From d13e5d36a3c55ddafa78af24fbc091e64a4146ce Mon Sep 17 00:00:00 2001 From: d33bs Date: Tue, 18 Feb 2025 08:23:55 -0700 Subject: [PATCH 1/7] add doi info and minor touch-ups --- CITATION.cff | 7 +++++++ readme.md | 5 +++++ 2 files changed, 12 insertions(+) diff --git a/CITATION.cff b/CITATION.cff index 6cda1b06..abecfcfe 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -17,11 +17,18 @@ authors: - given-names: Erik family-names: Serrano orcid: 'https://orcid.org/0000-0003-4188-9080' + - given-names: Vincent + family-names: Rubinetti + orcid: 'https://orcid.org/0000-0002-4655-3773' - given-names: Gregory family-names: Way orcid: 'https://orcid.org/0000-0002-0503-9348' repository-code: 'https://github.com/cytomining/CytoTable' url: 'https://cytomining.github.io/CytoTable/' +identifiers: + - description: Software DOI + type: doi + value: "10.5281/zenodo.14888111" abstract: >- Transform CellProfiler and DeepProfiler data for processing image-based profiling readouts with Pycytominer and other Cytomining tools. keywords: diff --git a/readme.md b/readme.md index 4cb161c9..301bb68d 100644 --- a/readme.md +++ b/readme.md @@ -2,6 +2,11 @@ # CytoTable +![PyPI - Version](https://img.shields.io/pypi/v/cytotable) +[![Build Status](https://github.com/cytomining/cytotable/actions/workflows/test.yml/badge.svg?branch=main)](https://github.com/cytomining/cytotable/actions/workflows/test.yml?query=branch%3Amain) +[![Poetry](https://img.shields.io/endpoint?url=https://python-poetry.org/badge/v0.json)](https://python-poetry.org/) +[![Software DOI badge](https://zenodo.org/badge/DOI/10.5281/zenodo.14888111.svg)](https://doi.org/10.5281/zenodo.14888111) + ![dataflow](https://raw.githubusercontent.com/cytomining/cytotable/main/docs/source/_static/dataflow.svg?raw=true) _Diagram showing data flow relative to this project._ From 45844f9663585c4e16180e271da008fe42c4d84c Mon Sep 17 00:00:00 2001 From: d33bs Date: Tue, 18 Feb 2025 08:24:04 -0700 Subject: [PATCH 2/7] change to shorter name --- .github/workflows/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index d586edb5..d4d974ca 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -11,7 +11,7 @@ on: - cron: "0 7 * * 3" jobs: - run_tests: + tests: strategy: matrix: # matrixed execution for parallel gh-action performance increases From 10a202e363c7c8312b4a7635a24c084e4e200020 Mon Sep 17 00:00:00 2001 From: d33bs Date: Tue, 18 Feb 2025 08:24:12 -0700 Subject: [PATCH 3/7] linting --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 17ac0013..64c907f6 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -50,7 +50,7 @@ repos: hooks: - id: blacken-docs - repo: https://github.com/PyCQA/bandit - rev: 1.8.2 + rev: 1.8.3 hooks: - id: bandit args: ["-c", "pyproject.toml"] From 8849351c635f8c273291d5e76d2cc48db02e8e16 Mon Sep 17 00:00:00 2001 From: d33bs Date: Tue, 18 Feb 2025 08:33:38 -0700 Subject: [PATCH 4/7] update name --- .github/workflows/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index d4d974ca..93bcff84 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -47,7 +47,7 @@ jobs: # smaller tests first. run_large_data_tests: runs-on: ubuntu-22.04 - needs: run_tests + needs: tests steps: - name: Checkout uses: actions/checkout@v4 From febc65d81725f8021aab6b878b74577133884301 Mon Sep 17 00:00:00 2001 From: d33bs Date: Mon, 14 Apr 2025 08:58:21 -0600 Subject: [PATCH 5/7] update cff to include others --- CITATION.cff | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index abecfcfe..ea01e412 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -11,15 +11,21 @@ authors: - given-names: David family-names: Bunten orcid: 'https://orcid.org/0000-0001-6041-3665' - - given-names: Faisal - family-names: Alquaddoomi - orcid: 'https://orcid.org/0000-0003-4297-8747' + - given-names: Jenna + family-names: Tomkinson + orcid: 'https://orcid.org/0000-0003-2676-5813' - given-names: Erik family-names: Serrano orcid: 'https://orcid.org/0000-0003-4188-9080' + - given-names: Michael + family-names: Lippincott + orcid: 'https://orcid.org/0000-0002-8637-1448' - given-names: Vincent family-names: Rubinetti orcid: 'https://orcid.org/0000-0002-4655-3773' + - given-names: Faisal + family-names: Alquaddoomi + orcid: 'https://orcid.org/0000-0003-4297-8747' - given-names: Gregory family-names: Way orcid: 'https://orcid.org/0000-0002-0503-9348' From 430b876a787678ec7ddc325f172c7424160f18fe Mon Sep 17 00:00:00 2001 From: d33bs Date: Tue, 15 Apr 2025 11:52:08 -0600 Subject: [PATCH 6/7] add ken --- CITATION.cff | 3 +++ 1 file changed, 3 insertions(+) diff --git a/CITATION.cff b/CITATION.cff index ea01e412..408c4f23 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -20,6 +20,9 @@ authors: - given-names: Michael family-names: Lippincott orcid: 'https://orcid.org/0000-0002-8637-1448' + - family-names: Brewer + given-names: Kenneth + orcid: 'https://orcid.org/0000-0003-4030-0254' - given-names: Vincent family-names: Rubinetti orcid: 'https://orcid.org/0000-0002-4655-3773' From 2586f0751ab417abd1a311455bb654cbd5115aa4 Mon Sep 17 00:00:00 2001 From: d33bs Date: Fri, 25 Apr 2025 14:52:13 -0600 Subject: [PATCH 7/7] Update .pre-commit-config.yaml --- .pre-commit-config.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 64c907f6..405f1472 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -12,11 +12,11 @@ repos: - id: check-added-large-files - id: check-toml - repo: https://github.com/python-poetry/poetry - rev: 2.1.1 + rev: 2.1.2 hooks: - id: poetry-check - repo: https://github.com/tox-dev/pyproject-fmt - rev: "v2.5.0" + rev: "v2.5.1" hooks: - id: pyproject-fmt - repo: https://github.com/codespell-project/codespell @@ -37,7 +37,7 @@ repos: - mdformat-myst - mdformat-gfm - repo: https://github.com/adrienverge/yamllint - rev: v1.35.1 + rev: v1.37.0 hooks: - id: yamllint exclude: ".pre-commit-config.yaml" @@ -56,7 +56,7 @@ repos: args: ["-c", "pyproject.toml"] additional_dependencies: ["bandit[toml]"] - repo: https://github.com/PyCQA/isort - rev: 6.0.0 + rev: 6.0.1 hooks: - id: isort - repo: https://github.com/jendrikseipp/vulture @@ -72,7 +72,7 @@ repos: hooks: - id: validate-cff - repo: https://github.com/PyCQA/pylint - rev: v3.3.4 + rev: v3.3.6 hooks: - id: pylint name: pylint