rekado pushed a commit to branch wip-python-team
in repository guix.
commit 854c42e30c3e8a9828278abada23473c370e689f
Author: Marco Baggio <[email protected]>
AuthorDate: Mon Apr 29 15:16:29 2024 +0200
gnu: Add python-metacells.
* gnu/packages/bioinformatics.scm (python-metacells): New variable.
Co-authored-by: Ricardo Wurmus <[email protected]>
Change-Id: I4fc760dc4317bde79c815f441ad0cc453248990a
---
gnu/packages/bioinformatics.scm | 69 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 69 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index aa6bce5591..907c3ee548 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2333,6 +2333,75 @@ provides data pre-processing functionality such as
dimensionality reduction
and gene expression visualization.")
(license license:gpl2+)))
+(define-public python-metacells
+ (package
+ (name "python-metacells")
+ (version "0.9.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "metacells" version))
+ (sha256
+ (base32 "02f63nxz6b60vl6s4n9vapaysnq1w5f3x7c179rh2rr7j2k5cf1y"))))
+ #;
+ (properties '((tunable? . #t)))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ ;; The package "python-igraph" has been deprecated in favor of
+ ;; just "igraph".
+ (add-after 'unpack 'rename-igraph
+ (lambda _
+ (substitute* "requirements.txt"
+ (("python-igraph") "igraph"))))
+ (add-after 'unpack 'do-not-tune
+ (lambda _
+ ;; Without this they pass -march=native to the compiler.
+ (setenv "WHEEL" "1")))
+ ;; Numba needs a writable dir to cache functions.
+ (add-before 'check 'set-numba-cache-dir
+ (lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp")))
+ (add-before 'build 'build-extensions
+ (lambda _
+ (invoke "python" "setup.py" "build_ext" "--inplace"))))))
+ (propagated-inputs (list python-anndata
+ python-cvxpy
+ python-fastcluster
+ python-importlib-metadata
+ python-numpy
+ python-pandas
+ python-psutil
+ python-igraph
+ python-pyyaml
+ python-scanpy
+ python-scipy
+ python-threadpoolctl
+ python-umap-learn))
+ (native-inputs (list python-black
+ python-bumpversion
+ python-flake8
+ python-isort
+ python-mypy
+ python-mypy-extensions
+ python-pylint
+ python-pytest
+ python-pytest-cov
+ python-sphinx
+ python-sphinx-rtd-theme
+ python-tox
+ python-twine))
+ (home-page "https://github.com/tanaylab/metacells.git";)
+ (synopsis "Single-cell RNA Sequencing Analysis")
+ (description "The metacells package implements the improved metacell
+algorithm for single-cell RNA sequencing (scRNA-seq) data analysis within the
+scipy framework, and projection algorithm based on it. The original metacell
+algorithm was implemented in R. The Python package contains various
+algorithmic improvements and is scalable for larger data sets (millions of
+cells).")
+ (license license:expat)))
+
(define-public python-parabam
(package
(name "python-parabam")
