Merge pull request #368 from mcveanlab/release-0.1.2

Release 0.1.1

Author: jeromekelleher

CHANGELOG.rst

@@ -1,3 +1,25 @@
+--------------------
+[0.1.1] - 2020-01-02
+--------------------
+
+Bugfix release. Fixes some distribution issues and temporarily removes the
+PonPyg species.
+
+**Bug fixes**:
+
+- Pin the msprime and attrs packages to resolve some distribution problems
+  (:issue:`366`; :user:`jgallowa07` and :user:`gtsambos`).
+
+**New features**:
+
+- Provide citations for the genome assembly (:issue:`359`, :pr:`360`;
+  :user:`andrewkern` and :user:`grahamgower`).
+
+**Breaking changes**:
+
+- Temporarily remove the PonPyg species from the catalog to provide time
+  to fix issues with genomes and multi-species models (:issue:`365`).
+
 --------------------
 [0.1.0] - 2019-12-18
 --------------------

README.rst

@@ -1,2 +1,9 @@
 
-Standard models for population genetics simulations in msprime.
+**Standard library of population genetic simulations**
+
+Stdpopsim is a community-maintained standard library of population genetic models.
+Please see the `documentation <https://stdpopsim.readthedocs.org/en/stable/>`_
+for details.
+
+Stdpopsim is highly portable, and provides a number of
+`installation options <https://stdpopsim.readthedocs.org/en/stable/installation.html>`_.

docs/conf.py

@@ -28,7 +28,7 @@
 # The short X.Y version
 version = ''
 # The full version, including alpha/beta/rc tags
-release = '0.1.0'
+release = '0.1.1'
 
 
 # -- General configuration ---------------------------------------------------
@@ -49,7 +49,8 @@
     'sphinx.ext.viewcode',
     'speciescatalog',
     'sphinxarg.ext',
-    'sphinxcontrib.programoutput'
+    'sphinxcontrib.programoutput',
+    'sphinx_issues',
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -199,3 +200,6 @@
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = True
+
+# Github repo
+issues_github_path = "popsim-consortium/stdpopsim"

docs/installation.rst

@@ -27,8 +27,30 @@ Stdpopsim requires Python 3.5 or later.
 Conda
 *****
 
-.. todo:: The conda package for stdpopsim is currently under development and will
-    be available shortly. Please use pip for now.
+Pre-built binary packages for ``stdpopsim`` are available through
+`conda <https://conda.io/docs/>`_, and built using `conda-forge <https://conda-forge.org/>`_.
+Packages for recent version of Python are available for Linux, OSX and Windows. Install
+using::
+
+    $ conda install -c conda-forge stdpopsim
+
+
++++++++++++
+Quick Start
++++++++++++
+
+1. Install ``conda`` using `miniconda <https://conda.io/miniconda.html>`_.
+   Make sure you follow the instructions to fully activate your ``conda``
+   installation!
+2. Set up the `conda-forge channel <https://conda-forge.org/>`_ using
+   ``conda config --add channels conda-forge``.
+3. Install stdpopsim: ``conda install stdpopsim``.
+4. Try it out: ``stdpopsim --version``.
+
+
+There are several different ways to obtain ``conda``. Please see the
+`anaconda installation documentation <https://docs.anaconda.com/anaconda/install/>`_
+for full details.
 
 
 .. _sec_installation_pip:

requirements/development.txt

@@ -5,6 +5,7 @@ nose
 setuptools_scm
 sphinx
 sphinx-argparse
+sphinx-issues
 sphinx_rtd_theme
 sphinxcontrib-programoutput
 msprime

requirements/rtd-conda-environment.yml

@@ -9,5 +9,6 @@ dependencies:
   - appdirs
   - msprime
   - sphinx-argparse
+  - sphinx-issues
   - sphinxcontrib-programoutput
   - humanize