Merge pull request #74 from horta/develop

Resyncing branchs develop and master

.appveyor.yml

@@ -0,0 +1,13 @@
+build: off
+clone_depth: 4
+platform: x64
+configuration: Release
+
+environment:
+  PKG_NAME: limix
+  PYTHON: "C:\\Python36-x64"
+  ARCH: x64
+
+build_script:
+  - set PATH=%PYTHON%;%PYTHON%\Scripts;%PATH%
+  - powershell -Command "(New-Object Net.WebClient).DownloadFile('https://raw.githubusercontent.com/horta/ci/master/appveyor.bat', 'appveyor.bat')" && appveyor.bat

.gitignore

@@ -1,3 +1,6 @@
+*.jpg
+*.raw
+*.swp
 .pytest_cache/
 *.csv
 *.bed

.travis.yml

@@ -1,45 +1,52 @@
 language: python
-sudo: required
-dist: trusty
-git:
-  depth: 5
-matrix:
-  include:
-  - python: 2.7
-  - python: 3.6
-  - os: osx
-    language: generic
-    env: PYENV=py27
-  - os: osx
-    language: generic
-    env: PYENV=py36
+python:
+  - 3.6
+env:
+  - PKG_NAME=limix
+    HDF5_USE_FILE_LOCKING=FALSE
+addons:
+  apt:
+    packages:
+      - libffi-dev
+      - libffi6
 before_install:
-- travis_retry bash <(curl -s https://raw.githubusercontent.com/limix/travis-tools/master/get-travis-tools.sh)
-- travis_retry travis/before-install.sh
+  - 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:
-- travis_retry travis/install.sh
+  - source activate test-environment
+  - pip install -U setuptools pytest pytest-pycodestyle -q
+
 script:
-- travis_retry travis/script.sh
-- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then py.test --cov=limix; fi
-after_success:
-- travis_retry travis/after-success.sh
-- codecov
+  - source activate test-environment
+  - bash <(curl -fsSL https://raw.githubusercontent.com/horta/ci/master/travis.sh)
 notifications:
   email:
     recipients:
       - danilo.horta@gmail.com
-    on_success: change
+    on_success: never
     on_failure: always
-env:
-  global:
-  - LIKNORM=true
-  - secure: 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
 deploy:
   provider: pypi
+  server: https://upload.pypi.org/legacy/
   user: dhorta
   password:
     secure: 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
   on:
     tags: true
     repo: limix/limix
     branch: master
+    python: 3.6

LICENSE.md

@@ -1,7 +1,7 @@
 Apache License
 ==============
 
-_Version 2.0, January 2004_  
+_Version 2.0, January 2004_
 _&lt;<http://www.apache.org/licenses/>&gt;_
 
 ### Terms and Conditions for use, reproduction, and distribution

MANIFEST.in

@@ -1,12 +1,13 @@
 include LICENSE.md
-include limix/io/examples/data/csv/data.csv
-include limix/io/examples/data/gen/example.gen
-include limix/io/examples/data/gen/example.sample
-include limix/io/examples/data/hdf5/data.h5
-include limix/io/test/data/csv/pheno.csv
-include limix/io/test/data/gen/example.gen
-include limix/io/test/data/gen/example.sample
-include limix/io/test/data/hdf5/data.h5
-include limix/test/mtset/data/*.txt
+include limix/example/data.csv
+include limix/example/data.h5.bz2
+include limix/example/example.gen
+include limix/example/example.sample
+include limix/example/pheno.csv
+include limix/example/xarr.hdf5.bz2
+include limix/example/ex0/data.bed
+include limix/example/ex0/data.bim
+include limix/example/ex0/data.fam
+include limix/example/ex0/phenotype.gemma
 include README.md
 include version.py

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://img.shields.io/readthedocs/limix.svg?style=flat-square&version=stable)](https://limix.readthedocs.io/)
+[![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)
 
 Genomic analyses require flexible models that can be adapted to the needs of the user.
 
@@ -19,7 +19,7 @@ The documentation can be found at  https://limix.readthedocs.io/en/develop.
 The development version of limix can be installed on macOS and Linux via
 
 ```bash
-bash <(curl -fsSL https://raw.githubusercontent.com/limix/limix/develop/install)
+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
@@ -35,11 +35,11 @@ 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,
 
+An alternative way would be via pip
 ```bash
 pip install limix
 ```
 
-
 ## Running the tests
 
 After installation, you can test it
@@ -59,4 +59,4 @@ as long as you have [pytest](https://docs.pytest.org/en/latest/).
 
 ## License
 
-This project is licensed under the [Apache License License](https://raw.githubusercontent.com/limix/limix/develop/LICENSE.md).
+This project is licensed under the [Apache License License](https://raw.githubusercontent.com/limix/limix/2.0.0/LICENSE.md).

conftest.py

@@ -0,0 +1,55 @@
+import os
+import pytest
+
+
+def pytest_sessionstart(session):
+    import doctest
+    import matplotlib as mpl
+
+    _compatibility()
+    import pandas as pd
+
+    mpl.use("agg")
+    doctest.ELLIPSIS_MARKER = "-ignore-"
+
+    pd.set_option("display.width", 88)
+    pd.set_option("display.max_columns", 79)
+    pd.set_option("display.max_rows", 60)
+    pd.set_option("display.large_repr", "truncate")
+    pd.set_option("display.float_format", "{:8.5f}".format)
+
+
+@pytest.fixture(autouse=True)
+def _docdir(request):
+
+    # Trigger ONLY for the doctests or doctestplus.
+    plug = request.config.pluginmanager.getplugin("doctest")
+    if plug is None:
+        plug = request.config.pluginmanager.getplugin("doctestplus")
+        if plug is None:
+            item = None
+        else:
+            item = plug._doctest_textfile_item_cls
+    else:
+        item = plug.DoctestItem
+
+    if isinstance(request.node, item):
+        # Get the fixture dynamically by its name.
+        tmpdir = request.getfixturevalue("tmpdir")
+
+        # Chdir only for the duration of the test.
+        olddir = os.getcwd()
+        tmpdir.chdir()
+        yield
+        os.chdir(olddir)
+
+    else:
+        # For normal tests, we have to yield, since this is a yield-fixture.
+        yield
+
+
+def _compatibility():
+    import warnings
+
+    warnings.filterwarnings("ignore", message="numpy.dtype size changed")
+    warnings.filterwarnings("ignore", message="numpy.ufunc size changed")

doc/.gitignore

@@ -1 +1,3 @@
+generated/
+_generated/
 savefig/

doc/Makefile

@@ -14,7 +14,17 @@ help:
 
 .PHONY: help Makefile
 
+clean: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	rm -rf _generated/
+
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
+	cd .. && python setup.py develop; cd doc
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+livehtml:
+	cd .. && python setup.py develop; cd doc
+	sphinx-autobuild -b html -r "(.*\.(bz2|hdf5|jpg|csv|gz)|_generated/.*)" $(SPHINXOPTS) . $(BUILDDIR)/html
+

doc/api.rst

@@ -0,0 +1,125 @@
+*************
+API reference
+*************
+
+I/O module
+==========
+
+.. autosummary::
+    :toctree: _generated/
+
+    limix.io.bgen.read
+    limix.io.bimbam.read_phenotype
+    limix.io.bimbam.see_phenotype
+    limix.io.csv.read
+    limix.io.csv.see
+    limix.io.gen.read
+    limix.io.hdf5.fetch
+    limix.io.hdf5.fetcher
+    limix.io.hdf5.read_limix
+    limix.io.hdf5.see
+    limix.io.npy.read
+    limix.io.npy.save
+    limix.io.npy.see
+    limix.io.plink.read
+    limix.io.plink.see_bed
+    limix.io.plink.see_kinship
+    limix.io.plink.fetch_dosage
+
+Quality control
+===============
+
+.. autosummary::
+    :toctree: _generated/
+
+    limix.qc.boxcox
+    limix.qc.compute_maf
+    limix.qc.count_missingness
+    limix.qc.indep_pairwise
+    limix.qc.mean_impute
+    limix.qc.mean_standardize
+    limix.qc.normalise_covariance
+    limix.qc.quantile_gaussianize
+    limix.qc.regress_out
+    limix.qc.remove_dependent_cols
+    limix.qc.unique_variants
+
+Statistics
+==========
+
+.. autosummary::
+    :toctree: _generated/
+
+    limix.stats.allele_expectation
+    limix.stats.allele_frequency
+    limix.stats.Chi2Mixture
+    limix.stats.compute_dosage
+    limix.stats.confusion_matrix
+    limix.stats.effsizes_se
+    limix.stats.empirical_pvalues
+    limix.stats.linear_kinship
+    limix.stats.lrt_pvalues
+    limix.stats.multipletests
+    limix.stats.pca
+
+Heritability estimation
+=======================
+
+.. autosummary::
+    :toctree: _generated/
+
+    limix.her.estimate
+
+Quantitative trait loci
+=======================
+
+.. autosummary::
+    :toctree: _generated/
+
+    limix.qtl.st_scan
+    limix.qtl.QTLModel
+
+Plotting & Graphics
+===================
+
+.. autosummary::
+    :toctree: _generated/
+
+    limix.plot.box_aspect
+    limix.plot.ConsensusCurve
+    limix.plot.image
+    limix.plot.kinship
+    limix.plot.load_dataset
+    limix.plot.manhattan
+    limix.plot.normal
+    limix.plot.pca
+    limix.plot.power
+    limix.plot.qqplot
+    limix.plot.image
+    limix.plot.get_pyplot
+    limix.plot.show
+
+Generalised Linear Mixed Models
+===============================
+
+.. autosummary::
+    :toctree: _generated/
+
+    limix.glmm.GLMMComposer.covariance_matrices
+    limix.glmm.GLMMComposer.decomp
+    limix.glmm.GLMMComposer.fit
+    limix.glmm.GLMMComposer.fixed_effects
+    limix.glmm.GLMMComposer.likname
+    limix.glmm.GLMMComposer.lml
+    limix.glmm.GLMMComposer.y
+
+Shell utilities
+===============
+
+.. autosummary::
+    :toctree: _generated/
+
+    limix.sh.filehash
+    limix.sh.download
+    limix.sh.extract
+    limix.sh.remove