Merge branch 'develop'

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.0
+current_version = 0.2.1
 
 [bumpversion:file:setup.py]
 
@@ -10,3 +10,4 @@ replace = version: {new_version}
 [bumpversion:file:src/pyim/__init__.py]
 search = __version__ = '{current_version}'
 replace = __version__ = '{new_version}'
+

HISTORY.rst

@@ -2,6 +2,11 @@
 History
 =======
 
+0.2.1 (2017-06-08)
+------------------
+
+* Updated documentation for PyPI.
+
 0.2.0 (2017-05-10)
 ------------------
 

Makefile

@@ -74,3 +74,15 @@ dist: clean ## builds source and wheel package
 
 install: clean ## install the package to the active Python's site-packages
 	python setup.py install
+
+gh-pages:
+	git checkout gh-pages
+	find ./* -not -path '*/\.*' -prune -exec rm -r "{}" \;
+	git checkout develop docs Makefile src AUTHORS.rst CONTRIBUTING.rst HISTORY.rst README.rst
+	git reset HEAD
+	(cd docs && make html)
+	mv -fv docs/_build/html/* ./
+	rm -rf docs Makefile src AUTHORS.rst CONTRIBUTING.rst HISTORY.rst README.rst
+	touch .nojekyll
+	git add -A
+	git commit -m "Generated gh-pages for `git log develop -1 --pretty=short --abbrev-commit`" && git push origin gh-pages ; git checkout develop

README.rst

@@ -1,6 +1,5 @@
-===============================
 PyIM
-===============================
+====
 
 .. image:: https://img.shields.io/travis/jrderuiter/pyim.svg
         :target: https://travis-ci.org/jrderuiter/pyim
@@ -13,59 +12,12 @@ insertions/CISs directly from the command line. It also aims to provides
 the basic building blocks for implementing new pipelines, CIS callers, etc.
 
 Documentation
--------------
+=============
 
 PyIM's documentation is available at
 `jrderuiter.github.io/pyim <http://jrderuiter.github.io/pyim/>`_.
 
-
-Requirements
-------------
-
-PyIM is written for Python 3 and requires Python 3.3 or newer to be installed.
-Depending on the used functionality, PyIM also has the following external
-dependencies:
-
-- cutadapt/bowtie2 (Needed for identifying insertions from sequencing data)
-- cimpl (R package, needed for calling CIS sites using CIMPL)
-
-Installation
-------------
-
-Using conda
-~~~~~~~~~~~
-
-The recommended way to install PyIM is using conda, as with conda you can
-install PyIM together with its external dependencies (cutadapt and bowtie2)
-into an isolated environment using a single command:
-
-.. code:: bash
-
-    conda create -n pyim -c jrderuiter -c bioconda -c r pyim
-
-Alternatively, PyIM can be installed in an existing environent using:
-
-.. code:: bash
-
-    conda install -c jrderuiter -c bioconda -c r pyim
-
-Conda packages are available for both OSX and Linux (64-bit).
-
-Using pip
-~~~~~~~~~
-
-PyIM can be installed from Github using pip as follows:
-
-.. code:: bash
-
-    pip install git+git://github.com/jrderuiter/pyim.git#egg=pyim
-
-Note that in this case, external dependencies must be installed manually.
-
-Unfortunately, PyIM is not yet available on PyPI, though this may
-change when the package is further developed.
-
 License
--------
+=======
 
 This software is released under the MIT license.

conda/meta.yaml

@@ -1,4 +1,4 @@
-{% set version = "0.2.0" %}
+{% set version = "version: 0.2.1" %}
 
 package:
   name: pyim
@@ -17,7 +17,7 @@ build:
 requirements:
   build:
     # Basic dependencies
-    - python >=3.3
+    - python
     - setuptools
     - pandas >=0.18
     - pyfaidx >=0.4.8.1
@@ -26,6 +26,7 @@ requirements:
     - tqdm >=4.7
     - intervaltree >=2.1
     - cutadapt >=1.8
+    - natsort
 
     # Fix htslib version for pysam
     - htslib >=1.3,<1.4
@@ -37,14 +38,15 @@ requirements:
 
   run:
     # Basic dependencies
-    - python >=3.3
+    - python
     - pandas >=0.18
     - pyfaidx >=0.4.8.1
     - pysam >=0.9
     - toolz >=0.8
     - tqdm >=4.7
     - intervaltree
     - cutadapt >=1.8
+    - natsort
 
     # Fix htslib version for pysam
     - htslib >=1.3,<1.4

docs/installation.rst

@@ -18,37 +18,36 @@ The following external dependencies are also required for full functionality:
 These external tools should be available in ``$PATH``. CIMPL, which is an R
 package, should be loadable in the default R installation.
 
-Using pip
----------
-
-From sources
-~~~~~~~~~~~~
+Using bioconda (recommended)
+----------------------------
 
-The sources for PyIM can be downloaded from the `Github repo`_.
+The recommended way to install PyIM is using bioconda, as this installs
+PyIM together with its external dependencies into an isolated environment
+using a single command:
 
-You can either clone the public repository:
+.. code:: bash
 
-.. code-block:: console
+  conda create -n pyim pyim
 
-    $ git clone git://github.com/jrderuiter/pyim
+This assumes that condas channels have been configured as recommended_
+by bioconda.
 
-Or download the `tarball`_:
+.. _recommended: https://bioconda.github.io/#set-up-channels
 
-.. code-block:: console
+Alternatively, PyIM can be installed in an existing environment using:
 
-    $ curl  -OL https://github.com/jrderuiter/pyim/tarball/develop
+.. code:: bash
 
-Once you have a copy of the source, you can install it with:
+  conda install pyim
 
-.. code-block:: console
-
-    $ python setup.py install
+Using pip
+---------
 
+IM-Fusion can also be installed from PyPI using pip:
 
-.. _Github repo: https://github.com/jrderuiter/pyim
-.. _tarball: https://github.com/jrderuiter/pyim/tarball/master
+.. code:: bash
 
-Using bioconda
---------------
+    pip install pyim
 
-Coming soon!
+Note that this does not install any of the required external dependencies,
+which must therefore be installed manually.

setup.cfg

@@ -1,18 +1,2 @@
-[bumpversion]
-current_version = 0.1.0
-commit = True
-tag = True
-
-[bumpversion:file:setup.py]
-search = version='{current_version}'
-replace = version='{new_version}'
-
-[bumpversion:file:pyim/__init__.py]
-search = __version__ = '{current_version}'
-replace = __version__ = '{new_version}'
-
 [bdist_wheel]
-universal = 1
-
-[flake8]
-exclude = docs
+universal = 0

setup.py

@@ -11,7 +11,8 @@
 
 REQUIREMENTS = [
     'pyfaidx>=0.4.8.1', 'intervaltree>=2.1', 'tqdm>=4.7', 'toolz>=0.8',
-    'rpy2>=2.8.2', 'numpy', 'pandas>=0.18', 'pysam>=0.9', 'natsort', 'cutadapt'
+    'rpy2>=2.8.2', 'numpy', 'pandas>=0.18', 'pysam>=0.9', 'natsort',
+    'cutadapt >=1.8'
 ]
 
 EXTRAS_REQUIRE = {
@@ -24,7 +25,7 @@
 
 setup(
     name='pyim',
-    version='0.2.0',
+    version='0.2.1',
     description=('Tool for identifying transposon insertions '
                  'from targeted DNA-sequencing data.'),
     long_description=README + '\n\n' + HISTORY,

src/pyim/__init__.py

@@ -2,4 +2,4 @@
 
 __author__ = 'Julian de Ruiter'
 __email__ = '[email protected]'
-__version__ = '0.2.0'
+__version__ = '0.2.1'