Merge pull request #9 from NeurodataWithoutBorders/dev

CI tests via gh actions

.github/workflows/integration_tests.yml

@@ -0,0 +1,25 @@
+name: integration tests
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    name: integration tests
+    steps:
+    - uses: actions/checkout@v1
+    - name: Install
+      run: pip install -e .
+    - name: Install packages needed for tests
+      # pyright 1.1.336 can produce annoying errors
+      run: pip install pytest pytest-cov pyright==1.1.335
+    - name: Run pyright
+      run: cd lindi && pyright
+    - name: Run tests and collect coverage
+      run: pytest --cov lindi --cov-report=xml --cov-report=term tests/
+    # - uses: codecov/codecov-action@v3
+    #   with:
+    #     token: ${{ secrets.CODECOV_TOKEN }}
+    #     fail_ci_if_error: true
+    #     file: ./coverage.xml
+    #     flags: unittests

.github/workflows/linter_checks.yml

@@ -0,0 +1,22 @@
+name: linter-checks
+
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    name: Linter checks
+    steps:
+    - uses: actions/checkout@v1
+    - name: Install
+      run: pip install -e .
+    - name: Install packages needed for tests
+      # pyright 1.1.336 can produce annoying errors
+      run: pip install pyright==1.1.335 flake8
+    - name: Run flake8
+      run: cd lindi && flake8 --config ../.flake8
+    - name: Run pyright
+      run: cd lindi && pyright

.vscode/tasks/test.sh

@@ -2,5 +2,6 @@
 set -ex
 
 # black --check .
+flake8 .
 pyright
 pytest --cov=lindi --cov-report=xml --cov-report=term tests/

devel/old_tests/test_lindi_client.py

@@ -15,7 +15,9 @@ def test_lindi_client():
     for k in acquisition.keys():
         print(k)
 
-    x = client["acquisition/ElectricalSeriesAp"]["data"]
+    aa = client["acquisition/ElectricalSeriesAp"]
+    assert isinstance(aa, LindiGroup)
+    x = aa["data"]
     assert isinstance(x, LindiDataset)
 
     print(x.shape)

examples/example1.py

@@ -1,6 +1,7 @@
 import numpy as np
 import h5py
 import tempfile
+import lindi
 from lindi import LindiH5Store, LindiClient, LindiDataset
 from _check_equal import _check_equal
 
@@ -76,8 +77,9 @@ def example1():
             G1 = h5f["group"]
             G2 = client["group"]
             for k, v in G1.attrs.items():
-                assert k in G2.attrs
-                assert _check_equal(v, G2.attrs[k])
+                if not isinstance(G2, lindi.LindiReference):
+                    assert k in G2.attrs
+                    assert _check_equal(v, G2.attrs[k])
 
             print("Comparing root group")
             for k, v in h5f.attrs.items():

examples/try_pynwb.py

@@ -28,4 +28,4 @@ def try_pynwb():
 
 
 if __name__ == "__main__":
-    try_pynwb()
+    try_pynwb()

lindi/LindiClient/LindiAttributes.py

@@ -5,7 +5,7 @@
 class LindiAttributes:
     def __init__(self, *, _object: Union[zarr.Group, zarr.Array]):
         self._object = _object
-    
+
     def get(self, key, default=None):
         return self._object.attrs.get(key, default)
 

lindi/LindiClient/LindiClient.py

@@ -1,7 +1,7 @@
 from typing import Union
 import json
 import tempfile
-from altair import Literal
+from typing import Literal
 from fsspec import FSMap
 import zarr
 import urllib.request

lindi/LindiClient/__init__.py

@@ -2,3 +2,4 @@
 from .LindiGroup import LindiGroup  # noqa: F401
 from .LindiDataset import LindiDataset  # noqa: F401
 from .LindiAttributes import LindiAttributes  # noqa: F401
+from .LindiGroup import LindiReference  # noqa: F401

lindi/LindiH5Store/LindiH5Store.py

@@ -481,7 +481,7 @@ def _get_chunk_names_for_dataset(chunk_coords_shape: List[int]) -> List[str]:
         return names
 
 
-def _reformat_json(x: bytes):
+def _reformat_json(x: Union[bytes, None]) -> Union[bytes, None]:
     if x is None:
         return None
     return json.dumps(json.loads(x.decode("utf-8"))).encode("utf-8")

lindi/__init__.py

@@ -1,2 +1,2 @@
-from .LindiClient import LindiClient, LindiGroup, LindiDataset, LindiAttributes  # noqa: F401
+from .LindiClient import LindiClient, LindiGroup, LindiDataset, LindiAttributes, LindiReference  # noqa: F401
 from .LindiH5Store import LindiH5Store, LindiH5StoreOpts  # noqa: F401

pyproject.toml

@@ -11,6 +11,7 @@ numcodecs = "^0.12.1"
 zarr = "^2.16.1"
 h5py = "^3.10.0"
 remfile = "^0.1.9"
+fsspec = "^2023.12.2"
 
 [tool.poetry.dev-dependencies]
 pytest = "^7.4.4"