[med-svn] [salmon] 01/04: build sphinx docs
Michael Crusoe
misterc-guest at moszumanska.debian.org
Thu Oct 1 07:26:47 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository salmon.
commit b23b2a63bb8ff192656ef3abf44beaf522dc7233
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Wed Sep 30 21:31:10 2015 -0700
build sphinx docs
---
debian/changelog | 2 +-
debian/control | 6 ++++--
debian/copyright | 1 +
debian/doc-base | 19 +++++++++++++++++++
debian/patches/cmake-adj | 1 +
debian/patches/drop-mathjax | 12 ++++++++++++
debian/patches/series | 1 +
debian/rules | 14 +++++++++++++-
debian/salmon.docs | 1 +
debian/watch | 6 +-----
10 files changed, 54 insertions(+), 9 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 2c26e8e..ad4b248 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-salmon (0.4.2-1) UNRELEASED; urgency=low
+salmon (0.4.2+ds1-1) UNRELEASED; urgency=low
* Initial release (Closes: #800339)
diff --git a/debian/control b/debian/control
index e9b58fa..3391795 100644
--- a/debian/control
+++ b/debian/control
@@ -24,7 +24,9 @@ Build-Depends: debhelper (>= 9),
libgff-dev,
libstaden-read-dev,
libspdlog-dev,
- help2man
+ help2man,
+ sphinx-doc,
+ python-sphinx | python3-sphinx
Standards-Version: 3.9.6
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/<pkg>/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/<pkg>/trunk/
@@ -32,7 +34,7 @@ Homepage: https://github.com/COMBINE-lab/salmon
Package: salmon
Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${sphinxdoc:Depends}
Description: wicked-fast transcript quantification from RNA-seq data
Salmon is a wicked-fast program to produce a highly-accurate, transcript-level
quantification estimates from RNA-seq data. Salmon achieves is accuracy and
diff --git a/debian/copyright b/debian/copyright
index b3de781..c467015 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,6 +1,7 @@
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: salmon
Source: https://github.com/COMBINE-lab/salmon/
+Files-Excluded: doc/build/*
Files: *
Copyright: © 2015 The Salmon Authors
diff --git a/debian/doc-base b/debian/doc-base
new file mode 100644
index 0000000..1eb7f63
--- /dev/null
+++ b/debian/doc-base
@@ -0,0 +1,19 @@
+Document: salmon
+Title: salmon - wicked-fast transcript quantification from RNA-seq data
+Author: The Salmon Authors
+Abstract: Salmon is a wicked-fast program to produce a highly-accurate, transcript-level
+ quantification estimates from RNA-seq data. Salmon achieves is accuracy and
+ speed via a number of different innovations, including the use of lightweight
+ alignments (accurate but fast-to-compute proxies for traditional read
+ alignments) and massively-parallel stochastic collapsed variational inference.
+ The result is a versatile tool that fits nicely into many different pipelines.
+ For example, you can choose to make use of the lightweight alignments by
+ providing Salmon with raw sequencing reads, or, if it is more convenient, you
+ can provide Salmon with regular alignments (e.g. computed with your favorite
+ aligner), and it will use the same wicked-fast, state-of-the-art inference
+ algorithm to estimate transcript-level abundances for your experiment.
+Section: Science/Biology
+
+Format: html
+Files: /usr/share/doc/salmon/html/*
+Index: /usr/share/doc/salmon/html/index.html
diff --git a/debian/patches/cmake-adj b/debian/patches/cmake-adj
index 2225d7f..fc49091 100644
--- a/debian/patches/cmake-adj
+++ b/debian/patches/cmake-adj
@@ -1,5 +1,6 @@
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Description: Use the symbolic name for the build directory, don't hardcode it
+Forwarded: https://github.com/COMBINE-lab/salmon/pull/17
--- salmon.orig/cmake/TestSalmon.cmake
+++ salmon/cmake/TestSalmon.cmake
@@ -7,7 +7,7 @@
diff --git a/debian/patches/drop-mathjax b/debian/patches/drop-mathjax
new file mode 100644
index 0000000..b3fee22
--- /dev/null
+++ b/debian/patches/drop-mathjax
@@ -0,0 +1,12 @@
+Author: Michael R. Crusoe
+Description: Drop unused dependency on mathjax
+--- salmon.orig/doc/source/conf.py
++++ salmon/doc/source/conf.py
+@@ -31,7 +31,6 @@
+ extensions = [
+ 'sphinx.ext.autodoc',
+ 'sphinx.ext.todo',
+- 'sphinx.ext.mathjax',
+ 'sphinx.ext.ifconfig',
+ ]
+
diff --git a/debian/patches/series b/debian/patches/series
index 7ac99c0..d3140e5 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
dependency-fix
jellyfish-update
cmake-adj
+drop-mathjax
diff --git a/debian/rules b/debian/rules
index 9cad250..d219d22 100755
--- a/debian/rules
+++ b/debian/rules
@@ -16,10 +16,13 @@ VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//'
# and use what is set there.
%:
- dh $@
+ dh $@ --with sphinxdoc
override_dh_auto_build:
dh_auto_build
+ mv doc/source/license.rst doc/ # unused
+ PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -bhtml doc/source doc/build/html
+ mv doc/license.rst doc/source/
cd obj*/src && \
help2man --no-discard-stderr --no-info --name="highly-accurate, transcript-level quantification estimates from RNA-seq data"\
salmon > ../../debian/salmon.1 && \
@@ -27,3 +30,12 @@ override_dh_auto_build:
--version-string="${VERSION}" --no-info "salmon --no-version-check $${option}" \
--include=../../debian/salmon-$${option}-man-include \
> ../../debian/salmon-$${option}.1; done
+
+override_dh_auto_clean:
+ dh_auto_clean
+ rm -f debian/*.1
+ rm -Rf sample_data
+ cd doc && $(MAKE) clean
+
+get-orig-source:
+ uscan --verbose --force-download --repack --compression xz
diff --git a/debian/salmon.docs b/debian/salmon.docs
new file mode 100644
index 0000000..8137b04
--- /dev/null
+++ b/debian/salmon.docs
@@ -0,0 +1 @@
+doc/build/html
diff --git a/debian/watch b/debian/watch
index c0b7f12..a23367b 100644
--- a/debian/watch
+++ b/debian/watch
@@ -1,10 +1,6 @@
version=3
# Uncomment to find new files on Github
# - when using releases:
+opts=filenamemangle=s/.+\/v?(\d\S*)\.tar\.gz/salmon-$1\.tar\.gz/,dversionmangle=s/[~\+]ds[0-9]*//,repacksuffix=+ds1 \
https://github.com/COMBINE-lab/salmon/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
# Remark: frequently you can do s/#PREFIX#/v?/ since 'v' or nothing is quite common but there are other prefixes possible
-
-
-# if you need to repack and choose +dfsg prefix
-# opts=dversionmangle=s/[~\+]dfsg[0-9]*// \
-#
--
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