mirtop (0.4.25-1) unstable; urgency=medium

  * Team upload.
  * New upstream version 0.4.25
  * Bump Standards-Version to 4.6.1 (no changes needed)

[dgit import unpatched mirtop 0.4.25-1]

19 files changed, 388 insertions, 0 deletions

diff --git a/debian/README.test b/debian/README.test
new file mode 100644
index 0000000..805a6f7
--- /dev/null
+++ b/debian/README.test
@@ -0,0 +1,10 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by running the provided test:
+
+    sh run-unit-test
+
+in order to confirm its integrity.
+
+
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..5dc8ddb
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,63 @@
+mirtop (0.4.25-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream version 0.4.25
+  * Bump Standards-Version to 4.6.1 (no changes needed)
+
+ -- Nilesh Patra <nilesh@debian.org>  Sun, 29 May 2022 11:23:26 +0530
+
+mirtop (0.4.24-1) unstable; urgency=medium
+
+  * Team Upload.
+  [ Matúš Kalaš ]
+  * Update citations
+  * Pretty-printed metadata & removed double-quotes
+
+  [ Nilesh Patra ]
+  * New upstream version 0.4.24
+  * Add python3-all to test-dep
+  * Run cme
+  * Update d/u/metadata
+
+ -- Nilesh Patra <nilesh@debian.org>  Mon, 15 Nov 2021 16:15:14 +0530
+
+mirtop (0.4.23-2) unstable; urgency=medium
+
+  * Team Upload.
+
+  [ Shruti Sridhar ]
+  * Add autopkgtests
+
+  [ Nilesh Patra ]
+  * d/p/fix-circular-import.patch: Fix circular import
+
+ -- Nilesh Patra <nilesh@debian.org>  Wed, 30 Jun 2021 18:18:19 +0000
+
+mirtop (0.4.23-1) unstable; urgency=medium
+
+  * New upstream version
+  * Standards-Version: 4.4.1
+  * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
+  * Remove trailing whitespace in debian/copyright
+  * Set upstream metadata fields: Repository, Repository-Browse.
+
+ -- Steffen Moeller <moeller@debian.org>  Thu, 05 Dec 2019 11:43:49 +0100
+
+mirtop (0.4.21-1) unstable; urgency=medium
+
+  * Team upload.
+
+  [ Karolis Kalantojus ]
+  * Remove duplicated patch lines
+
+  [ Andreas Tille ]
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+
+ -- Andreas Tille <tille@debian.org>  Thu, 01 Aug 2019 15:24:03 +0200
+
+mirtop (0.3.17-1) unstable; urgency=medium
+
+  * Initial release (Closes: #903582)
+
+ -- Karolis Kalantojus <karolis.kalantojus@gmail.com>  Sat, 09 Mar 2019 16:02:00 +0000
diff --git a/debian/clean b/debian/clean
new file mode 100644
index 0000000..1535275
--- /dev/null
+++ b/debian/clean
@@ -0,0 +1 @@
+mirtop/version.py
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..f41cdfb
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,60 @@
+Source: mirtop
+Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+Uploaders: Steffen Moeller <moeller@debian.org>,
+           Karolis Kalantojus <karolis.kalantojus@gmail.com>
+Section: science
+Testsuite: autopkgtest-pkg-python
+Priority: optional
+Build-Depends: debhelper-compat (= 13),
+               dh-python,
+               python3-all,
+               python3-setuptools,
+               python3-sphinx,
+               python3-recommonmark,
+               python3-pysam,
+               python3-pybedtools,
+               python3-pandas,
+               python3-biopython
+Standards-Version: 4.6.1
+Vcs-Browser: https://salsa.debian.org/med-team/mirtop
+Vcs-Git: https://salsa.debian.org/med-team/mirtop.git
+Homepage: https://github.com/miRTop/mirtop
+
+Package: python3-mirtop
+Architecture: all
+Section: python
+Depends: ${python3:Depends},
+         ${misc:Depends},
+         ${sphinxdoc:Depends},
+         python3-pysam,
+         python3-pybedtools,
+         python3-pandas,
+         python3-biopython
+Description: annotate miRNAs with a standard mirna/isomir naming (Python 3)
+ The main goal of this project is to create a reflection group on metazoan
+ microRNAs (miRNAs), open to all interested researchers, to identify blockages
+ and develop standards and guidelines to improve miRNA research, resources and
+ communication. This can go through the use of standardized file formats, gene
+ and variants nomenclature guidelines, and advancements in miRNA biology
+ understanding. The group will eventually also aim at expanding its breadth to
+ the development of novel tools, data resources, and best-practices guidelines
+ to benefit the scientific community by providing high confidence validated
+ research and analysis strategies, regardless the expertise in this field.
+ This package provides the Python modules for mirtop to execute correctly.
+
+Package: mirtop
+Architecture: all
+Depends: ${python3:Depends},
+         ${misc:Depends},
+         python3-mirtop
+Description: annotate miRNAs with a standard mirna/isomir naming
+ The main goal of this project is to create a reflection group on metazoan
+ microRNAs (miRNAs), open to all interested researchers, to identify blockages
+ and develop standards and guidelines to improve miRNA research, resources and
+ communication. This can go through the use of standardized file formats, gene
+ and variants nomenclature guidelines, and advancements in miRNA biology
+ understanding. The group will eventually also aim at expanding its breadth to
+ the development of novel tools, data resources, and best-practices guidelines
+ to benefit the scientific community by providing high confidence validated
+ research and analysis strategies, regardless the expertise in this field.
+ This package provides the command line interface to mirtop.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..d438693
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,32 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: mirtop
+Source: https://github.com/miRTop/mirtop
+Files-Excluded: mirtop/version.py
+
+Files: *
+Copyright: 2018 Lorena Pantano <lpantano@iscb.org>
+                Shruthi Bhat Bandyadka
+License: Expat
+
+Files: debian/*
+Copyright: 2018 Steffen Moeller <moeller@debian.org>
+License: Expat
+
+License: Expat
+ Permission is hereby granted, free of charge, to any person obtaining a
+ copy of this software and associated documentation files (the "Software"),
+ to deal in the Software without restriction, including without limitation
+ the rights to use, copy, modify, merge, publish, distribute, sublicense,
+ and/or sell copies of the Software, and to permit persons to whom the
+ Software is furnished to do so, subject to the following conditions:
+ .
+ The above copyright notice and this permission notice shall be included
+ in all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+ OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+ IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+ CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+ TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..c231a64
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,3 @@
+README.md
+debian/README*
+debian/tests/run-unit-test
diff --git a/debian/mirtop.install b/debian/mirtop.install
new file mode 100644
index 0000000..114184c
--- /dev/null
+++ b/debian/mirtop.install
@@ -0,0 +1 @@
+debian/python3-mirtop/usr/bin/mirtop usr/bin
diff --git a/debian/mirtop.manpages b/debian/mirtop.manpages
new file mode 100644
index 0000000..b19f8c8
--- /dev/null
+++ b/debian/mirtop.manpages
@@ -0,0 +1 @@
+build/man/*
diff --git a/debian/patches/fix-circular-import.patch b/debian/patches/fix-circular-import.patch
new file mode 100644
index 0000000..aeb61b8
--- /dev/null
+++ b/debian/patches/fix-circular-import.patch
@@ -0,0 +1,29 @@
+Description: import module in needed functions to fix circular import
+Author: Nilesh Patra <nilesh@debian.org>
+Last-Update: 2021-06-30
+--- a/mirtop/bam/bam.py
++++ b/mirtop/bam/bam.py
+@@ -15,7 +15,6 @@
+ from mirtop.mirna.realign import isomir, hits, reverse_complement
+ from mirtop.mirna.mapper import get_primary_transcript, guess_database
+ from mirtop.bam import filter
+-from mirtop.gff import body
+ from mirtop.mirna.annotate import annotate
+ from mirtop.libs import sql
+ 
+@@ -72,6 +71,7 @@
+ def low_memory_bam(bam_fn, sample, out_handle, args):
+     if args.genomic:
+         raise ValueError("low-memory option is not compatible with genomic coordinates.")
++    from mirtop.gff import body
+     precursors = args.precursors
+     bam_fn = _sam_to_bam(bam_fn)
+     bam_fn = _bam_sort(bam_fn)
+@@ -100,6 +100,7 @@
+ def low_memory_genomic_bam(bam_fn, sample, out_handle, args):
+     logger.info("Reading BAM file in low memory mode.")
+     logger.warning("This is under development and variants can be unexact.")
++    from mirtop.gff import body
+     precursors = args.precursors
+     bam_fn = _sam_to_bam(bam_fn)
+     bam_fn = _bam_sort(bam_fn)
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..fc41e34
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+spelling
+fix-circular-import.patch
diff --git a/debian/patches/spelling b/debian/patches/spelling
new file mode 100644
index 0000000..543456c
--- /dev/null
+++ b/debian/patches/spelling
@@ -0,0 +1,83 @@
+From: Karolis Kalantojus <karolis.kalantojus@gmail.com>
+Subject: Fix spelling typos
+--- a/CODE_OF_CONDUCT.md
++++ b/CODE_OF_CONDUCT.md
+@@ -1,4 +1,4 @@
+-* miRTop is dedicated to providing a harassment-free enviroment for everyone, regardless of gender, sexual orientation, disability, physical appearance, body size, race, religion, or choice of text editor. We do not tolerate harassment of participants in any form.
++* miRTop is dedicated to providing a harassment-free environment for everyone, regardless of gender, sexual orientation, disability, physical appearance, body size, race, religion, or choice of text editor. We do not tolerate harassment of participants in any form.
+ * All communication should be appropriate for a professional audience including people of many different backgrounds. Sexual language and imagery is not appropriate for any event.
+ * Be kind to others. Do not insult or put down other attendees.
+ * Behave professionally. Remember that harassment and sexist, racist, or exclusionary jokes are not appropriate.
+--- a/README.md
++++ b/README.md
+@@ -48,7 +48,7 @@ Installation
+ 
+ ### develop version
+ 
+-Thes best solution is to install conda to get an independent enviroment.
++Thes best solution is to install conda to get an independent environment.
+ 
+ ```
+ wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh
+--- a/docs/code_structure.md
++++ b/docs/code_structure.md
+@@ -7,7 +7,7 @@
+     * `tune`: if option `--clean` is on, filter according generic rules
+     * `clean_hits`: get the top hits
+ * mirtop/gff
+-  * __init.py__ wraps the convertion process to GFF3
++  * __init.py__ wraps the conversion process to GFF3
+   * __body.py__ `create` will create the line according GFF format established.
+     * `read_gff_line`: Inside a for loop to read line of the file. It'll return and structure key:value dictionary for each column.
+   * __header.py__ generate header and read header section.
+--- a/docs/how_to_contribute.md
++++ b/docs/how_to_contribute.md
+@@ -4,7 +4,7 @@
+ 
+ **You need first to clone and install the tool in [develop mode](installation.html)**
+ 
+-Let's say that you want to add a new operation to `mirtop`, for instance, similar to the `stats` command to work with sGFF3 files. Assume a `test` function for this exmaple to just read the file and print `Hello GFF3.`
++Let's say that you want to add a new operation to `mirtop`, for instance, similar to the `stats` command to work with sGFF3 files. Assume a `test` function for this example to just read the file and print `Hello GFF3.`
+ 
+ * Create the folder inside `mirtop/test`. The create to empty files named:
+  * `test.py`
+--- a/docs/installation.md
++++ b/docs/installation.md
+@@ -16,7 +16,7 @@ pip install --upgrade --no-deps git+http
+ 
+ ## install develop version
+ 
+-Thes best solution is to install conda to get an independent enviroment.
++Thes best solution is to install conda to get an independent environment.
+ 
+ ```
+ wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh
+@@ -33,4 +33,4 @@ git fetch origin dev
+ git checkout dev
+ 
+ python setup.py develop
+-```
+\ No newline at end of file
++```
+--- a/mirtop/libs/do.py
++++ b/mirtop/libs/do.py
+@@ -32,7 +32,7 @@ def find_bash():
+     raise IOError("Could not find bash in any standard location. Needed for unix pipes")
+ 
+ def find_cmd(cmd):
+-    """Find comand in session
++    """Find command in session
+     """
+     try:
+         return subprocess.check_output(["which", cmd]).strip()
+--- a/mirtop/libs/fastq.py
++++ b/mirtop/libs/fastq.py
+@@ -54,7 +54,7 @@ def splitext_plus(fn):
+         *fn(str)*: file name.
+ 
+     Returns:
+-        *base, ext(str, str)*: basename and extesion.
++        *base, ext(str, str)*: basename and extension.
+     """
+     base, ext = os.path.splitext(fn)
+     if ext in [".gz", ".bz2", ".zip"]:
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..99ea6e2
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,21 @@
+#!/usr/bin/make -f
+
+export DH_VERBOSE = 1
+export PYBUILD_NAME=mirtop
+
+%:
+	dh $@ --with python3,sphinxdoc --buildsystem=pybuild
+
+override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+	# No tests, yet
+	@echo "Not testing."
+endif
+
+override_dh_install:
+	dh_install
+	rm debian/python3-mirtop/usr/bin/mirtop
+
+override_dh_auto_build:
+	dh_auto_build
+	PYTHONPATH=. python3 -m sphinx -N -bman docs/ build/man # Manpage generator
diff --git a/debian/salsa-ci.yml b/debian/salsa-ci.yml
new file mode 100644
index 0000000..33c3a64
--- /dev/null
+++ b/debian/salsa-ci.yml
@@ -0,0 +1,4 @@
+---
+include:
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/source/options b/debian/source/options
new file mode 100644
index 0000000..cb61fa5
--- /dev/null
+++ b/debian/source/options
@@ -0,0 +1 @@
+extend-diff-ignore = "^[^/]*[.]egg-info/"
diff --git a/debian/tests/control b/debian/tests/control
new file mode 100644
index 0000000..70ba335
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @, python3-all, python3-nose, samtools, bedtools, seqan-apps
+Restrictions: allow-stderr
diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test
new file mode 100644
index 0000000..81aa06f
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,20 @@
+#!/bin/bash
+set -e
+
+CUR_DIR=`pwd`
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+  AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+  trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a ${CUR_DIR}/test/ $AUTOPKGTEST_TMP
+cp -a ${CUR_DIR}/data/ $AUTOPKGTEST_TMP
+
+cd $AUTOPKGTEST_TMP
+
+for py in $(py3versions -s 2> /dev/null)
+do
+    echo "Testing with $py in $(pwd):"
+    nosetests3 -v
+    
+done
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..0056727
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,49 @@
+---
+Reference:
+  - Author: >
+      Thomas Desvignes and Karen Eilbeck and Ioannis S. Vlachos
+      and Bastian Fromm and Yin Lu and Marc K. Halushka and Michael Hackenberg
+      and Gianvito Urgese and Elisa Ficarra and Shruthi Bandyadka
+      and Jason Sydes and Peter Batzel and John H. Postlethwait
+      and Phillipe Loher and Eric Londin and Aristeidis G. Telonis
+      and Isidore Rigoutsos and Lorena Pantano Rubino
+    Title: >
+      miRTOP: An open source community project for the development
+      of a unified format file for miRNA data [version 1; not peer reviewed]
+    Year: 2018
+    Journal: F1000Research
+    Volume: 7
+    Number: ISCB Comm. J.
+    Pages: 953 (Slides)
+    DOI: 10.7490/f1000research.1115724.1
+    eprint: https://f1000research.com/slides/7-953#
+  - Author: >
+      Thomas Desvignes and Phillipe Loher and Karen Eilbeck and Jeffery Ma
+      and Gianvito Urgese and Bastian Fromm and Jason Sydes
+      and Ernesto Aparicio-Puerta and Victor Barrera and Roderic Espín
+      and Florian Thibord and Xavier Bofill-De Ros and Eric Londin
+      and Aristeidis G Telonis and Elisa Ficarra and Marc R Friedländer
+      and John H Postlethwait and Isidore Rigoutsos and Michael Hackenberg
+      and Ioannis S Vlachos and Marc K Halushka and Lorena Pantano
+    Title: >
+      Unification of miRNA and isomiR research: the mirGFF3 format
+      and the mirtop API
+    Year: 2019
+    Journal: Bioinformatics
+    Month: 8
+    Pages: btz675
+    DOI: 10.1093/bioinformatics/btz675
+    PMID: 31504201
+Registry:
+  - Name: OMICtools
+    Entry: OMICS_31718
+  - Name: bio.tools
+    Entry: mirtop
+  - Name: conda:bioconda
+    Entry: mirtop
+Archive: GitHub
+Repository: https://github.com/miRTop/mirtop
+Repository-Browse: https://github.com/miRTop/mirtop
+Bug-Database: https://github.com/miRTop/mirtop/issues
+Bug-Submit: https://github.com/miRTop/mirtop/issues/new
+Changelog: https://github.com/miRTop/mirtop/tags
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..47dbba2
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=4
+opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%mirtop-$1.tar.gz%" \
+   https://github.com/miRTop/mirtop/tags \
+   (?:.*?/)?v?(\d[\d.]*)\.tar\.gz debian uupdate