* [bug#48774] [PATCH] Fix build of python-scanpy
@ 2021-06-01 8:33 Roel Janssen
2021-06-04 11:54 ` Mathieu Othacehe
0 siblings, 1 reply; 3+ messages in thread
From: Roel Janssen @ 2021-06-01 8:33 UTC (permalink / raw)
To: 48774
[-- Attachment #1: Type: text/plain, Size: 346 bytes --]
Dear Guix,
The attached two patches update python-anndata and python-scanpy, which
effectively fix the build for python-scanpy.
python-anndata switched to a PEP518 setup instead of the regular Python
"setup.py" approach. So with some help on IRC, I added custom phases
inspired by the python-tinycss2 package.
Kind regards,
Roel Janssen
[-- Attachment #2: 0001-gnu-python-anndata-Update-to-0.7.6.patch --]
[-- Type: text/x-patch, Size: 3114 bytes --]
From 04527e305c96addea2c231b901758339e576d146 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Tue, 1 Jun 2021 10:20:10 +0200
Subject: [PATCH 1/2] gnu: python-anndata: Update to 0.7.6.
* gnu/packages/python-xyz.scm (python-anndata): Update to 0.7.6.
---
gnu/packages/python-xyz.scm | 35 +++++++++++++++++++++++++----------
1 file changed, 25 insertions(+), 10 deletions(-)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index a5cc04edaf..973123b385 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -21046,28 +21046,41 @@ N-dimensional arrays for Python.")
(define-public python-anndata
(package
(name "python-anndata")
- (version "0.7.1")
+ (version "0.7.6")
(source
(origin
(method url-fetch)
(uri (pypi-uri "anndata" version))
(sha256
(base32
- "0rnfbpr55j1a1bi2kd4mz444741hrn74kz90h5rnjr59jmpfnh09"))))
+ "1ch8yp0xmag6z0kl01pljm35lbbwax7lrimfhiclpkd4m6xngk53"))))
(build-system python-build-system)
(arguments
- `(#:phases
+ `(#:tests? #f ; The tarball from PyPi doesn't include tests.
+ #:phases
(modify-phases %standard-phases
- (add-after 'unpack 'delete-inconvenient-tests
- (lambda _
- ;; This test depends on python-scikit-learn.
- (delete-file "anndata/tests/test_inplace_subset.py")
- #t))
(delete 'check)
- (add-after 'install 'check
+ (add-before 'build 'relax-dependency-requirements
+ (lambda _
+ ;; We need to upgrade python-pandas to avoid
+ ;; https://github.com/pandas-dev/pandas/issues/35446
+ (substitute* "pyproject.toml"
+ (("pandas>=1.1.1") "pandas>=1.0.5"))))
+ (replace 'build
+ (lambda _
+ ;; ZIP does not support timestamps before 1980.
+ (setenv "SOURCE_DATE_EPOCH" "315532800")
+ (invoke "flit" "build")))
+ (replace 'install
(lambda* (#:key inputs outputs #:allow-other-keys)
(add-installed-pythonpath inputs outputs)
- (invoke "pytest" "-vv"))))))
+ (let ((out (assoc-ref outputs "out")))
+ (for-each (lambda (wheel)
+ (format #true wheel)
+ (invoke "python" "-m" "pip" "install"
+ wheel (string-append "--prefix=" out)))
+ (find-files "dist" "\\.whl$")))
+ #t)))))
(propagated-inputs
`(("python-h5py" ,python-h5py)
("python-importlib-metadata" ,python-importlib-metadata)
@@ -21080,6 +21093,8 @@ N-dimensional arrays for Python.")
(native-inputs
`(("python-joblib" ,python-joblib)
("python-pytest" ,python-pytest)
+ ("python-toml" ,python-toml)
+ ("python-flit" ,python-flit)
("python-setuptools-scm" ,python-setuptools-scm)))
(home-page "https://github.com/theislab/anndata")
(synopsis "Annotated data for data analysis pipelines")
--
2.31.1
[-- Attachment #3: 0002-gnu-python-scanpy-Update-to-1.7.2.patch --]
[-- Type: text/x-patch, Size: 3560 bytes --]
From 094705a4ee2c46e8ed1b98c39c03b2a21c688c5e Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Tue, 1 Jun 2021 10:25:12 +0200
Subject: [PATCH 2/2] gnu: python-scanpy: Update to 1.7.2.
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.7.2.
---
gnu/packages/bioinformatics.scm | 25 +++++++++++++++++++++----
1 file changed, 21 insertions(+), 4 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1f018befe6..2b64a04150 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -122,6 +122,7 @@
#:use-module (gnu packages popt)
#:use-module (gnu packages protobuf)
#:use-module (gnu packages python)
+ #:use-module (gnu packages python-build)
#:use-module (gnu packages python-check)
#:use-module (gnu packages python-compression)
#:use-module (gnu packages python-science)
@@ -11096,14 +11097,14 @@ in RNA-seq data.")
(define-public python-scanpy
(package
(name "python-scanpy")
- (version "1.4.6")
+ (version "1.7.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "scanpy" version))
(sha256
(base32
- "0s2b6cvaigx4wzw3850qb93sjwwxbzh22kpbp498zklc5rjpbz4l"))))
+ "0c66adnfizsyk0h8bv2yhmay876z0klpxwpn4z6m71wly7yplpmd"))))
(build-system python-build-system)
(arguments
`(#:phases
@@ -11114,12 +11115,25 @@ in RNA-seq data.")
(delete-file-recursively "scanpy/tests/notebooks")
(delete-file "scanpy/tests/test_clustering.py")
(delete-file "scanpy/tests/test_datasets.py")
+ (delete-file "scanpy/tests/test_highly_variable_genes.py")
;; TODO: I can't get the plotting tests to work, even with Xvfb.
(delete-file "scanpy/tests/test_plotting.py")
(delete-file "scanpy/tests/test_preprocessing.py")
(delete-file "scanpy/tests/test_read_10x.py")
+ ;; The following tests need anndata.tests, which aren't included
+ ;; in the final python-anndata package.
+ (delete-file "scanpy/tests/test_combat.py")
+ (delete-file "scanpy/tests/test_embedding_plots.py")
+ (delete-file "scanpy/tests/test_normalization.py")
+ (delete-file "scanpy/tests/test_pca.py")
+ (delete-file "scanpy/tests/external/test_scrublet.py")
+
+ ;; The following tests requires 'scanorama', which isn't
+ ;; packaged yet.
+ (delete-file "scanpy/tests/external/test_scanorama_integrate.py")
+
(setenv "PYTHONPATH"
(string-append (getcwd) ":"
(getenv "PYTHONPATH")))
@@ -11144,11 +11158,14 @@ in RNA-seq data.")
("python-seaborn" ,python-seaborn)
("python-statsmodels" ,python-statsmodels)
("python-tables" ,python-tables)
+ ("python-pytoml" ,python-pytoml)
("python-tqdm" ,python-tqdm)
("python-umap-learn" ,python-umap-learn)))
(native-inputs
- `(("python-pytest" ,python-pytest)
- ("python-setuptools-scm" ,python-setuptools-scm)))
+ `(("python-leidenalg" ,python-leidenalg)
+ ("python-pytest" ,python-pytest)
+ ("python-setuptools-scm" ,python-setuptools-scm)
+ ("python-sinfo" ,python-sinfo)))
(home-page "https://github.com/theislab/scanpy")
(synopsis "Single-Cell Analysis in Python.")
(description "Scanpy is a scalable toolkit for analyzing single-cell gene
--
2.31.1
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [bug#48774] [PATCH] Fix build of python-scanpy
2021-06-01 8:33 [bug#48774] [PATCH] Fix build of python-scanpy Roel Janssen
@ 2021-06-04 11:54 ` Mathieu Othacehe
2021-06-04 21:58 ` bug#48774: " Roel Janssen
0 siblings, 1 reply; 3+ messages in thread
From: Mathieu Othacehe @ 2021-06-04 11:54 UTC (permalink / raw)
To: Roel Janssen; +Cc: 48774
Hello Roel,
> The attached two patches update python-anndata and python-scanpy, which
> effectively fix the build for python-scanpy.
Both patches look fine to me.
Thanks,
Mathieu
^ permalink raw reply [flat|nested] 3+ messages in thread
* bug#48774: [PATCH] Fix build of python-scanpy
2021-06-04 11:54 ` Mathieu Othacehe
@ 2021-06-04 21:58 ` Roel Janssen
0 siblings, 0 replies; 3+ messages in thread
From: Roel Janssen @ 2021-06-04 21:58 UTC (permalink / raw)
To: Mathieu Othacehe; +Cc: 48774-done
Hi Mathieu,
On Fri, 2021-06-04 at 13:54 +0200, Mathieu Othacehe wrote:
>
> Hello Roel,
>
> > The attached two patches update python-anndata and python-scanpy,
> > which
> > effectively fix the build for python-scanpy.
>
> Both patches look fine to me.
>
Thanks for looking at them! I rebuilt python-scanpy with these patches
on the latest master, and pushed these patches.
Kind regards,
Roel Janssen
^ permalink raw reply [flat|nested] 3+ messages in thread
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2021-06-01 8:33 [bug#48774] [PATCH] Fix build of python-scanpy Roel Janssen
2021-06-04 11:54 ` Mathieu Othacehe
2021-06-04 21:58 ` bug#48774: " Roel Janssen
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