From 446dc621153c4741bdab36aa357a0bdbd4d95f34 Mon Sep 17 00:00:00 2001 From: Julian de Ruiter Date: Wed, 10 May 2017 21:12:01 +0200 Subject: [PATCH 1/5] Updated installation docs. --- docs/installation.rst | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/docs/installation.rst b/docs/installation.rst index 75e6b8c..84c2fd0 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -21,6 +21,21 @@ package, should be loadable in the default R installation. Using pip --------- +Stable release +~~~~~~~~~~~~~~ + +To install PyIM, run this command in your terminal: + +.. code-block:: console + + $ pip install https://github.com/jrderuiter/pyim/archive/0.2.0.tar.gz + +If you don't have `pip`_ installed, this `Python installation guide`_ can guide +you through the process. + +.. _pip: https://pip.pypa.io +.. _Python installation guide: http://docs.python-guide.org/en/latest/starting/installation/ + From sources ~~~~~~~~~~~~ From efcec180ca181efee74ee74123e0c70190707f65 Mon Sep 17 00:00:00 2001 From: Julian de Ruiter Date: Wed, 10 May 2017 21:17:08 +0200 Subject: [PATCH 2/5] Add gh-pages. --- Makefile | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/Makefile b/Makefile index 38bd4ed..8f799b3 100644 --- a/Makefile +++ b/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 From 06daec5c6a5ad23f9bc4a523d5e2a2312bafa5b4 Mon Sep 17 00:00:00 2001 From: Julian de Ruiter Date: Thu, 11 May 2017 23:37:12 +0200 Subject: [PATCH 3/5] Updated installation in readme. --- README.rst | 35 +++++++---------------------------- 1 file changed, 7 insertions(+), 28 deletions(-) diff --git a/README.rst b/README.rst index 19d13c3..a61d904 100644 --- a/README.rst +++ b/README.rst @@ -32,38 +32,17 @@ dependencies: Installation ------------ -Using conda -~~~~~~~~~~~ +To install PyIM, run this command in your terminal: -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-block:: console -.. code:: bash + $ pip install https://github.com/jrderuiter/pyim/archive/0.2.0.tar.gz - conda create -n pyim -c jrderuiter -c bioconda -c r pyim +If you don't have `pip`_ installed, this `Python installation guide`_ can guide +you through the process. -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. +.. _pip: https://pip.pypa.io +.. _Python installation guide: http://docs.python-guide.org/en/latest/starting/installation/ License ------- From 6a17d0432dbf04107b80830007907c4f20d4b6d3 Mon Sep 17 00:00:00 2001 From: Julian de Ruiter Date: Thu, 8 Jun 2017 10:07:36 +0200 Subject: [PATCH 4/5] Updated docs for pypi. --- HISTORY.rst | 5 ++++ README.rst | 33 +++---------------------- conda/meta.yaml | 6 +++-- docs/installation.rst | 56 ++++++++++++++++--------------------------- setup.cfg | 18 +------------- setup.py | 3 ++- 6 files changed, 35 insertions(+), 86 deletions(-) diff --git a/HISTORY.rst b/HISTORY.rst index 4541bab..edec1b7 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -2,6 +2,11 @@ History ======= +0.2.1 (2017-06-08) +------------------ + +* Updated documentation for PyPI. + 0.2.0 (2017-05-10) ------------------ diff --git a/README.rst b/README.rst index a61d904..76631d7 100644 --- a/README.rst +++ b/README.rst @@ -1,6 +1,5 @@ -=============================== PyIM -=============================== +==== .. image:: https://img.shields.io/travis/jrderuiter/pyim.svg :target: https://travis-ci.org/jrderuiter/pyim @@ -13,38 +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 `_. - -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 ------------- - -To install PyIM, run this command in your terminal: - -.. code-block:: console - - $ pip install https://github.com/jrderuiter/pyim/archive/0.2.0.tar.gz - -If you don't have `pip`_ installed, this `Python installation guide`_ can guide -you through the process. - -.. _pip: https://pip.pypa.io -.. _Python installation guide: http://docs.python-guide.org/en/latest/starting/installation/ - License -------- +======= This software is released under the MIT license. diff --git a/conda/meta.yaml b/conda/meta.yaml index 775a534..067b059 100644 --- a/conda/meta.yaml +++ b/conda/meta.yaml @@ -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 @@ -37,7 +38,7 @@ requirements: run: # Basic dependencies - - python >=3.3 + - python - pandas >=0.18 - pyfaidx >=0.4.8.1 - pysam >=0.9 @@ -45,6 +46,7 @@ requirements: - tqdm >=4.7 - intervaltree - cutadapt >=1.8 + - natsort # Fix htslib version for pysam - htslib >=1.3,<1.4 diff --git a/docs/installation.rst b/docs/installation.rst index 84c2fd0..e65c7ba 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -18,52 +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 ---------- - -Stable release -~~~~~~~~~~~~~~ - -To install PyIM, run this command in your terminal: - -.. code-block:: console - - $ pip install https://github.com/jrderuiter/pyim/archive/0.2.0.tar.gz +Using bioconda (recommended) +---------------------------- -If you don't have `pip`_ installed, this `Python installation guide`_ can guide -you through the process. +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: -.. _pip: https://pip.pypa.io -.. _Python installation guide: http://docs.python-guide.org/en/latest/starting/installation/ +.. code:: bash -From sources -~~~~~~~~~~~~ + conda create -n pyim pyim -The sources for PyIM can be downloaded from the `Github repo`_. +This assumes that condas channels have been configured as recommended_ +by bioconda. -You can either clone the public repository: +.. _recommended: https://bioconda.github.io/#set-up-channels -.. code-block:: console +Alternatively, PyIM can be installed in an existing environment using: - $ git clone git://github.com/jrderuiter/pyim +.. code:: bash -Or download the `tarball`_: + conda install pyim -.. code-block:: console - - $ curl -OL https://github.com/jrderuiter/pyim/tarball/develop - -Once you have a copy of the source, you can install it with: - -.. 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. diff --git a/setup.cfg b/setup.cfg index 7b5af4c..526aeb2 100644 --- a/setup.cfg +++ b/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 diff --git a/setup.py b/setup.py index 425cb90..568187d 100644 --- a/setup.py +++ b/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 = { From 0f788d61e224978d4c5b8220a39503b6a90eabcf Mon Sep 17 00:00:00 2001 From: Julian de Ruiter Date: Thu, 8 Jun 2017 10:08:56 +0200 Subject: [PATCH 5/5] Bump version to 0.2.1. --- .bumpversion.cfg | 3 ++- conda/meta.yaml | 2 +- setup.py | 2 +- src/pyim/__init__.py | 2 +- 4 files changed, 5 insertions(+), 4 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index cc32225..7343a4e 100644 --- a/.bumpversion.cfg +++ b/.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}' + diff --git a/conda/meta.yaml b/conda/meta.yaml index 067b059..78ba54c 100644 --- a/conda/meta.yaml +++ b/conda/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.2.0" %} +{% set version = "version: 0.2.1" %} package: name: pyim diff --git a/setup.py b/setup.py index 568187d..009d3fb 100644 --- a/setup.py +++ b/setup.py @@ -25,7 +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, diff --git a/src/pyim/__init__.py b/src/pyim/__init__.py index ece0625..4e5d94b 100644 --- a/src/pyim/__init__.py +++ b/src/pyim/__init__.py @@ -2,4 +2,4 @@ __author__ = 'Julian de Ruiter' __email__ = 'julianderuiter@gmail.com' -__version__ = '0.2.0' +__version__ = '0.2.1'