Support dependencies (#20)

* * add test_batch.py
* * add print
* add 1-D boolean indexing support
* add support for zarr
* bug fix test_dsetview.py
* optional zarr dependency
* include python versions in pythonapp.yml
* update MANIFEST.in
* add requirements-dev.txt
* add coverage report
* Update pythonapp.yml

.github/workflows/workflow.yml

@@ -0,0 +1,38 @@
+name: Python application
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7, 3.8]
+
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt -r requirements-dev.txt
+    - name: Install lazy_ops
+      run: |
+        pip install -e .
+    - name: Generate coverage report
+      run: |
+        pip install pytest
+        pip install pytest-cov
+        pytest --cov=./ --cov-report=xml
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v1
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        file: ./coverage.xml
+        flags: unittests
+        name: codecov-umbrella
+        yml: ./codecov.yml

MANIFEST.in

@@ -0,0 +1 @@
+include requirements.txt requirements-dev.txt

README.md

@@ -1,6 +1,6 @@
 # lazy_ops
 
-<strong>Lazy transposing and slicing of h5py Datasets</strong>
+<strong>Lazy transposing and slicing of h5py Datasets and zarr arrays</strong>
 
 ## Installation
 

lazy_ops/__init__.py

@@ -1,2 +1,4 @@
 from lazy_ops.lazy_loading import DatasetView
 from lazy_ops.lazy_loading import lazy_transpose
+
+from .version import version as __version__

lazy_ops/lazy_loading.py

@@ -28,11 +28,11 @@
 from abc import ABCMeta, abstractmethod
 from typing import Union
 import h5py
-import zarr
+installed_dataset_types = h5py.Dataset
 
 class DatasetView(metaclass=ABCMeta):
 
-    def __new__(cls, dataset: Union[h5py.Dataset,zarr.core.Array] = None, slice_index=(np.index_exp[:],()), axis_order=None):
+    def __new__(cls, dataset: installed_dataset_types = None, slice_index=(np.index_exp[:],()), axis_order=None):
         """
         Args:
           dataset:     the underlying dataset
@@ -43,16 +43,17 @@ def __new__(cls, dataset: Union[h5py.Dataset,zarr.core.Array] = None, slice_inde
         """
         if cls == DatasetView:
             if isinstance(dataset,h5py.Dataset):
-                dsetview = DatasetViewh5py(dataset=dataset)
-            elif isinstance(dataset,zarr.core.Array):
-                dsetview = DatasetViewzarr(dataset=dataset)
-            else:
-                raise TypeError("DatasetView requires either an h5py dataset or a zarr array as first argument")
-            return dsetview
+                return DatasetViewh5py(dataset=dataset)
+            elif HAVE_ZARR:
+                if isinstance(dataset,zarr.core.Array):
+                    return DatasetViewzarr(dataset=dataset)
+            elif str(z1).find("zarr") != -1:
+                raise TypeError("To use DatasetView with a zarr array install zarr: \n pip install zarr\n")
+            raise TypeError("DatasetView requires either an h5py dataset or a zarr array as first argument")
         else:
             return super().__new__(cls)
 
-    def __init__(self, dataset: Union[h5py.Dataset,zarr.core.Array] = None, slice_index=(np.index_exp[:],()), axis_order=None):
+    def __init__(self, dataset: installed_dataset_types = None, slice_index=(np.index_exp[:],()), axis_order=None):
         """
         Args:
           dataset:     the underlying dataset
@@ -364,7 +365,7 @@ def read_direct(self, dest, source_sel=None, dest_sel=None):
         self.dataset.read_direct(reversed_dest, source_sel=reversed_slice_key, dest_sel=reversed_dest_sel)
         np.copyto(dest, reversed_dest.transpose(axis_order_read))
 
-def lazy_transpose(dset: Union[h5py.Dataset,zarr.core.Array], axes=None):
+def lazy_transpose(dset: installed_dataset_types, axes=None):
     """ Array lazy transposition, not passing axis argument reverses the order of dimensions
     Args:
       dset: h5py dataset
@@ -385,11 +386,11 @@ def __new__(cls,dataset):
         h5py.Dataset.__init__(_self, dataset.id)
         return _self
 
-class DatasetViewzarr(DatasetView, zarr.core.Array):
-
-    def __new__(cls,dataset):
-
-        _self = super().__new__(cls)
-        zarr.core.Array.__init__(_self, dataset.store, path=dataset.path)
-        return _self
-
+try:
+    import zarr
+    from .lazy_loading_zarr import DatasetViewzarr
+    installed_dataset_types = Union[installed_dataset_types,zarr.core.Array]
+    HAVE_ZARR = True
+except ImportError:
+    HAVE_ZARR = False
+    DatasetViewzarr = None

lazy_ops/lazy_loading_zarr.py

@@ -0,0 +1,11 @@
+import zarr
+from .lazy_loading import DatasetView
+
+class DatasetViewzarr(DatasetView, zarr.core.Array):
+
+    def __new__(cls,dataset):
+
+        _self = super().__new__(cls)
+        zarr.core.Array.__init__(_self, dataset.store, path=dataset.path)
+        return _self
+

lazy_ops/version.py

@@ -0,0 +1 @@
+version = '0.2.1'

requirements-dev.txt

@@ -0,0 +1,2 @@
+h5py
+zarr

setup.py

@@ -1,17 +1,29 @@
 from setuptools import setup, find_packages
 
+with open('requirements.txt', "r") as f:
+    install_requires = f.read().split()
+
+with open("lazy_ops/version.py", "r") as fv:
+    exec(fv.read())
+
 with open("README.md", "r") as fh:
     long_description = fh.read()
 
 setup(
     name="lazy_ops",
-    version="0.1.2",
+    version=version,
     url="https://github.com/ben-dichter-consulting/lazy_ops",
-    description="Lazy slicing and transpose operations for h5py",
+    description="Lazy slicing and transpose operations for h5py and zarr",
     long_description=long_description,
     long_description_content_type="text/markdown",
     author="Daniel Sotoude, Ben Dichter",
     author_email="[email protected], [email protected]",
     packages=find_packages(),
-    install_requires=['numpy', 'h5py'],
+    install_requires=install_requires,
+    classifiers=['Operating System :: OS Independent',
+                 'Development Status :: 3 - Alpha',
+                 'License :: OSI Approved :: BSD License',
+                 'Programming Language :: Python :: 3.6',
+                 'Programming Language :: Python :: 3.7',
+                 ],
 )

tox.ini

@@ -3,7 +3,7 @@ envlist = py35, py36, py37, py38
 [testenv]
 # install testing framework
 deps =
-    -rrequirements.txt
+    -rrequirements-dev.txt
     pytest
 # run the tests
 commands = pytest