CI: Bump pre-commit hooks and fix isort installation failure

.flake8

@@ -1,5 +1,7 @@
 [flake8]
 ignore =
-	E203,  # E203: whitespace before ':'
-	W503  # W503: line break before binary operator
+	# E203: whitespace before ':'
+	E203,
+	# W503: line break before binary operator
+	W503
 max-line-length = 100

.pre-commit-config.yaml

@@ -2,7 +2,7 @@ default_language_version:
   python: python3.8
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v4.4.0
     hooks:
       - id: check-added-large-files
       - id: check-case-conflict
@@ -13,31 +13,31 @@ repos:
       - id: end-of-file-fixer
       - id: trailing-whitespace
   - repo: https://github.com/alessandrojcm/commitlint-pre-commit-hook
-    rev: v9.0.0
+    rev: v9.4.0
     hooks:
         - id: commitlint
           stages:
             - commit-msg
           additional_dependencies: ['conventional-changelog-conventionalcommits']
   - repo: https://github.com/pycqa/isort
-    rev: 5.10.1
+    rev: 5.12.0
     hooks:
       - id: isort
   - repo: https://github.com/psf/black
-    rev: 22.6.0
+    rev: 22.12.0
     hooks:
       - id: black
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.1.0
+    rev: v2.2.2
     hooks:
       - id: codespell
         args: ["-x", ".codespellignorelines"]
   - repo: https://github.com/PyCQA/pydocstyle
-    rev: 6.1.1
+    rev: 6.3.0
     hooks:
       - id: pydocstyle
-        additional_dependencies: ["toml"]
+        additional_dependencies: ["tomli"]
   - repo: https://github.com/PyCQA/flake8
-    rev: 5.0.4
+    rev: 6.0.0
     hooks:
       - id: flake8

docs/source/synthesis_methodology.rst

@@ -13,7 +13,7 @@ Basically, the workflow used in BBP to generate the cell morphologies is the fol
 
 * collect biological data,
 * calibrate the models on these data,
-* synthetized the cells according to the calibration parameters.
+* synthesized the cells according to the calibration parameters.
 
 This package aims at running the calibration process, then calling each part of the
 production workflow on a small use case and computing some validation metrics. Once the

src/synthesis_workflow/validation.py

@@ -698,7 +698,7 @@ def plot_path_distance_fits(
             # Plot points
             plt.scatter(x, y, c="red", label="Outliers")
             plt.scatter(x_clean, y_clean, c="blue", label="Clean points")
-            plt.scatter(x_synth, y_synth, c="green", label="Synthetized points")
+            plt.scatter(x_synth, y_synth, c="green", label="Synthesized points")
 
             try:
                 # Plot fit function