[med-svn] [Git][med-team/ghmm][master] 3 commits: Revert attempt to port to lapacke to write an autopkgtest first (lapacke-port is in branch lapacke)
Andreas Tille (@tille)
gitlab at salsa.debian.org
Sat Jan 13 09:29:52 GMT 2024
Andreas Tille pushed to branch master at Debian Med / ghmm
Commits:
12c1c750 by Andreas Tille at 2024-01-13T07:22:08+01:00
Revert attempt to port to lapacke to write an autopkgtest first (lapacke-port is in branch lapacke)
- - - - -
13ac651d by Andreas Tille at 2024-01-13T08:45:44+01:00
Fix: SyntaxWarning: "is" with a literal. Did you mean "=="?
- - - - -
34de7138 by Andreas Tille at 2024-01-13T10:23:27+01:00
Fix clean target
- - - - -
5 changed files:
- debian/changelog
- debian/control
- + debian/patches/python3_syntax.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,10 +1,11 @@
ghmm (0.9~rc3-5) UNRELEASED; urgency=medium
* Team upload.
- * Do not build-depends on atlas
- Closes: #1056673
* Standards-Version: 4.6.2 (routine-update)
* Avoid explicitly specifying -Wl,--as-needed linker flag.
+ * Fix: SyntaxWarning: "is" with a literal. Did you mean "=="?
+ * Fix clean target
+ Closes: #1044649
-- Andreas Tille <tille at debian.org> Thu, 11 Jan 2024 17:06:32 +0100
=====================================
debian/control
=====================================
@@ -9,8 +9,8 @@ Build-Depends: debhelper-compat (= 13),
pkg-config,
libxml2-dev,
libgsl-dev,
- libblas-dev | libblas.so,
- liblapacke-dev,
+ libatlas-base-dev,
+ liblapack-dev,
zlib1g-dev,
swig
Standards-Version: 4.6.2
@@ -25,7 +25,6 @@ Depends: ${shlibs:Depends},
${misc:Depends},
python3,
libghmm1
-Recommends: libopenblas0 | libblis4
Description: General Hidden-Markov-Model library - tools
The General Hidden Markov Model Library (GHMM) is a C library with
additional Python3 bindings implementing a wide range of types of
=====================================
debian/patches/python3_syntax.patch
=====================================
@@ -0,0 +1,82 @@
+Description: Fix: SyntaxWarning: "is" with a literal. Did you mean "=="?
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 11 Jan 2024 17:06:32 +0100
+
+--- a/HMMEd/HMMEditingContext.py
++++ b/HMMEd/HMMEditingContext.py
+@@ -39,10 +39,10 @@ class HMMEditingContext(object):
+ self.modeltype = mtype
+ # check whether the parameter is an EmissionDomain
+ if isinstance(parameter, ghmm.EmissionDomain):
+- if parameter.CDataType is "int":
++ if parameter.CDataType == "int":
+ self.HMM = ObjectHMM(State, Transition, alphabet=parameter, etype=0)
+ self.modeltype |= ghmmwrapper.kDiscreteHMM
+- elif parameter.CDataType is "double":
++ elif parameter.CDataType == "double":
+ self.HMM = ObjectHMM(State, Transition, emissionClass=ContinuousMixtureDistribution, etype=1)
+ self.modeltype |= ghmmwrapper.kContinuousHMM
+ else:
+--- a/HMMEd/HMMEditor.py
++++ b/HMMEd/HMMEditor.py
+@@ -433,7 +433,7 @@ class HMMGraphEditor(SAGraphEditor):
+ filetypes = (("XML", ".xml"),
+ )
+ )
+- if file is "":
++ if file == "":
+ print("cancelled")
+ else:
+ self.fileName = file
+@@ -468,7 +468,7 @@ class HMMGraphEditor(SAGraphEditor):
+ filetypes = ( ("XML", ".xml"),
+ )
+ )
+- if file is not "":
++ if file != "":
+ self.fileName = file
+ self.dirty = 0
+ self.G.writeXML(self.fileName)
+--- a/HMMEd/ObjectHMM.py
++++ b/HMMEd/ObjectHMM.py
+@@ -645,9 +645,9 @@ class State(VertexObject):
+ self.fixed = ValidatingBool(False)
+
+ def __setattr__(self, name, value):
+- if name is "emission":
++ if name == "emission":
+ self.Emission.set(value)
+- elif name is "name":
++ elif name == "name":
+ try:
+ if self.itsHMM is not None:
+ vname = self.labeling
+@@ -662,9 +662,9 @@ class State(VertexObject):
+ #object.__setattr__(self, name, value)
+
+ def __getattr__(self, name):
+- if name is "emission":
++ if name == "emission":
+ return self.Emission.get()
+- elif name is "name":
++ elif name == "name":
+ return self.labeling
+ else:
+ return self.__dict__[name]
+@@ -1050,14 +1050,14 @@ class Transition(EdgeObject):
+ return "Transition from %d to %d with probability %f" % (self.tail.id, self.head.id, self.GetWeight())
+
+ def __setattr__(self, name, value):
+- if name is "p":
++ if name == "p":
+ self.SetWeight(value)
+ else:
+ self.__dict__[name] = value
+ #object.__setattr__(self, name, value)
+
+ def __getattr__(self, name):
+- if name is "p":
++ if name == "p":
+ return self.GetWeight()
+ else:
+ return self.__dict__[name]
=====================================
debian/patches/series
=====================================
@@ -3,4 +3,5 @@ pythonpaths.patch
fix_libxml2_config.patch
2to3.patch
python3_build_system.patch
-lapacke.patch
+#lapacke.patch
+python3_syntax.patch
=====================================
debian/rules
=====================================
@@ -30,13 +30,16 @@ override_dh_auto_clean:
find . -name Makefile -delete
find . \( -name "*.o" -o -name "*.lo" \) -delete
rm -f ghmmwrapper/ghmmwrapper.py ghmmwrapper/ghmmwrapper_wrap.c
- rm -rf HMMEd/build/ ghmmwrapper/build/
+ rm -rf HMMEd/build/ ghmmwrapper/build/ HMMEd/HMMEd.egg-info HMMEd/dist
+ rm -rf ghmmwrapper/ghmmwrapper.egg-info ghmmwrapper/dist
rm -f config.h config.log config.status
rm -f libtool stamp-h1 tests/chmm_test.2JNcXz
rm -f tools/ghmm-config
rm -rf ghmm/.deps/ tests/.deps/ tools/.deps/
+ rm -rf ghmm/ghmmconfig.h
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/33d3d42554998e4fc75f0632ccc7a035f8bcd9a4...34de713884e6588f9ad4696d3f3a61f04943f99a
--
View it on GitLab: https://salsa.debian.org/med-team/ghmm/-/compare/33d3d42554998e4fc75f0632ccc7a035f8bcd9a4...34de713884e6588f9ad4696d3f3a61f04943f99a
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