Patches for pdf docs, Pyrex compatibility, dir()/help() fixes #1
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Do ``cd doc; make`` and open ``doc/latex_new/Pygr.pdf``.
cnestedlist.pyx and cdict.py. Also updated .gitignore to exclude
build targets intervaldb.o and libnclist.a.
This patch fixes setup.py, which was giving the following output on
Mac OS X 10.6 (included below for those with the same error):
{{{
$ python setup.py --verbose build
running build
running build_py
not copying pygr/__init__.py (output up-to-date)
not copying pygr/annotation.py (output up-to-date)
not copying pygr/blast.py (output up-to-date)
not copying pygr/classutil.py (output up-to-date)
not copying pygr/coordinator.py (output up-to-date)
not copying pygr/Data.py (output up-to-date)
not copying pygr/dbfile.py (output up-to-date)
not copying pygr/downloader.py (output up-to-date)
not copying pygr/graphquery.py (output up-to-date)
not copying pygr/logger.py (output up-to-date)
not copying pygr/mapping.py (output up-to-date)
not copying pygr/metabase.py (output up-to-date)
not copying pygr/nlmsa_utils.py (output up-to-date)
not copying pygr/parse_blast.py (output up-to-date)
not copying pygr/schema.py (output up-to-date)
not copying pygr/seqdb.py (output up-to-date)
not copying pygr/sequence.py (output up-to-date)
not copying pygr/sequtil.py (output up-to-date)
not copying pygr/sqlgraph.py (output up-to-date)
not copying pygr/translationDB.py (output up-to-date)
not copying pygr/xnestedlist.py (output up-to-date)
not copying pygr/apps/__init__.py (output up-to-date)
not copying pygr/apps/catalog_downloads.py (output up-to-date)
not copying pygr/apps/leelabdb.py (output up-to-date)
not copying pygr/apps/maf2nclist.py (output up-to-date)
not copying pygr/apps/maf2VSgraph.py (output up-to-date)
not copying pygr/apps/seqref.py (output up-to-date)
not copying pygr/apps/splicegraph.py (output up-to-date)
not copying pygr/apps/ucsc_ensembl_annot.py (output up-to-date)
running build_ext
skipping 'pygr.seqfmt' extension (up-to-date)
pyrexc pygr/cdict.pyx --> pygr/cdict.c
~/pygr/pygr/cdict.pyx:95:4: __new__ method of extension type will change semantics in a future version of Pyrex. Use __cinit__ instead.
~/pygr/pygr/cdict.pyx:160:4: __new__ method of extension type will change semantics in a future version of Pyrex. Use __cinit__ instead.
~/pygr/pygr/cdict.pyx:212:4: __new__ method of extension type will change semantics in a future version of Pyrex. Use __cinit__ instead.
~/pygr/pygr/cdict.pyx:261:4: __new__ method of extension type will change semantics in a future version of Pyrex. Use __cinit__ instead.
~/pygr/pygr/cdict.pyx:407:4: __new__ method of extension type will change semantics in a future version of Pyrex. Use __cinit__ instead.
~/pygr/pygr/cdict.pyx:212:22: Warning: 'not None' will become the default in a future version of Pyrex. Use 'or None' to allow passing None.
building 'pygr.cdict' extension
gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -O2 -DNDEBUG -g -O3 -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c pygr/cgraph.c -o build/temp.macosx-10.6-intel-2.7/pygr/cgraph.o
gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -O2 -DNDEBUG -g -O3 -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c pygr/cdict.c -o build/temp.macosx-10.6-intel-2.7/pygr/cdict.o
pygr/cdict.c:1:2: error: #error Do not use this file, it is the result of a failed Pyrex compilation.
pygr/cdict.c:1:2: error: #error Do not use this file, it is the result of a failed Pyrex compilation.
lipo: can't figure out the architecture type of: ~/tmp/ccWaoUlh.out
error: command 'gcc-4.2' failed with exit status 1
}}}
There is still a separate warning on the 'or None' argument:
{{{
$ python setup.py build --verbose
running build
running build_py
running build_ext
pyrexc pygr/cnestedlist.pyx --> pygr/cnestedlist.c
~/pygr/pygr/cnestedlist.pyx:167:42: Warning: 'not None' will become the default in a future version of Pyrex. Use 'or None' to allow passing None.
building 'pygr.cnestedlist' extension
gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -O2 -DNDEBUG -g -O3 -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c pygr/intervaldb.c -o build/temp.macosx-10.6-intel-2.7/pygr/intervaldb.o
gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -O2 -DNDEBUG -g -O3 -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c pygr/cnestedlist.c -o build/temp.macosx-10.6-intel-2.7/pygr/cnestedlist.o
gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -O2 -DNDEBUG -g -O3 -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c pygr/apps/maf2nclist.c -o build/temp.macosx-10.6-intel-2.7/pygr/apps/maf2nclist.o
gcc-4.2 -arch i386 -arch x86_64 -isysroot / -g -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -isysroot / -g build/temp.macosx-10.6-intel-2.7/pygr/intervaldb.o build/temp.macosx-10.6-intel-2.7/pygr/cnestedlist.o build/temp.macosx-10.6-intel-2.7/pygr/apps/maf2nclist.o -o build/lib.macosx-10.6-intel-2.7/pygr/cnestedlist.so
}}}
Essentially, Pyrex has a transition period where every argument
needs to be explicitly declared with 'or None' or 'not None'.
This is because the default is currently 'or None', but it
will be changed to 'not None'. Explicit declarations will
work either way. See:
http://www.cosc.canterbury.ac.nz/greg.ewing/python/Pyrex/version/Doc/Release_Notes_0.9.9.html
…-the-box. Root cause of the dir() issue was that defaultPath was not getting inspected, which broke expectations set by the tutorial. Root cause of the help() issue is the __getattr__ method in ResourcePath, which did not return a string when asked for __name__ by the help method.
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Hi Chris,
I'm a friend of Titus' and made a few quick changes that significantly increased the out-of-the-box usability of pygr for me.
With these changes, I think people should be able to run the tutorial "as is". Will tell you if that's not the case.