python3Packages.snappy: init at 3.2 #415184

noiioiu · 2025-06-09T04:26:53Z

SnapPy is a program and python module for studying the topology and geometry of 3-manifolds.

Things done

Add a 👍 reaction to pull requests you find important.

pkgs/development/python-modules/snappy/default.nix

pkgs/development/python-modules/tkinter-gl/default.nix

pkgs/development/python-modules/snappy/default.nix

dotlambda · 2025-06-21T00:38:22Z

pkgs/development/python-modules/tkinter-gl/default.nix

+
+  postInstall = ''
+    cp -r src/tkinter_gl/tk $out/${python.sitePackages}/tkinter_gl/
+    patchelf --set-rpath ${lib.makeLibraryPath [ libGL ]} \


This should really be fixed upstream.

Source is here, but there are no releases and I haven't tried compiling it.

I created a package for tkgl and added it as a dependency of tkinter-gl instead of patching the compiled ones, the tests still run.

noiioiu · 2025-06-22T02:35:02Z

aarch64-linux build failed

What was the error?

noiioiu · 2025-06-22T03:18:58Z

error: Cannot build '/nix/store/1cba3fckayf1gnzrwxm0n4aq70p0kmqr-python3.12-cypari-2.5.5.drv'.
       Reason: builder failed with exit code 1.
       Output paths:
         /nix/store/148d6lzr52xnn18hkvqwxdrk3b1dg8ql-python3.12-cypari-2.5.5
         /nix/store/f1zm2bk5s9hmlaksmas74j7qp2h34lw7-python3.12-cypari-2.5.5-dist
       Last 25 log lines:
       > copying cypari/memory.py -> build/lib.linux-aarch64-cpython-312/cypari
       > copying cypari/py2tests.py -> build/lib.linux-aarch64-cpython-312/cypari
       > copying cypari/test.py -> build/lib.linux-aarch64-cpython-312/cypari
       > copying cypari/version.py -> build/lib.linux-aarch64-cpython-312/cypari
       > copying cypari/py3tests.py -> build/lib.linux-aarch64-cpython-312/cypari
       > copying cypari/tests.py -> build/lib.linux-aarch64-cpython-312/cypari
       > running build_ext
       > Building gmp ...
       > Extracting gmp source code ...
       > Configuring gmp with ./configure --build=x86_64-none-none --prefix=/build/source/libcache/gmp --with-pic
       > checking build system type... x86_64-none-none
       > checking host system type... x86_64-none-none
       > checking for a BSD-compatible install... /nix/store/6sb7gak61cwcg3p5grnhhyndi5hz935y-coreutils-9.7/bin/install -c
       > checking whether build environment is sane... yes
       > checking for a thread-safe mkdir -p... /nix/store/6sb7gak61cwcg3p5grnhhyndi5hz935y-coreutils-9.7/bin/mkdir -p
       > checking for gawk... gawk
       > checking whether make sets $(MAKE)... yes
       > checking whether make supports nested variables... yes
       > checking whether to enable maintainer-specific portions of Makefiles... no
       > checking ABI=64
       > checking compiler gcc -O2 -pedantic -fomit-frame-pointer -m64 ... no
       > configure: error: could not find a working compiler, see config.log for details
       > ***Failed to build PARI library***
       >
       > ERROR Backend subprocess exited when trying to invoke build_wheel
       For full logs, run:
         nix log /nix/store/1cba3fckayf1gnzrwxm0n4aq70p0kmqr-python3.12-cypari-2.5.5.drv

Ok, it looks like the source of the bug is here. The script will need to be patched.

noiioiu · 2025-07-07T11:03:03Z

Still can't build, I think it's enough to mark darwin as broken for now. I don’t have the energy to review anymore.

Cypari is now marked as broken on darwin.

alejo7797 · 2025-08-16T15:09:31Z

Thank you for taking the time to package SnapPy and its dependencies!
May I suggest adding a small pkgs/by-name/sn/snappy-topology/package.nix wrapper?

The attribute name is not too important, but unfortunately pkgs.snappy is taken.
I think snappy-topology is okay; I couldn't find any recommendations upstream.

noiioiu · 2025-08-18T17:55:37Z

Thank you for taking the time to package SnapPy and its dependencies! May I suggest adding a small pkgs/by-name/sn/snappy-topology/package.nix wrapper?

The attribute name is not too important, but unfortunately pkgs.snappy is taken. I think snappy-topology is okay; I couldn't find any recommendations upstream.

OK it has been added.

alejo7797

I have a few suggestions for changes which I hope are helpful.

pkgs/development/python-modules/snappy/default.nix

alejo7797 · 2025-08-19T01:59:06Z

pkgs/development/python-modules/snappy/default.nix

+  snappy-15-knots,
+  snappy-manifolds,
+  spherogram,
+  sphinx,


Suggested change

sphinx,

sphinxHook,

A suggestion: I wonder if it might be good to build the docs using Nixpkgs' sphinxHook?
There's a few other changes to the derivation needed to make this work, shown below.

Please ignore my suggestions if I'm missing some important reason for not doing this!

alejo7797 · 2025-08-19T02:00:01Z

pkgs/development/python-modules/snappy/default.nix

+  pname = "snappy";
+  version = "3.2";
+  pyproject = true;
+


Suggested change

outputs = [

"out"

"doc"

];

Re: sphinxHook

I think this can cause problems with nix-shell. Or does this fix it?

I think that avoids issues? I tried running nix-shell -I nixpkgs=. -p "python3.withPackages (ps: [ps.snappy])", then SnapPy, and clicking on the "SnapPy Help" button opened the documentation in my browser correctly.

Admittedly, I'm not sure if we'll enjoy the advantages of separating the documentation into its own output with that in place. The idea is to reduce the closure size of packages that just want to use the snappy libraries, but I think the doc output always gets pulled in the way things are now.

Alright, it seems to work. Maybe the SnapPy gui should be in a separate output then? But I'm not really sure how to do that.

alejo7797 · 2025-08-19T02:02:21Z

pkgs/development/python-modules/snappy/default.nix

+  postPatch = ''
+    substituteInPlace setup.py \
+      --replace-fail "/usr/include/GL" "${libGL.dev}/include/GL" \
+      --replace-fail "'python/doc'" "'$out/${python.sitePackages}/snappy/doc'"


Suggested change

--replace-fail "'python/doc'" "'$out/${python.sitePackages}/snappy/doc'"

substituteInPlace python/app_menus.py \

--replace-fail "os.path.join(os.path.dirname(snappy_dir), 'doc')" \

"os.path.join('${placeholder "doc"}', 'share', 'doc', '$name', 'html')"

Re: sphinxHook. For the help pages to be found within SnapPy.

alejo7797 · 2025-08-19T02:04:45Z

pkgs/development/python-modules/snappy/default.nix

+    sphinx
+    sphinx-rtd-theme
+  ];


Suggested change

sphinx

sphinx-rtd-theme

];

];

nativeBuildInputs = [

sphinxHook

sphinx-rtd-theme

];

sphinxRoot = "doc_src";

Re: sphinxHook. Actually implementing it.

alejo7797 · 2025-08-19T02:05:37Z

pkgs/development/python-modules/snappy/default.nix

+
+  buildInputs = [
+    libGL
+    libX11


Suggested change

libX11

Repeat from above: SnapPy builds fine without this for me?

I have removed it, it seems it is not necessary.

alejo7797 · 2025-08-19T02:07:32Z

pkgs/development/python-modules/snappy/default.nix

+
+  env.NIX_CFLAGS_COMPILE = toString [
+    "-I${libGL.dev}/include"
+    "-I${libX11.dev}/include"
+  ];
+


Suggested change

env.NIX_CFLAGS_COMPILE = toString [

"-I${libGL.dev}/include"

"-I${libX11.dev}/include"

];

I don't think this needs to be specified manually. Correct me if I'm wrong.

It seems to build without these, I don't remember why I thought they were necessary.

alejo7797 · 2025-08-19T02:11:48Z

pkgs/development/python-modules/snappy/default.nix

+  ];
+
+  postInstall = ''
+    ${python.interpreter} setup.py build_docs


Suggested change

${python.interpreter} setup.py build_docs

Re: sphinxHook. Not needed with that in use.

alejo7797

Following up on #415184 (comment):

Yeah I'm not sure how to build SnapPy without the GUI but these changes might sort of solve the problem. The idea being that if you want to run the SnapPy GUI and have the documentation work you install pkgs.snappy-topology, and if you just want to have the pkgs.python3Packages.snappy to import into, e.g. Sage, then you don't end up with the documentation in your shell closure.

Not sure if this way of going about things is okay.
Maybe someone with more experience can say.

pkgs/development/python-modules/snappy/default.nix

+  spherogram,
+  sphinxHook,
+  sphinx-rtd-theme,
+  tkinter-gl,


noiioiu · 2025-08-19T22:05:47Z

pkgs/development/python-modules/snappy/default.nix

+    substituteInPlace python/app_menus.py \
+      --replace-fail "os.path.join(os.path.dirname(snappy_dir), 'doc')" \
+                     "os.path.join('${placeholder "doc"}', 'share', 'doc', '$name', 'html')"


This would cause python3Packages.snappy to install a broken version of the gui?

Yeah :/ The only thing that doesn't work, though, is opening the HTML documentation from the SnapPy GUI (which makes sense if withDocs = false). Since the docs are also on snappy.computop.org maybe not including the docs by default is okay? It looks like this is essentially what happens in Nixpkgs for other Python packages using sphinxHook to build their documentation.

A little broken is still broken, and installing broken software is much worse than including a few extra megabytes of html.

Yeah I'm going to have to agree with that.

So, what should I do for now? Leave it as is?

Looks good to me as it is now. Upstream expects the documentation to be somewhere on the system.

alejo7797

Hi, I took a look at the tkgl derivation definition.
Using tcl.mkTclDerivation would be more idiomatic.
I have some other small suggestions for changes.

pkgs/by-name/tk/tkgl/package.nix

alejo7797 · 2025-08-27T18:44:01Z

pkgs/by-name/tk/tkgl/package.nix

+    "--with-tclinclude=${lib.getDev tcl}/include"
+    "--with-tk=${lib.getLib tk}/lib"
+    "--with-tkinclude=${lib.getDev tk}/include"
+    "--libdir=${placeholder "out"}/lib"


Suggested change

"--libdir=${placeholder "out"}/lib"

This gets taken care of by stdenv.

alejo7797 · 2025-08-27T18:46:14Z

pkgs/by-name/tk/tkgl/package.nix

+    substituteInPlace Makefile.in \
+      --replace-fail "install: all install-binaries install-libraries install-doc" \
+                 "install: all install-binaries"


Suggested change

substituteInPlace Makefile.in \

--replace-fail "install: all install-binaries install-libraries install-doc" \

"install: all install-binaries"

I think it's cleaner to specify installTargets.

alejo7797 · 2025-08-27T18:46:57Z

pkgs/by-name/tk/tkgl/package.nix

+    "--with-tkinclude=${lib.getDev tk}/include"
+    "--libdir=${placeholder "out"}/lib"
+  ];
+


Suggested change

installTargets = [

"install-binaries"

];

alejo7797

So it turns out sphinxHook supports a postInstallSphinx step.
Using this simplifies getting SnapPy to find the documentation.

alejo7797 · 2025-09-01T18:55:11Z

pkgs/development/python-modules/snappy/default.nix

+    substituteInPlace python/app_menus.py \
+      --replace-fail "os.path.join(os.path.dirname(snappy_dir), 'doc')" \
+                     "os.path.join('${placeholder "doc"}', 'share', 'doc', '$name', 'html')"


Suggested change

substituteInPlace python/app_menus.py \

--replace-fail "os.path.join(os.path.dirname(snappy_dir), 'doc')" \

"os.path.join('${placeholder "doc"}', 'share', 'doc', '$name', 'html')"

Found a better way to handle this.

alejo7797 · 2025-09-01T18:55:49Z

pkgs/development/python-modules/snappy/default.nix

+  sphinxRoot = "doc_src";
+


Suggested change

sphinxRoot = "doc_src";

Let's move this down after postInstall.

alejo7797 · 2025-09-01T18:59:25Z

pkgs/development/python-modules/snappy/default.nix

+  postInstall = ''
+    cp -r freedesktop/share $out/
+  '';
+


Suggested change

sphinxRoot = "doc_src";

postInstallSphinx = ''

ln -s ''${!outputDoc}/share/doc/$name/html $out/${python.sitePackages}/snappy/doc

'';

Sorry for my earlier suggestion, I feel that this way of handling the documentation will give less friction.
For example, this avoids a warning during the checkPhase.

alejo7797 · 2025-09-02T04:42:36Z

Nixpkgs bumped cython to version 3.1.2 and now cypari won't build.
I'm not sure what this should mean for this PR. I see these two options:

Pin the version of cython used by cypari to 3.0.12 as is done upstream.
Patch cypari as in Fix build with Cython 3.1 3-manifolds/CyPari#3.

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noiioiu added 7 commits September 1, 2025 22:57

tkgl: init at 1.2.1-unstable-2025-06-01

e556683

python3Packages.tkinter-gl: use tkgl

0d141f7

python3Packages.cypari: add patch for aarch-64

63c2bae

python3Packages.cypari: Mark as broken on darwin

b78e53c

python3Packages.cypari: move ln to preBuild

7b17a44

python3Packages.snappy: init at 3.2

1ba16be

snappy-topology: init at 3.2

8505f88

noiioiu force-pushed the SnapPy branch from 85c5748 to 8505f88 Compare September 2, 2025 03:58

+  outputs = [
+    "out"
+    "doc"
+  ];

	substituteInPlace Makefile.in \
	--replace-fail "install: all install-binaries install-libraries install-doc" \
	"install: all install-binaries"

+  installTargets = [
+    "install-binaries"
+  ];

	substituteInPlace python/app_menus.py \
	--replace-fail "os.path.join(os.path.dirname(snappy_dir), 'doc')" \
	"os.path.join('${placeholder "doc"}', 'share', 'doc', '$name', 'html')"

+  sphinxRoot = "doc_src";
+  postInstallSphinx = ''
+    ln -s ''${!outputDoc}/share/doc/$name/html $out/${python.sitePackages}/snappy/doc
+  '';

Uh oh!

python3Packages.snappy: init at 3.2 #415184

Are you sure you want to change the base?

python3Packages.snappy: init at 3.2 #415184

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