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=================
Developer's guide
=================
Code organization
=================
The top level directory is organized in the following
directories:
:file:`pysam`
Code specific to pysam.
:file:`doc`
The documentation. To build the latest documentation, first install
`Sphinx`_ and then type::
make -C doc html
:file:`tests`
Code and data for testing and benchmarking.
:file:`htslib`
Source code from `htslib`_ shipped with pysam. See
:file:`import.py` about importing.
:file:`samtools`
Source code from `samtools`_ shipped with pysam. See
:file:`import.py` about importing.
:file:`bcftools`
Source code from `bcftools`_ shipped with pysam. See
:file:`import.py` about importing.
Python language level
=====================
Pysam currently requires Python 3.6 as a minimum language level.
For example, this means that the following comparatively recent
language features and library functions are available for use:
* f-strings
* ``raise ... from None``
* :meth:`str.startswith`, :meth:`str.endswith`, :meth:`str.rstrip`, etc
However in particular the the following should not be used in
pysam source code or infrastructure scripts:
* :meth:`str.removeprefix`, :meth:`str.removesuffix` (new in 3.9)
* walrus ``:=`` operator (new in 3.8)
Importing new versions of htslib and samtools
=============================================
See instructions in :file:`import.py` to import the latest
versions of `htslib`_, `samtools`_ and `bcftools`_.
Unit testing
============
Unit tests are in the :file:`tests` directory. To run all unit tests,
run::
pytest tests
Most tests use test data from the :file:`tests/*_data` directories.
Some of these test data files are generated from other files in these
directories, which is done by running ``make`` in each directory::
make -C tests/pysam_data
# etc
Alternatively if any :file:`tests/*_data/all.stamp` file is not already
present, running the unit tests should generate that directory's data
files automatically.
Benchmarking
============
To run the benchmarking suite, make sure that `pytest-benchmark
<https://github.com/ionelmc/pytest-benchmark>`_ is installed. To run
all benchmarks, type::
pytest tests/*_bench.py
See :ref:`Benchmarking` for more on this topic.
Contributors
============
Please see Github for a list of all contributors:
https://github.com/pysam-developers/pysam/graphs/contributors
Many thanks to all contributors for helping in making pysam
useful.
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