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gnu: conda: Update to 4.8.3.

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* gnu/packages/package-management.scm (python-conda): Define as deprecated
alias for conda.
(python2-conda): Remove variable.
(conda)[arguments]: Add phases "fix-permissions",
"correct-python-executable-name", "do-not-use-python-root-as-prefix", and
"init"; remove phase "remove-failing-tests"; update "check" phase.
[inputs]: Add python-wrapper.
[native-inputs]: Move them all to...
[propagated-inputs]: ...this field.  Add python-conda-package-handling,
python-tqdm, and zstd.
[description]: Remove line about Conda as a library.
This commit is contained in:
Ricardo Wurmus 2020-08-13 00:00:54 +02:00
parent c9ec3c0763
commit 638ef1e81d
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1 changed files with 103 additions and 108 deletions
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gnu/packages/package-management.scm
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@ -782,10 +782,10 @@ (define-public python-conda-package-handling
extracting, creating, and converting between formats.")
(license license:bsd-3)))
(define-public python-conda
(define-public conda
(package
(name "python-conda")
(version "4.3.16")
(name "conda")
(version "4.8.3")
(source
(origin
(method git-fetch)
@ -795,58 +795,118 @@ (define-public python-conda
(file-name (git-file-name name version))
(sha256
(base32
"1qwy0awx4qf2pbk8z2b7q6wdcq7mvwpxxjhg27mbirdvs5hw7hb2"))))
"0iv1qzk21jsk6vdp3106xvpvl68zgfdqb3kyzpya87jhkl204l7r"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-permissions
(lambda _
;; This file is no longer writable after downloading with
;; 'git-fetch'
(make-file-writable
"tests/conda_env/support/saved-env/environment.yml")
#t))
(add-after 'unpack 'correct-python-executable-name
(lambda* (#:key inputs #:allow-other-keys)
(let ((python (assoc-ref inputs "python-wrapper")))
#;
(substitute* "conda/common/path.py"
(("python_version or ''")
"python_version or '3'"))
(substitute* "conda/core/initialize.py"
(("python_exe = join")
(format #f "python_exe = \"~a/bin/python\" #"
python))))
#t))
(add-after 'unpack 'do-not-use-python-root-as-prefix
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(python (assoc-ref inputs "python-wrapper")))
(substitute* "tests/core/test_initialize.py"
(("\"\"\"\\) % conda_prefix")
(format #f "\"\"\") % \"~a\"" python))
(("CONDA_PYTHON_EXE \"%s\"' % join\\(conda_prefix")
(format #f "CONDA_PYTHON_EXE \"%s\"' % join(\"~a\""
python))
(("conda_prefix = abspath\\(sys.prefix\\)")
(format #f "conda_prefix = abspath(\"~a\")" out)))
(substitute* "conda/base/context.py"
(("os.chdir\\(sys.prefix\\)")
(format #f "os.chdir(\"~a\")" out))
(("sys.prefix, '.condarc'")
(format #f "\"~a\", '.condarc'" out))
(("return abspath\\(sys.prefix\\)")
(format #f "return abspath(\"~a\")" out))
(("os.path.join\\(sys.prefix, bin_dir, exe\\)")
(format #f "\"~a/bin/conda\"" out))
(("'CONDA_EXE', sys.executable")
(format #f "'CONDA_EXE', \"~a/bin/conda\"" out))))
#t))
(add-before 'build 'create-version-file
(lambda _
(with-output-to-file "conda/.version"
(lambda () (display ,version)))
#t))
(add-before 'check 'remove-failing-tests
(lambda _
;; These tests require internet/network access
(let ((network-tests '("test_cli.py"
"test_create.py"
"test_export.py"
"test_fetch.py"
"test_history.py"
"test_info.py"
"test_install.py"
"test_priority.py"
"conda_env/test_cli.py"
"conda_env/test_create.py"
"conda_env/specs/test_notebook.py"
"conda_env/utils/test_notebooks.py"
"core/test_index.py"
"core/test_repodata.py")))
(with-directory-excursion "tests"
(for-each delete-file network-tests)
;; FIXME: This test creates a file, then deletes it and tests
;; that the file was deleted. For some reason it fails when
;; building with guix, but does not when you run it in the
;; directory left when you build with the --keep-failed
;; option
(delete-file "gateways/disk/test_delete.py")
;; This file is no longer writable after downloading with 'git-fetch'
(make-file-writable "conda_env/support/saved-env/environment.yml")
#t))))
(replace 'check
(lambda _
(setenv "HOME" "/tmp")
(invoke "py.test"))))))
(native-inputs
`(("python-cytoolz" ,python-cytoolz)
("python-ruamel.yaml" ,python-ruamel.yaml)
("python-requests" ,python-requests)
(invoke "py.test" "-vv"
"-k"
(string-append
"not integration"
;; This one reports a newer version of conda than
;; expected.
" and not test_auto_update_conda"
;; This fails because the output directory is not a
;; Conda environment.
" and not test_list"
;; This fails because we patched the default root
;; prefix.
" and not test_default_target_is_root_prefix"
;; TODO: I don't understand what this failure means
" and not test_PrefixData_return_value_contract"
;; TODO: same here
" and not test_install_1"
;; Not sure if this is really wrong. This fails because
;; /gnu/store/...python-conda-4.8.3/bin/python
;; is not /gnu/store/...python-wrapper-3.8.2/bin/python
" and not test_make_entry_point"))))
(add-after 'install 'init
;; This writes a whole bunch of shell initialization files to the
;; prefix directory. Many features of conda can only be used after
;; running "conda init".
(lambda* (#:key inputs outputs #:allow-other-keys)
(add-installed-pythonpath inputs outputs)
(setenv "HOME" "/tmp")
;; "conda init" insists on using sudo, because it is hell-bent on
;; modifying system files.
(mkdir-p "/tmp/fake-sudo")
(with-output-to-file "/tmp/fake-sudo/sudo"
(lambda () (format #t "#!~/bin/sh~%exec $@" (which "sh"))))
(chmod "/tmp/fake-sudo/sudo" #o700)
(setenv "PATH" (string-append "/tmp/fake-sudo:"
(getenv "PATH")))
(invoke (string-append (assoc-ref outputs "out")
"/bin/conda")
"init"))))))
(inputs
`(("python-wrapper" ,python-wrapper)))
(propagated-inputs
`(("python-anaconda-client" ,python-anaconda-client)
("python-conda-package-handling" ,python-conda-package-handling)
("python-cytoolz" ,python-cytoolz)
("python-pycosat" ,python-pycosat)
("python-pytest" ,python-pytest)
("python-responses" ,python-responses)
("python-pyyaml" ,python-pyyaml)
("python-anaconda-client" ,python-anaconda-client)))
("python-requests" ,python-requests)
("python-responses" ,python-responses)
("python-ruamel.yaml" ,python-ruamel.yaml)
("python-tqdm" ,python-tqdm)
;; XXX: This is dragged in by libarchive and is needed at runtime.
("zstd" ,zstd)))
(home-page "https://github.com/conda/conda")
(synopsis "Cross-platform, OS-agnostic, system-level binary package manager")
(description
@ -854,76 +914,11 @@ (define-public python-conda
is the package manager used by Anaconda installations, but it may be used for
other systems as well. Conda makes environments first-class citizens, making
it easy to create independent environments even for C libraries. Conda is
written entirely in Python.
This package provides Conda as a library.")
written entirely in Python.")
(license license:bsd-3)))
(define-public python2-conda
(let ((base (package-with-python2
(strip-python2-variant python-conda))))
(package (inherit base)
(native-inputs
`(("python2-enum34" ,python2-enum34)
,@(package-native-inputs base))))))
(define-public conda
(package (inherit python-conda)
(name "conda")
(arguments
(substitute-keyword-arguments (package-arguments python-conda)
((#:phases phases)
`(modify-phases ,phases
(replace 'build
(lambda* (#:key outputs #:allow-other-keys)
;; This test fails when run before installation.
(delete-file "tests/test_activate.py")
;; Fix broken defaults
(substitute* "conda/base/context.py"
(("return sys.prefix")
(string-append "return \"" (assoc-ref outputs "out") "\""))
(("return (prefix_is_writable\\(self.root_prefix\\))" _ match)
(string-append "return False if self.root_prefix == self.conda_prefix else "
match)))
;; The util/setup-testing.py is used to build conda in
;; application form, rather than the default, library form.
;; With this, we are able to run commands like `conda --help`
;; directly on the command line
(invoke "python" "utils/setup-testing.py" "build_py")))
(replace 'install
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(target (string-append out "/lib/python"
(python-version
(assoc-ref inputs "python"))
"/site-packages/")))
;; The installer aborts if the target directory is not on
;; PYTHONPATH.
(setenv "PYTHONPATH"
(string-append target ":" (getenv "PYTHONPATH")))
;; And it aborts if the directory doesn't exist.
(mkdir-p target)
(invoke "python" "utils/setup-testing.py" "install"
(string-append "--prefix=" out)))))
;; The "activate" and "deactivate" scripts don't need wrapping.
;; They also break when they are renamed.
(add-after 'wrap 'undo-wrap
(lambda* (#:key outputs #:allow-other-keys)
(with-directory-excursion (string-append (assoc-ref outputs "out") "/bin/")
(delete-file "deactivate")
(rename-file ".deactivate-real" "deactivate")
(delete-file "activate")
(rename-file ".activate-real" "activate")
#t)))))))
(description
"Conda is a cross-platform, Python-agnostic binary package manager. It
is the package manager used by Anaconda installations, but it may be used for
other systems as well. Conda makes environments first-class citizens, making
it easy to create independent environments even for C libraries. Conda is
written entirely in Python.")))
(define-public python-conda
(deprecated-package "python-conda" conda))
(define-public gwl
(package