256/397: gnu: instrain: Update to 1.9.0.

[guix-commits]

rekado pushed a commit to branch python-team
in repository guix.

commit 005b38aa812c5252b5ccf320a1a205af05607ed5
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Sun Jan 12 12:52:34 2025 +0100

    gnu: instrain: Update to 1.9.0.
    
    * gnu/packages/bioinformatics.scm (instrain): Update to 1.9.0.
    [source]: Fetch git repository.
    [build-system]: Use pyproject-build-system.
    [arguments]: Disable tests.
    [inputs]: Move all from here...
    [propagated-inputs]: ...to here; remove python-boto3, python-numba,
    python-scikit-learn, and python-drep.
    [native-inputs]: Add python-boto3, python-setuptools, and python-wheel.
    
    Change-Id: Ied1e909a6b22518908b95a43b8db5f35bd6c6ac6
---
 gnu/packages/bioinformatics.scm | 40 +++++++++++++++++++++++++---------------
 1 file changed, 25 insertions(+), 15 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c872801fe1..6ab1449d27 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -19028,44 +19028,54 @@ set.")
 (define-public instrain
   (package
     (name "instrain")
-    (version "1.5.4")
+    (version "1.9.0")
     (source
      (origin
-       (method url-fetch)
-       (uri (pypi-uri "inStrain" version))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/MrOlm/instrain";)
+             ;; There are no tags.
+             (commit "168f3f777b45139a9f6099f68974105b45e2d8ba")))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "05w1lw75x4lwkzg4qpi055g7hdjp9rnc4ksbxg2hfgksq9djk0hx"))))
-    (build-system python-build-system)
+         "1wc69ggyiacm1slb678239lqmf1g5dlb4alwsbp14gi6393gj9fg"))))
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
+     (list
+      ;; Tests assume that test files exist (they don't) and are located in
+      ;; the developer's home directory.
+      #:tests? #false
+      #:phases
+      '(modify-phases %standard-phases
          (add-after 'unpack 'patch-relative-imports
            (lambda _
+             (substitute* (find-files "test/tests" "test_.*\\.py")
+               (("from test_utils import BTO")
+                "from .test_utils import BTO")
+               (("import test_utils") "from . import test_utils"))
              (substitute* "docker/run_instrain.py"
                (("from s3_utils")
                 "from .s3_utils")
                (("from job_utils")
                 "from .job_utils")))))))
-    (inputs
+    (propagated-inputs
      (list python-biopython-1.73
-           python-boto3
            python-h5py
            python-lmfit
            python-matplotlib
            python-networkx
-           python-numba
            python-numpy
            python-pandas
            python-psutil
            python-pysam
-           python-scikit-learn
            python-seaborn
-           python-tqdm
-           ;; drep is needed for deprecated plot utilities
-           python-drep))
+           python-tqdm))
     (native-inputs
-     (list python-pytest))
+     (list python-boto3
+           python-pytest
+           python-setuptools
+           python-wheel))
     (home-page "https://github.com/MrOlm/inStrain";)
     (synopsis "Calculation of strain-level metrics")
     (description