Add github actions testing/CI script.

Change to Tuple for 3.8 compatibility.
Add more return values to utils.
Add resolve to manifest test.
Add PurePosixPath to manifest path for flattening across platforms.

.github/workflows/abc_atlas_access_ci.yaml

@@ -0,0 +1,26 @@
+name: ci/ab_atlas_access
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+jobs:
+  test:
+    name: ${{ matrix.python-version }}, ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ "macos-latest", "windows-latest", "ubuntu-latest" ]
+        python-version: [ "3.8", "3.9", "3.10", "3.11" ]
+      fail-fast: false
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install
+        run: |
+          python -m pip install --upgrade pip
+          pip install .
+      - name: Test
+        run: pytest tests

src/abc_atlas_access/abc_atlas_cache/cloud_cache.py

@@ -1,6 +1,6 @@
 from typing import List, Optional, Union
 from abc import ABC, abstractmethod
-from pathlib import Path
+from pathlib import Path, PurePosixPath
 import json
 import warnings
 import tqdm
@@ -174,8 +174,12 @@ def list_all_downloaded_manifests(self) -> list:
         Return a list of all of the manifest files that have been
         downloaded for this dataset
         """
-        output = [self.manifest_prefix + str(x).split('releases/')[-1]
-                  for x in self.cache_dir.glob("releases/*/manifest.json")]
+        # Use PurePosixPath for to enforce consistent formatting across
+        # platforms.
+        output = [
+            self.manifest_prefix + str(PurePosixPath(x)).split('releases/')[-1]
+            for x in self.cache_dir.glob("releases/*/manifest.json")
+        ]
         output.sort()
         return output
 

tests/abc_atlas_cache/test_manifest.py

@@ -108,7 +108,7 @@ def test_metadata_file_attributes(self):
         assert file_obj.url == 'https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/metadata/Allen-CCF-2020/20230630/parcellation.csv'  # noqa: E501
         assert file_obj.version == '20230630'
         assert file_obj.file_size == 41197
-        assert file_obj.local_path == cache_path / 'metadata/Allen-CCF-2020/20230630/parcellation.csv'  # noqa: E501
+        assert file_obj.local_path == (cache_path / 'metadata/Allen-CCF-2020/20230630/parcellation.csv').resolve()  # noqa: E501
         assert file_obj.file_type == 'csv'
         assert file_obj.relative_path == 'metadata/Allen-CCF-2020/20230630/parcellation.csv'  # noqa: E501
         assert file_obj.file_hash == 'aea6f6925d7c84f4e5a2d022cbc9c7bb'
@@ -128,7 +128,7 @@ def test_image_volume_file_attributes(self):
         assert file_obj.url == 'https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/image_volumes/MERFISH-C57BL6J-638850-CCF/20230630/resampled_annotation_boundary.nii.gz'  # noqa: E501
         assert file_obj.version == '20230630'
         assert file_obj.file_size == 1548196
-        assert file_obj.local_path == cache_path / 'image_volumes/MERFISH-C57BL6J-638850-CCF/20230630/resampled_annotation_boundary.nii.gz'  # noqa: E501
+        assert file_obj.local_path == (cache_path / 'image_volumes/MERFISH-C57BL6J-638850-CCF/20230630/resampled_annotation_boundary.nii.gz').resolve()  # noqa: E501
         assert file_obj.file_type == 'nii.gz'
         assert file_obj.relative_path == 'image_volumes/MERFISH-C57BL6J-638850-CCF/20230630/resampled_annotation_boundary.nii.gz'  # noqa: E501
         assert file_obj.file_hash == "1ce4be21528fa6cbfb462a117552477d"
@@ -148,7 +148,7 @@ def test_expresion_matrix_file_attributes(self):
         assert file_obj.url == 'https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/expression_matrices/WMB-10Xv2/20230630/WMB-10Xv2-Isocortex-2-log2.h5ad'  # noqa: E501
         assert file_obj.version == '20230630'
         assert file_obj.file_size == 9444387082
-        assert file_obj.local_path == cache_path / 'expression_matrices/WMB-10Xv2/20230630/WMB-10Xv2-Isocortex-2-log2.h5ad'  # noqa: E501
+        assert file_obj.local_path == (cache_path / 'expression_matrices/WMB-10Xv2/20230630/WMB-10Xv2-Isocortex-2-log2.h5ad').resolve()  # noqa: E501
         assert file_obj.file_type == 'h5ad'
         assert file_obj.relative_path == 'expression_matrices/WMB-10Xv2/20230630/WMB-10Xv2-Isocortex-2-log2.h5ad'  # noqa: E501
         assert file_obj.file_hash == "6cf8b3556e625b090c196ff5bb5f6cdd"

tests/abc_atlas_cache/utils.py

@@ -1,4 +1,4 @@
-from typing import Optional
+from typing import Optional, Tuple
 import boto3
 import hashlib
 from moto import mock_aws
@@ -22,7 +22,7 @@ def create_manifest_dict(version: str,
                          metadata_file: str = 'metadata_file.csv',
                          test_directory: str = 'test_directory',
                          file_hash: Optional[str] = None,
-                         location: str = 'us-east-1') -> tuple[dict, str, str]:
+                         location: str = 'us-east-1') -> Tuple[dict, str, str]:
     """
     """
     if file_hash is None:
@@ -91,7 +91,7 @@ def create_manifest_dict(version: str,
 def add_file_to_manifest(
         file_attribute: CacheFileAttributes,
         manifest: dict
-):
+) -> dict:
     """
     """
     split_file = file_attribute.relative_path.split('/')
@@ -131,7 +131,7 @@ def add_file_to_manifest(
 def add_directory_to_manifest(
         file_attribute: CacheFileAttributes,
         manifest: dict
-):
+) -> dict:
     """
     """
     split_file = file_attribute.relative_path.split('/')
@@ -163,7 +163,7 @@ def add_directory_to_manifest(
     return manifest
 
 
-def hash_data(data):
+def hash_data(data) -> str:
     hasher = hashlib.md5()
     hasher.update(data)
     return hasher.hexdigest()