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Update to brainreg v1 compliance #255

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merged 3 commits into from
Nov 6, 2023
Merged

Update to brainreg v1 compliance #255

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072ed8b
Update to brainreg v1 compliance
willGraham01 Nov 3, 2023
4529b36
Drop py3.8, add py3.11
willGraham01 Nov 6, 2023
e17bb01
cellfinder-core (tensorflow <2.12) does not support py3.11
willGraham01 Nov 6, 2023
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2 changes: 1 addition & 1 deletion .github/workflows/test_and_deploy.yml
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Expand Up @@ -46,7 +46,7 @@ jobs:
- os: windows-latest
python-version: "3.9"
- os: ubuntu-latest
python-version: "3.8"
python-version: "3.10"
steps:
- uses: neuroinformatics-unit/actions/test@v2
with:
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2 changes: 1 addition & 1 deletion cellfinder/main.py
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Expand Up @@ -42,7 +42,7 @@

def main():
suppress_tf_logging(tf_suppress_log_messages)
from brainreg.main import main as register
from brainreg.core.main import main as register

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from cellfinder.tools import prep

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4 changes: 2 additions & 2 deletions cellfinder/tools/parser.py
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Expand Up @@ -16,8 +16,8 @@
check_positive_float,
check_positive_int,
)
from brainreg.cli import atlas_parse, geometry_parser, niftyreg_parse
from brainreg.cli import backend_parse as brainreg_backend_parse
from brainreg.core.cli import atlas_parse, geometry_parser, niftyreg_parse
from brainreg.core.cli import backend_parse as brainreg_backend_parse

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from cellfinder_core.download.cli import (
download_directory_parser,
model_parser,
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2 changes: 1 addition & 1 deletion cellfinder/tools/prep.py
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Expand Up @@ -14,7 +14,7 @@
from bg_atlasapi import BrainGlobeAtlas
from brainglobe_utils.general.exceptions import CommandLineInputError
from brainglobe_utils.general.system import ensure_directory_exists
from brainreg.paths import Paths as BrainRegPaths
from brainreg.core.paths import Paths as BrainRegPaths

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from fancylog import fancylog

import cellfinder as program_for_log
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4 changes: 2 additions & 2 deletions pyproject.toml
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Expand Up @@ -3,7 +3,7 @@ name = "cellfinder"
description = "Automated 3D cell detection and registration of whole-brain images"
readme = "README.md"
license = { file = "LICENSE" }
requires-python = ">=3.8"
requires-python = ">=3.9"
authors = [
{ name = "Adam Tyson", email = "[email protected]" },
{ name = "Christian Niedworok" },
Expand All @@ -22,7 +22,7 @@ classifiers = [
"Intended Audience :: Science/Research",
]
dependencies = [
"brainreg",
"brainreg>=1.0.0",
"cellfinder-core>=0.2.4",
"configobj",
"fancylog>=0.0.7",
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3 changes: 1 addition & 2 deletions tox.ini
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@@ -1,10 +1,9 @@
# For more information about tox, see https://tox.readthedocs.io/en/latest/
[tox]
envlist = py{38,39,310}-{coredev}
envlist = py{39,310}-{coredev}

[gh-actions]
python =
3.8: py38
3.9: py39
3.10: py310

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