Abs store

.github/PULL_REQUEST_TEMPLATE.md

@@ -2,15 +2,9 @@
 
 TODO:
 * [ ] Add unit tests and/or doctests in docstrings
-* [ ] Unit tests and doctests pass locally under Python 3.6 (e.g., run ``tox -e py36`` or 
-  ``pytest -v --doctest-modules zarr``)
-* [ ] Unit tests pass locally under Python 2.7 (e.g., run ``tox -e py27`` or
-  ``pytest -v zarr``)
-* [ ] PEP8 checks pass (e.g., run ``tox -e py36`` or ``flake8 --max-line-length=100 zarr``)
 * [ ] Add docstrings and API docs for any new/modified user-facing classes and functions
 * [ ] New/modified features documented in docs/tutorial.rst
-* [ ] Doctests in tutorial pass (e.g., run ``tox -e py36`` or ``python -m doctest -o NORMALIZE_WHITESPACE -o ELLIPSIS docs/tutorial.rst``)
 * [ ] Changes documented in docs/release.rst
 * [ ] Docs build locally (e.g., run ``tox -e docs``)
 * [ ] AppVeyor and Travis CI passes
-* [ ] Test coverage to 100% (Coveralls passes)
+* [ ] Test coverage is 100% (Coveralls passes)

.pyup.yml

@@ -0,0 +1,24 @@
+# pyup.io config file
+# see https://pyup.io/docs/configuration/ for all available options
+
+schedule: every month
+
+requirements:
+  - requirements.txt:
+      pin: False
+      update: False
+  - requirements_test.txt:
+      pin: False
+      update: False
+  - requirements_rtfd.txt:
+      pin: False
+      update: False
+  - requirements_dev.txt:
+      pin: True
+      update: all
+  - requirements_dev_npy.txt:
+      pin: True
+      update: all
+  - requirements_dev_optional.txt:
+      pin: True
+      update: all

.travis.yml

@@ -11,15 +11,29 @@ addons:
     packages:
     - libdb-dev
 
-python:
-  - 2.7
-  - 3.4
-  - 3.5
-  - 3.6
+services:
+  - docker
+  - redis-server
+  - mongodb
+
+matrix:
+  include:
+    - python: 2.7
+    - python: 3.5
+    - python: 3.6
+    - python: 3.7
+      dist: xenial
+      sudo: true
+
+before_install:
+  - docker pull arafato/azurite
+  - mkdir ~/blob_emulator
+  - docker run -e executable=blob -d -t -p 10000:10000 -v ~/blob_emulator:/opt/azurite/folder arafato/azurite
+before_script:
+    - mongo mydb_test --eval 'db.createUser({user:"travis",pwd:"test",roles:["readWrite"]});'
 
 install:
-  - pip install -U pip setuptools wheel
-  - pip install -U tox-travis coveralls
+  - pip install -U pip setuptools wheel tox-travis coveralls
 
 script:
   - tox

CODE_OF_CONDUCT.md

@@ -0,0 +1,46 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team at zarr.conduct@gmail.com. The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/

appveyor.yml

@@ -2,67 +2,50 @@ branches:
   only:
     - master
 
+# the VS C++ compiler path, doesn't seem to exist in the PATH environment variable of
+# the Visual Studio 2017 build VM, due to which the pyosreplace package fails to build
+image: Visual Studio 2015
+
 environment:
 
   global:
     # SDK v7.0 MSVC Express 2008's SetEnv.cmd script will fail if the
     # /E:ON and /V:ON options are not enabled in the batch script intepreter
     # See: http://stackoverflow.com/a/13751649/163740
     CMD_IN_ENV: "cmd /E:ON /V:ON /C .\\build.cmd"
+    EMULATOR_LOC: C:\\Program Files (x86)\\Microsoft SDKs\\Azure\\Storage Emulator\\AzureStorageEmulator.exe
 
   matrix:
 
-    - PYTHON: "C:\\Python27"
-      PYTHON_VERSION: "2.7"
-      NUMPY_VERSION: "1.13.3"
-
     - PYTHON: "C:\\Python27-x64"
       PYTHON_VERSION: "2.7"
-      NUMPY_VERSION: "1.13.3"
-      DISTUTILS_USE_SDK: "1"
-
-    - PYTHON: "C:\\Python34"
-      NUMPY_VERSION: "1.13.3"
-      PYTHON_VERSION: "3.4"
-
-    - PYTHON: "C:\\Python34-x64"
-      PYTHON_VERSION: "3.4"
-      NUMPY_VERSION: "1.13.3"
       DISTUTILS_USE_SDK: "1"
 
-    - PYTHON: "C:\\Python35"
-      PYTHON_VERSION: "3.5"
-      NUMPY_VERSION: "1.13.3"
-
     - PYTHON: "C:\\Python35-x64"
       PYTHON_VERSION: "3.5"
-      NUMPY_VERSION: "1.13.3"
-
-    - PYTHON: "C:\\Python36"
-      PYTHON_VERSION: "3.6"
-      NUMPY_VERSION: "1.13.3"
 
     - PYTHON: "C:\\Python36-x64"
       PYTHON_VERSION: "3.6"
-      NUMPY_VERSION: "1.13.3"
 
-    - PYTHON: "C:\\Python36"
-      PYTHON_VERSION: "3.6"
-      NUMPY_VERSION: "1.14.0"
-
-    - PYTHON: "C:\\Python36-x64"
-      PYTHON_VERSION: "3.6"
-      NUMPY_VERSION: "1.14.0"
+    - PYTHON: "C:\\Python37-x64"
+      PYTHON_VERSION: "3.7"
 
 install:
   - "SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%"
+  - "%CMD_IN_ENV% python -m pip install -U pip setuptools wheel"
+  - "%CMD_IN_ENV% python -m pip install -rrequirements_test.txt"
+  - "%CMD_IN_ENV% python -m pip install -rrequirements_dev_npy.txt"
+  - "%CMD_IN_ENV% python -m pip install --no-binary=numcodecs -rrequirements_dev.txt"
+  - "%CMD_IN_ENV% python setup.py install"
+  - "%CMD_IN_ENV% python -m pip freeze"
 
 build: off
 
+before_test:
+  - '"%EMULATOR_LOC%" start'
+
 test_script:
-  - "%CMD_IN_ENV% python -m pip install -U pip setuptools wheel"
-  - "%CMD_IN_ENV% python -m pip install numpy==%NUMPY_VERSION%"
-  - "%CMD_IN_ENV% python -m pip install -rrequirements_dev.txt"
-  - "%CMD_IN_ENV% python setup.py install"
   - "%CMD_IN_ENV% python -m pytest -v --pyargs zarr"
-
+
+after_test:
+  - '"%EMULATOR_LOC%" stop'

docs/api/convenience.rst

@@ -10,3 +10,5 @@ Convenience functions (``zarr.convenience``)
 .. autofunction:: copy_all
 .. autofunction:: copy_store
 .. autofunction:: tree
+.. autofunction:: consolidate_metadata
+.. autofunction:: open_consolidated

docs/api/storage.rst

@@ -21,12 +21,22 @@ Storage (``zarr.storage``)
     .. automethod:: close
     .. automethod:: flush
 
+.. autoclass:: SQLiteStore
+
+    .. automethod:: close
+
+.. autoclass:: MongoDBStore
+.. autoclass:: RedisStore
 .. autoclass:: LRUStoreCache
 
     .. automethod:: invalidate
     .. automethod:: invalidate_values
     .. automethod:: invalidate_keys
 
+.. autoclass:: ABSStore
+
+.. autoclass:: ConsolidatedMetadataStore
+
 .. autofunction:: init_array
 .. autofunction:: init_group
 .. autofunction:: contains_array

docs/release.rst

@@ -1,6 +1,77 @@
 Release notes
 =============
 
+.. _release_2.3.0:
+
+2.3.0 (Work in Progress)
+------------------------
+
+Enhancements
+~~~~~~~~~~~~
+
+* New storage backend, backed by Azure Blob Storage,
+  class :class:`zarr.storage.ABSStore`.
+  All data is stored as Block blobs.
+
+* Add "consolidated" metadata as an experimental feature: use
+  :func:`zarr.convenience.consolidate_metadata` to copy all metadata from the various
+  metadata keys within a dataset hierarchy under a single key, and
+  :func:`zarr.convenience.open_consolidated` to use this single key. This can greatly
+  cut down the number of calls to the storage backend, and so remove a lot of overhead
+  for reading remote data. By :user:`Martin Durant <martindurant>`, :issue:`268`.
+
+* Support has been added for structured arrays with sub-array shape and/or nested fields. By
+  :user:`Tarik Onalan <onalant>`, :issue:`111`, :issue:`296`.
+
+* Adds the SQLite-backed :class:`zarr.storage.SQLiteStore` class enabling an
+  SQLite database to be used as the backing store for an array or group.
+  By :user:`John Kirkham <jakirkham>`, :issue:`368`, :issue:`365`.
+
+* Efficient iteration over arrays by decompressing chunkwise.
+  By :user:`Jerome Kelleher <jeromekelleher>`, :issue:`398`, :issue:`399`.
+
+* Adds the Redis-backed :class:`zarr.storage.RedisStore` class enabling a
+  Redis database to be used as the backing store for an array or group.
+  By :user:`Joe Hamman <jhamman>`, :issue:`299`, :issue:`372`.
+
+* Adds the MongoDB-backed :class:`zarr.storage.MongoDBStore` class enabling a
+  MongoDB database to be used as the backing store for an array or group.
+  By :user:`Joe Hamman <jhamman>`, :issue:`299`, :issue:`372`.
+
+Bug fixes
+~~~~~~~~~
+
+* The implementation of the :class:`zarr.storage.DirectoryStore` class has been modified to
+  ensure that writes are atomic and there are no race conditions where a chunk might appear
+  transiently missing during a write operation. By :user:`sbalmer <sbalmer>`, :issue:`327`,
+  :issue:`263`.
+
+* The required version of the `numcodecs <http://numcodecs.rtfd.io>`_ package has been upgraded
+  to 0.6.2, which has enabled some code simplification and fixes a failing test involving
+  msgpack encoding. By :user:`John Kirkham <jakirkham>`, :issue:`361`, :issue:`360`, :issue:`352`,
+  :issue:`355`, :issue:`324`.
+
+* Failing tests related to pickling/unpickling have been fixed. By :user:`Ryan Williams <ryan-williams>`,
+  :issue:`273`, :issue:`308`.
+
+* Ensure ``DictStore`` contains only ``bytes`` to facilitate comparisons and protect against writes.
+  By :user:`John Kirkham <jakirkham>`, :issue:`350`
+
+* Always use a ``tuple`` when indexing a NumPy ``ndarray``.
+  By :user:`John Kirkham <jakirkham>`, :issue:`376`
+
+Maintenance
+~~~~~~~~~~~
+
+* CI and test environments have been upgraded to include Python 3.7, drop Python 3.4, and
+  upgrade all pinned package requirements. :issue:`308`.
+
+* Corrects handling of ``NaT`` in ``datetime64`` and ``timedelta64`` in various
+  compressors (by :user:`John Kirkham <jakirkham>`; :issue:`344`).
+
+Acknowledgments
+~~~~~~~~~~~~~~~
+
 .. _release_2.2.0:
 
 2.2.0

docs/spec/v2.rst

@@ -140,13 +140,31 @@ the `NumPy documentation on Datetimes and Timedeltas
 <https://docs.scipy.org/doc/numpy/reference/arrays.datetime.html#datetime-units>`_.
 For example, ``"<M8[ns]"`` specifies a datetime64 data type with nanosecond time units.
 
-Structured data types (i.e., with multiple named fields) are encoded as a list
-of two-element lists, following `NumPy array protocol type descriptions (descr)
-<http://docs.scipy.org/doc/numpy/reference/arrays.interface.html#>`_. For
-example, the JSON list ``[["r", "|u1"], ["g", "|u1"], ["b", "|u1"]]`` defines a
-data type composed of three single-byte unsigned integers labelled "r", "g" and
-"b".
-
+Structured data types (i.e., with multiple named fields) are encoded
+as a list of lists, following `NumPy array protocol type descriptions
+(descr)
+<http://docs.scipy.org/doc/numpy/reference/arrays.interface.html#>`_. Each
+sub-list has the form ``[fieldname, datatype, shape]`` where ``shape``
+is optional. ``fieldname`` is a string, ``datatype`` is a string
+specifying a simple data type (see above), and ``shape`` is a list of
+integers specifying subarray shape. For example, the JSON list below
+defines a data type composed of three single-byte unsigned integer
+fields named "r", "g" and "b"::
+
+    [["r", "|u1"], ["g", "|u1"], ["b", "|u1"]]
+
+For example, the JSON list below defines a data type composed of three
+fields named "x", "y" and "z", where "x" and "y" each contain 32-bit
+floats, and each item in "z" is a 2 by 2 array of floats::
+
+    [["x", "<f4"], ["y", "<f4"], ["z", "<f4", [2, 2]]]
+
+Structured data types may also be nested, e.g., the following JSON
+list defines a data type with two fields "foo" and "bar", where "bar"
+has two sub-fields "baz" and "qux"::
+
+    [["foo", "<f4"], ["bar", [["baz", "<f4"], ["qux", "<i4"]]]] 
+
 .. _spec_v2_array_fill_value:
 
 Fill value encoding
@@ -235,7 +253,7 @@ keys like "foo/bar/0.0", "foo/bar/0.1", etc.
 To ensure consistent behaviour across different storage systems, logical paths
 MUST be normalized as follows:
 
-* Replace all backward slash characters ("\\") with forward slash characters
+* Replace all backward slash characters ("\\\\") with forward slash characters
   ("/")
 * Strip any leading "/" characters
 * Strip any trailing "/" characters
@@ -512,6 +530,10 @@ initially published to clarify ambiguities and add some missing information.
   either arrays or groups, and if absent then custom attributes should be treated as
   empty.
 
+* The specification now describes how structured datatypes with
+  subarray shapes and/or with nested structured data types are encoded
+  in array metadata (:issue:`111`, :issue:`296`).
+
 
 Changes from version 1 to version 2
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~