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Fix memory safety in TUV-x Python bindings for array returns#759

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K20shores merged 5 commits intodevelop-603-tuvx-examplesfrom
copilot/sub-pr-758
Jan 30, 2026
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Fix memory safety in TUV-x Python bindings for array returns#759
K20shores merged 5 commits intodevelop-603-tuvx-examplesfrom
copilot/sub-pr-758

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Copilot AI commented Jan 29, 2026 •
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The _run_tuvx function created NumPy arrays from pointers to local std::vector buffers. When the lambda returned, these vectors were destroyed, leaving dangling pointers in the NumPy arrays.

Changes

  • Heap allocation with RAII: Use std::unique_ptr<std::vector<double>> instead of stack-allocated vectors for automatic exception-safe cleanup
  • Capsule-based ownership transfer: Create py::capsule with custom deleter to manage vector lifetime, then atomically transfer ownership to NumPy arrays
  • Exception safety: Create each NumPy array immediately after its capsule to prevent use-after-free if array construction throws

Implementation

// Before: stack allocation causes dangling pointers
std::vector<double> photolysis_rates(n_photolysis * (n_layers + 1));
py::array_t<double> py_photolysis = py::array_t<double>({n_photolysis, n_layers + 1}, photolysis_rates.data());
return py_photolysis;  // dangling pointer when vector destroyed

// After: heap allocation with capsule ownership
auto photolysis_rates = std::make_unique<std::vector<double>>(n_photolysis * (n_layers + 1));
double* photolysis_data = photolysis_rates->data();
auto photolysis_capsule = py::capsule(photolysis_rates.get(), [](void* v) { delete reinterpret_cast<std::vector<double>*>(v); });
photolysis_rates.release();
py::array_t<double> py_photolysis = py::array_t<double>({n_photolysis, n_layers + 1}, photolysis_data, photolysis_capsule);
return py_photolysis;  // capsule ensures cleanup when array destroyed

Applied to all five output arrays: photolysis_rates, heating_rates, dose_rates, actinic_flux, spectral_irradiance.

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Copilot AI mentioned this pull request Jan 29, 2026
Merged
Copilot AI and others added 4 commits January 29, 2026 21:51
@K20shores
Fix memory safety issue in TUV-x Python bindings
5c6a7dc 
Allocate output arrays on heap and use py::capsule to manage lifetime.
This prevents dangling pointers when local vectors are destroyed.

Co-authored-by: K20shores <[email protected]>
@K20shores
Improve exception safety using std::unique_ptr
e643296 
Use RAII-based memory management with std::unique_ptr instead of raw
pointers to ensure automatic cleanup if exceptions occur during
allocation or array construction.

Co-authored-by: K20shores <[email protected]>
@K20shores
Fix double-delete issue in ownership transfer
b8694cb 
Store data pointers before releasing unique_ptrs to prevent double-delete
if exceptions occur during numpy array construction.

Co-authored-by: K20shores <[email protected]>
@K20shores
Ensure atomic ownership transfer from capsule to array
4cd673c 
Create each numpy array immediately after its capsule to prevent
use-after-free if exceptions occur during array construction.

Co-authored-by: K20shores <[email protected]>
Copilot AI changed the title [WIP] WIP address feedback from PR #758 for TUV-x examples and tutorial Fix memory safety in TUV-x Python bindings for array returns Jan 29, 2026
Copilot AI requested a review from K20shores January 29, 2026 21:59
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codecov-commenter commented Jan 29, 2026 •
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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 71.49%. Comparing base (73f6b65) to head (4cd673c).

Additional details and impacted files 
@@                    Coverage Diff                     @@
##           develop-603-tuvx-examples     #759   +/-   ##
==========================================================
  Coverage                      71.49%   71.49%           
==========================================================
  Files                            114      114           
  Lines                           8726     8726           
==========================================================
  Hits                            6239     6239           
  Misses                          2487     2487
Flag Coverage Δ
cpp_fortran 65.87% <ø> (ø)
javascript 92.56% <ø> (ø)
python 73.26% <ø> (ø)

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@K20shores K20shores marked this pull request as ready for review January 30, 2026 00:03
@K20shores K20shores merged commit 4936536 into develop-603-tuvx-examples Jan 30, 2026
45 of 50 checks passed
@K20shores K20shores deleted the copilot/sub-pr-758 branch January 30, 2026 00:03
K20shores added a commit that referenced this pull request Jan 30, 2026
@mattldawson @K20shores
TUV-x Examples and Tutorial (#758)
7cf369f 
* add v5.4 wavelength grid

* add v5.4 height grid

* add profile read function

* add profile data for v5.4

* add remaining profiles

* add v5.4 aerosol radiator

* add draft tuv-x 5.4 example

* add test of tuv 5.4 against standalone tuv-x

* added ts1 config test and example

* add TUV-x yaml configs

* tighten tolerances on tuv-x standalone tests

* allow in-place profile updates

* allow in-place grid element updates

* allow in-place radiator array updates

* start tuv-x jupyter notebook

* add second TUV-x tutorial

* typos

* add tuv-x dockerfile action

* address copilot comments and action failures

* try to address fortran and python action failures

* attempting to pull the fork head instead of main

* Update tutorials/8.tuv-x_standard_configurations.ipynb

Co-authored-by: Kyle Shores <[email protected]>

* merge main into develop-603-tuvx-examples

* packaging configs

* ignoring duplicate named nc files

* Fix memory safety in TUV-x Python bindings for array returns (#759)

* Initial plan

* Fix memory safety issue in TUV-x Python bindings

Allocate output arrays on heap and use py::capsule to manage lifetime.
This prevents dangling pointers when local vectors are destroyed.

Co-authored-by: K20shores <[email protected]>

* Improve exception safety using std::unique_ptr

Use RAII-based memory management with std::unique_ptr instead of raw
pointers to ensure automatic cleanup if exceptions occur during
allocation or array construction.

Co-authored-by: K20shores <[email protected]>

* Fix double-delete issue in ownership transfer

Store data pointers before releasing unique_ptrs to prevent double-delete
if exceptions occur during numpy array construction.

Co-authored-by: K20shores <[email protected]>

* Ensure atomic ownership transfer from capsule to array

Create each numpy array immediately after its capsule to prevent
use-after-free if exceptions occur during array construction.

Co-authored-by: K20shores <[email protected]>

---------

Co-authored-by: copilot-swe-agent[bot] <[email protected]>
Co-authored-by: K20shores <[email protected]>

* [WIP] Update TUV-x examples and tutorial based on feedback (#760)

* Initial plan

* Align Run() docstring array dimensions with C interface and Python bindings

Co-authored-by: K20shores <[email protected]>

* Use consistent dimension labels with underscores in Run() docstring

Co-authored-by: K20shores <[email protected]>

---------

Co-authored-by: copilot-swe-agent[bot] <[email protected]>
Co-authored-by: K20shores <[email protected]>

* responding to pr comments

* adding ffmpeg

---------

Co-authored-by: Kyle Shores <[email protected]>
Co-authored-by: Copilot <[email protected]>
Co-authored-by: K20shores <[email protected]>
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