From ebfb54774216db778a14c0adc5c992a89e41e7ed Mon Sep 17 00:00:00 2001 From: Peter Kruczkiewicz Date: Thu, 12 Jul 2018 11:33:15 -0500 Subject: [PATCH] Update README.rst name change and development instructions --- README.rst | 53 +++++++++++++++++++++++++++++++++++++++++++---------- 1 file changed, 43 insertions(+), 10 deletions(-) diff --git a/README.rst b/README.rst index db88ad2..5d7634c 100644 --- a/README.rst +++ b/README.rst @@ -4,7 +4,7 @@ |license| |nbsp| |citest| |nbsp| |pypi| |nbsp| |conda| .. |logo| image:: logo.png - :target: https://github.com/phac-nml/bio_hansel + :target: https://github.com/phac-nml/biohansel .. |pypi| image:: https://badge.fury.io/py/bio-hansel.svg :target: https://pypi.python.org/pypi/bio_hansel/ .. |license| image:: https://img.shields.io/badge/License-Apache%20v2.0-blue.svg @@ -26,7 +26,7 @@ Works on genome assemblies (FASTA files) or reads (FASTQ files)! Accepts Gzipped Citation ======== -If you find this tool useful, please cite as: +If you find the ``biohansel`` tool useful, please cite as: .. epigraph:: @@ -38,11 +38,11 @@ If you find this tool useful, please cite as: Requirements and Dependencies ============================= -This tool has only been tested on Linux (specifically Arch Linux). It may or may not work on OSX. +Each new build of ``biohansel`` is automatically tested on Linux using `Continuous Integration `_. ``biohansel`` has been confirmed to work on Mac OSX (versions 10.13.5 Beta and 10.12.6) when installed with Conda_. -These are the dependencies required for ``bio_hansel``: +These are the dependencies required for ``biohansel``: -- Python_ (>=v3.5) +- Python_ (>=v3.6) - numpy_ >=1.12.1 - pandas_ >=0.20.1 - pyahocorasick_ >=1.1.6 @@ -55,7 +55,7 @@ Installation With Conda_ ----------- -Install ``bio_hansel`` from Bioconda_ with Conda_ (`Conda installation instructions `_): +Install ``biohansel`` from Bioconda_ with Conda_ (`Conda installation instructions `_): .. code-block:: bash @@ -63,13 +63,13 @@ Install ``bio_hansel`` from Bioconda_ with Conda_ (`Conda installation instructi conda config --add channels defaults conda config --add channels conda-forge conda config --add channels bioconda - # install bio_hansel + # install biohansel conda install bio_hansel With pip_ from PyPI_ --------------------- -Install ``bio_hansel`` from PyPI_ with pip_: +Install ``biohansel`` from PyPI_ with pip_: .. code-block:: bash @@ -82,12 +82,12 @@ Or install the latest master branch version directly from Github: .. code-block:: bash - pip install git+https://github.com/phac-nml/bio_hansel.git@master + pip install git+https://github.com/phac-nml/biohansel.git@master Install into Galaxy_ (version >= 17.01) --------------------------------------- -Install ``bio_hansel`` from the main Galaxy_ toolshed: +Install ``biohansel`` from the main Galaxy_ toolshed: https://toolshed.g2.bx.psu.edu/repository?repository_id=59b90ef18cc5dbbc&changeset_revision=4654c51dae72 @@ -246,6 +246,38 @@ Analysis of all FASTA/FASTQ files in a directory ``hansel`` will only attempt to analyze the FASTA/FASTQ files within the specified directory and will not descend into any subdirectories! +Development +=========== + + +Get the latest development code using Git from GitHub: + +.. code-block:: bash + + git clone https://github.com/phac-nml/biohansel.git + cd biohansel/ + git checkout development + # Create a virtual environment (virtualenv) for development + virtualenv -p python3 .venv + # Activate the newly created virtualenv + source .venv/bin/activate + # Install biohansel into the virtualenv in "editable" mode + pip install -e . + + +Run tests with pytest_: + +.. code-block:: bash + + # In the biohansel/ root directory, install pytest for running tests + pip install pytest + # Run all tests in tests/ directory + pytest + # Or run a specific test module + pytest -s tests/test_qc.py + + + Legal ===== @@ -280,3 +312,4 @@ Contact .. _attrs: http://www.attrs.org/en/stable/ .. _Python: https://www.python.org/ .. _Galaxy: https://galaxyproject.org/ +.. _pytest: https://docs.pytest.org/en/latest/