source: framspy/FramsticksCLI.py @ 1011

from math import sqrt
from subprocess import Popen, PIPE, check_output
from enum import Enum
from typing import List  # to be able to specify a type hint of list(something)
from itertools import count  # for tracking multiple instances
import json
import sys, os
import argparse
import numpy as np


class FramsticksCLI:
        """Runs Framsticks CLI (command-line) executable and communicates with it using standard input and output.
        You can perform basic operations like mutation, crossover, and evaluation of genotypes.
        This way you can perform evolution controlled by python as well as access and manipulate genotypes.
        You can even design and use in evolution your own genetic representation implemented entirely in python.

        You need to provide one or two parameters when you run this class: the path to Framsticks CLI
        and the name of the Framsticks CLI executable (if it is non-standard). See::
                FramsticksCLI.py -h"""

        PRINT_FRAMSTICKS_OUTPUT: bool = False  # set to True for debugging
        DETERMINISTIC: bool = False  # set to True to have the same results on each run

        GENO_SAVE_FILE_FORMAT = Enum('GENO_SAVE_FILE_FORMAT', 'NATIVEFRAMS RAWGENO')  # how to save genotypes
        OUTPUT_DIR = "scripts_output"
        STDOUT_ENDOPER_MARKER = "FileObject.write"  # we look for this message on Framsticks CLI stdout to detect when Framsticks created a file with the result we expect

        FILE_PREFIX = 'framspy_'

        RANDOMIZE_CMD = "rnd" + "\n"
        SETEXPEDEF_CMD = "expdef standard-eval" + "\n"
        GETSIMPLEST_CMD = "getsimplest"
        GETSIMPLEST_FILE = "simplest.gen"
        EVALUATE_CMD = "evaluate eval-allcriteria.sim"
        EVALUATE_FILE = "genos_eval.json"
        CROSSOVER_CMD = "crossover"
        CROSSOVER_FILE = "child.gen"
        DISSIMIL_CMD = "dissimil"
        DISSIMIL_FILE = "dissimilarity_matrix.gen"
        ISVALID_CMD = "isvalid"
        ISVALID_FILE = "validity.gen"
        MUTATE_CMD = "mutate"
        MUTATE_FILE = "mutant.gen"

        CLI_INPUT_FILE = "genotypes.gen"

        _next_instance_id = count(0)  # "static" counter incremented when a new instance is created. Used for unique filenames


        def __init__(self, framspath, framsexe, pid=""):
                self.pid = pid if pid is not None else ""
                self.id = next(FramsticksCLI._next_instance_id)
                self.frams_path = framspath
                self.frams_exe = framsexe if framsexe is not None else 'frams.exe' if os.name == "nt" else 'frams.linux'
                self.writing_path = None
                mainpath = os.path.join(self.frams_path, self.frams_exe)
                exe_call = [mainpath, '-Q', '-s', '-c', '-icliutils.ini']  # -c will be ignored in Windows Framsticks (this option is meaningless because the Windows version does not support color console, so no need to deactivate this feature using -c)
                exe_call_to_get_version = [mainpath, '-V']
                exe_call_to_get_path = [mainpath, '-?']
                try:
                        print("\n".join(self.__readAllOutput(exe_call_to_get_version)))
                        help = self.__readAllOutput(exe_call_to_get_path)
                        for helpline in help:
                                if 'dDIRECTORY' in helpline:
                                        self.writing_path = helpline.split("'")[1]
                except FileNotFoundError:
                        print("Could not find Framsticks executable ('%s') in the given location ('%s')." % (self.frams_exe, self.frams_path))
                        sys.exit(1)
                print("Temporary files with results will be saved in detected writable working directory '%s'" % self.writing_path)
                self.__spawnFramsticksCLI(exe_call)


        def __readAllOutput(self, command):
                frams_process = Popen(command, stdout=PIPE, stderr=PIPE, stdin=PIPE)
                return [line.decode('utf-8').rstrip() for line in iter(frams_process.stdout.readlines())]


        def __spawnFramsticksCLI(self, args):
                # the child app (Framsticks CLI) should not buffer outputs and we need to immediately read its stdout, hence we use pexpect/wexpect
                print('Spawning Framsticks CLI for continuous stdin/stdout communication... ', end='')
                if os.name == "nt":  # Windows:
                        import wexpect  # https://pypi.org/project/wexpect/
                        # https://github.com/raczben/wexpect/tree/master/examples
                        self.child = wexpect.spawn(' '.join(args))
                else:
                        import pexpect  # https://pexpect.readthedocs.io/en/stable/
                        self.child = pexpect.spawn(' '.join(args))
                        self.child.setecho(False)  # linux only
                print('OK.')

                self.__readFromFramsCLIUntil("UserScripts.autoload")
                print('Performing a basic test 1/3... ', end='')
                assert self.getSimplest("1") == "X"
                print('OK.')
                print('Performing a basic test 2/3... ', end='')
                assert self.isValid("X[0:0]") is True
                print('OK.')
                print('Performing a basic test 3/3... ', end='')
                assert self.isValid("X[0:0],") is False
                print('OK.')
                if not self.DETERMINISTIC:
                        self.child.sendline(self.RANDOMIZE_CMD)
                self.child.sendline(self.SETEXPEDEF_CMD)


        def closeFramsticksCLI(self):
                # End gracefully by sending end-of-file character: ^Z or ^D
                # Without -Q argument ("quiet mode"), Framsticks CLI would print "Shell closed." for goodbye.
                self.child.sendline(chr(26 if os.name == "nt" else 4))


        def __getPrefixedFilename(self, filename: str) -> str:
                # Returns filename with unique instance id appended so there is no clash when many instances of this class use the same Framsticks CLI executable
                return FramsticksCLI.FILE_PREFIX + self.pid + str(chr(ord('A') + self.id)) + '_' + filename


        def __saveGenotypeToFile(self, genotype, name, mode, saveformat):
                relname = self.__getPrefixedFilename(name)
                absname = os.path.join(self.writing_path, relname)
                if mode == 'd':  # special mode, 'delete'
                        if os.path.exists(absname):
                                os.remove(absname)
                else:
                        outfile = open(absname, mode)
                        if saveformat == self.GENO_SAVE_FILE_FORMAT["RAWGENO"]:
                                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.close()
                return relname, absname


        def __readFromFramsCLIUntil(self, until_marker: str):
                while True:
                        self.child.expect('\n')
                        msg = str(self.child.before)
                        if self.PRINT_FRAMSTICKS_OUTPUT or msg.startswith("[ERROR]"):
                                print(msg)
                        if until_marker in msg:
                                break


        def __runCommand(self, command, genotypes, result_file_name, saveformat) -> List[str]:
                filenames_rel = []  # list of file names with input data for the command
                filenames_abs = []  # same list but absolute paths actually used
                if saveformat == self.GENO_SAVE_FILE_FORMAT["RAWGENO"]:
                        for i in range(len(genotypes)):
                                # plain text format = must have a separate file for each genotype
                                rel, abs = self.__saveGenotypeToFile(genotypes[i], "genotype" + str(i) + ".gen", "w", self.GENO_SAVE_FILE_FORMAT["RAWGENO"])
                                filenames_rel.append(rel)
                                filenames_abs.append(abs)
                elif saveformat == self.GENO_SAVE_FILE_FORMAT["NATIVEFRAMS"]:
                        self.__saveGenotypeToFile(None, self.CLI_INPUT_FILE, 'd', None)  # 'd'elete: ensure there is nothing left from the last run of the program because we "a"ppend to file in the loop below
                        for i in range(len(genotypes)):
                                rel, abs = self.__saveGenotypeToFile(genotypes[i], self.CLI_INPUT_FILE, "a", self.GENO_SAVE_FILE_FORMAT["NATIVEFRAMS"])
                        #  since we use the same file in the loop above, add this file only once (i.e., outside of the loop)
                        filenames_rel.append(rel)
                        filenames_abs.append(abs)

                result_file_name = self.__getPrefixedFilename(result_file_name)
                cmd = command + " " + " ".join(filenames_rel) + " " + result_file_name
                self.child.sendline(cmd + '\n')
                self.__readFromFramsCLIUntil(self.STDOUT_ENDOPER_MARKER)
                filenames_abs.append(os.path.join(self.writing_path, self.OUTPUT_DIR, result_file_name))
                return filenames_abs  # last element is a path to the file containing results


        def __cleanUpCommandResults(self, filenames):
                """Deletes files with results just created by the command."""
                for name in filenames:
                        os.remove(name)


        def getSimplest(self, genetic_format) -> str:
                assert len(genetic_format) == 1, "Genetic format should be a single character"
                files = self.__runCommand(self.GETSIMPLEST_CMD + " " + genetic_format + " ", [], self.GETSIMPLEST_FILE, self.GENO_SAVE_FILE_FORMAT["RAWGENO"])
                with open(files[-1]) as f:
                        genotype = "".join(f.readlines())
                self.__cleanUpCommandResults(files)
                return genotype


        def evaluate(self, genotype: str):
                """
                Returns:
                        Dictionary -- genotype evaluated with self.EVALUATE_COMMAND. Note that for whatever reason (e.g. incorrect genotype),
                        the dictionary you will get may be empty or partially empty and may not have the fields you expected, so handle such cases properly.
                """
                files = self.__runCommand(self.EVALUATE_CMD, [genotype], self.EVALUATE_FILE, self.GENO_SAVE_FILE_FORMAT["NATIVEFRAMS"])
                with open(files[-1]) as f:
                        data = json.load(f)
                if len(data) > 0:
                        self.__cleanUpCommandResults(files)
                        return data
                else:
                        print("Evaluating genotype: no performance data was returned in", self.EVALUATE_FILE)  # we do not delete files here
                        return None


        def mutate(self, genotype: str) -> str:
                files = self.__runCommand(self.MUTATE_CMD, [genotype], self.MUTATE_FILE, self.GENO_SAVE_FILE_FORMAT["RAWGENO"])
                with open(files[-1]) as f:
                        newgenotype = "".join(f.readlines())
                self.__cleanUpCommandResults(files)
                return newgenotype


        def crossOver(self, genotype1: str, genotype2: str) -> str:
                files = self.__runCommand(self.CROSSOVER_CMD, [genotype1, genotype2], self.CROSSOVER_FILE, self.GENO_SAVE_FILE_FORMAT["RAWGENO"])
                with open(files[-1]) as f:
                        child_genotype = "".join(f.readlines())
                self.__cleanUpCommandResults(files)
                return child_genotype


        def dissimilarity(self, genotype_list: List[str]) -> np.ndarray:
                """
                Returns:
                        A square array with dissimilarities of each pair of genotypes.
                """
                files = self.__runCommand(self.DISSIMIL_CMD, genotype_list, self.DISSIMIL_FILE, self.GENO_SAVE_FILE_FORMAT["NATIVEFRAMS"])
                with open(files[-1]) as f:
                        dissimilarity_matrix = np.genfromtxt(f, dtype=np.float64, comments='#', encoding=None, delimiter='\t')
                # We would like to skip column #1 while reading and read everything else, but... https://stackoverflow.com/questions/36091686/exclude-columns-from-genfromtxt-with-numpy
                # This would be too complicated, so strings (names) in column #1 become NaN as floats (unless they accidentally are valid numbers) - not great, not terrible
                square_matrix = dissimilarity_matrix[:, 2:]  # get rid of two first columns (fitness and name)
                EXPECTED_SHAPE = (len(genotype_list), len(genotype_list))
                # print(square_matrix)
                assert square_matrix.shape == EXPECTED_SHAPE, f"Not a correct dissimilarity matrix, expected {EXPECTED_SHAPE} "
                for i in range(len(square_matrix)):
                        assert square_matrix[i][i] == 0, "Not a correct dissimilarity matrix, diagonal expected to be 0"
                assert (square_matrix == square_matrix.T).all(), "Probably not a correct dissimilarity matrix, expecting symmetry, verify this"
                self.__cleanUpCommandResults(files)
                return square_matrix


        def isValid(self, genotype: str) -> bool:
                files = self.__runCommand(self.ISVALID_CMD, [genotype], self.ISVALID_FILE, self.GENO_SAVE_FILE_FORMAT["RAWGENO"])
                with open(files[-1]) as f:
                        valid = f.readline() == "1"
                self.__cleanUpCommandResults(files)
                return valid


def parseArguments():
        parser = argparse.ArgumentParser(description='Run this program with "python -u %s" if you want to disable buffering of its output.' % sys.argv[0])
        parser.add_argument('-path', type=ensureDir, required=True, help='Path to Framsticks CLI without trailing slash.')
        parser.add_argument('-exe', required=False, help='Executable name. If not given, "frams.exe" or "frams.linux" is assumed.')
        parser.add_argument('-genformat', required=False, help='Genetic format for the demo run, for example 4, 9, or S. If not given, f1 is assumed.')
        parser.add_argument('-pid', required=False, help='Unique ID of this process. Only relevant when you run multiple instances of this class simultaneously but as separate processes, and they use the same Framsticks CLI executable. This value will be appended to the names of created files to avoid conflicts.')
        return parser.parse_args()


def ensureDir(string):
        if os.path.isdir(string):
                return string
        else:
                raise NotADirectoryError(string)


if __name__ == "__main__":
        # A demo run.

        # TODO ideas:
        # - check_validity with three levels (invalid, corrected, valid)
        # - "vectorize" some operations (isvalid, evaluate) so that a number of genotypes is handled in one call
        # - use threads for non-blocking reading from frams' stdout and thus not relying on specific strings printed by frams
        # - a pool of binaries run at the same time, balance load - in particular evaluation
        # - if we read genotypes in "org:" format anywhere: import https://pypi.org/project/framsreader/0.1.2/ 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.
        #    So far we don't read, but we should use the proper writer to handle all special cases like quoting etc.

        parsed_args = parseArguments()
        framsCLI = FramsticksCLI(parsed_args.path, parsed_args.exe, parsed_args.pid)

        simplest = framsCLI.getSimplest('1' if parsed_args.genformat is None else parsed_args.genformat)
        print("\tSimplest genotype:", simplest)
        parent1 = framsCLI.mutate(simplest)
        parent2 = parent1
        MUTATE_COUNT = 10
        for x in range(MUTATE_COUNT):  # example of a chain of 20 mutations
                parent2 = framsCLI.mutate(parent2)
        print("\tParent1 (mutated simplest):", parent1)
        print("\tParent2 (Parent1 mutated %d times):" % MUTATE_COUNT, parent2)
        offspring = framsCLI.crossOver(parent1, parent2)
        print("\tCrossover (Offspring):", offspring)
        print('\tDissimilarity of Parent1 and Offspring:', framsCLI.dissimilarity([parent1, offspring])[0, 1])
        print('\tPerformance of Offspring:', framsCLI.evaluate(offspring))
        print('\tValidity of Offspring:', framsCLI.isValid(offspring))

        framsCLI.closeFramsticksCLI()