Feature/send config data to analysis (#232)

* * use pathlib module for file paths
* send in packing config data directly to analysis

* Process arguments inside `doloop` function

cellpack/autopack/Analysis.py

@@ -33,7 +33,7 @@
 from cellpack.autopack.plotly_result import PlotlyAnalysis
 from cellpack.autopack.upy import colors as col
 from cellpack.autopack.upy.colors import map_colors
-from cellpack.autopack.utils import check_paired_key, get_paired_key
+from cellpack.autopack.utils import check_paired_key, get_paired_key, get_seed_list
 from cellpack.autopack.writers import Writer
 from cellpack.autopack.writers.ImageWriter import ImageWriter
 import concurrent.futures
@@ -2342,17 +2342,10 @@ def pack_one_seed(
 
     def doloop(
         self,
-        number_of_packings,
+        recipe_data,
+        packing_config_data,
         bounding_box,
         get_distance_distribution=True,
-        plot_figures=True,
-        show_grid=True,
-        seed_list=None,
-        config_name="default",
-        recipe_version="1.0.0",
-        image_export_options=None,
-        parallel=False,
-        save_gradient_data_as_image=False,
     ):
         """
         Runs multiple packings of the same recipe in a loop. This workflow
@@ -2363,26 +2356,17 @@ def doloop(
 
         Parameters
         ----------
-        number_of_packing : int
-            Number of repeats of a packing. Default: 1
-        bounding_box : np.ndarray
-            bounding box from the environment
+        recipe_data: dict
+            Dictionary containing recipe data
+        packing_config_data: dict
+            Dictionary containing packing configuration data
+        bounding_box: list
+            List of two lists containing the minimum and maximum coordinates
+            of the bounding box
         get_distance_distribution: bool
-            specify whether to calculate distance distributions
-        render: bool
-            ???
-        plot_figures: bool
-            specify whether to save figures generated by the analyses
-        show_grid: bool
-            specify whether to display packing grid in browser
-        fbox_bb: ???
-            ???
-        seed_list: List
-            list of seeds to use for the packing (for reproducibility)
-        config_name: string
-            name of the configuration used for the packing
-        recipe_version: string
-            version of the recipe used for the packing
+            Whether to calculate and store distance and angle distributions
+        seed_list: list
+            List of seeds to use for packings
 
         Outputs
         -------
@@ -2393,6 +2377,16 @@ def doloop(
             distributions as applicable for each seed, and a combined image
             across seeds
         """
+        number_of_packings = packing_config_data["number_of_packings"]
+        plot_figures = packing_config_data.get("save_plot_figures", True)
+        show_grid = packing_config_data["show_grid_plot"]
+        image_export_options = packing_config_data.get("image_export_options")
+        parallel = packing_config_data.get("parallel", False)
+        save_gradient_data_as_image = packing_config_data.get(
+            "save_gradient_data_as_image", False
+        )
+
+        seed_list = get_seed_list(packing_config_data, recipe_data)
         if seed_list is None:
             seed_list = self.getHaltonUnique(number_of_packings)
         packing_basename = self.env.base_name

cellpack/bin/pack.py

@@ -1,5 +1,5 @@
 import fire
-from os import path
+from pathlib import Path
 import logging
 import logging.config
 import time
@@ -12,10 +12,9 @@
 from cellpack.autopack.loaders.config_loader import ConfigLoader
 from cellpack.autopack.loaders.recipe_loader import RecipeLoader
 from cellpack.autopack.loaders.analysis_config_loader import AnalysisConfigLoader
-from cellpack.autopack.utils import get_seed_list
 
 ###############################################################################
-log_file_path = path.abspath(path.join(__file__, "../../logging.conf"))
+log_file_path = Path(__file__).parent.parent / "logging.conf"
 logging.config.fileConfig(log_file_path, disable_existing_loggers=False)
 log = logging.getLogger()
 ###############################################################################
@@ -30,8 +29,6 @@ def pack(recipe, config_path=None, analysis_config_path=None):
 
     :return: void
     """
-    log.info(f"Running in {__file__}")
-
     packing_config_data = ConfigLoader(config_path).config
     recipe_data = RecipeLoader(
         recipe, packing_config_data["save_converted_recipe"]
@@ -58,21 +55,10 @@ def pack(recipe, config_path=None, analysis_config_path=None):
         )
         log.info(f"saving to {env.out_folder}")
 
-        seed_list = get_seed_list(packing_config_data, recipe_data)
-
         analyze.doloop(
-            packing_config_data["number_of_packings"],
+            recipe_data,
+            packing_config_data,
             env.boundingBox,
-            plot_figures=packing_config_data.get("save_plot_figures", True),
-            show_grid=packing_config_data["show_grid_plot"],
-            seed_list=seed_list,
-            config_name=packing_config_data["name"],
-            recipe_version=recipe_data["version"],
-            image_export_options=packing_config_data.get("image_export_options"),
-            parallel=packing_config_data.get("parallel", False),
-            save_gradient_data_as_image=packing_config_data.get(
-                "save_gradient_data_as_image", False
-            ),
         )
         if analysis_config_path is not None:
             analyze.run_analysis_workflow(