Lint setup fix

.github/workflows/test_and_deploy.yml

@@ -6,49 +6,28 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.8
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install .[dev]
-      - name: Lint
-        run: |
-          black ./ --check
-          flake8
+      - uses: brainglobe/actions/lint@v1
+
   test:
     needs: lint
+    name: ${{ matrix.os }} py${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: [3.7, 3.8]
-        exclude:
-          - os: macos-latest
-            python-version: 3.7
-          - os: windows-latest
-            python-version: 3.7
+        # Run all supported Python versions on linux
+        python-version: ["3.7", "3.8", "3.9"]
+        os: [ubuntu-latest]
+        # Include one windows and macos run
+        include:
+        - os: macos-latest
+          python-version: "3.9"
+        - os: windows-latest
+          python-version: "3.9"
+
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python
-        uses: actions/setup-python@v2
+      - uses: brainglobe/actions/test@v1
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install .[dev]
-      - name: Test
-        run: pytest
-      - name: Coveralls
-        env:
-            GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: |
-            pip install coveralls
-            coveralls --service=github
 
   deploy:
     needs: test
@@ -59,7 +38,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v1
         with:
-          python-version: "3.7"
+          python-version: "3.x"
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip

.gitignore

@@ -114,6 +114,7 @@ venv/
 ENV/
 env.bak/
 venv.bak/
+.envrc
 
 # Spyder project settings
 .spyderproject

.pre-commit-config.yaml

@@ -1,13 +1,36 @@
 repos:
--   repo: https://github.com/python/black
-    rev: 20.8b1
-    hooks:
-    - id: black
-      pass_filenames: true
--   repo: https://gitlab.com/pycqa/flake8
-    rev: 3.7.9
-    hooks:
-    - id: flake8
-      pass_filenames: true
-      # this seems to need to be here in addition to setup.cfg
-      exclude: __init__.py
+    - repo: https://github.com/pycqa/isort
+      rev: 5.10.1
+      hooks:
+          - id: isort
+            types: [text]
+            types_or: [python, cython]
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v4.3.0
+      hooks:
+          - id: check-docstring-first
+          - id: check-executables-have-shebangs
+          - id: check-merge-conflict
+          - id: check-toml
+          - id: end-of-file-fixer
+          - id: mixed-line-ending
+            args: [--fix=lf]
+          - id: requirements-txt-fixer
+          - id: trailing-whitespace
+            # 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
+      hooks:
+          - id: flake8
+    - repo: https://github.com/psf/black
+      rev: 22.3.0
+      hooks:
+          - id: black
+    - repo: https://github.com/pre-commit/mirrors-mypy
+      rev: v0.961
+      hooks:
+          - id: mypy
+            additional_dependencies:
+                - types-requests

LICENSE

@@ -26,4 +26,4 @@ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

@@ -14,7 +14,7 @@
 ![banner](https://github.com/brainglobe/bg-atlasapi/blob/master/docs/img/banner.jpeg)
 
 
-The brainglobe atlas API (BG-AtlasAPI) provides a common interface for programmers to download and process brain atlas data from multiple sources. 
+The brainglobe atlas API (BG-AtlasAPI) provides a common interface for programmers to download and process brain atlas data from multiple sources.
 
 ## Atlases available
 
@@ -44,7 +44,7 @@ To see a list of atlases use `bg_atlasapi.show_atlases`
 ```python
 from bg_atlasapi import show_atlases
 show_atlases()
-#                                Brainglobe Atlases                               
+#                                Brainglobe Atlases
 # ╭──────────────────────────────────┬────────────┬───────────────┬──────────────╮
 # │ Name                             │ Downloaded │ Local version │    Latest    │
 # │                                  │            │               │   version    │
@@ -61,7 +61,7 @@ show_atlases()
 
 **Using the atlases**
 
-All the features of each atlas can be accessed via the `BrainGlobeAtlas` class. 
+All the features of each atlas can be accessed via the `BrainGlobeAtlas` class.
 
 
 e.g. for the 25um Allen Mouse Brain Atlas:
@@ -119,7 +119,7 @@ pprint(VISp)
 #  'structure_id_path': [997, 8, 567, 688, 695, 315, 669, 385]}
 ```
 
-### Note on coordinates in `bg-atlasapi` 
+### Note on coordinates in `bg-atlasapi`
 Working with both image coordinates and cartesian coordinates in the same space can be confusing! In `bg-atlasapi`, the origin is always assumed to be in the upper left corner of the image (sectioning along the first dimension), the "ij" convention. This means that when plotting meshes and points using cartesian systems, you might encounter confusing behaviors coming from the fact that in cartesian plots one axis is inverted with respect to  ij coordinates (vertical axis increases going up, image row indexes increase going down). To make things as consistent as possible, in `bg-atlasapi` the 0 of the meshes coordinates is assumed to coincide with the 0 index of the images stack, and meshes coordinates increase following the direction stack indexes increase.
 To deal with transformations between your data space and `bg-atlasapi`, you might find helpful the [bg-space](https://github.com/brainglobe/bg-space) package.
 
@@ -134,4 +134,3 @@ Someone might have already asked a question you might have, so if you're not sur
 The BrainGlobe project is generously supported by the Sainsbury Wellcome Centre and the Institute of Neuroscience, Technical University of Munich, with funding from Wellcome, the Gatsby Charitable Foundation and the Munich Cluster for Systems Neurology - Synergy.
 
 <img src='https://brainglobe.info/images/logos_combined.png' width="550">
-

bg_atlasapi/bg_atlas.py

@@ -1,14 +1,13 @@
-from pathlib import Path
 import tarfile
+from io import StringIO
+from pathlib import Path
+
 import requests
 from rich import print as rprint
 from rich.console import Console
-from io import StringIO
-from bg_atlasapi.utils import _rich_atlas_metadata
-
-
-from bg_atlasapi import utils, config, core, descriptors
 
+from bg_atlasapi import config, core, descriptors, utils
+from bg_atlasapi.utils import _rich_atlas_metadata
 
 COMPRESSED_FILENAME = "atlas.tar.gz"
 

bg_atlasapi/cli.py

@@ -1,8 +1,9 @@
-from bg_atlasapi.list_atlases import show_atlases
-from bg_atlasapi.update_atlases import update_atlas, install_atlas
-from bg_atlasapi.config import cli_modify_config
 import click
 
+from bg_atlasapi.config import cli_modify_config
+from bg_atlasapi.list_atlases import show_atlases
+from bg_atlasapi.update_atlases import install_atlas, update_atlas
+
 
 @click.command()
 @click.argument("command")

bg_atlasapi/config.py

@@ -6,9 +6,10 @@
 BRAINGLOBE_CONFIG_DIR.
 """
 
-import os
 import configparser
+import os
 from pathlib import Path
+
 import click
 
 CONFIG_FILENAME = "bg_config.conf"

bg_atlasapi/core.py

@@ -1,21 +1,21 @@
-from pathlib import Path
-import pandas as pd
-import numpy as np
-from collections import UserDict
 import warnings
+from collections import UserDict
+from pathlib import Path
 
+import numpy as np
+import pandas as pd
 from bg_space import AnatomicalSpace
 
-from bg_atlasapi.utils import read_json, read_tiff
-from bg_atlasapi.structure_class import StructuresDict
 from bg_atlasapi.descriptors import (
-    METADATA_FILENAME,
-    STRUCTURES_FILENAME,
-    REFERENCE_FILENAME,
     ANNOTATION_FILENAME,
     HEMISPHERES_FILENAME,
     MESHES_DIRNAME,
+    METADATA_FILENAME,
+    REFERENCE_FILENAME,
+    STRUCTURES_FILENAME,
 )
+from bg_atlasapi.structure_class import StructuresDict
+from bg_atlasapi.utils import read_json, read_tiff
 
 
 class Atlas:

bg_atlasapi/list_atlases.py

@@ -1,14 +1,13 @@
-from rich.table import Table
-from rich import print as rprint
-from rich.panel import Panel
-
-from bg_atlasapi import config, utils, descriptors
-
-
 """
     Some functionality to list all available and downloaded brainglobe atlases
 """
 
+from rich import print as rprint
+from rich.panel import Panel
+from rich.table import Table
+
+from bg_atlasapi import config, descriptors, utils
+
 
 def get_downloaded_atlases():
     """Get a list of all the downloaded atlases and their version.

bg_atlasapi/structure_class.py

@@ -1,6 +1,7 @@
-import meshio as mio
-from collections import UserDict
 import warnings
+from collections import UserDict
+
+import meshio as mio
 
 from bg_atlasapi.structure_tree_util import get_structures_tree
 

bg_atlasapi/update_atlases.py

@@ -1,6 +1,7 @@
-from rich import print as rprint
 import shutil
 
+from rich import print as rprint
+
 from bg_atlasapi.bg_atlas import BrainGlobeAtlas, _version_str_from_tuple
 from bg_atlasapi.list_atlases import get_downloaded_atlases
 

bg_atlasapi/utils.py

@@ -1,19 +1,20 @@
+import configparser
 import json
-import tifffile
-import requests
 import logging
-import configparser
+
+import requests
+import tifffile
+from rich.panel import Panel
+from rich.pretty import Pretty
 from rich.progress import (
     BarColumn,
     DownloadColumn,
+    Progress,
     TextColumn,
-    TransferSpeedColumn,
     TimeRemainingColumn,
-    Progress,
+    TransferSpeedColumn,
 )
 from rich.table import Table
-from rich.panel import Panel
-from rich.pretty import Pretty
 from rich.text import Text
 
 logging.getLogger("urllib3").setLevel(logging.WARNING)

pyproject.toml

@@ -18,4 +18,8 @@ exclude = '''
     | examples
   )/
 )
-'''
+'''
+
+[tool.isort]
+multi_line_output = 3
+include_trailing_comma = true

pytest.ini

@@ -1,2 +1,2 @@
 [pytest]
-addopts = --cov=bg_atlasapi
+addopts = --cov=bg_atlasapi

requirements.txt

@@ -1,9 +1,9 @@
+bg-space>=0.5.0
+click
+meshio
 numpy
-tifffile
-treelib
 pandas
 requests
-meshio
-click
 rich>=9.0.0
-bg-space>=0.5.0
+tifffile
+treelib

requirements_dev.txt

@@ -1,10 +1,8 @@
-sphinx
-sphinx_rtd_theme
-pydoc-markdown
-pytest-cov
-pytest
-gitpython
-coverage
-pre-commit
 black
-flake8
+coverage
+flake8
+gitpython
+isort
+pre - commit
+pytest
+pytest - cov

setup.py

@@ -1,4 +1,4 @@
-from setuptools import setup, find_namespace_packages
+from setuptools import find_namespace_packages, setup
 
 with open("requirements.txt") as f:
     requirements = f.read().splitlines()

tests/conftest.py

@@ -1,9 +1,11 @@
-import pytest
-from bg_atlasapi.bg_atlas import BrainGlobeAtlas
-import tempfile
 import shutil
+import tempfile
 from pathlib import Path
 
+import pytest
+
+from bg_atlasapi.bg_atlas import BrainGlobeAtlas
+
 
 @pytest.fixture()
 def atlas():