sharlatan pushed a commit to branch python-team
in repository guix.
commit 964c653a099d470a274d4f1f2e7b3a6e54946dc9
Author: Nicolas Graves <ngra...@ngraves.fr>
AuthorDate: Mon Mar 31 08:18:41 2025 +0200
gnu: taxtastic: Update to 0.11.1.
* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.11.1.
[build-system]: Switch to pyproject-build-system.
[arguments]{test-flags}: Ignore failing test.
{phases}: Improve style with gexp. Update phase
'prepare-directory. Improve phase 'check with test-flags inclusion.
[native-inputs]: Add python-setuptools, python-wheel.
[propagated-inputs]: Sort inputs. Replace python-psycopg2 by both
python-psycopg and python-psycopg2-binary. Add python-sqlparse.
Signed-off-by: Sharlatan Hellseher <sharlata...@gmail.com>
---
gnu/packages/bioinformatics.scm | 69 ++++++++++++++++++++++-------------------
1 file changed, 37 insertions(+), 32 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0f59f73448..1215e67117 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12414,7 +12414,7 @@ Cuffdiff or Ballgown programs.")
(define-public taxtastic
(package
(name "taxtastic")
- (version "0.9.2")
+ (version "0.11.1")
(source (origin
;; The Pypi version does not include tests.
(method git-fetch)
@@ -12424,42 +12424,47 @@ Cuffdiff or Ballgown programs.")
(file-name (git-file-name name version))
(sha256
(base32
- "1k6wg9ych1j3srnhdny1y4470qlhfg730rb3rm3pq7l7gw62vmgb"))))
- (build-system python-build-system)
+ "18h3vlyx9qp7xymd8ra6jn5h0vzlpzgcd75kslqyv2qcg1a7scc4"))))
+ (build-system pyproject-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'prepare-directory
- (lambda _
- ;; This test fails, but the error is not caught by the test
- ;; framework, so the tests fail...
- (substitute* "tests/test_taxit.py"
- (("self.cmd_fails\\(''\\)")
- "self.cmd_fails('nothing')"))
- ;; This version file is expected to be created with git describe.
- (mkdir-p "taxtastic/data")
- (with-output-to-file "taxtastic/data/ver"
- (lambda () (display ,version)))))
- (replace 'check
- ;; Note, this fails to run with "-v" as it tries to write to a
- ;; closed output stream.
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (invoke "python" "-m" "unittest"))))
- ;; This fails because it cannot find psycopg2 even though it is
- ;; available.
- (delete 'sanity-check))))
+ (list
+ #:test-flags #~(list "-k" "not test_new_nodes02")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'prepare-directory
+ (lambda _
+ ;; This package is unknown to pypi.
+ (substitute* '("requirements.txt" "setup.py")
+ ((".*psycopg-binary.*") ""))
+ ;; This test fails, but the error is not caught by the test
+ ;; framework, so the tests fail...
+ (substitute* "tests/test_taxit.py"
+ (("self.cmd_fails\\(''\\)")
+ "self.cmd_fails('nothing')"))
+ ;; This version file is expected to be created with git describe.
+ (mkdir-p "taxtastic/data")
+ (with-output-to-file "taxtastic/data/ver"
+ (lambda () (display #$version)))))
+ (replace 'check
+ ;; Note, this fails to run with "-v" as it tries to write to a
+ ;; closed output stream.
+ (lambda* (#:key tests? test-flags #:allow-other-keys)
+ (when tests?
+ (apply invoke "python" "-m" "unittest" test-flags)))))))
+ (native-inputs
+ (list python-setuptools python-wheel))
(propagated-inputs
- (list python-sqlalchemy
+ (list python-biopython
python-decorator
- python-biopython
- python-pandas
- python-psycopg2
+ python-dendropy
python-fastalite
- python-pyyaml
- python-six
python-jinja2
- python-dendropy))
+ python-pandas
+ python-psycopg
+ python-psycopg2-binary
+ python-pyyaml
+ python-sqlalchemy-2
+ python-sqlparse))
(home-page "https://github.com/fhcrc/taxtastic";)
(synopsis "Tools for taxonomic naming and annotation")
(description
