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File tree restructure #17

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16 changes: 15 additions & 1 deletion .gitignore
Original file line number Diff line number Diff line change
@@ -1,9 +1,23 @@
# General ignore patterns
*
!*.*
!*/

# Ignore build artifacts and temporary files
*.o
*.so
*.a
*.asv
*~
doc*/

# Ignore Sphinx build output but include source files
doc/build/
doc/source/.*
!doc/source/*.rst
!doc/source/conf.py

# Include all non-build documentation files
!doc/
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Hi @pritkc , thank you for your work. I would just remove these lines and for now leave only your line 14, where we exclude the doc/build path.

You also want to exclude the path that you have specified in your Doxyfile: in the HTML_OUTPUT variable, that is HTML_OUTPUT = doc/api_docs/cpp

Suggested change
doc/source/.*
!doc/source/*.rst
!doc/source/conf.py
# Include all non-build documentation files
!doc/
doc/api_docs/cpp


# Add makefile
!Makefile
36 changes: 18 additions & 18 deletions Doxyfile
Original file line number Diff line number Diff line change
Expand Up @@ -99,7 +99,7 @@ OUTPUT_LANGUAGE = English
# Possible values are: None, LTR, RTL and Context.
# The default value is: None.

OUTPUT_TEXT_DIRECTION = None
# OUTPUT_TEXT_DIRECTION = None

# If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member
# descriptions after the members that are listed in the file and class
Expand Down Expand Up @@ -267,7 +267,7 @@ ALIASES =
# A mapping has the form "name=value". For example adding "class=itcl::class"
# will allow you to use the command class in the itcl::class meaning.

TCL_SUBST =
# TCL_SUBST =

# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources
# only. Doxygen will then generate output that is more tailored for C. For
Expand Down Expand Up @@ -829,7 +829,7 @@ WARN_LOGFILE =
# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
# Note: If this tag is empty the current directory is searched.

INPUT = README.md src/mole_C++ examples/examples_C++
INPUT = README.md src/cpp examples/cpp

# This tag can be used to specify the character encoding of the source files
# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
Expand Down Expand Up @@ -1120,15 +1120,15 @@ VERBATIM_HEADERS = YES
# generated with the -Duse_libclang=ON option for CMake.
# The default value is: NO.

CLANG_ASSISTED_PARSING = NO
# CLANG_ASSISTED_PARSING = NO

# If clang assisted parsing is enabled you can provide the compiler with command
# line options that you would normally use when invoking the compiler. Note that
# the include paths will already be set by doxygen for the files and directories
# specified with INPUT and INCLUDE_PATH.
# This tag requires that the tag CLANG_ASSISTED_PARSING is set to YES.

CLANG_OPTIONS =
# CLANG_OPTIONS =

# If clang assisted parsing is enabled you can provide the clang parser with the
# path to the compilation database (see:
Expand All @@ -1138,7 +1138,7 @@ CLANG_OPTIONS =
# Note: The availability of this option depends on whether or not doxygen was
# generated with the -Duse_libclang=ON option for CMake.

CLANG_DATABASE_PATH =
# CLANG_DATABASE_PATH =

#---------------------------------------------------------------------------
# Configuration options related to the alphabetical class index
Expand All @@ -1156,7 +1156,7 @@ ALPHABETICAL_INDEX = YES
# Minimum value: 1, maximum value: 20, default value: 5.
# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.

COLS_IN_ALPHA_INDEX = 5
# COLS_IN_ALPHA_INDEX = 5

# In case all classes in a project start with a common prefix, all classes will
# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag
Expand All @@ -1181,7 +1181,7 @@ GENERATE_HTML = YES
# The default directory is: html.
# This tag requires that the tag GENERATE_HTML is set to YES.

HTML_OUTPUT = docs/DOXY_C++
HTML_OUTPUT = doc/api_docs/cpp

# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
# generated HTML page (for example: .htm, .php, .asp).
Expand Down Expand Up @@ -1292,7 +1292,7 @@ HTML_COLORSTYLE_GAMMA = 80
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.

HTML_TIMESTAMP = NO
# HTML_TIMESTAMP = NO

# If the HTML_DYNAMIC_MENUS tag is set to YES then the generated HTML
# documentation will contain a main index with vertical navigation menus that
Expand Down Expand Up @@ -1584,7 +1584,7 @@ FORMULA_FONTSIZE = 10
# The default value is: YES.
# This tag requires that the tag GENERATE_HTML is set to YES.

FORMULA_TRANSPARENT = YES
# FORMULA_TRANSPARENT = YES

# The FORMULA_MACROFILE can contain LaTeX \newcommand and \renewcommand commands
# to create new LaTeX commands to be used in formulas as building blocks. See
Expand Down Expand Up @@ -1892,7 +1892,7 @@ LATEX_HIDE_INDICES = NO
# The default value is: NO.
# This tag requires that the tag GENERATE_LATEX is set to YES.

LATEX_SOURCE_CODE = NO
# LATEX_SOURCE_CODE = NO

# The LATEX_BIB_STYLE tag can be used to specify the style to use for the
# bibliography, e.g. plainnat, or ieeetr. See
Expand All @@ -1908,7 +1908,7 @@ LATEX_BIB_STYLE = plain
# The default value is: NO.
# This tag requires that the tag GENERATE_LATEX is set to YES.

LATEX_TIMESTAMP = NO
# LATEX_TIMESTAMP = NO

# The LATEX_EMOJI_DIRECTORY tag is used to specify the (relative or absolute)
# path from which the emoji images will be read. If a relative path is entered,
Expand Down Expand Up @@ -1982,7 +1982,7 @@ RTF_EXTENSIONS_FILE =
# The default value is: NO.
# This tag requires that the tag GENERATE_RTF is set to YES.

RTF_SOURCE_CODE = NO
# RTF_SOURCE_CODE = NO

#---------------------------------------------------------------------------
# Configuration options related to the man page output
Expand Down Expand Up @@ -2087,7 +2087,7 @@ DOCBOOK_OUTPUT = docbook
# The default value is: NO.
# This tag requires that the tag GENERATE_DOCBOOK is set to YES.

DOCBOOK_PROGRAMLISTING = NO
# DOCBOOK_PROGRAMLISTING = NO

#---------------------------------------------------------------------------
# Configuration options for the AutoGen Definitions output
Expand Down Expand Up @@ -2274,7 +2274,7 @@ EXTERNAL_PAGES = YES
# powerful graphs.
# The default value is: YES.

CLASS_DIAGRAMS = YES
# CLASS_DIAGRAMS = YES

# You can include diagrams made with dia in doxygen documentation. Doxygen will
# then run dia to produce the diagram and insert it in the documentation. The
Expand Down Expand Up @@ -2316,14 +2316,14 @@ DOT_NUM_THREADS = 0
# The default value is: Helvetica.
# This tag requires that the tag HAVE_DOT is set to YES.

DOT_FONTNAME = Helvetica
# DOT_FONTNAME = Helvetica

# The DOT_FONTSIZE tag can be used to set the size (in points) of the font of
# dot graphs.
# Minimum value: 4, maximum value: 24, default value: 10.
# This tag requires that the tag HAVE_DOT is set to YES.

DOT_FONTSIZE = 10
# DOT_FONTSIZE = 10

# By default doxygen will tell dot to use the default font as specified with
# DOT_FONTNAME. If you specify a different font using DOT_FONTNAME you can set
Expand Down Expand Up @@ -2549,7 +2549,7 @@ MAX_DOT_GRAPH_DEPTH = 0
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.

DOT_TRANSPARENT = NO
# DOT_TRANSPARENT = NO

# Set the DOT_MULTI_TARGETS tag to YES to allow dot to generate multiple output
# files in one run (i.e. multiple -o and -T options on the command line). This
Expand Down
2 changes: 1 addition & 1 deletion Makefile
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ ARMA = /home/johnny/armadillo-10.2.1

export

SUBDIRS = src/mole_C++ examples/examples_C++ tests/tests_C++
SUBDIRS = src/cpp examples/cpp tests/cpp

all clean: $(SUBDIRS)
$(SUBDIRS):
Expand Down
34 changes: 17 additions & 17 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -71,26 +71,26 @@ to build the C++ version if you are just interested in using MOLE from MATLAB/Oc

Here are instructions on how to run the provided examples and tests for both the C++ and MATLAB versions of the library to help you quickly get started with MOLE.

* **tests_C++:**
* **tests/cpp:**
These tests, which are automatically executed upon constructing the library's C++ version, play a crucial role in verifying the correct installation of MOLE and its dependencies. There are four tests in total.

* **tests_MATLAB:**
We encourage MATLAB users to execute these tests before using MOLE by entering the `tests_MATLAB` directory and executing `run_tests.m` from MATLAB. These tests are analogous to those contained in `tests_C++`.
* **tests/matlab:**
We encourage MATLAB users to execute these tests before using MOLE by entering the `tests/matlab` directory and executing `run_tests.m` from MATLAB. These tests are analogous to those contained in `tests/cpp`.

* **examples_C++:**
* **examples/cpp:**
These will be automatically built after calling `make`. We encourage C++ users to make this their entry point to familiarize themselves with this library version. The four examples are self-contained and adequately documented, and they solve typical PDEs.

* **examples_MATLAB:**
* **examples/matlab:**
Most of our examples are provided in the MATLAB scripting language. Over 30 examples range from linear one-dimensional PDEs to highly nonlinear multidimensional PDEs.


5: Documentation
----------------

The folder `doc_MATLAB` contains generated documentation about the MATLAB/Octave API.
It was generated with a tool called [_m2html_](https://www.gllmflndn.com/software/matlab/m2html). However, for a quick start on MOLE's MATLAB/Octave version, we recommend starting with this short [guide](https://github.com/jcorbino/mole/blob/master/CSRC%20Report%20on%20MOLE.pdf).
The folder `doc/api_docs/matlab` contains generated documentation about the MATLAB/Octave API.
It was generated with a tool called [_m2html_](https://www.gllmflndn.com/software/matlab/m2html). However, for a quick start on MOLE's MATLAB/Octave version, we recommend starting with this short [guide](https://github.com/csrc-sdsu/mole/blob/master/doc/assets/manuals/CSRC%20Report%20on%20MOLE.pdf).

For C++ users, we provide a short [guide](https://github.com/jcorbino/mole/blob/master/MOLE_C%2B%2B_Quick_Guide.pdf) to MOLE's C++ flavor. However, for those in need of more details to interact with the library, we suggest to follow these instructions:
For C++ users, we provide a short [guide](https://github.com/csrc-sdsu/mole/blob/master/doc/assets/manuals/MOLE_C%2B%2B_Quick_Guide.pdf) to MOLE's C++ flavor. However, for those in need of more details to interact with the library, we suggest to follow these instructions:

To generate the C++ documentation, execute:

Expand All @@ -106,7 +106,7 @@ Performing non-unary operations involving operands constructed over different gr
6: Community Guidelines
-----------------------

We welcome contributions to MOLE, whether they involve adding new functionalities, providing examples, addressing existing issues, reporting bugs, or requesting new features. Please refer to our [Contribution Guidelines](https://github.com/jcorbino/mole/blob/master/CONTRIBUTING.md) for more details.
We welcome contributions to MOLE, whether they involve adding new functionalities, providing examples, addressing existing issues, reporting bugs, or requesting new features. Please refer to our [Contribution Guidelines](https://github.com/csrc-sdsu/mole/blob/master/CONTRIBUTING.md) for more details.


7: Citations
Expand All @@ -120,11 +120,11 @@ the library [![DOI](https://joss.theoj.org/papers/10.21105/joss.06288/status.svg

Now, some cool pictures obtained with MOLE:

![Obtained with curvilinear operators](images/4thOrder.png)
![Obtained with curvilinear operators](images/4thOrder2.png)
![Obtained with curvilinear operators](images/4thOrder3.png)
![Obtained with curvilinear operators](images/grid2.png)
![Obtained with curvilinear operators](images/grid.png)
![Obtained with curvilinear operators](images/WavyGrid.png)
![Obtained with curvilinear operators](images/wave2D.png)
![Obtained with curvilinear operators](images/burgers.png)
![Obtained with curvilinear operators](doc/assets/img/4thOrder.png)
![Obtained with curvilinear operators](doc/assets/img/4thOrder2.png)
![Obtained with curvilinear operators](doc/assets/img/4thOrder3.png)
![Obtained with curvilinear operators](doc/assets/img/grid2.png)
![Obtained with curvilinear operators](doc/assets/img/grid.png)
![Obtained with curvilinear operators](doc/assets/img/WavyGrid.png)
![Obtained with curvilinear operators](doc/assets/img/wave2D.png)
![Obtained with curvilinear operators](doc/assets/img/burgers.png)
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113 changes: 113 additions & 0 deletions doc/api_docs/cpp/README_8md.html
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@@ -0,0 +1,113 @@
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