Rnachipintegrator

--------------------------

* Add option to compute distances from gene TES only (``--edge=tes``)
(`PR 77 <https://github.com/fls-bioinformatics-core/RnaChipIntegrator/pull/78>`_).
* Add ``CITATION.cff`` file and updated information on how to cite
``RnaChipIntegrator`` (`PR 78 <https://github.com/fls-bioinformatics-core/RnaChipIntegrator/pull/78>`_).
* Update the installation documentation and metadata
(`PR 85 <https://github.com/fls-bioinformatics-core/RnaChipIntegrator/pull/85>`_,
`PR 86 <https://github.com/fls-bioinformatics-core/RnaChipIntegrator/pull/86>`_).
* Add automated CI testing and deployment to PyPI via GitHub Actions,
and add support for Python 3.9
(`PR 74 <https://github.com/fls-bioinformatics-core/RnaChipIntegrator/pull/74>`_).
* Drop support for Python 2.7
(`PR 76 <https://github.com/fls-bioinformatics-core/RnaChipIntegrator/pull/76>`_).

--------------------------

--------------------------

* Add support for Python 3 (3.5, 3.6, 3.7 and 3.8)
(`PR 69 <https://github.com/fls-bioinformatics-core/RnaChipIntegrator/pull/69>`_,
`PR 71 <https://github.com/fls-bioinformatics-core/RnaChipIntegrator/pull/71>`_).

--------------------------

--------------------------

* Implement batch mode operation which allows a single run of
``RnaChipIntegrator`` to iterate over any combination of
multiple cutoffs (via new ``--cutoffs`` option) and multiple
peaks and genes files (via new ``--peaks`` and ``--genes``
options)
(`PR 58 <https://github.com/fls-bioinformatics-core/RnaChipIntegrator/pull/58>`_).
* Drop support for Python 2.6
(`PR 66 <https://github.com/fls-bioinformatics-core/RnaChipIntegrator/pull/66>`_).

--------------------------

--------------------------

* Fix bug in gene-centric analysis when using ``--edge=both``,
which meant valid peaks could sometimes be dropped from the
results
(`PR 60 <https://github.com/fls-bioinformatics-core/RnaChipIntegrator/pull/60>`_).
* New ``--peak_id`` option enables peak names to be read from
an ``ID`` column in the peaks file, which will be carried
through to the output files
(`PR 56 <https://github.com/fls-bioinformatics-core/RnaChipIntegrator/pull/56>`_).
* New ``--analyses`` option enables specific analyses to be
selected (i.e. either peak-centric only, gene-centric only,
or both peak- and gene-centric)
(`PR 46 <https://github.com/fls-bioinformatics-core/RnaChipIntegrator/pull/46>`_).

--------------------------

--------------------------

* Update description of 'direction' in the documentation and
the XLSX file, to clarify the meaning of the terms 'upstream'
and downstream' in the program outputs.
* Update documentation to explain how comments, header lines,
and lines with 'bad' data, are handled by the program when
reading in the input files.
* Add a section on 'known problems' to the documentation.

--------------------------

--------------------------

* Bugfix release: fixes bug which crashed the program if
``--cutoff=0`` was specified together with ``--xlsx``.

--------------------------