Add Nix flake for deterministic Nix builds (attempt 2) by ThatOtherAndrew · Pull Request #909 · digraphs/Digraphs

ThatOtherAndrew · 2026-03-20T07:49:45Z

Nix is a functional programming language used for deterministic builds, by pinning environment "inputs" (e.g. gcc) to a specific version. This allows for a universal and deterministic nix build command which replaces the need for autogen, configure, and make.

This is a recreation of a previous PR (#906) which was messed up due to accidentally committing multiple features to the main branch. I have learned from my mistake and one sleepless night later my changes are properly branched now. oops!

Copilot

Pull request overview

Adds Nix flake support to enable deterministic nix build / nix develop workflows for building the GAP Digraphs package from this repository.

Changes:

Introduce flake.nix defining a digraphs derivation and a development shell.
Pin Nixpkgs via flake.lock for reproducible builds.
Ignore the default Nix build symlink (result) in .gitignore.

Reviewed changes

Copilot reviewed 1 out of 3 changed files in this pull request and generated 5 comments.

File	Description
flake.nix	Defines Nix flake outputs (package + devShell) and the build/install steps for Digraphs.
flake.lock	Pins `nixpkgs` revision/hash to make builds deterministic.
.gitignore	Ignores the `result` symlink created by `nix build`.

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Copilot · 2026-03-20T07:53:29Z

flake.nix

+            configurePhase = ''
+              runHook preConfigure
+
+              # Generate the configure script
+              mkdir -p gen
+              aclocal -Wall --force
+              autoconf -Wall -f
+              autoheader -Wall -f
+
+              # Run configure, pointing at the GAP root
+              ./configure --with-gaproot=${gaproot}
+
+              runHook postConfigure
+            '';


The custom configurePhase calls ./configure without passing the standard Nix configure flags (e.g., --prefix=$out, build/host flags, and any configureFlags), which can lead to incorrect paths and reduced portability (especially for cross builds). Prefer using the default configurePhase with configureFlags = [ "--with-gaproot=..." ]; or, if keeping a custom phase, invoke ./configure with the standard flags included.

Copilot · 2026-03-20T07:53:29Z

flake.nix

+            nativeBuildInputs = with pkgs; [
+              autoconf
+              automake
+              gcc


nativeBuildInputs includes gcc, but this flake advertises Darwin support as well; forcing gcc can cause toolchain mismatches or failures on macOS where the default stdenv compiler is clang. Consider relying on stdenv.cc (already provided by mkDerivation) and drop gcc, or select an appropriate stdenv/toolchain per-system.

Suggested change

gcc

Copilot · 2026-03-20T07:53:30Z

flake.nix

+
+            buildPhase = ''
+              runHook preBuild
+              make


The overridden buildPhase runs plain make, which bypasses the standard stdenv make flags (including parallelism and any makeFlags). To keep builds consistent and faster under Nix, either use the default buildPhase or call make with the stdenv-provided flags.

Suggested change

make

make $makeFlags

Copilot · 2026-03-20T07:53:30Z

flake.nix

+            configurePhase = ''
+              runHook preConfigure
+
+              # Generate the configure script
+              mkdir -p gen
+              aclocal -Wall --force
+              autoconf -Wall -f
+              autoheader -Wall -f
+
+              # Run configure, pointing at the GAP root
+              ./configure --with-gaproot=${gaproot}
+
+              runHook postConfigure
+            '';
+


This flake reimplements the repo's existing ./autogen.sh logic inline. Using the script directly (or autoreconfHook) would reduce drift if the autogen steps change in the future and keeps the build definition simpler.

Suggested change

configurePhase = ''

runHook preConfigure

# Generate the configure script

mkdir -p gen

aclocal -Wall --force

autoconf -Wall -f

autoheader -Wall -f

# Run configure, pointing at the GAP root

./configure --with-gaproot=${gaproot}

runHook postConfigure

'';

preConfigure = ''

./autogen.sh

'';

configureFlags = [

"--with-gaproot=${gaproot}"

];

Copilot · 2026-03-20T07:53:30Z

flake.nix

+              # Copy GAP source files
+              cp -r gap "$out/digraphs/"
+              cp -r lib "$out/digraphs/" 2>/dev/null || true
+              cp -r doc "$out/digraphs/" 2>/dev/null || true
+              cp -r data "$out/digraphs/" 2>/dev/null || true
+              cp -r tst "$out/digraphs/" 2>/dev/null || true
+
+              # Copy the compiled shared object
+              cp -r bin "$out/digraphs/"
+
+              # Copy package metadata files
+              cp PackageInfo.g "$out/digraphs/"
+              cp init.g "$out/digraphs/"
+              cp read.g "$out/digraphs/"
+              cp -r makedoc.g "$out/digraphs/" 2>/dev/null || true
+              cp LICENSE "$out/digraphs/" 2>/dev/null || true
+              cp CHANGELOG.md "$out/digraphs/" 2>/dev/null || true
+              cp README.md "$out/digraphs/" 2>/dev/null || true
+


The installPhase uses cp ... 2>/dev/null || true to ignore missing paths, which can silently produce incomplete outputs if a directory unexpectedly disappears or is renamed. Prefer explicit if [ -d ... ]; then ...; fi (or a single copy of an explicit file list) so packaging failures are surfaced when the layout changes.

Suggested change

# Copy GAP source files

cp -r gap "$out/digraphs/"

cp -r lib "$out/digraphs/" 2>/dev/null || true

cp -r doc "$out/digraphs/" 2>/dev/null || true

cp -r data "$out/digraphs/" 2>/dev/null || true

cp -r tst "$out/digraphs/" 2>/dev/null || true

# Copy the compiled shared object

cp -r bin "$out/digraphs/"

# Copy package metadata files

cp PackageInfo.g "$out/digraphs/"

cp init.g "$out/digraphs/"

cp read.g "$out/digraphs/"

cp -r makedoc.g "$out/digraphs/" 2>/dev/null || true

cp LICENSE "$out/digraphs/" 2>/dev/null || true

cp CHANGELOG.md "$out/digraphs/" 2>/dev/null || true

cp README.md "$out/digraphs/" 2>/dev/null || true

# Copy GAP source files (required)

cp -r gap "$out/digraphs/"

# Copy optional GAP directories if they exist

if [ -d lib ]; then

cp -r lib "$out/digraphs/"

fi

if [ -d doc ]; then

cp -r doc "$out/digraphs/"

fi

if [ -d data ]; then

cp -r data "$out/digraphs/"

fi

if [ -d tst ]; then

cp -r tst "$out/digraphs/"

fi

# Copy the compiled shared object (required)

cp -r bin "$out/digraphs/"

# Copy required package metadata files

cp PackageInfo.g "$out/digraphs/"

cp init.g "$out/digraphs/"

cp read.g "$out/digraphs/"

# Copy optional metadata / documentation files if they exist

if [ -f makedoc.g ]; then

cp makedoc.g "$out/digraphs/"

fi

if [ -f LICENSE ]; then

cp LICENSE "$out/digraphs/"

fi

if [ -f CHANGELOG.md ]; then

cp CHANGELOG.md "$out/digraphs/"

fi

if [ -f README.md ]; then

cp README.md "$out/digraphs/"

fi

codecov · 2026-03-20T14:30:52Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 97.35%. Comparing base (1f56fb0) to head (8c8a9fd).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #909   +/-   ##
=======================================
  Coverage   97.35%   97.35%           
=======================================
  Files          50       50           
  Lines       21045    21045           
  Branches      639      639           
=======================================
  Hits        20489    20489           
  Misses        491      491           
  Partials       65       65

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reiniscirpons

Hi Andromeda, thanks for the PR! I'm not a nix user myself, but think its a good effort to try and package Digraphs for simpler installation.

Some comments:

It seems the flake only lists gap itself as a dependency, but Digraphs depends on other gap packages such as datastructures and io (see the Dependencies record in PackageInfo.g (https://github.com/digraphs/Digraphs/blob/main/PackageInfo.g#L560) for more info). The gap dependency may or may not package them, and may or may not package the right versions of these packages, so its probably a good idea to explicitly set them as dependencies.

This of course introduces some headache, since as far as I know neither the datastructures nor io are available as nix packages. Of course, in theory we could make flakes available for these packages too, but now these would also need to be maintained etc, which can quickly get out of hand. I think this should be a community rather than single author effort to make it maintainable, but at the moment nix is not used much in the community as far as I can tell.

Gap has its own package manager: the PackageManager package (documentation: https://gap-packages.github.io/PackageManager/doc/chap0_mj.html , github: https://github.com/gap-packages/PackageManager) by @mtorpey . It solves quite a lot of headaches related to building and installing gap packages and their dependencies, and if I understand correctly it should be able to build Digraphs too (including a development version). So maybe it would be possible to simplify the script by having a separate flake for PackageManager, and then all this flake would do is call the PackageManager InstallPackage command from gap?
Before merging this PR we would probably want to add some CI job for testing the nix builds. Otherwise it is a very high probability that this file will just go out-of-sync or break as we update the package. At the same time, I'm not sure if any of the current maintainers of digraphs would be able to fix any nix-related issues, since we are not nix users ourselves.

Overall I think its a good effort and probably quite useful for other nix users wanting to install digraphs, but I'm not sure we will merge this PR in the near future mainly due to a lack of nix support in the gap ecosystem and lack of nix know-how among the digraphs maintainers. So don't feel like you need to spend much more time fixing any of the issues above.

If you are interested in gap packaging in general, it might be a good idea to talk to Michael at one of the meetings about the PackageManager package. Thanks again!

reiniscirpons · 2026-03-25T22:30:28Z

flake.nix

+              mkdir -p gen
+              aclocal -Wall --force
+              autoconf -Wall -f
+              autoheader -Wall -f


Suggested change

mkdir -p gen

aclocal -Wall --force

autoconf -Wall -f

autoheader -Wall -f

./autogen.sh

I think the preferred method for generating the configure script is via the autogen.sh script. But I'm not sure if there is some technical nix reason to prefer the more explicit instructions.

ThatOtherAndrew added 2 commits March 20, 2026 03:46

Create Nix flake

1547c22

Add Nix build output to .gitignore

8c8a9fd

Copilot AI review requested due to automatic review settings March 20, 2026 07:49

Copilot started reviewing on behalf of ThatOtherAndrew March 20, 2026 07:50 View session

Copilot AI reviewed Mar 20, 2026

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reiniscirpons reviewed Mar 25, 2026

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Add Nix flake for deterministic Nix builds (attempt 2)#909

Add Nix flake for deterministic Nix builds (attempt 2)#909
ThatOtherAndrew wants to merge 2 commits intodigraphs:mainfrom
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