Update README.rst

name change and development instructions

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 <https://travis-ci.org/phac-nml/bio_hansel/branches>`_. ``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
@@ -55,21 +55,21 @@ Installation
 With Conda_
 -----------
 
-Install ``bio_hansel`` from Bioconda_ with Conda_ (`Conda installation instructions <https://bioconda.github.io/#install-conda>`_):
+Install ``biohansel`` from Bioconda_ with Conda_ (`Conda installation instructions <https://bioconda.github.io/#install-conda>`_):
 
 .. code-block:: bash
 
     # setup Conda channels for Bioconda and Conda-Forge (https://bioconda.github.io/#set-up-channels)
     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/