Reorganize code, removing _orig submodule (#76)

* reorganize for easier development

* fix docstring typo

Author: mfschubert

CHANGELOG.md

@@ -1,6 +1,7 @@
 # Change log
 
 ## Unreleased
+- Restructure codebase to integrate code originally in the `_orig` submodule within the main `src/fmmax` modules, separating the code available under the two licenses to the top (AGPL) and bottom (MIT) of each file.
 
 ## 1.4.2 (July 10, 2025)
 - Avoid use of `jax.pure_callback` in the eigendecomposition. This requires jax newer than 0.4.36.

README.md

@@ -71,7 +71,7 @@ If you use FMMAX, please consider citing [our paper](https://opg.optica.org/oe/f
 ```
 
 ## License
-Some portions of FMMAX were created while the author was employed by Meta or by Meta collaborators, with copyright owned by Meta and available under the [MIT license](https://github.com/facebookresearch/fmmax/blob/main/LICENSE2). Other portions were created or substantially changed subsequently (copyright not owned by Meta) and are available under the [AGPL](https://github.com/facebookresearch/fmmax/blob/main/LICENSE). These are split on a file-by-file basis, with the file header indicating which license is applicable.
+Some portions of FMMAX were created while the author was employed by Meta or by Meta collaborators, with copyright owned by Meta and available under the [MIT license](https://github.com/facebookresearch/fmmax/blob/main/LICENSE2). Other portions were created or substantially changed subsequently (copyright not owned by Meta) and are available under the [AGPL](https://github.com/facebookresearch/fmmax/blob/main/LICENSE). Throughout the codebase, a given file may contain code that is owned by Meta, and code which is not. In such a file, the code owned by Meta will be at the end separated by a comment.
 
 ## References
 - [2012 Liu] V. Liu and S. Fan, [S4: A free electromagnetic solver for layered structures structures](https://www.sciencedirect.com/science/article/pii/S0010465512001658), _Comput. Phys. Commun._ **183**, 2233-2244 (2012).

src/fmmax/__init__.py

@@ -1,4 +1,22 @@
-# Copyright (c) 2025 Martin F. Schubert
+# FMMAX
+# Copyright (C) 2025 Martin F. Schubert
+
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Affero General Public License for more details.
+
+# You should have received a copy of the GNU Affero General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+"""FMMAX: Fourier modal method with jax.
+
+Copyright (c) Martin F. Schubert
+"""
 
 __version__ = "v1.4.2"