Summary of Errors
Summary of Errors
- Ensembl
[ensembl] failed to resolve: 'NoneType' object has no attribute 'text' - 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. `
- National Cancer Institute Thesaurus
[ncit] issue parsing: Issue in NCItGetter with date 2026-04-13 and fmt %B %d, %Y - DepMap
[DepMap] failed to resolve: Expecting value: line 1 column 1 (char 0) - SIGNOR
[SIGNOR] failed to resolve: HTTPSConnectionPool(host='signor.uniroma2.it', port=443): Max retries exceeded with url: /downloads.php (Caused by ConnectTimeoutError(<HTTPSConnection(host='signor.uniroma2.it', port=443) at 0x7ff81090a330>, 'Connection to signor.uniroma2.it timed out. (connect timeout=15)'))
Ensembl
Using class: EnsemblGetter
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/ensembl.py", line 24, in get
manifest = soup.find(**{"class": "box-header"}).text
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'text'
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.
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 2026-04-13 and fmt %B %d, %Y
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)
SIGNOR
Using class: SignorGetter
Traceback (most recent call last):
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connection.py", line 204, in _new_conn
sock = connection.create_connection(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/util/connection.py", line 85, in create_connection
raise err
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/util/connection.py", line 73, in create_connection
sock.connect(sa)
TimeoutError: timed out
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 787, in urlopen
response = self._make_request(
^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 488, in _make_request
raise new_e
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 464, in _make_request
self._validate_conn(conn)
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 1093, in _validate_conn
conn.connect()
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connection.py", line 759, in connect
self.sock = sock = self._new_conn()
^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connection.py", line 213, in _new_conn
raise ConnectTimeoutError(
urllib3.exceptions.ConnectTimeoutError: (<HTTPSConnection(host='signor.uniroma2.it', port=443) at 0x7ff81090a330>, 'Connection to signor.uniroma2.it timed out. (connect timeout=15)')
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/adapters.py", line 645, in send
resp = conn.urlopen(
^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 841, in urlopen
retries = retries.increment(
^^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/util/retry.py", line 535, in increment
raise MaxRetryError(_pool, url, reason) from reason # type: ignore[arg-type]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='signor.uniroma2.it', port=443): Max retries exceeded with url: /downloads.php (Caused by ConnectTimeoutError(<HTTPSConnection(host='signor.uniroma2.it', port=443) at 0x7ff81090a330>, 'Connection to signor.uniroma2.it timed out. (connect timeout=15)'))
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/signor.py", line 26, in get
soup = get_soup(URL)
^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/pystow/utils/__init__.py", line 871, in get_soup
res = requests.get(url, verify=verify, timeout=timeout or 15, headers=headers)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/api.py", line 73, in get
return request("get", url, params=params, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/api.py", line 59, in request
return session.request(method=method, url=url, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/sessions.py", line 592, in request
resp = self.send(prep, **send_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/sessions.py", line 706, in send
r = adapter.send(request, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/adapters.py", line 666, in send
raise ConnectTimeout(e, request=request)
requests.exceptions.ConnectTimeout: HTTPSConnectionPool(host='signor.uniroma2.it', port=443): Max retries exceeded with url: /downloads.php (Caused by ConnectTimeoutError(<HTTPSConnection(host='signor.uniroma2.it', port=443) at 0x7ff81090a330>, 'Connection to signor.uniroma2.it timed out. (connect timeout=15)'))