bug#63277: python-anaconda-client and conda fail

bug#63277: python-anaconda-client and conda fail

[Etienne B. Roesch]

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Hi,

I am new to guix, but it looks like both python-anaconda-client and conda
fail to build, as ci.guix also confirms. I wish I could readily help, but I
am really new to this :)

Etienne

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bug#63277: python-anaconda-client and conda fail

[Hugo Buddelmeijer]

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

[1] https://guix.gnu.org/manual/en/html_node/Sending-a-Patch-Series.html

bug#63277: [PATCH 1/5] gnu: Add python-conda-package-streaming.

[Hugo Buddelmeijer]

* gnu/packages/python-xyz.scm (python-conda-package-streaming): New variable.
---
 gnu/packages/python-xyz.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

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

bug#63277: [PATCH 2/5] gnu: python-conda-package-handling: Update to 2.1.0

[Hugo Buddelmeijer]

* 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(-)

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

bug#63277: [PATCH 3/5] gnu: conda: Remove python-anaconda-client dependency.

[Hugo Buddelmeijer]

* gnu/packages/package-management.scm (conda): Remove python-anaconda-client dependency.
---
 gnu/packages/package-management.scm | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

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

bug#63277: [PATCH 4/5] gnu: python-defusedxml: Update to 0.7.1.

[Hugo Buddelmeijer]

* gnu/packages/xml.scm (defused-python): Update to 0.7.1.
---
 gnu/packages/xml.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

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

bug#63277: [PATCH 5/5] gnu: python-anaconda-client: Update to 1.11.2

[Hugo Buddelmeijer]

* 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(-)

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

bug#63277: python-anaconda-client and conda fail

[Hugo Buddelmeijer]

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

bug#63277: python-anaconda-client and conda fail

[Hugo Buddelmeijer]

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:
>
> 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

bug#63277: python-anaconda-client and conda fail

[Simon Tournier]

Hi,

On Mon, 11 Sep 2023 at 10:08, Hugo Buddelmeijer <hugo@buddelmeijer.nl> wrote:

> The conda package seems to be fixed, and python-anaconda-client also
> builds. So I think this can be closed.

Thanks for the follow-up.  I am closing.

Feel free to reopen if I misread.

Cheers,
simon