[med-svn] [Git][med-team/python-cogent][master] Several changes to make test suite work; Packaging needs **lots** of cleanups; ...

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / python-cogent


Commits:
c3c8c7d0 by Andreas Tille at 2020-01-08T12:16:12+01:00
Several changes to make test suite work; Packaging needs **lots** of cleanups; packaging needed scitrack first

- - - - -


4 changed files:

- debian/changelog
- debian/control
- debian/patches/sphinx.patch
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -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 at debian.org>  Tue, 07 Jan 2020 20:12:00 +0100
 


=====================================
debian/control
=====================================
@@ -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
=====================================
@@ -1,5 +1,14 @@
 --- 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
=====================================
@@ -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



View it on GitLab: https://salsa.debian.org/med-team/python-cogent/commit/c3c8c7d0e19fb742b9a97d313ad90f3a2261adff

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-cogent/commit/c3c8c7d0e19fb742b9a97d313ad90f3a2261adff
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