Merge pull request #240183 from alxsimon/master
This commit is contained in:
commit
9bd0bea1f4
|
@ -813,6 +813,12 @@
|
||||||
fingerprint = "B422 CFB1 C9EF 73F7 E1E2 698D F53E 3233 42F7 A6D3A";
|
fingerprint = "B422 CFB1 C9EF 73F7 E1E2 698D F53E 3233 42F7 A6D3A";
|
||||||
}];
|
}];
|
||||||
};
|
};
|
||||||
|
alxsimon = {
|
||||||
|
email = "alexis.simon@normalesup.org";
|
||||||
|
github = "alxsimon";
|
||||||
|
githubId = 9567176;
|
||||||
|
name = "Alexis Simon";
|
||||||
|
};
|
||||||
alyaeanyx = {
|
alyaeanyx = {
|
||||||
email = "alyaeanyx@mailbox.org";
|
email = "alyaeanyx@mailbox.org";
|
||||||
github = "alyaeanyx";
|
github = "alyaeanyx";
|
||||||
|
|
58
pkgs/development/python-modules/demes/default.nix
Normal file
58
pkgs/development/python-modules/demes/default.nix
Normal file
|
@ -0,0 +1,58 @@
|
||||||
|
{ lib
|
||||||
|
, buildPythonPackage
|
||||||
|
, fetchPypi
|
||||||
|
, setuptools-scm
|
||||||
|
, ruamel-yaml
|
||||||
|
, attrs
|
||||||
|
, pythonOlder
|
||||||
|
, pytestCheckHook
|
||||||
|
, pytest-xdist
|
||||||
|
, numpy
|
||||||
|
}:
|
||||||
|
|
||||||
|
buildPythonPackage rec {
|
||||||
|
pname = "demes";
|
||||||
|
version = "0.2.3";
|
||||||
|
format = "pyproject";
|
||||||
|
disabled = pythonOlder "3.7";
|
||||||
|
|
||||||
|
src = fetchPypi {
|
||||||
|
inherit pname version;
|
||||||
|
hash = "sha256-nmE7ZbR126J3vKdR3h83qJ/V602Fa6J3M6IJnIqCNhc=";
|
||||||
|
};
|
||||||
|
|
||||||
|
nativeBuildInputs = [
|
||||||
|
setuptools-scm
|
||||||
|
];
|
||||||
|
|
||||||
|
propagatedBuildInputs = [
|
||||||
|
ruamel-yaml
|
||||||
|
attrs
|
||||||
|
];
|
||||||
|
|
||||||
|
postPatch = ''
|
||||||
|
# remove coverage arguments to pytest
|
||||||
|
sed -i '/--cov/d' setup.cfg
|
||||||
|
'';
|
||||||
|
|
||||||
|
nativeCheckInputs = [
|
||||||
|
pytestCheckHook
|
||||||
|
pytest-xdist
|
||||||
|
numpy
|
||||||
|
];
|
||||||
|
|
||||||
|
disabledTestPaths = [
|
||||||
|
"tests/test_spec.py"
|
||||||
|
];
|
||||||
|
|
||||||
|
pythonImportsCheck = [
|
||||||
|
"demes"
|
||||||
|
];
|
||||||
|
|
||||||
|
meta = with lib; {
|
||||||
|
description = "Tools for describing and manipulating demographic models";
|
||||||
|
homepage = "https://github.com/popsim-consortium/demes-python";
|
||||||
|
license = licenses.isc;
|
||||||
|
maintainers = with maintainers; [ alxsimon ];
|
||||||
|
};
|
||||||
|
}
|
63
pkgs/development/python-modules/demesdraw/default.nix
Normal file
63
pkgs/development/python-modules/demesdraw/default.nix
Normal file
|
@ -0,0 +1,63 @@
|
||||||
|
{ lib
|
||||||
|
, stdenv
|
||||||
|
, buildPythonPackage
|
||||||
|
, fetchPypi
|
||||||
|
, setuptools-scm
|
||||||
|
, demes
|
||||||
|
, matplotlib
|
||||||
|
, numpy
|
||||||
|
, scipy
|
||||||
|
, pythonOlder
|
||||||
|
, pytestCheckHook
|
||||||
|
, pytest-xdist
|
||||||
|
, mpmath
|
||||||
|
}:
|
||||||
|
|
||||||
|
buildPythonPackage rec {
|
||||||
|
pname = "demesdraw";
|
||||||
|
version = "0.4.0";
|
||||||
|
format = "pyproject";
|
||||||
|
disabled = pythonOlder "3.7";
|
||||||
|
|
||||||
|
src = fetchPypi {
|
||||||
|
inherit pname version;
|
||||||
|
hash = "sha256-n7dz+kYf2yyr66TBx452W6z4qT6bT81u0J4aMAYuGCc=";
|
||||||
|
};
|
||||||
|
|
||||||
|
nativeBuildInputs = [
|
||||||
|
setuptools-scm
|
||||||
|
];
|
||||||
|
|
||||||
|
propagatedBuildInputs = [
|
||||||
|
demes
|
||||||
|
matplotlib
|
||||||
|
numpy
|
||||||
|
scipy
|
||||||
|
];
|
||||||
|
|
||||||
|
postPatch = ''
|
||||||
|
# remove coverage arguments to pytest
|
||||||
|
sed -i '/--cov/d' setup.cfg
|
||||||
|
'';
|
||||||
|
|
||||||
|
# This variable is needed to suppress the "Trace/BPT trap: 5" error in Darwin's checkPhase.
|
||||||
|
# Not sure of the details, but we can avoid it by changing the matplotlib backend during testing.
|
||||||
|
env.MPLBACKEND = lib.optionalString stdenv.isDarwin "Agg";
|
||||||
|
|
||||||
|
nativeCheckInputs = [
|
||||||
|
pytestCheckHook
|
||||||
|
pytest-xdist
|
||||||
|
mpmath
|
||||||
|
];
|
||||||
|
|
||||||
|
pythonImportsCheck = [
|
||||||
|
"demesdraw"
|
||||||
|
];
|
||||||
|
|
||||||
|
meta = with lib; {
|
||||||
|
description = "Drawing functions for Demes demographic models";
|
||||||
|
homepage = "https://github.com/grahamgower/demesdraw";
|
||||||
|
license = licenses.isc;
|
||||||
|
maintainers = with maintainers; [ alxsimon ];
|
||||||
|
};
|
||||||
|
}
|
81
pkgs/development/python-modules/msprime/default.nix
Normal file
81
pkgs/development/python-modules/msprime/default.nix
Normal file
|
@ -0,0 +1,81 @@
|
||||||
|
{ lib
|
||||||
|
, buildPythonPackage
|
||||||
|
, fetchPypi
|
||||||
|
, setuptools-scm
|
||||||
|
, pythonOlder
|
||||||
|
, gsl
|
||||||
|
, numpy
|
||||||
|
, newick
|
||||||
|
, tskit
|
||||||
|
, demes
|
||||||
|
, pytest
|
||||||
|
, pytest-xdist
|
||||||
|
, scipy
|
||||||
|
}:
|
||||||
|
|
||||||
|
buildPythonPackage rec {
|
||||||
|
pname = "msprime";
|
||||||
|
version = "1.2.0";
|
||||||
|
format = "pyproject";
|
||||||
|
disabled = pythonOlder "3.8";
|
||||||
|
|
||||||
|
src = fetchPypi {
|
||||||
|
inherit pname version;
|
||||||
|
hash = "sha256-YAJa2f0w2CenKubnYLbP8HodDhabLB2hAkyw/CPkp6o=";
|
||||||
|
};
|
||||||
|
|
||||||
|
nativeBuildInputs = [
|
||||||
|
setuptools-scm
|
||||||
|
gsl
|
||||||
|
];
|
||||||
|
|
||||||
|
buildInputs = [
|
||||||
|
gsl
|
||||||
|
];
|
||||||
|
|
||||||
|
propagatedBuildInputs = [
|
||||||
|
numpy
|
||||||
|
newick
|
||||||
|
tskit
|
||||||
|
demes
|
||||||
|
];
|
||||||
|
|
||||||
|
nativeCheckInputs = [
|
||||||
|
pytest
|
||||||
|
pytest-xdist
|
||||||
|
scipy
|
||||||
|
];
|
||||||
|
|
||||||
|
checkPhase = ''
|
||||||
|
runHook preCheck
|
||||||
|
|
||||||
|
# avoid adding the current directory to sys.path
|
||||||
|
# https://docs.pytest.org/en/7.1.x/explanation/pythonpath.html#invoking-pytest-versus-python-m-pytest
|
||||||
|
# need pythonPackages.stdpopsim
|
||||||
|
# need pythonPackages.bintrees
|
||||||
|
# need pythonPachages.python_jsonschema_objects
|
||||||
|
# ModuleNotFoundError: No module named 'lwt_interface.dict_encoding_testlib'
|
||||||
|
# fails for python311
|
||||||
|
# fails for python311
|
||||||
|
pytest -v --import-mode append \
|
||||||
|
--ignore=tests/test_demography.py \
|
||||||
|
--ignore=tests/test_algorithms.py \
|
||||||
|
--ignore=tests/test_provenance.py \
|
||||||
|
--ignore=tests/test_dict_encoding.py \
|
||||||
|
--deselect=tests/test_ancestry.py::TestSimulator::test_debug_logging \
|
||||||
|
--deselect=tests/test_ancestry.py::TestSimulator::test_debug_logging_dtwf
|
||||||
|
|
||||||
|
runHook postCheck
|
||||||
|
'';
|
||||||
|
|
||||||
|
pythonImportsCheck = [
|
||||||
|
"msprime"
|
||||||
|
];
|
||||||
|
|
||||||
|
meta = with lib; {
|
||||||
|
description = "Simulate genealogical trees and genomic sequence data using population genetic models";
|
||||||
|
homepage = "https://github.com/tskit-dev/msprime";
|
||||||
|
license = licenses.gpl3Plus;
|
||||||
|
maintainers = with maintainers; [ alxsimon ];
|
||||||
|
};
|
||||||
|
}
|
45
pkgs/development/python-modules/newick/default.nix
Normal file
45
pkgs/development/python-modules/newick/default.nix
Normal file
|
@ -0,0 +1,45 @@
|
||||||
|
{ lib
|
||||||
|
, buildPythonPackage
|
||||||
|
, fetchFromGitHub
|
||||||
|
, setuptools-scm
|
||||||
|
, pythonOlder
|
||||||
|
, pytestCheckHook
|
||||||
|
}:
|
||||||
|
|
||||||
|
buildPythonPackage rec {
|
||||||
|
pname = "newick";
|
||||||
|
version = "1.9.0";
|
||||||
|
format = "pyproject";
|
||||||
|
disabled = pythonOlder "3.7";
|
||||||
|
|
||||||
|
src = fetchFromGitHub {
|
||||||
|
owner = "dlce-eva";
|
||||||
|
repo = "python-newick";
|
||||||
|
rev = "v${version}";
|
||||||
|
hash = "sha256-TxyR6RYvy2oIcDNZnHrExtPYGspyWOtZqNy488OmWwk=";
|
||||||
|
};
|
||||||
|
|
||||||
|
nativeBuildInputs = [
|
||||||
|
setuptools-scm
|
||||||
|
];
|
||||||
|
|
||||||
|
postPatch = ''
|
||||||
|
# remove coverage arguments to pytest
|
||||||
|
sed -i '/--cov/d' setup.cfg
|
||||||
|
'';
|
||||||
|
|
||||||
|
nativeCheckInputs = [
|
||||||
|
pytestCheckHook
|
||||||
|
];
|
||||||
|
|
||||||
|
pythonImportsCheck = [
|
||||||
|
"newick"
|
||||||
|
];
|
||||||
|
|
||||||
|
meta = with lib; {
|
||||||
|
description = "A python package to read and write the Newick format";
|
||||||
|
homepage = "https://github.com/dlce-eva/python-newick";
|
||||||
|
license = licenses.asl20;
|
||||||
|
maintainers = with maintainers; [ alxsimon ];
|
||||||
|
};
|
||||||
|
}
|
45
pkgs/development/python-modules/pyslim/default.nix
Normal file
45
pkgs/development/python-modules/pyslim/default.nix
Normal file
|
@ -0,0 +1,45 @@
|
||||||
|
{ lib
|
||||||
|
, buildPythonPackage
|
||||||
|
, fetchPypi
|
||||||
|
, setuptools-scm
|
||||||
|
, pythonOlder
|
||||||
|
, msprime
|
||||||
|
, numpy
|
||||||
|
, tskit
|
||||||
|
}:
|
||||||
|
|
||||||
|
buildPythonPackage rec {
|
||||||
|
pname = "pyslim";
|
||||||
|
version = "1.0.3";
|
||||||
|
format = "pyproject";
|
||||||
|
disabled = pythonOlder "3.7";
|
||||||
|
|
||||||
|
src = fetchPypi {
|
||||||
|
inherit pname version;
|
||||||
|
hash = "sha256-BRfv5AcdRpnvk7zGeYYWweh+foFEOSZjz3pTjX8KOnA=";
|
||||||
|
};
|
||||||
|
|
||||||
|
nativeBuildInputs = [
|
||||||
|
setuptools-scm
|
||||||
|
];
|
||||||
|
|
||||||
|
propagatedBuildInputs = [
|
||||||
|
msprime
|
||||||
|
tskit
|
||||||
|
numpy
|
||||||
|
];
|
||||||
|
|
||||||
|
# Requires non-packaged software SLiM
|
||||||
|
doCheck = false;
|
||||||
|
|
||||||
|
pythonImportsCheck = [
|
||||||
|
"pyslim"
|
||||||
|
];
|
||||||
|
|
||||||
|
meta = with lib; {
|
||||||
|
description = "Tools for dealing with tree sequences coming to and from SLiM";
|
||||||
|
homepage = "https://github.com/tskit-dev/pyslim";
|
||||||
|
license = licenses.mit;
|
||||||
|
maintainers = with maintainers; [ alxsimon ];
|
||||||
|
};
|
||||||
|
}
|
46
pkgs/development/python-modules/tskit/default.nix
Normal file
46
pkgs/development/python-modules/tskit/default.nix
Normal file
|
@ -0,0 +1,46 @@
|
||||||
|
{ lib
|
||||||
|
, buildPythonPackage
|
||||||
|
, fetchPypi
|
||||||
|
, setuptools-scm
|
||||||
|
, pythonOlder
|
||||||
|
, numpy
|
||||||
|
, jsonschema
|
||||||
|
, svgwrite
|
||||||
|
}:
|
||||||
|
|
||||||
|
buildPythonPackage rec {
|
||||||
|
pname = "tskit";
|
||||||
|
version = "0.5.5";
|
||||||
|
format = "pyproject";
|
||||||
|
disabled = pythonOlder "3.7";
|
||||||
|
|
||||||
|
src = fetchPypi {
|
||||||
|
inherit pname version;
|
||||||
|
hash = "sha256-phhBTAHAPlBnmzSiLmPYDMg1Mui85NZacni3WuYAc6c=";
|
||||||
|
};
|
||||||
|
|
||||||
|
nativeBuildInputs = [
|
||||||
|
setuptools-scm
|
||||||
|
];
|
||||||
|
|
||||||
|
propagatedBuildInputs = [
|
||||||
|
numpy
|
||||||
|
jsonschema
|
||||||
|
svgwrite
|
||||||
|
];
|
||||||
|
|
||||||
|
# Pypi does not include test folder and too complex to compile from GitHub source
|
||||||
|
# will ask upstream to include tests in pypi
|
||||||
|
doCheck = false;
|
||||||
|
|
||||||
|
pythonImportsCheck = [
|
||||||
|
"tskit"
|
||||||
|
];
|
||||||
|
|
||||||
|
meta = with lib; {
|
||||||
|
description = "The tree sequence toolkit";
|
||||||
|
homepage = "https://github.com/tskit-dev/tskit";
|
||||||
|
license = licenses.mit;
|
||||||
|
maintainers = with maintainers; [ alxsimon ];
|
||||||
|
};
|
||||||
|
}
|
|
@ -2517,6 +2517,10 @@ self: super: with self; {
|
||||||
|
|
||||||
deluge-client = callPackage ../development/python-modules/deluge-client { };
|
deluge-client = callPackage ../development/python-modules/deluge-client { };
|
||||||
|
|
||||||
|
demes = callPackage ../development/python-modules/demes { };
|
||||||
|
|
||||||
|
demesdraw = callPackage ../development/python-modules/demesdraw { };
|
||||||
|
|
||||||
demetriek = callPackage ../development/python-modules/demetriek { };
|
demetriek = callPackage ../development/python-modules/demetriek { };
|
||||||
|
|
||||||
demjson3 = callPackage ../development/python-modules/demjson3 { };
|
demjson3 = callPackage ../development/python-modules/demjson3 { };
|
||||||
|
@ -6586,6 +6590,8 @@ self: super: with self; {
|
||||||
|
|
||||||
msoffcrypto-tool = callPackage ../development/python-modules/msoffcrypto-tool { };
|
msoffcrypto-tool = callPackage ../development/python-modules/msoffcrypto-tool { };
|
||||||
|
|
||||||
|
msprime = callPackage ../development/python-modules/msprime { };
|
||||||
|
|
||||||
mss = callPackage ../development/python-modules/mss { };
|
mss = callPackage ../development/python-modules/mss { };
|
||||||
|
|
||||||
msrestazure = callPackage ../development/python-modules/msrestazure { };
|
msrestazure = callPackage ../development/python-modules/msrestazure { };
|
||||||
|
@ -6830,6 +6836,8 @@ self: super: with self; {
|
||||||
|
|
||||||
newversion = callPackage ../development/python-modules/newversion { };
|
newversion = callPackage ../development/python-modules/newversion { };
|
||||||
|
|
||||||
|
newick = callPackage ../development/python-modules/newick { };
|
||||||
|
|
||||||
nexia = callPackage ../development/python-modules/nexia { };
|
nexia = callPackage ../development/python-modules/nexia { };
|
||||||
|
|
||||||
nextcloudmonitor = callPackage ../development/python-modules/nextcloudmonitor { };
|
nextcloudmonitor = callPackage ../development/python-modules/nextcloudmonitor { };
|
||||||
|
@ -9540,6 +9548,8 @@ self: super: with self; {
|
||||||
|
|
||||||
pysingleton = callPackage ../development/python-modules/pysingleton { };
|
pysingleton = callPackage ../development/python-modules/pysingleton { };
|
||||||
|
|
||||||
|
pyslim = callPackage ../development/python-modules/pyslim { };
|
||||||
|
|
||||||
pyslurm = callPackage ../development/python-modules/pyslurm {
|
pyslurm = callPackage ../development/python-modules/pyslurm {
|
||||||
inherit (pkgs) slurm;
|
inherit (pkgs) slurm;
|
||||||
};
|
};
|
||||||
|
@ -12609,6 +12619,8 @@ self: super: with self; {
|
||||||
|
|
||||||
trytond = callPackage ../development/python-modules/trytond { };
|
trytond = callPackage ../development/python-modules/trytond { };
|
||||||
|
|
||||||
|
tskit = callPackage ../development/python-modules/tskit { };
|
||||||
|
|
||||||
ttach = callPackage ../development/python-modules/ttach { };
|
ttach = callPackage ../development/python-modules/ttach { };
|
||||||
|
|
||||||
ttls = callPackage ../development/python-modules/ttls { };
|
ttls = callPackage ../development/python-modules/ttls { };
|
||||||
|
|
Loading…
Reference in a new issue