Update runs started to fail for some Python projects

[rikardn]

Is there an existing issue for this?

• I have searched the existing issues

Package ecosystem

requirement.txt for Python package

Package manager version

pip 24.3.1

Language version

Python 3.13

Manifest location and content before the Dependabot update

https://github.com/pharmpy/pharmpy/blob/main/requirements.txt

dependabot.yml content

https://github.com/pharmpy/pharmpy/blob/main/.github/dependabot.yml

Updated dependency

No response

What you expected to see, versus what you actually saw

Since 2 days the update runs labled like pip in /. - Update #945847166 fails. Nothing in particular has changed on our side.

Native package manager behavior

No response

Images of the diff or a link to the PR, issue, or logs

The failed run: https://github.com/pharmpy/pharmpy/actions/runs/12701561660

The error:

Dependabot
Dependabot encountered an error performing the update

Error: The updater encountered one or more errors.

For more information see: https://github.com/pharmpy/pharmpy/network/updates/945847166 (write access to the repository is required to view the log)

The text following the link:

Dependabot encountered an unknown error

Dependabot failed to update your dependencies because an unexpected error occurred. See the logs for more details.
[Troubleshoot Dependabot errors](https://docs.github.com/github/managing-security-vulnerabilities/troubleshooting-dependabot-errors)

The full raw log:

2025-01-10T01:30:49.1862864Z Current runner version: '2.321.0'
2025-01-10T01:30:49.1889046Z ##[group]Operating System
2025-01-10T01:30:49.1890015Z Ubuntu
2025-01-10T01:30:49.1890639Z 24.04.1
2025-01-10T01:30:49.1891184Z LTS
2025-01-10T01:30:49.1891702Z ##[endgroup]
2025-01-10T01:30:49.1892256Z ##[group]Runner Image
2025-01-10T01:30:49.1892865Z Image: ubuntu-24.04
2025-01-10T01:30:49.1893386Z Version: 20250105.1.0
2025-01-10T01:30:49.1894477Z Included Software: https://github.com/actions/runner-images/blob/ubuntu24/20250105.1/images/ubuntu/Ubuntu2404-Readme.md
2025-01-10T01:30:49.1895817Z Image Release: https://github.com/actions/runner-images/releases/tag/ubuntu24%2F20250105.1
2025-01-10T01:30:49.1896730Z ##[endgroup]
2025-01-10T01:30:49.1897466Z ##[group]Runner Image Provisioner
2025-01-10T01:30:49.1898096Z 2.0.404.1
2025-01-10T01:30:49.1898563Z ##[endgroup]
2025-01-10T01:30:49.1900772Z ##[group]GITHUB_TOKEN Permissions
2025-01-10T01:30:49.1902894Z Actions: read
2025-01-10T01:30:49.1903732Z Attestations: read
2025-01-10T01:30:49.1904426Z Checks: read
2025-01-10T01:30:49.1904915Z Contents: read
2025-01-10T01:30:49.1905450Z Deployments: read
2025-01-10T01:30:49.1906006Z Discussions: read
2025-01-10T01:30:49.1906540Z Issues: read
2025-01-10T01:30:49.1907041Z Metadata: read
2025-01-10T01:30:49.1907703Z Packages: read
2025-01-10T01:30:49.1908259Z Pages: read
2025-01-10T01:30:49.1908747Z PullRequests: read
2025-01-10T01:30:49.1909327Z RepositoryProjects: read
2025-01-10T01:30:49.1909915Z SecurityEvents: read
2025-01-10T01:30:49.1910422Z Statuses: read
2025-01-10T01:30:49.1910941Z ##[endgroup]
2025-01-10T01:30:49.1914026Z Secret source: None
2025-01-10T01:30:49.1914985Z Prepare workflow directory
2025-01-10T01:30:49.2221254Z Prepare all required actions
2025-01-10T01:30:49.2257599Z Getting action download info
2025-01-10T01:30:49.3802278Z Download action repository 'github/dependabot-action@main' (SHA:0be28d6deb5d265a40277828ea3d2ae001dc6f5d)
2025-01-10T01:30:49.7246194Z Complete job name: Dependabot
2025-01-10T01:30:49.7996636Z ##[group]Run mkdir -p  ./dependabot-job-945847166-1736472639
2025-01-10T01:30:49.7997710Z �[36;1mmkdir -p  ./dependabot-job-945847166-1736472639�[0m
2025-01-10T01:30:49.8028427Z shell: /usr/bin/bash -e {0}
2025-01-10T01:30:49.8029209Z ##[endgroup]
2025-01-10T01:30:49.8289503Z ##[group]Run github/dependabot-action@main
2025-01-10T01:30:49.8290150Z env:
2025-01-10T01:30:49.8290541Z   DEPENDABOT_DISABLE_CLEANUP: 1
2025-01-10T01:30:49.8291059Z   DEPENDABOT_ENABLE_CONNECTIVITY_CHECK: 0
2025-01-10T01:30:49.8291904Z   GITHUB_TOKEN: ***
2025-01-10T01:30:49.8292699Z   GITHUB_DEPENDABOT_JOB_TOKEN: ***
2025-01-10T01:30:49.8293572Z   GITHUB_DEPENDABOT_CRED_TOKEN: ***
2025-01-10T01:30:49.8294080Z ##[endgroup]
2025-01-10T01:30:50.0465851Z 🤖 ~ starting update ~
2025-01-10T01:30:50.0482915Z Fetching job details
2025-01-10T01:30:50.5399947Z ##[group]Pulling updater images
2025-01-10T01:30:50.5445370Z Pulling image ghcr.io/dependabot/dependabot-updater-pip:8e121fd1af90dbea64a9ced4640478e7e41fff9e...
2025-01-10T01:31:05.9037614Z Pulled image ghcr.io/dependabot/dependabot-updater-pip:8e121fd1af90dbea64a9ced4640478e7e41fff9e
2025-01-10T01:31:05.9052183Z Pulling image ghcr.io/github/dependabot-update-job-proxy/dependabot-update-job-proxy:v2.0.20250106164350@sha256:3d7f1451fb945866f192cc64a691e821bce337de6218d58b47ff8098ecc42e7a...
2025-01-10T01:31:06.3379207Z Pulled image ghcr.io/github/dependabot-update-job-proxy/dependabot-update-job-proxy:v2.0.20250106164350@sha256:3d7f1451fb945866f192cc64a691e821bce337de6218d58b47ff8098ecc42e7a
2025-01-10T01:31:06.3381703Z ##[endgroup]
2025-01-10T01:31:06.3382208Z Starting update process
2025-01-10T01:31:06.6482594Z Created proxy container: c618cf01d29bb5b35e2c90013cffb744a39ca8d1d1e6ed2054f31497fc6d277b
2025-01-10T01:31:06.9120720Z Created container: d39d930db805b2e7b0a0e6933127b43c4881f252aa76323dd564727064335cc9
2025-01-10T01:31:06.9854594Z   proxy | 2025/01/10 01:31:06 proxy starting, commit: e49a3703db0cef7fcf7e11a692ff8007307c9711
2025-01-10T01:31:06.9863068Z   proxy | 2025/01/10 01:31:06 Listening (:1080)
2025-01-10T01:31:07.0801759Z updater | Updating certificates in /etc/ssl/certs...
2025-01-10T01:31:07.8271587Z updater | rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL
2025-01-10T01:31:07.8362801Z updater | 1 added, 0 removed; done.
2025-01-10T01:31:07.8363536Z Running hooks in /etc/ca-certificates/update.d...
2025-01-10T01:31:07.8372810Z updater | done.
2025-01-10T01:31:09.5785018Z updater | 2025/01/10 01:31:09 INFO <job_945847166> Starting job processing
2025-01-10T01:31:09.5845569Z 2025/01/10 01:31:09 INFO <job_945847166> Job definition: {"job":{"allowed-updates":[{"dependency-type":"direct","update-type":"all"}],"commit-message-options":{"prefix":null,"prefix-development":null,"include-scope":null},"credentials-metadata":[{"type":"git_source","host":"github.com"}],"debug":null,"dependencies":null,"dependency-groups":[{"name":"dask","rules":{"patterns":["dask","distributed"]}}],"dependency-group-to-refresh":null,"existing-pull-requests":[[{"dependency-name":"lxml","dependency-version":"4.6.2"}],[{"dependency-name":"jinja2","dependency-version":"2.11.3"}],[{"dependency-name":"pyyaml","dependency-version":"5.4"}],[{"dependency-name":"lxml","dependency-version":"4.6.3"}],[{"dependency-name":"pygments","dependency-version":"2.7.4"}],[{"dependency-name":"sympy","dependency-version":"1.8"}],[{"dependency-name":"idna","dependency-version":"3.1"}],[{"dependency-name":"sphinx","dependency-version":"3.5.4"}],[{"dependency-name":"websocket-client","dependency-version":"0.58.0"}],[{"dependency-name":"networkx","dependency-version":"2.5.1"}],[{"dependency-name":"psutil","dependency-version":"5.8.0"}],[{"dependency-name":"pep517","dependency-version":"0.10.0"}],[{"dependency-name":"docker","dependency-version":"5.0.0"}],[{"dependency-name":"msgpack","dependency-version":"1.0.2"}],[{"dependency-name":"html5lib","dependency-version":"1.1"}],[{"dependency-name":"numpy","dependency-version":"1.20.2"}],[{"dependency-name":"pandas","dependency-version":"1.2.4"}],[{"dependency-name":"sphinx","dependency-version":"4.0.0"}],[{"dependency-name":"sphinx","dependency-version":"4.0.1"}],[{"dependency-name":"markupsafe","dependency-version":"2.0.0"}],[{"dependency-name":"jinja2","dependency-version":"3.0.0"}],[{"dependency-name":"dask","dependency-version":"2021.5.0"}],[{"dependency-name":"markupsafe","dependency-version":"2.0.1"}],[{"dependency-name":"jinja2","dependency-version":"3.0.1"}],[{"dependency-name":"sphinx","dependency-version":"4.0.2"}],[{"dependency-name":"pydata-sphinx-theme","dependency-version":"0.6.3"}],[{"dependency-name":"idna","dependency-version":"3.2"}],[{"dependency-name":"dask[distributed]","dependency-version":"2021.6.0"}],[{"dependency-name":"dask","dependency-version":"2021.6.0"}],[{"dependency-name":"dask","dependency-version":"2021.6.1"}],[{"dependency-name":"distributed","dependency-version":"2021.6.2"}],[{"dependency-name":"dask","dependency-version":"2021.6.2"}],[{"dependency-name":"pandas","dependency-version":"1.3.0"}],[{"dependency-name":"sphinx","dependency-version":"4.0.3"}],[{"dependency-name":"networkx","dependency-version":"2.6.1"}],[{"dependency-name":"dask","dependency-version":"2021.7.0"}],[{"dependency-name":"sphinx","dependency-version":"4.1.0"}],[{"dependency-name":"distributed","dependency-version":"2021.7.0"}],[{"dependency-name":"sphinx","dependency-version":"4.1.1"}],[{"dependency-name":"dask","dependency-version":"2021.7.1"}],[{"dependency-name":"pandas","dependency-version":"1.3.1"}],[{"dependency-name":"distributed","dependency-version":"2021.7.1"}],[{"dependency-name":"distributed","dependency-version":"2021.7.2"}],[{"dependency-name":"ipykernel","dependency-version":"6.1.0"}],[{"dependency-name":"distributed","dependency-version":"2021.8.0"}],[{"dependency-name":"dask","dependency-version":"2021.8.0"}],[{"dependency-name":"ipykernel","dependency-version":"6.2.0"}],[{"dependency-name":"distributed","dependency-version":"2021.8.1"}],[{"dependency-name":"dask","dependency-version":"2021.8.1"}],[{"dependency-name":"lark-parser","dependency-version":"0.12.0"}],[{"dependency-name":"ipykernel","dependency-version":"6.3.1"}],[{"dependency-name":"dask","dependency-version":"2021.9.0"}],[{"dependency-name":"distributed","dependency-version":"2021.9.0"}],[{"dependency-name":"ipykernel","dependency-version":"6.4.0"}],[{"dependency-name":"ipykernel","dependency-version":"6.4.1"}],[{"dependency-name":"dask","dependency-version":"2021.9.1"}],[{"dependency-name":"distributed","dependency-version":"2021.9.1"}],[{"dependency-name":"jsonschema","dependency-version":"4.0.0"}],[{"dependency-name":"jsonschema","dependency-version":"4.0.1"}],[{"dependency-name":"jsonschema","dependency-version":"4.1.0"}],[{"dependency-name":"jsonschema","dependency-version":"4.1.1"}],[{"dependency-name":"ipykernel","dependency-version":"6.4.2"}],[{"dependency-name":"jsonschema","dependency-version":"4.1.2"}],[{"dependency-name":"distributed","dependency-version":"2021.10.0"}],[{"dependency-name":"docutils","dependency-version":"0.18"}],[{"dependency-name":"packaging","dependency-version":"21.2"}],[{"dependency-name":"ipykernel","dependency-version":"6.5.0"}],[{"dependency-name":"jsonschema","dependency-version":"4.2.0"}],[{"dependency-name":"distributed","dependency-version":"2021.11.0"}],[{"dependency-name":"jsonschema","dependency-version":"4.2.1"}],[{"dependency-name":"distributed","dependency-version":"2021.11.1"}],[{"dependency-name":"ipykernel","dependency-version":"6.5.1"}],[{"dependency-name":"distributed","dependency-version":"2021.11.2"}],[{"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2025-01-10T01:31:09.6262111Z updater | 2025/01/10 01:31:09 INFO <job_945847166> Started process PID: 1071 with command: {} git config --global credential.helper '!/home/dependabot/common/lib/dependabot/../../bin/git-credential-store-immutable --file /home/dependabot/dependabot-updater/git.store' {}
2025-01-10T01:31:09.6415435Z updater | 2025/01/10 01:31:09 INFO <job_945847166> Process PID: 1071 completed with status: pid 1071 exit 0
2025-01-10T01:31:09.6416988Z updater | 2025/01/10 01:31:09 INFO <job_945847166> Total execution time: 0.02 seconds
2025-01-10T01:31:09.6460559Z updater | 2025/01/10 01:31:09 INFO <job_945847166> Started process PID: 1079 with command: {} git config --global --replace-all url.https://github.com/.insteadOf ssh://git@github.com/ {}
2025-01-10T01:31:09.6494486Z updater | 2025/01/10 01:31:09 INFO <job_945847166> Process PID: 1079 completed with status: pid 1079 exit 0
2025-01-10T01:31:09.6495321Z 2025/01/10 01:31:09 INFO <job_945847166> Total execution time: 0.0 seconds
2025-01-10T01:31:09.6502946Z updater | 2025/01/10 01:31:09 INFO <job_945847166> Started process PID: 1086 with command: {} git config --global --add url.https://github.com/.insteadOf ssh://git@github.com: {}
2025-01-10T01:31:09.6537947Z updater | 2025/01/10 01:31:09 INFO <job_945847166> Process PID: 1086 completed with status: pid 1086 exit 0
2025-01-10T01:31:09.6539311Z 2025/01/10 01:31:09 INFO <job_945847166> Total execution time: 0.0 seconds
2025-01-10T01:31:09.6543645Z updater | 2025/01/10 01:31:09 INFO <job_945847166> Started process PID: 1093 with command: {} git config --global --add url.https://github.com/.insteadOf git@github.com: {}
2025-01-10T01:31:09.6581914Z updater | 2025/01/10 01:31:09 INFO <job_945847166> Process PID: 1093 completed with status: pid 1093 exit 0
2025-01-10T01:31:09.6582983Z 2025/01/10 01:31:09 INFO <job_945847166> Total execution time: 0.0 seconds
2025-01-10T01:31:09.6587464Z updater | 2025/01/10 01:31:09 INFO <job_945847166> Started process PID: 1100 with command: {} git config --global --add url.https://github.com/.insteadOf git@github.com/ {}
2025-01-10T01:31:09.6628575Z updater | 2025/01/10 01:31:09 INFO <job_945847166> Process PID: 1100 completed with status: pid 1100 exit 0
2025-01-10T01:31:09.6631206Z updater | 2025/01/10 01:31:09 INFO <job_945847166> Total execution time: 0.0 seconds
2025-01-10T01:31:09.6640496Z updater | 2025/01/10 01:31:09 INFO <job_945847166> Started process PID: 1107 with command: {} git config --global --add url.https://github.com/.insteadOf git://github.com/ {}
2025-01-10T01:31:09.6675530Z updater | 2025/01/10 01:31:09 INFO <job_945847166> Process PID: 1107 completed with status: pid 1107 exit 0
2025-01-10T01:31:09.6676293Z 2025/01/10 01:31:09 INFO <job_945847166> Total execution time: 0.0 seconds
2025-01-10T01:31:09.6691726Z updater | 2025/01/10 01:31:09 INFO <job_945847166> Started process PID: 1114 with command: {} git clone --no-tags --depth 1 --recurse-submodules --shallow-submodules https://github.com/pharmpy/pharmpy /home/dependabot/dependabot-updater/repo {}
2025-01-10T01:31:09.7854217Z   proxy | 2025/01/10 01:31:09 [002] GET https://github.com:443/pharmpy/pharmpy/info/refs?service=git-upload-pack
2025-01-10T01:31:09.7861701Z   proxy | 2025/01/10 01:31:09 [002] * authenticating git server request (host: github.com)
2025-01-10T01:31:09.8547506Z   proxy | 2025/01/10 01:31:09 [002] 200 https://github.com:443/pharmpy/pharmpy/info/refs?service=git-upload-pack
2025-01-10T01:31:09.8952269Z   proxy | 2025/01/10 01:31:09 [004] POST https://github.com:443/pharmpy/pharmpy/git-upload-pack
2025-01-10T01:31:09.8953313Z 2025/01/10 01:31:09 [004] * authenticating git server request (host: github.com)
2025-01-10T01:31:10.0001238Z   proxy | 2025/01/10 01:31:09 [004] 200 https://github.com:443/pharmpy/pharmpy/git-upload-pack
2025-01-10T01:31:10.0323616Z   proxy | 2025/01/10 01:31:10 [006] POST https://github.com:443/pharmpy/pharmpy/git-upload-pack
2025-01-10T01:31:10.0324822Z 2025/01/10 01:31:10 [006] * authenticating git server request (host: github.com)
2025-01-10T01:31:10.2815118Z   proxy | 2025/01/10 01:31:10 [006] 200 https://github.com:443/pharmpy/pharmpy/git-upload-pack
2025-01-10T01:31:10.6599553Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Process PID: 1114 completed with status: pid 1114 exit 0
2025-01-10T01:31:10.6600641Z 2025/01/10 01:31:10 INFO <job_945847166> Total execution time: 0.99 seconds
2025-01-10T01:31:10.6606742Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Started process PID: 1159 with command: {} git -C /home/dependabot/dependabot-updater/repo ls-files --stage {}
2025-01-10T01:31:10.6679928Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Process PID: 1159 completed with status: pid 1159 exit 0
2025-01-10T01:31:10.6689028Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Total execution time: 0.01 seconds
2025-01-10T01:31:10.6745578Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Started process PID: 1174 with command: {} git config --global credential.helper '!/home/dependabot/common/lib/dependabot/../../bin/git-credential-store-immutable --file /home/dependabot/dependabot-updater/git.store' {}
2025-01-10T01:31:10.6788079Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Process PID: 1174 completed with status: pid 1174 exit 0
2025-01-10T01:31:10.6789634Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Total execution time: 0.0 seconds
2025-01-10T01:31:10.6827733Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Started process PID: 1182 with command: {} git config --global --replace-all url.https://github.com/.insteadOf ssh://git@github.com/ {}
2025-01-10T01:31:10.6841339Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Process PID: 1182 completed with status: pid 1182 exit 0
2025-01-10T01:31:10.6842500Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Total execution time: 0.01 seconds
2025-01-10T01:31:10.6847627Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Started process PID: 1189 with command: {} git config --global --add url.https://github.com/.insteadOf ssh://git@github.com: {}
2025-01-10T01:31:10.6884376Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Process PID: 1189 completed with status: pid 1189 exit 0
2025-01-10T01:31:10.6885525Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Total execution time: 0.0 seconds
2025-01-10T01:31:10.6891356Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Started process PID: 1196 with command: {} git config --global --add url.https://github.com/.insteadOf git@github.com: {}
2025-01-10T01:31:10.6928792Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Process PID: 1196 completed with status: pid 1196 exit 0
2025-01-10T01:31:10.6929926Z 2025/01/10 01:31:10 INFO <job_945847166> Total execution time: 0.0 seconds
2025-01-10T01:31:10.6933540Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Started process PID: 1203 with command: {} git config --global --add url.https://github.com/.insteadOf git@github.com/ {}
2025-01-10T01:31:10.6972249Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Process PID: 1203 completed with status: pid 1203 exit 0
2025-01-10T01:31:10.6973074Z 2025/01/10 01:31:10 INFO <job_945847166> Total execution time: 0.0 seconds
2025-01-10T01:31:10.6984031Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Started process PID: 1210 with command: {} git config --global --add url.https://github.com/.insteadOf git://github.com/ {}
2025-01-10T01:31:10.7020974Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Process PID: 1210 completed with status: pid 1210 exit 0
2025-01-10T01:31:10.7022954Z 2025/01/10 01:31:10 INFO <job_945847166> Total execution time: 0.0 seconds
2025-01-10T01:31:10.7027847Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Started process PID: 1217 with command: {} git rev-parse HEAD {}
2025-01-10T01:31:10.7065081Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Process PID: 1217 completed with status: pid 1217 exit 0
2025-01-10T01:31:10.7066092Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Total execution time: 0.0 seconds
2025-01-10T01:31:10.7108689Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Started process PID: 1232 with command: {} git config --global credential.helper '!/home/dependabot/common/lib/dependabot/../../bin/git-credential-store-immutable --file /home/dependabot/dependabot-updater/git.store' {}
2025-01-10T01:31:10.7151044Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Process PID: 1232 completed with status: pid 1232 exit 0
2025-01-10T01:31:10.7152924Z 2025/01/10 01:31:10 INFO <job_945847166> Total execution time: 0.0 seconds
2025-01-10T01:31:10.7159060Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Started process PID: 1240 with command: {} git config --global --replace-all url.https://github.com/.insteadOf ssh://git@github.com/ {}
2025-01-10T01:31:10.7198983Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Process PID: 1240 completed with status: pid 1240 exit 0
2025-01-10T01:31:10.7199980Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Total execution time: 0.0 seconds
2025-01-10T01:31:10.7204185Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Started process PID: 1247 with command: {} git config --global --add url.https://github.com/.insteadOf ssh://git@github.com: {}
2025-01-10T01:31:10.7245701Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Process PID: 1247 completed with status: pid 1247 exit 0
2025-01-10T01:31:10.7246518Z 2025/01/10 01:31:10 INFO <job_945847166> Total execution time: 0.0 seconds
2025-01-10T01:31:10.7252518Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Started process PID: 1254 with command: {} git config --global --add url.https://github.com/.insteadOf git@github.com: {}
2025-01-10T01:31:10.7293514Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Process PID: 1254 completed with status: pid 1254 exit 0
2025-01-10T01:31:10.7294388Z 2025/01/10 01:31:10 INFO <job_945847166> Total execution time: 0.0 seconds
2025-01-10T01:31:10.7297999Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Started process PID: 1261 with command: {} git config --global --add url.https://github.com/.insteadOf git@github.com/ {}
2025-01-10T01:31:10.7338719Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Process PID: 1261 completed with status: pid 1261 exit 0
2025-01-10T01:31:10.7343062Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Total execution time: 0.0 seconds
2025-01-10T01:31:10.7344230Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Started process PID: 1268 with command: {} git config --global --add url.https://github.com/.insteadOf git://github.com/ {}
2025-01-10T01:31:10.7384848Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Process PID: 1268 completed with status: pid 1268 exit 0
2025-01-10T01:31:10.7385403Z 2025/01/10 01:31:10 INFO <job_945847166> Total execution time: 0.0 seconds
2025-01-10T01:31:10.7389779Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Started process PID: 1275 with command: {} git rev-parse HEAD {}
2025-01-10T01:31:10.7428701Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Process PID: 1275 completed with status: pid 1275 exit 0
2025-01-10T01:31:10.7429496Z 2025/01/10 01:31:10 INFO <job_945847166> Total execution time: 0.0 seconds
2025-01-10T01:31:10.8110964Z updater | 2025/01/10 01:31:10 INFO <job_945847166> Dependabot is using Python version '3.13'.
2025-01-10T01:31:10.9446824Z   proxy | 2025/01/10 01:31:10 [008] POST /update_jobs/945847166/record_ecosystem_versions
2025-01-10T01:31:11.0384829Z   proxy | 2025/01/10 01:31:11 [008] 204 /update_jobs/945847166/record_ecosystem_versions
2025-01-10T01:31:11.0419069Z updater | 2025/01/10 01:31:11 INFO <job_945847166> Base commit SHA: 79e1794250b639352d6df12ad162946169e8de60
2025-01-10T01:31:11.0427524Z updater | 2025/01/10 01:31:11 INFO <job_945847166> Finished job processing
2025-01-10T01:31:12.8028457Z updater | 2025/01/10 01:31:12 INFO <job_945847166> Starting job processing
2025-01-10T01:31:12.8703184Z updater | 2025/01/10 01:31:12 INFO <job_945847166> Started process PID: 1288 with command: {} pyenv versions {}
2025-01-10T01:31:12.9220255Z updater | 2025/01/10 01:31:12 INFO <job_945847166> Process PID: 1288 completed with status: pid 1288 exit 0
2025-01-10T01:31:12.9220839Z updater | 2025/01/10 01:31:12 INFO <job_945847166> Total execution time: 0.06 seconds
2025-01-10T01:31:12.9624196Z updater | 2025/01/10 01:31:12 INFO <job_945847166> Started process PID: 1332 with command: {} pyenv local 3.13 {}
2025-01-10T01:31:12.9991940Z updater | 2025/01/10 01:31:12 INFO <job_945847166> Process PID: 1332 completed with status: pid 1332 exit 0
2025-01-10T01:31:12.9992771Z 2025/01/10 01:31:12 INFO <job_945847166> Total execution time: 0.04 seconds
2025-01-10T01:31:13.0009699Z updater | 2025/01/10 01:31:13 INFO <job_945847166> Started process PID: 1376 with command: {} pyenv exec pip --version {}
2025-01-10T01:31:14.2970838Z updater | 2025/01/10 01:31:14 INFO <job_945847166> Process PID: 1376 completed with status: pid 1376 exit 0
2025-01-10T01:31:14.2971759Z 2025/01/10 01:31:14 INFO <job_945847166> Total execution time: 1.3 seconds
2025-01-10T01:31:14.2972964Z updater | 2025/01/10 01:31:14 INFO <job_945847166> Package manager pip, Info : pip 24.0 from /usr/local/.pyenv/versions/3.13.1/lib/python3.13/site-packages/pip (python 3.13)
2025-01-10T01:31:14.2973901Z 
2025-01-10T01:31:14.2995085Z updater | 2025/01/10 01:31:14 INFO <job_945847166> Detected package manager : pip
2025-01-10T01:31:14.3002760Z updater | 2025/01/10 01:31:14 INFO <job_945847166> Started process PID: 1469 with command: {} pyenv versions {}
2025-01-10T01:31:14.3705108Z updater | 2025/01/10 01:31:14 INFO <job_945847166> Process PID: 1469 completed with status: pid 1469 exit 0
2025-01-10T01:31:14.3706028Z 2025/01/10 01:31:14 INFO <job_945847166> Total execution time: 0.07 seconds
2025-01-10T01:31:14.3715497Z updater | 2025/01/10 01:31:14 INFO <job_945847166> Started process PID: 1544 with command: {} pyenv local 3.13 {}
2025-01-10T01:31:14.4077931Z updater | 2025/01/10 01:31:14 INFO <job_945847166> Process PID: 1544 completed with status: pid 1544 exit 0
2025-01-10T01:31:14.4079559Z 2025/01/10 01:31:14 INFO <job_945847166> Total execution time: 0.04 seconds
2025-01-10T01:31:14.4084874Z updater | 2025/01/10 01:31:14 INFO <job_945847166> Started process PID: 1588 with command: {} pyenv exec pip --version {}
2025-01-10T01:31:14.7671994Z updater | 2025/01/10 01:31:14 INFO <job_945847166> Process PID: 1588 completed with status: pid 1588 exit 0
2025-01-10T01:31:14.7674278Z 2025/01/10 01:31:14 INFO <job_945847166> Total execution time: 0.36 seconds
2025-01-10T01:31:14.7675603Z 2025/01/10 01:31:14 INFO <job_945847166> Package manager pip, Info : pip 24.0 from /usr/local/.pyenv/versions/3.13.1/lib/python3.13/site-packages/pip (python 3.13)
2025-01-10T01:31:14.7676490Z 
2025-01-10T01:31:14.7676787Z updater | 2025/01/10 01:31:14 INFO <job_945847166> Detected python version: 3.13.1
2025-01-10T01:31:14.7677690Z 2025/01/10 01:31:14 INFO <job_945847166> Detected python major minor version: 3.13
2025-01-10T01:31:14.7683800Z updater | 2025/01/10 01:31:14 INFO <job_945847166> Started process PID: 1681 with command: {} pyenv exec python --version {}
2025-01-10T01:31:14.8370780Z updater | 2025/01/10 01:31:14 INFO <job_945847166> Process PID: 1681 completed with status: pid 1681 exit 0
2025-01-10T01:31:14.8371670Z 2025/01/10 01:31:14 INFO <job_945847166> Total execution time: 0.07 seconds
2025-01-10T01:31:14.8508492Z updater | 2025/01/10 01:31:14 INFO <job_945847166> Started process PID: 1753 with command: pyenv exec python3 /opt/python/run.py
2025-01-10T01:31:16.8725456Z updater | 2025/01/10 01:31:16 INFO <job_945847166> Process PID: 1753 completed with status: pid 1753 exit 0
2025-01-10T01:31:16.8744464Z updater | 2025/01/10 01:31:16 INFO <job_945847166> Total execution time: 2.02 seconds
2025-01-10T01:31:16.9220540Z updater | 2025/01/10 01:31:16 INFO <job_945847166> Detected python version: 3.13.1
2025-01-10T01:31:16.9221361Z 2025/01/10 01:31:16 INFO <job_945847166> Detected python major minor version: 3.13
2025-01-10T01:31:16.9253494Z updater | 2025/01/10 01:31:16 INFO <job_945847166> Detected python version: 3.13.1
2025-01-10T01:31:16.9254313Z 2025/01/10 01:31:16 INFO <job_945847166> Detected python major minor version: 3.13
2025-01-10T01:31:16.9265400Z updater | 2025/01/10 01:31:16 ERROR <job_945847166> undefined method `captures' for nil
2025-01-10T01:31:16.9269224Z updater | 2025/01/10 01:31:16 ERROR <job_945847166> /home/dependabot/python/lib/dependabot/python/file_parser.rb:341:in `evaluate_condition'
2025-01-10T01:31:16.9270653Z 2025/01/10 01:31:16 ERROR <job_945847166> /home/dependabot/python/lib/dependabot/python/file_parser.rb:323:in `marker_satisfied?'
2025-01-10T01:31:16.9271922Z 2025/01/10 01:31:16 ERROR <job_945847166> /home/dependabot/python/lib/dependabot/python/file_parser.rb:310:in `blocking_marker?'
2025-01-10T01:31:16.9273418Z 2025/01/10 01:31:16 ERROR <job_945847166> /home/dependabot/python/lib/dependabot/python/file_parser.rb:257:in `block in requirement_dependencies'
2025-01-10T01:31:16.9274860Z 2025/01/10 01:31:16 ERROR <job_945847166> /home/dependabot/python/lib/dependabot/python/file_parser.rb:254:in `each'
2025-01-10T01:31:16.9276297Z updater | 2025/01/10 01:31:16 ERROR <job_945847166> /home/dependabot/python/lib/dependabot/python/file_parser.rb:254:in `requirement_dependencies'
2025-01-10T01:31:16.9277803Z 2025/01/10 01:31:16 ERROR <job_945847166> /home/dependabot/python/lib/dependabot/python/file_parser.rb:54:in `parse'
2025-01-10T01:31:16.9279367Z 2025/01/10 01:31:16 ERROR <job_945847166> /home/dependabot/dependabot-updater/lib/dependabot/dependency_snapshot.rb:229:in `parse_files!'
2025-01-10T01:31:16.9281299Z 2025/01/10 01:31:16 ERROR <job_945847166> /home/dependabot/dependabot-updater/vendor/ruby/3.3.0/gems/sorbet-runtime-0.5.11577/lib/types/private/methods/call_validation.rb:270:in `bind_call'
2025-01-10T01:31:16.9282848Z 2025/01/10 01:31:16 ERROR <job_945847166> /home/dependabot/dependabot-updater/vendor/ruby/3.3.0/gems/sorbet-runtime-0.5.11577/lib/types/private/methods/call_validation.rb:270:in `validate_call'
2025-01-10T01:31:16.9285221Z updater | 2025/01/10 01:31:16 ERROR <job_945847166> /home/dependabot/dependabot-updater/vendor/ruby/3.3.0/gems/sorbet-runtime-0.5.11577/lib/types/private/methods/_methods.rb:277:in `block in _on_method_added'
2025-01-10T01:31:16.9287139Z 2025/01/10 01:31:16 ERROR <job_945847166> /home/dependabot/dependabot-updater/lib/dependabot/dependency_snapshot.rb:189:in `block in initialize'
2025-01-10T01:31:16.9288703Z 2025/01/10 01:31:16 ERROR <job_945847166> /home/dependabot/dependabot-updater/lib/dependabot/dependency_snapshot.rb:187:in `each'
2025-01-10T01:31:16.9289559Z 2025/01/10 01:31:16 ERROR <job_945847166> /home/dependabot/dependabot-updater/lib/dependabot/dependency_snapshot.rb:187:in `initialize'
2025-01-10T01:31:16.9290575Z updater | 2025/01/10 01:31:16 ERROR <job_945847166> /home/dependabot/dependabot-updater/vendor/ruby/3.3.0/gems/sorbet-runtime-0.5.11577/lib/types/private/methods/call_validation.rb:270:in `bind_call'
2025-01-10T01:31:16.9291762Z 2025/01/10 01:31:16 ERROR <job_945847166> /home/dependabot/dependabot-updater/vendor/ruby/3.3.0/gems/sorbet-runtime-0.5.11577/lib/types/private/methods/call_validation.rb:270:in `validate_call'
2025-01-10T01:31:16.9292945Z 2025/01/10 01:31:16 ERROR <job_945847166> /home/dependabot/dependabot-updater/vendor/ruby/3.3.0/gems/sorbet-runtime-0.5.11577/lib/types/private/methods/_methods.rb:277:in `block in _on_method_added'
2025-01-10T01:31:16.9294137Z 2025/01/10 01:31:16 ERROR <job_945847166> /home/dependabot/dependabot-updater/lib/dependabot/dependency_snapshot.rb:38:in `new'
2025-01-10T01:31:16.9294988Z updater | 2025/01/10 01:31:16 ERROR <job_945847166> /home/dependabot/dependabot-updater/lib/dependabot/dependency_snapshot.rb:38:in `create_from_job_definition'
2025-01-10T01:31:16.9296040Z 2025/01/10 01:31:16 ERROR <job_945847166> /home/dependabot/dependabot-updater/vendor/ruby/3.3.0/gems/sorbet-runtime-0.5.11577/lib/types/private/methods/call_validation.rb:270:in `bind_call'
2025-01-10T01:31:16.9297230Z updater | 2025/01/10 01:31:16 ERROR <job_945847166> /home/dependabot/dependabot-updater/vendor/ruby/3.3.0/gems/sorbet-runtime-0.5.11577/lib/types/private/methods/call_validation.rb:270:in `validate_call'
2025-01-10T01:31:16.9298698Z 2025/01/10 01:31:16 ERROR <job_945847166> /home/dependabot/dependabot-updater/vendor/ruby/3.3.0/gems/sorbet-runtime-0.5.11577/lib/types/private/methods/_methods.rb:277:in `block in _on_method_added'
2025-01-10T01:31:16.9299772Z updater | 2025/01/10 01:31:16 ERROR <job_945847166> /home/dependabot/dependabot-updater/lib/dependabot/update_files_command.rb:22:in `block in perform_job'
2025-01-10T01:31:16.9300796Z 2025/01/10 01:31:16 ERROR <job_945847166> /home/dependabot/dependabot-updater/vendor/ruby/3.3.0/gems/opentelemetry-api-1.4.0/lib/opentelemetry/trace/tracer.rb:37:in `block in in_span'
2025-01-10T01:31:16.9301905Z updater | 2025/01/10 01:31:16 ERROR <job_945847166> /home/dependabot/dependabot-updater/vendor/ruby/3.3.0/gems/opentelemetry-api-1.4.0/lib/opentelemetry/trace.rb:70:in `block in with_span'
2025-01-10T01:31:16.9302974Z 2025/01/10 01:31:16 ERROR <job_945847166> /home/dependabot/dependabot-updater/vendor/ruby/3.3.0/gems/opentelemetry-api-1.4.0/lib/opentelemetry/context.rb:87:in `with_value'
2025-01-10T01:31:16.9303985Z 2025/01/10 01:31:16 ERROR <job_945847166> /home/dependabot/dependabot-updater/vendor/ruby/3.3.0/gems/opentelemetry-api-1.4.0/lib/opentelemetry/trace.rb:70:in `with_span'
2025-01-10T01:31:16.9305153Z updater | 2025/01/10 01:31:16 ERROR <job_945847166> /home/dependabot/dependabot-updater/vendor/ruby/3.3.0/gems/opentelemetry-api-1.4.0/lib/opentelemetry/trace/tracer.rb:37:in `in_span'
2025-01-10T01:31:16.9306143Z updater | 2025/01/10 01:31:16 ERROR <job_945847166> /home/dependabot/dependabot-updater/lib/dependabot/update_files_command.rb:18:in `perform_job'
2025-01-10T01:31:16.9306944Z updater | 2025/01/10 01:31:16 ERROR <job_945847166> /home/dependabot/dependabot-updater/lib/dependabot/base_command.rb:37:in `run'
2025-01-10T01:31:16.9307612Z 2025/01/10 01:31:16 ERROR <job_945847166> bin/update_files.rb:46:in `<main>'
2025-01-10T01:31:16.9554128Z   proxy | 2025/01/10 01:31:16 [011] POST /update_jobs/945847166/record_update_job_unknown_error
2025-01-10T01:31:17.0198739Z   proxy | 2025/01/10 01:31:17 [011] 204 /update_jobs/945847166/record_update_job_unknown_error
2025-01-10T01:31:17.0272533Z   proxy | 2025/01/10 01:31:17 [013] POST /update_jobs/945847166/record_update_job_error
2025-01-10T01:31:17.0704452Z   proxy | 2025/01/10 01:31:17 [013] 204 /update_jobs/945847166/record_update_job_error
2025-01-10T01:31:17.0812512Z   proxy | 2025/01/10 01:31:17 [015] POST /update_jobs/945847166/record_update_job_unknown_error
2025-01-10T01:31:17.1417276Z   proxy | 2025/01/10 01:31:17 [015] 204 /update_jobs/945847166/record_update_job_unknown_error
2025-01-10T01:31:17.1891803Z   proxy | 2025/01/10 01:31:17 [017] PATCH /update_jobs/945847166/mark_as_processed
2025-01-10T01:31:17.2570243Z   proxy | 2025/01/10 01:31:17 [017] 204 /update_jobs/945847166/mark_as_processed
2025-01-10T01:31:17.2578338Z updater | 2025/01/10 01:31:17 INFO <job_945847166> Finished job processing
2025-01-10T01:31:17.2591029Z updater | 2025/01/10 01:31:17 INFO Results:
2025-01-10T01:31:17.2591811Z Dependabot encountered '1' error(s) during execution, please check the logs for more details.
2025-01-10T01:31:17.2592305Z +--------------------+
2025-01-10T01:31:17.2592952Z |       Errors       |
2025-01-10T01:31:17.2593287Z +--------------------+
2025-01-10T01:31:17.2593592Z | update_files_error |
2025-01-10T01:31:17.2593792Z +--------------------+
2025-01-10T01:31:17.3921200Z Failure running container d39d930db805b2e7b0a0e6933127b43c4881f252aa76323dd564727064335cc9
2025-01-10T01:31:17.4648988Z Cleaned up container d39d930db805b2e7b0a0e6933127b43c4881f252aa76323dd564727064335cc9
2025-01-10T01:31:17.4763110Z   proxy | 2025/01/10 01:31:17 0/8 calls cached (0%)
2025-01-10T01:31:17.4764581Z   proxy | 2025/01/10 01:31:17 Posting metrics to remote API endpoint
2025-01-10T01:31:17.8301284Z ##[error]Dependabot encountered an error performing the update

Error: The updater encountered one or more errors.

For more information see: https://github.com/pharmpy/pharmpy/network/updates/945847166 (write access to the repository is required to view the log)
2025-01-10T01:31:17.8308817Z 🤖 ~ finished: error reported to Dependabot ~
2025-01-10T01:31:17.8399619Z Post job cleanup.
2025-01-10T01:31:17.9685739Z Cleaning up orphan processes

Smallest manifest that reproduces the issue

No response