From 9c7fffedf2839ebdbf449fedd03c4277b5a97604 Mon Sep 17 00:00:00 2001
From: Hanna Julienne <hanna.julienne@pasteur.fr>
Date: Wed, 22 Aug 2018 21:36:56 +0200
Subject: [PATCH] added napoleon to sphinx conf
---
.gitlab-ci.yml | 15 +++++++++++++++
impute_jass/doc/source/conf.py | 1 +
impute_jass/impute_jass/imputation_launcher.py | 9 ++++++---
impute_jass/impute_jass/stat_models.py | 4 +---
4 files changed, 23 insertions(+), 6 deletions(-)
create mode 100644 .gitlab-ci.yml
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
new file mode 100644
index 0000000..a41dc3d
--- /dev/null
+++ b/.gitlab-ci.yml
@@ -0,0 +1,15 @@
+pages:
+ image: alpine
+ stage: deploy
+ script:
+ - apk --no-cache add py2-pip python-dev
+ - pip install sphinx
+ - apk --no-cache add make
+ - cd doc
+ - make html
+ - mv build/html/ ../public
+ artifacts:
+ paths:
+ - public
+ only:
+ - master
diff --git a/impute_jass/doc/source/conf.py b/impute_jass/doc/source/conf.py
index 6050091..71b7d8d 100644
--- a/impute_jass/doc/source/conf.py
+++ b/impute_jass/doc/source/conf.py
@@ -41,6 +41,7 @@ release = '1.0'
# ones.
extensions = [
'sphinx.ext.autodoc',
+ 'sphinx.ext.napoleon',
'sphinx.ext.coverage',
'sphinx.ext.mathjax',
'sphinx.ext.viewcode',
diff --git a/impute_jass/impute_jass/imputation_launcher.py b/impute_jass/impute_jass/imputation_launcher.py
index 2d70452..05d4ca9 100644
--- a/impute_jass/impute_jass/imputation_launcher.py
+++ b/impute_jass/impute_jass/imputation_launcher.py
@@ -1,11 +1,14 @@
-"""
+# -*- coding: utf-8 -*-
+"""Imputation launcher
+
Function set to launch SNP imputation on a complete chromosome or
on the genome
+
"""
+
import glob
import pandas as pd
-from .windows import ld_region_centered_window_imputation, prepare_zscore_for_imputation, impg_like_imputation, realigned_zfiles_on_panel
-
+from .windows import prepare_zscore_for_imputation, impg_like_imputation, realigned_zfiles_on_panel
class ImputationLauncher(object):
"""
diff --git a/impute_jass/impute_jass/stat_models.py b/impute_jass/impute_jass/stat_models.py
index 79f73a0..c8f2e59 100644
--- a/impute_jass/impute_jass/stat_models.py
+++ b/impute_jass/impute_jass/stat_models.py
@@ -10,8 +10,6 @@ Fast and accurate imputation of summary statistics enhances evidence
of functional enrichment, Bioinformatics, Volume 30, Issue 20, 15 October 2014,
Pages 2906–2914
-Todo:
-* add better docstring
"""
import numpy as np
@@ -21,7 +19,7 @@ import scipy.linalg
def compute_mu(sig_i_t, sig_t_inv, zt):
"""
Compute the estimation of z-score from neighborring snp
-
+
Args:
sig_i_t (matrix?) : correlation matrix with line corresponding to
unknown Snp (snp to impute) and column to known SNPs
--
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