build: ⬆️ update configuration files for improved linting and formattingUpdate linting and formatting configurations (#1749)

* chore: update pre-commit configuration for argument formatting and versioning

* chore: 🚨 update ruff version to v0.8.4 and comment out prettier configuration

Pre Commit mirrors prettier is archived

* chore: remove commented-out prettier configuration from pre-commit config

* chore: ✨ add empty file for actionlint

* chore: ✨ add initial actionlint configuration file

* ci: ➖ disable black and isort linters in trunk configuration

* build: ⬆️ update configuration files for improved linting and formatting

* refactor: simplify file writing logic in PklVisualizer

* refactor: streamline file handling in ExportResults and ensure safe YAML loading

* test: skip tests for Python versions lower than 3.9

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* fix: update YAML loading to use deprecated method for compatibility

* refactor: ♻️ simplify file opening logic in RIXSConverter

* refactor: simplify Poetry installation logic in CI workflow

* test: skip tests for Python versions lower than 3.9

* test: skip tests and import for Python versions lower than 3.9

* test: add Python version check for tests requiring Python 3.9 or higher

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: Anselmoo

.github/actionlint.yaml

@@ -61,11 +61,7 @@ jobs:
       - name: Install Poetry and dependencies with dev-dependencies
         run: |
           python -m pip install --upgrade pip
-          # if [ "${{ matrix.os }}" == "windows-latest" ]; then
-          #   pip install poetry
-          # else
           pip install poetry
-          # fi
           poetry config virtualenvs.create true
           poetry config virtualenvs.in-project true
           poetry config virtualenvs.path .venv

.github/workflows/python-ci.yml

@@ -16,17 +16,17 @@ repos:
       - id: check-merge-conflict
       - id: check-case-conflict
       - id: check-added-large-files
-        args: ["--maxkb=1000"]
+        args: [--maxkb=1000]
         exclude: \.ipynb
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.3
+    rev: v0.8.4
     hooks:
       - id: ruff
         files: spectrafit/
       - id: ruff-format
         files: spectrafit/
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.13.0
+    rev: v1.14.0
     hooks:
       - id: mypy
         additional_dependencies:
@@ -45,9 +45,3 @@ repos:
     hooks:
       - id: pydocstyle
         additional_dependencies: [toml>=0.10.2]
-  - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "v4.0.0-alpha.8"
-    hooks:
-      - id: prettier
-        files: '\.(md|js|css)$'
-        args: [--prose-wrap=always]

.pre-commit-config.yaml

@@ -17,14 +17,15 @@ runtimes:
     - python@3.10.8
 # This is the section where you manage your linters. (https://docs.trunk.io/check/configuration)
 lint:
+  disabled:
+    - black
+    - isort
   enabled:
     - actionlint@1.7.4
     - bandit@1.8.0
-    - black@24.10.0
     - checkov@3.2.334
     - git-diff-check
     - hadolint@2.12.1-beta
-    - isort@5.13.2
     - markdownlint@0.43.0
     - mypy@1.13.0
     - osv-scanner@1.9.1

.trunk/trunk.yaml

@@ -106,8 +106,9 @@ def lorentzian(
             Union[NDArray[np.float64], float]: Lorentzian distribution of `x` given.
         """
         sigma = fwhml * Constants.fwhml2sig
-        return np.array(amplitude / (1 + ((1.0 * x - center) / sigma) ** 2)) / (
-            pi * sigma
+        return np.array(
+            amplitude / (1 + ((1.0 * x - center) / sigma) ** 2) / (pi * sigma),
+            dtype=np.float64,
         )
 
     @staticmethod
@@ -292,7 +293,7 @@ def _norm(
         """
         if abs(sigma) < 1.0e-13:
             sigma = 1.0e-13
-        return np.subtract(x, center) / sigma
+        return np.array(np.subtract(x, center) / sigma, dtype=np.float64)
 
     @staticmethod
     def erf(
@@ -1587,7 +1588,7 @@ def solve_local_fitting(
 
         for key, _kwarg in peak_kwargs.items():
             val += getattr(DistributionModels(), key[0])(x, **_kwarg)
-        return val - data
+        return np.array(val - data, dtype=np.float64)
 
     @staticmethod
     def solve_global_fitting(

poetry.lock

@@ -514,9 +514,7 @@ def export_report(self, report: Dict[Any, Any], args: FnameAPI) -> None:
             prefix=args.prefix,
             suffix=args.suffix,
             folder=args.folder,
-        ).open(
-            "wb+",
-        ) as f:
+        ).open("wb+") as f:
             tomli_w.dump(report, f)
 
     @staticmethod

spectrafit/models.py

@@ -111,12 +111,8 @@ def save(self, data: Any, fname: Path, export_format: str) -> None:
             format=export_format,
         )
 
-        with (
-            pure_fname(fname)
-            .with_suffix(".json")
-            .open("w+", encoding="utf-8") as outfile
-        ):
-            json.dump(data, outfile, indent=4)
+        with open(pure_fname(fname).with_suffix(".json"), "w+", encoding="utf-8") as f:
+            json.dump(data, f, indent=4)
 
     def get_type(self, value: Any) -> Union[Dict[str, Any], str]:
         """Get the type of the value.

spectrafit/plugins/notebook.py

@@ -182,20 +182,11 @@ def save(self, data: Any, fname: Path, export_format: str) -> None:
             with (
                 pure_fname(fname)
                 .with_suffix(f".{export_format}")
-                .open(
-                    "w",
-                    encoding="utf-8",
-                ) as f
+                .open("w", encoding="utf-8") as f
             ):
                 json.dump(self.numpydict2listdict(data), f, indent=4)
         elif export_format in {"toml", "lock"}:
-            with (
-                pure_fname(fname)
-                .with_suffix(f".{export_format}")
-                .open(
-                    "wb",
-                ) as f
-            ):
+            with pure_fname(fname).with_suffix(f".{export_format}").open("wb") as f:
                 tomli_w.dump(self.numpydict2listdict(data), f, multiline_strings=False)
         elif export_format == "npy":
             np.save(pure_fname(fname).with_suffix(f".{export_format}"), data)

spectrafit/plugins/pkl_visualizer.py

@@ -6,6 +6,7 @@
 import shutil
 
 from pathlib import Path
+import sys
 from typing import Any
 from typing import Dict
 from typing import Tuple
@@ -25,10 +26,16 @@
 from spectrafit.plugins.pkl_converter import ExportData
 from spectrafit.plugins.pkl_converter import PklConverter
 from spectrafit.plugins.pkl_visualizer import PklVisualizer
-from spectrafit.plugins.pptx_converter import PPTXConverter
-from spectrafit.plugins.rixs_converter import RIXSConverter
 
 
+if sys.version_info >= (3, 9):
+    from spectrafit.plugins.pptx_converter import PPTXConverter
+    from spectrafit.plugins.rixs_converter import RIXSConverter
+else:
+    pytest.mark.skip("Requires Python 3.9 or higher", allow_module_level=True)
+
+
+@pytest.mark.skipif(sys.version_info < (3, 9), reason="Requires Python 3.9 or higher")
 class TestFileConverter:
     """Test the file converter plugin."""
 
@@ -301,6 +308,7 @@ def reference_dataframe() -> pd.DataFrame:
     )
 
 
+@pytest.mark.skipif(sys.version_info < (3, 9), reason="Requires Python 3.9 or higher")
 class TestDataConverter:
     """Test DataConverter class."""
 
@@ -512,6 +520,7 @@ def tmp_file_pkl_nested(
     return tmp_file
 
 
+@pytest.mark.skipif(sys.version_info < (3, 9), reason="Requires Python 3.9 or higher")
 class TestPklConverter:
     """Test PklConverter."""
 
@@ -686,6 +695,7 @@ def test_cmd_pkl_converter(
         )
 
 
+@pytest.mark.skipif(sys.version_info < (3, 9), reason="Requires Python 3.9 or higher")
 class TestPklAsGraph:
     """Test the pkl visualizer."""
 
@@ -803,6 +813,7 @@ def fixture_tmp_list_dict_rixs(
     return fname, keys
 
 
+@pytest.mark.skipif(sys.version_info < (3, 9), reason="Requires Python 3.9 or higher")
 class TestRixsConverter:
     """Test the rixs converter."""
 
@@ -859,7 +870,7 @@ def test_save(
         if export_format == "npy":
             data_npy = np.load(fname.parent / f"{fname.stem}.npy", allow_pickle=True)
             assert isinstance(data_npy, np.ndarray)
-            assert np.allclose(data_npy.item()[keys[0]], data[keys[0]])
+            assert np.allclose(data_npy.item()[keys[0]], data[keys[0]])  # type: ignore
 
         if export_format == "npz":
             data_npz = np.load(fname.parent / f"{fname.stem}.npz", allow_pickle=True)
@@ -1039,6 +1050,7 @@ def test_cmd_pkl_converter(
 """
 
 
+@pytest.mark.skipif(sys.version_info < (3, 9), reason="Requires Python 3.9 or higher")
 class TestPPTXConverter:
     """Test the pptx converter."""
 

spectrafit/plugins/rixs_converter.py

@@ -1,6 +1,7 @@
 """Test of the RIXS Visualizer."""
 
 from pathlib import Path
+import sys
 from typing import Any
 from typing import Tuple
 
@@ -9,25 +10,29 @@
 import pytest
 
 from numpy.typing import NDArray
-from spectrafit.plugins.rixs_converter import RIXSConverter
-from spectrafit.plugins.rixs_visualizer import RIXSApp
-from spectrafit.plugins.rixs_visualizer import RIXSFigure
-from spectrafit.plugins.rixs_visualizer import RIXSVisualizer
 
+if sys.version_info >= (3, 9):
+    from spectrafit.plugins.rixs_converter import RIXSConverter
+    from spectrafit.plugins.rixs_visualizer import RIXSApp
+    from spectrafit.plugins.rixs_visualizer import RIXSFigure
+    from spectrafit.plugins.rixs_visualizer import RIXSVisualizer
+else:
+    pytest.mark.skip("Requires Python 3.9 or higher", allow_module_level=True)
 
+
+@pytest.mark.skipif(sys.version_info < (3, 9), reason="Requires Python 3.9 or higher")
 @pytest.fixture(scope="module", autouse=True, name="test_data")
 def fixture_test_data() -> (
     Tuple[NDArray[np.float64], NDArray[np.float64], NDArray[np.float64]]
 ):
     """Test data."""
-    space_x_y = np.arange(0, 10, 0.1)
+    space_x_y = np.arange(0, 10, 0.1, dtype=np.float64)
     space_x, space_y = np.meshgrid(space_x_y, space_x_y)
     return space_x_y, space_x_y, np.sin(space_x) * np.cos(space_y)
 
 
 # Write test  RIXSFigure
-
-
+@pytest.mark.skipif(sys.version_info < (3, 9), reason="Requires Python 3.9 or higher")
 class TestRixsFigure:
     """Test of the RIXS Figure."""
 
@@ -59,6 +64,7 @@ def test_create_rixs_figure(self, test_data: NDArray[np.float64]) -> None:
         assert isinstance(fig_xas, go.Figure)
 
 
+@pytest.mark.skipif(sys.version_info < (3, 9), reason="Requires Python 3.9 or higher")
 class TestRIXSApp:
     """Test of the App."""
 

spectrafit/plugins/test/test_converter.py

@@ -662,7 +662,7 @@ def assert_isinstance(
     def test_key_not_available(self) -> None:
         """Test if the key is not available."""
         args = {"autopeak": True, "global_": 0}
-        x = np.arange(0, 10, 0.1)
+        x = np.arange(0, 10, 0.1, dtype=np.float64)
         data = (
             np.sin(np.arange(0, 10, 0.1)) ** 3 + 2 * np.cos(np.arange(0, 10, 0.1)) ** 2
         )
@@ -705,17 +705,17 @@ def test_plateau_size(self) -> None:
     def test_distance(self) -> None:
         """Test if the distance is calculated correctly."""
         args = {"autopeak": True, "global_": 0}
-        x = 3 * np.arange(10, dtype=np.float64)
-        data = 3 * np.exp(10, dtype=np.float64)
+        x = 3.0 * np.arange(10, dtype=np.float64)
+        data = 3.0 * np.exp(10, dtype=np.float64)
 
-        auto = AutoPeakDetection(x=x, data=data, args=args)
+        auto = AutoPeakDetection(x=x, data=data, args=args)  # type: ignore
         _val = auto.estimate_distance
         assert not isclose(_val, 1.0)
 
     def test_autopeakdetection_mean(self) -> None:
         """Test of auto default detection with negative values."""
         args = {"autopeak": True, "global_": 0}
-        x = np.arange(0, 10, 0.1)
+        x = np.arange(0, 10, 0.1, dtype=np.float64)
         data = (
             np.sin(np.arange(0, 10, 0.1)) ** 3 + 2 * np.cos(np.arange(0, 10, 0.1)) ** 2
         )