diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 69 |
1 files changed, 37 insertions, 32 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 38ea51417c..3bf6b73ce2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12432,7 +12432,7 @@ 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) @@ -12442,42 +12442,47 @@ 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 |