Dependency Dashboard

This issue lists Renovate updates and detected dependencies. Read the [Dependency Dashboard](https://docs.renovatebot.com/key-concepts/dashboard/) docs to learn more.
[View this repository on the Mend.io Web Portal](https://developer.mend.io/github/DiamondLightSource/python-relion).

## Config Migration Needed

- [ ] Select this checkbox to let Renovate create an automated Config Migration PR.

## Pending Approval

The following branches are pending approval. To create them, click on a checkbox below.

- [ ] Update all dependencies (`dials_data`, `gemmi`, `graphviz`, `htcondor`, `importlib_metadata`, `ispyb`, `matplotlib`, `mrcfile`, `opencv-python`, `opencv-python-headless`, `pandas`, `plotly`, `pytest-mock`, `sphinx-rtd-theme`, `starfile`, `workflows`, `zocalo`)
- [ ] Update actions/checkout action to v6
- [ ] Update all dependencies (major) (`Sphinx`, `htcondor`, `importlib_metadata`, `ispyb`, `numpy`, `pandas`, `plotly`, `pytest-cov`, `sphinx-rtd-theme`, `workflows`, `zocalo`)
- [ ] Update github/codeql-action action to v4
- [ ] 🔐 **Create all pending approval PRs at once** 🔐

## Open

The following updates have all been created. To force a retry/rebase of any, click on a checkbox below.

- [ ] [Update dependency pydantic to v1.10.13 [SECURITY]](../pull/204)
- [ ] [Update dependency pillow to v10.3.0 [SECURITY]](../pull/203)
- [ ] [Update dependency pytest to v9 [SECURITY]](../pull/205)
- [ ] **Click on this checkbox to rebase all open PRs at once**

## Detected Dependencies

dockerfile (1)

Dockerfile (1)

- `nvidia/cuda 10.2-devel-centos7`

github-actions (1)

.github/workflows/codeql.yml (4)

- `actions/checkout v3` → [Updates: `v6`]
- `github/codeql-action v2` → [Updates: `v4`]
- `github/codeql-action v2` → [Updates: `v4`]
- `github/codeql-action v2` → [Updates: `v4`]

helm-values (1)

Helm/values.yaml

pep621 (1)

pyproject.toml (1)

- `setuptools >= 40.6.0`

pip_requirements (3)

requirements_dev.txt (18)

- `bump2version ==1.0.1`
- `dials_data ==2.4.81` → [Updates: `==2.4.141`]
- `gemmi ==0.6.5` → [Updates: `==0.7.5`]
- `graphviz ==0.20.2` → [Updates: `==0.21`]
- `ispyb ==10.0.0` → [Updates: `==10.2.4`, `==12.0.0`]
- `matplotlib ==3.8.3` → [Updates: `==3.10.9`]
- `mrcfile ==1.5.0` → [Updates: `==1.5.4`]
- `opencv-python ==4.9.0.80` → [Updates: `==4.13.0.92`]
- `pandas ==2.2.1` → [Updates: `==2.3.3`, `==3.0.2`]
- `pillow ==10.2.0` → [Updates: `==10.3.0`]
- `plotly ==5.20.0` → [Updates: `==5.24.1`, `==6.7.0`]
- `pydantic ==1.10.7` → [Updates: `==1.10.13`]
- `pytest-cov ==4.1.0` → [Updates: `==7.1.0`]
- `pytest-mock ==3.12.0` → [Updates: `==3.15.1`]
- `pytest ==8.1.1` → [Updates: `==9.0.3`]
- `starfile ==0.5.6` → [Updates: `==0.5.13`]
- `workflows ==2.26` → [Updates: `==2.28`, `==3.4`]
- `zocalo ==0.30.2` → [Updates: `==0.32.0`, `==1.4.0`]

requirements_doc.txt (10)

- `gemmi ==0.6.5` → [Updates: `==0.7.5`]
- `ispyb ==10.0.0` → [Updates: `==10.2.4`, `==12.0.0`]
- `matplotlib ==3.8.3` → [Updates: `==3.10.9`]
- `mrcfile ==1.5.0` → [Updates: `==1.5.4`]
- `pandas ==2.2.1` → [Updates: `==2.3.3`, `==3.0.2`]
- `pillow ==10.2.0` → [Updates: `==10.3.0`]
- `plotly ==5.20.0` → [Updates: `==5.24.1`, `==6.7.0`]
- `pydantic ==1.10.7` → [Updates: `==1.10.13`]
- `Sphinx ==4.5.0` → [Updates: `==9.1.0`]
- `sphinx-rtd-theme ==1.0.0` → [Updates: `==1.3.0`, `==3.1.0`]

requirements.txt (14)

- `gemmi ==0.6.5` → [Updates: `==0.7.5`]
- `htcondor ==23.5.2` → [Updates: `==23.10.29`, `==25.8.2`]
- `importlib_metadata ==7.0.2` → [Updates: `==7.2.1`, `==9.0.0`]
- `matplotlib ==3.8.3` → [Updates: `==3.10.9`]
- `mrcfile ==1.5.0` → [Updates: `==1.5.4`]
- `numpy ==1.26.4` → [Updates: `==2.4.4`]
- `opencv-python-headless ==4.9.0.80` → [Updates: `==4.13.0.92`]
- `pandas ==2.2.1` → [Updates: `==2.3.3`, `==3.0.2`]
- `pillow ==10.2.0` → [Updates: `==10.3.0`]
- `plotly ==5.20.0` → [Updates: `==5.24.1`, `==6.7.0`]
- `pydantic ==1.10.7` → [Updates: `==1.10.13`]
- `starfile ==0.5.6` → [Updates: `==0.5.13`]
- `workflows ==2.26` → [Updates: `==2.28`, `==3.4`]
- `zocalo ==0.30.2` → [Updates: `==0.32.0`, `==1.4.0`]

setup-cfg (1)

setup.cfg (1)

- `pydantic ==1.10.7` → [Updates: `==1.10.13`]

---

- [ ] Check this box to trigger a request for Renovate to run again on this repository

Start with the Renovate Dependency Dashboard and inspect the existing security pull requests before changing anything. Review requirements_dev.txt, requirements_doc.txt, requirements.txt, pyproject.toml, setup.cfg, Dockerfile, Helm/values.yaml, and .github/workflows/codeql.yml to understand the listed updates. Done means the selected dependency updates are applied and the repository checks pass.

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