Commit 33a1e999 authored by Dmitry Kalinkin's avatar Dmitry Kalinkin
Browse files

snakemake: 8.14.0 -> 8.19.3

parent 5f021139

pkgs/applications/science/misc/snakemake/assets.nix

0 → 100644
+67 −0
Original line number Diff line number Diff line 
{ fetchurl }:

{

  "snakemake/LICENSE.md" = fetchurl {

    url = "https://raw.githubusercontent.com/snakemake/snakemake/main/LICENSE.md";

    sha256 = "84a1a82b05c80637744d3fe8257235c15380efa6cc32608adf4b21f17af5d2b8";

  };

  "pygments/LICENSE" = fetchurl {

    url = "https://raw.githubusercontent.com/pygments/pygments/master/LICENSE";

    sha256 = "a9d66f1d526df02e29dce73436d34e56e8632f46c275bbdffc70569e882f9f17";

  };

  "tailwindcss/LICENSE" = fetchurl {

    url = "https://raw.githubusercontent.com/tailwindlabs/tailwindcss/master/LICENSE";

    sha256 = "60e0b68c0f35c078eef3a5d29419d0b03ff84ec1df9c3f9d6e39a519a5ae7985";

  };

  "tailwindcss/tailwind.css" = fetchurl {

    url = "https://cdn.tailwindcss.com/3.0.23?plugins=forms@0.4.0,typography@0.5.2";

    sha256 = "8a597dc918fb62e05db23a5f810327a045a62c57cfda16646075138a6ac696fa";

  };

  "react/LICENSE" = fetchurl {

    url = "https://raw.githubusercontent.com/facebook/react/main/LICENSE";

    sha256 = "da6d3703ed11cbe42bd212c725957c98da23cbff1998c05fa4b3d976d1a58e93";

  };

  "react/react.production.min.js" = fetchurl {

    url = "https://cdnjs.cloudflare.com/ajax/libs/react/18.2.0/umd/react.production.min.js";

    sha256 = "4b4969fa4ef3594324da2c6d78ce8766fbbc2fd121fff395aedf997db0a99a06";

  };

  "react/react-dom.production.min.js" = fetchurl {

    url = "https://cdnjs.cloudflare.com/ajax/libs/react-dom/18.2.0/umd/react-dom.production.min.js";

    sha256 = "21758ed084cd0e37e735722ee4f3957ea960628a29dfa6c3ce1a1d47a2d6e4f7";

  };

  "vega/vega.js" = fetchurl {

    url = "https://cdnjs.cloudflare.com/ajax/libs/vega/5.21.0/vega.js";

    sha256 = "b34c43055ef5d39a093e937522955dc359fbaec6c5b0259ae2de4c9da698e9fe";

  };

  "vega/LICENSE" = fetchurl {

    url = "https://raw.githubusercontent.com/vega/vega/main/LICENSE";

    sha256 = "63727832aaf62004a2b249c933e327f3c90caf49e41a72f4bf436edf632cbda8";

  };

  "vega-lite/vega-lite.js" = fetchurl {

    url = "https://cdnjs.cloudflare.com/ajax/libs/vega-lite/5.2.0/vega-lite.js";

    sha256 = "6eb7f93121cd9f44cf8640244f87c5e143f87c7a0b6cd113da4a9e41e3adf0aa";

  };

  "vega-lite/LICENSE" = fetchurl {

    url = "https://raw.githubusercontent.com/vega/vega-lite/next/LICENSE";

    sha256 = "f618900fd0d64046963b29f40590cdd1e341a2f41449f99110d82fd81fea808c";

  };

  "vega-embed/vega-embed.js" = fetchurl {

    url = "https://cdnjs.cloudflare.com/ajax/libs/vega-embed/6.20.8/vega-embed.js";

    sha256 = "4e546c1f86eb200333606440e92f76e2940b905757018d9672cd1708e4e6ff0a";

  };

  "vega-embed/LICENSE" = fetchurl {

    url = "https://raw.githubusercontent.com/vega/vega-embed/next/LICENSE";

    sha256 = "32df67148f0fc3db0eb9e263a7b75d07f1eb14c61955005a4a39c6918d10d137";

  };

  "heroicons/LICENSE" = fetchurl {

    url = "https://raw.githubusercontent.com/tailwindlabs/heroicons/master/LICENSE";

    sha256 = "60e0b68c0f35c078eef3a5d29419d0b03ff84ec1df9c3f9d6e39a519a5ae7985";

  };

  "prop-types/prop-types.min.js" = fetchurl {

    url = "https://cdnjs.cloudflare.com/ajax/libs/prop-types/15.7.2/prop-types.min.js";

    sha256 = "4c88350517ee82aa4f3368e67ef1a453ca6636dcfa6449b4e3d6faa5c877066e";

  };

  "prop-types/LICENSE" = fetchurl {

    url = "https://raw.githubusercontent.com/facebook/prop-types/main/LICENSE";

    sha256 = "f657f99d3fb9647db92628e96007aabb46e5f04f33e49999075aab8e250ca7ce";

  };

}

pkgs/applications/science/misc/snakemake/assets.sed

0 → 100644
+9 −0
Original line number Diff line number Diff line 
/Asset(.*/ {               # find Asset declaration

s/: Asset(/ = fetchurl {/; # replace leading

  :b;                      # a label

  $!N;                     # if not EOF, include next line

  s/",/";/;                # provide separators between attributes

  /)/!bb;                  # repeat until a closing bracket is located

  s/),/};/;                # provide separators between assets

  p                        # output what we have

}

pkgs/applications/science/misc/snakemake/default.nix

+113 −8
Original line number Diff line number Diff line 
{ lib

, fetchFromGitHub

, fetchpatch

, fetchurl

, python3

, runtimeShell

, stress

}:



python3.pkgs.buildPythonApplication rec {

  pname = "snakemake";

  version = "8.14.0";

  version = "8.19.3";

  format = "setuptools";



  src = fetchFromGitHub {

    owner = "snakemake";

    repo = pname;

    rev = "refs/tags/v${version}";

    hash = "sha256-6oguN4u4OUDXpDsbueSBNwtWgLCaKmgq3w/d/MsMh7Y=";

    hash = "sha256-DWlMF/aNRCYDfTP41ALaGJFBTBjHxqZtx/0PtD/37KY=";

    # https://github.com/python-versioneer/python-versioneer/issues/217

    postFetch = ''

      sed -i "$out"/snakemake/_version.py -e 's#git_refnames = ".*"#git_refnames = " (tag: v${version})"#'

    '';

  };



  patches = [

    # Avoid downloading if files are provided

    # https://github.com/snakemake/snakemake/pull/3072

    (fetchpatch {

      url = "https://github.com/snakemake/snakemake/commit/ea89ec2f20faa0db303fdab0eafa640c9147cc14.diff";

      hash = "sha256-gzmto3Kusk40kPH29DkvYcJgAx2VAOq3mw5vPSCp5mI=";

    })

  ];



  postPatch = ''

    patchShebangs --build tests/

    patchShebangs --host snakemake/executors/jobscript.sh

    substituteInPlace snakemake/shell.py \

      --replace "/bin/sh" "${runtimeShell}"

  '';

    substituteInPlace tests/common.py \

      --replace-fail 'os.environ["PYTHONPATH"] = os.getcwd()' "pass" \

      --replace-fail 'del os.environ["PYTHONPATH"]' "pass"

    substituteInPlace snakemake/unit_tests/__init__.py \

      --replace-fail '"unit_tests/templates"' '"'"$PWD"'/snakemake/unit_tests/templates"'

  '' + (let

    assets = import ./assets.nix { inherit fetchurl; };

  in

    # Use fetchPypi once https://github.com/snakemake/snakemake/pull/3073 is available

    lib.concatStrings (lib.mapAttrsToList (name: file: ''

      echo install -D "${file}" snakemake/assets/data/${name}

      install -D "${file}" snakemake/assets/data/${name}

    '') assets));



  propagatedBuildInputs = with python3.pkgs; [

    appdirs
@@ -41,6 +62,7 @@ python3.pkgs.buildPythonApplication rec { 
    nbformat

    psutil

    pulp

    pygments

    pyyaml

    requests

    reretry
@@ -66,16 +88,97 @@ python3.pkgs.buildPythonApplication rec { 
    numpy

    pandas

    pytestCheckHook

    pytest-mock

    requests-mock

    snakemake-executor-plugin-cluster-generic

    snakemake-storage-plugin-fs

    stress

  ];



  disabledTestPaths = [

    "tests/test_conda_python_3_7_script/test_script.py"

  pytestFlagsArray = [

    "tests/tests.py"

    "tests/test_expand.py"

    "tests/test_io.py"

    "tests/test_schema.py"

    "tests/test_executor_test_suite.py"

    "tests/test_api.py"

  ];



  # Some will be disabled via https://github.com/snakemake/snakemake/pull/3074

  disabledTests = [

    # requires network connection

    "test_deploy_sources"

    "test_modules_meta_wrapper"

    "test_module_complex"

    "test_module_complex2"

    "test_module_with_script"

    "test_module_report"

    "test_load_metawrapper"

    # requires conda

    "test_archive"

    "test_script"

    "test_conda"

    "test_conda_list_envs"

    "test_upstream_conda"

    "test_deploy_script"

    "test_deploy_hashing"

    "test_conda_custom_prefix"

    "test_conda_cmd_exe"

    "test_wrapper"

    "test_wrapper_local_git_prefix"

    "test_singularity_conda"

    "test_issue635"

    "test_issue1093"

    "test_jupyter_notebook"

    "test_jupyter_notebook_draft"

    "test_converting_path_for_r_script"

    "test_conda_named"

    "test_conda_function"

    "test_conda_pin_file"

    "test_conda_python_script"

    "test_conda_python_3_7_script"

    "test_prebuilt_conda_script"

    "test_conda_global"

    "test_script_pre_py39"

    "test_resource_string_in_cli_or_profile"

    "test_conda"

    "test_env_modules"

    "test_script_pre_py39"

    # requires graphviz

    "test_filegraph"

    # requires s3

    "test_storage"

    "test_default_storage"

    "test_output_file_cache_storage"

    # requires peppy and eido

    "test_pep"

    # requires perl

    "test_shadow"

    # requires snakemake-storage-plugin-http

    "test_ancient"

    "test_modules_prefix"

    # weird

    "test_strict_mode"

    "test_issue1256"

    "test_issue2574"

    # requires apptainer

    "test_singularity"

    "test_singularity_cluster"

    "test_singularity_invalid"

    "test_singularity_module_invalid"

    "test_singularity_none"

    "test_singularity_global"

    "test_cwl_singularity"

    "test_issue1083"

    "test_github_issue78"

    "test_container"

    "test_shell_exec"

    "test_containerized"

    # future-proofing

    "conda"

    "singularity"

    "apptainer"

    "container"

  ];



  pythonImportsCheck = [
@@ -86,6 +189,8 @@ python3.pkgs.buildPythonApplication rec { 
    export HOME="$(mktemp -d)"

  '';



  passthru.updateScript = ./update.sh;



  meta = with lib; {

    homepage = "https://snakemake.github.io";

    license = licenses.mit;

pkgs/applications/science/misc/snakemake/update.sh

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+21 −0
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#!/usr/bin/env nix-shell

#!nix-shell -i bash -p curl common-updater-scripts gnused nixfmt-rfc-style



set -eu -o pipefail



version=${1:-$(curl -s https://api.github.com/repos/snakemake/snakemake/releases/latest | jq --raw-output '.tag_name[1:]')}

update-source-version snakemake $version



basedir="$(dirname "$0")"

cat <<EOF > "$basedir/assets.nix"

{ fetchurl }:

{

EOF

outlink="$basedir/src"

nix-build . -A snakemake.src -o "$outlink"

sed "$outlink"/snakemake/assets/__init__.py -n -f "$basedir/assets.sed" >> "$basedir/assets.nix"

rm "$outlink"

cat <<EOF >> "$basedir/assets.nix"

}

EOF

nixfmt "$basedir/assets.nix"