[med-svn] [Git][med-team/mapdamage][master] 9 commits: New upstream version 2.2.1+dfsg

Steffen Möller gitlab at salsa.debian.org
Mon Jun 29 23:27:28 BST 2020



Steffen Möller pushed to branch master at Debian Med / mapdamage


Commits:
a9e55a3f by Steffen Moeller at 2020-06-30T00:19:26+02:00
New upstream version 2.2.1+dfsg
- - - - -
2b0f7dbf by Steffen Moeller at 2020-06-30T00:19:26+02:00
routine-update: New upstream version

- - - - -
a9183ef7 by Steffen Moeller at 2020-06-30T00:19:26+02:00
Update upstream source from tag 'upstream/2.2.1+dfsg'

Update to upstream version '2.2.1+dfsg'
with Debian dir ec833f08eed026cce3b5bf83a617566c9bb0b0da
- - - - -
a977ce61 by Steffen Moeller at 2020-06-30T00:19:27+02:00
routine-update: Standards-Version: 4.5.0

- - - - -
3a2b9ba2 by Steffen Moeller at 2020-06-30T00:19:27+02:00
routine-update: debhelper-compat 13

- - - - -
1d67166f by Steffen Moeller at 2020-06-30T00:19:33+02:00
routine-update: Add salsa-ci file

- - - - -
bde56cdd by Steffen Moeller at 2020-06-30T00:19:33+02:00
routine-update: Rules-Requires-Root: no

- - - - -
8df98553 by Steffen Moeller at 2020-06-30T00:19:36+02:00
Set upstream metadata fields: Bug-Submit, Repository, Repository-Browse.

Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html


Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html

- - - - -
1faef07a by Steffen Moeller at 2020-06-30T00:26:20+02:00
New upstream version.

- - - - -


9 changed files:

- README.md
- bin/mapDamage
- debian/changelog
- debian/control
- debian/rules
- + debian/salsa-ci.yml
- debian/upstream/metadata
- mapdamage/version.py
- setup.py


Changes:

=====================================
README.md
=====================================
@@ -1,29 +1,33 @@
 ## mapDamage
 
-[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/mapdamage2/README.html) [![Conda](https://img.shields.io/conda/dn/bioconda/mapdamage2.svg)](https://anaconda.org/bioconda/mapdamage2/files) ![Conda](https://anaconda.org/bioconda/mapdamage2/badges/latest_release_date.svg) ![Conda](https://anaconda.org/bioconda/mapdamage2/badges/version.svg) [![Project Status: Inactive – The project has reached a stable, usable state but is no longer being actively developed; support/maintenance will be provided as time allows.](https://www.repostatus.org/badges/latest/inactive.svg)](https://www.repostatus.org/#inactive)
+[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/mapdamage2/README.html) [![Conda](https://img.shields.io/conda/dn/bioconda/mapdamage2.svg)](https://anaconda.org/bioconda/mapdamage2/files) 
 
+![Conda](https://anaconda.org/bioconda/mapdamage2/badges/latest_release_date.svg) ![Conda](https://anaconda.org/bioconda/mapdamage2/badges/version.svg) [![Project Status: Inactive – The project has reached a stable, usable state but is no longer being actively developed; support/maintenance will be provided as time allows.](https://www.repostatus.org/badges/latest/inactive.svg)](https://www.repostatus.org/#inactive)
 
 #### `bioconda` installation
 
-- python3 version **2.2.0**
-```
-conda install -c bioconda mapdamage2=2.2.0
-```
+* python3 version **2.2.1**
 
-- python3 version **2.2.0** **with** R and 4 mandatory packages for the Bayesian inference:
+``` 
+conda install -c bioconda mapdamage2=2.2.1
 ```
-conda install -c bioconda mapdamage2=2.2.0=pyr36_1
+
+* python3 version **2.2.1** **with** R and 4 mandatory packages for the Bayesian inference:
+
+``` 
+conda install -c bioconda mapdamage2=2.2.1=pyr36_1
 ```
 
 ---
 
 ### Important
 
-- From version `2.2.0` the `master` branch is requiring **python3** as `python2` is not supported from 2020-01-01.
+* From version `2.2.1` the `master` branch is requiring **python3** as `python2` is not supported from 2020-01-01.
 
-- Users with versions dating prior to June 12 2013 please update. A nasty bug that caused the statistical part of `mapDamage` to use half of the data for estimation of the damage parameters, sorry for the inconvenience..
+* Users with versions dating prior to June 12 2013 please update. A nasty bug that caused the statistical part of `mapDamage` to use half of the data for estimation of the damage parameters, sorry for the inconvenience..
 
 ### Introduction
+
 Complete documentation, instructions, examples, screenshots and FAQ are available at [this address](http://ginolhac.github.io/mapDamage/).
 
 [mapDamage2](https://geogenetics.ku.dk/publications/mapdamage2.0/) is a computational framework written in **Python3** and **R**, which tracks and quantifies DNA damage patterns
@@ -31,31 +35,30 @@ among ancient DNA sequencing reads generated by Next-Generation Sequencing platf
 
 `mapDamage` was developed at the [Centre for GeoGenetics](https://geogenetics.ku.dk/) by the [Orlando Group ](https://geogenetics.ku.dk/research_groups/palaeomix_group/).
 
-
 ### Citation
+
 If you use this program, please cite the following publication:  
 Jónsson H, Ginolhac A, Schubert M, Johnson P, Orlando L.
 [mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters.
 _Bioinformatics_ 23rd April 2013. doi: 10.1093/bioinformatics/btt193](http://bioinformatics.oxfordjournals.org/content/early/2013/05/17/bioinformatics.btt193)
 
-
 The original `mapDamage1` was published in the following article:  
 Ginolhac A, Rasmussen M, Gilbert MT, Willerslev E, Orlando L.
 [mapDamage: testing for damage patterns in ancient DNA sequences. _Bioinformatics_ 2011 **27**(15):2153-5
 http://bioinformatics.oxfordjournals.org/content/27/15/2153](http://bioinformatics.oxfordjournals.org/content/27/15/2153)
 
-
 ### Test the no-stats part and rescaling
 
 you can test `mapDamage` by running:
 
-```
+``` 
 cd mapDamage/mapdamage/
 python3 mp_test.py
 ```
 
 should return
-```
+
+``` 
 Started with the command: /usr/local/bin/mapDamage -i tests/test.bam -r tests/fake1.fasta -d tests/results --no-stats
 	Reading from 'tests/test.bam'
 	Writing results to 'tests/results/'
@@ -69,7 +72,7 @@ Ran 2 tests in 3.357s
 OK
 ```
 
-
 ### Contact
+
 Please report bugs and suggest possible improvements to Aurélien Ginolhac, Mikkel Schubert or Hákon Jónsson by email:
 ginolhac at gmail.com, mikkelsch at gmail.com or jonsson.hakon at gmail.com.


=====================================
bin/mapDamage
=====================================
@@ -139,20 +139,6 @@ def _check_mm_option():
             raise SystemExit("The --mapdamage-modules path (path=%s) must contain the mapdamage module" % path_to_mm)
     return path_to_mm
 
-def is_paired(alignfile):
-    """
-    check if an alignment file contains paired end data by
-    looking at the first 100 reads
-    """
-
-    n = 0
-    for read in alignfile:
-        if read.is_paired:
-            return True
-        n += 1
-        if n == 100:
-            return False
-
 
 def main():
     start_time = time.time()
@@ -241,14 +227,6 @@ def main():
     else:
         in_bam = pysam.Samfile(options.filename)
 
-    # exit SAM/BAM is paired (look at top 100 reads)
-    if is_paired(in_bam):
-        logger.error("alignment file must be single-ended")
-        sys.stderr.write("alignment file must be single-ended\n")
-        sys.exit(1)
-    # reset SAM/BAM to the begining
-    in_bam = pysam.Samfile(options.filename)
-
     reflengths = dict(list(zip(in_bam.references, in_bam.lengths)))
     # check if references in SAM/BAM are the same in the fasta reference file
     fai_lengths = mapdamage.seq.read_fasta_index(options.ref + ".fai")


=====================================
debian/changelog
=====================================
@@ -1,3 +1,17 @@
+mapdamage (2.2.1+dfsg-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream version
+  * Standards-Version: 4.5.0 (routine-update)
+  * debhelper-compat 13 (routine-update)
+  * Add salsa-ci file (routine-update)
+  * Rules-Requires-Root: no (routine-update)
+  * Set upstream metadata fields: Bug-Submit, Repository,
+    Repository-Browse (routine-update)
+  * d/rules: Improved post-build cleansing
+
+ -- Steffen Moeller <moeller at debian.org>  Tue, 30 Jun 2020 00:19:37 +0200
+
 mapdamage (2.2.0+dfsg-1) unstable; urgency=medium
 
   * New upstream version


=====================================
debian/control
=====================================
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 Uploaders: Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
                python3,
                dh-python,
                python3-setuptools,
@@ -13,10 +13,11 @@ Build-Depends: debhelper-compat (= 12),
                r-cran-gam <!nocheck>,
                r-cran-ggplot2 <!nocheck>,
                r-cran-inline <!nocheck>
-Standards-Version: 4.4.1
+Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/mapdamage
 Vcs-Git: https://salsa.debian.org/med-team/mapdamage.git
 Homepage: https://ginolhac.github.io/mapDamage/
+Rules-Requires-Root: no
 
 Package: mapdamage
 Architecture: all


=====================================
debian/rules
=====================================
@@ -27,3 +27,5 @@ override_dh_python3:
 override_dh_auto_clean:
 	dh_auto_clean
 	rm -f mapdamage/_version.py
+	rm -f mapdamage/tests/results/Fragmisincorporation_plot.pdf mapdamage/tests/results/Fragmisincorporation_plot.pdf mapdamage/tests/results/Length_plot.pdf mapdamage/tests/results/Length_plot.pdf
+	rm -f mapdamage/tests/fake1.fasta.fai mapdamage/tests/results/3pGtoA_freq.txt mapdamage/tests/results/5pCtoT_freq.txt mapdamage/tests/results/Runtime_log.txt mapdamage/tests/results/dnacomp.txt mapdamage/tests/results/lgdistribution.txt mapdamage/tests/results/misincorporation.txt mapdamage/tests/test.rescaled.sam


=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml


=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,4 @@
+Bug-Submit: https://github.com/ginolhac/mapDamage/issues/new
 Reference:
 - Author: >
     Hákon Jónsson and Aurélien Ginolhac and Mikkel Schubert and
@@ -26,3 +27,5 @@ Registry:
 - Name: conda:bioconda
   Entry: mapdamage2
 Bug-Database: https://github.com/ginolhac/mapDamage/issues
+Repository: https://github.com/ginolhac/mapDamage.git
+Repository-Browse: https://github.com/ginolhac/mapDamage


=====================================
mapdamage/version.py
=====================================
@@ -2,4 +2,4 @@
 try:
     from mapdamage._version import __version__
 except ImportError:
-    __version__ = "2.2.0"
+    __version__ = "2.2.1"


=====================================
setup.py
=====================================
@@ -35,7 +35,7 @@ def setup_version():
         version = subprocess.check_output(("git", "describe", "--always", "--tags", "--dirty"))
         with open(os.path.join("mapdamage", "_version.py"), "w") as handle:
             handle.write("#!/usr/bin/env python\n")
-            handle.write("__version__ = %r\n" % (version.strip(),))
+            handle.write("__version__ = %r\n" % (version.decode("utf-8").strip(),))
     except (subprocess.CalledProcessError, OSError) as error:
         raise SystemExit("Could not determine mapDamage version: %s" % (error,))
 



View it on GitLab: https://salsa.debian.org/med-team/mapdamage/-/compare/90380206100e9dd6c74af3b0deae952371ccbcbd...1faef07a2d8b4839f0d5ec7e2a44b81caef5620c

-- 
View it on GitLab: https://salsa.debian.org/med-team/mapdamage/-/compare/90380206100e9dd6c74af3b0deae952371ccbcbd...1faef07a2d8b4839f0d5ec7e2a44b81caef5620c
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