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biology/libsbml: Fix build with Python 3.10

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Obtained from:	4f01a15fde (based on)
This commit is contained in:
Po-Chuan Hsieh 2021-11-02 05:18:34 +08:00
parent ec3016d98f
commit 8ad9338b22
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GPG Key ID: 9A4BD10F002DD04B
2 changed files with 280 additions and 1 deletions
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2
biology/libsbml/Makefile
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@ -35,7 +35,7 @@ LIBXML2_USE= GNOME=libxml2
LIBXML2_USES= gnome
PYTHON_BUILD_DEPENDS= swig:devel/swig
PYTHON_CMAKE_BOOL= WITH_PYTHON
PYTHON_USES= python:-3.9
PYTHON_USES= python:3.6+
PYTHON_CMAKE_ON= WITH_SWIG
RUBY_BUILD_DEPENDS= swig:devel/swig
RUBY_CMAKE_BOOL= WITH_RUBY

279
biology/libsbml/files/patch-src-bindings-python-doc-converter-rewrite_pydoc.py Normal file
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@ -0,0 +1,279 @@
Obtained from: https://github.com/sbmlteam/libsbml/commit/4f01a15fde1d8afa9eaffb4c13dfc83a3404f183 (based on)
--- src/bindings/python/doc-converter/rewrite_pydoc.py.orig 2020-11-25 11:03:01 UTC
+++ src/bindings/python/doc-converter/rewrite_pydoc.py
@@ -118,7 +118,273 @@ import re
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: