~ruther/guix-local

940fd33cad2a8b66c6065bb466007f4502d6a1e3 — Sharlatan Hellseher 4 months ago c94d575 
gnu: python-cellbender: Update to 0.3.2.

* gnu/packages/bioinformatics.scm (python-cellbender): Update to 0.3.2.
[arguments] <phases>: Add 'relax-requirements.
[propagated-inputs]: Remove python-scikit-learn, python-sphinx,
python-sphinx-argparse, python-sphinx-autodoc-typehints,
python-sphinx-rtd-theme, and python-sphinxcontrib-programoutput; add
python-loompy, python-lxml-html-clean, python-nbconvert,
python-notebook, python-psutil, and python-pytorch.
[native-inputs]: Add python-setuptools.

Change-Id: I79473da4ca33b648fd9bd19f21dc91edb4a12cc3
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
patch browse .tar.gz 
1 files changed, 24 insertions(+), 11 deletions(-)

M gnu/packages/bioinformatics.scm

M gnu/packages/bioinformatics.scm => gnu/packages/bioinformatics.scm +24 -11
@@ 2496,33 2496,46 @@ cell types.  Cell2cell is suitable for single-cell RNA sequencing
(define-public python-cellbender
  (package
    (name "python-cellbender")
    (version "0.2.2")
    (version "0.3.2")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/broadinstitute/CellBender")
             (commit (string-append "v" version))))
              (url "https://github.com/broadinstitute/CellBender")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "0h9d9pznffdbya631hkk7b7jwjrgx5saqssar1d42qbyvdji3hgy"))))
         "1sdw4dv881ll8ylxcp06xa74c3wvrdyzpwfilzk8i1pwgrdrgb3f"))))
    (build-system pyproject-build-system)
    (arguments
     (list #:tests? #false)) ;there are none
     (list
      #:tests? #f ;there are none
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'relax-requirements
            (lambda _
              ;; See:
              ;; <https://github.com/broadinstitute/CellBender/issues/426>,
              ;; <https://github.com/broadinstitute/CellBender/issues/416>.
              (substitute* "requirements.txt"
                (("(notebook|ipython|jupyter.*)")"")
                (("<.*") "\n")))))))
    (native-inputs
     (list python-setuptools))
    (propagated-inputs
     (list python-anndata
           python-loompy
           python-lxml-html-clean
           python-matplotlib
           python-nbconvert
           python-notebook
           python-numpy
           python-pandas
           python-psutil
           python-pyro-ppl
           python-scikit-learn
           python-pytorch
           python-scipy
           python-sphinx
           python-sphinx-argparse
           python-sphinx-autodoc-typehints
           python-sphinx-rtd-theme
           python-sphinxcontrib-programoutput
           python-tables))
    (home-page "https://cellbender.rtfd.io/")
    (synopsis "Eliminate technical artifacts from single-cell RNA-seq data")