Chore: Fix lint

.copier-answers.yml

@@ -1,6 +1,6 @@
 # Changes here will be overwritten by Copier
 
-_commit: 0.1.59
+_commit: 0.1.63
 _src_path: git@bbpgitlab.epfl.ch:neuromath/python-template.git
 author_email: bbp-ou-cells@groupes.epfl.ch
 author_name: bbp-ou-cells

.pre-commit-config.yaml

@@ -1,8 +1,6 @@
-default_language_version:
-  python: python3.9
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.6.0
     hooks:
       - id: check-added-large-files
       - id: check-case-conflict
@@ -13,22 +11,22 @@ repos:
       - id: end-of-file-fixer
       - id: trailing-whitespace
   - repo: https://github.com/alessandrojcm/commitlint-pre-commit-hook
-    rev: v9.5.0
+    rev: v9.17.0
     hooks:
         - id: commitlint
           stages:
             - commit-msg
           additional_dependencies: ['conventional-changelog-conventionalcommits']
   - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
   - repo: https://github.com/psf/black
-    rev: 23.9.1
+    rev: 24.8.0
     hooks:
       - id: black
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
+    rev: v2.3.0
     hooks:
       - id: codespell
         args: ["-x", ".codespellignorelines"]
@@ -38,6 +36,6 @@ repos:
       - id: pydocstyle
         additional_dependencies: ["tomli"]
   - repo: https://github.com/PyCQA/flake8
-    rev: 6.1.0
+    rev: 7.1.1
     hooks:
       - id: flake8

examples/parameter_update/compare.py

@@ -1,4 +1,5 @@
 """Example of comparison."""
+
 import json
 
 import pandas as pd

setup.py

@@ -1,4 +1,5 @@
 """Setup for the synthesis-workflow package."""
+
 import importlib
 from pathlib import Path
 

src/morphval/__init__.py

@@ -1,4 +1,5 @@
 """Morphology Statistical Validation Package."""
+
 import pkg_resources
 
 __version__ = pkg_resources.get_distribution("synthesis_workflow").version

src/morphval/common.py

@@ -1,4 +1,5 @@
 """Private helper functions of the validation module."""
+
 import contextlib
 import json
 import os

src/morphval/validation.py

@@ -1,4 +1,5 @@
 """Statistical validation tools."""
+
 import copy
 from collections import namedtuple
 from decimal import Decimal

src/morphval/validation_main.py

@@ -1,4 +1,5 @@
 """Main module of MorphVal package."""
+
 import collections
 import os
 import time

src/synthesis_workflow/__init__.py

@@ -1,4 +1,5 @@
 """Workflow for neuronal synthesis validation."""
+
 import pkg_resources
 from morphio import SectionType  # noqa
 

src/synthesis_workflow/circuit.py

@@ -1,4 +1,5 @@
 """Functions for slicing mvd3 circuit files to place specific cells only."""
+
 import logging
 from pathlib import Path
 

src/synthesis_workflow/extra/insitu_validation.py

@@ -1,4 +1,5 @@
 """In-situ validation functions for synthesis in atlas."""
+
 from pathlib import Path
 
 import matplotlib

src/synthesis_workflow/extra/make_map.py

@@ -1,4 +1,5 @@
 """Make a atlas map from scatter data."""
+
 from copy import copy
 
 import matplotlib

src/synthesis_workflow/fit_utils.py

@@ -1,4 +1,5 @@
 """Some functions used to fit path distances with depth."""
+
 from typing import Sequence
 from typing import Tuple
 

src/synthesis_workflow/morphology_combos/__init__.py

@@ -1,2 +1,3 @@
 """Module to create and modify morphologie combos with dataframes."""
+
 from .create_me_combos import *  # noqa

src/synthesis_workflow/morphology_combos/create_me_combos.py

@@ -1,4 +1,5 @@
 """Functions to create and modify combos dataframe."""
+
 import json
 import logging
 from pathlib import Path

src/synthesis_workflow/synthesis.py

@@ -1,4 +1,5 @@
 """Functions for synthesis to be used by luigi tasks."""
+
 import logging
 import os
 import re

src/synthesis_workflow/tasks/circuit.py

@@ -1,4 +1,5 @@
 """Luigi tasks for circuit and atlas processings."""
+
 import pickle
 from copy import deepcopy
 from functools import partial
@@ -243,9 +244,11 @@ def run(self):
             mtype_taxonomy_path,
             CircuitConfig().atlas_path,
             self.density_factor,
-            mask=self.input()["boundary"].path
-            if CreateBoundaryMask().boundary_thickness > 0
-            else None,
+            mask=(
+                self.input()["boundary"].path
+                if CreateBoundaryMask().boundary_thickness > 0
+                else None
+            ),
             seed=self.seed,
             region=CircuitConfig().region,
         )

src/synthesis_workflow/tasks/cli.py

@@ -1,4 +1,5 @@
 """CLI for validation workflows."""
+
 import argparse
 import inspect
 import logging

src/synthesis_workflow/tasks/config.py

@@ -1,4 +1,5 @@
 """Configurations for luigi tasks."""
+
 import logging
 import shutil
 import warnings

src/synthesis_workflow/tasks/diametrizer.py

@@ -1,4 +1,5 @@
 """Luigi tasks to diametrize cells."""
+
 import logging
 import os
 import sys

src/synthesis_workflow/tasks/synthesis.py

@@ -1,4 +1,5 @@
 """Luigi tasks for morphology synthesis."""
+
 import json
 import logging
 from pathlib import Path

src/synthesis_workflow/tasks/vacuum_synthesis.py

@@ -1,4 +1,5 @@
 """Luigi tasks for morphology synthesis in vacuum."""
+
 import json
 import logging
 
@@ -104,7 +105,7 @@ class PlotVacuumMorphologies(WorkflowTask):
     """Plot morphologies to obtain annotations.
 
     Attributes:
-        vacuum_synth_morphology_path (str): Column name to use from the morphlogy DataFrame.
+        vacuum_synth_morphology_path (str): Column name to use from the morphology DataFrame.
     """
 
     pdf_filename = PathParameter(

src/synthesis_workflow/tasks/validation.py

@@ -1,4 +1,5 @@
 """Luigi tasks for validation of synthesis."""
+
 import json
 import logging
 import pickle

src/synthesis_workflow/tasks/workflows.py

@@ -1,4 +1,5 @@
 """Luigi tasks for validation workflows."""
+
 import configparser
 import json
 import pickle
@@ -70,9 +71,11 @@ def run(self):
         if sample is None:
             sample = SliceCircuit().n_cells
         config["cells"] = {
-            "mtypes": json.dumps(list(SynthesisConfig().mtypes))
-            if SynthesisConfig().mtypes is not None
-            else "",
+            "mtypes": (
+                json.dumps(list(SynthesisConfig().mtypes))
+                if SynthesisConfig().mtypes is not None
+                else ""
+            ),
             "sample": str(sample),
         }
         config["planes"] = {

src/synthesis_workflow/tools.py

@@ -1,4 +1,5 @@
 """Some tool functions used in synthesis."""
+
 import glob
 import json
 import logging

src/synthesis_workflow/utils.py

@@ -1,4 +1,5 @@
 """Utils functions."""
+
 import json
 import logging
 from pathlib import Path

src/synthesis_workflow/vacuum_synthesis.py

@@ -1,4 +1,5 @@
 """Functions for synthesis in vacuum to be used by luigi tasks."""
+
 import itertools
 
 import matplotlib.pyplot as plt

src/synthesis_workflow/validation.py

@@ -1,4 +1,5 @@
 """Functions for validation of synthesis to be used by luigi tasks."""
+
 # pylint: disable=too-many-lines
 import itertools
 import json
@@ -451,7 +452,7 @@ def _plot_layers(x_pos, atlas, ax):
             layer_bounds[:, 0],
             layer_bounds[:, 1],
             alpha=0.5,
-            label=f"layer {layer+1}",
+            label=f"layer {layer + 1}",
         )
 
 

src/version.py

@@ -1,2 +1,3 @@
 """Package version."""
+
 VERSION = "1.2.0.dev1"

tests/__init__.py

@@ -1,4 +1,5 @@
 """Tests suite for the synthesis-workflow package."""
+
 from configparser import ConfigParser
 
 

tests/conftest.py

@@ -1,4 +1,5 @@
 """Configuration for the pytest test suite."""
+
 # pylint: disable=redefined-outer-name
 import json
 import os

tests/morphval/test_validation.py

@@ -1,4 +1,5 @@
 """Test the `morphval.validation` module."""
+
 from copy import deepcopy
 
 import pytest

tests/morphval/test_validation_main.py

@@ -1,4 +1,5 @@
 """Tests for the morphval package."""
+
 from pathlib import Path
 
 import pkg_resources

tests/test_O1_workflow.py

@@ -1,4 +1,5 @@
 """Tests for workflows module."""
+
 import luigi
 import numpy as np
 import pytest

tests/test_cli.py

@@ -1,4 +1,5 @@
 """Tests for the synthesis_workflow.cli module."""
+
 import re
 
 from synthesis_workflow.tasks import cli

tests/test_fit_utils.py

@@ -1,4 +1,5 @@
 """Tests for the synthesis_workflow.fit_utils module."""
+
 # pylint: disable=redefined-outer-name
 import numpy as np
 import pytest

tests/test_utils.py

@@ -1,4 +1,5 @@
 """Tests for utils module."""
+
 import json
 
 import pandas as pd

tests/test_vacuum_workflow.py

@@ -1,4 +1,5 @@
 """Tests for workflows module."""
+
 import shutil
 
 import luigi

tox.ini

@@ -21,12 +21,7 @@ setenv =
     COVERAGE_FILE = {env:COVERAGE_FILE:.coverage-{envname}}
     PIP_INDEX_URL = {env:PIP_INDEX_URL:https://bbpteam.epfl.ch/repository/devpi/simple}
     PIP_EXTRA_INDEX_URL = {env:PIP_EXTRA_INDEX_URL:https://pypi.python.org/simple}
-deps =
-    min_versions: Requirements-Builder
 commands =
-    min_versions: requirements-builder --level=min --extras=test -o {envtmpdir}/requirements_min.txt setup.py
-    min_versions: pip install -r {envtmpdir}/requirements_min.txt
-    min_versions: pip freeze
     pytest \
         -n {env:PYTEST_NPROCS:3} \
         --dist loadgroup \
@@ -72,6 +67,12 @@ commands =
 
 [testenv:min_versions]
 basepython = python3.9
+deps =
+    Requirements-Builder
+commands_pre =
+    requirements-builder --level=min --extras=test -o {envtmpdir}/requirements_min.txt setup.py
+    pip install -r {envtmpdir}/requirements_min.txt
+    pip freeze
 
 [testenv:lint]
 basepython = python3.9