clean2

scripts/bokeh_plot/components/convert_data.py

@@ -16,7 +16,7 @@ def prepare_time_data(time_data_list, keypair, timepairs):
     export = data.to_dict(orient="list")
     return export
 
-# include yaml names and keys
+
 def prepare_size_data(size_data, keypair, sizepairs):
     """Returns a dictionary containing the given data in the format for the size plot."""
     key, keyname = keypair

scripts/bokeh_plot/components/helpers.py

@@ -1,6 +1,5 @@
 """Helper functions."""
 
-
 def convert_dic_to_list(data):
     """Returns a list containing the values of the given list as strings."""
     return [str(i) for i in data]

scripts/bokeh_plot/components/plot_css_html.py

@@ -118,6 +118,7 @@ def get_button_style():
         }
     """]
 
+
 def get_global_style():
     """Returns the global CSS style."""
     return """

scripts/bokeh_plot/plot.py

@@ -1,8 +1,6 @@
 from components.log_init import log_init
 log_init(snakemake.log[0]) # type: ignore
 
-import csv
-import os
 import pandas as pd
 
 from bokeh.layouts import column, row
@@ -79,9 +77,11 @@ def create_plot():
     with open(SIZE_INPUT, "r", encoding="utf-8") as size_file, open(TIME_INPUT, "r", encoding="utf-8") as timing_file:
         time_data = pd.read_csv(timing_file, delimiter="\t")
         size_data = pd.read_csv(size_file, delimiter="\t")
+
     for key in KEYS.keys():
         time_dic = prepare_time_data(time_data, (key, KEYS[key]), TIME["NAMES"])
         size_dic = prepare_size_data(size_data, (key, KEYS[key]), SIZE["NAMES"])
+
         time_x_range = round(max(time_dic["wall_clock_time_in_seconds"]) * 1.05, 3)
         size_x_range = round(max(size_dic["GB_TOTAL_SIZE"]) * 1.05, 3)
 
@@ -96,8 +96,8 @@ def create_plot():
         vercel_div = create_vercel_div()
         all_elements = column(both_plots, vercel_div, sizing_mode="scale_both")
         tabs.append(TabPanel(child=all_elements, title=KEYS[key]))
+
     add_description_tab(tabs)
-
     save(Tabs(tabs=tabs, sizing_mode="scale_both", stylesheets=[get_tab_style(), get_global_style()]))
 
 create_plot()

scripts/plot_parameters.yaml

@@ -11,6 +11,7 @@ KEYS:
   U: U
   U+R: "U and R"
 
+
 TIME:
   FORMAT:
     - determine_query_length_in_seconds
@@ -28,15 +29,15 @@ TIME:
     load_index_in_seconds: "Load index"
     load_index_percentage: "Load index percentage"
     compute_minimiser_avg_in_seconds: "Compute minimizer (avg)"
-    compute_minimiser_max_percentage: "Compute minimizer (max) percentage"
+    compute_minimiser_avg_percentage: "Compute minimizer (avg) percentage"
     compute_minimiser_max_in_seconds: "Compute minimizer (max)"
     compute_minimiser_max_percentage: "Compute minimizer (max) percentage"
     query_ibf_avg_in_seconds: "Query IBF (avg)"
-    query_ibf_max_percentage: "Query IBF (max) percentage"
+    query_ibf_avg_percentage: "Query IBF (avg) percentage"
     query_ibf_max_in_seconds: "Query IBF (max)"
     query_ibf_max_percentage: "Query IBF (max) percentage"
     generate_results_avg_in_seconds: "Generate results (avg)"
-    generate_results_max_percentage: "Generate results (max) percentage"
+    generate_results_avg_percentage: "Generate results (avg) percentage"
     generate_results_max_in_seconds: "Generate results (max)"
     generate_results_max_percentage: "Generate results (max) percentage"
 
@@ -58,93 +59,3 @@ SIZE:
     LEVEL_2_AVG_LOAD_FACTOR: "Level 2: Avg load factor"
     LEVEL_3_AVG_LOAD_FACTOR: "Level 3: Avg load factor"
     GB_TOTAL_SIZE: "Total size"
-
-# SIZE:
-#   FORMAT:
-#     LEVEL_0: "Level 0"
-#     LEVEL_1: "Level 1"
-#     LEVEL_2: "Level 2"
-#     LEVEL_3: "Level 3"
-#   HOVER:
-#     SUBKEY_VALUE: "SUBKEY_VALUE"
-#     SIZE: "Size"
-#     # LEVEL_0_BITSIZE: "Level 0 size"
-#     # LEVEL_1_BITSIZE: "Level 1 size"
-#     # LEVEL_2_BITSIZE: "Level 2 size"
-#     # LEVEL_3_BITSIZE: "Level 3 size"
-#   ADVANCED_HOVER:
-#     SUBKEY_VALUE: "SUBKEY_VALUE"
-#     SIZE: "Size"
-#     AVG_LOAD_FACTOR: "Avg load factor"
-#     # LEVEL_0_BIT_SIZE: "Level 0 size"
-#     # LEVEL_1_BIT_SIZE: "Level 1 size"
-#     # LEVEL_2_BIT_SIZE: "Level 2 size"
-#     # LEVEL_3_BIT_SIZE: "Level 3 size"
-#     # LEVEL_0_AVG_LOAD_FACTOR: "Level 0 avg load factor"
-#     # LEVEL_1_AVG_LOAD_FACTOR: "Level 1 avg load factor"
-#     # LEVEL_2_AVG_LOAD_FACTOR: "Level 2 avg load factor"
-#     # LEVEL_3_AVG_LOAD_FACTOR: "Level 3 avg load factor"
-
-# KEYS_FORMAT:
-#   - "alpha"
-#   - "hash"
-#   - "kmer"
-#   - "relaxed-fpr"
-#   - "none"
-#   - "U"
-#   - "U+R"
-
-# KEYS_NAMES:
-#   - "alpha"
-#   - "hash"
-#   - "k-mer"
-#   - "relaxed-fpr"
-#   - "no U no R"
-#   - "U"
-#   - "U and R"
-
-# TIME_FORMAT:
-#   - "SUBKEY"
-#   - "determine_query_length_in_seconds"
-#   - "query_file_io_in_seconds"
-#   - "load_index_in_seconds"
-#   - "compute_minimiser_max_in_seconds"
-#   - "query_ibf_max_in_seconds"
-#   - "generate_results_max_in_seconds"
-
-# TIME_NAMES:
-#   - "Determine query length"
-#   - "Queryfile IO"
-#   - "Load index"
-#   - "Compute minimizer (max)"
-#   - "Query IBF (max)"
-#   - "Generate results (max)"
-
-# TIME_HOVER:
-#   - "Determine query length"
-#   - "Queryfile IO"
-#   - "Load index"
-#   - "Compute minimizer (max)"
-#   - "Query IBF (max)"
-#   - "Generate results (max)"
-
-# TIME_HOVER_ADVANCED:
-#   - "Determine query length"
-#   - "Queryfile IO"
-#   - "Load index"
-#   - "Compute minimizer (max)"
-#   - "Query IBF (max)"
-#   - "Generate results (max)"
-
-# SIZE_FORMAT:
-#   - "SUBKEY"
-#   - "LEVEL_0"
-#   - "LEVEL_1"
-#   - "LEVEL_2"
-#   - "LEVEL_3"
-
-# SIZE_NAMES:
-#   - "Level 0"
-#   - "Level 1"
-#   - "Level 2"
-#   - "Level 3"