Merge branch 'staging/migrate-old-recipes' of https://github.com/meso…

…scope/cellpack into staging/migrate-old-recipes

README.md

@@ -6,19 +6,16 @@
 
 algorithm to pack molecular recipes
 
+### Prerequisite 
+1. Install Conda: https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html
 
 ### Setup 
-1. create a virtual env: `conda create -n autopack`
-2. `activate autopack`
+1. create a virtual env: `conda create -n autopack python=3.9`
+2. `conda activate autopack`
 3. `pip install -e .[dev]`
 
-### Run analysis code
-By default analyze will run all packing methods on `cellpack/test-recipes/NM_Analysis_FigureB1.0.json
-Examples:
-* `analyze -o [PATH/TO/OUTPUT/FOLDER]` will create subfolders for each packing method at your output folder
-* To run just one packing method: `analyze -o [PATH/TO/OUTPUT/FOLDER] -p jitter`
-* To change the dimension of the packing: `analyze -r cellpack/test-recipes/NM_Analysis_FigureC1.json  -o /Users/meganriel-mehan/Dropbox/cellPack/NM_Analysis_C_1 -d 3`
-* Turn off plotly plot: `analyze -o [PATH/TO/OUTPUT/FOLDER] -ng` or `analyze -o [PATH/TO/OUTPUT/FOLDER] --no-grid-plot`
+### Run pack code
+1. example pack recipe : `pack -r  cellpack/test-recipes/NM_Analysis_FigureB1.0.json  -c packing-configs/run.json`
 
 ### Run conversion code 
 * To convert to simularium and view at https://staging.simularium.allencell.org/viewer

cellpack/__init__.py

@@ -6,7 +6,7 @@
 __email__ = "[email protected]"
 # Do not edit this string manually, always use bumpversion
 # Details in CONTRIBUTING.md
-__version__ = "1.0.1"
+__version__ = "1.0.3"
 
 from .autopack.loaders.recipe_loader import RecipeLoader  # noqa: F401
 

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.0.1
+current_version = 1.0.3
 commit = True
 tag = True
 

setup.py

@@ -44,10 +44,10 @@
     "panda3d==1.10.10",
     "pmw==2.0.1",
     "scipy>=1.6.2",
-    "simulariumio>=1.2.0",
+    "simulariumio>=1.6.2",
     "plotly>=5.3.1",
     "pycollada==0.7.2",
-    "pyembree>=0.1.12",
+    "pyembree>=0.1.8",
     "pymunk>=6.2.0",
     "trimesh>=3.9.34",
 ]
@@ -98,6 +98,6 @@
     url="https://github.com/mesoscope/cellpack",
     # Do not edit this string manually, always use bumpversion
     # Details in CONTRIBUTING.rst
-    version="1.0.1",
+    version="1.0.3",
     zip_safe=False,
 )