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BlueBrain
NeuroM
Commits
fa584992
Unverified
Commit
fa584992
authored
9 months ago
by
Eleftherios Zisis
Committed by
GitHub
9 months ago
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Add python3.13 & remove EOL python3.8 (#1132)
parent
f1304bbe
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4 changed files
.github/workflows/run-tox.yml
+1
-1
1 addition, 1 deletion
.github/workflows/run-tox.yml
neurom/__init__.py
+4
-5
4 additions, 5 deletions
neurom/__init__.py
pyproject.toml
+3
-3
3 additions, 3 deletions
pyproject.toml
tox.ini
+3
-4
3 additions, 4 deletions
tox.ini
with
11 additions
and
13 deletions
.github/workflows/run-tox.yml
+
1
−
1
View file @
fa584992
...
@@ -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
...
...
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Click to expand it.
neurom/__init__.py
+
4
−
5
View file @
fa584992
...
@@ -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
...
...
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pyproject.toml
+
3
−
3
View file @
fa584992
...
@@ -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$|examples\/.*\.py$'
...
...
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tox.ini
+
3
−
4
View file @
fa584992
...
@@ -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
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