From 5e97a1075620dfd2445d8cf037ec216cb86812ee Mon Sep 17 00:00:00 2001 From: natsukium Date: Fri, 19 May 2023 19:53:49 +0900 Subject: [PATCH 1/2] python3Packages.acebinf: remove This library was introduced as a dependency of "truvari" but is no longer used. Also, "pyvcf" on which it depends, cannot be built due to the removal of "use_2to3". --- .../python-modules/acebinf/default.nix | 28 ------------------- pkgs/top-level/python-aliases.nix | 1 + pkgs/top-level/python-packages.nix | 2 -- 3 files changed, 1 insertion(+), 30 deletions(-) delete mode 100644 pkgs/development/python-modules/acebinf/default.nix diff --git a/pkgs/development/python-modules/acebinf/default.nix b/pkgs/development/python-modules/acebinf/default.nix deleted file mode 100644 index 7889e007d83ee..0000000000000 --- a/pkgs/development/python-modules/acebinf/default.nix +++ /dev/null @@ -1,28 +0,0 @@ -{ 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 ]; - }; -} diff --git a/pkgs/top-level/python-aliases.nix b/pkgs/top-level/python-aliases.nix index 882c75b9aed8a..bc530590cb13f 100644 --- a/pkgs/top-level/python-aliases.nix +++ b/pkgs/top-level/python-aliases.nix @@ -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 diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index 9f2309f864cfd..68153a8f76476 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -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 { }; From 8e5964963fd6fce214ff6339c2f040b043ad49a9 Mon Sep 17 00:00:00 2001 From: natsukium Date: Fri, 19 May 2023 20:02:38 +0900 Subject: [PATCH 2/2] python3Packages.pyvcf: remove This library was introduced as a dependency of "truvari" but is no longer used. Also, it can no longer be built due to the removal of "use_2to3". --- .../python-modules/pyvcf/default.nix | 33 ------------------- pkgs/top-level/python-aliases.nix | 1 + pkgs/top-level/python-packages.nix | 2 -- 3 files changed, 1 insertion(+), 35 deletions(-) delete mode 100644 pkgs/development/python-modules/pyvcf/default.nix diff --git a/pkgs/development/python-modules/pyvcf/default.nix b/pkgs/development/python-modules/pyvcf/default.nix deleted file mode 100644 index 1efcdd4d22423..0000000000000 --- a/pkgs/development/python-modules/pyvcf/default.nix +++ /dev/null @@ -1,33 +0,0 @@ -{ 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 - }; -} diff --git a/pkgs/top-level/python-aliases.nix b/pkgs/top-level/python-aliases.nix index bc530590cb13f..53b9ccd520b4d 100644 --- a/pkgs/top-level/python-aliases.nix +++ b/pkgs/top-level/python-aliases.nix @@ -251,6 +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 diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index 68153a8f76476..6d9722e67e3b1 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -10043,8 +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 { };