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

   1 {
   2   buildPythonPackage,
   3   lib,
   4   setuptools,
   5   stdenv,
   6   fetchFromGitHub,
   7   installShellFiles,
   8   git,
   9   coreutils,
  10   versioneer,
  11   # core
  12   platformdirs,
  13   chardet,
  14   iso8601,
  15   humanize,
  16   fasteners,
  17   packaging,
  18   patool,
  19   tqdm,
  20   annexremote,
  21   looseversion,
  22   git-annex,
  23   # downloaders
  24   boto3,
  25   keyrings-alt,
  26   keyring,
  27   msgpack,
  28   requests,
  29   # publish
  30   python-gitlab,
  31   # misc
  32   argcomplete,
  33   pyperclip,
  34   python-dateutil,
  35   # duecredit
  36   duecredit,
  37   distro,
  38   # win
  39   colorama,
  40   # python-version-dependent
  41   pythonOlder,
  42   importlib-metadata,
  43   typing-extensions,
  44   # tests
  45   pytest-xdist,
  46   pytestCheckHook,
  47   p7zip,
  48   curl,
  49   httpretty,
  50 }:
  51
  52 buildPythonPackage rec {
  53   pname = "datalad";
  54   version = "1.1.5";
  55   pyproject = true;
  56
  57   src = fetchFromGitHub {
  58     owner = "datalad";
  59     repo = "datalad";
  60     tag = version;
  61     hash = "sha256-XwzYlSP2MbEb0U3tuVOq3NNqLTS08UzSfSFBidHbpAY=";
  62   };
  63
  64   postPatch = ''
  65     substituteInPlace datalad/distribution/create_sibling.py \
  66       --replace-fail "/bin/ls" "${coreutils}/bin/ls"
  67     # Remove vendorized versioneer.py
  68     rm versioneer.py
  69   '';
  70
  71   nativeBuildInputs = [
  72     installShellFiles
  73     git
  74   ];
  75
  76   build-system = [
  77     setuptools
  78     versioneer
  79   ];
  80
  81   dependencies =
  82     optional-dependencies.core ++ optional-dependencies.downloaders ++ optional-dependencies.publish;
  83
  84   optional-dependencies = {
  85     core =
  86       [
  87         platformdirs
  88         chardet
  89         distro
  90         iso8601
  91         humanize
  92         fasteners
  93         packaging
  94         patool
  95         tqdm
  96         annexremote
  97         looseversion
  98       ]
  99       ++ lib.optionals stdenv.hostPlatform.isWindows [ colorama ]
 100       ++ lib.optionals (pythonOlder "3.10") [ importlib-metadata ]
 101       ++ lib.optionals (pythonOlder "3.11") [ typing-extensions ];
 102     downloaders = [
 103       boto3
 104       keyrings-alt
 105       keyring
 106       msgpack
 107       requests
 108     ];
 109     downloaders-extra = [
 110       # requests-ftp # not in nixpkgs yet
 111     ];
 112     publish = [ python-gitlab ];
 113     misc = [
 114       argcomplete
 115       pyperclip
 116       python-dateutil
 117     ];
 118     duecredit = [ duecredit ];
 119   };
 120
 121   postInstall = ''
 122     installShellCompletion --cmd datalad \
 123          --bash <($out/bin/datalad shell-completion) \
 124          --zsh  <($out/bin/datalad shell-completion)
 125     wrapProgram $out/bin/datalad --prefix PYTHONPATH : "$PYTHONPATH"
 126   '';
 127
 128   preCheck = ''
 129     export HOME=$TMPDIR
 130   '';
 131
 132   # tests depend on apps in $PATH which only will get installed after the test
 133   disabledTests = [
 134     # No such file or directory: 'datalad'
 135     "test_script_shims"
 136     "test_cfg_override"
 137     "test_completion"
 138     "test_nested_pushclone_cycle_allplatforms"
 139     "test_create_sub_gh3463"
 140     "test_create_sub_dataset_dot_no_path"
 141     "test_cfg_passthrough"
 142     "test_addurls_stdin_input_command_line"
 143     "test_run_datalad_help"
 144     "test_status_custom_summary_no_repeats"
 145     "test_quoting"
 146
 147     #  No such file or directory: 'git-annex-remote-[...]"
 148     "test_create"
 149     "test_ensure_datalad_remote_maybe_enable"
 150
 151     # "git-annex: unable to use external special remote git-annex-remote-datalad"
 152     "test_ria_postclonecfg"
 153     "test_ria_postclone_noannex"
 154     "test_ria_push"
 155     "test_basic_scenario"
 156     "test_annex_get_from_subdir"
 157     "test_ensure_datalad_remote_init_and_enable_needed"
 158     "test_ensure_datalad_remote_maybe_enable[False]"
 159     "test_ensure_datalad_remote_maybe_enable[True]"
 160     "test_create_simple"
 161     "test_create_alias"
 162     "test_storage_only"
 163     "test_initremote"
 164     "test_read_access"
 165     "test_ephemeral"
 166     "test_initremote_basic_fileurl"
 167     "test_initremote_basic_httpurl"
 168     "test_remote_layout"
 169     "test_version_check"
 170     "test_gitannex_local"
 171     "test_push_url"
 172     "test_url_keys"
 173     "test_obtain_permission_root"
 174     "test_source_candidate_subdataset"
 175     "test_update_fetch_all"
 176     "test_add_archive_dirs"
 177     "test_add_archive_content"
 178     "test_add_archive_content_strip_leading"
 179     "test_add_archive_content_zip"
 180     "test_add_archive_content_absolute_path"
 181     "test_add_archive_use_archive_dir"
 182     "test_add_archive_single_file"
 183     "test_add_delete"
 184     "test_add_archive_leading_dir"
 185     "test_add_delete_after_and_drop"
 186     "test_add_delete_after_and_drop_subdir"
 187     "test_override_existing_under_git"
 188     "test_copy_file_datalad_specialremote"
 189     "test_download_url_archive"
 190     "test_download_url_archive_from_subdir"
 191     "test_download_url_archive_trailing_separator"
 192     "test_download_url_need_datalad_remote"
 193     "test_datalad_credential_helper - assert False"
 194
 195     # need internet access
 196     "test_clone_crcns"
 197     "test_clone_datasets_root"
 198     "test_reckless"
 199     "test_autoenabled_remote_msg"
 200     "test_ria_http_storedataladorg"
 201     "test_gin_cloning"
 202     "test_nonuniform_adjusted_subdataset"
 203     "test_install_datasets_root"
 204     "test_install_simple_local"
 205     "test_install_dataset_from_just_source"
 206     "test_install_dataset_from_just_source_via_path"
 207     "test_datasets_datalad_org"
 208     "test_get_cached_dataset"
 209     "test_cached_dataset"
 210     "test_cached_url"
 211     "test_anonymous_s3"
 212     "test_protocols"
 213     "test_get_versioned_url_anon"
 214     "test_install_recursive_github"
 215     "test_failed_install_multiple"
 216
 217     # pbcopy not found
 218     "test_wtf"
 219
 220     # CommandError: 'git -c diff.ignoreSubmodules=none -c core.quotepath=false ls-files -z -m -d' failed with exitcode 128
 221     "test_subsuperdataset_save"
 222   ];
 223
 224   nativeCheckInputs = [
 225     p7zip
 226     pytest-xdist
 227     pytestCheckHook
 228     git-annex
 229     curl
 230     httpretty
 231   ];
 232
 233   pytestFlagsArray = [
 234     # Deprecated in 3.13. Use exc_type_str instead.
 235     "-W"
 236     "ignore::DeprecationWarning"
 237   ];
 238
 239   pythonImportsCheck = [ "datalad" ];
 240
 241   meta = {
 242     description = "Keep code, data, containers under control with git and git-annex";
 243     homepage = "https://www.datalad.org";
 244     license = lib.licenses.mit;
 245     maintainers = with lib.maintainers; [ renesat ];
 246   };
 247 }