[bug#60009] Update python-graphviz and other Python updates.

[bug#60009] Update python-graphviz and other Python updates.

[Ricardo Wurmus]

This patch series updates some bioinformatics packages.  In doing so it
has to touch python-graphviz, which leads to a large number of rebuilds.

-- 
Ricardo

[bug#60009] [PATCH 01/18] gnu: python-graphviz: Update to 0.20.1.

[Ricardo Wurmus]

* gnu/packages/graphviz.scm (python-graphviz): Update to 0.20.1.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom "check" phase; add "prepare-check" phase.
[native-inputs]: Remove python-mock.
---
 gnu/packages/graphviz.scm | 23 +++++++++++------------
 1 file changed, 11 insertions(+), 12 deletions(-)

diff --git a/gnu/packages/graphviz.scm b/gnu/packages/graphviz.scm
index 51c1de3932..7c2cb1eae0 100644
--- a/gnu/packages/graphviz.scm
+++ b/gnu/packages/graphviz.scm
@@ -2,7 +2,7 @@
 ;;; Copyright © 2013, 2015, 2021 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2015, 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Theodoros Foradis <theodoros@foradis.org>
-;;; Copyright © 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2017, 2018, 2019, 2022 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Gábor Boskovits <boskovits@gmail.com>
 ;;; Copyright © 2018 Mathieu Lirzin <mthl@gnu.org>
@@ -32,6 +32,7 @@
 (define-module (gnu packages graphviz)
   #:use-module (guix packages)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system pyproject)
   #:use-module (guix build-system python)
   #:use-module (guix download)
   #:use-module (guix git-download)
@@ -180,27 +181,25 @@ (define-public graphviz-2.38
 (define-public python-graphviz
   (package
     (name "python-graphviz")
-    (version "0.13.2")
+    (version "0.20.1")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "graphviz" version ".zip"))
               (sha256
                (base32
-                "009alrilzx0v7kl41khbq7k6k8b8pxyvbsi1b1ai933f6kpbxb30"))))
-    (build-system python-build-system)
+                "1y1b956r01kg7qarkkrivhn71q64k0gbq6bcybd4gfd3v95g2n4c"))))
+    (build-system pyproject-build-system)
     (arguments
-     '(#:phases (modify-phases %standard-phases
-                  (replace 'check
-                    (lambda* (#:key tests #:allow-other-keys)
-                      (if tests
-                          (invoke "pytest" "-vv")
-                          (format #t "test suite not run~%"))
-                      #t)))))
+     (list
+      #:phases
+      '(modify-phases %standard-phases
+         (add-before 'check 'prepare-chec
+           ;; Needed for fontconfig cache directories
+           (lambda _ (setenv "HOME" (getcwd)))))))
     (native-inputs
      (list unzip
            ;; For tests.
            graphviz
-           python-mock
            python-pytest
            python-pytest-cov
            python-pytest-mock))
-- 
2.36.1

[bug#60009] [PATCH 02/18] gnu: python-hyperopt: Update to 0.2.7.

[Ricardo Wurmus]

* gnu/packages/machine-learning.scm (python-hyperopt): Update to 0.2.7.
[arguments]: Adjust check phase; disable test_distribution_rvs test.
[build-system]: Use pyproject-build-system.
[propagated-inputs]: Add python-py4j.
[native-inputs]: Remove python-ipython and python-ipyparallel.
---
 gnu/packages/machine-learning.scm | 36 ++++++++++++++++---------------
 1 file changed, 19 insertions(+), 17 deletions(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index fc8de01066..3dbe54a24a 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1552,35 +1552,39 @@ (define-public vowpal-wabbit
 (define-public python-hyperopt
   (package
     (name "python-hyperopt")
-    (version "0.2.5")
+    (version "0.2.7")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "hyperopt" version))
        (sha256
-        (base32 "1k4ma8ci0bxghw7g4ms944zak1pi83yv2d6bxd7fcslm1zalfq5w"))))
-    (build-system python-build-system)
+        (base32 "0jd1ghmm423kbhjvd6pxq92y5vkz25390687fcnd7fshh3jrmy0v"))))
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
+     (list
+      #:phases
+      '(modify-phases %standard-phases
          (replace 'check
-           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+           (lambda* (#:key tests? #:allow-other-keys)
              (when tests?
-               (add-installed-pythonpath inputs outputs)
-               (invoke "python" "-m" "pytest" "--ignore"
+               (invoke "python" "-m" "pytest"
                        ;; Needs python-pyspark.
-                       "hyperopt/tests/test_spark.py"
+                       "--ignore" "hyperopt/tests/integration/test_spark.py"
                        ;; Needs both python-scikit-learn and python-lightgbm.
-                       "--ignore" "hyperopt/tests/test_atpe_basic.py"
+                       "--ignore" "hyperopt/tests/unit/test_atpe_basic.py"
                        ;; The tests below need python-lightgbm.
-                       "-k" (string-append "not test_branin"
-                                           " and not test_distractor"
-                                           " and not test_q1lognormal"
-                                           " and not test_quadratic1"
-                                           " and not test_twoarms"))))))))
+                       "-k"
+                       (string-append "not test_branin"
+                                      " and not test_distractor"
+                                      " and not test_q1lognormal"
+                                      " and not test_quadratic1"
+                                      " and not test_twoarms"
+                                      ;; XXX Type error with this version of scipy
+                                      " and not test_distribution_rvs"))))))))
     (propagated-inputs
      (list python-cloudpickle
            python-future
+           python-py4j
            python-networkx
            python-numpy
            python-scipy
@@ -1588,8 +1592,6 @@ (define-public python-hyperopt
            python-tqdm))
     (native-inputs
      (list python-black
-           python-ipython
-           python-ipyparallel
            python-nose
            python-pymongo
            python-pytest))
-- 
2.36.1

[bug#60009] [PATCH 03/18] gnu: python-biopython: Update to 1.80.

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.80.
[build-system]: Use pyproject-build-system.
[arguments]: Remove trailing #T from build phase.
---
 gnu/packages/bioinformatics.scm | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 207f3c3d28..52abe152ee 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1237,21 +1237,21 @@ (define-public perl-bio-db-hts
 (define-public python-biopython
   (package
     (name "python-biopython")
-    (version "1.76")
+    (version "1.80")
     (source (origin
               (method url-fetch)
               ;; use PyPi rather than biopython.org to ease updating
               (uri (pypi-uri "biopython" version))
               (sha256
                (base32
-                "0wlch9xpa0fpgjzyxi6jsfca6iakaq9a05927xg8vqnmvaccnwrq"))))
-    (build-system python-build-system)
+                "0hqf3jsxn2sphcx81fx7x3i69sarpjsi70fzw98f8rw7z2d5x02j"))))
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
+     '(#:phases
        (modify-phases %standard-phases
          (add-before 'check 'set-home
            ;; Some tests require a home directory to be set.
-           (lambda _ (setenv "HOME" "/tmp") #t)))))
+           (lambda _ (setenv "HOME" "/tmp"))))))
     (propagated-inputs
      (list python-numpy))
     (home-page "https://biopython.org/")
-- 
2.36.1

[bug#60009] [PATCH 04/18] gnu: python-hicmatrix: Update to 16.

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 16.
[build-system]: Use pyproject-build-system.
[arguments]: Shuffle the quote.
---
 gnu/packages/bioinformatics.scm | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 52abe152ee..82801e7eeb 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13373,7 +13373,7 @@ (define-public python-cooltools
 (define-public python-hicmatrix
   (package
     (name "python-hicmatrix")
-    (version "15")
+    (version "16")
       (source
         (origin
           ;;Pypi sources do not contain any test
@@ -13384,11 +13384,12 @@ (define-public python-hicmatrix
           (file-name (git-file-name name version))
           (sha256
             (base32
-             "1dshjxgb16sdfg9k1bhw2yhyngac04k4ca7aqy8g3i3pprr068r5"))))
-    (build-system python-build-system)
+             "00b9l62j4knrsdp7l3pawi9cqcsl09diycbhmmnar850bzssmq4f"))))
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
+     (list
+      #:phases
+      '(modify-phases %standard-phases
          (replace 'check
            (lambda* (#:key tests? #:allow-other-keys)
              (when tests?
-- 
2.36.1

[bug#60009] [PATCH 05/18] gnu: python-pygenometracks: Update to 3.5.

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm (python-pygenometracks): Update to 3.5.
[build-system]: Use pyproject-build-system.
[arguments]: Quote phases instead of full list of arguments; remove trailing #T
from build phase.
---
 gnu/packages/bioinformatics.scm | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 82801e7eeb..e6a8789ea6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13466,25 +13466,25 @@ (define-public python-hicexplorer
 (define-public python-pygenometracks
   (package
     (name "python-pygenometracks")
-    (version "3.3")
+    (version "3.5")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pyGenomeTracks" version))
        (sha256
         (base32
-         "16laa0wnf4qn9fb9ych4w1vqhqwjss70v0y0f6wp4gwqfrlgac0f"))))
-    (build-system python-build-system)
+         "1l7smg2gc1vm2181lzmdnywb11gp6s6z6j444dbsigv65car8z8p"))))
+    (build-system pyproject-build-system)
     (arguments
-     `(#:tests? #f ; there are none
-       #:phases
-       (modify-phases %standard-phases
+     (list
+      #:tests? #f                       ;there are none
+      #:phases
+      '(modify-phases %standard-phases
          (add-after 'unpack 'relax-requirements
            (lambda _
              (substitute* "setup.py"
                (("matplotlib ==3.1.1")
-                "matplotlib >=3.1.1"))
-             #t)))))
+                "matplotlib >=3.1.1")))))))
     (propagated-inputs
      (list python-future
            python-gffutils
-- 
2.36.1

[bug#60009] [PATCH 06/18] gnu: python-hicexplorer: Update to 3.7.2.

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm (python-hicexplorer): Update to 3.7.2.
[build-system]: Use pyproject-build-system.
[arguments]: Use gexp; remove phase "loosen-up-requirements"; add test-flags
to skip some tests; add phase "remove-dependency-on-krbalancing" to remove a
dependency on an unlicensed package; add phase "fix-references"; add phase
"run-only-low-mem-tests".
[propagated-inputs]: Remove python-configparser and python-six; add
python-biopython, python-cleanlab-1, python-fit-nbinom, python-graphviz,
python-hic2cool, python-hicmatrix, python-hyperopt, python-imbalanced-learn,
python-ipykernel, python-psutil, python-pybedtools, python-pygenometracks,
python-scikit-learn, and python-tqdm.
[native-inputs]: Add graphviz.
---
 gnu/packages/bioinformatics.scm | 106 ++++++++++++++++++++++++++++----
 1 file changed, 94 insertions(+), 12 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e6a8789ea6..ea33311a2c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13413,7 +13413,7 @@ (define-public python-hicmatrix
 (define-public python-hicexplorer
   (package
     (name "python-hicexplorer")
-    (version "2.1.4")
+    (version "3.7.2")
     (source
      (origin
        ;; The latest version is not available on Pypi.
@@ -13424,32 +13424,114 @@ (define-public python-hicexplorer
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0q5gpbzmrkvygqgw524q36b4nrivcmyi5v194vsx0qw7b3gcmq08"))))
-    (build-system python-build-system)
+         "1yavgxry38g326z10bclvdf8glmma05fxj5m73h15m1r2l9xmw3v"))))
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'loosen-up-requirements
-           (lambda _
-             (substitute* "setup.py"
-               (("==") ">="))
-             #t)))))
+     (list
+      #:test-flags
+      '(list "hicexplorer/test/general/"
+             "--ignore" "hicexplorer/test/general/test_hicTADClassifier.py"
+             "--ignore" "hicexplorer/test/general/test_hicTrainTADClassifier.py"
+             "-k"
+             (string-append
+              ;; Unknown chromosome: ChrX
+              "not test_build_matrix_restrictionCutFile_two"
+              ;; fixture 'keepSelfLigation' not found
+              " and not test_build_matrix_restrictionCutFile_six"
+              ;; ValueError: object dtype is not supported by sparse matrices
+              " and not test_hic_transfer_obs_exp_perChromosome"
+
+              ;; No KR balancing available
+              " and not test_correct_matrix_KR_partial_cool"
+              " and not test_correct_matrix_KR_cool"
+              " and not test_correct_matrix_KR_H5"))
+      #:phases
+      #~(modify-phases %standard-phases
+          ;; See https://github.com/deeptools/Knight-Ruiz-Matrix-balancing-algorithm/issues/23
+          (add-after 'unpack 'remove-dependency-on-krbalancing
+            (lambda _
+              (substitute* "hicexplorer/hicCorrectMatrix.py"
+                (("from krbalancing import.*") "")
+                (("( *)assert\\(args.correctionMethod == 'KR'\\)" m indent)
+                 (string-append m "\n"
+                                indent "log.error('krbalancing not available')\n"
+                                indent "exit(1)")))
+              (substitute* "setup.py"
+                (("\"krbalancing >= 0.0.5\",") ""))
+              (substitute* "requirements.txt"
+                (("krbalancing >= 0.0.5") ""))))
+          (add-after 'unpack 'fix-references
+            (lambda _
+              (let ((site (string-append #$output "/lib/python"
+                                         #$(version-major+minor
+                                            (package-version python))
+                                         "/site-packages")))
+                (substitute* "hicexplorer/lib/tadClassifier.py"
+                  (("model_location = site.getsitepackages\\(\\)\\[0\\]")
+                   (string-append "model_location = \"" site "\""))))
+              (substitute* "hicexplorer/hicFindRestSite.py"
+                (("subprocess.check_output\\(\\[\"cat\"")
+                 (string-append "subprocess.check_output([\""
+                                (which "cat") "\""))
+                (("cmd = 'sort -k1")
+                 (string-append "cmd = '" (which "sort") " -k1")))))
+          ;; The tests aim to detect available memory and run more tests when
+          ;; there is more available memory.  Let's run them deterministically
+          ;; instead and don't run any tests that require more than 1GB of
+          ;; RAM.
+          (add-after 'unpack 'run-only-low-mem-tests
+            (lambda _
+              (with-directory-excursion "hicexplorer/test"
+                (substitute* '("trivial_runs/test_hicBuildMatrix_trivial_runs_2.py"
+                               "trivial_runs/test_hicAggregateContacts_trivial_runs_five.py"
+                               "trivial_runs/test_hicAggregateContacts_trivial_runs_four.py"
+                               "trivial_runs/test_hicAggregateContacts_trivial_runs.py"
+                               "trivial_runs/test_hicAggregateContacts_trivial_runs_two_1.py"
+                               "trivial_runs/test_hicBuildMatrix_trivial_runs.py"
+                               "trivial_runs/test_hicAggregateContacts_trivial_runs_two_3.py"
+                               "trivial_runs/test_hicAggregateContacts_trivial_runs_three.py"
+                               "trivial_runs/test_hicAggregateContacts_trivial_runs_two.py"
+                               "trivial_runs/test_hicAggregateContacts_trivial_runs_two_2.py"
+                               "trivial_runs/test_hicAggregateContacts_trivial_runs_six.py"
+                               "general/test_hicDifferentialTAD.py"
+                               "general/test_hicDetectLoops.py"
+                               "general/test_hicPlotMatrix.py"
+                               "general/test_hicHyperoptDetectLoops.py"
+                               "general/test_hicCreateThresholdFile.py"
+                               "general/test_hicMergeDomains.py"
+                               "general/test_hicHyperoptDetectLoopsHiCCUPS.py"
+                               "general/test_hicAggregateContacts.py"
+                               "general/test_hicInterIntraTAD.py")
+                  (("^memory =.*") "memory = 1\n"))))))))
     (propagated-inputs
      (list python-biopython
-           python-configparser
+           python-cleanlab-1
            python-cooler
+           python-fit-nbinom
            python-future
+           python-graphviz
+           python-hic2cool
+           python-hicmatrix
+           python-hyperopt
+           python-imbalanced-learn
            python-intervaltree
+           python-ipykernel
            python-jinja2
            python-matplotlib
            python-numpy
            python-pandas
+           python-psutil
+           python-pybedtools
            python-pybigwig
+           python-pygenometracks
            python-pysam
+           python-scikit-learn
            python-scipy
-           python-six
            python-tables
+           python-tqdm
            python-unidecode))
+    (native-inputs
+     (list graphviz)) ;for hicexplorer/test/test_compute_function.py
     (home-page "https://hicexplorer.readthedocs.io")
     (synopsis "Process, analyze and visualize Hi-C data")
     (description
-- 
2.36.1

[bug#60009] [PATCH 07/18] gnu: python-dna-features-viewer: Update to 3.1.1.

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm (python-dna-features-viewer):
Update to 3.1.1.
[build-system]: Use pyproject-build-system.
[arguments]: Add build phase to fix a compatibility problem with biopython.
[propagated-inputs]: Add python-packaging.
---
 gnu/packages/bioinformatics.scm | 23 ++++++++++++++++++-----
 1 file changed, 18 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ea33311a2c..371bf1077a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -16597,18 +16597,31 @@ (define-public python-pybbi
 (define-public python-dna-features-viewer
   (package
     (name "python-dna-features-viewer")
-    (version "3.0.3")
+    (version "3.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "dna_features_viewer" version))
        (sha256
         (base32
-         "0vci6kg2id6r6rh3cifq7ccnh7j0mb8iqg3hji6rva0ayrdqzafc"))))
-    (build-system python-build-system)
-    (arguments '(#:tests? #false)) ; there are none
+         "10a5pmh73spdgfml88zjqg1rn2j2zdxn06ir8a5q3arspyqvyqcb"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:tests? #false ;there are none
+      #:phases
+      '(modify-phases %standard-phases
+         ;; See https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer/issues/73
+         ;; and https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer/pull/74
+         (add-after 'unpack 'fix-biopython-compatibility
+           (lambda _
+             (substitute* "dna_features_viewer/biotools.py"
+               (("zip\\(aa1 \\+ \"\\*\", aa3 \\+ \\[\"\\*\"\\]\\)")
+                "zip(aa1 + ('*',), aa3 + ('*',))")))))))
     (propagated-inputs
-     (list python-biopython python-matplotlib))
+     (list python-biopython
+           python-matplotlib
+           python-packaging))
     (home-page
      "https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer")
     (synopsis "Plot features from DNA sequences")
-- 
2.36.1

[bug#60009] [PATCH 08/18] gnu: python-bokeh: Skip failing PIL test.

[Ricardo Wurmus]

The result seems fine, so don't worry about it.

* gnu/packages/python-xyz.scm (python-bokeh)[arguments]: Ignore failing
test_transform_PIL test.
---
 gnu/packages/python-xyz.scm | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 8591423116..c63ba212b0 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -15465,7 +15465,10 @@ (define-public python-bokeh
                (delete-file "tests/unit/bokeh/models/test_sources.py")
                (delete-file "tests/unit/bokeh/embed/test_bundle.py")
 
-               (invoke "pytest" "-v")))))))
+               ;; XXX: This one test transforms a gif of a red box.  It
+               ;; transforms it all right but the base64 doesn't look as
+               ;; expected, probably because of a change in pillow.
+               (invoke "pytest" "-v" "-k" "not test_transform_PIL")))))))
     (propagated-inputs
      (list node-lts
            python-jinja2
-- 
2.36.1

[bug#60009] [PATCH 09/18] gnu: sqlite-next: Update to 3.40.0.

[Ricardo Wurmus]

* gnu/packages/sqlite.scm (sqlite-next): Update to 3.40.0.
---
 gnu/packages/sqlite.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/sqlite.scm b/gnu/packages/sqlite.scm
index 71cc923a3a..930dc8041d 100644
--- a/gnu/packages/sqlite.scm
+++ b/gnu/packages/sqlite.scm
@@ -7,7 +7,7 @@
 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2016 David Craven <david@craven.ch>
 ;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Marius Bakke <marius@gnu.org>
-;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2017, 2022 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017 Jelle Licht <jlicht@fsfe.org>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Alex Vong <alexvong1995@gmail.com>
-- 
2.36.1

[bug#60009] [PATCH 10/18] gnu: python-apsw: Update to 3.40.0.0.

[Ricardo Wurmus]

* gnu/packages/databases.scm (python-apsw): Update to 3.40.0.0.
[source]: Remove obsolete patch.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add python-cython.
[arguments]: Move build-extensions phase before build phase.
* gnu/local.mk (dist_patch_DATA): Remove patch.
* gnu/packages/patches/python-apsw-3.39.2.1-test-fix.patch: Remove file.
---
 gnu/local.mk                                  |  1 -
 gnu/packages/databases.scm                    | 36 +++++++++----------
 .../python-apsw-3.39.2.1-test-fix.patch       | 27 --------------
 3 files changed, 18 insertions(+), 46 deletions(-)
 delete mode 100644 gnu/packages/patches/python-apsw-3.39.2.1-test-fix.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 6e12f9cdb1..295be3c67c 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1719,7 +1719,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-3-fix-tests.patch			\
   %D%/packages/patches/python-3-hurd-configure.patch		\
   %D%/packages/patches/python-3-no-static-lib.patch		\
-  %D%/packages/patches/python-apsw-3.39.2.1-test-fix.patch	\
   %D%/packages/patches/python-aionotify-0.2.0-py3.8.patch	\
   %D%/packages/patches/python-argcomplete-1.11.1-fish31.patch	\
   %D%/packages/patches/python-cross-compile.patch		\
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index b74762789a..9d1eec5ea0 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -173,6 +173,7 @@ (define-module (gnu packages databases)
   #:use-module (guix build-system go)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system perl)
+  #:use-module (guix build-system pyproject)
   #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system ruby)
@@ -3590,7 +3591,7 @@ (define-public python-pickleshare
 (define-public python-apsw
   (package
     (name "python-apsw")
-    (version "3.39.2.1")
+    (version "3.40.0.0")
     ;; The compressed release has fetching functionality disabled.
     (source
      (origin
@@ -3600,24 +3601,23 @@ (define-public python-apsw
              version "/apsw-" version ".zip"))
        (sha256
         (base32
-         "06x3qgg71xz8l3kz8gz04wkfp5f6zfrg476a4mm1c5hikqyw6ykj"))
-       ;; Cherry-picked from upstream, remove when bumping to 3.39.3.
-       (patches
-        (search-patches "python-apsw-3.39.2.1-test-fix.patch"))))
-    (build-system python-build-system)
-    (native-inputs (list unzip))
-    (inputs (list sqlite-next))         ;SQLite 3.39 required.
+         "02sgja00azvd08wi2wm105apmhp2644s7aw9b1zdg3dkcwjnsiad"))))
+    (build-system pyproject-build-system)
+    (native-inputs
+     (list python-cython unzip))
+    (inputs (list sqlite-next))         ;SQLite 3.40 required.
     (arguments
-     (list #:phases
-           #~(modify-phases %standard-phases
-               (replace 'build
-                 (lambda _
-                   (invoke "python" "setup.py" "build" "--enable-all-extensions"
-                           "--enable=load_extension")))
-               (add-after 'build 'build-test-helper
-                 (lambda _
-                   (invoke "gcc" "-fPIC" "-shared" "-o" "./testextension.sqlext"
-                           "-I." "-Isqlite3" "src/testextension.c"))))))
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'build 'build-extensions
+            (lambda _
+              (invoke "python" "setup.py" "build" "--enable-all-extensions"
+                      "--enable=load_extension")))
+          (add-after 'build 'build-test-helper
+            (lambda _
+              (invoke "gcc" "-fPIC" "-shared" "-o" "./testextension.sqlext"
+                      "-I." "-Isqlite3" "src/testextension.c"))))))
     (home-page "https://github.com/rogerbinns/apsw/")
     (synopsis "Another Python SQLite Wrapper")
     (description
diff --git a/gnu/packages/patches/python-apsw-3.39.2.1-test-fix.patch b/gnu/packages/patches/python-apsw-3.39.2.1-test-fix.patch
deleted file mode 100644
index cc233e3ccd..0000000000
--- a/gnu/packages/patches/python-apsw-3.39.2.1-test-fix.patch
+++ /dev/null
@@ -1,27 +0,0 @@
-From 1111f902075169bd0d96cdd10607ef8499f0fed5 Mon Sep 17 00:00:00 2001
-From: Roger Binns <rogerb@rogerbinns.com>
-Date: Mon, 5 Sep 2022 07:12:25 -0700
-Subject: [PATCH] Deal with mismatched SQLITE_ENABLE_COLUMN_METADATA
-
-Address #363
----
- apsw/tests.py   | 2 +-
- 1 files changed, 1 insertions(+), 1 deletion(-)
-
-diff --git a/apsw/tests.py b/apsw/tests.py
-index b4a94d3..256ead0 100644
---- a/apsw/tests.py
-+++ b/apsw/tests.py
-@@ -772,8 +772,8 @@ class APSW(unittest.TestCase):
-         c.execute("drop table foo; create table foo (%s)" % (", ".join(["[%s] %s" % (n, t) for n, t in cols]), ))
-         c.execute("insert into foo([x a space]) values(1)")
-         c.execute("create temp table two(fred banana); insert into two values(7); create temp view three as select fred as [a space] from two")
--        has_full=any(o=="ENABLE_COLUMN_METADATA" or o.startswith("ENABLE_COLUMN_METADATA=") for o in apsw.compile_options)
-+        has_full=any(o=="ENABLE_COLUMN_METADATA" or o.startswith("ENABLE_COLUMN_METADATA=") for o in apsw.compile_options) if apsw.using_amalgamation else hasattr(c, "description_full")
-         for row in c.execute("select * from foo"):
-             self.assertEqual(cols, c.getdescription())
-             self.assertEqual(has_full, hasattr(c, "description_full"))
-
-base-commit: f628374c5857d940067ef26c9ea4e85a08a94f76
---
-2.37.2
-- 
2.36.1

[bug#60009] [PATCH 11/18] gnu: python-cgatcore: Update to 0.6.14.

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm (python-cgatcore): Update to 0.6.14.
[build-system]: Use pyproject-build-system.
[arguments]: Disable broken tests with #:test-flags; do not replace 'check
phase; add phase 'sqlite-compatibility.
[native-inputs]: Drop input labels.
---
 gnu/packages/bioinformatics.scm | 50 ++++++++++++++++++++-------------
 1 file changed, 31 insertions(+), 19 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 371bf1077a..4044ff625e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -16081,7 +16081,7 @@ (define-public python-pyliftover
 (define-public python-cgatcore
   (package
     (name "python-cgatcore")
-    (version "0.6.7")
+    (version "0.6.14")
     ;; The version of pypi does not include test data.
     (source (origin
               (method git-fetch)
@@ -16091,11 +16091,22 @@ (define-public python-cgatcore
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "17vk88v1bx7x02ibzkc9i7ir4b5p1hcjr38jpsfzyzxr68352d5k"))))
-    (build-system python-build-system)
+                "0fjjaski39j8b7v21wldmbwwsfhicngajah7n4skafi56kdck33p"))))
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
+     (list
+      #:test-flags
+      '(list "-k"
+             (string-append
+              ;; This test actually does what it should, but the check fails with
+              ;; TypeError: cannot unpack non-iterable Namespace object
+              "not test_start_and_stop_are_logged_with_argparse"
+              ;; These all attempt to connect to localhost with SSH
+              " and not test_job_should_use_TMPDIR_and_clean_up"
+              " and not test_job_should_use_TMPDIR_and_clean_up_after_fail"
+              " and not test_job_should_write_to_explicit_temp_and_not_clean_up"))
+      #:phases
+      '(modify-phases %standard-phases
          (add-after 'unpack 'fix-references
            (lambda _
              (substitute* "cgatcore/pipeline/execution.py"
@@ -16103,21 +16114,22 @@ (define-public python-cgatcore
                (("executable=\"/bin/bash\"")
                 (string-append "executable=\"" (which "bash") "\""))
                (("\\\\time") (which "time")))))
-         (delete 'check)
-         (add-after 'install 'check
-           (lambda* (#:key tests? inputs outputs #:allow-other-keys)
-             (when tests?
-               (add-installed-pythonpath inputs outputs)
-               ;; Requires network access
-               (delete-file "tests/test_pipeline_execution.py")
-               (invoke "python" "-m" "pytest" "-v")))))))
+         (add-after 'unpack 'sqlite-compatibility
+           (lambda _
+             ;; Load apsw (and thus newer sqlite3) before importing Python's
+             ;; older sqlite3 library.
+             (substitute* "cgatcore/pipeline/__init__.py"
+               (("import os")
+                (string-append "import os\nimport apsw")))
+             (substitute* "tests/template_pipeline.py"
+               (("import sys" m)
+                (string-append "import apsw\n" m))))))))
     (native-inputs
-     `(("python-pytest" ,python-pytest)
-       ("lsof" ,lsof)
-       ("hostname" ,inetutils)
-       ("openssl" ,openssl)))
-    (inputs
-     (list time))
+     (list python-pytest
+           lsof
+           inetutils
+           openssl))
+    (inputs (list time))
     (propagated-inputs
      (list python-apsw
            python-gevent
-- 
2.36.1

[bug#60009] [PATCH 12/18] gnu: python-flask-restful: Update to 0.3.9.

[Ricardo Wurmus]

* gnu/packages/python-web.scm (python-flask-restful): Update to 0.3.9.
[source]: Remove patch.
[build-system]: Use pyproject-build-system.
[arguments]: Disable "test_redirect" test; remove 'fix-imports phase.
[native-inputs]: Replace python-nose with python-pytest.
* gnu/local.mk (dist_patch_DATA): Remove patch.
* gnu/packages/patches/python-flask-restful-werkzeug-compat.patch: Remove file.
---
 gnu/local.mk                                  |  1 -
 ...python-flask-restful-werkzeug-compat.patch | 36 -------------------
 gnu/packages/python-web.scm                   | 31 +++++++---------
 3 files changed, 12 insertions(+), 56 deletions(-)
 delete mode 100644 gnu/packages/patches/python-flask-restful-werkzeug-compat.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 295be3c67c..60a422fd7e 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1728,7 +1728,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-docopt-pytest6-compat.patch	\
   %D%/packages/patches/python-execnet-read-only-fix.patch	\
   %D%/packages/patches/python-fixtures-remove-monkeypatch-test.patch	\
-  %D%/packages/patches/python-flask-restful-werkzeug-compat.patch	\
   %D%/packages/patches/python-ipython-documentation-chars.patch	\
   %D%/packages/patches/python-ipython-documentation-repro.patch	\
   %D%/packages/patches/python-keras-integration-test.patch	\
diff --git a/gnu/packages/patches/python-flask-restful-werkzeug-compat.patch b/gnu/packages/patches/python-flask-restful-werkzeug-compat.patch
deleted file mode 100644
index 0e928ef455..0000000000
--- a/gnu/packages/patches/python-flask-restful-werkzeug-compat.patch
+++ /dev/null
@@ -1,36 +0,0 @@
-We need one patch on top of 0.3.8 for compatibility with Werkzeug 1.0.
-
-Taken from upstream:
-https://github.com/flask-restful/flask-restful/commit/73376a488907af3042b52678ac4c23f8a8911e5b
-
-diff --git a/tests/test_api.py b/tests/test_api.py
-index f7f8e661..6795d362 100644
---- a/tests/test_api.py
-+++ b/tests/test_api.py
-@@ -445,7 +445,9 @@ def test_handle_non_api_error(self):
- 
-         resp = app.get("/foo")
-         self.assertEquals(resp.status_code, 404)
--        self.assertEquals('text/html', resp.headers['Content-Type'])
-+        # in newer versions of werkzeug this is `text/html; charset=utf8`
-+        content_type, _, _ = resp.headers['Content-Type'].partition(';')
-+        self.assertEquals('text/html', content_type)
- 
-     def test_non_api_error_404_catchall(self):
-         app = Flask(__name__)
-diff --git a/tests/test_reqparse.py b/tests/test_reqparse.py
-index 2f1fbedf..9776f17c 100644
---- a/tests/test_reqparse.py
-+++ b/tests/test_reqparse.py
-@@ -2,9 +2,9 @@
- import unittest
- from mock import Mock, patch
- from flask import Flask
--from werkzeug import exceptions, MultiDict
-+from werkzeug import exceptions
- from werkzeug.wrappers import Request
--from werkzeug.datastructures import FileStorage
-+from werkzeug.datastructures import FileStorage, MultiDict
- from flask_restful.reqparse import Argument, RequestParser, Namespace
- import six
- import decimal
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 7543e05f47..18c0b47b67 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -3924,35 +3924,28 @@ (define-public python-flask-jwt
 (define-public python-flask-restful
   (package
     (name "python-flask-restful")
-    (version "0.3.8")
+    (version "0.3.9")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "Flask-RESTful" version))
-        (patches (search-patches "python-flask-restful-werkzeug-compat.patch"))
         (sha256
          (base32
-          "05b9lzx5yc3wgml2bcq50lq35h66m8zpj6dc9advcb5z3acsbaay"))))
-    (build-system python-build-system)
+          "0gm5dz088v3d2k1dkcp9b3nnqpkk0fp2jly870hijj2xhc5nbv6c"))))
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'fix-imports
-           (lambda _
-             (substitute* "flask_restful/__init__.py"
-               (("flask\\.helpers") "flask.scaffold")))))))
+     ;; This test fails because '/' is not 'http://localhost/'.
+     (list #:test-flags '(list "-k" "not test_redirect")))
     (propagated-inputs
-      (list python-aniso8601 python-flask python-pytz))
+     (list python-aniso8601 python-flask python-pytz))
     (native-inputs
-      (list ;; Optional dependency of Flask. Tests need it.
-            python-blinker python-mock ; For tests
-            python-nose))  ;for tests
-    (home-page
-      "https://www.github.com/flask-restful/flask-restful/")
-    (synopsis
-      "Flask module for creating REST APIs")
+     (list python-blinker
+           python-mock
+           python-pytest))
+    (home-page "https://www.github.com/flask-restful/flask-restful/")
+    (synopsis "Flask module for creating REST APIs")
     (description
-      "This package contains a Flask module for creating REST APIs.")
+     "This package contains a Flask module for creating REST APIs.")
     (license license:bsd-3)))
 
 (define-public python-flask-basicauth
-- 
2.36.1

[bug#60009] [PATCH 13/18] gnu: python-marshmallow: Update to 3.19.0.

[Ricardo Wurmus]

* gnu/packages/python-xyz.scm (python-marshmallow): Update to 3.19.0.
[build-system]: Use pyproject-build-system.
[propagated-inputs]: Remove python-dateutil and python-simplejson; add
python-packaging.
[native-inputs]: Add python-flake8, python-flake8-bugbear, python-mypy,
python-pre-commit, and python-simplejson.
---
 gnu/packages/python-xyz.scm | 31 ++++++++++++++++++-------------
 1 file changed, 18 insertions(+), 13 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index c63ba212b0..7d9f420412 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -20953,24 +20953,29 @@ (define-public python-flex
 (define-public python-marshmallow
   (package
     (name "python-marshmallow")
-    (version "3.9.1")
+    (version "3.19.0")
     (source
      (origin
-      (method url-fetch)
-      (uri (pypi-uri "marshmallow" version))
-      (sha256
-       (base32
-        "0kizhh3mnhpa08wfnsv1gagy22bpxzxszgbiylkhpz1d8qvwrykk"))))
-    (build-system python-build-system)
+       (method url-fetch)
+       (uri (pypi-uri "marshmallow" version))
+       (sha256
+        (base32
+         "0y6vpq2p5841kcw2qil68la0rx9z1vmxzj3dxjv99kjhsq7jq0wh"))))
+    (build-system pyproject-build-system)
     (propagated-inputs
-     (list python-dateutil python-simplejson))
+     (list python-packaging))
     (native-inputs
-     (list python-pytest python-pytz))
+     (list python-flake8
+           python-flake8-bugbear
+           python-mypy
+           python-pre-commit
+           python-pytest
+           python-pytz
+           python-simplejson))
     (home-page "https://github.com/marshmallow-code/marshmallow")
-    (synopsis "Convert complex datatypes to and from native
-     Python datatypes")
-    (description "@code{marshmallow} provides a library for converting
-     complex datatypes to and from native Python datatypes.")
+    (synopsis "Convert complex datatypes to and from native Python datatypes")
+    (description "@code{marshmallow} provides a library for converting complex
+datatypes to and from native Python datatypes.")
     (license license:expat)))
 
 (define-public python-marshmallow-jsonapi
-- 
2.36.1

[bug#60009] [PATCH 14/18] gnu: python-apispec: Update to 6.0.2.

[Ricardo Wurmus]

* gnu/packages/python-xyz.scm (python-apispec): Update to 6.0.2.
[build-system]: Use pyproject-build-system.
[arguments]: Disable test through test-flags, not by replacing the 'check
phase.
[propagated-inputs]: Remove python-pyyaml; add python-packaging.
[native-inputs]: Add python-flake8, python-flake8-bugbear, python-mypy,
python-pre-commit, and python-pyyaml.
---
 gnu/packages/python-xyz.scm | 39 ++++++++++++++++++++-----------------
 1 file changed, 21 insertions(+), 18 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 7d9f420412..37c2caf400 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -21011,33 +21011,36 @@ (define-public python-marshmallow-jsonapi
 (define-public python-apispec
   (package
     (name "python-apispec")
-    (version "4.0.0")
+    (version "6.0.2")
     (source
      (origin
-      (method url-fetch)
-      (uri (pypi-uri "apispec" version))
-      (sha256
+       (method url-fetch)
+       (uri (pypi-uri "apispec" version))
+       (sha256
         (base32
-          "12n4w5zkn4drcn8izq68vmixmqvz6abviqkdn4ip0kaax3jjh3in"))))
-    (build-system python-build-system)
+         "11vqxwdxmm7qmyhdbxk4gnx37nbzmn266ah92gi4pvzd76vq0vg7"))))
+    (build-system pyproject-build-system)
     (arguments
-     '(#:phases (modify-phases %standard-phases
-                  (replace 'check
-                    (lambda _
-                      (invoke "pytest" "-vv"
-                              ;; Disable validation tests since they require
-                              ;; the optional 'prance' library which is not
-                              ;; yet in Guix.
-                              "-k" "not openapi_tools_validate"))))))
+     (list
+      ;; Disable validation tests since they require
+      ;; the optional 'prance' library which is not
+      ;; yet in Guix.
+      #:test-flags '(list "-k" "not openapi_tools_validate")))
     (propagated-inputs
-     (list python-pyyaml))
+     (list python-packaging))
     (native-inputs
-     (list python-pytest python-marshmallow))
+     (list python-flake8
+           python-flake8-bugbear
+           python-marshmallow
+           python-mypy
+           python-pre-commit
+           python-pytest
+           python-pyyaml))
     (home-page "https://github.com/marshmallow-code/apispec")
     (synopsis "Swagger/OpenAPI specification generator")
     (description "@code{python-apispec} is a pluggable API specification
-     generator.  It currently supports the OpenAPI specification, formerly known
-     as Swagger.")
+generator.  It currently supports the OpenAPI specification, formerly known as
+Swagger.")
     (license license:expat)))
 
 (define-public python-apispec-webframeworks
-- 
2.36.1

[bug#60009] [PATCH 15/18] gnu: python-pyjwt: Update to 2.6.0.

[Ricardo Wurmus]

* gnu/packages/python-xyz.scm (python-pyjwt): Update to 2.6.0.
[build-system]: Use pyproject-build-system.
[arguments]: Remove.
[native-inputs]: Add pytohn-coverage, python-pre-commit, python-sphinx, and
python-sphinx-rtd-theme.
---
 gnu/packages/python-xyz.scm | 19 +++++++++----------
 1 file changed, 9 insertions(+), 10 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 37c2caf400..a6983e4411 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -4087,23 +4087,22 @@ (define-public python-text-unidecode
 (define-public python-pyjwt
   (package
     (name "python-pyjwt")
-    (version "2.4.0")
+    (version "2.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "PyJWT" version))
        (sha256
         (base32
-         "1fmbcwfw1463wjzwbcgg3s16rad6kfb1mc5y7jbkp6v9ihh0hafl"))))
-    (build-system python-build-system)
-    (arguments
-     '(#:phases (modify-phases %standard-phases
-                  (replace 'check
-                    (lambda* (#:key tests? #:allow-other-keys)
-                      (when tests?
-                        (invoke "pytest" "-vv")))))))
+         "1z85kwr945rbzrn5wabrsmck5x8disa9wc7b3y5gci7w65z5qa39"))))
+    (build-system pyproject-build-system)
     (native-inputs
-     (list python-cryptography python-pytest))
+     (list python-coverage
+           python-cryptography
+           python-pre-commit
+           python-pytest
+           python-sphinx
+           python-sphinx-rtd-theme))
     (home-page "https://github.com/progrium/pyjwt")
     (synopsis "JSON Web Token implementation in Python")
     (description
-- 
2.36.1

[bug#60009] [PATCH 16/18] gnu: python-flasgger: Update to 0.9.5.

[Ricardo Wurmus]

* gnu/packages/python-xyz.scm (python-flasgger): Update to 0.9.5.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom 'check phase; add 'prepare-check phase; disable
"test_swag" test via #:test-flags.
[native-inputs]: Add python-apispec-webframeworks and python-flask-jwt.
---
 gnu/packages/python-xyz.scm | 36 +++++++++++++++++++++---------------
 1 file changed, 21 insertions(+), 15 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index a6983e4411..e273e71fa0 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -21073,7 +21073,7 @@ (define-public python-apispec-webframeworks
 (define-public python-flasgger
   (package
     (name "python-flasgger")
-    (version "0.6.3")
+    (version "0.9.5")
     (source
       (origin
         (method git-fetch)
@@ -21082,29 +21082,35 @@ (define-public python-flasgger
               (commit version)))
         (file-name (git-file-name name version))
         (sha256
-          (base32 "0yydxsyjnc0clbrjqb1n7587l6cdqvwdagwxk5hkx01qwdfbkvpn"))))
-    (build-system python-build-system)
+          (base32 "0a2djgfq905a4in16068qz0ikg88dm4nbckaamhaz2v9khllr0bi"))))
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             (substitute* "Makefile"
-               (("flake8 flasgger --ignore=F403")
-                "flake8 flasgger --ignore=E731,F403"))
-             (invoke "py.test"))))))
+     (list
+      ;; This test fails due to missing fixtures
+      #:test-flags '(list "-k" "not test_swag")
+      #:phases
+      '(modify-phases %standard-phases
+        (add-after 'unpack 'prepare-check
+          (lambda _
+            ;; This requires a dummy package "flasgger_package" to be installed.
+            (delete-file "examples/package_example.py")
+            ;; These fail with an internal server error
+            (for-each delete-file '("examples/marshmallow_apispec.py"
+                                    "examples/validation.py")))))))
     (propagated-inputs
      (list python-flask python-pyyaml python-jsonschema python-mistune
            python-six))
     (native-inputs
-     (list python-decorator
+     (list python-apispec
+           python-apispec-webframeworks
+           python-decorator
            python-flake8
+           python-flask-jwt
            python-flask-restful
            python-flex
-           python-pytest
-           python-pytest-cov
            python-marshmallow
-           python-apispec))
+           python-pytest
+           python-pytest-cov))
     (home-page "https://github.com/rochacbruno/flasgger/")
     (synopsis "Extract Swagger specs from your Flask project")
     (description "@code{python-flasgger} allows extracting Swagger specs
-- 
2.36.1

[bug#60009] [PATCH 17/18] gnu: seqmagick: Update to 0.8.4.

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm (seqmagick): Update to 0.8.4.
[build-system]: Use pyproject-build-system.
[inputs]: Add python-pygtrie.
[native-inputs]: Replace python-nose with python-pytest.
---
 gnu/packages/bioinformatics.scm | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4044ff625e..e8a8ddc361 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6945,19 +6945,19 @@ (define-public seqan-1
 (define-public seqmagick
   (package
     (name "seqmagick")
-    (version "0.8.0")
+    (version "0.8.4")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "seqmagick" version))
        (sha256
         (base32
-         "0pf98da7i59q47gwrbx0wjk6xlvbybiwphw80w7h4ydjj0579a2b"))))
-    (build-system python-build-system)
+         "0c6skyig8fyylnbj4597pjj9h0dn36rkxrhwd34yrsc6k6f7r8a0"))))
+    (build-system pyproject-build-system)
     (inputs
-     (list python-biopython))
+     (list python-biopython python-pygtrie))
     (native-inputs
-     (list python-nose))
+     (list python-pytest))
     (home-page "https://github.com/fhcrc/seqmagick")
     (synopsis "Tools for converting and modifying sequence files")
     (description
-- 
2.36.1

[bug#60009] [PATCH 18/18] gnu: cnvkit: Update to 0.9.9.

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm (cnvkit): Update to 0.9.9.
[build-system]: Use pyproject-build-system.
[arguments]: Relax restriction on python-joblib.
[propagated-inputs]: Add python-pomegranate and python-scikit-learn.
---
 gnu/packages/bioinformatics.scm | 21 ++++++++++++++++-----
 1 file changed, 16 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e8a8ddc361..5e2e0796a0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14225,7 +14225,7 @@ (define-public nanopolish
 (define-public cnvkit
   (package
     (name "cnvkit")
-    (version "0.9.5")
+    (version "0.9.9")
     (source
      (origin
        (method git-fetch)
@@ -14234,17 +14234,28 @@ (define-public cnvkit
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0g2f78k68yglmj4fsfmgs8idqv3di9aj53fg0ld0hqljg8chhh82"))))
-    (build-system python-build-system)
+        (base32 "1q4l7jhr1k135an3n9aa9wsid5lk6fwxb0hcldrr6v6y76zi4gj1"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      '(modify-phases %standard-phases
+         ;; See upstream commit eee0f6eaec57d5c6e58142d661979f3aacc5f76a
+         (add-after 'unpack 'compatibility
+           (lambda _
+             (substitute* "setup.py"
+               (("'joblib.*") "")))))))
     (propagated-inputs
      (list python-biopython
            python-future
            python-matplotlib
            python-numpy
-           python-reportlab
            python-pandas
-           python-pysam
+           python-pomegranate
            python-pyfaidx
+           python-pysam
+           python-reportlab
+           python-scikit-learn
            python-scipy
            ;; R packages
            r-dnacopy))
-- 
2.36.1

[bug#60009] [PATCH 09/18] gnu: sqlite-next: Update to 3.40.0.

[zimoun]

Hi Ricardo,

On Mon, 12 Dec 2022 at 15:27, Ricardo Wurmus <rekado@elephly.net> wrote:
> * gnu/packages/sqlite.scm (sqlite-next): Update to 3.40.0.
> ---
>  gnu/packages/sqlite.scm | 2 +-
>  1 file changed, 1 insertion(+), 1 deletion(-)
>
> diff --git a/gnu/packages/sqlite.scm b/gnu/packages/sqlite.scm
> index 71cc923a3a..930dc8041d 100644
> --- a/gnu/packages/sqlite.scm
> +++ b/gnu/packages/sqlite.scm
> @@ -7,7 +7,7 @@
>  ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
>  ;;; Copyright © 2016 David Craven <david@craven.ch>
>  ;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Marius Bakke <marius@gnu.org>
> -;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
> +;;; Copyright © 2017, 2022 Ricardo Wurmus <rekado@elephly.net>
>  ;;; Copyright © 2017 Jelle Licht <jlicht@fsfe.org>
>  ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
>  ;;; Copyright © 2018 Alex Vong <alexvong1995@gmail.com>

This patch does not seem to update sqlite-next. :-)


Cheers,
simon

[bug#60009] [PATCH 08/18] gnu: python-bokeh: Skip failing PIL test.

[zimoun]

Hi Ricardo,

On Mon, 12 Dec 2022 at 15:27, Ricardo Wurmus <rekado@elephly.net> wrote:

> The result seems fine, so don't worry about it.

Is this intended to be in the commit message?


Cheers,
simon

[bug#60009] [PATCH 08/18] gnu: python-bokeh: Skip failing PIL test.

[Ricardo Wurmus]

zimoun <zimon.toutoune@gmail.com> writes:

> On Mon, 12 Dec 2022 at 15:27, Ricardo Wurmus <rekado@elephly.net> wrote:
>
>> The result seems fine, so don't worry about it.
>
> Is this intended to be in the commit message?

Yes.  The test compares base64-encoded gifs; the gifs look identical but
the base64-encoded data differs.  Hence the note in the commit message
that disabling this PIL test is probably fine.

-- 
Ricardo

[bug#60009] [PATCH 09/18] gnu: sqlite-next: Update to 3.40.0.

[Ricardo Wurmus]

zimoun <zimon.toutoune@gmail.com> writes:

> Hi Ricardo,
>
> On Mon, 12 Dec 2022 at 15:27, Ricardo Wurmus <rekado@elephly.net> wrote:
>> * gnu/packages/sqlite.scm (sqlite-next): Update to 3.40.0.
>> ---
>>  gnu/packages/sqlite.scm | 2 +-
>>  1 file changed, 1 insertion(+), 1 deletion(-)
>>
>> diff --git a/gnu/packages/sqlite.scm b/gnu/packages/sqlite.scm
>> index 71cc923a3a..930dc8041d 100644
>> --- a/gnu/packages/sqlite.scm
>> +++ b/gnu/packages/sqlite.scm
>> @@ -7,7 +7,7 @@
>>  ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
>>  ;;; Copyright © 2016 David Craven <david@craven.ch>
>>  ;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Marius Bakke <marius@gnu.org>
>> -;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
>> +;;; Copyright © 2017, 2022 Ricardo Wurmus <rekado@elephly.net>
>>  ;;; Copyright © 2017 Jelle Licht <jlicht@fsfe.org>
>>  ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
>>  ;;; Copyright © 2018 Alex Vong <alexvong1995@gmail.com>
>
> This patch does not seem to update sqlite-next. :-)

Yes, when I rebased on top of commit 50b36f688b43c219dc64a1ce7f6d5e08c0025089
my change disappeared.  That commit did not update python-apsw, which is
sensitive to the version of sqlite-next.

I wish we could express these dependencies as constraints so that people
know what other packages to pay attention to when updating something.

-- 
Ricardo

[bug#60009] [PATCH 08/18] gnu: python-bokeh: Skip failing PIL test.

[Simon Tournier]

Hi,

On Mon, 12 Dec 2022 at 21:10, Ricardo Wurmus <rekado@elephly.net> wrote:

> >> The result seems fine, so don't worry about it.

> Yes.  The test compares base64-encoded gifs; the gifs look identical but
> the base64-encoded data differs.  Hence the note in the commit message
> that disabling this PIL test is probably fine.

That also in the comment. :-)

Well, when I read it, I have been confused but this line, so maybe the
"about it." could be explicit: "about the failing test."

Cheers,
simon

[bug#60009] [PATCH 09/18] gnu: sqlite-next: Update to 3.40.0.

[Simon Tournier]

Hi,

On Mon, 12 Dec 2022 at 21:13, Ricardo Wurmus <rekado@elephly.net> wrote:

> Yes, when I rebased on top of commit 50b36f688b43c219dc64a1ce7f6d5e08c0025089
> my change disappeared.  That commit did not update python-apsw, which is
> sensitive to the version of sqlite-next.

Why not dropping this patch "gnu: sqlite-next: Update to 3.40.0." if
it is already merged?

Despite the comment for python-aspw,

--8<---------------cut here---------------start------------->8---
(inputs (list sqlite-next))         ;SQLite 3.39 required.
--8<---------------cut here---------------end--------------->8---

it builds fine with 3.40 [1].  Collateral damage avoided. :-)

1: http://ci.guix.gnu.org/build/224759/details


> I wish we could express these dependencies as constraints so that people
> know what other packages to pay attention to when updating something.

I totally agree!  Maybe the QA [2] will help; well, the QA service
seems having troubles with for 60009 [2] for unexpected reasons.
Today, the update looks like lottery. :-)  Sometime, a trivial update
here and then an unexpected break overthere.

2: https://qa.guix.gnu.org/issue/60009

Cheers,
simon

[bug#60009] [PATCH 09/18] gnu: sqlite-next: Update to 3.40.0.

[Ricardo Wurmus]

Simon Tournier <zimon.toutoune@gmail.com> writes:

> On Mon, 12 Dec 2022 at 21:13, Ricardo Wurmus <rekado@elephly.net> wrote:
>
>> Yes, when I rebased on top of commit 50b36f688b43c219dc64a1ce7f6d5e08c0025089
>> my change disappeared.  That commit did not update python-apsw, which is
>> sensitive to the version of sqlite-next.
>
> Why not dropping this patch "gnu: sqlite-next: Update to 3.40.0." if
> it is already merged?

Only because I didn’t notice before sending off the patch set ;)
I’ll drop it before merging the patches.

> Despite the comment for python-aspw,
>
> (inputs (list sqlite-next))         ;SQLite 3.39 required.
>
> it builds fine with 3.40 [1].  Collateral damage avoided. :-)
>
> 1: http://ci.guix.gnu.org/build/224759/details

Good good.  Could be that the difference between 3.39 and 3.40 is just
not big enough to matter.  What does matter is that it’s not just
“sqlite” but something more recent.

>> I wish we could express these dependencies as constraints so that people
>> know what other packages to pay attention to when updating something.
>
> I totally agree!  Maybe the QA [2] will help; well, the QA service
> seems having troubles with for 60009 [2] for unexpected reasons.
> Today, the update looks like lottery. :-)  Sometime, a trivial update
> here and then an unexpected break overthere.
>
> 2: https://qa.guix.gnu.org/issue/60009

I’ve been refreshing this page since I submitted the patch set; good to
know that the problems here are unexpected.

I have previously built packages with these changes on berlin, so there
are substitutes already.  I’ll go ahead and merge it if you have no
objections.

Thank you for the review!

-- 
Ricardo

[bug#60009] [PATCH 08/18] gnu: python-bokeh: Skip failing PIL test.

[Ricardo Wurmus]

Simon Tournier <zimon.toutoune@gmail.com> writes:

> Hi,
>
> On Mon, 12 Dec 2022 at 21:10, Ricardo Wurmus <rekado@elephly.net> wrote:
>
>> >> The result seems fine, so don't worry about it.
>
>> Yes.  The test compares base64-encoded gifs; the gifs look identical but
>> the base64-encoded data differs.  Hence the note in the commit message
>> that disabling this PIL test is probably fine.
>
> That also in the comment. :-)
>
> Well, when I read it, I have been confused but this line, so maybe the
> "about it." could be explicit: "about the failing test."

Okay, I’ll make the note a little more explicit.

Thanks for the comments!

-- 
Ricardo

[bug#60009] [PATCH 09/18] gnu: sqlite-next: Update to 3.40.0.

[Simon Tournier]

Hi,

On Tue, 13 Dec 2022 at 00:06, Ricardo Wurmus <rekado@elephly.net> wrote:

> I have previously built packages with these changes on berlin, so there
> are substitutes already.  I’ll go ahead and merge it if you have no
> objections.

No objection.  I have not built all the patch set neither but the series LGTM.

Please go ahead. :-)

Cheers,
simon

bug#60009: [PATCH 09/18] gnu: sqlite-next: Update to 3.40.0.

[Ricardo Wurmus]

Simon Tournier <zimon.toutoune@gmail.com> writes:

> Hi,
>
> On Tue, 13 Dec 2022 at 00:06, Ricardo Wurmus <rekado@elephly.net> wrote:
>
>> I have previously built packages with these changes on berlin, so there
>> are substitutes already.  I’ll go ahead and merge it if you have no
>> objections.
>
> No objection.  I have not built all the patch set neither but the series LGTM.
>
> Please go ahead. :-)

Thanks!  Merged.

-- 
Ricardo