Re-enabled conversion of equations arrays. Disabled works even worse

import argparse

import os

import re

import shutil

import sys

image_marker_pattern = re.compile(r'>>>image was here')

align_pattern = re.compile(r'.*:align: center')

modifiedFileFolder = "src/modifiedRst/"

modifiedRstFolder = "src/modifiedRst/"

safeRstFolder = "src/safeRst/"

# Since this is a proof of concept implementation,

# skip any rst files that are known to cause problems

skipFileList = ["pair_tersoff_zbl.rst"]

                # not an equation line, so simply queue it up for output as is

                modifiedFileLines.append(line)

    if doWriteModifiedFile:

        #print(*modifiedFileLines, sep="\n")

        # We're going to write out a modified file, so first copy the original rst

        # file into the original file folder.

        nameParts = filename.split("/")

        filenamePos = len(nameParts) - 1

        safeFilePath = "{0}{1}".format(safeRstFolder, nameParts[filenamePos])

        shutil.copyfile(filename, safeFilePath)

        print("modifiedFileLines has %d lines before align center cleanup" % len(modifiedFileLines))

        # First, go through the file and pull out the lines where there is

        # now an image file marker followed by an align center directive

        print("modifiedFileLines has %d lines after align center cleanup" % len(modifiedFileLines))

        # Now we can actually write out the new contents

        try:

            if not os.path.exists(modifiedFileFolder):

                os.makedirs(modifiedFileFolder)

            nameParts = filename.split("/")

            filenamePos = len(nameParts) - 1

            modFilePath = "{0}{1}".format(modifiedFileFolder, nameParts[filenamePos])

            modFilePath = "{0}{1}".format(modifiedRstFolder, nameParts[filenamePos])

            modRst = open(modFilePath, "w")

            for rstLine in modifiedFileLines:

                modRst.write(rstLine)

            modRst.close()

        except OSError:

            print('Error: Creating directory. ' + modifiedFileFolder)

            print('Error: Creating directory. ' + modifiedRstFolder)

    return imageCount

    parser = argparse.ArgumentParser(description='replace image markup in rst files with inline mathjax markup from .txt source of images')

    parser.add_argument('files',  metavar='file', nargs='+', help='one or more files to scan')

    parsed_args = parser.parse_args()

    print(parsed_args)

    # TODO: make originalRst folder and copy src/*.rst files into it

    if not os.path.exists(safeRstFolder):

        os.makedirs(safeRstFolder)

    if not os.path.exists(modifiedRstFolder):

        os.makedirs(modifiedRstFolder)

    # Because we may decide to add files to the skip list between runs,

    # if we have more than one file to process,

    # remove the modified file folder so we don't end up with

    # files from both original and modified folders

    # zombie modifications

    if len(parsed_args.files) > 1:

        for outputFile in os.listdir(modifiedFileFolder):

            filePath = os.path.join(modifiedFileFolder, outputFile)

        for outputFile in os.listdir(modifiedRstFolder):

            filePath = os.path.join(modifiedRstFolder, outputFile)

            try:

                if os.path.isfile(filePath):

                    os.unlink(filePath)

            except Exception as e:

                print(e)

                sys.exit(1)

        for safeFile in os.listdir(safeRstFolder):

            filePath = os.path.join(safeRstFolder, safeFile)

            try:

                if os.path.isfile(filePath):

                    os.unlink(filePath)

                sys.exit(1)

    for filename in parsed_args.files:

        print("filename: %s" % filename)

        doSkip = False

        for skipName in skipFileList:

            if filename.find(skipName) != -1: