Merge pull request #232816 from natsukium/python3Packages.pyvcf/remove (3ece3ad2) · Commits · nix / nixpkgs

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

deleted100644 → 0

+0 −28

Original line number	Diff line number	Diff line
		{ lib
		, buildPythonPackage
		, fetchPypi
		, pyvcf
		}:

		buildPythonPackage rec {
		pname = "ACEBinf";
		version = "1.0.2";

		src = fetchPypi {
		inherit pname version;
		sha256 = "1168pny671l6zfm2vv1pwspnflmzi7f4v8yldjl7zlz0b9cm5zlz";
		};

		buildInputs = [ pyvcf ];

		# no tests
		doCheck = false;
		pythonImportsCheck = [ "acebinf" ];

		meta = with lib; {
		homepage = "https://github.com/ACEnglish/acebinf";
		description = "Collection of simple utilities used when building bioinformatics tools";
		license = licenses.unlicense;
		maintainers = with maintainers; [ ris ];
		};
		}

deleted100644 → 0

+0 −33

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		{ lib
		, buildPythonPackage
		, fetchFromGitHub
		, pytest
		}:

		buildPythonPackage rec {
		pname = "PyVCF";
		version = "0.6.8";

		src = fetchFromGitHub {
		owner = "jamescasbon";
		repo = "PyVCF";
		rev = "476169cd457ba0caa6b998b301a4d91e975251d9";
		sha256 = "0qf9lwj7r2hjjp4bd4vc7nayrhblfm4qcqs4dbd43a6p4bj2jv5p";
		};

		nativeCheckInputs = [ pytest ];

		meta = with lib; {
		homepage = "https://pyvcf.readthedocs.io/en/latest/index.html";
		description = "A VCF (Variant Call Format) Parser for Python, supporting version 4.0 and 4.1";
		license = licenses.bsd3;
		maintainers = with maintainers; [ scalavision ];
		longDescription = ''
		The intent of this module is to mimic the csv module in the Python stdlib,
		as opposed to more flexible serialization formats like JSON or YAML.
		vcf will attempt to parse the content of each record based on the data
		types specified in the meta-information lines
		'';
		broken = true; # uses the 2to3 feature, that got removed in setuptools 0.58
		};
		}

+2 −0

Original line number	Diff line number	Diff line
		@@ -34,6 +34,7 @@ in

		mapAliases ({
		abodepy = jaraco-abode; # added 2023-02-01
		acebinf = throw "acebinf has been removed because it is abandoned and broken."; # Added 2023-05-19
		aioh2 = throw "aioh2 has been removed because it is abandoned and broken."; # Added 2022-03-30
		ansible-base = throw "ansible-base has been removed, because it is end of life"; # added 2022-03-30
		ansible-doctor = throw "ansible-doctor has been promoted to a top-level attribute"; # Added 2023-05-16
		@@ -250,6 +251,7 @@ mapAliases ({
		pytorchWithCuda = torchWithCuda; # added 2022-09-30
		pytorchWithoutCuda = torchWithoutCuda; # added 2022-09-30
		pytwitchapi = twitchapi; # added 2022-03-07
		pyvcf = throw "pyvcf has been removed, it was using setuptools 2to3 translation feature, which has been removed in setuptools 58"; # added 2023-05-19
		PyVirtualDisplay = pyvirtualdisplay; # added 2023-02-19
		qasm2image = throw "qasm2image is no longer maintained (since November 2018), and is not compatible with the latest pythonPackages.qiskit versions."; # added 2020-12-09
		Quandl = quandl; # added 2023-02-19

+0 −4

Original line number	Diff line number	Diff line
		@@ -28,8 +28,6 @@ self: super: with self; {

		accupy = callPackage ../development/python-modules/accupy { };

		acebinf = callPackage ../development/python-modules/acebinf { };

		acme = callPackage ../development/python-modules/acme { };

		acme-tiny = callPackage ../development/python-modules/acme-tiny { };
		@@ -10045,8 +10043,6 @@ self: super: with self; {

		pyvcd = callPackage ../development/python-modules/pyvcd { };

		pyvcf = callPackage ../development/python-modules/pyvcf { };

		pyvera = callPackage ../development/python-modules/pyvera { };

		pyverilog = callPackage ../development/python-modules/pyverilog { };