Merge branch 'master' into fsspec_w

Martin Durant · Martin Durant · commit f7327708aeef · 2020-10-08T11:21:28.000-04:00
diff --git a/.github/workflows/releases.yml b/.github/workflows/releases.yml
@@ -0,0 +1,61 @@
+name: Wheels
+
+on: [push, pull_request]
+
+jobs:
+  build_artifacts:
+    name: Build wheel on ubuntu-latest
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+
+    steps:
+      - uses: actions/checkout@v1
+        with:
+          submodules: true
+
+      - uses: actions/setup-python@v1
+        name: Install Python
+        with:
+          python-version: '3.8'
+
+      - name: Install PyBuild
+        run: |
+          python -m pip install build
+
+      - name: Build wheel and sdist
+        run: |
+          python -m build
+      - uses: actions/upload-artifact@v1
+        with:
+          name: releases
+          path: dist
+
+  test_dist_pypi:
+    needs: [build_artifacts]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/download-artifact@v1
+        with:
+          name: releases
+          path: dist
+
+      - name: test
+        run: |
+          ls
+          ls dist
+
+  upload_pypi:
+    needs: [build_artifacts]
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')
+    steps:
+      - uses: actions/download-artifact@v1
+        with:
+          name: releases
+          path: dist
+      - uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.pypi_password }}
+          # To test: repository_url: https://test.pypi.org/legacy/
diff --git a/.travis.yml b/.travis.yml
@@ -20,7 +20,6 @@ services:
 
 matrix:
   include:
-    - python: 3.5
     - python: 3.6
       env: BUILD_DOCS='true'
     - python: 3.7
@@ -39,7 +38,7 @@ before_script:
     - mongo mydb_test --eval 'db.createUser({user:"travis",pwd:"test",roles:["readWrite"]});'
 
 install:
-  - pip install -U pip setuptools wheel tox-travis coveralls mypy
+  - pip install -U pip setuptools wheel tox-travis coveralls mypy codecov
 
 script:
   - tox
@@ -48,3 +47,4 @@ script:
 
 after_success:
   - coveralls --service=travis-pro
+  - codecov
diff --git a/appveyor.yml b/appveyor.yml
@@ -18,9 +18,6 @@ environment:
 
   matrix:
 
-    - PYTHON: "C:\\Python35-x64"
-      PYTHON_VERSION: "3.5"
-
     - PYTHON: "C:\\Python36-x64"
       PYTHON_VERSION: "3.6"
 
diff --git a/codecov.yml b/codecov.yml
@@ -0,0 +1,9 @@
+coverage:
+  status:
+    project:
+      default:
+        target: 100
+        threshold: 0.1
+    patch:
+      default:
+        target: 100
diff --git a/docs/contributing.rst b/docs/contributing.rst
@@ -330,6 +330,11 @@ compatibility in some way.
 Release procedure
 ~~~~~~~~~~~~~~~~~
 
+.. note:: 
+
+   Most of the release process is now handled by github workflow which should
+   automatically push a release to PyPI if a tag is pushed. 
+
 Checkout and update the master branch::
 
     $ git checkout master
@@ -347,7 +352,6 @@ Tag the version (where "X.X.X" stands for the version number, e.g., "2.2.0")::
 
 Release source code to PyPI::
 
-    $ python setup.py register sdist
     $ twine upload dist/zarr-${version}.tar.gz
 
 Obtain checksum for release to conda-forge::
diff --git a/docs/release.rst b/docs/release.rst
@@ -2,16 +2,27 @@ Release notes
 =============
 
 
-Next release
+Next Release
 ------------
 
+This release will be the first release of Zarr not supporting Python 3.5.
+
+* End Python 3.5 support.
+  By :user:`Chris Barnes <clbarnes>`; :issue:`602`.
+
+2.5.0
+-----
+
+
+This release will be the last to support Python 3.5, next version of Zarr will be Python 3.6+.
+
 * `DirectoryStore` now uses `os.scandir`, which should make listing large store
   faster, :issue:`563`
   
 * Remove a few remaining Python 2-isms.
   By :user:`Poruri Sai Rahul <rahulporuri>`; :issue:`393`.
 
-* Fix minor bug in `N5Store`. 
+* Fix minor bug in `N5Store`.
   By :user:`gsakkis`, :issue:`550`.
 
 * Improve error message in Jupyter when trying to use the ``ipytree`` widget
@@ -24,8 +35,8 @@ Next release
   By :user:`Elliott Sales de Andrade <QuLogic>`; :issue:`442`
 
 * Many of the convenience functions to emit errors (``err_*`` from
-  ``zarr.errors``  have been replaced by ``ValueError`` subclasses. The
-  functions are deprecated and will be removed in the future. :issue:`590` )
+  ``zarr.errors``  have been replaced by ``ValueError`` subclasses. The corresponding
+  ``err_*`` function have been removed. :issue:`590`, :issue:`614`)
 
 * Improve consistency of terminology regarding arrays and datasets in the 
   documentation.
diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools>=40.8.0", "wheel"]
+build-backend = "setuptools.build_meta"
diff --git a/setup.py b/setup.py
@@ -1,5 +1,3 @@
-import sys
-
 from setuptools import setup
 
 DESCRIPTION = 'An implementation of chunked, compressed, ' \
@@ -35,7 +33,7 @@
             'ipytree',
         ],
     },
-    python_requires='>=3.5',
+    python_requires='>=3.6, <4',
     install_requires=dependencies,
     package_dir={'': '.'},
     packages=['zarr', 'zarr.tests'],
@@ -49,7 +47,6 @@
         'Topic :: Software Development :: Libraries :: Python Modules',
         'Operating System :: Unix',
         'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.5',
         'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
         'Programming Language :: Python :: 3.8',
diff --git a/tox.ini b/tox.ini
@@ -4,7 +4,7 @@
 # and then run "tox" from this directory.
 
 [tox]
-envlist = py35, py36, py37-npy{115,116,latest}, py38, docs
+envlist = py36, py37-npy{115,116,latest}, py38, docs
 
 [testenv]
 install_command = pip install --no-binary=numcodecs {opts} {packages}
diff --git a/zarr/convenience.py b/zarr/convenience.py
@@ -82,12 +82,8 @@ def open(store=None, mode='a', **kwargs):
         else:
             return open_group(store, mode=mode, **kwargs)
 
-    elif mode == 'a':
-        if contains_array(store, path):
-            return open_array(store, mode=mode, **kwargs)
-        elif contains_group(store, path):
-            return open_group(store, mode=mode, **kwargs)
-        elif 'shape' in kwargs:
+    elif mode == "a":
+        if "shape" in kwargs or contains_array(store, path):
             return open_array(store, mode=mode, **kwargs)
         else:
             return open_group(store, mode=mode, **kwargs)
diff --git a/zarr/errors.py b/zarr/errors.py
@@ -15,49 +15,35 @@ def __init__(self, *args):
         super().__init__(self._msg.format(*args))
 
 
-class ContainsGroupError(_BaseZarrError):
-    _msg = "path {0!r} contains a group"
+class _BaseZarrIndexError(IndexError):
+    _msg = ""
+
+    def __init__(self, *args):
+        super().__init__(self._msg.format(*args))
 
 
-def err_contains_group(path):
-    raise ContainsGroupError(path)  # pragma: no cover
+class ContainsGroupError(_BaseZarrError):
+    _msg = "path {0!r} contains a group"
 
 
 class ContainsArrayError(_BaseZarrError):
     _msg = "path {0!r} contains an array"
 
 
-def err_contains_array(path):
-    raise ContainsArrayError(path)  # pragma: no cover
-
-
 class ArrayNotFoundError(_BaseZarrError):
     _msg = "array not found at path %r' {0!r}"
 
 
-def err_array_not_found(path):
-    raise ArrayNotFoundError(path)  # pragma: no cover
-
-
 class GroupNotFoundError(_BaseZarrError):
     _msg = "group not found at path {0!r}"
 
 
-def err_group_not_found(path):
-    raise GroupNotFoundError(path)  # pragma: no cover
-
-
 class PathNotFoundError(_BaseZarrError):
     _msg = "nothing found at path {0!r}"
 
 
-def err_path_not_found(path):
-    raise PathNotFoundError(path)  # pragma: no cover
-
-
-def err_bad_compressor(compressor):
-    raise ValueError('bad compressor; expected Codec object, found %r' %
-                     compressor)
+class BadCompressorError(_BaseZarrError):
+    _msg = "bad compressor; expected Codec object, found {0!r}"
 
 
 class FSPathExistNotDir(GroupNotFoundError):
@@ -69,25 +55,23 @@ def __init__(self):
         super().__init__("object is read-only")
 
 
-def err_read_only():
-    raise ReadOnlyError()  # pragma: no cover
-
+class BoundsCheckError(_BaseZarrIndexError):
+    _msg = "index out of bounds for dimension with length {0}"
 
-def err_boundscheck(dim_len):
-    raise IndexError('index out of bounds for dimension with length {}'
-                     .format(dim_len))
 
-
-def err_negative_step():
-    raise IndexError('only slices with step >= 1 are supported')
+class NegativeStepError(IndexError):
+    def __init__(self):
+        super().__init__("only slices with step >= 1 are supported")
 
 
 def err_too_many_indices(selection, shape):
     raise IndexError('too many indices for array; expected {}, got {}'
                      .format(len(shape), len(selection)))
 
 
-def err_vindex_invalid_selection(selection):
-    raise IndexError('unsupported selection type for vectorized indexing; only '
-                     'coordinate selection (tuple of integer arrays) and mask selection '
-                     '(single Boolean array) are supported; got {!r}'.format(selection))
+class VindexInvalidSelectionError(_BaseZarrIndexError):
+    _msg = (
+        "unsupported selection type for vectorized indexing; only "
+        "coordinate selection (tuple of integer arrays) and mask selection "
+        "(single Boolean array) are supported; got {0!r}"
+    )
diff --git a/zarr/indexing.py b/zarr/indexing.py
@@ -5,8 +5,12 @@
 
 import numpy as np
 
-from zarr.errors import (err_boundscheck, err_negative_step,
-                         err_too_many_indices, err_vindex_invalid_selection)
+from zarr.errors import (
+    NegativeStepError,
+    err_too_many_indices,
+    VindexInvalidSelectionError,
+    BoundsCheckError,
+)
 
 
 def is_integer(x):
@@ -46,7 +50,7 @@ def normalize_integer_selection(dim_sel, dim_len):
 
     # handle out of bounds
     if dim_sel >= dim_len or dim_sel < 0:
-        err_boundscheck(dim_len)
+        raise BoundsCheckError(dim_len)
 
     return dim_sel
 
@@ -101,7 +105,7 @@ def __init__(self, dim_sel, dim_len, dim_chunk_len):
         # normalize
         self.start, self.stop, self.step = dim_sel.indices(dim_len)
         if self.step < 1:
-            err_negative_step()
+            raise NegativeStepError()
 
         # store attributes
         self.dim_len = dim_len
@@ -385,7 +389,7 @@ def wraparound_indices(x, dim_len):
 
 def boundscheck_indices(x, dim_len):
     if np.any(x < 0) or np.any(x >= dim_len):
-        err_boundscheck(dim_len)
+        raise BoundsCheckError(dim_len)
 
 
 class IntArrayDimIndexer(object):
@@ -756,7 +760,7 @@ def __getitem__(self, selection):
         elif is_mask_selection(selection, self.array):
             return self.array.get_mask_selection(selection, fields=fields)
         else:
-            err_vindex_invalid_selection(selection)
+            raise VindexInvalidSelectionError(selection)
 
     def __setitem__(self, selection, value):
         fields, selection = pop_fields(selection)
@@ -767,7 +771,7 @@ def __setitem__(self, selection, value):
         elif is_mask_selection(selection, self.array):
             self.array.set_mask_selection(selection, value, fields=fields)
         else:
-            err_vindex_invalid_selection(selection)
+            raise VindexInvalidSelectionError(selection)
 
 
 def check_fields(fields, dtype):
diff --git a/zarr/storage.py b/zarr/storage.py
@@ -40,7 +40,7 @@
 
 from zarr.errors import (
     MetadataError,
-    err_bad_compressor,
+    BadCompressorError,
     ContainsArrayError,
     ContainsGroupError,
     FSPathExistNotDir,
@@ -397,8 +397,8 @@ def _init_array_metadata(
     if compressor:
         try:
             compressor_config = compressor.get_config()
-        except AttributeError:
-            err_bad_compressor(compressor)
+        except AttributeError as e:
+            raise BadCompressorError(compressor) from e
 
     # obtain filters config
     if filters:

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,3 @@`
	`1`	`+[build-system]`
	`2`	`+requires = ["setuptools>=40.8.0", "wheel"]`
	`3`	`+build-backend = "setuptools.build_meta"`