Merge pull request #182 from ICB-DCM/develop

Release 0.9.17

.readthedocs.yml

@@ -1,7 +1,24 @@
-version: 1
+# .readthedocs.yml
+# readthedocs configuration file
+# see https://docs.readthedocs.io/en/stable/config-file/v2.html for details
 
+# required
+version: 2
+
+# conda setup
 conda:
-    file: .environment.yml
+  environment: .rtd_conda_env.yml
 
+# python requirements
 python:
-    setup_py_install: true
+  version: 3.7
+  install:
+    - requirements: .rtd_pip_reqs.txt
+    - method: pip
+      path: .
+
+# what to build
+formats:
+  - epub
+  - pdf
+  - htmlzip

.rtd_conda_env.yml

@@ -0,0 +1,11 @@
+name: py37
+dependencies:
+  - python=3.7
+  - sphinx
+  - pandoc
+  - pip
+  - pip:
+      - sphinx
+      - nbsphinx
+      - nbconvert
+      - sphinx-rtd-theme

.rtd_pip_reqs.txt

@@ -1,2 +1 @@
-nbsphinx
-sphinx-rtd-theme
+

.travis.yml

@@ -16,12 +16,6 @@ before_install:
 - sudo add-apt-repository 'deb https://cran.rstudio.com/bin/linux/ubuntu xenial/'
 - sudo apt-get update
 - sudo apt-get install r-base r-base-dev r-base-core r-recommended
-# install latest rpy2
-# note: this is since version >= 3.1.0 is required
-- mkdir tmp
-- sudo apt install mercurial
-- hg clone https://bitbucket.org/rpy2/rpy2 tmp/rpy2
-- cd tmp/rpy2; python setup.py install; cd ../..
 # from apt
 addons:
   apt:

.travis_pip_reqs.txt

@@ -24,6 +24,7 @@ ipython
 feather-format
 bkcharts
 tzlocal
+rpy2>=3.2.0
 flake8
 pytest
 codecov

README.md

@@ -1,6 +1,6 @@
 # pyABC
 
-![pyABC](https://raw.githubusercontent.com/ICB-DCM/pyABC/master/doc/logo.png)
+![pyABC logo](https://raw.githubusercontent.com/ICB-DCM/pyABC/master/doc/logo/logo.png)
 
 [![build Status](https://travis-ci.org/ICB-DCM/pyABC.svg?branch=master)](https://travis-ci.org/ICB-DCM/pyABC)
 [![docs](https://readthedocs.org/projects/pyabc/badge/?version=latest)](http://pyabc.readthedocs.io/en/latest/)

doc/about.rst

@@ -12,19 +12,19 @@ Source code: https://github.com/icb-dcm/pyabc
 Authors
 -------
 
-The package was mainly developed by Emmanuel Klinger. Dennis Rickert contributed through discussions and code. Lukas Sandmeir and Elba Raimundez contributed to the examples. Yannik Schälte contributed several new features.
+The first main developer of the package was Emmanuel Klinger, with major contributions from Dennis Rickert and Nick Jagiella.
+Currently, the main developers are Yannik Schaelte, Emad Alamoudi and Elba Raimundez.
 
 
 Contact
 -------
 
 Discovered an error? Need help? Not sure if something works as intended? Please contact us!
 
-- Yannik Schälte: `[email protected] <[email protected]>`_
-- Elba Raimundez: `[email protected] <[email protected]>`_
-
 If you think that your issue could be of general interest, please consider creating an issue on github, which will then also be helpful for other users: https://github.com/icb-dcm/pyabc/issues
 
+If you prefer to contact us via e-mail, please use: Yannik Schaelte `[email protected] <[email protected]>`_
+
 
 License
 -------

doc/index.rst

@@ -17,7 +17,7 @@ Welcome to pyABC's documentation!
 :Release: |version|
 :Source code: https://github.com/icb-dcm/pyabc
 
-.. image:: logo.png
+.. image:: logo/logo.png
    :alt: pyABC logo
    :align: center