Summary of Errors
Summary of Errors
- DepMap
[DepMap] failed to resolve: Expecting value: line 1 column 1 (char 0) - National Cancer Institute Thesaurus
[ncit] issue parsing: Issue in NCItGetter with date 2026-04-06 and fmt %B %d, %Y - Research Organization Registry `[ror] issue parsing: Could not look up zenodo/api_token and no default given.
This can be solved with one of the following:
- Set the ZENODO_API_TOKEN environment variable
- Windows, via GUI: https://www.computerhope.com/issues/ch000549.htm
- Windows, via CLI: https://learn.microsoft.com/en-us/windows-server/administration/windows-commands/set_1
- Mac OS: https://apple.stackexchange.com/questions/106778/how-do-i-set-environment-variables-on-os-x
- Linux: https://www.freecodecamp.org/news/how-to-set-an-environment-variable-in-linux/
-
Use the PyStow CLI from the command line to set the configuration like so:
$ pystow set zenodo api_token
This creates an INI file in /home/runner/.config/zenodo.ini with the configuration in the right place.
-
Create/edit an INI file in /home/runner/.config/zenodo.ini and manually fill it in by 1) creating a section inside it called [zenodo] and 2) setting a value for api_token =
that looks like: /home/runner/.config/zenodo.ini
[zenodo] api_token =
See https://github.com/cthoyt/pystow#%EF%B8%8F%EF%B8%8F-configuration for more information. `
DepMap
Using class: DepMapGetter
Traceback (most recent call last):
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/models.py", line 978, in json
return complexjson.loads(self.text, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.12.13/x64/lib/python3.12/json/__init__.py", line 346, in loads
return _default_decoder.decode(s)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.12.13/x64/lib/python3.12/json/decoder.py", line 338, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.12.13/x64/lib/python3.12/json/decoder.py", line 356, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 271, in iter_versions
yv = resolve(cls)
^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 193, in resolve
return _resolve_helper_cached(name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 606, in func_wrapper
return _call(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 459, in _call
return _calc_entry(core, key, func, args, kwds, _print)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 84, in _calc_entry
func_res = func(*args, **kwds)
^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 203, in _resolve_helper_cached
return getter.resolve()
^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 215, in resolve
version=cls.version,
^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 93, in version
if isinstance(cls._cache_prop, str):
^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 87, in _cache_prop
cls._cache = cls().get()
^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/depmap.py", line 23, in get
latest = next(release for release in res.json()["releaseData"] if release["isLatest"])
^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/models.py", line 982, in json
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
National Cancer Institute Thesaurus
Using class: NCItGetter
Traceback (most recent call last):
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 271, in iter_versions
yv = resolve(cls)
^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 193, in resolve
return _resolve_helper_cached(name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 606, in func_wrapper
return _call(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 459, in _call
return _calc_entry(core, key, func, args, kwds, _print)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 84, in _calc_entry
func_res = func(*args, **kwds)
^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 203, in _resolve_helper_cached
return getter.resolve()
^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 219, in resolve
date=cls.date,
^^^^^^^^
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 120, in date
raise ValueError(
ValueError: Issue in NCItGetter with date 2026-04-06 and fmt %B %d, %Y
Research Organization Registry
Using class: RORGetter
Traceback (most recent call last):
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 271, in iter_versions
yv = resolve(cls)
^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 193, in resolve
return _resolve_helper_cached(name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 606, in func_wrapper
return _call(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 459, in _call
return _calc_entry(core, key, func, args, kwds, _print)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 84, in _calc_entry
func_res = func(*args, **kwds)
^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 203, in _resolve_helper_cached
return getter.resolve()
^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 215, in resolve
version=cls.version,
^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 93, in version
if isinstance(cls._cache_prop, str):
^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 87, in _cache_prop
cls._cache = cls().get()
^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/ror.py", line 22, in get
version_info = ror_downloader.get_version_info(download=False)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/ror_downloader/api.py", line 227, in get_version_info
client = zenodo_client.Zenodo()
^^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/zenodo_client/api.py", line 117, in __init__
self.access_token = pystow.get_config(
^^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/pystow/config_api.py", line 161, in get_config
raise ConfigError(module=module, key=key)
pystow.config_api.ConfigError: Could not look up zenodo/api_token and no default given.
This can be solved with one of the following:
1. Set the ZENODO_API_TOKEN environment variable
- Windows, via GUI: https://www.computerhope.com/issues/ch000549.htm
- Windows, via CLI: https://learn.microsoft.com/en-us/windows-server/administration/windows-commands/set_1
- Mac OS: https://apple.stackexchange.com/questions/106778/how-do-i-set-environment-variables-on-os-x
- Linux: https://www.freecodecamp.org/news/how-to-set-an-environment-variable-in-linux/
2. Use the PyStow CLI from the command line to
set the configuration like so:
$ pystow set zenodo api_token <value>
This creates an INI file in /home/runner/.config/zenodo.ini
with the configuration in the right place.
3. Create/edit an INI file in /home/runner/.config/zenodo.ini and manually
fill it in by 1) creating a section inside it called [zenodo]
and 2) setting a value for api_token = <value> that looks like:
# /home/runner/.config/zenodo.ini
[zenodo]
api_token = <value>
See https://github.com/cthoyt/pystow#%EF%B8%8F%EF%B8%8F-configuration for more information.