Add new atlas (#133)

* Add new atlas * update pre-commit * require explicit use of Optional * update tox * update tox
brainglobe · Jan 6, 2023 · dbecd16 · dbecd16
1 parent 5835887
commit dbecd16
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Showing 5 changed files with 14 additions and 28 deletions.
diff --git a/.pre-commit-config.yaml b/.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://github.com/psf/black
-      rev: 22.3.0
+      rev: 22.10.0
       hooks:
           - id: black
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v0.961
+      rev: v0.990
       hooks:
           - id: mypy
             additional_dependencies:
+                - types-setuptools
                 - types-requests
diff --git a/README.md b/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:

diff --git a/bg_atlasapi/utils.py b/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.
 

diff --git a/tests/test_list_atlases.py b/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")

diff --git a/tox.ini b/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