Merge pull request #200 from ImperialCollegeLondon/switch-to-ruff

Switch to ruff for linting and formatting
ImperialCollegeLondon · Jan 8, 2025 · 460f51c · 460f51c
2 parents ee6bd1d + adb57cc
commit 460f51c
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diff --git a/.flake8 b/.flake8
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -4,20 +4,17 @@ repos:
     hooks:
       - id: check-merge-conflict
       - id: debug-statements
-  - repo: https://github.com/timothycrosley/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
-        additional_dependencies: [toml]
-  - repo: https://github.com/psf/black
-    rev: 23.3.0
-    hooks:
-      - id: black
-  - repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
-    hooks:
-      - id: flake8
-        additional_dependencies: [flake8-docstrings]
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.8.5
+    hooks:
+      # Run the linter.
+      - id: ruff
+        types_or: [ python, pyi, jupyter ]
+        args: [ --fix ]
+      # Run the formatter.
+      - id: ruff-format
+        types_or: [ python, pyi, jupyter ]
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.5.1
     hooks:

diff --git a/docs/source/_append_footbib.py b/docs/source/_append_footbib.py
@@ -1,4 +1,5 @@
 """Append a footbibliography directive to all .rst files in a directory."""
+
 import os
 import sys
 

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -1,6 +1,5 @@
 """Configuration file for the Sphinx documentation builder."""
 
-
 import os
 import sys
 

diff --git a/docs/source/examples/LEAN-differentiation.ipynb b/docs/source/examples/LEAN-differentiation.ipynb
@@ -24,20 +24,25 @@
    "source": [
     "import pyprobe\n",
     "import matplotlib.pyplot as plt\n",
+    "\n",
     "%matplotlib inline\n",
     "\n",
-    "info_dictionary = {'Name': 'Sample cell',\n",
-    "                   'Chemistry': 'NMC622',\n",
-    "                   'Nominal Capacity [Ah]': 0.04,\n",
-    "                   'Cycler number': 1,\n",
-    "                   'Channel number': 1,}\n",
-    "data_directory = '../../../tests/sample_data/neware'\n",
+    "info_dictionary = {\n",
+    "    \"Name\": \"Sample cell\",\n",
+    "    \"Chemistry\": \"NMC622\",\n",
+    "    \"Nominal Capacity [Ah]\": 0.04,\n",
+    "    \"Cycler number\": 1,\n",
+    "    \"Channel number\": 1,\n",
+    "}\n",
+    "data_directory = \"../../../tests/sample_data/neware\"\n",
     "\n",
     "# Create a cell object\n",
     "cell = pyprobe.Cell(info=info_dictionary)\n",
-    "cell.add_procedure(procedure_name='Sample',\n",
-    "                   folder_path = data_directory,\n",
-    "                   filename = 'sample_data_neware.parquet')"
+    "cell.add_procedure(\n",
+    "    procedure_name=\"Sample\",\n",
+    "    folder_path=data_directory,\n",
+    "    filename=\"sample_data_neware.parquet\",\n",
+    ")"
    ]
   },
   {
@@ -53,9 +58,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "final_cycle= cell.procedure['Sample'].experiment('Break-in Cycles').cycle(-1)\n",
+    "final_cycle = cell.procedure[\"Sample\"].experiment(\"Break-in Cycles\").cycle(-1)\n",
     "\n",
-    "final_cycle.plot(x='Time [hr]', y='Voltage [V]')"
+    "final_cycle.plot(x=\"Time [hr]\", y=\"Voltage [V]\")"
    ]
   },
   {
@@ -72,15 +77,38 @@
    "outputs": [],
    "source": [
     "from pyprobe.analysis import differentiation\n",
-    "discharge_dQdV = differentiation.differentiate_LEAN(input_data = final_cycle.discharge(0), \n",
-    "                                                    x = 'Capacity [Ah]', y='Voltage [V]', k = 10, gradient = 'dxdy')\n",
-    "charge_dQdV = differentiation.differentiate_LEAN(input_data = final_cycle.charge(0).constant_current(), \n",
-    "                                                 x = 'Capacity [Ah]', y='Voltage [V]', k = 10, gradient = 'dxdy')\n",
+    "\n",
+    "discharge_dQdV = differentiation.differentiate_LEAN(\n",
+    "    input_data=final_cycle.discharge(0),\n",
+    "    x=\"Capacity [Ah]\",\n",
+    "    y=\"Voltage [V]\",\n",
+    "    k=10,\n",
+    "    gradient=\"dxdy\",\n",
+    ")\n",
+    "charge_dQdV = differentiation.differentiate_LEAN(\n",
+    "    input_data=final_cycle.charge(0).constant_current(),\n",
+    "    x=\"Capacity [Ah]\",\n",
+    "    y=\"Voltage [V]\",\n",
+    "    k=10,\n",
+    "    gradient=\"dxdy\",\n",
+    ")\n",
     "\n",
     "fig, ax = plt.subplots()\n",
-    "discharge_dQdV.plot(x='Capacity [Ah]', y='d(Capacity [Ah])/d(Voltage [V])', ax=ax, label='Discharge', color='blue')\n",
-    "charge_dQdV.plot(x='Capacity [Ah]', y='d(Capacity [Ah])/d(Voltage [V])', ax=ax, label='Charge', color='red')\n",
-    "ax.set_ylabel('d(Capacity [Ah])/d(Voltage [V])')"
+    "discharge_dQdV.plot(\n",
+    "    x=\"Capacity [Ah]\",\n",
+    "    y=\"d(Capacity [Ah])/d(Voltage [V])\",\n",
+    "    ax=ax,\n",
+    "    label=\"Discharge\",\n",
+    "    color=\"blue\",\n",
+    ")\n",
+    "charge_dQdV.plot(\n",
+    "    x=\"Capacity [Ah]\",\n",
+    "    y=\"d(Capacity [Ah])/d(Voltage [V])\",\n",
+    "    ax=ax,\n",
+    "    label=\"Charge\",\n",
+    "    color=\"red\",\n",
+    ")\n",
+    "ax.set_ylabel(\"d(Capacity [Ah])/d(Voltage [V])\")"
    ]
   },
   {
@@ -96,13 +124,37 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "discharge_dQdV = differentiation.differentiate_LEAN(input_data = final_cycle.discharge(0), x = 'Capacity [mAh]', y='Voltage [V]', k = 10, gradient = 'dxdy')\n",
-    "charge_dQdV = differentiation.differentiate_LEAN(input_data = final_cycle.charge(0).constant_current(), x = 'Capacity [mAh]', y='Voltage [V]', k = 10, gradient = 'dxdy')\n",
+    "discharge_dQdV = differentiation.differentiate_LEAN(\n",
+    "    input_data=final_cycle.discharge(0),\n",
+    "    x=\"Capacity [mAh]\",\n",
+    "    y=\"Voltage [V]\",\n",
+    "    k=10,\n",
+    "    gradient=\"dxdy\",\n",
+    ")\n",
+    "charge_dQdV = differentiation.differentiate_LEAN(\n",
+    "    input_data=final_cycle.charge(0).constant_current(),\n",
+    "    x=\"Capacity [mAh]\",\n",
+    "    y=\"Voltage [V]\",\n",
+    "    k=10,\n",
+    "    gradient=\"dxdy\",\n",
+    ")\n",
     "\n",
     "fig, ax = plt.subplots()\n",
-    "discharge_dQdV.plot(x='Capacity [mAh]', y='d(Capacity [mAh])/d(Voltage [V])', ax=ax, label='Discharge', color='blue')\n",
-    "charge_dQdV.plot(x='Capacity [mAh]', y='d(Capacity [mAh])/d(Voltage [V])', ax=ax, label='Charge', color='red')\n",
-    "ax.set_ylabel('d(Capacity [mAh])/d(Voltage [V])')"
+    "discharge_dQdV.plot(\n",
+    "    x=\"Capacity [mAh]\",\n",
+    "    y=\"d(Capacity [mAh])/d(Voltage [V])\",\n",
+    "    ax=ax,\n",
+    "    label=\"Discharge\",\n",
+    "    color=\"blue\",\n",
+    ")\n",
+    "charge_dQdV.plot(\n",
+    "    x=\"Capacity [mAh]\",\n",
+    "    y=\"d(Capacity [mAh])/d(Voltage [V])\",\n",
+    "    ax=ax,\n",
+    "    label=\"Charge\",\n",
+    "    color=\"red\",\n",
+    ")\n",
+    "ax.set_ylabel(\"d(Capacity [mAh])/d(Voltage [V])\")"
    ]
   },
   {
@@ -118,12 +170,36 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "discharge_dQdV = differentiation.differentiate_LEAN(input_data = final_cycle.discharge(0), x = 'Cycle Capacity [Ah]', y='Voltage [V]', k = 10, gradient = 'dxdy')\n",
-    "charge_dQdV = differentiation.differentiate_LEAN(input_data = final_cycle.charge(0).constant_current(), x = 'Cycle Capacity [Ah]', y='Voltage [V]', k = 10, gradient = 'dxdy')\n",
+    "discharge_dQdV = differentiation.differentiate_LEAN(\n",
+    "    input_data=final_cycle.discharge(0),\n",
+    "    x=\"Cycle Capacity [Ah]\",\n",
+    "    y=\"Voltage [V]\",\n",
+    "    k=10,\n",
+    "    gradient=\"dxdy\",\n",
+    ")\n",
+    "charge_dQdV = differentiation.differentiate_LEAN(\n",
+    "    input_data=final_cycle.charge(0).constant_current(),\n",
+    "    x=\"Cycle Capacity [Ah]\",\n",
+    "    y=\"Voltage [V]\",\n",
+    "    k=10,\n",
+    "    gradient=\"dxdy\",\n",
+    ")\n",
     "\n",
     "fig, ax = plt.subplots()\n",
-    "discharge_dQdV.plot(x='Cycle Capacity [Ah]', y='d(Cycle Capacity [Ah])/d(Voltage [V])', ax=ax, label='Discharge', color='blue')\n",
-    "charge_dQdV.plot(x='Cycle Capacity [Ah]', y='d(Cycle Capacity [Ah])/d(Voltage [V])', ax=ax, label='Charge', color='red')"
+    "discharge_dQdV.plot(\n",
+    "    x=\"Cycle Capacity [Ah]\",\n",
+    "    y=\"d(Cycle Capacity [Ah])/d(Voltage [V])\",\n",
+    "    ax=ax,\n",
+    "    label=\"Discharge\",\n",
+    "    color=\"blue\",\n",
+    ")\n",
+    "charge_dQdV.plot(\n",
+    "    x=\"Cycle Capacity [Ah]\",\n",
+    "    y=\"d(Cycle Capacity [Ah])/d(Voltage [V])\",\n",
+    "    ax=ax,\n",
+    "    label=\"Charge\",\n",
+    "    color=\"red\",\n",
+    ")"
    ]
   }
  ],

diff --git a/docs/source/examples/analysing-GITT-data.ipynb b/docs/source/examples/analysing-GITT-data.ipynb
@@ -20,22 +20,26 @@
    "source": [
     "import pyprobe\n",
     "import matplotlib.pyplot as plt\n",
+    "\n",
     "%matplotlib inline\n",
     "\n",
-    "info_dictionary = {'Name': 'Sample cell',\n",
-    "                   'Chemistry': 'NMC622',\n",
-    "                   'Nominal Capacity [Ah]': 0.04,\n",
-    "                   'Cycler number': 1,\n",
-    "                   'Channel number': 1,}\n",
-    "data_directory = '../../../tests/sample_data/neware'\n",
+    "info_dictionary = {\n",
+    "    \"Name\": \"Sample cell\",\n",
+    "    \"Chemistry\": \"NMC622\",\n",
+    "    \"Nominal Capacity [Ah]\": 0.04,\n",
+    "    \"Cycler number\": 1,\n",
+    "    \"Channel number\": 1,\n",
+    "}\n",
+    "data_directory = \"../../../tests/sample_data/neware\"\n",
     "\n",
     "# Create a cell object\n",
     "cell = pyprobe.Cell(info=info_dictionary)\n",
-    "cell.add_procedure(procedure_name='Sample',\n",
-    "                   folder_path = data_directory,\n",
-    "                   filename = 'sample_data_neware.parquet')\n",
-    "print(cell.procedure['Sample'].experiment_names)\n",
-    "\n"
+    "cell.add_procedure(\n",
+    "    procedure_name=\"Sample\",\n",
+    "    folder_path=data_directory,\n",
+    "    filename=\"sample_data_neware.parquet\",\n",
+    ")\n",
+    "print(cell.procedure[\"Sample\"].experiment_names)"
    ]
   },
   {
@@ -52,9 +56,13 @@
    "outputs": [],
    "source": [
     "fig, ax = plt.subplots()\n",
-    "cell.procedure['Sample'].experiment('Break-in Cycles').plot(x='Time [hr]', y='Voltage [V]', ax=ax, label='Break-in Cycles', color='blue')\n",
-    "cell.procedure['Sample'].experiment('Discharge Pulses').plot(x='Time [hr]', y='Voltage [V]', ax=ax, label='Discharge Pulses', color='red')\n",
-    "ax.set_ylabel('Voltage [V]')"
+    "cell.procedure[\"Sample\"].experiment(\"Break-in Cycles\").plot(\n",
+    "    x=\"Time [hr]\", y=\"Voltage [V]\", ax=ax, label=\"Break-in Cycles\", color=\"blue\"\n",
+    ")\n",
+    "cell.procedure[\"Sample\"].experiment(\"Discharge Pulses\").plot(\n",
+    "    x=\"Time [hr]\", y=\"Voltage [V]\", ax=ax, label=\"Discharge Pulses\", color=\"red\"\n",
+    ")\n",
+    "ax.set_ylabel(\"Voltage [V]\")"
    ]
   },
   {
@@ -72,14 +80,18 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "reference_charge = cell.procedure['Sample'].experiment('Break-in Cycles').charge(-1)\n",
-    "cell.procedure['Sample'].set_SOC(reference_charge=reference_charge)\n",
+    "reference_charge = cell.procedure[\"Sample\"].experiment(\"Break-in Cycles\").charge(-1)\n",
+    "cell.procedure[\"Sample\"].set_SOC(reference_charge=reference_charge)\n",
     "\n",
     "fig, ax = plt.subplots()\n",
-    "cell.procedure['Sample'].experiment('Break-in Cycles').plot(x='Time [hr]', y='SOC', ax=ax, label='Break-in Cycles', color='blue')\n",
-    "cell.procedure['Sample'].experiment('Discharge Pulses').plot(x='Time [hr]', y='SOC', ax=ax, label='Discharge Pulses', color='red')\n",
-    "ax.set_ylabel('SOC')\n",
-    "plt.legend(loc='lower left')"
+    "cell.procedure[\"Sample\"].experiment(\"Break-in Cycles\").plot(\n",
+    "    x=\"Time [hr]\", y=\"SOC\", ax=ax, label=\"Break-in Cycles\", color=\"blue\"\n",
+    ")\n",
+    "cell.procedure[\"Sample\"].experiment(\"Discharge Pulses\").plot(\n",
+    "    x=\"Time [hr]\", y=\"SOC\", ax=ax, label=\"Discharge Pulses\", color=\"red\"\n",
+    ")\n",
+    "ax.set_ylabel(\"SOC\")\n",
+    "plt.legend(loc=\"lower left\")"
    ]
   },
   {
@@ -95,12 +107,18 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "pulsing_experiment = cell.procedure['Sample'].experiment('Discharge Pulses')\n",
+    "pulsing_experiment = cell.procedure[\"Sample\"].experiment(\"Discharge Pulses\")\n",
     "\n",
     "fig, ax = plt.subplots()\n",
-    "pulsing_experiment.plot(x='Experiment Time [hr]', y='Voltage [V]', ax=ax, label='Discharge Pulses', color='red')\n",
-    "ax.set_ylabel('Voltage [V]')\n",
-    "plt.legend(loc='lower left')"
+    "pulsing_experiment.plot(\n",
+    "    x=\"Experiment Time [hr]\",\n",
+    "    y=\"Voltage [V]\",\n",
+    "    ax=ax,\n",
+    "    label=\"Discharge Pulses\",\n",
+    "    color=\"red\",\n",
+    ")\n",
+    "ax.set_ylabel(\"Voltage [V]\")\n",
+    "plt.legend(loc=\"lower left\")"
    ]
   },
   {
@@ -117,6 +135,7 @@
    "outputs": [],
    "source": [
     "from pyprobe.analysis import pulsing\n",
+    "\n",
     "pulse_object = pulsing.Pulsing(input_data=pulsing_experiment)"
    ]
   },
@@ -134,9 +153,17 @@
    "outputs": [],
    "source": [
     "fig, ax = plt.subplots()\n",
-    "pulse_object.input_data.plot(x='Experiment Time [hr]', y='Voltage [V]', label='Full Experiment', color='blue', ax=ax)\n",
-    "pulse_object.pulse(4).plot(x='Experiment Time [hr]', y='Voltage [V]', label='Pulse 5', color='red', ax=ax)\n",
-    "ax.set_ylabel('Voltage [V]')"
+    "pulse_object.input_data.plot(\n",
+    "    x=\"Experiment Time [hr]\",\n",
+    "    y=\"Voltage [V]\",\n",
+    "    label=\"Full Experiment\",\n",
+    "    color=\"blue\",\n",
+    "    ax=ax,\n",
+    ")\n",
+    "pulse_object.pulse(4).plot(\n",
+    "    x=\"Experiment Time [hr]\", y=\"Voltage [V]\", label=\"Pulse 5\", color=\"red\", ax=ax\n",
+    ")\n",
+    "ax.set_ylabel(\"Voltage [V]\")"
    ]
   },
   {
@@ -187,9 +214,9 @@
    "outputs": [],
    "source": [
     "fig, ax = plt.subplots()\n",
-    "pulse_resistances.plot(x='SOC', y='R0 [Ohms]', ax=ax, label='R0', color='blue')\n",
-    "pulse_resistances.plot(x='SOC', y='R_10s [Ohms]', ax=ax, label='R_10s', color='red')\n",
-    "ax.set_ylabel('Resistance [Ohms]')"
+    "pulse_resistances.plot(x=\"SOC\", y=\"R0 [Ohms]\", ax=ax, label=\"R0\", color=\"blue\")\n",
+    "pulse_resistances.plot(x=\"SOC\", y=\"R_10s [Ohms]\", ax=ax, label=\"R_10s\", color=\"red\")\n",
+    "ax.set_ylabel(\"Resistance [Ohms]\")"
    ]
   }
  ],