63/105: gnu: python-biom-format: Use pyproject-build-system.

2024-12-25 Thread guix-commits
rekado pushed a commit to branch python-team
in repository guix.

commit f14cd2968de31ca66d462bbabbff88b27f223498
Author: Ricardo Wurmus 
AuthorDate: Tue Dec 17 11:28:01 2024 +0100

gnu: python-biom-format: Use pyproject-build-system.

* gnu/packages/bioinformatics.scm (python-biom-format)[build-system]: Use
pyproject-build-system.
[arguments]: Replace phase 'disable-broken-tests with #:test-flags; enable 
one
test; add phase 'build-extensions.
[native-inputs]: Remove python-nose.

Change-Id: I8399d9b05bdb6da89d8056d536ab7e25dc22f9c2
---
 gnu/packages/bioinformatics.scm | 48 +
 1 file changed, 15 insertions(+), 33 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c10983cc2d..1a551dfdc7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3479,48 +3479,30 @@ use-case, we encourage users to compose functions to 
achieve their goals.")
;; Delete generated C files.
(snippet
 '(for-each delete-file (find-files "." "\\.c")
-(build-system python-build-system)
+(build-system pyproject-build-system)
 (arguments
  (list
+  #:test-flags
+  '(list "-k"
+ (string-append ;; Unclear why this one fails.  There is no 
backtrace.
+"not test_to_dataframe_is_sparse"
+;; These need skbio, but that neeeds biom-format.
+" and not test_align_tree_intersect_obs"
+" and not test_align_tree_intersect_tips"
+" and not test_align_tree_sample"))
   #:phases
   '(modify-phases %standard-phases
  (add-after 'unpack 'use-cython
(lambda _ (setenv "USE_CYTHON" "1")))
+ (add-before 'check 'build-extensions
+   (lambda _
+ ;; Cython extensions have to be built before running the tests.
+ (invoke "python" "setup.py" "build_ext" "--inplace")))
  (add-after 'unpack 'pandas-compatibility
(lambda _
  (substitute* "biom/tests/test_table.py"
(("import pandas.util.testing")
-"import pandas.testing"
- (add-after 'unpack 'disable-broken-tests
-   (lambda _
- (substitute* "biom/tests/test_util.py"
-   (("^(.+)def test_biom_open_hdf5_no_h5py" m indent)
-(string-append indent
-   "@npt.dec.skipif(True, msg='Guix')\n"
-   m)))
- (substitute* "biom/tests/test_table.py"
-   (("^(.+)def test_from_hdf5_issue_731" m indent)
-(string-append indent
-   "@npt.dec.skipif(True, msg='Guix')\n"
-   m))
-   ;; Unclear why this one fails.  There is no backtrace.
-   (("^(.+)def test_to_dataframe_is_sparse" m indent)
-(string-append indent
-   "@npt.dec.skipif(True, msg='Guix')\n"
-   m))
-   ;; These need skbio, but that neeeds biom-format.
-   (("^(.+)def test_align_tree_intersect_obs" m indent)
-(string-append indent
-   "@npt.dec.skipif(True, msg='Guix')\n"
-   m))
-   (("^(.+)def test_align_tree_intersect_tips" m indent)
-(string-append indent
-   "@npt.dec.skipif(True, msg='Guix')\n"
-   m))
-   (("^(.+)def test_align_tree_sample" m indent)
-(string-append indent
-   "@npt.dec.skipif(True, msg='Guix')\n"
-   m
+"import pandas.testing")))
 (propagated-inputs
  (list python-anndata
python-click
@@ -3532,7 +3514,7 @@ use-case, we encourage users to compose functions to 
achieve their goals.")
;;python-scikit-bio ;mutually recursive dependency
python-scipy))
 (native-inputs
- (list python-cython python-pytest python-pytest-cov python-nose))
+ (list python-cython python-pytest python-pytest-cov))
 (home-page "https://www.biom-format.org";)
 (synopsis "Biological Observation Matrix (BIOM) format utilities")
 (description



63/105: gnu: python-biom-format: Use pyproject-build-system.

2024-12-21 Thread guix-commits
rekado pushed a commit to branch python-team
in repository guix.

commit b45f3f4318efcdf398a8d98868cb4bb2f80fd4cf
Author: Ricardo Wurmus 
AuthorDate: Tue Dec 17 11:28:01 2024 +0100

gnu: python-biom-format: Use pyproject-build-system.

* gnu/packages/bioinformatics.scm (python-biom-format)[build-system]: Use
pyproject-build-system.
[arguments]: Replace phase 'disable-broken-tests with #:test-flags; enable 
one
test; add phase 'build-extensions.
[native-inputs]: Remove python-nose.

Change-Id: I8399d9b05bdb6da89d8056d536ab7e25dc22f9c2
---
 gnu/packages/bioinformatics.scm | 48 +
 1 file changed, 15 insertions(+), 33 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c10983cc2d..1a551dfdc7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3479,48 +3479,30 @@ use-case, we encourage users to compose functions to 
achieve their goals.")
;; Delete generated C files.
(snippet
 '(for-each delete-file (find-files "." "\\.c")
-(build-system python-build-system)
+(build-system pyproject-build-system)
 (arguments
  (list
+  #:test-flags
+  '(list "-k"
+ (string-append ;; Unclear why this one fails.  There is no 
backtrace.
+"not test_to_dataframe_is_sparse"
+;; These need skbio, but that neeeds biom-format.
+" and not test_align_tree_intersect_obs"
+" and not test_align_tree_intersect_tips"
+" and not test_align_tree_sample"))
   #:phases
   '(modify-phases %standard-phases
  (add-after 'unpack 'use-cython
(lambda _ (setenv "USE_CYTHON" "1")))
+ (add-before 'check 'build-extensions
+   (lambda _
+ ;; Cython extensions have to be built before running the tests.
+ (invoke "python" "setup.py" "build_ext" "--inplace")))
  (add-after 'unpack 'pandas-compatibility
(lambda _
  (substitute* "biom/tests/test_table.py"
(("import pandas.util.testing")
-"import pandas.testing"
- (add-after 'unpack 'disable-broken-tests
-   (lambda _
- (substitute* "biom/tests/test_util.py"
-   (("^(.+)def test_biom_open_hdf5_no_h5py" m indent)
-(string-append indent
-   "@npt.dec.skipif(True, msg='Guix')\n"
-   m)))
- (substitute* "biom/tests/test_table.py"
-   (("^(.+)def test_from_hdf5_issue_731" m indent)
-(string-append indent
-   "@npt.dec.skipif(True, msg='Guix')\n"
-   m))
-   ;; Unclear why this one fails.  There is no backtrace.
-   (("^(.+)def test_to_dataframe_is_sparse" m indent)
-(string-append indent
-   "@npt.dec.skipif(True, msg='Guix')\n"
-   m))
-   ;; These need skbio, but that neeeds biom-format.
-   (("^(.+)def test_align_tree_intersect_obs" m indent)
-(string-append indent
-   "@npt.dec.skipif(True, msg='Guix')\n"
-   m))
-   (("^(.+)def test_align_tree_intersect_tips" m indent)
-(string-append indent
-   "@npt.dec.skipif(True, msg='Guix')\n"
-   m))
-   (("^(.+)def test_align_tree_sample" m indent)
-(string-append indent
-   "@npt.dec.skipif(True, msg='Guix')\n"
-   m
+"import pandas.testing")))
 (propagated-inputs
  (list python-anndata
python-click
@@ -3532,7 +3514,7 @@ use-case, we encourage users to compose functions to 
achieve their goals.")
;;python-scikit-bio ;mutually recursive dependency
python-scipy))
 (native-inputs
- (list python-cython python-pytest python-pytest-cov python-nose))
+ (list python-cython python-pytest python-pytest-cov))
 (home-page "https://www.biom-format.org";)
 (synopsis "Biological Observation Matrix (BIOM) format utilities")
 (description