Add new atlas

.pre-commit-config.yaml

@@ -20,17 +20,18 @@ repos:
  # bump2version produces whitespace in setup.cfg, so exclude to
  # not inferfere with versioning
  exclude: setup.cfg
- - repo: https://gitlab.com/pycqa/flake8
- rev: 3.9.2
+ - repo: https://github.com/pycqa/flake8
+ rev: 5.0.4
  hooks:
  - id: flake8
  - repo: https:/psf/black
- rev: 22.3.0
+ rev: 22.10.0
  hooks:
  - id: black
  - repo: https:/pre-commit/mirrors-mypy
- rev: v0.961
+ rev: v0.990
  hooks:
  - id: mypy
  additional_dependencies:
+ - types-setuptools
  - types-requests

README.md

@@ -36,6 +36,7 @@ A number of atlases are in development, but those available currently are:
 * [Waxholm Space atlas of the Sprague Dawley rat brain](https://doi.org/10.1016/j.neuroimage.2014.04.001) at 39 micron resolution
 * [3D Edge-Aware Refined Atlases Derived from the Allen Developing Mouse Brain Atlases](https://doi.org/10.7554/eLife.61408) (E13, E15, E18, P4, P14, P28 & P56)
 * [Princeton Mouse Brain Atlas](https://brainmaps.princeton.edu/2020/09/princeton-mouse-brain-atlas-links) at 20 micron resolution
+* [Kim Lab Developmental CCF (P56)](https://data.mendeley.com/datasets/2svx788ddf/1) at 10 micron resolution with 8 reference images - STP, LSFM (iDISCO) and MRI (a0, adc, dwo, fa, MTR, T2)
 
 ## Installation
 BG-AtlasAPI works with Python >3.6, and can be installed from PyPI with:

bg_atlasapi/utils.py

@@ -1,7 +1,7 @@
 import configparser
 import json
 import logging
-from typing import Callable
+from typing import Callable, Optional
 
 import requests
 import tifffile
@@ -130,7 +130,9 @@ def check_internet_connection(
 
 
 def retrieve_over_http(
- url, output_file_path, fn_update: Callable[[int, int], None] = None
+ url,
+ output_file_path,
+ fn_update: Optional[Callable[[int, int], None]] = None,
 ):
  """Download file from remote location, with progress bar.
 

tests/test_list_atlases.py

@@ -12,9 +12,6 @@ def test_get_downloaded_atlases():
  # Check that example is listed:
  assert "example_mouse_100um" in available_atlases
 
- # Check that all listed ar valid atlas names:
- assert all([len(a.split("_")) == 3 for a in available_atlases])
-
 
 def test_get_local_atlas_version():
  v = get_local_atlas_version("example_mouse_100um")

tox.ini

@@ -1,30 +1,15 @@
 # For more information about tox, see https://tox.readthedocs.io/en/latest/
 [tox]
-envlist = py{38,39,310}-{linux,windows}
+envlist = py{37,38,39,310}
 
 [gh-actions]
 python =
+ 3.7: py37
  3.8: py38
  3.9: py39
  3.10: py310
 
-[gh-actions:env]
-PLATFORM =
- ubuntu-latest: linux
- windows-latest: windows
-
 [testenv]
-platform =
- macos: darwin
- linux: linux
- windows: win32
-passenv =
- CI
- GITHUB_ACTIONS
- DISPLAY XAUTHORITY
- NUMPY_EXPERIMENTAL_ARRAY_FUNCTION
- PYVISTA_OFF_SCREEN
-deps =
- pytest # https://docs.pytest.org/en/latest/contents.html
- pytest-cov # https://pytest-cov.readthedocs.io/en/latest/
+extras =
+ dev
 commands = pytest -v --color=yes --cov=bg_atlasapi --cov-report=xml