Commit c3c8c7d0 authored by Andreas Tille's avatar Andreas Tille
Browse files

Several changes to make test suite work; Packaging needs **lots** of cleanups;... 

Several changes to make test suite work; Packaging needs **lots** of cleanups; packaging needed scitrack first
parent 4911cb9d

debian/changelog

+1 −0
Original line number Diff line number Diff line
@@ -14,6 +14,7 @@ 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.

  TODO: package scitrack (https://github.com/HuttleyLab/scitrack)



 -- Andreas Tille <tille@debian.org>  Tue, 07 Jan 2020 20:12:00 +0100

debian/control

+6 −2
Original line number Diff line number Diff line
@@ -10,11 +10,13 @@ Build-Depends: debhelper-compat (= 12), 
               python3-all-dev,

               python3-matplotlib,

               python3-numpy,

               python3-pandas,

               python3-setuptools,

               python3-sphinx,

               python3-numpydoc,

               python3-nbsphinx,

               python3-sphinxcontrib.bibtex,

               python3-tqdm,

               cython3,

               ncbi-blast+-legacy,

               bwa [any-amd64],
@@ -31,7 +33,8 @@ Build-Depends: debhelper-compat (= 12), 
               parsinsert,

               raxml [any-amd64 any-i386],

               rdp-classifier,

               rtax

               rtax,

               pandoc

Standards-Version: 4.4.1

Vcs-Browser: https://salsa.debian.org/med-team/python-cogent

Vcs-Git: https://salsa.debian.org/med-team/python-cogent.git
@@ -42,7 +45,8 @@ Architecture: any 
Depends: ${shlibs:Depends},

         ${misc:Depends},

         ${python3:Depends},

         python3-matplotlib

         python3-matplotlib,

         python3-pandas

Recommends: ncbi-blast+-legacy,

            bwa [any-amd64],

            cd-hit,

debian/patches/sphinx.patch

+9 −0
Original line number Diff line number Diff line 
--- a/doc/conf.py

+++ b/doc/conf.py

@@ -8,7 +8,7 @@ autosummary_generate = True

 numpydoc_class_members_toctree = False

 

 extensions = [

-    "numpydoc",

+#    "numpydoc",

     "sphinx.ext.todo",

     "sphinx.ext.doctest",

     "nbsphinx",

@@ -16,6 +16,7 @@ extensions = [

     "sphinx.ext.autodoc",

     "sphinx.ext.autosummary",

debian/rules

+7 −5
Original line number Diff line number Diff line
@@ -6,6 +6,8 @@ 


export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow



export PYBUILD_BEFORE_TEST=cp -r {dir}/tests/data {build_dir}



BUILDARCH := $(shell dpkg-architecture -qDEB_BUILD_ARCH)



FAILED_TESTS := test_infernal \
@@ -45,7 +47,7 @@ export PYBUILD_NAME=cogent 
include /usr/share/dpkg/default.mk



%:

	dh $@ --with python3 --buildsystem=pybuild

	dh $@ --with python3,sphinxdoc --buildsystem=pybuild



override_dh_clean:

	#These files are rebuilt on-the-fly
@@ -56,9 +58,9 @@ override_dh_clean: 
	rm -rf doc/_build

	dh_clean



override_dh_auto_build:

__override_dh_auto_build:

	dh_auto_build

	cd doc; $(MAKE) html

	set -x; cd doc; PYTHONPATH=$(CURDIR) http_proxy='127.0.0.1:9' $(MAKE) html

	# remove superfluous files and dirs

	find doc/_build -name "*.doctree*" -delete

	rm -f doc/_build/html/_sources/COGENT_LICENSE.txt
@@ -68,7 +70,7 @@ override_dh_auto_build: 


override_dh_shlibdeps:

	dh_shlibdeps

	dh_numpy

	dh_numpy3



override_dh_compress:

	dh_compress --exclude=.js --exclude=.fasta --exclude=.txt --exclude=.pdb
@@ -78,7 +80,7 @@ override_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_auto_test:

___override_dh_auto_test:

ifeq (,$(filter nocheck, $(DEB_BUILD_OPTIONS)))

	cp -a tests/alltests.py tests/alltests.py~

	# exclude tests known to fail