clean up and update V2 recipes and configs in example and tests folders (#403)

* fix plotly show error

* add save_plot_figures to config loader

* remove default for save_plot_figures

* archive recipes

* more archived recipe

* update v2 recipes and configs

* add template recipes to example

* Update default config options

* Set "browser" as the default renderer for plotly

* Update and format example recipes to remove singleton lists

* Update examples in README.md

* remove archived folder

---------

Co-authored-by: mogres <saurabh.mogre@alleninstitute.org>

Author: rugeli

README.md

@@ -30,9 +30,9 @@ pip install -e .
 ```
 
 ## Pack example recipes
-1. v1: `pack -r examples/recipes/v1/NM_Analysis_FigureB1.0.json -c examples/packing-configs/run.json`
-2. v2:  `pack -r examples/recipes/v2/one_sphere.json -c examples/packing-configs/run.json`
-3. Pack from remote server: `pack -r  github:recipes/NM_Analysis_FigureB1.0.json  -c examples/packing-configs/run.json`
+1. v1: `pack -r examples/recipes/v1/NM_Analysis_FigureB1.0.json`
+2. v2:  `pack -r examples/recipes/v2/spheres_in_a_box.json`
+3. Pack from remote server: `pack -r  github:recipes/NM_Analysis_FigureB1.0.json `
 
 **Stable Release:** `pip install cellpack`<br>
 **Development Head:** `pip install git+https://github.com/mesoscope/cellpack.git`

cellpack/autopack/Analysis.py

@@ -1179,7 +1179,7 @@ def doloop(
             across seeds
         """
         number_of_packings = packing_config_data["number_of_packings"]
-        plot_figures = packing_config_data.get("save_plot_figures", True)
+        plot_figures = packing_config_data["save_plot_figures"]
         show_grid = packing_config_data["show_grid_plot"]
         image_export_options = packing_config_data.get("image_export_options")
 

cellpack/autopack/loaders/config_loader.py

@@ -1,7 +1,6 @@
 # -*- coding: utf-8 -*-
-import os
-
 import json
+import os
 from json import encoder
 
 import cellpack.autopack as autopack
@@ -28,7 +27,7 @@ class ConfigLoader(object):
     default_values = {
         "clean_grid_cache": False,
         "format": "simularium",
-        "load_from_grid_file": False,
+        "load_from_grid_file": True,
         "inner_grid_method": "trimesh",
         "live_packing": False,
         "number_of_packings": 1,
@@ -43,9 +42,10 @@ class ConfigLoader(object):
         "save_analyze_result": False,
         "save_converted_recipe": False,
         "save_gradient_data_as_image": False,
+        "save_plot_figures": True,
         "show_grid_plot": False,
         "show_sphere_trees": False,
-        "show_progress_bar": False,
+        "show_progress_bar": True,
         "spacing": None,
         "upload_results": True,
         "use_periodicity": False,

cellpack/autopack/plotly_result.py

@@ -1,7 +1,11 @@
-from cellpack.autopack.upy.colors import create_divergent_color_map_with_scaled_values
-import plotly.graph_objects as go
-import plotly.colors as pcolors
 import numpy
+import plotly.colors as pcolors
+import plotly.graph_objects as go
+import plotly.io as pio
+
+from cellpack.autopack.upy.colors import create_divergent_color_map_with_scaled_values
+
+pio.renderers.default = "browser"
 
 
 class PlotlyAnalysis:

cellpack/tests/packing-configs/test_config.json

@@ -1,17 +1,8 @@
 {
     "name": "test_config",
-    "format": "simularium",
-    "inner_grid_method": "trimesh",
-    "live_packing": false,
-    "ordered_packing": false,
     "out": "cellpack/tests/outputs/",
     "overwrite_place_method": true,
     "place_method": "spheresSST",
     "save_analyze_result": true,
-    "show_grid_plot": false,
-    "spacing": null,
-    "parallel": false,
-    "use_periodicity": false,
-    "show_sphere_trees": true,
-    "upload_results": false
+    "show_sphere_trees": true
 }

cellpack/tests/packing-configs/test_gradient_data_image.json

@@ -3,7 +3,6 @@
     "save_analyze_result": true,
     "show_grid_plot": true,
     "spacing": 0.25,
-    "show_sphere_trees": false,
     "load_from_grid_file": true,
     "save_gradient_data_as_image": true,
     "image_export_options": {

cellpack/tests/packing-configs/test_grid_plot_config.json

@@ -1,7 +1,6 @@
 {
     "name": "show_grid_plot",
     "out": "cellpack/tests/outputs/",
-    "load_from_grid_file": false,
     "overwrite_place_method": true,
     "place_method": "spheresSST",
     "save_analyze_result": true,

cellpack/tests/packing-configs/test_image_config_base.json

@@ -1,18 +1,10 @@
 {
     "name": "test_image_config_base",
-    "format": "simularium",
-    "inner_grid_method": "trimesh",
-    "live_packing": false,
-    "ordered_packing": false,
-    "out": "out/",
     "overwrite_place_method": true,
     "place_method": "spheresSST",
     "save_analyze_result": true,
     "show_grid_plot": true,
-    "number_of_packings": 1,
     "spacing": 2.5,
-    "use_periodicity": false,
-    "show_sphere_trees": false,
     "load_from_grid_file": true,
     "save_converted_recipe": true,
     "image_export_options": {

cellpack/tests/packing-configs/test_image_config_convolved.json

@@ -1,18 +1,10 @@
 {
     "name": "test_image_config_convolved",
-    "format": "simularium",
-    "inner_grid_method": "trimesh",
-    "live_packing": false,
-    "ordered_packing": false,
     "out": "out/images/",
     "overwrite_place_method": true,
     "place_method": "spheresSST",
     "save_analyze_result": true,
-    "show_grid_plot": false,
-    "number_of_packings": 1,
     "spacing": 2.5,
-    "use_periodicity": false,
-    "show_sphere_trees": false,
     "load_from_grid_file": true,
     "save_converted_recipe": true,
     "image_export_options": {

cellpack/tests/packing-configs/test_image_config_solid_seg.json

@@ -1,22 +1,10 @@
 {
     "name": "test_image_config_solid_seg",
-    "format": "simularium",
-    "inner_grid_method": "trimesh",
-    "live_packing": false,
-    "ordered_packing": false,
-    "out": "out/",
     "overwrite_place_method": true,
     "place_method": "spheresSST",
     "save_analyze_result": true,
-    "show_grid_plot": false,
-    "number_of_packings": 1,
-    "spacing": null,
-    "use_periodicity": false,
-    "show_sphere_trees": false,
     "load_from_grid_file": true,
-    "save_converted_recipe": false,
     "save_plot_figures": false,
-    "parallel": false,
     "image_export_options": {
         "hollow": false,
         "voxel_size": [1,1,1],