[med-svn] [Git][med-team/libsbml][master] 7 commits: initialize changelog
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Wed Mar 30 22:24:33 BST 2022
Étienne Mollier pushed to branch master at Debian Med / libsbml
Commits:
11c51162 by Étienne Mollier at 2022-03-30T21:26:33+02:00
initialize changelog
- - - - -
4651e5be by Étienne Mollier at 2022-03-30T22:14:07+02:00
Add python3.10.patch from Frank T. Bergmann
Closes: #1008669
Thanks: Adrian Bunk
- - - - -
8d95a0ba by Étienne Mollier at 2022-03-30T22:18:23+02:00
d/control,d/t/autopkgtest-pkg-python.conf: enable superficial autopkgtest
- - - - -
9435ffbf by Étienne Mollier at 2022-03-30T22:22:19+02:00
update changelog
- - - - -
8abb8906 by Étienne Mollier at 2022-03-30T22:22:38+02:00
routine-update: Standards-Version: 4.6.0
- - - - -
6dcacf45 by Étienne Mollier at 2022-03-30T23:11:14+02:00
routine-update: Ready to upload to unstable
- - - - -
ad8a583f by Étienne Mollier at 2022-03-30T23:19:16+02:00
hm, remove autodep8 python for now
to work properly, the package must be built against all available
python versions, but it is only compiled for the default version,
so there is always one of the test that fail when two versions are
available.
- - - - -
4 changed files:
- debian/changelog
- debian/control
- + debian/patches/python3.10.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+libsbml (5.19.0+dfsg-2) unstable; urgency=medium
+
+ * Team upload.
+ * Add python3.10.patch from Frank T. Bergmann to fix FTBFS with python3.10.
+ Thanks to Adrian Bunk (Closes: #1008669)
+ * Standards-Version: 4.6.0 (routine-update)
+
+ -- Étienne Mollier <emollier at debian.org> Wed, 30 Mar 2022 22:25:04 +0200
+
libsbml (5.19.0+dfsg-1) unstable; urgency=medium
* New upstream version
=====================================
debian/control
=====================================
@@ -16,7 +16,7 @@ Build-Depends: debhelper-compat (= 13),
perl,
libperl-dev,
default-jdk-headless,
- default-jdk-doc,
+ default-jdk-doc,
dh-octave,
r-base-dev,
r-base-core,
@@ -30,9 +30,9 @@ Build-Depends: debhelper-compat (= 13),
cli-common-dev,
mono-runtime-common,
texlive-latex-base,
- rdfind,
+ rdfind,
texlive-latex-extra
-Standards-Version: 4.5.1
+Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/libsbml
Vcs-Git: https://salsa.debian.org/med-team/libsbml.git
Homepage: http://www.sbml.org/
@@ -71,7 +71,7 @@ Section: python
Depends: ${shlibs:Depends},
${misc:Depends},
${python3:Depends},
- swig2.0 | swig
+ swig
Provides: python3-sbml
Description: System Biology Markup Language library - Python3 bindings
LibSBML is a library designed to help you read, write, manipulate,
@@ -87,7 +87,7 @@ Section: java
Depends: ${shlibs:Depends},
${misc:Depends},
jarwrapper,
- default-jdk-doc
+ default-jdk-doc
Pre-Depends: ${misc:Pre-Depends}
Provides: libsbml-java
Description: System Biology Markup Language library - Java bindings
@@ -204,8 +204,6 @@ Architecture: all
Multi-Arch: foreign
Section: doc
Depends: ${misc:Depends}
-Breaks: libsbml5-python-doc
-Replaces: libsbml5-python-doc
Suggests: libsbml5-dev (= ${binary:Version})
Description: System Biology Markup Language library - Python3 documentation
LibSBML is a library designed to help you read, write, manipulate,
=====================================
debian/patches/python3.10.patch
=====================================
@@ -0,0 +1,277 @@
+Description: Copy classes for use in python 3.10 and above
+ The NullWriter and AbstractFormatter have been removed in 3.10
+Origin: upstream, https://github.com/sbmlteam/libsbml/commit/7843361b3fb6d13658928105e4635a01478ba70e
+Author: "Frank T. Bergmann" <fbergman at caltech.edu>
+Last-Update: 2021-10-11
+
+--- a/src/bindings/python/doc-converter/rewrite_pydoc.py
++++ b/src/bindings/python/doc-converter/rewrite_pydoc.py
+@@ -118,7 +118,267 @@
+ import sys
+ import os
+ import textwrap
+-from formatter import NullWriter, AbstractFormatter
++try:
++ from formatter import NullWriter, AbstractFormatter
++except Exception:
++ # issue 173 these classes have been removed in 3.10, so
++ # as per the 3.10 release notes: Existing users should copy whatever
++ # classes they use into their code. (Contributed by Dong-hee Na and
++ # Terry J. Reedy in bpo-42299.)
++ #
++ # So here they are:
++
++
++ class NullWriter:
++ """Minimal writer interface to use in testing & inheritance.
++ A writer which only provides the interface definition; no actions are
++ taken on any methods. This should be the base class for all writers
++ which do not need to inherit any implementation methods.
++ """
++ def __init__(self): pass
++ def flush(self): pass
++ def new_alignment(self, align): pass
++ def new_font(self, font): pass
++ def new_margin(self, margin, level): pass
++ def new_spacing(self, spacing): pass
++ def new_styles(self, styles): pass
++ def send_paragraph(self, blankline): pass
++ def send_line_break(self): pass
++ def send_hor_rule(self, *args, **kw): pass
++ def send_label_data(self, data): pass
++ def send_flowing_data(self, data): pass
++ def send_literal_data(self, data): pass
++
++ class AbstractFormatter:
++ """The standard formatter.
++ This implementation has demonstrated wide applicability to many writers,
++ and may be used directly in most circumstances. It has been used to
++ implement a full-featured World Wide Web browser.
++ """
++
++ # Space handling policy: blank spaces at the boundary between elements
++ # are handled by the outermost context. "Literal" data is not checked
++ # to determine context, so spaces in literal data are handled directly
++ # in all circumstances.
++
++ def __init__(self, writer):
++ self.writer = writer # Output device
++ self.align = None # Current alignment
++ self.align_stack = [] # Alignment stack
++ self.font_stack = [] # Font state
++ self.margin_stack = [] # Margin state
++ self.spacing = None # Vertical spacing state
++ self.style_stack = [] # Other state, e.g. color
++ self.nospace = 1 # Should leading space be suppressed
++ self.softspace = 0 # Should a space be inserted
++ self.para_end = 1 # Just ended a paragraph
++ self.parskip = 0 # Skipped space between paragraphs?
++ self.hard_break = 1 # Have a hard break
++ self.have_label = 0
++
++ def end_paragraph(self, blankline):
++ if not self.hard_break:
++ self.writer.send_line_break()
++ self.have_label = 0
++ if self.parskip < blankline and not self.have_label:
++ self.writer.send_paragraph(blankline - self.parskip)
++ self.parskip = blankline
++ self.have_label = 0
++ self.hard_break = self.nospace = self.para_end = 1
++ self.softspace = 0
++
++ def add_line_break(self):
++ if not (self.hard_break or self.para_end):
++ self.writer.send_line_break()
++ self.have_label = self.parskip = 0
++ self.hard_break = self.nospace = 1
++ self.softspace = 0
++
++ def add_hor_rule(self, *args, **kw):
++ if not self.hard_break:
++ self.writer.send_line_break()
++ self.writer.send_hor_rule(*args, **kw)
++ self.hard_break = self.nospace = 1
++ self.have_label = self.para_end = self.softspace = self.parskip = 0
++
++ def add_label_data(self, format, counter, blankline = None):
++ if self.have_label or not self.hard_break:
++ self.writer.send_line_break()
++ if not self.para_end:
++ self.writer.send_paragraph((blankline and 1) or 0)
++ if isinstance(format, str):
++ self.writer.send_label_data(self.format_counter(format, counter))
++ else:
++ self.writer.send_label_data(format)
++ self.nospace = self.have_label = self.hard_break = self.para_end = 1
++ self.softspace = self.parskip = 0
++
++ def format_counter(self, format, counter):
++ label = ''
++ for c in format:
++ if c == '1':
++ label = label + ('%d' % counter)
++ elif c in 'aA':
++ if counter > 0:
++ label = label + self.format_letter(c, counter)
++ elif c in 'iI':
++ if counter > 0:
++ label = label + self.format_roman(c, counter)
++ else:
++ label = label + c
++ return label
++
++ def format_letter(self, case, counter):
++ label = ''
++ while counter > 0:
++ counter, x = divmod(counter-1, 26)
++ # This makes a strong assumption that lowercase letters
++ # and uppercase letters form two contiguous blocks, with
++ # letters in order!
++ s = chr(ord(case) + x)
++ label = s + label
++ return label
++
++ def format_roman(self, case, counter):
++ ones = ['i', 'x', 'c', 'm']
++ fives = ['v', 'l', 'd']
++ label, index = '', 0
++ # This will die of IndexError when counter is too big
++ while counter > 0:
++ counter, x = divmod(counter, 10)
++ if x == 9:
++ label = ones[index] + ones[index+1] + label
++ elif x == 4:
++ label = ones[index] + fives[index] + label
++ else:
++ if x >= 5:
++ s = fives[index]
++ x = x-5
++ else:
++ s = ''
++ s = s + ones[index]*x
++ label = s + label
++ index = index + 1
++ if case == 'I':
++ return label.upper()
++ return label
++
++ def add_flowing_data(self, data):
++ if not data: return
++ prespace = data[:1].isspace()
++ postspace = data[-1:].isspace()
++ data = " ".join(data.split())
++ if self.nospace and not data:
++ return
++ elif prespace or self.softspace:
++ if not data:
++ if not self.nospace:
++ self.softspace = 1
++ self.parskip = 0
++ return
++ if not self.nospace:
++ data = ' ' + data
++ self.hard_break = self.nospace = self.para_end = \
++ self.parskip = self.have_label = 0
++ self.softspace = postspace
++ self.writer.send_flowing_data(data)
++
++ def add_literal_data(self, data):
++ if not data: return
++ if self.softspace:
++ self.writer.send_flowing_data(" ")
++ self.hard_break = data[-1:] == '\n'
++ self.nospace = self.para_end = self.softspace = \
++ self.parskip = self.have_label = 0
++ self.writer.send_literal_data(data)
++
++ def flush_softspace(self):
++ if self.softspace:
++ self.hard_break = self.para_end = self.parskip = \
++ self.have_label = self.softspace = 0
++ self.nospace = 1
++ self.writer.send_flowing_data(' ')
++
++ def push_alignment(self, align):
++ if align and align != self.align:
++ self.writer.new_alignment(align)
++ self.align = align
++ self.align_stack.append(align)
++ else:
++ self.align_stack.append(self.align)
++
++ def pop_alignment(self):
++ if self.align_stack:
++ del self.align_stack[-1]
++ if self.align_stack:
++ self.align = align = self.align_stack[-1]
++ self.writer.new_alignment(align)
++ else:
++ self.align = None
++ self.writer.new_alignment(None)
++
++ def push_font(self, font):
++ size, i, b, tt = font
++ if self.softspace:
++ self.hard_break = self.para_end = self.softspace = 0
++ self.nospace = 1
++ self.writer.send_flowing_data(' ')
++ if self.font_stack:
++ csize, ci, cb, ctt = self.font_stack[-1]
++ if size is AS_IS: size = csize
++ if i is AS_IS: i = ci
++ if b is AS_IS: b = cb
++ if tt is AS_IS: tt = ctt
++ font = (size, i, b, tt)
++ self.font_stack.append(font)
++ self.writer.new_font(font)
++
++ def pop_font(self):
++ if self.font_stack:
++ del self.font_stack[-1]
++ if self.font_stack:
++ font = self.font_stack[-1]
++ else:
++ font = None
++ self.writer.new_font(font)
++
++ def push_margin(self, margin):
++ self.margin_stack.append(margin)
++ fstack = filter(None, self.margin_stack)
++ if not margin and fstack:
++ margin = fstack[-1]
++ self.writer.new_margin(margin, len(fstack))
++
++ def pop_margin(self):
++ if self.margin_stack:
++ del self.margin_stack[-1]
++ fstack = filter(None, self.margin_stack)
++ if fstack:
++ margin = fstack[-1]
++ else:
++ margin = None
++ self.writer.new_margin(margin, len(fstack))
++
++ def set_spacing(self, spacing):
++ self.spacing = spacing
++ self.writer.new_spacing(spacing)
++
++ def push_style(self, *styles):
++ if self.softspace:
++ self.hard_break = self.para_end = self.softspace = 0
++ self.nospace = 1
++ self.writer.send_flowing_data(' ')
++ for style in styles:
++ self.style_stack.append(style)
++ self.writer.new_styles(tuple(self.style_stack))
++
++ def pop_style(self, n=1):
++ del self.style_stack[-n:]
++ self.writer.new_styles(tuple(self.style_stack))
++
++ def assert_line_data(self, flag=1):
++ self.nospace = self.hard_break = not flag
++ self.para_end = self.parskip = self.have_label = 0
+ try:
+ from htmllib import HTMLParser
+ except Exception:
=====================================
debian/patches/series
=====================================
@@ -10,3 +10,4 @@ javadoc.patch
remove_SBMLDoclet.patch
fix_build_issue.patch
fix_python_interpreter.patch
+python3.10.patch
View it on GitLab: https://salsa.debian.org/med-team/libsbml/-/compare/0e2eb925216e18e9017f5e1afd72f3bdaeed44d9...ad8a583f85c1f836adf20fdc179c6225c311f958
--
View it on GitLab: https://salsa.debian.org/med-team/libsbml/-/compare/0e2eb925216e18e9017f5e1afd72f3bdaeed44d9...ad8a583f85c1f836adf20fdc179c6225c311f958
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