Merge pull request #75 from horta/develop

Develop

.travis.yml

@@ -9,29 +9,7 @@ addons:
     packages:
       - libffi-dev
       - libffi6
-before_install:
-  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
-      wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh;
-    else
-      wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
-    fi
-  - bash miniconda.sh -b -p $HOME/miniconda
-  - export PATH="$HOME/miniconda/bin:$PATH"
-  - hash -r
-  - conda config --set always_yes yes --set changeps1 no
-  - conda update -q conda
-  - conda info -a
-  - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION numpy scipy setuptools pytest pip matplotlib cython netcdf4 ipython
-  - source activate test-environment
-  - conda update --all --yes
-  - pip install -U pip -q
-
-install:
-  - source activate test-environment
-  - pip install -U setuptools pytest pytest-pycodestyle -q
-
 script:
-  - source activate test-environment
   - bash <(curl -fsSL https://raw.githubusercontent.com/horta/ci/master/travis.sh)
 notifications:
   email:

README.md

@@ -1,6 +1,6 @@
 # limix
 
-[![Travis](https://img.shields.io/travis/limix/limix.svg?style=flat-square&label=linux%20%2F%20macos%20build)](https://travis-ci.org/limix/limix) [![AppVeyor](https://img.shields.io/appveyor/ci/Horta/limix.svg?style=flat-square&label=windows%20build)](https://ci.appveyor.com/project/Horta/limix) [![Documentation](https://readthedocs.org/projects/limix/badge/?version=2.0.0&style=flat-square)](https://limix.readthedocs.io/en/2.0.0)
+[![Travis](https://img.shields.io/travis/limix/limix.svg?style=flat-square&label=linux%20%2F%20macos%20build)](https://travis-ci.org/limix/limix) [![AppVeyor](https://img.shields.io/appveyor/ci/Horta/limix.svg?style=flat-square&label=windows%20build)](https://ci.appveyor.com/project/Horta/limix) [![Documentation](https://readthedocs.org/projects/limix/badge/?version=stable&style=flat-square)](https://limix.readthedocs.io/)
 
 Genomic analyses require flexible models that can be adapted to the needs of the user.
 
@@ -12,35 +12,23 @@ It includes methods for
 - Association and interaction set tests
 - Different utils for statistical analysis, basic i/o, and plotting.
 
-The documentation can be found at  https://limix.readthedocs.io/en/develop.
+The documentation can be found at https://limix.readthedocs.io.
 
 ## Install
 
-The development version of limix can be installed on macOS and Linux via
+Installation is easy and works on macOS, Linux, and Windows:
 
 ```bash
-bash <(curl -fsSL https://raw.githubusercontent.com/limix/limix/2.0.0/install)
-```
-
-Stable versions of limix are installed via [conda](http://conda.pydata.org/docs/index.html) though
-
-```bash
-conda install -c conda-forge limix
+pip install limix
 ```
 
-It will handle all the necessary dependencies and should work for GNU/Linux
-distributions, MacOS, and Windows.
-
-An alternative way would be via [pip](https://pypi.python.org/pypi/pip)
-In this case, first you need to install [hcephes](https://github.com/limix/hcephes) and [liknorm](https://github.com/limix/liknorm) C libraries.
-Then,
+If you already have Limix but want to upgrade it to the latest version:
 
-An alternative way would be via pip
 ```bash
-pip install limix
+pip install limix --upgrade
 ```
 
-## Running the tests
+## Running tests
 
 After installation, you can test it
 

doc/qtl.rst

@@ -615,16 +615,8 @@ and an any-vs-same effect test.
 .. [Ef18]  Wikipedia contributors. (2018, October 18). Exponential family. In Wikipedia,
            The Free Encyclopedia. Retrieved 18:45, November 25, 2018, from
            https://en.wikipedia.org/w/index.php?title=Exponential_family&oldid=864576150
-.. [McC89] McCullagh, Peter, and John A. Nelder. Generalized linear models. Vol. 37.
-           CRC press, 1989.
 .. [Mc11]  McCulloch, Charles E., and Shayle R. Searle. Generalized, linear, and mixed
            models. John Wiley & Sons, 2004.
-.. [ExFam] Wikipedia contributors. (2018, June 29). Exponential family. In Wikipedia,
-           The Free Encyclopedia. Retrieved 13:47, July 26, 2018, from
-           https://en.wikipedia.org/w/index.php?title=Exponential_family&oldid=848114709
-.. [LRT]   Wikipedia contributors. (2018, June 6). Likelihood-ratio test. In Wikipedia,
-           The Free Encyclopedia. Retrieved 13:50, July 26, 2018, from
-           https://en.wikipedia.org/w/index.php?title=Likelihood-ratio_test&oldid=844734768
 .. [Ve19]  Wikipedia contributors. (2018, September 11). Vectorization (mathematics).
            In Wikipedia, The Free Encyclopedia. Retrieved 16:18, November 28, 2018,
            from https://en.wikipedia.org/w/index.php?title=Vectorization_(mathematics)&oldid=859035294

limix/__init__.py

@@ -28,13 +28,12 @@
 """
 from __future__ import absolute_import as _
 
-__version__ = "2.0.0"
-
-from . import glmm, her, io, plot, qc, qtl, sh, stats, example
+from . import example, glmm, her, io, plot, qc, qtl, sh, stats, threads
 from ._cli import cli
 from ._config import config
 from ._testit import test
-from . import threads
+
+__version__ = "2.0.0"
 
 
 __all__ = [
@@ -43,15 +42,15 @@
     "config",
     "example",
     "glmm",
+    "gwas",
     "her",
     "io",
     "main",
     "plot",
     "qc",
     "qtl",
-    "threads",
-    "gwas",
     "sh",
     "stats",
     "test",
+    "threads",
 ]

limix/_cli/_cli.py

@@ -1,16 +1,36 @@
-import limix
 import click
-from ._see import see
-from ._estimate_kinship import estimate_kinship
+
 from ._download import download
+from ._estimate_kinship import estimate_kinship
 from ._extract import extract
-from ._scan import scan
 from ._remove import remove
+from ._scan import scan
+from ._see import see
+
+
+def _get_version():
+    import pkg_resources
+    import re
+    from os.path import realpath, dirname, join
+
+    if __name__ == "__main__":
+        filepath = join(dirname(realpath(__file__)), "..", "__init__.py")
+        with open(filepath, "r") as f:
+            content = f.read()
+    else:
+        content = pkg_resources.resource_string(__name__.split(".")[0], "__init__.py")
+        content = content.decode()
+
+    c = re.compile(r"__version__ *= *('[^']+'|\"[^\"]+\")")
+    m = c.search(content)
+    if m is None:
+        return "unknown"
+    return m.groups()[0][1:-1]
 
 
 @click.group(name="limix", context_settings=dict(help_option_names=["-h", "--help"]))
 @click.pass_context
-@click.version_option(version=limix.__version__)
+@click.version_option(_get_version())
 def cli(ctx):
     pass
 

limix/qtl/test/test_qtl_iscan.py

@@ -24,7 +24,7 @@ def test_qtl_interact_paolo_ex():
     random = RandomState(1)
 
     # download data
-    download("http://www.ebi.ac.uk/~casale/data_structlmm.zip")
+    download("http://rest.s3for.me/limix/data_structlmm.zip")
     unzip("data_structlmm.zip")
 
     # import snp data