debian/README.test

-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.

debian/average_nucleotide_identity.py.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.11.
+.TH AVERAGE_NUCLEOTIDE_IDENTITY.PY "1" "November 2019" "average_nucleotide_identity.py 0.2.9" "User Commands"
+.SH NAME
+average_nucleotide_identity.py \- average nucleotide identity
+.SH SYNOPSIS
+.B average_nucleotide_identity.py
+[\-h] [\-\-version] \fB\-o\fR OUTDIRNAME \fB\-i\fR INDIRNAME [\-v] [\-f] [\-s FRAGSIZE]
+[\-l LOGFILE] [\-\-skip_nucmer]
+[\-\-skip_blastn] [\-\-noclobber]
+[\-\-nocompress] [\-g] [\-\-gformat GFORMAT]
+[\-\-gmethod {mpl,seaborn}]
+[\-\-labels LABELS] [\-\-classes CLASSES]
+[\-m {ANIm,ANIb,ANIblastall,TETRA}]
+[\-\-scheduler {multiprocessing,SGE}]
+[\-\-workers WORKERS]
+[\-\-SGEgroupsize SGEGROUPSIZE]
+[\-\-SGEargs SGEARGS] [\-\-maxmatch]
+[\-\-nucmer_exe NUCMER_EXE]
+[\-\-filter_exe FILTER_EXE]
+[\-\-blastn_exe BLASTN_EXE]
+[\-\-makeblastdb_exe MAKEBLASTDB_EXE]
+[\-\-blastall_exe BLASTALL_EXE]
+[\-\-formatdb_exe FORMATDB_EXE]
+[\-\-write_excel] [\-\-rerender]
+[\-\-subsample SUBSAMPLE] [\-\-seed SEED]
+[\-\-jobprefix JOBPREFIX]
+.SH OPTIONS
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-version\fR
+show program's version number and exit
+.TP
+\fB\-o\fR OUTDIRNAME, \fB\-\-outdir\fR OUTDIRNAME
+Output directory (required)
+.TP
+\fB\-i\fR INDIRNAME, \fB\-\-indir\fR INDIRNAME
+Input directory name (required)
+.TP
+\fB\-v\fR, \fB\-\-verbose\fR
+Give verbose output
+.TP
+\fB\-f\fR, \fB\-\-force\fR
+Force file overwriting
+.TP
+\fB\-s\fR FRAGSIZE, \fB\-\-fragsize\fR FRAGSIZE
+Sequence fragment size for ANIb (default 1020)
+.TP
+\fB\-l\fR LOGFILE, \fB\-\-logfile\fR LOGFILE
+Logfile location
+.TP
+\fB\-\-skip_nucmer\fR
+Skip NUCmer runs, for testing (e.g. if output already
+present)
+.TP
+\fB\-\-skip_blastn\fR
+Skip BLASTN runs, for testing (e.g. if output already
+present)
+.TP
+\fB\-\-noclobber\fR
+Don't nuke existing files
+.TP
+\fB\-\-nocompress\fR
+Don't compress/delete the comparison output
+.TP
+\fB\-g\fR, \fB\-\-graphics\fR
+Generate heatmap of ANI
+.TP
+\fB\-\-gformat\fR GFORMAT
+Graphics output format(s) [pdf|png|jpg|svg] (default
+pdf,png,eps meaning three file formats)
+.TP
+\fB\-\-gmethod\fR {mpl,seaborn}
+Graphics output method (default mpl)
+.TP
+\fB\-\-labels\fR LABELS
+Path to file containing sequence labels
+.TP
+\fB\-\-classes\fR CLASSES
+Path to file containing sequence classes
+.TP
+\fB\-m\fR {ANIm,ANIb,ANIblastall,TETRA}, \fB\-\-method\fR {ANIm,ANIb,ANIblastall,TETRA}
+ANI method (default ANIm)
+.TP
+\fB\-\-scheduler\fR {multiprocessing,SGE}
+Job scheduler (default multiprocessing, i.e. locally)
+.TP
+\fB\-\-workers\fR WORKERS
+Number of worker processes for multiprocessing
+(default zero, meaning use all available cores)
+.TP
+\fB\-\-SGEgroupsize\fR SGEGROUPSIZE
+Number of jobs to place in an SGE array group (default
+10000)
+.TP
+\fB\-\-SGEargs\fR SGEARGS
+Additional arguments for qsub
+.TP
+\fB\-\-maxmatch\fR
+Override MUMmer to allow all NUCmer matches
+.TP
+\fB\-\-nucmer_exe\fR NUCMER_EXE
+Path to NUCmer executable
+.TP
+\fB\-\-filter_exe\fR FILTER_EXE
+Path to delta\-filter executable
+.TP
+\fB\-\-blastn_exe\fR BLASTN_EXE
+Path to BLASTN+ executable
+.TP
+\fB\-\-makeblastdb_exe\fR MAKEBLASTDB_EXE
+Path to BLAST+ makeblastdb executable
+.TP
+\fB\-\-blastall_exe\fR BLASTALL_EXE
+Path to BLASTALL executable
+.TP
+\fB\-\-formatdb_exe\fR FORMATDB_EXE
+Path to BLAST formatdb executable
+.TP
+\fB\-\-write_excel\fR
+Write Excel format output tables
+.TP
+\fB\-\-rerender\fR
+Rerender graphics output without recalculation
+.TP
+\fB\-\-subsample\fR SUBSAMPLE
+Subsample a percentage [0\-1] or specific number (1\-n)
+of input sequences
+.TP
+\fB\-\-seed\fR SEED
+Set random seed for reproducible subsampling.
+.TP
+\fB\-\-jobprefix\fR JOBPREFIX
+Prefix for SGE jobs (default ANI).
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.

debian/changelog

-python-pyani (0.2.9-1) UNRELEASED; urgency=medium
+python-pyani (0.2.9-1) unstable; urgency=medium
 
-  * Initial release (Closes: #<bug>)
+  * Initial release (Closes: #944663)
 
- -- Andreas Tille <tille@debian.org>  Wed, 13 Nov 2019 14:26:23 +0100
+ -- Andreas Tille <tille@debian.org>  Wed, 13 Nov 2019 15:38:25 +0100

debian/control

@@ -7,11 +7,14 @@ Build-Depends: debhelper-compat (= 12),
                dh-python,
                python3-all-dev,
                python3-setuptools,
-               python3-biopython,
-               python3-matplotlib,
-               python3-pandas,
-               python3-scipy,
-               python3-seaborn
+               python3-biopython <!nocheck>,
+               python3-matplotlib <!nocheck>,
+               python3-pandas <!nocheck>,
+               python3-scipy <!nocheck>,
+               python3-seaborn <!nocheck>,
+               mummer <!nocheck>,
+               ncbi-blast+ <!nocheck>,
+               python3-nose <!nocheck>
 Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/python-pyani
 Vcs-Git: https://salsa.debian.org/med-team/python-pyani.git
@@ -19,6 +22,7 @@ Homepage: https://github.com/widdowquinn/pyani
 
 Package: python3-pyani
 Architecture: any
+Section: python
 Depends: ${python3:Depends},
          ${misc:Depends},
          python3-setuptools,
@@ -26,7 +30,9 @@ Depends: ${python3:Depends},
          python3-matplotlib,
          python3-pandas,
          python3-scipy,
-         python3-seaborn
+         python3-seaborn,
+         mummer,
+         ncbi-blast+,
 Description: Python3 module for average nucleotide identity analyses
  Pyani is a Python3 module and script that provides support for
  calculating average nucleotide identity (ANI) and related measures for
@@ -34,6 +40,3 @@ Description: Python3 module for average nucleotide identity analyses
  output. Where available, it takes advantage of multicore systems, and
  can integrate with SGE/OGE-type job schedulers for the sequence
  comparisons.
- .
- Pyani also installs the script pyani.py, which enables command-line
- based analysis of genomes.

debian/createmanpages

+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+
+AUTHOR=".SH AUTHOR\n \
+This manpage was written by $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+progname=average_nucleotide_identity.py
+help2man --no-info --no-discard-stderr \
+         --name="average nucleotide identity" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=genbank_get_genomes_by_taxon.py
+help2man --no-info --no-discard-stderr \
+         --name="genbank get genomes by taxon" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+    http://liw.fi/manpages/
+EOT

debian/genbank_get_genomes_by_taxon.py.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.11.
+.TH GENBANK_GET_GENOMES_BY_TAXON.PY "1" "November 2019" "genbank_get_genomes_by_taxon.py 0.2.9" "User Commands"
+.SH NAME
+genbank_get_genomes_by_taxon.py \- genbank get genomes by taxon
+.SH SYNOPSIS
+.B genbank_get_genomes_by_taxon.py
+[\-h] \fB\-o\fR OUTDIRNAME [\-t TAXON] [\-v] [\-f]
+[\-\-noclobber] [\-l LOGFILE]
+[\-\-format FORMAT] \fB\-\-email\fR EMAIL
+[\-\-retries RETRIES]
+[\-\-batchsize BATCHSIZE]
+[\-\-timeout TIMEOUT]
+.SH OPTIONS
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-o\fR OUTDIRNAME, \fB\-\-outdir\fR OUTDIRNAME
+Output directory (required)
+.TP
+\fB\-t\fR TAXON, \fB\-\-taxon\fR TAXON
+NCBI taxonomy ID
+.TP
+\fB\-v\fR, \fB\-\-verbose\fR
+Give verbose output
+.TP
+\fB\-f\fR, \fB\-\-force\fR
+Force file overwriting
+.TP
+\fB\-\-noclobber\fR
+Don't nuke existing files
+.TP
+\fB\-l\fR LOGFILE, \fB\-\-logfile\fR LOGFILE
+Logfile location
+.TP
+\fB\-\-format\fR FORMAT
+Output file format [gbk|fasta]
+.TP
+\fB\-\-email\fR EMAIL
+Email associated with NCBI queries (required)
+.TP
+\fB\-\-retries\fR RETRIES
+Number of Entrez retry attempts per request.
+.TP
+\fB\-\-batchsize\fR BATCHSIZE
+Entrez record return batch size
+.TP
+\fB\-\-timeout\fR TIMEOUT
+Timeout for URL connection (s)
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.

debian/lintian-overrides

+# see https://lists.debian.org/debian-med/2018/06/msg00043.html
+python3-pyani: script-with-language-extension usr/bin/*.*

debian/manpages

+debian/*.1

debian/rules

@@ -5,3 +5,6 @@ export PYBUILD_NAME=pyani
 
 %:
 	dh $@ --with python3 --buildsystem=pybuild
+
+override_dh_installman:
+	dh_installman --language=C

debian/tests/control

-Tests: run-unit-test
-Depends: @
-Restrictions: allow-stderr

debian/tests/run-unit-test

-#!/bin/bash
-set -e
-
-pkg=#PACKAGENAME#
-
-export LC_ALL=C.UTF-8
-if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
-  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
-  # Double quote below to expand the temporary directory variable now versus
-  # later is on purpose.
-  # shellcheck disable=SC2064
-  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
-fi
-
-cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
-
-cd "${AUTOPKGTEST_TMP}"
-
-#do_stuff_to_test_package#