~ruther/guix-local: gnu: python-metacells: Simplify.

9d51f4ba0136a2914a3eb98f3e09d6551cecb76b — Sharlatan Hellseher 2 months ago bbc241a

gnu: python-metacells: Simplify.

* gnu/packages/bioinformatics.scm (python-metacells):
[arguments] <phases>: Merge 'set-numba-cache-dir and 'build-extension
into 'pre-check and just remove local source to prevent rebuilding
expansions for tests, it saves some compute time with the same output.
[native-inputs]: Add pybind11.

Change-Id: I95e6706813cc5d3167593440c714c5091303cb00
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

patch browse .tar.gz

1 files changed, 5 insertions(+), 6 deletions(-)

M gnu/packages/bioinformatics.scm

M gnu/packages/bioinformatics.scm => gnu/packages/bioinformatics.scm +5 -6

@@ 3259,12 3259,11 @@ and gene expression visualization.")
             (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
+          (add-before 'check 'pre-check
             (lambda _
-              (invoke "python" "setup.py" "build_ext" "--inplace"))))))
+              ;; Numba needs a writable dir to cache functions.
+              (setenv "NUMBA_CACHE_DIR" "/tmp")
+              (delete-file-recursively "metacells"))))))
     (propagated-inputs (list python-anndata
                              python-cvxpy
                              python-fastcluster


@@ 3278,7 3277,7 @@ and gene expression visualization.")
                              python-scipy
                              python-threadpoolctl
                              python-umap-learn))
-    (native-inputs (list python-pytest python-setuptools))
+    (native-inputs (list pybind11 python-pytest python-setuptools))
     (home-page "https://github.com/tanaylab/metacells.git")
     (synopsis "Single-cell RNA Sequencing Analysis")
     (description "The metacells package implements the improved metacell