From 51088c1de4899b7c0caedce8928e7ba744229c3f Mon Sep 17 00:00:00 2001
From: Emily <vcs@emily.moe>
Date: Sun, 22 Sep 2024 13:51:28 +0100
Subject: [PATCH] toil: drop
MIME-Version: 1.0
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This package has been broken since 24.05 (`pkg_resources` error when
running `toil --help`), and hasn’t built since Python 3.12 became
the default. There have been two major upstream releases since this
package was last updated. I tried to package the newest version, which
drops the boto dependency, but unfortunately it requires obsolete
versions of other Python libraries that we no longer package. Since
it’s been broken for this long anyway and can’t be updated,
let’s drop it for now.
---
 .../science/misc/toil/default.nix             | 90 -------------------
 pkgs/top-level/aliases.nix                    |  1 +
 pkgs/top-level/all-packages.nix               |  2 -
 3 files changed, 1 insertion(+), 92 deletions(-)
 delete mode 100644 pkgs/applications/science/misc/toil/default.nix

diff --git a/pkgs/applications/science/misc/toil/default.nix b/pkgs/applications/science/misc/toil/default.nix
deleted file mode 100644
index 9142676fff48..000000000000
--- a/pkgs/applications/science/misc/toil/default.nix
+++ /dev/null
@@ -1,90 +0,0 @@
-{ lib
-, fetchFromGitHub
-, python3
-, rsync
-}:
-
-python3.pkgs.buildPythonApplication rec {
-  pname = "toil";
-  version = "5.12.0";
-  format = "setuptools";
-
-  src = fetchFromGitHub {
-    owner = "DataBiosphere";
-    repo = pname;
-    rev = "refs/tags/releases/${version}";
-    hash = "sha256-cTpbQo9tPZifUO59vbnIa3XUinFJ2/5Slfe4yszglFM=";
-  };
-
-  propagatedBuildInputs = with python3.pkgs; [
-    addict
-    dill
-    docker
-    enlighten
-    psutil
-    py-tes
-    pypubsub
-    python-dateutil
-    pytz
-    pyyaml
-    requests
-    typing-extensions
-  ];
-
-  nativeCheckInputs = [
-    rsync
-  ] ++ (with python3.pkgs; [
-    boto
-    botocore
-    flask
-    pytestCheckHook
-    stubserver
-  ]);
-
-  pytestFlagsArray = [
-    "src/toil/test"
-  ];
-
-  pythonImportsCheck = [
-    "toil"
-  ];
-
-  disabledTestPaths = [
-    # Tests are reaching their timeout
-    "src/toil/test/docs/scriptsTest.py"
-    "src/toil/test/jobStores/jobStoreTest.py"
-    "src/toil/test/provisioners/aws/awsProvisionerTest.py"
-    "src/toil/test/src"
-    "src/toil/test/wdl"
-    "src/toil/test/utils/utilsTest.py"
-    "src/toil/test/cwl/cwlTest.py"
-    "src/toil/test/lib/test_ec2.py"
-    "src/toil/test/lib/aws/test_iam.py"
-    "src/toil/test/lib/aws/test_s3.py"
-  ];
-
-  disabledTests = [
-    # Tests fail starting with 5.7.1
-    "testServices"
-    "testConcurrencyWithDisk"
-    "testJobConcurrency"
-    "testNestedResourcesDoNotBlock"
-    "test_omp_threads"
-    "testFileSingle"
-    "testFileSingle10000"
-    "testFileSingleCheckpoints"
-    "testFileSingleNonCaching"
-    "testFetchJobStoreFiles"
-    "testFetchJobStoreFilesWSymlinks"
-    "testJobStoreContents"
-    "test_cwl_on_arm"
-    "test_cwl_toil_kill"
-  ];
-
-  meta = with lib; {
-    description = "Workflow engine written in pure Python";
-    homepage = "https://toil.ucsc-cgl.org/";
-    license = with licenses; [ asl20 ];
-    maintainers = with maintainers; [ veprbl ];
-  };
-}
diff --git a/pkgs/top-level/aliases.nix b/pkgs/top-level/aliases.nix
index 264c231fa20f..5c26945985f4 100644
--- a/pkgs/top-level/aliases.nix
+++ b/pkgs/top-level/aliases.nix
@@ -1559,6 +1559,7 @@ mapAliases ({
   tightvnc = throw "'tightvnc' has been removed as the version 1.3 is not maintained upstream anymore and is insecure"; # Added 2024-08-22
   tixati = throw "'tixati' has been removed from nixpkgs as it is unfree and unmaintained"; # Added 2023-03-17
   tkcvs = tkrev; # Added 2022-03-07
+  toil = throw "toil was removed as it was broken and requires obsolete versions of libraries"; # Added 2024-09-22
   tokodon = plasma5Packages.tokodon;
   tokyo-night-gtk = tokyonight-gtk-theme; # Added 2024-01-28
   tomcat_connectors = apacheHttpdPackages.mod_jk; # Added 2024-06-07
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index f41e712c6e30..c6d64eb987e2 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -18809,8 +18809,6 @@ with pkgs;
 
   todoist-electron = callPackage ../applications/misc/todoist-electron { };
 
-  toil = callPackage ../applications/science/misc/toil { };
-
   travis = callPackage ../development/tools/misc/travis { };
 
   tree-sitter = makeOverridable (callPackage ../development/tools/parsing/tree-sitter) {