debian/changelog

-python-cogent (2019.12.6a-1) UNRELEASED; urgency=medium
+python-cogent (2019.12.6a+dfsg-1) UNRELEASED; urgency=medium
 
   * New upstream version supporting Python3
     Closes: #937654, #935298
@@ -14,6 +14,9 @@ python-cogent (2019.12.6a-1) UNRELEASED; urgency=medium
   * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
     Repository-Browse.
   * Fix day-of-week for changelog entry 1.5.3-1.
+  * Remove minimized JS from former sphinx run
+  * Binary package is now python3-cogent3 which
+    Breaks/Provides/Replaces: python-cogent
   TODO: scitrack (#948415 in new)
         tinydb (https://salsa.debian.org/python-team/modules/tinydb #819649)
 

debian/control

@@ -39,7 +39,10 @@ Depends: ${shlibs:Depends},
          python3-tinydb
 Recommends: ncbi-blast+-legacy,
             dialign
-Suggests: python-cogent-doc,
+Suggests: python-cogent-doc
+Breaks: python-cogent
+Provides: python-cogent
+Replaces: python-cogent
 Description: framework for genomic biology
  PyCogent is a software library for genomic biology. It is a fully
  integrated and thoroughly tested framework for:

debian/copyright

 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: PyCogent
 Source: https://github.com/cogent3/cogent3/releases
+Files-Excluded: */_static
 
 Files: *
 Copyright: 2007-2012 The Cogent Project

debian/patches/fix_interpreter.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Tue, 07 Jan 2020 20:12:00 +0100
+Description: Fix broken interpreter lines
+
+--- a/src/cogent3/phylo/maximum_likelihood.py
++++ b/src/cogent3/phylo/maximum_likelihood.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python'
++#!/usr/bin/python3
+ from math import exp
+ 
+ from .least_squares import WLS
+--- a/src/cogent3/recalculation/__init__.py
++++ b/src/cogent3/recalculation/__init__.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/envthon
++#!/usr/bin/python3
+ __all__ = ["calculation", "definition", "scope", "setting"]
+ 
+ __author__ = "Peter Maxwell"
+--- a/src/cogent3/recalculation/setting.py
++++ b/src/cogent3/recalculation/setting.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python'
++#!/usr/bin/python3
+ """Instances of these classes are assigned to different parameter/scopes
+ by a parameter controller"""
+ 
+--- a/src/cogent3/align/dp_calculation.py
++++ b/src/cogent3/align/dp_calculation.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env/python
++#!/usr/bin/python3
+ 
+ import numpy
+ 
+--- a/src/cogent3/data/molecular_weight.py
++++ b/src/cogent3/data/molecular_weight.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env Python
++#!/usr/bin/python3
+ """Data for molecular weight calculations on proteins and nucleotides."""
+ 
+ __author__ = "Rob Knight"

debian/patches/series

 sphinx.patch
+fix_interpreter.patch

debian/patches/sphinx.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Tue, 07 Jan 2020 20:12:00 +0100
+Description: Work around failure in sphinx doc processing
+
 --- a/doc/conf.py
 +++ b/doc/conf.py
 @@ -8,7 +8,7 @@ autosummary_generate = True

debian/python3-cogent.install

-tests	usr/share/doc/python-cogent

debian/python3-cogent3.install

+tests	usr/share/doc/python3-cogent3

debian/python3-cogent3.lintian-overrides

+# Test suite needs all these files
+python3-cogent3: duplicated-compressed-file *

debian/rules

@@ -45,3 +45,6 @@ override_dh_installdocs:
 	dh_installdocs
 	rm -rf debian/$(DEB_SOURCE)/usr/share/doc/$(DEB_SOURCE)/html/_sources
 	find debian -name doctrees -type d | xargs rm -rf
+
+override_dh_python3:
+	dh_python3 --shebang=/usr/bin/python3

debian/tests/control

 Tests: run-unit-test
-Depends: @
+Depends: @, python3-pytest
 Restrictions: allow-stderr

debian/tests/run-unit-test

-#!/bin/sh -e
+#!/bin/bash
+set -e
 
-pkg=python-cogent
+pkg=python3-cogent3
 
+export LC_ALL=C.UTF-8
 if [ "$AUTOPKGTEST_TMP" = "" ] ; then
   AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
   trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
 fi
 
-cd $AUTOPKGTEST_TMP
-
-BUILDARCH=$(dpkg-architecture -qDEB_BUILD_ARCH)
-
-FAILED_TESTS="test_infernal \
-	      test_mothur \
-	      test_parsinsert \
-	      test_raxml_v730 \
-	      test_rtax \
-	      test_clustalw \
-	      test_mafft \
-	      test_unifrac \
-	      test_seqsim.test_analysis \
-	      test_seqsim.test_usage"
-
-ONLYAMD64_TESTS="test_bwa"
-
-# There are tests failing on certain architectures
-# We need to decide between not shipping cogent there or hiding
-# our eyes from these failures.  See README.source for further
-# explanation.
-FAIL_ON_ARMEL_TESTS="test_core.test_profile"
-                       
-
-FAIL_ON_PPC64_MIPS64EL="test_core.test_tree"
-
-FAIL_ON_I386_TESTS="test_maths.test_stats.test_test \
-	                      test_seqsim.test_sequence_generators"
-
-FAIL_ON_PPC64_TESTS=test_app.test_util
-
-FAIL_ON_S390X_TESTS=test_maths.test_optimisers
-
-FAIL_ON_MIPS_TESTS=test_seqsim.test_sequence_generators
-
-
-
-cp -a /usr/share/doc/${pkg}/tests/ .
-gunzip -r *
-
-
-# exclude tests known to fail
-	for tst in $FAILED_TESTS ; do sed -i "/$tst/d" tests/alltests.py ; done
-
-# avoid amd64 only tools on other architectures
-if [ "$BUILDARCH" = "amd64" ]; then
-	echo "bwa can be tested on amd64 arch"
-else
-	for tst in $ONLYAMD64_TESTS ; do sed -i "/$tst/d" tests/alltests.py ; done
-if [ "$BUILDARCH" = "$(filter $BUILDARCH, mips64el ppc64el ppc64)" ]; then
-	for tst in $FAIL_ON_PPC64_MIPS64EL ; do sed -i "/$tst/d" tests/alltests.py ; done
-fi
-if [ "$BUILDARCH" = "armel" ] ; then
-	for tst in $FAIL_ON_ARMEL_TESTS ; do sed -i "/$tst/d" tests/alltests.py ; done
-fi
-if [ "$BUILDARCH" = "ppc64" ] ; then
-	for tst in $FAIL_ON_PPC64_TESTS ; do sed -i "/$tst/d" tests/alltests.py ; done
-fi
-if [ "$BUILDARCH" = "s390x" ] ; then
-	for tst in $FAIL_ON_S390X_TESTS ; do sed -i "/$tst/d" tests/alltests.py ; done
-fi
-if [ "$BUILDARCH" = "mips" ] ; then
-	for tst in $FAIL_ON_MIPS_TESTS ; do sed -i "/$tst/d" tests/alltests.py ; done
-fi
-if [ "$BUILDARCH" = "$(filter $BUILDARCH, i386 kfreebsd-i386)" ] ; then
-	for tst in $FAIL_ON_I386_TESTS ; do sed -i "/$tst/d" tests/alltests.py ; done
-fi
-fi
+cd "$AUTOPKGTEST_TMP"
 
+cp -a /usr/share/doc/${pkg}/tests .
+unset GZIP
+for gz in `find . -name "*.gz"` ; do
+    if echo $gz | grep -q formattest.fasta.gz ; then continue ; fi
+    gunzip $gz
+done
 cd tests
-echo "lolo"
-python alltests.py
+
+pytest-3

debian/watch

 version=4
 
+opts="repacksuffix=+dfsg,dversionmangle=auto,repack,compression=xz" \
   https://github.com/cogent3/cogent3/releases .*/archive/@ANY_VERSION@@ARCHIVE_EXT@
 
 # Project moved to Github

doc/_static/require.min.js

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