Implementing templates via Jinja2

Added Class Hierarchy page (Correctly shows inheritance of classes and structs)
Added Class Member Functions page
Added Class Member Variables page
Added Class Member Typedefs page
Added Class Member Enumerations page
Added Namespace List page
Added Namespace Members page
Added Namespace Member Functions page
Added Namespace Member Variables page
Added Namespace Member Typedefs page
Added Namespace Member Enumerations page
Added Inherited member types and functions listings into the derived classes
Use title when listing groups in modules.md
Fix sometimes html sensitive characters (<>& etc.) not escaping properly
Fix if source file has markdown codeblock ``` it would mess up output file
Added "Implements" on member functions if they override a method from a base class
Fixed anchors in VuePress (e.g. #function-hello-world)
Fixed numbering of overloaded functions and their anchors
Replaced anchoring on GitBook to use VuePress style anchoring

Author: Matus Novak

.gitignore

@@ -109,3 +109,4 @@ dist/
 example/temp
 *-old
 .vscode
+temp/

README.md

@@ -1,7 +1,9 @@
-# doxybook
+# DoxyBook
 
 This python tool will take an xml output generated by the Doxygen and converts that into markdown to be used by GitBook or Vuepress.
 
+Version v3.0.0 uses Jinja templates to generate Markdown files. The v3.0.0 is a massive overhaul of the XML processing and Markdown generation. **See the commit to see the changes.** The new v3.0.0 version has many bugfixes alongside with some additional namespace related files added into the output. If you are looking for old non templated version v2.1.6 then look into branch [doxybook/tree/v2.1.6](https://github.com/matusnovak/doxybook/tree/v2.1.6).
+
 ## Live Demo
 
 See live demo here for [Gitbook here](https://matusnovak.github.io/doxybook/gitbook/api/classexample_1_1_animal.html) or [Vuepress here](https://matusnovak.github.io/doxybook/vuepress/api/classexample_1_1_animal.html).
@@ -10,7 +12,11 @@ Alternativelly, the markdown files are located in the `doxybook/example/gitbook/
 
 ## Requirements
 
-You need to have **python 3.6 or newer**. No additional python packages necessary, only the ones included by default in python itself.
+You need to have **python 3.6 or newer** and [Jinja2](http://jinja.pocoo.org/docs/2.10/intro/) package installed.
+
+## Memory usage
+
+Needs up to 100MiB of memory. Parsing super large projects can use up to 0.5GiB of memory. For example, a project consisting of 1000 Doxygen xml files can use 550MiB of memory, but I would be worried more about VuePress or GitBook memory usage while using that many files.
 
 ## Installation
 
@@ -83,15 +89,18 @@ This tool was designed to copy the file naming and structure of Doxygen html out
 All classes, namespaces, structures, and interfaces are generated, including the following additional files:
 
 * Directories (e.g. `dir_....md`)
-* Files - source code + file documentation (e.g. `filename_8h.md`)
-* Markdown pages through doxygen, highly do not recommend using this! (e.g. `md_src_....md`)
+* Files with source code + file documentation (e.g. `filename_8h.md`)
+* Markdown pages processed through doxygen, highly do not recommend using this! (e.g. `md_src_....md`)
+* Members (e.g. `class_xxx_yyy.md` or `namespace_xxx_yyy.md`)
 * Class List (e.g. `annotated.md`)
 * Class Index (e.g. `classes.md`)
-* Variable Index (e.g. `variables.md`)
-* Function Index (e.g. `functions.md`)
-* Enumeration Index (e.g. `enumerations.md`)
+* Class Members (e.g. `class_members.md`, `class_member_enums.md`, `class_member_functions.md`, `class_member_typedefs.md`, `class_member_variables.md`)
+* Class Hierarchy (.e.g `hierarchy.md`)
+* Namespace List (e.g. `namespaces.md`)
+* Namespace Members (e.g. `namespace_members.md`, `namespace_member_enums.md`, `namespace_member_functions.md`, `namespace_member_typedefs.md`, `namespace_member_variables.md`)
 * Modules/groups (e.g. `modules.md`)
-* Index page (if any) (e.g. `indexpage.md`)
+* Index page (if exists within Doxygen output as `indexpage.xml`) (e.g. `index.md`)
+* Any additional pages generated by Doxygen such as bugs, todo, tests
 
 See the example folder to see all files.
 
@@ -101,6 +110,7 @@ See the example folder to see all files.
 > python -m doxybook -h
 usage: __main__.py [-h] [-t TARGET] -i INPUT -o OUTPUT [-s SUMMARY] [-d DEBUG]
                    [--noindex NOINDEX] [--hints HINTS]
+                   [--ignoreerrors IGNOREERRORS]
 
 Convert doxygen XML output into GitBook or Vuepress markdown output.
 
@@ -119,11 +129,13 @@ optional arguments:
                         false)
   -d DEBUG, --debug DEBUG
                         Debug the class hierarchy (default: false)
-  --noindex NOINDEX     If set to true, no search keywords will be generated
-                        at the file headers (default: false)
   --hints HINTS         (Vuepress only) If set to true, hints will be
                         generated for the sections note, bug, and a warning
                         (default: true)
+  --ignoreerrors IGNOREERRORS
+                        If set to true, will continue to generate Markdown
+                        files even if an error has been detected (default:
+                        false)
 ```
 
 ## Detailed usage Vuepress
@@ -146,6 +158,10 @@ optional arguments:
 6. Run doxybook as: `doxybook -i temp/xml -o docs/api -s SUMMARY.md -t gitbook` (paths are relative) The `-s SUMMARY.md` is optional, if you provide a vaid path to the SUMMARY.md file then the doxybook will alter the contents with links to generated markdown files.
 7. Then build your GitBook as: `gitbook build`, or serve it as `gitbook serve` and go to `http://localhost:4000`, or upload the contents of `_book` folder into gh-pages on GitHub.
 
+## Having errors while generating markdown files?
+
+Run doxybook as `doxybook --ignoreerrors true -i ... -o ... -t ...`. The files will be generated, but some things may be missing.
+
 ## How does the SUMMARY.md work here? (Gitbook only)
 
 GitBook has a big fault that anything not listed in `SUMMARY.md` will get ignored. Therefore the doxybook needs to alter the `SUMMARY.md`. Yes, this is optional, in case GitBook will be fixed in the future. 
@@ -168,36 +184,59 @@ After running doxybook, the summary will become this code below. Notice how `* [
 # Summary
 
 * [Introduction](README.md)
-* [Documentation](docs/api/index.md)
-  * [Related Pages](docs/api/pages.md)
-    * [Bug List](docs/api/bug.md)
-    * [My Personal Index Page](docs/api/indexpage.md)
-    * [Markdown test](docs/api/md_src_markdown-demo.md)
-    * [Test List](docs/api/test.md)
-    * [Todo List](docs/api/todo.md)
-  * [Modules](docs/api/modules.md)
-    * [animals](docs/api/group__animals.md)
-  * [Class Index](docs/api/classes.md)
-  * [Class List](docs/api/annotated.md)
-    * [namespace example](docs/api/namespaceexample.md)
-      * [class Animal](docs/api/classexample_1_1_animal.md)
-        * [struct Result](docs/api/structexample_1_1_animal_1_1_result.md)
-      * [class Bird](docs/api/classexample_1_1_bird.md)
-      * [class CustomException](docs/api/classexample_1_1_custom_exception.md)
-      * [class SpecialBird](docs/api/classexample_1_1_special_bird.md)
-  * [Files](docs/api/files.md)
-    * [src/](docs/api/dir_68267d1309a1af8e8297ef4c3efbcdba.md)
-      * [animal.h](docs/api/animal_8h.md)
-      * [animal.h - source](docs/api/animal_8h_source.md)
-      * [bird.h](docs/api/bird_8h.md)
-      * [bird.h - source](docs/api/bird_8h_source.md)
-      * [example.h](docs/api/example_8h.md)
-      * [example.h - source](docs/api/example_8h_source.md)
-      * [special_bird.h](docs/api/special__bird_8h.md)
-      * [special_bird.h - source](docs/api/special__bird_8h_source.md)
-      * [utils/](docs/api/dir_313caf1132e152dd9b58bea13a4052ca.md)
-        * [exception.h](docs/api/exception_8h.md)
-        * [exception.h - source](docs/api/exception_8h_source.md)
+* [Documentation](api/index.md)
+  * [Related Pages](api/pages.md)
+    * [Bug List](api/bug.md)
+    * [My Personal Index Page](api/indexpage.md)
+    * [Markdown test](api/md_src_markdown-demo.md)
+    * [Test List](api/test.md)
+    * [Todo List](api/todo.md)
+  * [Modules](api/modules.md)
+    * [Some organism example](api/group__organism.md)
+      * [An animal group example](api/group__animals.md)
+  * [Class List](api/annotated.md)
+    * [namespace example](api/namespaceexample.md)
+      * [class example::Animal](api/classexample_1_1_animal.md)
+        * [struct example::Animal::Result](api/structexample_1_1_animal_1_1_result.md)
+      * [interface example::AnimalInterface](api/classexample_1_1_animal_interface.md)
+      * [class example::Bird](api/classexample_1_1_bird.md)
+      * [class example::CustomException](api/classexample_1_1_custom_exception.md)
+      * [class example::NumericException](api/classexample_1_1_numeric_exception.md)
+      * [class example::SpecialBird](api/classexample_1_1_special_bird.md)
+      * [namespace example::inner_namespace](api/namespaceexample_1_1inner__namespace.md)
+        * [class example::inner_namespace::Vector](api/classexample_1_1inner__namespace_1_1_vector.md)
+  * [Namespace List](api/namespaces.md)
+  * [Namespace Members](api/namespace_members.md)
+  * [Namespace Member Functions](api/namespace_member_functions.md)
+  * [Namespace Member Variables](api/namespace_member_variables.md)
+  * [Namespace Member Typedefs](api/namespace_member_typedefs.md)
+  * [Namespace Member Enumerations](api/namespace_member_enums.md)
+  * [Class Index](api/classes.md)
+  * [Class Hierarchy](api/hierarchy.md)
+  * [Class Members](api/class_members.md)
+  * [Class Member Functions](api/class_member_functions.md)
+  * [Class Member Variables](api/class_member_variables.md)
+  * [Class Member Typedefs](api/class_member_typedefs.md)
+  * [Class Member Enumerations](api/class_member_enums.md)
+  * [Files](api/files.md)
+    * [markdown-demo.md](api/markdown-demo_8md.md)
+    * [markdown-demo.md source](api/markdown-demo_8md_source.md)
+    * [src](api/dir_68267d1309a1af8e8297ef4c3efbcdba.md)
+      * [animal.h](api/animal_8h.md)
+      * [animal.h source](api/animal_8h_source.md)
+      * [animal_interface.h](api/animal__interface_8h.md)
+      * [animal_interface.h source](api/animal__interface_8h_source.md)
+      * [bird.h](api/bird_8h.md)
+      * [bird.h source](api/bird_8h_source.md)
+      * [config.h](api/config_8h.md)
+      * [config.h source](api/config_8h_source.md)
+      * [example.h](api/example_8h.md)
+      * [example.h source](api/example_8h_source.md)
+      * [special_bird.h](api/special__bird_8h.md)
+      * [special_bird.h source](api/special__bird_8h_source.md)
+      * [src/utils](api/dir_313caf1132e152dd9b58bea13a4052ca.md)
+        * [exception.h](api/exception_8h.md)
+        * [exception.h source](api/exception_8h_source.md)
 * [Something else](something-else.md)
 * [Go to my website](http://mywebsite.com/)
 ```
@@ -215,7 +254,7 @@ After running doxybook, the summary will become this code below. Notice how `* [
 ```
 MIT License
 
-Copyright (c) 2018 Matus Novak
+Copyright (c) 2019 Matus Novak
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

doxybook/__init__.py

@@ -1,140 +0,0 @@
-import argparse
-import sys
-import os
-import xml.etree.ElementTree
-
-from doxybook.loader import load_root
-from doxybook.kind import Kind
-from doxybook.node import Node
-from doxybook.cache import Cache
-from doxybook.generators import (
-    generate_annotated,
-    generate_class_index,
-    generate_dir,
-    generate_file,
-    generate_files,
-    generate_member,
-    generate_modules,
-    generate_page,
-    generate_pages,
-    generate_summary,
-    generate_function_index,
-    generate_variable_index,
-    generate_enum_index
-)
-from doxybook.config import config
-
-def write_groups(index_path: str, output_path: str, node: Node, cache: Cache):
-    for member in node.members:
-        if member.kind == Kind.GROUP:
-            generate_member(index_path, output_path, member.refid, cache)
-            write_groups(index_path, output_path, member, cache)
-
-def write_members(index_path: str, output_path: str, node: Node, cache: Cache):
-    for member in node.members:
-        if member.kind == Kind.STRUCT or member.kind == Kind.NAMESPACE or member.kind == Kind.CLASS or member.kind == Kind.INTERFACE:
-            generate_member(index_path, output_path, member.refid, cache)
-            write_members(index_path, output_path, member, cache)
-
-def main():
-    parser = argparse.ArgumentParser(description='Convert doxygen XML output into GitBook or Vuepress markdown output.')
-    parser.add_argument('-t', '--target', 
-        type=str, 
-        help='Select the target: Gitbook (default) or Vuepress, for example: "-t vuepress" or "-t gitbook"',
-        required=False,
-        default=config.target
-    )
-    parser.add_argument('-i', '--input', 
-        type=str, 
-        help='Path to doxygen generated xml folder',
-        required=True
-    )
-    parser.add_argument('-o', '--output', 
-        type=str, 
-        help='Path to the destination folder',
-        required=True
-    )
-    parser.add_argument('-s', '--summary', 
-        type=str, 
-        help='Path to the summary file which contains a link to index.md in the folder pointed by --input (default: false)',
-        required=False
-    )
-    parser.add_argument('-d', '--debug', 
-        type=bool, 
-        help='Debug the class hierarchy (default: false)',
-        required=False,
-        default=config.debug
-    )
-    parser.add_argument('--noindex', 
-        type=bool, 
-        help='If set to true, no search keywords will be generated at the file headers (default: false)',
-        required=False,
-        default=config.noindex
-    )
-    parser.add_argument('--hints', 
-        type=bool, 
-        help='(Vuepress only) If set to true, hints will be generated for the sections note, bug, and a warning (default: true)',
-        required=False,
-        default=config.hints
-    )
-
-    args = parser.parse_args()
-
-    if args.target != 'gitbook' and args.target != 'vuepress':
-        raise Exception('Unknown target: ' + str(args.target))
-
-    config.debug = args.debug
-    config.target = args.target
-    config.noindex = args.noindex
-    config.hints = args.hints
-
-    if args.summary and not os.path.exists(args.summary):
-        raise Exception('The provided summary file does not exist!')
-
-    if not os.path.exists(args.output) or not os.path.isdir(args.output):
-        raise Exception('The target output directory does not exist!')
-
-    os.makedirs(args.output, exist_ok=True)
-    cache = Cache()
-    root = load_root(cache, args.input)
-
-    # Generate Index
-    generate_class_index(args.output, root)
-    generate_function_index(args.output, root)
-    generate_variable_index(args.output, root)
-    generate_enum_index(args.output, root)
-
-    # Generate Class List
-    generate_annotated(args.input, args.output, root, cache)
-
-    # Write all members out
-    write_members(args.input, args.output, root, cache)
-
-    # Generate modules page
-    modules = generate_modules(args.input, args.output, root, cache)
-
-    # Write all grouos out
-    write_groups(args.input, args.output, root, cache)
-
-    # Generate pages page
-    pages = generate_pages(args.input, args.output, root, cache)
-
-    # Write all pages out
-    for child in root.members:
-        if child.kind == Kind.PAGE:
-            generate_page(args.input, args.output, child.refid, cache)
-
-    # Generate files page
-    files = generate_files(args.input, args.output, root, cache)
-
-    # Write all files out
-    for child in root.members:
-        if child.kind == Kind.FILE:
-            generate_member(args.input, args.output, child.refid, cache)
-            generate_file(args.input, args.output, child, cache)
-        if child.kind == Kind.DIR:
-            generate_dir(args.input, args.output, child, cache)
-
-    # Update summary
-    if args.summary:
-        generate_summary(args.output, args.summary, root, modules, pages, files)