Modelcif

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- Data that have been split over multiple mmCIF or BinaryCIF files can now
be combined into a single :class:`modelcif.System` object using the new
``add_to_system`` argument to :func:`modelcif.reader.read` (10).
- A new example, ``associated.py``, has been added to demonstrate reading
in data that has been split into multiple "associated" mmCIF files using
:class:`modelcif.associated.CIFFile`.

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- The new class :class:`modelcif.model.NotModeledResidueRange` allows for
the annotation of residue ranges that were explicitly not modeled.
Any residue marked as not-modeled in all models will be excluded from
the ``pdbx_poly_seq_scheme`` table.
- The ``util/make-mmcif.py`` script is now included in the installed package,
so can be run if desired with ``python3 -m modelcif.util.make_mmcif``.
- The ``make_mmcif`` utility script will now automatically add any
missing :class:`modelcif.model.NotModeledResidueRange` objects for
not-modeled residue ranges.

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- Reference information in the ``struct_ref`` mmCIF table is now supported
in addition to the ModelCIF-specific tables such as
``ma_target_ref_db_details``. :class:`modelcif.reference.TargetReference`
now inherits from ``ihm.reference.Sequence`` and allows for the full
database sequence, plus any differences between it and the modeled sequence,
to be recorded. The ``align_begin`` and ``align_end`` arguments are now
deprecated (34).

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- Bugfix: :class:`modelcif.SoftwareGroup` now allows for parameters to
be associated with each piece of software in the group, rather than
with the group as a whole (33).

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- :class:`modelcif.associated.File` now takes an optional ``data``
argument to allow describing any modeling input/output that is stored
in that file.
- RPM packages are now provided for Fedora and RedHat Enterprise Linux.

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- More examples have been added to demonstrate interconversion between
mmCIF and BinaryCIF, and to validate mmCIF files.
- A utility script ``util/make-mmcif.py`` has been added which can add
minimal ModelCIF-related tables to an mmCIF file, to add in deposition.
- The reader is now more robust when handling files that are not ModelCIF
compliant (31).
- The ``exptl`` table is no longer written to output mmCIF files, to conform
with wwPDB's recommendation. Instead, the
``struct.pdbx_structure_determination_methodology`` data item denotes
that the model is computational (29).