[med-svn] [Git][med-team/ghmm][master] 3 commits: Attempt to fix the installation for local builds (for instance with `debuild`)
Andreas Tille (@tille)
gitlab at salsa.debian.org
Mon Jan 15 14:49:59 GMT 2024
Andreas Tille pushed to branch master at Debian Med / ghmm
Commits:
762f0126 by Andreas Tille at 2024-01-13T15:18:54+01:00
Attempt to fix the installation for local builds (for instance with `debuild`)
While this makes the problem consistent between building in pbuilder and debuild it
installs to /usr/local (despite prefix is properly set) and thus breaks the build for both
--> patch deactivated
- - - - -
2f53d3ee by Andreas Tille at 2024-01-15T15:46:54+01:00
Try hard to get Python3 modules installed into proper dirs
- - - - -
defd83c4 by Andreas Tille at 2024-01-15T15:49:27+01:00
More syntax fixes
- - - - -
6 changed files:
- debian/control
- debian/ghmm.install
- debian/patches/python3_syntax.patch
- debian/patches/series
- + debian/patches/setuptools.patch
- debian/rules
Changes:
=====================================
debian/control
=====================================
@@ -4,6 +4,7 @@ Uploaders: Steffen Moeller <moeller at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
+ dh-sequence-python3,
d-shlibs,
python3-dev,
pkg-config,
@@ -23,6 +24,7 @@ Package: ghmm
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
+ ${python3:Depends},
python3,
libghmm1
Description: General Hidden-Markov-Model library - tools
=====================================
debian/ghmm.install
=====================================
@@ -1,3 +1,3 @@
usr/bin
usr/share/ghmm/ghmm.dtd*
-usr/lib/python3*/site-packages/* usr/lib/ghmm
+#usr/lib/python3*
=====================================
debian/patches/python3_syntax.patch
=====================================
@@ -80,3 +80,23 @@ Last-Update: Thu, 11 Jan 2024 17:06:32 +0100
return self.GetWeight()
else:
return self.__dict__[name]
+--- a/ghmmwrapper/ghmm.py
++++ b/ghmmwrapper/ghmm.py
+@@ -1355,7 +1355,7 @@ class HMMOpenFactory(HMMFactory):
+ result = []
+ for i in range(nrModels):
+ cmodel = getModel(i)
+- if emission_domain is 'd':
++ if emission_domain == 'd':
+ emission_domain = Alphabet(cmodel.alphabet)
+ if modelType & ghmmwrapper.kLabeledStates:
+ labelDomain = LabelDomain(cmodel.label_alphabet)
+@@ -2865,7 +2865,7 @@ class DiscreteEmissionHMM(HMM):
+
+ if self.hasFlags(kSilentStates):
+ raise NotImplementedError("Sorry, training of models containing silent states not yet supported.")
+- if R is -1:
++ if R == -1:
+ R = int(math.ceil(.5*math.log(math.sqrt(len(trainingSequences)))))
+ #print R
+ if R <= 1:
=====================================
debian/patches/series
=====================================
@@ -5,3 +5,4 @@ fix_libxml2_config.patch
python3_build_system.patch
#lapacke.patch
python3_syntax.patch
+# setuptools.patch
=====================================
debian/patches/setuptools.patch
=====================================
@@ -0,0 +1,29 @@
+Description: Attempt to fix the installation for local builds (for instance with `debuild`)
+ While this makes the problem consistent between building in pbuilder and debuild it
+ installs to /usr/local (despite prefix is properly set) and thus breaks the build for both
+ --> patch deactivated
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 11 Jan 2024 17:06:32 +0100
+
+--- a/HMMEd/setup.py
++++ b/HMMEd/setup.py
+@@ -35,7 +35,7 @@
+ #
+ ################################################################################
+
+-from distutils.core import setup,Extension
++from setuptools import setup, Extension
+
+
+ setup(name="HMMEd",
+--- a/ghmmwrapper/setup.py
++++ b/ghmmwrapper/setup.py
+@@ -35,7 +35,7 @@
+ #
+ ################################################################################
+
+-from distutils.core import setup,Extension
++from setuptools import setup, Extension
+
+ setup(name="ghmmwrapper",
+ version="0.8",
=====================================
debian/rules
=====================================
@@ -1,17 +1,28 @@
#!/usr/bin/make -f
-#export DH_VERBOSE = 1
+
+export DH_VERBOSE = 1
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+export PYBUILD_NAME=HMMEd
+
%:
dh $@
override_dh_auto_configure:
- dh_auto_configure -- --enable-atlas
+ dh_auto_configure --sourcedirectory=$(CURDIR) -- --enable-atlas
+ dh_auto_configure --buildsystem=pybuild --sourcedirectory=HMMEd
+
+override_dh_auto_build:
+ dh_auto_build
+ dh_auto_build --buildsystem=pybuild --sourcedirectory=HMMEd
+
+override_dh_auto_install:
+ dh_auto_install
+ dh_auto_install --buildsystem=pybuild --sourcedirectory=HMMEd
override_dh_install:
dh_install
- find $(CURDIR)/debian/tmp -name "*.pyc" -delete
d-shlibmove --commit \
--multiarch \
--devunversioned \
@@ -22,8 +33,18 @@ override_dh_install:
cd $(CURDIR)/debian/ghmm/usr/bin/ && mv cluster ghmm-cluster
sed -i -e 's@ [^ ]*-f\(file\|debug\)-prefix-map=[^ ]*@@g' \
$(CURDIR)/debian/ghmm/usr/bin/ghmm-config
- find debian -name __pycache__ | xargs rm -rf
find debian -name libghmm.la -delete
+ # temporarily copy over ghmmwrapper to the pybuild created dir
+ mkdir -p debian/python3-HMMEd/usr/lib/python3/dist-packages
+ mv debian/tmp/usr/local/lib/python3.11/dist-packages/ghmmwrapper-0.8-py3*.egg debian/python3-HMMEd/usr/lib/python3/dist-packages/ghmm
+ rm -rf debian/tmp/usr/local
+ find debian -type d -name __pycache__ | xargs rm -rf
+
+override_dh_python3:
+ # We do not provide a package python3-HMMEd thus copy the pybuild installed files over to ghmm
+ mv debian/python3-HMMEd/usr/bin/* debian/ghmm/usr/bin
+ mv debian/python3-HMMEd/usr/lib debian/ghmm/usr
+ dh_python3 -p ghmm
override_dh_auto_clean:
if [ -r Makefile ]; then $(MAKE) clean; fi
@@ -42,4 +63,3 @@ override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
$(MAKE) --directory=tests
endif
-
View it on GitLab: https://salsa.debian.org/med-team/ghmm/-/compare/34de713884e6588f9ad4696d3f3a61f04943f99a...defd83c42c30fab4d4ed456455d196bef5665c7d
--
View it on GitLab: https://salsa.debian.org/med-team/ghmm/-/compare/34de713884e6588f9ad4696d3f3a61f04943f99a...defd83c42c30fab4d4ed456455d196bef5665c7d
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