From fa584992338592607472c7a235ce6f23aab1e3d0 Mon Sep 17 00:00:00 2001
From: Eleftherios Zisis <eleftherios.zisis@epfl.ch>
Date: Mon, 14 Oct 2024 14:38:26 +0200
Subject: [PATCH] Add python3.13 & remove EOL python3.8 (#1132)

---
 .github/workflows/run-tox.yml | 2 +-
 neurom/__init__.py            | 9 ++++-----
 pyproject.toml                | 6 +++---
 tox.ini                       | 7 +++----
 4 files changed, 11 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/run-tox.yml b/.github/workflows/run-tox.yml
index 5dfcdaaa..cd5864bb 100644
--- a/.github/workflows/run-tox.yml
+++ b/.github/workflows/run-tox.yml
@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       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:
     - uses: actions/checkout@v4
diff --git a/neurom/__init__.py b/neurom/__init__.py
index 4a8c5242..4a4e2f37 100644
--- a/neurom/__init__.py
+++ b/neurom/__init__.py
@@ -32,7 +32,7 @@
     Load a morphology
 
     >>> 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
 
@@ -43,16 +43,15 @@
     files it finds and returns a list of morphologies
 
     >>> import numpy as np  # For mean value calculation
-    >>> pop = nm.load_morphologies('some/data/directory')
-    >>> for m in pop:
-    ...     print 'mean section length', np.mean(nm.get('section_lengths', m))
+    >>> pop = nm.load_morphologies('tests/data/valid_set')
+    >>> mean_section_lengths = [np.mean(nm.get('section_lengths', m)) for m in pop]
 
     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
 
     >>> import neurom as nm
     >>> 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)]
 """
 from importlib.metadata import version
diff --git a/pyproject.toml b/pyproject.toml
index 6deabda7..2d266887 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -9,7 +9,7 @@ build-backend = "setuptools.build_meta"
 name = "neurom"
 description = "NeuroM: a light-weight neuron morphology analysis package"
 readme = "README.md"
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 license = { file = "LICENSE.txt" }
 authors = [
     { name = "Blue Brain Project, EPFL" },
@@ -19,7 +19,6 @@ classifiers = [
     "Intended Audience :: Education",
     "Intended Audience :: Science/Research",
     "Programming Language :: Python",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
@@ -78,10 +77,11 @@ testpaths = [
 [tool.black]
 line-length = 100
 target-version = [
-    'py38',
     'py39',
     'py310',
     'py311',
+    'py312',
+    'py313',
 ]
 skip-string-normalization = true
 include = 'neurom\/.*\.py$|tests\/.*\.py$|doc\/source\/conf\.py$|setup\.py$|examples\/.*\.py$'
diff --git a/tox.ini b/tox.ini
index 89c07dd9..8d569dae 100644
--- a/tox.ini
+++ b/tox.ini
@@ -10,7 +10,7 @@ envlist =
     coverage
     tutorial
     check-packaging
-    py{38,39,310,311,312,313}
+    py{39,310,311,312,313}
 
 [testenv]
 deps =
@@ -97,9 +97,8 @@ convention = google
 
 [gh-actions]
 python =
-  3.8: py38, lint
-  3.9: py39, docs
+  3.9: py39, lint
   3.10: py310, tutorial
   3.11: py311, check-packaging
-  3.12: py312
+  3.12: py312, docs
   3.13: py313