# Third-Party Notices

This notice describes third-party material relevant to FlashDEG source and
binary releases. FlashDEG-owned code is distributed under the MIT License; see
the top-level `LICENSE`.

Release artifacts should include:

- `LICENSE`
- `THIRD_PARTY_NOTICES.md`
- `LICENSES/`

## Bundled Third-Party Code

### SciPy L-BFGS-B

FlashDEG vendors a copy of SciPy's C translation of L-BFGS-B under
`third_party/scipy_lbfgsb/`.

- License: BSD-3-Clause
- License file: `LICENSES/scipy-lbfgsb/LICENSE.txt`
- Source metadata: `LICENSES/scipy-lbfgsb/SOURCE.txt`

SciPy's C translation is derived from the original Fortran L-BFGS-B 3.0
implementation by Ciyou Zhu, Richard Byrd, Jorge Nocedal, and Jose Luis
Morales. The local FlashDEG header removes SciPy's Python/Numpy wrapper and
exports the low-level `setulb` routine for direct C/C++ use.

`third_party/scipy_lbfgsb/lapack_shims.cpp` is FlashDEG-owned glue code, not
SciPy code. It is used only when the selected BLAS/LAPACK backend does not
provide the LAPACK Fortran ABI symbols required by the vendored L-BFGS-B code.

### GUI gene-symbol maps (Ensembl: human, Drosophila)

The desktop GUI ships gene-ID → gene-symbol lookup tables as external files in a
`gene_maps/` folder next to the application (not embedded in the executable),
used only to offer a gene-ID ↔ symbol display toggle in the results view:

- `gui_app/gene_maps/gene_symbols_human.tsv.gz` — human (Ensembl ENSG ↔ symbol).
- `gui_app/gene_maps/gene_symbols_fly.tsv.gz` — *Drosophila melanogaster*
  (FlyBase FBgn ↔ symbol).

Both are generated from Ensembl BioMart by `gui_app/scripts/fetch-gene-symbols.ps1`
(datasets `hsapiens_gene_ensembl` / `dmelanogaster_gene_ensembl`, attributes
`ensembl_gene_id` + `external_gene_name`).

- Source: Ensembl (https://www.ensembl.org), GRCh38 (human) and BDGP6 (fly).
- Ensembl genome-annotation data is freely available for use; gene display
  names are largely HGNC-derived (human) / FlyBase-derived (Drosophila). See
  Ensembl's terms: https://www.ensembl.org/info/about/legal/disclaimer.html
- The files are data only (no code) and are used for display in the GUI; they
  do not affect any analysis result.

## External Build And Runtime Dependencies

FlashDEG release builds normally use the following external dependencies. These
projects are not vendored in this repository unless a binary artifact
explicitly bundles their shared libraries.

### Eigen

FlashDEG uses Eigen for dense linear algebra when `FLASHDEG_USE_EIGEN=ON`.

- License: MPL-2.0, with some files under more permissive licenses
- License file: `LICENSES/eigen/LICENSE.txt`

### Boost.Math

FlashDEG uses Boost.Math for special functions and statistical distributions
when `FLASHDEG_USE_BOOST_MATH=ON`.

- License: Boost Software License 1.0
- License file: `LICENSES/boost/LICENSE.txt`

### BLAS / LAPACK / OpenBLAS

FlashDEG can link to OpenBLAS or another BLAS/LAPACK implementation when
`FLASHDEG_USE_BLAS=ON`.

- OpenBLAS license: BSD-3-Clause
- OpenBLAS license file: `LICENSES/openblas/LICENSE.txt`
- Reference LAPACK license file: `LICENSES/blas-lapack/LICENSE.txt`

If a binary release bundles an OpenBLAS, BLAS, LAPACK, Accelerate, MKL, or other
numerical shared library, include the exact license files supplied by that
binary dependency package.

## Source-Repository Test Fixtures

The public source repository can contain small test fixtures that are not part
of the user-facing FlashDEG binary.

### PyDESeq2 Port / Reimplementation

FlashDEG's early statistical core and `pydeseq2_*` implementation files were
written as a C++ port/reimplementation of PyDESeq2's DESeq2-like workflow.
PyDESeq2 is MIT-licensed; see `LICENSES/pydeseq2/LICENSE.txt`.

PyDESeq2 itself is not bundled in FlashDEG release binaries.

### PyDESeq2 Fixture Subset

`tests/fixtures/pyde_reference/` contains a small copied subset of PyDESeq2 CSV
test fixtures.

- Upstream project: PyDESeq2
- License: MIT
- License files:
  - `LICENSES/pydeseq2/LICENSE.txt`
- Source metadata: `LICENSES/pydeseq2/SOURCE.txt`