From 55c40c87ab1aeb63ff8253fd4fefcc1ad1b52b99 Mon Sep 17 00:00:00 2001 From: d33bs Date: Mon, 8 Sep 2025 15:25:49 -0600 Subject: [PATCH 1/2] address readme typos and content --- readme.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/readme.md b/readme.md index 52200d46..2bf512d8 100644 --- a/readme.md +++ b/readme.md @@ -13,17 +13,17 @@ _Diagram showing data flow relative to this project._ ## Summary -CytoTable enables single-cell morphology data analysis by cleaning and transforming CellProfiler (`.csv` or `.sqlite`), cytominer-database (`.sqlite`), and DeepProfiler (`.npz`), and other sources such as IN Carta data output data at scale. +CytoTable enables single-cell morphology data analysis by cleaning and transforming CellProfiler (`.csv` or `.sqlite`), cytominer-database (`.sqlite`), and DeepProfiler (`.npz`), and other sources such as IN Carta output data at scale. CytoTable creates parquet files for both independent analysis and for input into [Pycytominer](https://github.com/cytomining/pycytominer). The output files (such as [Parquet](https://parquet.apache.org/) and [anndata](https://github.com/scverse/anndata) file formats) have a documented data model, including referenceable schema where appropriate (for validation within Pycytominer or other image-based profiling projects). -> 📔 Check out our demonstration notebook for a one-stop reference of how to use CytoTable. +> 📔🧑‍🏫 Check out our demonstration notebook for a one-stop reference of how to use CytoTable. > [CytoTable mise en place (general overview)](https://cytomining.github.io/CytoTable/examples/cytotable_mise_en_place_general_overview.html) > -> 📓 Consider also checking out our demonstration notebook covering how to use cloud-based data sources with CytoTable. -> [CytoTable mise en place (general overview)](https://cytomining.github.io/CytoTable/examples/cytotable_from_the_cloud.html) +> 📓☁️ Consider also checking out our demonstration notebook covering how to use cloud-based data sources with CytoTable. +> [CytoTable from the cloud (cloud-based overview)](https://cytomining.github.io/CytoTable/examples/cytotable_from_the_cloud.html) -The name for the project is inspired from: +The name for the project is inspired by: - __Cyto__: "1. (biology) cell." ([Wiktionary: Cyto-](https://en.wiktionary.org/wiki/cyto-)) - __Table__: @@ -61,7 +61,7 @@ At scale, CytoTable transforms data into file formats which can be directly inte ## References -- [pycytominer](https://github.com/cytomining/pycytominer) +- [Pycytominer](https://github.com/cytomining/pycytominer) - [cytominer-database](https://github.com/cytomining/cytominer-database) - [DeepProfiler](https://github.com/cytomining/DeepProfiler) - [CellProfiler](https://github.com/CellProfiler/CellProfiler) From 340e7392d6c49b3c20e5e0c79229b09cec661639 Mon Sep 17 00:00:00 2001 From: d33bs Date: Mon, 8 Sep 2025 15:28:08 -0600 Subject: [PATCH 2/2] 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 3a1ae431..833b8614 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -46,7 +46,7 @@ repos: hooks: - id: black - repo: https://github.com/asottile/blacken-docs - rev: 1.19.1 + rev: 1.20.0 hooks: - id: blacken-docs - repo: https://github.com/PyCQA/bandit