CPP MOLE 2.0 grid implementation + error handling by Tony-Drummond · Pull Request #442 · csrc-sdsu/mole

Tony-Drummond · 2026-08-18T18:54:45Z

What type of PR is this? (check all applicable)

Description

Objective
Bring the C++ implementation into compliance with the MOLE 2.0
API, numerical behavior, testing, documentation, and packaging standards.

mole/
├── cpp/
| │── cmake/
| │── doc/
| │── examples
| |── src/
| │ ├── boundaries
| │ └── grids
| │ └── include
| │ └── operators
| │ └── sys
| │ └── utils
| |── tests
Figure 1. C++ MOLE 2.0 implementation. Bolded subdirectories names are the ones impacted by this PR and related Git issues.
This PR implements first steps of CPP MOLE 2.0 implementation:

Adopt new CPP software organization into the directory structure in Figure 1 (below)
Implement MOLE Errors handling and reporting system.
Implement C++ regression tests for the MOLE Errors module and use examples for documentation
Implement MOLE Grid classes and related data structures
Implement C++ regression tests for the MOLE Grid classes + Error handling/tracking, and basic examples for documentation

Related Issues & Documents

Issues, #437 (cpp directory reorganization) , #438 (error handling), #440 (cpp grid implementation)

I have created an Issue that is paired with this PR
Closes MOLE v2.0.0 Development: Adopt new CPP software organization into the directory structure #437
Closes Add C++ implementations of the MOLE Error Handling and the MOLE Grid data structures and core functionalities #438
Closes Add debugging API for the MOLE Grid 2.0 implementations #440

QA Instructions, Screenshots, Recordings

Tests and examples for creating grid are included. There are several tests of the full CPP functionality included here.

To build:

cd mole/cpp (notice that while we are moving from MOLE 1.2 to MOLE 2.0, the new CPP development is organized using the directory structure shown above). Thus, to build the C++, start from the subdirectory mole/cpp
mkdir build; cd build create a new subdirectory build and enter that new subdirectory
cmake .. will prepare to build the MOLE cpp library and include all software dependencies
make will manually build the MOLE library, examples and tests
cd examples/grids to run different examples of grid creation, or
cd tests to run any of the different tests of the library (>120 tests of the current C++ MOLE API)

Keep-open request

I am requesting maintainer review for keep-open.

Reason:

Added/updated tests?

_We encourage you to test all code included with MOLE, including examples.

Yes
No, and this is why: please replace this line with details on why tests
have not been included
I need help with writing tests

Read Contributing Guide and Code of Conduct

📖 I have read the MOLE Contributing Guide: https://github.com/csrc-sdsu/mole/blob/main/CONTRIBUTING.md
📖 I have read the MOLE Code of Conduct: https://github.com/csrc-sdsu/mole/blob/main/CODE_OF_CONDUCT.md

[optional] Are there any post deployment tasks we need to perform?

[optional] What gif best describes this PR or how it makes you feel?

Bumps [pillow](https://github.com/python-pillow/Pillow) from 12.1.1 to 12.3.0. - [Release notes](https://github.com/python-pillow/Pillow/releases) - [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst) - [Commits](python-pillow/Pillow@12.1.1...12.3.0) --- updated-dependencies: - dependency-name: pillow dependency-version: 12.3.0 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com>

Fix version specification for Pillow in requirements.txt Signed-off-by: Christopher Paolini <paolini@engineering.sdsu.edu>

Added debugging information to CMake configuration step. Signed-off-by: Christopher Paolini <paolini@engineering.sdsu.edu>

New directory structure with new implementations for MOLE grids, arrays, errors, and utilities. New README files in every subdirectory fixed errors

Added debugging information to CMake configuration step. Signed-off-by: Christopher Paolini <paolini@engineering.sdsu.edu>

New directory structure with new implementations for MOLE grids, arrays, errors, and utilities. New README files in every subdirectory fixed errors grid basic struct makegrid added Including DEBUGING MODE Adding testing and build utilities CMakefiles are updated

…_0_grid_implementation

Parses variadic <attribute, value> pairs into a gridRaw, validates dimensionality, cell counts, topology and isPeriodic length at parse time, then narrows into gridParams1D/2D/3D and calls makeGrid. Failures return a gridNull carrying the error stack. isPeriodic takes a pointer to a vector<bool> so its size can be checked against dim.

29 cases covering parse-time validation through runChecks and dimension dispatch through the gridBuilder macro, including isPeriodic size mismatches and out-of-order attributes.

Four examples covering 1D construction, 2D with periodicity, argument order independence, and parse-time error reporting.

Bumps [pillow](https://github.com/python-pillow/Pillow) from 12.1.1 to 12.3.0. - [Release notes](https://github.com/python-pillow/Pillow/releases) - [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst) - [Commits](python-pillow/Pillow@12.1.1...12.3.0) --- updated-dependencies: - dependency-name: pillow dependency-version: 12.3.0 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com>

Fix version specification for Pillow in requirements.txt Signed-off-by: Christopher Paolini <paolini@engineering.sdsu.edu>

Bumps [pillow](https://github.com/python-pillow/Pillow) from 12.1.1 to 12.3.0. - [Release notes](https://github.com/python-pillow/Pillow/releases) - [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst) - [Commits](python-pillow/Pillow@12.1.1...12.3.0) --- updated-dependencies: - dependency-name: pillow dependency-version: 12.3.0 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com>

Fix version specification for Pillow in requirements.txt Signed-off-by: Christopher Paolini <paolini@engineering.sdsu.edu>

Added the example/sys files

Adds gridBase::applyDebugMode and a debug_mode overload of each grid1D/2D/3D constructor. The mode is applied once at construction and is not stored. The trigger is isValidatedGrid() rather than hasGridErrors(): a grid carries MOLE_ERR_GRID_UNCHECKED until validation clears it, and mergeErrors folds upstream errors into the same stack, so a valid grid can hold errors it did not cause. Aborting on those would end user programs over grids that are fine. Reporting is non-destructive in every mode, so a caller can still print or write the log afterwards. Makes gridBase's constructor protected and gridNull's private, reachable only through makeGridNull. Both classes are internal. 15 new tests, all binaries green.

Parses a debug pair carrying a MOLE debug mode and applies it to the resulting grid. Dispatch moves into buildGrid so that every path, including both failure paths, funnels through one point. The debug pair has to come first: parsing stops at an unrecognized attribute name, so a trailing debug pair is never read on the calls that need it. Documented in the header and asserted in the tests.

Codes 14-17 mapped to empty strings; code 16 is logged by gridBuilder on an unknown attribute, so users saw a bare code with no message. Renumbers the dictionary comments (011-017, not 001-007) and corrects the gridBuilder range to 10-99.

valeriabarra and others added 24 commits August 11, 2026 21:42

Bump version

651ec44

Update RELEASING notes for MOLE.jl releases

8445521

grid basic struct

d6266b2

Correct Pillow version in requirements.txt

f4cd3dc

Fix version specification for Pillow in requirements.txt Signed-off-by: Christopher Paolini <paolini@engineering.sdsu.edu>

makegrid added

8e71163

ensure subdirs exist

cf3a0a2

validate grid added

209807d

Enhance CMake step with debug output

ebd1a2e

Added debugging information to CMake configuration step. Signed-off-by: Christopher Paolini <paolini@engineering.sdsu.edu>

MOLE grids, errors and utilities

6db0017

New directory structure with new implementations for MOLE grids, arrays, errors, and utilities. New README files in every subdirectory fixed errors

grid basic struct

35735d8

makegrid added

598e572

ensure subdirs exist

f153daf

validate grid added

192f537

Enhance CMake step with debug output

ba272c1

Added debugging information to CMake configuration step. Signed-off-by: Christopher Paolini <paolini@engineering.sdsu.edu>

Merge branch 'dev/MOLE_2.0' into cpp_dev/mole2_0_grid_implementation

7bec474

Including DEBUGING MODE

e23653c

Adding testing and build utilities

bb81610

Merge remote-tracking branch 'origin/dev/MOLE_2.0' into cpp_dev/mole2…

88b3304

…_0_grid_implementation

Update README.md

0f8342f

test: add regression tests for gridBuilder

dff0e9c

29 cases covering parse-time validation through runChecks and dimension dispatch through the gridBuilder macro, including isPeriodic size mismatches and out-of-order attributes.

docs: add gridBuilder examples

b9114e0

Four examples covering 1D construction, 2D with periodicity, argument order independence, and parse-time error reporting.

Tony-Drummond added Enhancement New feature or request Tests C++ Issues related to the MOLE C++ API Unit Testing Something fails in the auto-testing phases MOLE-2.0 Ideas and issues relating to the MOLE 2.0 development branch and or update. labels Aug 18, 2026

Tony-Drummond requested a review from jbrzensk August 18, 2026 18:57

Tony-Drummond requested review from joehellmers, mdumett and valeriabarra August 18, 2026 18:57

dependabot Bot and others added 13 commits August 18, 2026 13:30

Correct Pillow version in requirements.txt

d1c862e

Fix version specification for Pillow in requirements.txt Signed-off-by: Christopher Paolini <paolini@engineering.sdsu.edu>

Correct Pillow version in requirements.txt

6804c3c

Fix version specification for Pillow in requirements.txt Signed-off-by: Christopher Paolini <paolini@engineering.sdsu.edu>

Correct Pillow version in requirements.txt

b42f606

Fix version specification for Pillow in requirements.txt Signed-off-by: Christopher Paolini <paolini@engineering.sdsu.edu>

updated README.md files + more examples

6416cb4

Added the example/sys files

Update MOLE_errors.h

062dc16

updating .gitignore

d1f5d9a

updating .gitignore

90d352e

Update MOLE_errors.h

710f5bb

Navigation Menu

Uh oh!

CPP MOLE 2.0 grid implementation + error handling - #442

CPP MOLE 2.0 grid implementation + error handling#442
Tony-Drummond wants to merge 37 commits into
dev/MOLE_2.0from
cpp_dev/mole2_0_grid_implementation

Tony-Drummond commented Aug 18, 2026

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

5 participants

Uh oh!

Conversation

Tony-Drummond commented Aug 18, 2026

What type of PR is this? (check all applicable)

Description

Related Issues & Documents

QA Instructions, Screenshots, Recordings

Keep-open request

Added/updated tests?

Read Contributing Guide and Code of Conduct

[optional] Are there any post deployment tasks we need to perform?

[optional] What gif best describes this PR or how it makes you feel?

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

5 participants