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Overlay: Python: SpyNNaker & deps

master
David Crompton 2024-07-31 15:15:35 -04:00
parent 1cac1e66d9
commit dad965e198
2 changed files with 583 additions and 1 deletions
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2
overlays/python-packages.nix
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@ -30,4 +30,4 @@ final: final-py: prev-py: {
numpy
];
};
}
} // (import ./spynnaker.nix final final-py prev-py)

582
overlays/spynnaker.nix Normal file
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@ -0,0 +1,582 @@
final: final-py: prev-py: let
SpiNNFrontEndCommon_C_Models = final.stdenv.mkDerivation {
pname = "SpiNNFrontEndCommon";
version = "1!7.1.1";
src = final.fetchFromGitHub {
owner = "SpiNNakerManchester";
repo = "SpiNNFrontEndCommon";
rev = "c3f8c980fd51d40032524150c563feac787532ae";
hash = "sha256-lJwoFmICQdnLaalFcFGnLnGiE+puuV2fQHM1wqHiiFY=";
};
buildInputs = with final; [
final-py.spinn_common
which
gcc-arm-embedded-10
(final-py.python.withPackages (p: with p; [
SpiNNUtilities
]))
];
preConfigure = ''
mkdir SPINN_DIRS
cp -r ${final-py.spinn_common}/SPINN_DIRS/* SPINN_DIRS
chmod +rw -R SPINN_DIRS
export SPINN_DIRS=$PWD/SPINN_DIRS
export GNUTOOLS=${final.gcc-arm-embedded-10}
export GNUBIN=$GNUTOOLS/bin
export C_LOGS_DICT=$PWD/spinn_front_end_common/common_model_binaries/logs.sqlite3
pushd c_common
'';
installPhase = ''
popd
mkdir $out
cp -r * $out
'';
};
spynnaker_c = final.stdenv.mkDerivation {
pname = "spynnaker";
version = "1!7.1.1";
src = final.fetchFromGitHub {
owner = "SpiNNakerManchester";
repo = "sPyNNaker";
rev = "6f7455badeeea223dda85cd0aab9e5f5086f843b";
hash = "sha256-zXssngB+A6zoH5X2FOI10biUNXNlwh0tySje/JMoZ0w=";
};
buildInputs = with final; [
(final-py.python.withPackages (p: with p; [
SpiNNFrontEndCommon
]))
gcc-arm-embedded-10
];
preConfigure = ''
mkdir SPINN_DIRS
cp -r ${SpiNNFrontEndCommon_C_Models}/SPINN_DIRS/* SPINN_DIRS
chmod +rw -R SPINN_DIRS
export SPINN_DIRS=$PWD/SPINN_DIRS
export GNUTOOLS=${final.gcc-arm-embedded-10}
export GNUBIN=$GNUTOOLS/bin
SLLT_TAG=https://spinnakermanchester.github.io/spinnaker_tools/sllt.tag
COMMON_TAG=https://spinnakermanchester.github.io/spinn_common/common.tag
FEC_TAG=https://spinnakermanchester.github.io/SpiNNFrontEndCommon/c/fec.tag
pushd neural_modelling
export NEURAL_MODELLING_DIRS=$PWD
touch logs.sqlite3
export C_LOGS_DICT=$PWD/logs.sqlite3
'';
installPhase = ''
popd
mkdir $out
cp -r * $out
'';
};
in {
morphio = final-py.toPythonModule ( final.stdenv.mkDerivation rec {
pname = "morphio";
version = "3.3.9";
src = final.fetchFromGitHub {
owner = "BlueBrain";
repo = "MorphIO";
rev = "v${version}";
fetchSubmodules = true;
hash = "sha256-qPHuKb9dSnSgEXzeI94Zf3VpMBBssQ0y8lCVzzYB+rA=";
};
nativeBuildInputs = (with final; [
cmake
ninja
hdf5
final-py.numpy
]);
cmakeFlags = [
"-DMorphIO_CXX_WARNINGS=OFF"
];
postInstall = ''
mkdir -p $out/${final-py.python.sitePackages}
mv ../morphio $out/${final-py.python.sitePackages}
cp binds/python/_morphio.* $out/${final-py.python.sitePackages}/morphio/
'';
});
csa = final-py.buildPythonPackage rec {
pname = "csa";
version = "0.1.12";
src = final.fetchFromGitHub {
owner = "INCF";
repo = "csa";
rev = "v${version}";
hash = "sha256-QtgqpYD0PtMoiobCEe0SkKF6HiiypctOWht9EnhlhKM=";
};
propagatedBuildInputs = with final-py; [
numpy
matplotlib
];
};
nineml = final-py.buildPythonPackage rec {
pname = "nineml";
version = "25-04-2020";
src = final.fetchFromGitHub {
owner = "INCF";
repo = "nineml-python";
rev = "062a2ac8a9be97cee4dad02938e3858e051cf07c";
hash = "sha256-Tyil4lnqQlzQthp6L77+pAjDywHDQC3NIp39BRgIfzY=";
};
postPatch = ''
sed -e 's/collections.Iterable/collections.abc.Iterable/g' -i nineml/utils/iterables.py
sed -e 's/sympy.numbers/sympy.core.numbers/g' -i nineml/abstraction/componentclass/visitors/validators/general.py
'';
buildInputs = with final-py; [
pip
];
propagatedBuildInputs = with final-py; [
lxml
pyyaml
h5py
future
sympy
numpy
numpydoc
nose
];
};
lazyarray = final-py.buildPythonPackage rec {
pname = "lazyarray";
version = "0.5.2";
src = final.fetchFromGitHub {
owner = "NeuralEnsemble";
repo = "lazyarray";
rev = "9d60f2c307a70d7bd65fbfe3cb2a96391fd88bf9";
hash = "sha256-D4KzICEdCoA1S8uKRU76Q6PfcolbuZsLAtDIm4a94wo=";
};
doCheck = false; # Py2 code
propagatedBuildInputs = with final-py; [
numpy
];
};
pynn = final-py.buildPythonPackage rec {
pname = "pyNN";
version = "0.12.1";
src = final.fetchFromGitHub {
owner = "NeuralEnsemble";
repo = "PyNN";
rev = "${version}";
hash = "sha256-X7U4aSA6J45++2mTPGWi+N6QtuH0muQtSrH6CWziNJg=";
};
buildInputs = with final-py; [
pip
];
propagatedBuildInputs = with final-py; [
nineml
numpy
lazyarray
neo
quantities
morphio
brian2
nest
neuronpy
];
doCheck = false;
};
boilerplates = final-py.buildPythonPackage rec {
pname = "boilerplates";
version = "1.1.1";
src = final.fetchFromGitHub {
owner = "mbdevpl";
repo = "python-boilerplates";
rev = "v${version}";
hash = "sha256-u6Gdtgqo4s40vMZhgEonil7OWsbOSFbnBO2PgOzWXmY=";
};
# Fix circular dependency
postPatch = ''
echo "" > ./requirements.txt
echo 'VERSION = "${version}"' > ./boilerplates/_version.py
'';
disabledTests = [
"test_git_repo"
"test_logging"
];
nativeBuildInputs = with final-py; [
pytestCheckHook
];
propagatedBuildInputs = with final-py; [
colorlog
sentry-sdk
executing
pure-eval
asttokens
argcomplete
GitPython
packaging
semver
docutils
];
};
version-query = final-py.buildPythonPackage rec {
pname = "version-query";
version = "1.5.5";
src = final.fetchFromGitHub {
owner = "mbdevpl";
repo = "version-query";
rev = "v${version}";
hash = "sha256-b5G1YwT3RSWusNsT4kq8aBCzzs0UfoJrPMUH8KuaqX0=";
};
postPatch = ''
echo 'VERSION = "${version}"' > ./version_query/_version.py
'';
doCheck = false;
propagatedBuildInputs = with final-py; [
boilerplates
];
};
ebrains-drive = final-py.buildPythonPackage rec {
pname = "ebrains-drive";
version = "20-02-2024";
src = final.fetchFromGitHub {
owner = "HumanBrainProject";
repo = "ebrains-drive";
rev = "3be240da78b23488cf01dc9768423bb962673c8d";
hash = "sha256-eYbAHGu0h9K5FYos10GGUwSMdDgVcslz2wf6XFY5yjo=";
};
postPatch = ''
sed -e 's/__version__ = predict_version_str()/__version__ = "0.6.0"/g' -i setup.py
'';
# no more strings.lowercase
doCheck = false;
propagatedBuildInputs = with final-py; [
version-query
requests
tqdm
];
};
SpiNNUtilities = final-py.buildPythonPackage {
pname = "SpiNNUtilities";
version = "1!7.1.1";
src = final.fetchFromGitHub {
owner = "SpiNNakerManchester";
repo = "SpiNNUtils";
rev = "37beeec7ad5489af8e644dfdf511108f27146951";
hash = "sha256-oB3uxDTX7CFvftqDxYqJ0A4RLfK4/JH1FVoAJMcUEa4=";
};
# Tests depend on writable home
postPatch = ''
mkdir $NIX_BUILD_TOP/fake_home
export HOME=$NIX_BUILD_TOP/fake_home
export SKIP_PING_TESTS="true"
'';
nativeBuildInputs = with final-py; [
pytestCheckHook
];
disabledTests = [
"test_localhost"
];
buildInputs = with final-py; [
httpretty
testfixtures
];
propagatedBuildInputs = with final-py; [
appdirs
numpy
pyyaml
requests
typing-extensions
];
};
SpiNNMachine = final-py.buildPythonPackage {
pname = "SpiNNMachine";
version = "1!7.1.1";
src = final.fetchFromGitHub {
owner = "SpiNNakerManchester";
repo = "SpiNNMachine";
rev = "a798e7b12200d66f6fb9c6ed0af3f0fa85abd7be";
hash = "sha256-+9/ZK72SgI3seSCwCBVMPP1VL6r83SkQ4n3S1WkVCac=";
};
nativeBuildInputs = with final-py; [
pytestCheckHook
];
buildInputs = with final-py; [
testfixtures
];
propagatedBuildInputs = with final-py; [
SpiNNUtilities
];
};
SpiNNaker_PACMAN = final-py.buildPythonPackage {
pname = "SpiNNaker_PACMAN";
version = "1!7.1.1";
src = final.fetchFromGitHub {
owner = "SpiNNakerManchester";
repo = "PACMAN";
rev = "adc5ed196b8ac661365c5ec67b4107932548deab";
hash = "sha256-ITe0fqDg/4r1xwFYXHpl0kL0Ek3d2s+SbQvRtWk1eF4=";
};
nativeBuildInputs = with final-py; [
pytestCheckHook
];
buildInputs = with final-py; [
testfixtures
];
propagatedBuildInputs = with final-py; [
SpiNNMachine
jsonschema
];
};
SpiNNMan = final-py.buildPythonPackage {
pname = "SpiNNMan";
version = "1!7.1.1";
src = final.fetchFromGitHub {
owner = "SpiNNakerManchester";
repo = "SpiNNMan";
rev = "8b0e8192125c5856769ff302480e2c17b08d1b5f";
hash = "sha256-54JE5Vl1mcdBCHR4HOk4l7muZHePvufrwhgJZ11aX2A=";
};
nativeBuildInputs = with final-py; [
pytestCheckHook
];
buildInputs = with final-py; [
testfixtures
];
disabledTests = [
"test_create_job"
];
propagatedBuildInputs = with final-py; [
SpiNNMachine
SpiNNUtilities
websocket-client
];
};
spalloc = final-py.buildPythonPackage {
pname = "spalloc";
version = "1!7.1.1";
src = final.fetchFromGitHub {
owner = "SpiNNakerManchester";
repo = "spalloc";
rev = "25f5d0874269996f2c36175885e9bbe7895ed4af";
hash = "sha256-Tck2VGV5ZO1PKHEY/OLoIVvj5AWCyVqtXca514vWmTA=";
};
nativeBuildInputs = with final-py; [
pytestCheckHook
];
buildInputs = with final-py; [
mock
];
propagatedBuildInputs = with final-py; [
SpiNNUtilities
jsonschema
];
};
spinnaker_tools = final.stdenv.mkDerivation {
pname = "spinnaker_tools";
version = "1!7.1.1";
src = final.fetchFromGitHub {
owner = "SpiNNakerManchester";
repo = "spinnaker_tools";
rev = "26dd8651d7af8371ca1d5927524d1af2527dd041";
hash = "sha256-Ppow52pfzVi9Jh7cVSow6OmNMLmudMq4lRZOeCJyMU8=";
};
propagatedBuildInputs = with final; [
perl
gcc-arm-embedded-10
];
postPatch = ''
patchShebangs ./tools
'';
preConfigure = ''
export SPINN_DIRS=$PWD
export GNUTOOLS=${final.gcc-arm-embedded-10}
export GNUBIN=$GNUTOOLS/bin
chmod +x ./tools/*
'';
installPhase = ''
mkdir $out
cp -r * $out
'';
};
spinn_common = final.stdenv.mkDerivation {
pname = "spinn_common";
version = "1!7.1.1";
src = final.fetchFromGitHub {
owner = "SpiNNakerManchester";
repo = "spinn_common";
rev = "fa5f769a7e8bab42b6932557c0deaebc1d7f2016";
hash = "sha256-aQpIkPWhKT+Uw4svKfibR7SEeKwNPqv86skSLNv2Z3Q=";
};
nativeBuildInputs = [
final-py.spinnaker_tools
];
preConfigure = ''
mkdir SPINN_DIRS
cp -r ${final-py.spinnaker_tools}/* SPINN_DIRS
chmod +rw -R SPINN_DIRS
export SPINN_DIRS=$PWD/SPINN_DIRS
export GNUTOOLS=${final.gcc-arm-embedded-10}
export GNUBIN=$GNUTOOLS/bin
'';
postInstall = ''
cp -r SPINN_DIRS $out
'';
};
SpiNNFrontEndCommon = final-py.buildPythonPackage {
pname = "SpiNNFrontEndCommon";
version = "1!7.1.1";
src = SpiNNFrontEndCommon_C_Models;
nativeBuildInputs = with final-py; [
pytestCheckHook
];
buildInputs = with final-py; [
httpretty
testfixtures
];
disabledTestPaths = [
"fec_local_tests/test_java_caller.py"
"unittests/interface/test_java_caller.py"
];
propagatedBuildInputs = with final-py; [
ebrains-drive
scipy
SpiNNMan
SpiNNaker_PACMAN
spalloc
SpiNNFrontEndCommon_C_Models
];
};
spinnaker_testbase = final-py.buildPythonPackage {
pname = "spinnaker_testbase";
version = "1!7.1.1";
src = final.fetchFromGitHub {
owner = "SpiNNakerManchester";
repo = "TestBase";
rev = "324aa4c9f8348aa21c88611bb7ccf7585c783415";
hash = "sha256-YBDaFr7oDx53LBQN+V8CXpNTIGSLBDRyq4pNMBxankI=";
};
nativeBuildInputs = with final-py; [
pytestCheckHook
];
buildInputs = with final-py; [
testfixtures
];
propagatedBuildInputs = with final-py; [
SpiNNFrontEndCommon
matplotlib
];
};
spynnaker = final-py.buildPythonPackage {
pname = "spynnaker";
version = "1!7.1.1";
src = spynnaker_c;
nativeBuildInputs = with final-py; [
pytestCheckHook
];
buildInputs = with final-py; [
testfixtures
spinnaker_testbase
];
propagatedBuildInputs = with final-py; [
SpiNNFrontEndCommon
matplotlib
quantities
neo
lazyarray
scipy
csa
pynn
];
# All these tests depend on connecting to the SpiNNaker or Network
disabledTestPaths = [
"proxy_integration_tests/"
"spynnaker_integration_tests/"
"test_whole_board/"
"unittests/test_from_file_connector.py"
"unittests/model_tests/"
"unittests/test_using_virtual_board/"
"unittests/test_integration_using_virtual_board/"
"unittests/test_pop_views_assembly/test_getting.py"
"unittests/test_pop_views_assembly/test_idmixin.py"
"unittests/test_pop_views_assembly/test_models.py"
"unittests/test_pop_views_assembly/test_population.py"
"unittests/test_pop_views_assembly/test_record.py"
"unittests/test_pop_views_assembly/test_views.py"
"unittests/test_populations/test_population.py"
"unittests/test_sata_connectors/"
"unittests/test_spinnaker_link_connectors/"
"unittests/test_populations/test_vertex.py"
"unittests/utilities_tests/test_utility_calls.py"
];
};
}