fix libhomfly on OSX

[dimpase]

as reported on ​sage-devel linking on OSX fails with "duplicate symbol" errors.

[libhomfly-1.0r2] libtool: link: cc -dynamiclib -Wl,-undefined -Wl,dynamic_lookup -o .libs/libhomfly.0.dylib  .libs/bound.o .libs/control.o .libs/dllink.o .libs/homfly.o .libs/knot.o .libs/model.o .libs/order.o .libs/poly.o   -lgc -L/Volumes/Sage/sage/local/lib  -g -O2 -Wl,-rpath -Wl,/Volumes/Sage/sage/local/lib   -install_name  /Volumes/Sage/sage/local/lib/libhomfly.0.dylib -compatibility_version 1 -current_version 1.0 -Wl,-single_module -Wl,-exported_symbols_list,.libs/libhomfly-symbols.expsym
[libhomfly-1.0r2] duplicate symbol _first in:
[libhomfly-1.0r2]     .libs/bound.o
[libhomfly-1.0r2]     .libs/control.o
[libhomfly-1.0r2] duplicate symbol _list in:
[libhomfly-1.0r2]     .libs/bound.o
[libhomfly-1.0r2]     .libs/control.o
...

there is also an error in poly.c, where a non-void function returns nothing. This is trivially fixed by

diff --git a/lib/poly.c b/lib/poly.c
index 48e9a68..307d1de 100644
--- a/lib/poly.c
+++ b/lib/poly.c
@@ -76,7 +76,7 @@ char *p_show(Poly *p)
   {
     fprintf(stream, "0");
     fclose(stream);
-    return;
+    return NULL;
   }
 
   for (first = 1, pt = p->term, pend = pt+p->len; pt != pend; ++pt)

---

As it was being fixed, more problems were uncovered, and then a pesky GC bug, that went away after adding an explicit GC_INIT() call.

It appears that all is fixed by ​https://github.com/miguelmarco/libhomfly/pull/11

the (official!) tarball is here: ​https://github.com/miguelmarco/libhomfly/releases/download/1.02r4/libhomfly-1.02r4.tar.gz

[dimpase]

I have a fix for the C code madness, now onto some cython trouble, hopefully minor:

sage -t --warn-long 231.9 src/sage/libs/homfly.pyx
**********************************************************************
File "src/sage/libs/homfly.pyx", line 65, in sage.libs.homfly.homfly_polynomial_string
Failed example:
    from sage.libs.homfly import homfly_polynomial_string # optional - libhomfly
Exception raised:
    Traceback (most recent call last):
      File "/Volumes/Sage/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 515, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/Volumes/Sage/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 885, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.libs.homfly.homfly_polynomial_string[0]>", line 1, in <module>
        from sage.libs.homfly import homfly_polynomial_string # optional - libhomfly
    ImportError: dlopen(/Volumes/Sage/sage/local/lib/python2.7/site-packages/sage/libs/homfly.so, 2): Symbol not found: _fmemopen
      Referenced from: /Volumes/Sage/sage/local/lib/libhomfly.0.dylib
      Expected in: flat namespace
     in /Volumes/Sage/sage/local/lib/libhomfly.0.dylib
**********************************************************************

[dimpase]

duh, there is no fmemopen on OSX, as simple as this...

[dimpase]

C changes proposed to upstream: ​https://github.com/miguelmarco/libhomfly/pull/8

[dimpase]

still, for OSX we need to update GC to a very recent version, see ​https://github.com/miguelmarco/libhomfly/pull/8 for details.

[dimpase]

the last remaining problem was the lack of GC_INIT() call in the library (something that is apparently not needed on Linux, but the docs say that that some platforms might need it...)

With ​https://github.com/miguelmarco/libhomfly/pull/11 it is all fixed, also on the current Sage's GC version on OSX.

---

New commits:

​a3c3ac7

new version and checksum

[dimpase]

NB: the tarball is just a proof of concept, corresponding to commit b68b5b2aac2e89b17312208080562f5754d3da2d on ​https://github.com/dimpase/libhomfly

Once the upstream is done with merging, we should get the official tarball...

[mmarco]

I made a new release upstream. It is ​https://github.com/miguelmarco/libhomfly/releases/tag/1.02r4

The tarball is at ​https://github.com/miguelmarco/libhomfly/archive/1.02r4.tar.gz

[git]

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

​c623d6b

new version and checksum

[git]

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

​5b5e57b

new version and checksum; minor SPKG.txt update

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​7f277d9

tarball needs autoreconf run, thus updated

[dimpase]

I had to update the tarball from github by running autoreconf -if and re-tarring then.

Should all be ready now.

[dimpase]

One little detail about GC_INIT(): it is not needed on the current Boehm GC master at ​https://github.com/ivmai/bdwgc, but is needed on few releases (7.4 and 7.6), as well as on the current Sage's version of GC.

No it builds with SAGE_CHECK=yes, and all the relevant Sage tests pass, too, on OSX 10.12 as well as on Linux.

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​f3349e0

use the official tarball

[dimpase]

OK, so now even the tarball is official!

[dimpase]

I think we need a menu choice saying "Fixes fully merged in the current upstream release". :-)