forked from tribes/guix
gnu: conda: Update to 25.9.1.
* gnu/packages/package-management.scm (conda): Update to 25.9.1. Use G-Expressions, move all propagated-inputs to inputs, as it's a final command. [arguments] <test-flags>: Ignored test files are reworked to keep just bare minimal of unit tests, more attention is required to resolve the rest, rework skipped tests. Run test in parallel. <phases>: Remove 'use-older-pytest, 'fix-ruamel-yaml-dependency, and 'create-version-file'; add 'fix-pytest-config, 'set-default-solver-to-classic, 'set-version, 'pre-check, and 'wrap-executable. [inputs]: Add python-archspec, python-boltons, python-boto3, python-charset-normalizer, python-conda-package-handling, python-conda-content-trust, python-distro, python-frozendict, python-jsonpatch, python-menuinst, python-packaging, python-platformdirs, python-pluggy, python-pycosat, python-requests, python-ruamel.yaml, python-setuptools, python-tqdm, python-truststore, and python-zstandard. [propagated-inputs]: Remove python-anaconda-client, python-boto3, python-conda-package-handling, python-cytoolz, python-mock, python-pluggy, python-pycosat, python-pytest, python-pyyaml, python-requests, python-responses, python-ruamel.yaml-0.16, python-tqdm, and zstd. [native-inputs]: Remove python-coverage, python-pytest-cov, and python-wheel; add nss-certs-for-test, patchelf, python-hatch-vcs, python-anaconda-client, python-flask, python-hatchling, python-importlib-resources, python-pexpect, python-pytest, python-pytest-mock, python-pytest-rerunfailures, python-pytest-split, python-pytest-xdist, python-responses, and python-werkzeug. Fixes: guix/guix#3928 Change-Id: Ie8b463e1614d1477b169cf1cf4f94328f49fc4f2
This commit is contained in:
Sharlatan Hellseher
@@ -1432,83 +1432,116 @@ manage (install/update) them for you.")
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(define-public conda
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(package
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(name "conda")
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(version "22.9.0")
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(version "25.9.1")
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/conda/conda")
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(commit version)))
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(url "https://github.com/conda/conda")
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(commit version)))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"16vz4vx311ry9w35mi5wna8p8n3abd6wdqrpqzjfdlwv7hcr44s4"))))
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(base32 "1s8xxc8rfayfq6p3iwgp9v3hbanp30ciw7cznppn1qk1l9fy7nxj"))))
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(build-system pyproject-build-system)
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(arguments
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(list
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;; tests: 1616 passed, 169 skipped, 12 xfailed, 673 warnings
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#:test-flags
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'(list
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"--ignore=tests/cli/test_main_clean.py"
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"--ignore=tests/cli/test_main_rename.py"
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"-k" (string-append
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"not "
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(string-join
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(list
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"integration"
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;; This one reports a newer version of conda than
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;; expected; conda-1.5.2-py27_0 instead of
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;; conda-1.3.5-py27_0.
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"test_auto_update_conda"
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;; This fails because the output directory is not a
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;; Conda environment.
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"test_list"
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;; This fails because we patched the default root
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;; prefix.
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"test_default_target_is_root_prefix"
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;; This fails because of missing features in python-flaky.
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"test_no_features"
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;; These fail because they require network access
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"test_no_ssl"
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"test_run_readonly_env"
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"test_run_returns_int"
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"test_run_returns_nonzero_errorlevel"
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"test_run_returns_zero_errorlevel"
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"test_run_uncaptured"
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;; TODO: I don't understand what this failure means
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"test_PrefixData_return_value_contract"
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;; TODO: same here
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"test_install_1"
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;; Not sure if this is really wrong. This fails because
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;; /gnu/store/...conda-22.9.0/bin/python
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;; is not /gnu/store/...python-wrapper-3.9.9/bin/python
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"test_make_entry_point"
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"test_get_python_info" "test__get_python_info"
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"test_install_conda_csh"
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"test_install_conda_fish")
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" and not ")))
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#~(list "-m" "not integration"
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"--numprocesses" (number->string (min 8 (parallel-job-count)))
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;; Tests try to search for system level packages and fail with
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;; error: The following packages are missing from the target
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;; environment: patch, ca-certificates, zlib ...
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"--ignore=tests/cli/test_subcommands.py"
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;; ModuleNotFoundError: No module named 'conda_libmamba_solver'
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"--ignore=tests/test_solvers.py"
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;; Network access is required.
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"--ignore=tests/trust/test_signature_verification.py"
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"-k" (string-join
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;; XXX: Issues salad: network access, can't detect Conda
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;; environemnt, assertion failed; review if they may be
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;; fixed.
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(list "not test_PrefixData_return_value_contract"
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"test__get_python_info"
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"test_auto_update_conda"
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"test_build_version_shows_as_changed "
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"test_cannot_rename_base_env_by_name"
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"test_cannot_rename_base_env_by_path"
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"test_conda_doctor_happy_path"
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"test_conda_doctor_happy_path_verbose"
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"test_conda_pip_interop_dependency_satisfied_by_pip"
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"test_create_env_json"
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"test_denylist_channels"
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"test_dont_update_packages_with_version_constraints"
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"test_environment"
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"test_exit_codes"
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"test_explicit_missing_cache_entries"
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"test_explicit_packages"
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"test_export_explicit_format_validation_errors"
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"test_export_ignore_channels_flag"
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"test_export_no_builds_format"
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"test_export_override_channels_and_ignore_channels_"
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"test_export_package_alphabetical_ordering"
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"test_export_pip_dependencies_handling"
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"test_export_preserves_channels_from_installed_"
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"test_export_regular_format_consistency"
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"test_export_with_pip_dependencies_integration"
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"test_extrapolate"
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"test_fields_all"
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"test_fields_invalid"
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"test_file_locking_not_supported"
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"test_file_locking_supported"
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"test_frozen_env_cep22"
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"test_get_packages_behavior_with_interoperability"
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"test_get_python_info"
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"test_health_check_ran"
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"test_info_envs_frozen"
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"test_install_1"
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"test_install_from_extracted_package"
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"test_installer_installs_explicit"
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"test_is_active_prefix"
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"test_list_all_known_prefixes_with_none_values_error"
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"test_list_argument_variations"
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"test_list_json"
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"test_list_package"
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"test_list_revisions"
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"test_load_entrypoints_importerror"
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"test_multiline_run_command"
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"test_post_solve_action_raises_exception"
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"test_post_solve_invoked"
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"test_post_transaction_raises_exception"
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"test_pre_solve_invoked"
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"test_pre_transaction_raises_exception"
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"test_print_unexpected_error_message_upload_2"
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"test_protected_dirs_error_for_rename"
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"test_remove_all"
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"test_remove_all_keep_env"
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"test_run_readonly_env"
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"test_run_returns_int"
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"test_run_returns_zero_errorlevel"
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"test_solve_1"
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"test_transaction_hooks_invoked"
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"test_update"
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"test_validate_subdir_config"
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"test_validate_subdir_config_invalid_subdir")
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" and not "))
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#:phases
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#~(modify-phases %standard-phases
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;; The default version of pytest does not support these options.
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(add-after 'unpack 'use-older-pytest
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(add-after 'unpack 'fix-pytest-config
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(lambda _
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(substitute* "setup.cfg"
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(("--xdoctest-.*") ""))))
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(add-after 'unpack 'fix-ruamel-yaml-dependency
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(lambda _
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(substitute* "setup.py"
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(("ruamel_yaml_conda") "ruamel.yaml"))))
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(substitute* "pyproject.toml"
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(("--cov.*") ""))))
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(add-after 'unpack 'correct-python-executable-name
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(lambda* (#:key inputs #:allow-other-keys)
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(let ((python (assoc-ref inputs "python-wrapper")))
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(lambda _
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(let ((python #$(this-package-input "python-wrapper")))
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(substitute* "conda/core/initialize.py"
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(("python_exe = join")
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(format #f "python_exe = \"~a/bin/python\" #"
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python))))))
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(add-after 'unpack 'do-not-use-python-root-as-prefix
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(let ((out (assoc-ref outputs "out"))
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(python (assoc-ref inputs "python-wrapper")))
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;; XXX: Proper wrap CONDA_EXE, CONDA_ENVS_PATH, CONDA_PKGS_DIRS.
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(lambda _
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(let ((python #$(this-package-input "python-wrapper")))
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(substitute* "tests/core/test_initialize.py"
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(("\"\"\"\\) % conda_prefix")
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(format #f "\"\"\") % ~s" python))
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@@ -1516,57 +1549,95 @@ manage (install/update) them for you.")
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(format #f "CONDA_PYTHON_EXE \"%s\"' % join(~s"
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python))
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(("conda_prefix = abspath\\(sys.prefix\\)")
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(format #f "conda_prefix = abspath(~s)" out)))
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(format #f "conda_prefix = abspath(~s)" #$output)))
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(substitute* "conda/base/context.py"
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(("os.chdir\\(sys.prefix\\)")
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(format #f "os.chdir(~s)" out))
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(format #f "os.chdir(~s)" #$output))
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(("sys.prefix, '.condarc'")
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(format #f "~s, '.condarc'" out))
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(format #f "~s, '.condarc'" #$output))
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(("return abspath\\(sys.prefix\\)")
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(format #f "return abspath(~s)" out))
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(format #f "return abspath(~s)" #$output))
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(("os.path.join\\(sys.prefix, bin_dir, exe\\)")
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(format #f "\"~a/bin/conda\"" out))
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(format #f "\"~a/bin/conda\"" #$output))
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(("'CONDA_EXE', sys.executable")
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(format #f "'CONDA_EXE', \"~a/bin/conda\"" out))))))
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(add-before 'build 'create-version-file
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(lambda _
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(with-output-to-file "conda/.version"
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(lambda () (display #$version)))))
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(format #f "'CONDA_EXE', \"~a/bin/conda\"" #$output))))))
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(add-after 'create-entrypoints 'init
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;; This writes a whole bunch of shell initialization files to the
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;; prefix directory. Many features of conda can only be used after
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;; running "conda init".
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(add-installed-pythonpath inputs outputs)
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;; prefix directory. Many features of conda can only be used
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;; after running "conda init".
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(lambda _
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(setenv "HOME" "/tmp")
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(invoke (string-append (assoc-ref outputs "out")
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"/bin/conda")
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"init"))))))
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(invoke (string-append #$output "/bin/conda") "init")))
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(add-after 'unpack 'set-default-solver-to-classic
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;; XXX: Remove when conda-libmamba-solver is packaged.
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(lambda _
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(substitute* "conda/base/constants.py"
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(("DEFAULT_SOLVER: Final = \"libmamba\"")
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"DEFAULT_SOLVER: Final = \"classic\""))))
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(add-before 'build 'set-version
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(lambda _
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(setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)))
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(add-before 'check 'pre-check
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(lambda _
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;; TODO: Package libsolv, libmamba, and conda-libmamba-solver:
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;; <https://github.com/openSUSE/libsolv>,
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;; <https://github.com/conda/conda-libmamba-solver>,
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;; <https://github.com/mamba-org/mamba>.
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(setenv "CONDA_CLASSIC_SOLVER" "classic")
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(setenv "CONDA_DEFAULT_SOLVER" "classic")
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(setenv "CONDA_TEST_SOLVERS" "classic")
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(setenv "HOME" "/tmp")))
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(add-after 'wrap 'wrap-executable
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(lambda _
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(wrap-program (string-append #$output "/bin/conda")
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`("CONDA_EXE" prefix
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(,(string-append #$output "/bin/conda")))
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`("CONDA_ENVS_PATH" prefix
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(,(string-append "$HOME/.conda/envs")))
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`("CONDA_PKGS_DIRS" prefix
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(,(string-append "$HOME/.conda/pkgs")))))))))
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(native-inputs
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(list nss-certs-for-test
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patchelf
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python-hatch-vcs
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python-anaconda-client
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python-flaky
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python-flask
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python-hatchling
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python-importlib-resources
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python-pexpect
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python-pytest
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python-pytest-mock
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python-pytest-rerunfailures
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python-pytest-split
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python-pytest-timeout
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python-pytest-xdist
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python-pytest-xprocess
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python-responses
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python-werkzeug))
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(inputs
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(list python-wrapper))
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(propagated-inputs
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(list python-anaconda-client
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(list python-archspec
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python-boltons
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python-boto3
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python-charset-normalizer
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;; python-conda-libmamba-solver ;TODO: not packaged yet
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python-conda-package-handling
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python-cytoolz
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python-mock
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python-conda-content-trust
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python-distro
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python-frozendict
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python-jsonpatch
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python-menuinst
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python-packaging
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python-platformdirs
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python-pluggy
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python-pycosat
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python-pytest
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python-pyyaml
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python-requests
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python-responses
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python-ruamel.yaml-0.16
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python-ruamel.yaml
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python-setuptools
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python-tqdm
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;; XXX: This is dragged in by libarchive and is needed at runtime.
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zstd))
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(native-inputs
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(list python-coverage
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python-flaky
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python-pytest-cov
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python-pytest-timeout
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python-pytest-xprocess
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python-wheel))
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python-truststore
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python-wrapper ;XXX: Check if it's actually required
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python-zstandard))
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(home-page "https://github.com/conda/conda")
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(synopsis "Cross-platform, OS-agnostic, system-level binary package manager")
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(description
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Block a user