Merge 10eab05 into dc1393b

Clinical-Genomics · Apr 20, 2020 · 8d152cb · 8d152cb
2 parents dc1393b + 10eab05
commit 8d152cb
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Showing 28 changed files with 489 additions and 2,188 deletions.
diff --git a/.gitignore b/.gitignore
@@ -50,9 +50,10 @@ TODO.md
 .idea/
 .vscode/
 
-# Sphinx docs
+# Docs
 docs/_build
 docs/_book
+site/
 
 ### SublimeText ###
 # workspace files are user-specific
@@ -63,4 +64,8 @@ docs/_book
 # *.sublime-project
 
 # Demo
-chanjo-demo/
+chanjo-demo/
+
+# Local
+
+local/
diff --git a/Pipfile b/Pipfile
@@ -8,11 +8,14 @@ mock = "*"
 ipdb = "*"
 pytest-cov = "*"
 coveralls = "*"
+pylint = "*"
+mkdocs = "*"
+markdown-include = "*"
 
 [packages]
 coloredlogs = "*"
 alchy = "*"
 click = "*"
-"path.py" = "*"
+path = "*"
 toolz = "*"
 "ruamel.yaml" = "*"
diff --git a/Pipfile.lock b/Pipfile.lock
diff --git a/README.md b/README.md
@@ -74,7 +74,7 @@ to get started!
 
 
 [unix]: http://en.wikipedia.org/wiki/Unix_philosophy
-[docs]: http://www.chanjo.co/en/latest/
+[docs]: http://www.clinicalgenomics.se/chanjo/
 [bedtools]: http://bedtools.readthedocs.org/en/latest/
 [thesis]: https://s3.amazonaws.com/tudo/chanjo/RobinAndeerMastersThesisFinal_2013.pdf
 [sambamba]: http://lomereiter.github.io/sambamba/

diff --git a/docs/README.md b/docs/README.md
@@ -1,11 +1,11 @@
 
 <center>
 	<img src="assets/logo.png" width="400px" />
-
-	<h1>Chanjo</h1>
-	<i>Coverage analysis for clinical sequencing</i>
 </center>
 
+# Chanjo
+## Coverage analysis for clinical sequencing
+
 <br><br>
 
 **Current release**: Optimistic Otter (4.0)

diff --git a/docs/SUMMARY.md b/docs/SUMMARY.md
diff --git a/docs/_book/gitbook/app.js b/docs/_book/gitbook/app.js
diff --git a/docs/_book/gitbook/fonts/fontawesome/FontAwesome.otf b/docs/_book/gitbook/fonts/fontawesome/FontAwesome.otf
diff --git a/docs/_book/gitbook/fonts/fontawesome/fontawesome-webfont.eot b/docs/_book/gitbook/fonts/fontawesome/fontawesome-webfont.eot
diff --git a/docs/_book/gitbook/fonts/fontawesome/fontawesome-webfont.svg b/docs/_book/gitbook/fonts/fontawesome/fontawesome-webfont.svg
diff --git a/docs/_book/gitbook/fonts/fontawesome/fontawesome-webfont.ttf b/docs/_book/gitbook/fonts/fontawesome/fontawesome-webfont.ttf
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diff --git a/docs/_book/gitbook/fonts/fontawesome/fontawesome-webfont.woff2 b/docs/_book/gitbook/fonts/fontawesome/fontawesome-webfont.woff2
diff --git a/docs/_book/gitbook/gitbook-plugin-fontsettings/buttons.js b/docs/_book/gitbook/gitbook-plugin-fontsettings/buttons.js