refactor: Improve code readability and reducing code duplications (#127)

* refactor: Improve code readability and  reducing code duplications

- Using tuples to reperesent the non-diagonal elements via dictionary

* feat: Update poetry-core version and add pytest configuration with new tests for LigandFieldTheory

* test: Mark eigensolver_invalid_input test as expected failure due to unimplemented functionality

* chore: 🗃️ Moving test file

* chore: Clean up configuration files and update changelog formatting

* refactor: Improve test readability by formatting and organizing parameterized tests

* style: Format code for improved readability by adjusting line breaks and spacing

* fix: Correct comment from 'd3' to 'd2' for clarity in batch processing logic

* chore: Update pyproject.toml for improved dependency formatting and linting rules

* refactor: Enhance type hinting and improve code readability in tools and test files

* style: Improve docstring formatting and add missing method descriptions in matrices.py

.github/dependabot.yml

@@ -9,4 +9,3 @@ updates:
     directory: "/" # Location of package manifests
     schedule:
       interval: "weekly"
-

.github/workflows/docker-image.yml

@@ -15,4 +15,4 @@ jobs:
     steps:
     - uses: actions/checkout@v2
     - name: Build the Docker image
-      run: docker build . --file Dockerfile --tag tanabesugano:$(date +%s)
+      run: docker build . --file Dockerfile --tag tanabesugano:$(date +%s)

CHANGELOG.md

@@ -7,4 +7,4 @@
 * Add `poetry` for dependecy mangament
   * `setup.py` depends now on the `project.toml`
 * Modified the `GitHub-Actions`
-* Introduced `TanabeSugano` batch for extending analysis of correlation matrices
+* Introduced `TanabeSugano` batch for extending analysis of correlation matrices

pyproject.toml

@@ -38,31 +38,31 @@ classifiers = [
 include = ["LICENSE"]
 exclude = ["test/**/*.py", "example/**", "ts-diagrams/**"]
 
-        [tool.poetry.dependencies]
-        python = ">=3.9,<4.0"
-        pandas = ">=1.2.4,<4.0.0"
-        numpy = [
-                  { version = "^1.24.4", python = ">=3.8,<3.9" },
-                  { version = "^1.26.4", python = ">=3.9,<3.10" },
-                  { version = "^2.0.2", python = ">=3.10,<3.13" },
-        ]
-        matplotlib = "^3.4.2"
-        prettytable = ">=2.1,<4.0"
-        plotly = { version = "^5.13.1", optional = true }
-        update = "^0.0.1"
+[tool.poetry.dependencies]
+python = ">=3.9,<4.0"
+pandas = ">=1.2.4,<4.0.0"
+numpy = [
+        { version = "^1.24.4", python = ">=3.8,<3.9" },
+        { version = "^1.26.4", python = ">=3.9,<3.10" },
+        { version = "^2.0.2", python = ">=3.10,<3.13" },
+]
+matplotlib = "^3.4.2"
+prettytable = ">=2.1,<4.0"
+plotly = { version = "^5.13.1", optional = true }
+update = "^0.0.1"
 
-        [tool.poetry.group.dev.dependencies]
-        pytest = ">=7.2,<9.0"
-        pytest-clarity = "^1.0.1"
-        pytest-cov = ">=4,<6"
-        flake8 = ">=6,<8"
-        black = ">=22.12,<25.0"
-        isort = "^5.11.4"
-        pytest-console-scripts = "^1.3.1"
-        ruff = "^0.7.0"
+[tool.poetry.group.dev.dependencies]
+pytest = ">=7.2,<9.0"
+pytest-clarity = "^1.0.1"
+pytest-cov = ">=4,<6"
+flake8 = ">=6,<8"
+black = ">=22.12,<25.0"
+isort = "^5.11.4"
+pytest-console-scripts = "^1.3.1"
+ruff = "^0.7.0"
 
 [build-system]
-requires = ["poetry-core>=1.0.0"]
+requires = ["poetry-core>=1.1.0"]
 build-backend = "poetry.core.masonry.api"
 
 [tool.poetry.scripts]
@@ -73,14 +73,24 @@ plotly = ["plotly"]
 
 [tool.ruff]
 lint.select = ["ALL"]
-lint.ignore = ["N806"]
+lint.ignore = ["UP006", "UP007", "N801", "N802", "N803", "N806"]
 target-version = "py38"
 src = ["tanabesugano"]
 
+[tool.ruff.lint.per-file-ignores]
+"tanabesugano/test/*" = ["PT006", "ANN001", "ANN201", "D103", "PLR2004", "S101"]
+
 [tool.ruff.lint.isort]
 known-first-party = ["umf"]
 force-single-line = true
 lines-between-types = 1
 lines-after-imports = 2
 known-third-party = ["poetry.core"]
 required-imports = ["from __future__ import annotations"]
+
+[tool.pytest.ini_options]
+markers = """
+    xfail: mark test as expecting to fail
+    skip: mark test as skipped
+"""
+addopts = "-v --cov=tanabesugano"

tanabesugano/__init__.py

@@ -1,4 +1,5 @@
 """tanabesugano: A Python package for Tanabe-Sugano diagrams."""
+
 from __future__ import annotations
 
 

tanabesugano/batch.py

@@ -33,14 +33,18 @@ def __init__(
                 "The range of `B` is based on the three values: start, stop, steps!",
             )
         self.B = np.linspace(
-            B[0], B[1], int(B[2]),
+            B[0],
+            B[1],
+            int(B[2]),
         )  # Racah-Parameter B in wavenumbers
         if len(C) != 3:
             raise KeyError(
                 "The range of `C` is based on the three values: start, stop, steps!",
             )
         self.C = np.linspace(
-            C[0], C[1], int(C[2]),
+            C[0],
+            C[1],
+            int(C[2]),
         )  # Racah-Parameter C in wavenumbers
 
         if slater:
@@ -63,7 +67,7 @@ def calculation(self) -> None:
         for _Dq in self.Dq:
             for _B in self.B:
                 for _C in self.C:
-                    if self.d_count == 2:  # d3
+                    if self.d_count == 2:  # d2
                         states = matrices.d2(Dq=_Dq, B=_B, C=_C).solver()
                         self.result.append(
                             {

tanabesugano/cmd.py

@@ -103,7 +103,9 @@ def plot(self) -> None:
             ls="--",
         )
         self.label_plot(
-            "DD excitations -Diagram", r"$dd-state-energy\,(1/cm)$", r"$10Dq\,(1/cm)$",
+            "DD excitations -Diagram",
+            r"$dd-state-energy\,(1/cm)$",
+            r"$10Dq\,(1/cm)$",
         )
         plt.show()
 
@@ -128,8 +130,7 @@ def savetxt(self) -> None:
         ).to_csv(Path(f"{self.title_DD}.csv"), index=False)
 
     def calculation(self) -> None:
-        """Is filling the self.result with the iTS states of over-iterated energy range
-        """
+        """Is filling the self.result with the iTS states of over-iterated energy range"""
         result = []
         for dq in self.df["Energy"]:
             if self.d_count == 2:  # d2
@@ -197,8 +198,7 @@ def subsplit_states(states: dict) -> dict:
         return rearranged_states
 
     def ci_cut(self, dq_ci: float = None) -> None:
-        """Extracting the atomic-termsymbols for a specific dq depending on the oxidation state
-        """
+        """Extracting the atomic-termsymbols for a specific dq depending on the oxidation state"""
         if self.d_count == 2:  # d2
             states = matrices.d2(Dq=dq_ci / 10.0, B=self.B, C=self.C).solver()
             self.ts_print(states, dq_ci=dq_ci)
@@ -366,7 +366,10 @@ def cmd_line() -> None:
 
     parser = argparse.ArgumentParser(description=description)
     parser.add_argument(
-        "-d", type=int, default=6, help="Number of unpaired electrons (default d5)",
+        "-d",
+        type=int,
+        default=6,
+        help="Number of unpaired electrons (default d5)",
     )
     parser.add_argument(
         "-Dq",
@@ -398,7 +401,10 @@ def cmd_line() -> None:
         "1.)",
     )
     parser.add_argument(
-        "-n", type=int, default=500, help="Number of roots (default nroots = 500)",
+        "-n",
+        type=int,
+        default=500,
+        help="Number of roots (default nroots = 500)",
     )
     parser.add_argument(
         "-ndisp",