Add initial version of updated tools from #1533

#! /usr/bin/env python3

# LAMMPS Documentation Utilities

#

# Scan for duplicate anchor labels in documentation files

#

# Copyright (C) 2019 E. Anne Gunn

# Based largely on doc_anchor_check.py by Richard Berger

#

# This program is free software: you can redistribute it and/or modify

# it under the terms of the GNU General Public License as published by

# the Free Software Foundation, either version 3 of the License, or

# (at your option) any later version.

#

# This program is distributed in the hope that it will be useful,

# but WITHOUT ANY WARRANTY; without even the implied warranty of

# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

# GNU General Public License for more details.

#

# You should have received a copy of the GNU General Public License

# along with this program.  If not, see <http://www.gnu.org/licenses/>.

import argparse

import os

import re

import sys

# We only want to replace image lines where image is

# pulled from Eqs subfolder

image_pattern = re.compile(r'.*image:: Eqs/(.*)\.jpg')

tex_eq_pattern = re.compile(r'\$\$')

latex_begin_eq_pattern = re.compile(r'\\begin{equation}')

latex_end_eq_pattern = re.compile(r'\\end{equation}')

latex_begin_eqArray_pattern = re.compile(r'\\begin{eqnarray\*}')

latex_end_eqArray_pattern = re.compile(r'\\end{eqnarray\*}')

imageMarker = ">>>image was here"

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

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

modifiedFileFolder = "src/modifiedRst/"

# Since this is a proof of concept implementation,

# skip any rst files that are known to cause problems

skipFileList = ["pair_tersoff_zbl.rst"]

runReport = {

}

def checkForEquationStart(texLine):

    eqType = None

    texMatch = tex_eq_pattern.match(texLine)

    if texMatch:

        eqType = "texMatch"

    else:

        eqMatch = latex_begin_eq_pattern.match(texLine)

        if eqMatch:

            eqType = "eqMatch"

        else:

            eqArrayMatch = latex_begin_eqArray_pattern.match(texLine)

            if eqArrayMatch:

                eqType = "eqArrayMatch"

    return eqType

def checkForEquationEnd(texLine, eqType):

    endPattern = tex_eq_pattern

    if eqType == "texMatch":

        endPattern = tex_eq_pattern

    elif eqType == "eqMatch":

        endPattern = latex_end_eq_pattern

    elif eqType == "eqArrayMatch":

        endPattern = latex_end_eqArray_pattern

    else:

        print("***error: unexpected eqType %s, will look for tex delimiter" % eqType)

    endMatch = endPattern.match(texLine)

    endFound = endMatch is not None

    if endFound:

        print("found pattern end, line: %s" % texLine)

    return endFound

def startMathjax():

    mathjaxLines = []

    mathjaxLines.append(".. math::\n\n")

    return mathjaxLines

def endMathjax(mathjaxLines):

    mathjaxLines.append("\n")

    mathjaxLines.append("%s\n" % imageMarker)

    return mathjaxLines

def processFile(filename):

    print("in processFile for filename: %s" % filename)

    imageCount = 0

    modifiedFileLines = []

    doWriteModifiedFile = False

    with open(filename, 'rt') as f:

        for line_number, line in enumerate(f):

            m = image_pattern.match(line)

            if m:

                fileroot = m.group(1)

                print("fileroot: {0}".format(fileroot))

                imageCount += 1

                texFilename = "src/Eqs/{0}.tex".format(fileroot)

                print("will try to open %s" % texFilename)

                eqType = None

                eqLines = []

                try:

                    with open(texFilename, 'rt', encoding='utf-8') as t:

                        print("%s file opened ok" % texFilename)

                        eqLines = startMathjax()

                        try:

                            for dummy, texLine in enumerate(t):

                                #print(texLine)

                                if eqType == None:

                                    eqType = checkForEquationStart(texLine)

                                    if eqType != None:

                                        print("equation type: {0}".format(eqType))

                                else:

                                    endFound = checkForEquationEnd(texLine, eqType)

                                    if endFound != True:

                                        eqLines.append(texLine)

                                    else:

                                        eqType = None

                                        eqLines = endMathjax(eqLines)

                                        print("Equation lines will be:")

                                        print("-----------------------------")

                                        print(*eqLines, sep="\n")

                                        print("-----------------------------")

                        except UnicodeDecodeError:

                            print("UnicodeDecodeError reading file file %s, image markup will be left in place" % texFilename)

                            break

                except EnvironmentError:

                    error = "could not open source tex file {0}, line: {1}".format(texFilename, line)

                    print(error)

                    print("image markup will be left in place")

                    if filename not in runReport:

                        runReport[filename] = []

                    runReport[filename].append(error)

                    # put the image line we could not replace back into the output

                    eqLines.append(line)

                if len(eqLines) > 0:

                    modifiedFileLines.extend(eqLines)

                    doWriteModifiedFile = True

                    eqLines = []

            else:

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

                modifiedFileLines.append(line)

    if doWriteModifiedFile:

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

        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

        deleteLines = []

        for lineNumber, line in enumerate(modifiedFileLines):

            m = image_marker_pattern.match(line)

            if m:

                print("found image marker in line %d" % lineNumber)

                n = align_pattern.match(modifiedFileLines[lineNumber+1])

                if n:

                    print("found align center")

                    deleteLines.append(lineNumber)

                    deleteLines.append(lineNumber+1)

        #When deleting, always work from the back of the list to the front

        for lineNumber in reversed(deleteLines):

            print(lineNumber)

            del modifiedFileLines[lineNumber]

        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])

            modRst = open(modFilePath, "w")

            for rstLine in modifiedFileLines:

                modRst.write(rstLine)

            modRst.close()

        except OSError:

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

    return imageCount

def main():

    fileCount = 0

    totalImageCount = 0

    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()

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

    # 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

    # zombie modifications

    if len(parsed_args.files) > 1:

        for outputFile in os.listdir(modifiedFileFolder):

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

            try:

                if os.path.isfile(filePath):

                    os.unlink(filePath)

            except Exception as e:

                print(e)

                sys.exit(1)

    for filename in parsed_args.files:

        doSkip = False

        for skipName in skipFileList:

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

                print("skipping file: %s" % filename)

                doSkip = True

                runReport[filename] = ["skipped based on skipFileList"]

                break

        if not doSkip:

            fileCount += 1

            ic = processFile(filename)

            totalImageCount += ic

    print("============================================")

    print("Processed %d rst files." % fileCount)

    print("Found %d image lines." % totalImageCount)

    for fileKey in runReport:

        print("--------------------------------------------")

        print("run report for %s:" % fileKey)

        print(*runReport[fileKey], sep="\n")

    print("============================================")

if __name__ == "__main__":

    main()

#! /usr/bin/env python3

# LAMMPS Documentation Utilities

#

# Scan for duplicate anchor labels in documentation files

#

# Copyright (C) 2017 Richard Berger

#

# This program is free software: you can redistribute it and/or modify

# it under the terms of the GNU General Public License as published by

# the Free Software Foundation, either version 3 of the License, or

# (at your option) any later version.

#

# This program is distributed in the hope that it will be useful,

# but WITHOUT ANY WARRANTY; without even the implied warranty of

# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

# GNU General Public License for more details.

#

# You should have received a copy of the GNU General Public License

# along with this program.  If not, see <http://www.gnu.org/licenses/>.

import re

import sys

import argparse

def main():

    parser = argparse.ArgumentParser(description='scan for duplicate anchor labels in documentation files')

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

    parsed_args = parser.parse_args()

    anchor_pattern = re.compile(r'^\.\. _(.*):$')

    anchors = {}

    for filename in parsed_args.files:

        #print("filename: %s" % filename)

        with open(filename, 'rt') as f:

            for line_number, line in enumerate(f):

                m = anchor_pattern.match(line)

                if m:

                    label = m.group(1)

                    #print("found label: %s" % label)

                    if label in anchors:

                        anchors[label].append((filename, line_number+1))

                    else:

                        anchors[label] = [(filename, line_number+1)]

    print("found %d anchor labels" % len(anchors))

    count = 0

    for label in sorted(anchors.keys()):

        if len(anchors[label]) > 1:

            print(label)

            count += 1

            for filename, line_number in anchors[label]:

                print(" - %s:%d" % (filename, line_number))

    if count > 0:

        print("Found %d anchor label errors." % count)

        sys.exit(1)

    else:

        print("No anchor label errors.")

if __name__ == "__main__":

    main()

      entry_points = {

          "console_scripts": ['txt2html = lammpsdoc.txt2html:main',

                              'txt2rst  = lammpsdoc.txt2rst:main',

                              'doc_anchor_check = lammpsdoc.doc_anchor_check:main ']

                              'rst_anchor_check = lammpsdoc.rst_anchor_check:main ']

      },

)