cmdstan: bump to 2.25.0 #108843
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cmdstan: bump to 2.25.0 #108843
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prusnak
requested changes
Jan 9, 2021
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| let | ||
| name = "cmdstan"; | ||
| version = "2.25.0"; | ||
| in stdenv.mkDerivation { | ||
| name = "${name}-${version}"; |
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Suggested change
| let | |
| name = "cmdstan"; | |
| version = "2.25.0"; | |
| in stdenv.mkDerivation { | |
| name = "${name}-${version}"; | |
| stdenv.mkDerivation rec { | |
| pname = "cmdstan"; | |
| version = "2.25.0"; |
|
|
||
| src = fetchurl { | ||
| url = "https://github.com/stan-dev/cmdstan/releases/download/v2.17.1/cmdstan-2.17.1.tar.gz"; | ||
| sha256 = "1vq1cnrkvrvbfl40j6ajc60jdrjcxag1fi6kff5pqmadfdz9564j"; | ||
| url = |
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src = fetchFromGitHub {
owner = "stan-dev";
repo = pname;
rev = "v${version}";
sha256 = "TODO";
};
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This package, cmdstan, uses the stanc3 binary. stanc3 upstream uses nix, but the default.nix pins nixpkgs 19.09.
I haven't figured out a working stanc3 derivation on nixpkgs-unstable that doesn't use import-from-derivation (see below).
Using the release tarball with fetchTarball includes the binaries from stanc3 so it works fine. Using fetchFromGitHub excludes the bin/ directory so it doesn't work.
{ stdenv, fetchFromGitHub, python, runtimeShell, bash, gnumake, gcc }:
let
stanc3 = import (fetchTarball {
url = "https://github.com/stan-dev/stanc3/archive/v2.25.0.tar.gz";
sha256 = "sha256:01iak3ac2hzdrjbyfcsbqiizjd2b4jmb422fxxia0vcw799jwhay";
});
in stdenv.mkDerivation rec {
pname = "cmdstan";
version = "2.25.0";
src = fetchFromGitHub {
owner = "stan-dev";
repo = "cmdstan";
rev = "v${version}";
sha256 = "sha256:1s49rhak2phkzqfjx1xmj74frqi79p99n3kcmndm3fbq6b695ag1";
fetchSubmodules = true;
};
buildFlags = [ "build" ];
enableParallelBuilding = true;
postPatch = ''
substituteInPlace stan/lib/stan_math/make/libraries \
--replace "/usr/bin/env bash" ${bash}/bin/bash
substituteInPlace stan/lib/stan_math/lib/boost_1.72.0/bootstrap.sh \
--replace '`which echo`' echo
patchShebangs .
mkdir bin
cp -r ${stanc3}/bin/* bin
'';
# Hack to avoid TMPDIR in RPATHs.
# Copied from https://github.com/NixOS/nixpkgs/commit/f5c568446a12dbf58836925c5487e5cdad1fa578
preFixup = ''
rm -rf "$(pwd)"
mkdir "$(pwd)"
'';
doCheck = false;
checkInputs = [ python ];
checkPhase = "python ./runCmdStanTests.py src/test/interface"; # see #5368
installPhase = ''
mkdir -p $out/opt $out/bin
cp -r . $out/opt/cmdstan
ln -s $out/opt/cmdstan/bin/stanc $out/bin/stanc
ln -s $out/opt/cmdstan/bin/stansummary $out/bin/stansummary
cat > $out/bin/stan <<EOF
#!${runtimeShell}
export PATH="$PATH":${gcc}/bin
${gnumake}/bin/make -C $out/opt/cmdstan "\$(realpath "\$1")"
EOF
chmod a+x $out/bin/stan
'';
meta = {
description = "Command-line interface to Stan";
longDescription = ''
Stan is a probabilistic programming language implementing full Bayesian
statistical inference with MCMC sampling (NUTS, HMC), approximate Bayesian
inference with Variational inference (ADVI) and penalized maximum
likelihood estimation with Optimization (L-BFGS).
'';
homepage = "https://mc-stan.org/interfaces/cmdstan.html";
license = stdenv.lib.licenses.bsd3;
platforms = stdenv.lib.platforms.all;
};
}
| }; | ||
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| buildFlags = [ "build" ]; | ||
| enableParallelBuilding = true; | ||
|
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| # Hack to avoid TMPDIR in RPATHs. | ||
| # Copied from https://github.com/NixOS/nixpkgs/commit/f5c568446a12dbf58836925c5487e5cdad1fa578 | ||
| preFixup = ''rm -rf "$(pwd)" && mkdir "$(pwd)" ''; |
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Suggested change
| preFixup = ''rm -rf "$(pwd)" && mkdir "$(pwd)" ''; | |
| preFixup = '' | |
| rm -rf "$(pwd)" | |
| mkdir "$(pwd)" | |
| ''; |
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| patchPhase = '' | ||
| substituteInPlace stan/lib/stan_math/make/libraries --replace "/usr/bin/env bash" ${bash}/bin/bash | ||
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||
| patchShebangs . | ||
| ''; |
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Suggested change
| patchPhase = '' | |
| substituteInPlace stan/lib/stan_math/make/libraries --replace "/usr/bin/env bash" ${bash}/bin/bash | |
| patchShebangs . | |
| ''; | |
| postPhase = '' | |
| substituteInPlace stan/lib/stan_math/make/libraries --replace "/usr/bin/env bash" ${bash}/bin/bash | |
| patchShebangs . | |
| ''; |
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I can't find any documentation on postPhase. Is that a typo?
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Yeah it is. I meant postPatch.
|
As I mentioned in #108843 (comment), I don't know how to do this without IFD. So I'm closing this for now. |
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Motivation for this change
Things done
sandboxinnix.confon non-NixOS linux)nix-shell -p nixpkgs-review --run "nixpkgs-review wip"./result/bin/)nix path-info -Sbefore and after)