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zarr-developers / zarr / 1340 / 2
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22 Jan 2019 12:52PM UTC coverage: 98.838% (+0.007%) from 98.831%
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Add SQLiteStore (#368)

* Create an SQLite-backed mutable mapping

Implements a key-value store using SQLite. As this is a builtin module
in Python and a common database to use in various languages, this should
have high utility and be very portable. Not to mention many databases
provide an SQLite language on top regardless of the internal
representation. So this can be a great template for users wishing to
work with Zarr in their preferred database.

* Test SQLiteStore

Try using the `SQLiteStore` everywhere one would use another store and
make sure that it behaves correctly. This includes simple key-value
store usage, creating hierarchies, and storing arrays.

* Export `SQLiteStore` to the top-level namespace

* Include some SQLiteStore examples

Provide a few examples of how one might use `SQLiteStore` to store
arrays or groups. These examples are taken with minor modifications from
the `LMDBStore` examples.

* Demonstrate the `SQLiteStore` in the tutorial

Includes a simple example borrowed from `LMDBStore`'s tutorial example,
which shows how to create and use an `SQLiteStore`.

* Provide API documentation for `SQLiteStore`

* Make a release note for `SQLiteStore`

* Use unique extension for `SQLiteStore` files

Otherwise we may end up opening a different databases' files and try to
use them with SQLite only to run into errors. This caused the doctests
to fail previously. Changing the extension as we have done should avoid
these conflicts.

* Only close SQLite database when requested

Instead of opening, committing, and closing the SQLite database for
every operation, limit these to user requested operations. Namely commit
only when the user calls `flush`. Also close only when the user calls
`close`. This should make operations with SQLite much more performant
than when we automatically committed and closed after every user
operation.

* Update docs to show how to close `SQLiteStore`

As users need... (continued)

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