Skip to content
Snippets Groups Projects
Unverified Commit fa584992 authored by Eleftherios Zisis's avatar Eleftherios Zisis Committed by GitHub
Browse files

Add python3.13 & remove EOL python3.8 (#1132)

parent f1304bbe
No related branches found
No related tags found
No related merge requests found
...@@ -12,7 +12,7 @@ jobs: ...@@ -12,7 +12,7 @@ jobs:
runs-on: ubuntu-latest runs-on: ubuntu-latest
strategy: strategy:
matrix: matrix:
python-version: ['3.8', '3.9', '3.10', '3.11', '3.12'] python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
steps: steps:
- uses: actions/checkout@v4 - uses: actions/checkout@v4
......
...@@ -32,7 +32,7 @@ Examples: ...@@ -32,7 +32,7 @@ Examples:
Load a morphology Load a morphology
>>> import neurom as nm >>> import neurom as nm
>>> m = nm.load_morphology('some/data/path/morph_file.swc') >>> m = nm.load_morphology('tests/data/swc/Neuron.swc')
Obtain some morphometrics using the get function Obtain some morphometrics using the get function
...@@ -43,16 +43,15 @@ Examples: ...@@ -43,16 +43,15 @@ Examples:
files it finds and returns a list of morphologies files it finds and returns a list of morphologies
>>> import numpy as np # For mean value calculation >>> import numpy as np # For mean value calculation
>>> pop = nm.load_morphologies('some/data/directory') >>> pop = nm.load_morphologies('tests/data/valid_set')
>>> for m in pop: >>> mean_section_lengths = [np.mean(nm.get('section_lengths', m)) for m in pop]
... print 'mean section length', np.mean(nm.get('section_lengths', m))
Apply a function to a selection of neurites in a morphology or morphology population. Apply a function to a selection of neurites in a morphology or morphology population.
This example gets the number of points in each axon in a morphology population This example gets the number of points in each axon in a morphology population
>>> import neurom as nm >>> import neurom as nm
>>> filter = lambda n : n.type == nm.AXON >>> filter = lambda n : n.type == nm.AXON
>>> mapping = lambda n : len(n.points) >>> mapping = lambda n, section_type : len(n.points)
>>> n_points = [n for n in nm.iter_neurites(pop, mapping, filter)] >>> n_points = [n for n in nm.iter_neurites(pop, mapping, filter)]
""" """
from importlib.metadata import version from importlib.metadata import version
......
...@@ -9,7 +9,7 @@ build-backend = "setuptools.build_meta" ...@@ -9,7 +9,7 @@ build-backend = "setuptools.build_meta"
name = "neurom" name = "neurom"
description = "NeuroM: a light-weight neuron morphology analysis package" description = "NeuroM: a light-weight neuron morphology analysis package"
readme = "README.md" readme = "README.md"
requires-python = ">=3.8" requires-python = ">=3.9"
license = { file = "LICENSE.txt" } license = { file = "LICENSE.txt" }
authors = [ authors = [
{ name = "Blue Brain Project, EPFL" }, { name = "Blue Brain Project, EPFL" },
...@@ -19,7 +19,6 @@ classifiers = [ ...@@ -19,7 +19,6 @@ classifiers = [
"Intended Audience :: Education", "Intended Audience :: Education",
"Intended Audience :: Science/Research", "Intended Audience :: Science/Research",
"Programming Language :: Python", "Programming Language :: Python",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.11",
...@@ -78,10 +77,11 @@ testpaths = [ ...@@ -78,10 +77,11 @@ testpaths = [
[tool.black] [tool.black]
line-length = 100 line-length = 100
target-version = [ target-version = [
'py38',
'py39', 'py39',
'py310', 'py310',
'py311', 'py311',
'py312',
'py313',
] ]
skip-string-normalization = true skip-string-normalization = true
include = 'neurom\/.*\.py$|tests\/.*\.py$|doc\/source\/conf\.py$|setup\.py$|examples\/.*\.py$' include = 'neurom\/.*\.py$|tests\/.*\.py$|doc\/source\/conf\.py$|setup\.py$|examples\/.*\.py$'
......
...@@ -10,7 +10,7 @@ envlist = ...@@ -10,7 +10,7 @@ envlist =
coverage coverage
tutorial tutorial
check-packaging check-packaging
py{38,39,310,311,312,313} py{39,310,311,312,313}
[testenv] [testenv]
deps = deps =
...@@ -97,9 +97,8 @@ convention = google ...@@ -97,9 +97,8 @@ convention = google
[gh-actions] [gh-actions]
python = python =
3.8: py38, lint 3.9: py39, lint
3.9: py39, docs
3.10: py310, tutorial 3.10: py310, tutorial
3.11: py311, check-packaging 3.11: py311, check-packaging
3.12: py312 3.12: py312, docs
3.13: py313 3.13: py313
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment