Changeset 1105

Timestamp:

03/13/21 00:46:26 (4 years ago)

Author:

Maciej Komosinski

Message:

Using the "framsfiles" module to write genotypes to a file instead of an ad-hoc code

File:

• framspy/FramsticksCLI.py (modified) (4 diffs)

framspy/FramsticksCLI.py

@@ -7 +7 @@
 import argparse
 import numpy as np
-import framsreader  # only needed for mutation: https://pypi.org/project/framsreader
+from framsfiles import reader as framsreader
+from framsfiles import writer as framswriter
 
 
@@ -36 +37 @@
         GETSIMPLEST_CMD = "getsimplest"
         GETSIMPLEST_FILE = "simplest.gen"
-        EVALUATE_CMD = "evaluate eval-allcriteria.sim" # the .sim file must be compatible with the standard-eval expdef
+        EVALUATE_CMD = "evaluate eval-allcriteria.sim"  # the .sim file must be compatible with the standard-eval expdef
         EVALUATE_FILE = "genos_eval.json"
         CROSSOVER_CMD = "crossover"
@@ -127 +128 @@
                                 outfile.write(genotype)
                         else:
-                                outfile.write("org:\n")
-                                outfile.write("genotype:~\n")
-                                outfile.write(genotype + "~\n\n")  # TODO proper quoting of special characters in genotype...
+                                outfile.write(framswriter.from_collection({"_classname": "org", "genotype": genotype}))
+                                outfile.write("\n")
                         outfile.close()
                 return relname, absname
@@ -304 +304 @@
         # - "vectorize" crossover so that many genotypes is handled in one call. Even better, use .so/.dll direct communication to CLI
         # - use threads for non-blocking reading from frams' stdout and thus not relying on specific strings printed by frams
-        # - a pool of binaries running simultaneously, balance load - in particular evaluation
-        # - if we read genotypes in "org:" format anywhere: import https://pypi.org/project/framsreader and use it if successful,
-        #    if not then print a message "framsreader not available, using simple internal method to save a genotype" and proceed as it is now.
-        #    We should use the proper writer to handle all special cases like quoting special characters etc.
+        # - a pool of binaries running simultaneously, balance load - in particular, evaluation
 
         parsed_args = parseArguments()