[med-svn] [Git][med-team/pyensembl][master] tinytimer - missed while executing command line

[Steffen Möller (@moeller)]

Steffen Möller pushed to branch master at Debian Med / pyensembl


Commits:
403939bc by Steffen Möller at 2025-08-01T18:44:42+01:00
tinytimer - missed while executing command line

$ pyensembl install --release 111 --species homo_sapiens
Traceback (most recent call last):
  File "/usr/bin/pyensembl", line 33, in <module>
    sys.exit(load_entry_point('pyensembl==2.3.13', 'console_scripts', 'pyensembl')())
             ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/bin/pyensembl", line 25, in importlib_load_entry_point
    return next(matches).load()
           ~~~~~~~~~~~~~~~~~~^^
  File "/usr/lib/python3.13/importlib/metadata/__init__.py", line 179, in load
    module = import_module(match.group('module'))
  File "/usr/lib/python3.13/importlib/__init__.py", line 88, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<frozen importlib._bootstrap>", line 1387, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1360, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1331, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 935, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 1026, in exec_module
  File "<frozen importlib._bootstrap>", line 488, in _call_with_frames_removed
  File "/usr/lib/python3/dist-packages/pyensembl/shell.py", line 43, in <module>
    import pkg_resources
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 3661, in <module>
    @_call_aside
     ^^^^^^^^^^^
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 3645, in _call_aside
    f(*args, **kwargs)
    ~^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 3674, in _initialize_master_working_set
    working_set = _declare_state('object', 'working_set', WorkingSet._build_master())
                                                          ~~~~~~~~~~~~~~~~~~~~~~~~^^
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 654, in _build_master
    ws.require(__requires__)
    ~~~~~~~~~~^^^^^^^^^^^^^^
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 1066, in require
    needed = self.resolve(parse_requirements(requirements))
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 893, in resolve
    dist = self._resolve_dist(
        req, best, replace_conflicting, env, installer, required_by, to_activate
    )
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 934, in _resolve_dist
    raise DistributionNotFound(req, requirers)
pkg_resource.DistributionNotFound: The 'tinytimer<1.0.0,>=0.0.0' distribution was not found and is required by pyensembl

- - - - -


3 changed files:

- debian/changelog
- debian/control
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+pyensembl (2.3.13-3) UNRELEASED; urgency=medium
+
+  * Need to remove tinytimer from resources.txt to avoid error message
+    at runtime checking dependencies.
+  * Standards-Version: 4.7.2
+
+ -- Steffen Moeller <moeller at debian.org>  Fri, 01 Aug 2025 18:41:38 +0100
+
 pyensembl (2.3.13-2) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/control
=====================================
@@ -17,7 +17,7 @@ Build-Depends: debhelper-compat (= 13),
                python3-pytest <!nocheck>,
 #              python3-tinytimer # only run during tests that are not run because of
 #              demand for internet access
-Standards-Version: 4.7.0
+Standards-Version: 4.7.2
 Homepage: https://github.com/openvax/pyensembl
 Vcs-Browser: https://salsa.debian.org/med-team/pyensembl
 Vcs-Git: https://salsa.debian.org/med-team/pyensembl.git


=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
 skip-benchmark.patch
+no_tinytimer_in_requirements.txt



View it on GitLab: https://salsa.debian.org/med-team/pyensembl/-/commit/403939bc9e479d171253ced8b5eccba3cafc3cea

-- 
View it on GitLab: https://salsa.debian.org/med-team/pyensembl/-/commit/403939bc9e479d171253ced8b5eccba3cafc3cea
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