Functionalizer

==============

.. warning:: Changes in this release may require an additional ``--`` after the
``--morphologies`` flag for proper command line argument parsing.

Changes:
- Add a new filter that allows to assign morphologies to spines.
See also FUNCZ-301_.
- Add the column ``edge_type_id`` to gap-junction output to conform with
the SONATA specification.
- Load all node attributes and make them conditional at the same time.
Should avoid having to specify bogus attributes when using projections.
See also FUNCZ-307_.

==============

Breaking Changes:
- Write section types out with the correct
`MorphIO convention`_.
See also FUNCZ-289_.

Changes:
- Allow unsigned integer types for SONATA input. Restricted to a maximum
of 32 bits.
See also FUNCZ-291_.

==============

.. warning:: Changes in this release will yield different results compared
to previous versions when re-running circuits.

Breaking Changes:
- Replace the random number generating library. Switch to using the tried
and tested Random123 library. See also HPCTM-1294_.
- Run the `TouchRules` filter by default in structural mode. See also
FUNCZ-255_.

Changes:
- Fix a regression that led to duplicated gap-junction ids. See also
FUNCZ-287_.

===============

Breaking Changes:
- Drop the `SynapseProperties` filter by default in structural mode.
Space savings are small, but time savings seem worthwhile. See
also FUNCZ-265_.

Changes:
- Produce `debug` output by default. See also FUNCZ-281_.
- Reduce the output of the cluster startup script to display important
information more prominently. Spykfunc will not require the flag
``-p spark.master=…`` any longer when launched with ``sm_run``.
See also FUNCZ-275_.
- Generalize :class:`~recipe.parts.touch_connections.ConnectionRule`,
where ``<mTypeRule to="…" …`` is now superseded by ``<rule toMType="…" …``
and additional selection criteria may be specified.
- Store metadata about previous tool invocations and add recipe, filters
used. See also HPCTM-1425_.
- Track touches dropped and raise an exception if touches are removed
filters like synaptic property generation. See also FUNCZ-274_.
- Rework user interface to require the flags ``--recipe`` and
``--morphologies``, previously positional arguments, when using
filters. Drop ``--parquet`` and ``--touches`` and use positional
arguments instead, auto-detecting the input file type.
- Allow to not specify any filters or use the ``--merge`` flag to process
several inputs of **non-overlapping** edge populations. See also
FUNCZ-279_.

.. note:: If a source—target connection appears in more than one input,
synapses for this input may not be sorted in a reproducible
way.

==============

Changes:
- Fix a bug where the afferent section type of too many sections was
changed. See also FUNCZ-269_.
- Factor some recipe reading code out into its own module. See also
FUNCZ-183_.
- Sort within each output partition to have completely reproducible
output. See also FUNCZ-262_.
- Change the input parameters to require ``--from <circuit_file> <population>``
and ``--to <circuit_file> <population>``. Both source and target parameters
can differ, allowing to specify different circuit files and/or populations.
Note that the ``--circuit <circuit_file>`` is replaced by this feature.
- Add support for NodeSets with ``--from-nodeset <nodesets_file> <nodeset>``
and ``--to-nodeset <nodesets_file> <nodeset>``, filtering the populations
specified by the ``--from``/``--to`` parameters. Both source and target
parameters can differ, allowing different nodesets files and/or nodesets.
- Change: Refactoring to introduce support for SONATA files natively through
Libsonata. Note that MVD and/or other legacy files are no longer supported.
See also FUNCZ-263_.

==============

Changes:
- Shuffle the data loading order to perform almost all I/O after recipe
parsing and setup.
Added an option ``--dry-run`` to read minimal data and verify the
recipe.
See also FUNCZ-248_.