pycytominer

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Bug: get an error in pycytominer/__init__.py it was fixed coming back to the previous commit

10

### Example code with output I get an error when I try to use `pycytominer/__init__.py` in the cluster. code: ---- cd ~/ebs_tmp/${PROJECT_NAME}/workspace/software/pycytominer/ mkdir -p ../../log/${BATCH_ID}/ parallel \ --max-procs ${MAXPROCS} \...

PaulaLlanos

Bumps [jinja2](https://github.com/pallets/jinja) from 3.1.3 to 3.1.4. Release notes Sourced from jinja2's releases. 3.1.4 This is the Jinja 3.1.4 security release, which fixes security issues and bugs but does not otherwise...

dependabot[bot]

### Example code with output I'm currently working with a dataset that doesn't utilize CellProfiler features. As a result, it has different compartments: ```text compartments = ['Primary', 'Cells', 'F Actin',...

axiomcura

docs: add pydocsstyle linting and switch to mkdocs

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# Description I was working on #382 and couldn't figure out how to resolve some sphinx build errors with opaque error messages. I decided to take this opportunity to switch...

kenibrewer

bug: Failing docs build

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I just noticed that our docs build hasn't updated since 1.0.1. https://pycytominer.readthedocs.io/en/stable/ @d33bs You recently changed something about how we are authenticating with RTD right? Is this something that you...

kenibrewer

Complete Docker-Sponsored Open Source (DSOS) application process

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This issue continues work towards efforts mentioned in #214 to gain Docker-Sponsored Open Source (DSOS) sponsorship based on feedback received from Docker. This work may involve additional updates to how...

d33bs

Switch to more stable test data path for `CellLocations` tests

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Erin's suggestion in https://github.com/broadinstitute/cellpainting-gallery/issues/80#issuecomment-1986375614 was to move away from JUMP since it is the most likely to change in the future - just checking if you've seen this advice. If...

kenibrewer

> Here's another possible change at your discretion. This would make it a bit easier with the context management. > > 1. Move `./build/docker/Dockerfile` to `./Dockerfile` > 2. Add the...

d33bs

https://github.com/cytomining/pycytominer/pull/387 introduced Bandit checks. Two S108 violations in pycytominer.cyto_utils.collate were left unaddressed at that time and were instead given `# noqa: S108` ignores. Acceptance Criteria: - [ ] There are...

kenibrewer

#387 introduced Bandit checks. Several S101 violations in `pycytominer.cyto_utils` were left unaddressed at that time and were instead given `# noqa: S101` ignores. Acceptance Criteria: - There are no `#...

kenibrewer