From 5b0696a0f7129346edbe1721ec3a81833a674a04 Mon Sep 17 00:00:00 2001 From: Neil Shephard Date: Fri, 1 Nov 2024 12:56:45 +0000 Subject: [PATCH] build: minimal set of dependencies This runs the code on the minimal reproducible example that @jjriley1 is developing on [jjriley1/slam_3UIs:jjriley1/1-tidy-up](https://github.com/jjriley1/slam_3UIs/tree/jjriley1/1-tidy-up). Installing in a clean virtual environment the script at least runs against commit `0d00ec98253919a3cf5a4b34e5e6bde771acfb1e` (and `fb93e864390e2a3517ffb7ee2bed5ab2cc923a9c`) although currently because of hard coded files in `pipeline_slam_3UIs/pipeline.yaml` no processing is undertaken with the sample files that have been provided. I expect the dependencies to grow as we add more functionality and have deliberately left `pandas`, `numpy` and `matplotlib` as dependencies as they will be used to do the legwork that the various R scripts currently do. --- pyproject.toml | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 1b997ca..eea53ea 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -36,16 +36,15 @@ keywords = [ "slamseq", ] dependencies = [ - #"cgatcore", - #"cgat-apps@git+https://github.com/cgat-developers/cgat-apps", - #"cgat-flow@git+https://github.com/cgat-developers/cgat-flow", - #"cgat-report", - #"heapq", + "apsw", + "cgatcore", + "gevent", "matplotlib", "numpy", "pandas", "pysam", "ruffus", + "sqlalchemy", ]