feature: ✨ fix syntax by adding missing commas in function signatures (…

…#1656)

* chore: 🚨 remove unused hooks for black, isort, flake8, pylint, and pyupgrade

* build: 🧑‍💻 add `RUFF` and remove unused packages from poetry.lock and pyproject.toml

* chore: ✨ add Ruff linter and formatter to pre-commit configuration

* chore: ✨ configure Ruff linter to fix all issues and extend ignore rules

* chore: ✨ fix syntax by adding missing commas in function signatures

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

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

* chore: ✨ include 'spectrafit/' directory in Ruff and Ruff-format hooks

---------

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

.pre-commit-config.yaml

@@ -18,26 +18,13 @@ repos:
       - id: check-added-large-files
         args: ["--maxkb=1000"]
         exclude: \.ipynb
-  - repo: https://github.com/psf/black.git
-    rev: 24.10.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.7.0
     hooks:
-      - id: black
-  - repo: https://github.com/asottile/blacken-docs
-    rev: 1.19.0
-    hooks:
-      - id: blacken-docs
-        additional_dependencies: [black>=24.1.1]
-  - repo: https://github.com/PyCQA/isort.git
-    rev: 5.13.2
-    hooks:
-      - id: isort
-        additional_dependencies: [toml>=0.10.2]
-  - repo: https://github.com/PyCQA/flake8.git
-    rev: 7.1.1
-    hooks:
-      - id: flake8
-        exclude: ^spectrafit/test/, ^examples/
-        entry: flake8  --max-doc-length 100 --max-line-length  88 --ignore E203,W503,W605
+      - id: ruff
+        files: spectrafit/
+      - id: ruff-format
+        files: spectrafit/
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.11.2
     hooks:
@@ -58,19 +45,9 @@ repos:
     hooks:
       - id: pydocstyle
         additional_dependencies: [toml>=0.10.2]
-  - repo: https://github.com/PyCQA/pylint
-    rev: "v3.3.1"
-    hooks:
-      - id: pylint
-        additional_dependencies: [toml>=0.10.2, numpy>=1.23.4, pydantic>=2.1]
   - 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]
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v3.18.0
-    hooks:
-      - id: pyupgrade
-        args: [--py38-plus]

docs/examples/example9_2.ipynb

@@ -19,9 +19,10 @@
     "# Loading packages and default data\n",
     "from spectrafit.plugins import notebook as nb\n",
     "import pandas as pd\n",
+    "\n",
     "df = pd.read_csv(\n",
     "    \"https://raw.githubusercontent.com/Anselmoo/spectrafit/main/Examples/data.csv\"\n",
-    ")\n"
+    ")"
    ]
   },
   {
@@ -135,7 +136,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "spn.solver_model(initial_model=initial_model)\n"
+    "spn.solver_model(initial_model=initial_model)"
    ]
   },
   {
@@ -174,7 +175,7 @@
     "    color=cs.MoonAkiColor(),\n",
     "    font=cs.MoonAkiFont(),\n",
     ")\n",
-    "spn.solver_model(initial_model=initial_model)\n"
+    "spn.solver_model(initial_model=initial_model)"
    ]
   },
   {
@@ -216,7 +217,7 @@
     "    color=cs.DevOpsDarkColor(),\n",
     "    font=cs.DevOpsDarkFont(),\n",
     ")\n",
-    "spn.solver_model(initial_model=initial_model)\n"
+    "spn.solver_model(initial_model=initial_model)"
    ]
   },
   {
@@ -262,7 +263,7 @@
     "    color=cs.ColorBlindColor(),\n",
     "    font=cs.ColorBlindFont(),\n",
     ")\n",
-    "spn.solver_model(initial_model=initial_model)\n"
+    "spn.solver_model(initial_model=initial_model)"
    ]
   },
   {
@@ -301,7 +302,7 @@
     "    color=cs.DevOpsLightColor(),\n",
     "    font=cs.DevOpsLightFont(),\n",
     ")\n",
-    "spn.solver_model(initial_model=initial_model)\n"
+    "spn.solver_model(initial_model=initial_model)"
    ]
   },
   {

docs/examples/example9_3.ipynb

@@ -21,6 +21,7 @@
     "# Loading packages and default data\n",
     "from spectrafit.plugins import notebook as nb\n",
     "import pandas as pd\n",
+    "\n",
     "df = pd.read_csv(\n",
     "    \"https://raw.githubusercontent.com/Anselmoo/spectrafit/main/Examples/data.csv\"\n",
     ")"
@@ -41,7 +42,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "spn = nb.SpectraFitNotebook(df=df, x_column=\"Energy\", y_column=\"Noisy\", fname=\"example9_3\")"
+    "spn = nb.SpectraFitNotebook(\n",
+    "    df=df, x_column=\"Energy\", y_column=\"Noisy\", fname=\"example9_3\"\n",
+    ")"
    ]
   },
   {
@@ -69,11 +72,11 @@
     "    {\n",
     "        \"gaussian\": {\n",
     "            \"amplitude\": {\"max\": 2, \"min\": 0, \"vary\": True, \"value\": 0.3},\n",
-    "            \"center\": {\"max\": 2., \"min\": 0, \"vary\": True, \"value\": 2},\n",
+    "            \"center\": {\"max\": 2.0, \"min\": 0, \"vary\": True, \"value\": 2},\n",
     "            \"fwhmg\": {\"max\": 0.3, \"min\": 0.02, \"vary\": True, \"value\": 0.1},\n",
     "        }\n",
     "    },\n",
-    "     {\n",
+    "    {\n",
     "        \"gaussian\": {\n",
     "            \"amplitude\": {\"max\": 2, \"min\": 0, \"vary\": True, \"value\": 0.3},\n",
     "            \"center\": {\"max\": 3.5, \"min\": 1.5, \"vary\": True, \"value\": 2.5},\n",
@@ -168,7 +171,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "spn.solver_model(initial_model=initial_model, show_plot=False, show_peaks=True)\n"
+    "spn.solver_model(initial_model=initial_model, show_plot=False, show_peaks=True)"
    ]
   },
   {

docs/examples/example9_6.ipynb

@@ -80,11 +80,11 @@
     "    {\n",
     "        \"gaussian\": {\n",
     "            \"amplitude\": {\"max\": 2, \"min\": 0, \"vary\": True, \"value\": 0.3},\n",
-    "            \"center\": {\"max\": 2., \"min\": 0, \"vary\": True, \"value\": 2},\n",
+    "            \"center\": {\"max\": 2.0, \"min\": 0, \"vary\": True, \"value\": 2},\n",
     "            \"fwhmg\": {\"max\": 0.3, \"min\": 0.02, \"vary\": True, \"value\": 0.1},\n",
     "        }\n",
     "    },\n",
-    "     {\n",
+    "    {\n",
     "        \"gaussian\": {\n",
     "            \"amplitude\": {\"max\": 2, \"min\": 0, \"vary\": True, \"value\": 0.3},\n",
     "            \"center\": {\"max\": 3.5, \"min\": 1.5, \"vary\": True, \"value\": 2.5},\n",