(address . bug-guix@gnu.org)
CAPX-MzA4uZv5Heu2O6n-=7oRLFGfUWdy+6r9VYDCmF6XOeJVJg@mail.gmail.com
python-anaconda-client and conda fail
- Done
Details
- 3 participants
- Etienne B. Roesch
- Hugo Buddelmeijer
- Simon Tournier
- Owner
- unassigned
- Submitted by
- Etienne B. Roesch
- Severity
- normal
E
H
(address . 63277@debbugs.gnu.org)
CA+Jv8O02Aqc-y8WmkXR3=zFDjBmN+-SnFt6Ca+eCkQaRa70HJw@mail.gmail.com
Hi Etienne,
I've noticed that conda (22.9.0) does not build as well, and have
resolved the issue in my local guix clone.
It required these changes:
- Add python-conda-package-streaming 0.7.0.
- Upgrade python-conda-package-handling from 1.7.3 to 2.1.0 (which has
python-conda-package-streaming as a dependency).
- Remove python-anaconda-client as a dependency of conda.
- Make conda a dependency of python-anaconda-client.
I'm also relatively new to guix. I think it is prefered to have small
patches, so I will send four patches for each of the above steps to
this issue as described in [1]. Then hopefully someone will review
them and merge them. Then after that it might be worthwhile to update
conda itself too.
Some notes:
- python-conda-package-streaming has conda itself as an optional
dependency for testing. I have therefore disabled all the tests.
- python-conda-package-streaming also removes the need for libarchive,
which apparently required some workarounds, so those are also removed.
- It is not clear to me why python-anaconda-client was a dependency of
conda in the first place, so maybe I'm missing something.
- I've also fixed some linting warnings on the existing packages.
Cheers,
Hugo
H
[PATCH 1/5] gnu: Add python-conda-package-streaming.
(address . 63277@debbugs.gnu.org)(name . Hugo Buddelmeijer)(address . hugo@buddelmeijer.nl)
324846ea5414ea4c382de41e604c19d8566c7cf6.1683547087.git.hugo@buddelmeijer.nl
* gnu/packages/python-xyz.scm (python-conda-package-streaming): New variable.
---
gnu/packages/python-xyz.scm | 31 +++++++++++++++++++++++++++++++
1 file changed, 31 insertions(+)
Toggle diff (46 lines)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index a5c99a6f20..c627e456e1 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -1688,6 +1688,37 @@ (define-public python-clyent
by @code{binstar}, @code{binstar-build}, and @code{chalmers}.")
(license license:bsd-3)))
+(define-public python-conda-package-streaming
+ (package
+ (name "python-conda-package-streaming")
+ (version "0.7.0")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "conda_package_streaming" version))
+ (sha256
+ (base32
+ "01a8yhfiww3ac0glnb41iqcrz5n6ya1k0w4vwc5wg06qcp6ipbq2"))))
+ (build-system pyproject-build-system)
+ (arguments
+ ;; All tests require conda to be installed. However conda requires
+ ;; python-conda-package-handling, which requires
+ ;; python-conda-package-streaming (this package), so the tests
+ ;; cannot be run.
+ `(#:tests? #f))
+ (propagated-inputs (list python-requests python-zstandard))
+ (native-inputs (list python-pytest
+ python-pytest-cov
+ python-pytest-mock
+ python-flit
+ python-bottle
+ python-boto3))
+ (home-page "https://github.com/conda/conda-package-streaming")
+ (synopsis
+ "Download metadata from conda packages without transferring entire file.")
+ (description
+ "Download conda metadata from packages without transferring entire file. Get metadata from local .tar.bz2 packages without reading entire files.")
+ (license license:bsd-3)))
+
(define-public python-babel
(package
(name "python-babel")
base-commit: d1aba42ad4e1909faa21d484975c5954c778e002
--
2.39.2
H
[PATCH 2/5] gnu: python-conda-package-handling: Update to 2.1.0
(address . 63277@debbugs.gnu.org)(name . Hugo Buddelmeijer)(address . hugo@buddelmeijer.nl)
fdb18beeabd100567599263bb76f75d43ef19e10.1683547087.git.hugo@buddelmeijer.nl
* gnu/packages/package-management.scm (python-conda-package-handling): Update to 2.1.0
---
gnu/packages/package-management.scm | 21 ++++++++-------------
1 file changed, 8 insertions(+), 13 deletions(-)
Toggle diff (48 lines)
diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index 9869dfaacf..1ebc95077b 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -952,7 +952,7 @@ (define-public python-anaconda-client
(define-public python-conda-package-handling
(package
(name "python-conda-package-handling")
- (version "1.7.3")
+ (version "2.1.0")
(source
(origin
(method git-fetch)
@@ -962,25 +962,20 @@ (define-public python-conda-package-handling
(file-name (git-file-name name version))
(sha256
(base32
- "1dq6f5ks3cinb355x712bls9bvv6bli6x3c43sdkqvawdw8xgv9j"))))
+ "17k363s2ad8cfngyrazzqvq287dab64ssah2rhzj4h7v1mfy47bm"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
- (add-after 'unpack 'use-unmodified-libarchive
- (lambda _
- (substitute* "setup.py"
- (("archive_and_deps") "archive"))))
(replace 'check
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (add-installed-pythonpath inputs outputs)
- (invoke "pytest" "-vv" "tests"))))))
+ (lambda* (#:key tests? inputs outputs #:allow-other-keys)
+ (when tests?
+ (add-installed-pythonpath inputs outputs)
+ (invoke "pytest" "-vv" "tests")))))))
(propagated-inputs
- (list python-six python-tqdm))
- (inputs
- (list libarchive))
+ (list python-conda-package-streaming))
(native-inputs
- (list python-cython python-pytest python-pytest-cov
+ (list python-wheel python-pytest python-pytest-cov
python-pytest-mock python-mock))
(home-page "https://conda.io")
(synopsis "Create and extract conda packages of various formats")
--
2.39.2
H
[PATCH 3/5] gnu: conda: Remove python-anaconda-client dependency.
(address . 63277@debbugs.gnu.org)(name . Hugo Buddelmeijer)(address . hugo@buddelmeijer.nl)
49e908fe2967fc31209c1fbce36370969b209daa.1683547087.git.hugo@buddelmeijer.nl
* gnu/packages/package-management.scm (conda): Remove python-anaconda-client dependency.
---
gnu/packages/package-management.scm | 10 ++++------
1 file changed, 4 insertions(+), 6 deletions(-)
Toggle diff (34 lines)
diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index 1ebc95077b..2e2c116c33 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -1101,23 +1101,21 @@ (define-public conda
(inputs
(list python-wrapper))
(propagated-inputs
- (list python-anaconda-client
- python-boto3
+ (list python-boto3
python-conda-package-handling
python-cytoolz
python-pluggy
python-pycosat
- python-pytest
python-pyyaml
python-requests
python-responses
python-ruamel.yaml
- python-tqdm
- ;; XXX: This is dragged in by libarchive and is needed at runtime.
- zstd))
+ python-tqdm))
(native-inputs
(list python-coverage
python-flaky
+ python-mock
+ python-pytest
python-pytest-timeout
python-pytest-xprocess))
(home-page "https://github.com/conda/conda")
--
2.39.2
H
[PATCH 4/5] gnu: python-defusedxml: Update to 0.7.1.
(address . 63277@debbugs.gnu.org)(name . Hugo Buddelmeijer)(address . hugo@buddelmeijer.nl)
2834aeee4ebcbd41a9f7e15ea291dad459c38bca.1683547087.git.hugo@buddelmeijer.nl
* gnu/packages/xml.scm (defused-python): Update to 0.7.1.
---
gnu/packages/xml.scm | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
Toggle diff (26 lines)
diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm
index 2bc4f66c01..c4ab832bc5 100644
--- a/gnu/packages/xml.scm
+++ b/gnu/packages/xml.scm
@@ -1439,16 +1439,16 @@ (define-public xlsx2csv
(define-public python-defusedxml
(package
(name "python-defusedxml")
- (version "0.6.0")
+ (version "0.7.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "defusedxml" version))
(sha256
(base32
- "1xbp8fivl3wlbyg2jrvs4lalaqv1xp9a9f29p75wdx2s2d6h717n"))))
+ "0s9ym98jrd819v4arv9gmcr6mgljhxd9q866sxi5p4c5n4nh7cqv"))))
(build-system python-build-system)
- (home-page "https://bitbucket.org/tiran/defusedxml")
+ (home-page "https://github.com/tiran/defusedxml")
(synopsis "XML bomb protection for Python stdlib modules")
(description
"Defusedxml provides XML bomb protection for Python stdlib modules.")
--
2.39.2
H
[PATCH 5/5] gnu: python-anaconda-client: Update to 1.11.2
(address . 63277@debbugs.gnu.org)(name . Hugo Buddelmeijer)(address . hugo@buddelmeijer.nl)
c9d38caf6137502e1848eb9a203c4f73a3bdcf92.1683547087.git.hugo@buddelmeijer.nl
* gnu/packages/package-management.scm (python-anaconda-client): Update to 1.11.2.
---
gnu/packages/package-management.scm | 17 ++++++++---------
1 file changed, 8 insertions(+), 9 deletions(-)
Toggle diff (46 lines)
diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index 2e2c116c33..ea5679fb44 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -900,7 +900,7 @@ (define-public rpm
(define-public python-anaconda-client
(package
(name "python-anaconda-client")
- (version "1.8.0")
+ (version "1.11.2")
(source
(origin
(method git-fetch)
@@ -910,10 +910,10 @@ (define-public python-anaconda-client
(file-name (git-file-name name version))
(sha256
(base32
- "1vyk0g0gci4z9psisb8h50zi3j1nwfdg1jw3j76cxv0brln0v3fw"))))
+ "1cd1ycpa9b4i5hn7fqksddk6iky2ap6gw6f3l8fy95ypdjyk2z3d"))))
(build-system python-build-system)
(propagated-inputs
- (list python-clyent python-nbformat python-pyyaml python-requests))
+ (list python-clyent python-nbformat python-pyyaml python-requests python-requests-toolbelt python-tqdm python-defusedxml python-conda-package-handling conda))
(native-inputs
(list python-coverage
python-dateutil
@@ -934,12 +934,11 @@ (define-public python-anaconda-client
"tests/test_authorizations.py"
"tests/test_login.py"
"tests/test_whoami.py"
- "utils/notebook/tests/test_data_uri.py"
- "utils/notebook/tests/test_base.py"
- "utils/notebook/tests/test_downloader.py"
- "inspect_package/tests/test_conda.py")))
- (with-directory-excursion "binstar_client"
- (for-each delete-file network-tests)))
+ "tests/utils/notebook/test_data_uri.py"
+ "tests/utils/notebook/test_base.py"
+ "tests/utils/notebook/test_downloader.py"
+ "tests/utils/test_conda.py")))
+ (for-each delete-file network-tests))
#t)))))
(home-page "https://github.com/Anaconda-Platform/anaconda-client")
(synopsis "Anaconda Cloud command line client library")
--
2.39.2
H
python-anaconda-client and conda fail
(address . 63277@debbugs.gnu.org)
CA+Jv8O20DgGHqd7JwEcb77P3MouiTLw3M3LLj-cT7y+0CGKPEQ@mail.gmail.com
Sending the patches seems to have worked out just fine. Except that
number 2 got in my own spam folder.
I forgot that I also needed to update python-defusedxml to 0.7.1.
Using guix does feel a bit like a moving target. It is good to learn
how to fix such issues yourself, because they will pop-up often. The
Contributing section [1] of the manual is a good place to start.
Something unrelated: my desktop (gnome) looks sooo much sharper it
seems, so kudos to whoever improved that!
Cheers,
Hugo
H
(address . 63277@debbugs.gnu.org)
CA+Jv8O3_Zf4CEq6V87oZ96iLcS5OB33UVaaG-hMBfFc_TwdcQw@mail.gmail.com
The conda package seems to be fixed, and python-anaconda-client also
builds. So I think this can be closed.
On Mon, 8 May 2023 at 14:22, Hugo Buddelmeijer <hugo@buddelmeijer.nl> wrote:
Toggle quote (17 lines)
>
> Sending the patches seems to have worked out just fine. Except that
> number 2 got in my own spam folder.
>
> I forgot that I also needed to update python-defusedxml to 0.7.1.
>
> Using guix does feel a bit like a moving target. It is good to learn
> how to fix such issues yourself, because they will pop-up often. The
> Contributing section [1] of the manual is a good place to start.
>
> Something unrelated: my desktop (gnome) looks sooo much sharper it
> seems, so kudos to whoever improved that!
>
> Cheers,
> Hugo
>
> [1] https://guix.gnu.org/manual/en/html_node/Contributing.html
S
Re: bug#63277: python-anaconda-client and conda fail
87jzswhe9d.fsf@gmail.com
Closed
?