From c5e731cc56594db4486265731e28979e50d46d5b Mon Sep 17 00:00:00 2001 From: Ruge Li <91452427+rugeli@users.noreply.github.com> Date: Thu, 9 Nov 2023 12:53:04 -0800 Subject: [PATCH] Maintenance/update readme (#211) * fix readme aws link * fix example recipe paths * add v2 recipe * add v2 one sphere recipe in readme --- README.md | 5 +++-- cellpack/autopack/upy/simularium/simularium_helper.py | 4 +++- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index a356e0f02..cbbea9878 100644 --- a/README.md +++ b/README.md @@ -15,8 +15,9 @@ algorithm to pack molecular recipes 3. `pip install -e .[dev]` ### Run pack code -1. example pack recipe : `pack -r examples/recipes/v1/NM_Analysis_FigureB1.0.json -c packing-configs/run.json` -2. example pack from remote : `pack -r github:recipes/NM_Analysis_FigureB1.0.json -c packing-configs/run.json` +1. example pack v1 recipe : `pack -r examples/recipes/v1/NM_Analysis_FigureB1.0.json -c examples/packing-configs/run.json` +2. example pack v2 recipe : `pack -r examples/recipes/v2/one_sphere.json -c examples/packing-configs/run.json` +3. example pack from remote : `pack -r github:recipes/NM_Analysis_FigureB1.0.json -c examples/packing-configs/run.json` ### Run conversion code * To convert to simularium and view at https://staging.simularium.allencell.org/viewer diff --git a/cellpack/autopack/upy/simularium/simularium_helper.py b/cellpack/autopack/upy/simularium/simularium_helper.py index ba6c8508d..1965c28c8 100644 --- a/cellpack/autopack/upy/simularium/simularium_helper.py +++ b/cellpack/autopack/upy/simularium/simularium_helper.py @@ -1392,7 +1392,9 @@ def post_and_open_file(self, file_name, open_results_in_browser=True): try: url = simulariumHelper.store_results_to_s3(simularium_file) except Exception as e: - aws_readme_url = "https://github.com/mesoscope/cellpack/blob/feature/main/README.md#aws-s3" + aws_readme_url = ( + "https://github.com/mesoscope/cellpack/blob/main/README.md#aws-s3" + ) if isinstance(e, NoCredentialsError): print( f"need to configure your aws account, find instructions here: {aws_readme_url}"