Dcicsnovault

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`PR 223 Index Delete Retry <https://github.com/4dn-dcic/snovault/pull/223>`_

* Retry delete_index in case of an error,
likely related to a snapshot occurring at the same time as the delete operation.
Give it two minutes (12 tries) to succeed.

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`PR 224 Use dcicutils 4.0 <https://github.com/4dn-dcic/snovault/pull/224>`_

**NOTE:** The breaking change here is the use of ``dcicutils 4.x``.

* This accepts ``dcicutils 4.0``.
* Minor change to ``.gitignore`` to add ``.python-cmd``.
* Constrains ``boto3``, ``botocore``, ``boto3-stubs``, and ``botocore-stubs``.

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`PR 222 Invalidation Scope Fix (C4-854) <https://github.com/4dn-dcic/snovault/pull/222>`_

* Repairs several important cases in invalidation scope by revising the core algorithm,
which is now described in the ``filter_invalidation_scope`` docstring.
* Should work correctly for object fields, links beyond depth ``1`` and ``*``.
* Other small changes include repairing the test script
and allowing indexer worker runs to re-use testapp for 100 iterations
(thus preserving cache, probably speeding up indexing and reducing DB load)

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`PR 221 Remove embeds of unmappable properties <https://github.com/4dn-dcic/snovault/pull/221>`_

* Here, we remove embeds of properties that cannot be mapped within our system,
namely those that fall under ``additionalProperties`` or ``patternProperties`` in our schema.

* As far as I understand things, since these fields cannot be mapped, adding them to an item's embedding list
will not work regardless of the changes here, specifically the explicit removal of the properties
from the default embeds in ``find_default_embeds_for_schema``.
Thus, no properties in the schema defined under ``additionalProperties`` or ``patternProperties`` can be embedded
or used for invalidation scope with our current set-up,
and significant refactoring would be required to make these work.

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`PR 220 Further upgrader version fix <https://github.com/4dn-dcic/snovault/pull/220>`_

The recent upgrader fix (in v.5.6.0) added the default version of ``1`` for upgrader calls,
but not all calls to the upgrader were included in the fix.
Specifically, the upgrader call within ``resources.py`` is still resulting in errors.
We fix that here, as well as the call within the possibly defunct ``batchupgrade.py`` for good measure.
(Grepping ``snovault`` for ``upgrader.upgrade`` didn't reveal any other instances of calls to the upgrader to fix.)