From unknown Sun Aug 17 01:51:24 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#48774] [PATCH] Fix build of python-scanpy Resent-From: Roel Janssen Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 01 Jun 2021 08:35:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 48774 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 48774@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.16225364419187 (code B ref -1); Tue, 01 Jun 2021 08:35:01 +0000 Received: (at submit) by debbugs.gnu.org; 1 Jun 2021 08:34:01 +0000 Received: from localhost ([127.0.0.1]:35714 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lnzqQ-0002Ng-Oj for submit@debbugs.gnu.org; Tue, 01 Jun 2021 04:34:01 -0400 Received: from lists.gnu.org ([209.51.188.17]:57512) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lnzqI-0002NQ-8g for submit@debbugs.gnu.org; Tue, 01 Jun 2021 04:33:48 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:36986) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lnzqI-0003xu-2E for guix-patches@gnu.org; Tue, 01 Jun 2021 04:33:42 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:50288) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lnzqH-0008U6-RT for guix-patches@gnu.org; Tue, 01 Jun 2021 04:33:41 -0400 Received: from [143.121.198.253] (port=37750) by fencepost.gnu.org with esmtpsa (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lnzqG-0004Gx-Fr for guix-patches@gnu.org; Tue, 01 Jun 2021 04:33:41 -0400 From: Roel Janssen Message-ID: <4ee322e7-2aaf-750a-bee7-4bbc8d7bd64b@gnu.org> Date: Tue, 1 Jun 2021 10:33:34 +0200 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:78.0) Gecko/20100101 Thunderbird/78.8.1 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="------------C74DDF4A038D59D606F47B56" Content-Language: en-US X-Spam-Score: -2.3 (--) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) This is a multi-part message in MIME format. --------------C74DDF4A038D59D606F47B56 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit 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 --------------C74DDF4A038D59D606F47B56 Content-Type: text/x-patch; charset=UTF-8; name="0001-gnu-python-anndata-Update-to-0.7.6.patch" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="0001-gnu-python-anndata-Update-to-0.7.6.patch" >From 04527e305c96addea2c231b901758339e576d146 Mon Sep 17 00:00:00 2001 From: Roel Janssen 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 --------------C74DDF4A038D59D606F47B56 Content-Type: text/x-patch; charset=UTF-8; name="0002-gnu-python-scanpy-Update-to-1.7.2.patch" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="0002-gnu-python-scanpy-Update-to-1.7.2.patch" >From 094705a4ee2c46e8ed1b98c39c03b2a21c688c5e Mon Sep 17 00:00:00 2001 From: Roel Janssen 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 --------------C74DDF4A038D59D606F47B56-- From unknown Sun Aug 17 01:51:24 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#48774] [PATCH] Fix build of python-scanpy Resent-From: Mathieu Othacehe Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 04 Jun 2021 11:55:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 48774 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Roel Janssen Cc: 48774@debbugs.gnu.org Received: via spool by 48774-submit@debbugs.gnu.org id=B48774.162280767921718 (code B ref 48774); Fri, 04 Jun 2021 11:55:01 +0000 Received: (at 48774) by debbugs.gnu.org; 4 Jun 2021 11:54:39 +0000 Received: from localhost ([127.0.0.1]:45661 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lp8PP-0005eD-8M for submit@debbugs.gnu.org; Fri, 04 Jun 2021 07:54:39 -0400 Received: from eggs.gnu.org ([209.51.188.92]:47904) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lp8PN-0005e1-He for 48774@debbugs.gnu.org; Fri, 04 Jun 2021 07:54:37 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:57022) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lp8PI-0007XI-97 for 48774@debbugs.gnu.org; Fri, 04 Jun 2021 07:54:32 -0400 Received: from [2a01:e0a:19b:d9a0:45b5:a14a:5c75:5737] (port=52112 helo=meije) by fencepost.gnu.org with esmtpsa (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lp8PH-0001M9-Pn; Fri, 04 Jun 2021 07:54:32 -0400 From: Mathieu Othacehe References: <4ee322e7-2aaf-750a-bee7-4bbc8d7bd64b@gnu.org> Date: Fri, 04 Jun 2021 13:54:29 +0200 In-Reply-To: <4ee322e7-2aaf-750a-bee7-4bbc8d7bd64b@gnu.org> (Roel Janssen's message of "Tue, 1 Jun 2021 10:33:34 +0200") Message-ID: <87tumdetfu.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/27.2 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: -2.3 (--) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) 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 From unknown Sun Aug 17 01:51:24 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: Roel Janssen Subject: bug#48774: closed (Re: bug#48774: [PATCH] Fix build of python-scanpy) Message-ID: References: <4ee322e7-2aaf-750a-bee7-4bbc8d7bd64b@gnu.org> X-Gnu-PR-Message: they-closed 48774 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 48774@debbugs.gnu.org Date: Fri, 04 Jun 2021 21:59:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1622843942-9952-1" This is a multi-part message in MIME format... ------------=_1622843942-9952-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #48774: [PATCH] Fix build of python-scanpy which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 48774@debbugs.gnu.org. --=20 48774: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D48774 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1622843942-9952-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 48774-done) by debbugs.gnu.org; 4 Jun 2021 21:58:23 +0000 Received: from localhost ([127.0.0.1]:47989 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lpHpe-0002ZW-PT for submit@debbugs.gnu.org; Fri, 04 Jun 2021 17:58:22 -0400 Received: from eggs.gnu.org ([209.51.188.92]:60558) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lpHpa-0002Z9-Ea for 48774-done@debbugs.gnu.org; Fri, 04 Jun 2021 17:58:21 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:56862) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lpHpV-0007pT-5U for 48774-done@debbugs.gnu.org; Fri, 04 Jun 2021 17:58:13 -0400 Received: from 2001-1c02-0b21-6200-c9cf-5ac8-4ac9-c58e.cable.dynamic.v6.ziggo.nl ([2001:1c02:b21:6200:c9cf:5ac8:4ac9:c58e]:54656) by fencepost.gnu.org with esmtpsa (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lpHpU-00037t-Ry; Fri, 04 Jun 2021 17:58:13 -0400 Message-ID: Subject: Re: bug#48774: [PATCH] Fix build of python-scanpy From: Roel Janssen To: Mathieu Othacehe Date: Fri, 04 Jun 2021 23:58:09 +0200 In-Reply-To: <87tumdetfu.fsf@gnu.org> References: <4ee322e7-2aaf-750a-bee7-4bbc8d7bd64b@gnu.org> <87tumdetfu.fsf@gnu.org> Content-Type: text/plain; charset="UTF-8" User-Agent: Evolution 3.40.1 (3.40.1-1.fc34) MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 48774-done Cc: 48774-done@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) 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 ------------=_1622843942-9952-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 1 Jun 2021 08:34:01 +0000 Received: from localhost ([127.0.0.1]:35714 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lnzqQ-0002Ng-Oj for submit@debbugs.gnu.org; Tue, 01 Jun 2021 04:34:01 -0400 Received: from lists.gnu.org ([209.51.188.17]:57512) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lnzqI-0002NQ-8g for submit@debbugs.gnu.org; Tue, 01 Jun 2021 04:33:48 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:36986) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lnzqI-0003xu-2E for guix-patches@gnu.org; Tue, 01 Jun 2021 04:33:42 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:50288) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lnzqH-0008U6-RT for guix-patches@gnu.org; Tue, 01 Jun 2021 04:33:41 -0400 Received: from [143.121.198.253] (port=37750) by fencepost.gnu.org with esmtpsa (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lnzqG-0004Gx-Fr for guix-patches@gnu.org; Tue, 01 Jun 2021 04:33:41 -0400 To: guix-patches@gnu.org From: Roel Janssen Subject: [PATCH] Fix build of python-scanpy Message-ID: <4ee322e7-2aaf-750a-bee7-4bbc8d7bd64b@gnu.org> Date: Tue, 1 Jun 2021 10:33:34 +0200 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:78.0) Gecko/20100101 Thunderbird/78.8.1 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="------------C74DDF4A038D59D606F47B56" Content-Language: en-US X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: submit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) This is a multi-part message in MIME format. --------------C74DDF4A038D59D606F47B56 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit 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 --------------C74DDF4A038D59D606F47B56 Content-Type: text/x-patch; charset=UTF-8; name="0001-gnu-python-anndata-Update-to-0.7.6.patch" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="0001-gnu-python-anndata-Update-to-0.7.6.patch" >From 04527e305c96addea2c231b901758339e576d146 Mon Sep 17 00:00:00 2001 From: Roel Janssen 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 --------------C74DDF4A038D59D606F47B56 Content-Type: text/x-patch; charset=UTF-8; name="0002-gnu-python-scanpy-Update-to-1.7.2.patch" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="0002-gnu-python-scanpy-Update-to-1.7.2.patch" >From 094705a4ee2c46e8ed1b98c39c03b2a21c688c5e Mon Sep 17 00:00:00 2001 From: Roel Janssen 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 --------------C74DDF4A038D59D606F47B56-- ------------=_1622843942-9952-1--