# Integration tests
These tests use [pytest](https://docs.pytest.org/en/stable/) to ensure two
objectives (during CI):
1. Test the python interface at [`src/pyo.rs`](https://github.com/carrascomj/rust_sbml/blob/trunk/src/pyo.rs).
2. Ensure the parser is consistent with [libSBML](https://github.com/sbmlteam/libsbml).
The benchmarks are ignored during CI.
## Benchmarks
> The benchmarks are obviously unfair since **rust_sbml** does not cover the entire
[SBML level 3 core specification](https://www.degruyter.com/view/journals/jib/16/2/article-20190021.xml).
Moreover, it does not check for consistency with the extra [plugin FBC](sbml.org/Documents/Specifications/SBML_Level_3/Packages/fbc), and
ignores namespaces (the rest of the packages are not implemented).
Download bigg model (_E. coli_ core is on the repository already):
```shell
curl -L -O http://bigg.ucsd.edu/static/models/RECON1.xml
mv RECON1.xml tests_integration
```
Install required dev dependencies (a compatible version of python is required):
```shell
pip install pytest pytest-benchmark rust_sbml cobra
```
Run the tests from the root of this repository:
```shell
pytest tests_integration
```
Results:
```
----------------------------------------------------------------------------------------------- benchmark: 4 tests -----------------------------------------------------------------------------------------------
Name (time in ms) Min Max Mean StdDev Median IQR Outliers OPS Rounds Iterations
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
test_benchmark_rust_sbml_small 36.8397 (1.0) 86.1893 (1.0) 39.4792 (1.0) 9.3725 (1.0) 37.5944 (1.0) 0.8622 (1.0) 1;2 25.3298 (1.0) 27 1
test_benchmark_libsbml_small 169.6363 (4.60) 230.0817 (2.67) 180.0127 (4.56) 24.5311 (2.62) 170.0557 (4.52) 0.8629 (1.00) 1;1 5.5552 (0.22) 6 1
test_benchmark_rust_sbml_big 1,570.5220 (42.63) 1,627.4761 (18.88) 1,592.6992 (40.34) 20.9688 (2.24) 1,587.9476 (42.24) 16.3945 (19.01) 2;1 0.6279 (0.02) 5 1
test_benchmark_libsbml_big 5,961.8366 (161.83) 6,595.0936 (76.52) 6,258.9519 (158.54) 236.3963 (25.22) 6,218.8225 (165.42) 310.7440 (360.39) 2;0 0.1598 (0.01) 5 1
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
```