyzer.enums import LLCPhases, LLCSpaceGroups, LLCMillerIndices
 from sastools.analyzer.llcphase import LLCPhase
 
@@ -26,13 +28,13 @@ def _calculate_a_H1(self, d: float, h: int, k: int) -> float:
         return a_H1
 
     def calculate_lattice_parameters(
-        self, d_meas: list[float], phase: LLCPhases = LLCPhases.H1
+        self, d_meas: List[float], phase: LLCPhases = LLCPhases.H1
     ) -> None:
         """Calculate lattice parameters of hexagonal phase using a list
         of measured lattice plane distances `d_meas`.
 
         Args:
-            d_meas (list[float]): Measured lattice plane distances.
+            d_meas (List[float]): Measured lattice plane distances.
             phase (LLCPhases, optional): The hexagonal phase of the system. Defaults to LLCPhases.H1.
 
         Raises:
@@ -43,7 +45,7 @@ def calculate_lattice_parameters(
                 f"Chosen LLC phase '{phase}' is not (yet) supported."
             )
         self._exact_phase = phase
-        for i, j in enumerate(d_meas):
+        for i, _ in enumerate(d_meas):
             a_i = self._calculate_a_H1(
                 d_meas[i], self.miller_indices[0][i], self.miller_indices[1][i]
             )
@@ -64,18 +66,18 @@ def space_group(self) -> LLCSpaceGroups:
         return self._space_group
 
     @property
-    def miller_indices(self) -> tuple[list[int], list[int], list[int]]:
+    def miller_indices(self) -> Tuple[List[int], List[int], List[int]]:
         """Get miller indices of hexagonal phase."""
         self._miller_indices = LLCMillerIndices[self._space_group.name].value
         return self._miller_indices
 
     @property
-    def lattice_parameters(self) -> list[float]:
+    def lattice_parameters(self) -> List[float]:
         """Get lattice parameters of hexagonal phase."""
         return self._lattice_parameters
 
     @property
-    def phase_information(self) -> dict:
+    def phase_information(self) -> Dict:
         """Get full phase information of hexagonal phase."""
         self._phase_information = dict(
             phase=self.exact_phase.value,
@@ -107,15 +109,15 @@ def _calculate_a_V1(self, d: float, h: int, k: int, l: int) -> float:
 
     def calculate_lattice_parameters(
         self,
-        d_meas: list[float],
+        d_meas: List[float],
         phase: LLCPhases = LLCPhases.V1,
         space_group: LLCSpaceGroups = LLCSpaceGroups.IA3D,
     ) -> None:
         """Calculate lattice parameters of cubic phase using a list of
         measured lattice plane distances `d_meas`.
 
         Args:
-            d_meas (list[float]): Measured lattice plane distances.
+            d_meas (List[float]): Measured lattice plane distances.
             phase (LLCPhases, optional): The cubic phase of the system. Defaults to LLCPhases.V1.
             space_group (LLCSpaceGroups, optional): The space group corresponding to the cubic phase. Defaults to LLCSpaceGroups.IA3D.
 
@@ -137,13 +139,13 @@ def calculate_lattice_parameters(
             )
             self._lattice_parameters.append(a_i)
 
-    def calculate_d_reciprocal(self, peak_center: list[float]) -> None:
+    def calculate_d_reciprocal(self, peak_center: List[float]) -> None:
         """Calculate the reciprocal lattice plane distances
         `d_reciprocal` from the `peak_centers` determined through
         lorentzian fitting.
 
         Args:
-            peak_center (list[float]): Peak centers determined by lorentzian fitting for the cubic phase.
+            peak_center (List[float]): Peak centers determined by lorentzian fitting for the cubic phase.
         """
         self._d_reciprocal = [peak / (2 * np.pi) for peak in peak_center]
 
@@ -180,20 +182,20 @@ def space_group(self, space_group: LLCSpaceGroups) -> None:
         self._space_group = space_group
 
     @property
-    def miller_indices(self) -> tuple[list[int], list[int], list[int]]:
+    def miller_indices(self) -> Tuple[List[int], List[int], List[int]]:
         """Get miller indices of cubic phase."""
         if self.space_group is None:
             raise ValueError("space_group property has to be provided first.")
         self._miller_indices = LLCMillerIndices[self._space_group.name].value
         return self._miller_indices
 
     @property
-    def lattice_parameters(self) -> list[float]:
+    def lattice_parameters(self) -> List[float]:
         """Get lattice parameters of cubic phase."""
         return self._lattice_parameters
 
     @property
-    def phase_information(self) -> dict:
+    def phase_information(self) -> Dict:
         """Get full phase information of cubic phase."""
         self._phase_information = dict(
             phase=self.exact_phase.value,
@@ -202,12 +204,12 @@ def phase_information(self) -> dict:
         return self._phase_information
 
     @property
-    def d_reciprocal(self) -> list[float]:
+    def d_reciprocal(self) -> List[float]:
         """Get reciprocal lattice plane distances of cubic phase."""
         return self._d_reciprocal
 
     @property
-    def sqrt_miller(self) -> list[int]:
+    def sqrt_miller(self) -> List[int]:
         """Get square roots of miller indices of cubic phase."""
         return self._sqrt_miller
 
@@ -226,13 +228,13 @@ def __repr__(self) -> str:
         return "Lamellar LLC Phase"
 
     def calculate_lattice_parameters(
-        self, d_meas: list[float], phase: LLCPhases = LLCPhases.LA
+        self, d_meas: List[float], phase: LLCPhases = LLCPhases.LA
     ) -> None:
         """Calculate lattice parameters of lamellar phase using a list
         of measured lattice plane distances `d_meas`.
 
         Args:
-            d_meas (list[float]): Measured lattice plane distances.
+            d_meas (List[float]): Measured lattice plane distances.
             phase (LLCPhases, optional): The lamellar phase of the system. Defaults to LLCPhases.LA.
 
         Raises:
@@ -265,12 +267,12 @@ def miller_indices(self) -> None:
         return self._miller_indices
 
     @property
-    def lattice_parameters(self) -> list[float]:
+    def lattice_parameters(self) -> List[float]:
         """Get lattice parameters of lamellar phase."""
         return self._lattice_parameters
 
     @property
-    def phase_information(self) -> dict:
+    def phase_information(self) -> Dict:
         """Get full phase information of lamellar phase."""
         self._phase_information = dict(
             phase=self.exact_phase.value,
@@ -293,13 +295,13 @@ def __repr__(self) -> str:
         return "Indeterminate LLC Phase"
 
     def calculate_lattice_parameters(
-        self, d_meas: list[float], phase: LLCPhases = LLCPhases.INDETERMINATE
+        self, d_meas: List[float], phase: LLCPhases = LLCPhases.INDETERMINATE
     ) -> None:
         """Do not use this method! Indeterminate phases have no lattice
         parameters.
 
         Args:
-            d_meas (list[float]): Measured lattice plane distances.
+            d_meas (List[float]): Measured lattice plane distances.
             phase (LLCPhases, optional): Indeterminate phase. Defaults to LLCPhases.INDETERMINATE.
 
         Raises:
@@ -330,7 +332,7 @@ def lattice_parameters(self) -> None:
         return self._lattice_parameters
 
     @property
-    def phase_information(self) -> dict:
+    def phase_information(self) -> Dict:
         """Get full phase information of indeterminate phase."""
         self._phase_information = dict(
             phase=self.exact_phase.value,