clean code

.gitattributes

@@ -5,4 +5,4 @@ tests/* linguist-documentation
 scheme/examples/* linguist-documentation
 python/numpy.i linguist-vendored
 src/support/mt19937ar.c linguist-vendored
-src/support/meep_mt.h linguist-language=C++
+src/support/meep_mt.h linguist-language=C++

.github/dependabot.yml

@@ -0,0 +1,11 @@
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "daily"
+
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: monthly

.github/workflows/build-ci.yml

@@ -1,10 +1,10 @@
-name: CI
+name: run tests
 
 on:
-  push:
-    branches: [ master ]
   pull_request:
-    branches: [ master ]
+  push:
+  schedule:
+    - cron: 0 2 * * * # run at 2 AM UTC
   workflow_dispatch:
 
 jobs:

.github/workflows/pre-commit.yml

@@ -0,0 +1,16 @@
+---
+name: pre-commit
+
+on:
+  pull_request:
+  push:
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+      - uses: pre-commit/[email protected]

.gitignore

@@ -15,6 +15,11 @@
 _build
 .vscode
 .idea
+python/examples/.ipynb_checkpoints/
+h5utils/
+hdf5/
+extra/
+configure~
 
 # autotools stuff
 Makefile

.pre-commit-config.yaml

@@ -0,0 +1,112 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "08b4be84be2d74173246b7c9b6c22212a6c15a2d"
+    hooks:
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+
+  # - repo: https://github.com/hakancelik96/unimport
+  #   rev: df8eb1a4c91acb84da197828af8157708968b596
+  #   hooks:
+  #     - id: unimport
+  #       args: [--remove, --include-star-import]
+  # - repo: https://github.com/pycqa/isort
+  #   rev: "12cc5fbd67eebf92eb2213b03c07b138ae1fb448"
+  #   hooks:
+  #     - id: isort
+  #       files: "python/.*"
+  #       args: ["--profile", "black", "--filter-files"]
+
+  - repo: https://github.com/psf/black
+    rev: "4f1772e2aed8356e57b923eacf45f813ec3324a0"
+    hooks:
+      - id: black
+
+  # - repo: https://gitlab.com/pycqa/flake8
+  #   rev: "21d3c70d676007470908d39b73f0521d39b3b997"
+  #   hooks:
+  #     - id: flake8
+
+  # - repo: https://github.com/kynan/nbstripout
+  #   rev: 8cafdcc393232045208137698dbeb42d6e0dd9e8
+  #   hooks:
+  #     - id: nbstripout
+  #       files: ".ipynb"
+
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v2.37.3
+    hooks:
+      - id: pyupgrade
+        args: [--py37-plus, --keep-runtime-typing]
+
+  # - repo: https://github.com/codespell-project/codespell
+  #   rev: 4d782511b3999c243feb3858cd7062270eb13291
+  #   hooks:
+  #     - id: codespell
+  #       args: ["-L TE,TE/TM,te,ba,FPR,fpr_spacing,ro"]
+
+  # - repo: https://github.com/shellcheck-py/shellcheck-py
+  #   rev: f87a493c6596a5338d69395905a4e13ed65584f6
+  #   hooks:
+  #     - id: shellcheck
+
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: dc89c436469616a7c48293ec60c8e21e9d95be08 # Use the ref you want to point at
+    hooks:
+      - id: python-use-type-annotations
+
+  - repo: https://github.com/PyCQA/bandit
+    rev: 97501817e621db9975dfa6a2a1d36370942d1812
+    hooks:
+      - id: bandit
+        args: [--exit-zero]
+        # ignore all tests, not just tests data
+        exclude: ^tests/
+  - repo: https://github.com/pre-commit/mirrors-clang-format
+    rev: 'v14.0.6'  # Use the sha / tag you want to point at
+    hooks:
+    -   id: clang-format
+  # - repo: https://github.com/pre-commit/mirrors-mypy
+  #   rev: "214c33306afe17f1cc7d2d55e4da705b6ebe0627"
+  #   hooks:
+  #     - id: mypy
+  #       exclude: ^(docs/|example-plugin/|tests/fixtures)
+  #       additional_dependencies:
+  #         - "pydantic"
+  # - repo: https://github.com/terrencepreilly/darglint
+  #   rev: master
+  #   hooks:
+  #     - id: darglint
+
+  # - repo: https://github.com/pycqa/pydocstyle
+  #   rev: ""
+  #   hooks:
+  #     - id: pydocstyle
+  # - repo: https://github.com/asottile/reorder_python_imports
+  #   rev: 2b2f0c74acdb3de316e23ceb7dd0d7945c354050
+  #   hooks:
+  #     - id: reorder-python-imports
+  # - repo: https://github.com/PyCQA/pylint
+  #   rev: v2.14.1
+  #   hooks:
+  #     - id: pylint
+  #       args: [--exit-zero]
+  # - repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
+  #   rev: 6565d773ca281682d7062d4c0be74538cc474cc9
+  #   hooks:
+  #     - id: pretty-format-java
+  #       args: [--autofix]
+  #     - id: pretty-format-kotlin
+  #       args: [--autofix]
+  #     - id: pretty-format-yaml
+  #       args: [--autofix, --indent, "2"]
+  # - repo: https://github.com/adrienverge/yamllint.git
+  #   rev: v1.21.0 # or higher tag
+  #   hooks:
+  #       - id: yamllint
+  #         args: [--format, parsable, --strict]
+  # - repo: https://github.com/jumanjihouse/pre-commit-hook-yamlfmt
+  #   rev: 0.1.0 # or specific tag
+  #   hooks:
+  #       - id: yamlfmt

.sourcery.yaml

@@ -0,0 +1,2 @@
+refactor:
+  python_version: '3.7'

AUTHORS

@@ -17,4 +17,4 @@ Ian Williamson <[email protected]>
 Andreas Hoenselaar <[email protected]>
 Ben Bartlett <[email protected]>
 Krishna Gadepalli <[email protected]>
-Mo Chen <[email protected]>
+Mo Chen <[email protected]>

codemeta.json

@@ -2,7 +2,8 @@
   "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
   "@type": "SoftwareSourceCode",
   "name": "Meep",
-  "description": "Meep is a free and open-source software package for electromagnetics simulation via the finite-difference time-domain (FDTD) method spanning a broad range of applications.",
+  "description":
+      "Meep is a free and open-source software package for electromagnetics simulation via the finite-difference time-domain (FDTD) method spanning a broad range of applications.",
   "url": "https://github.com/NanoComp/meep",
   "codeRepository": "https://github.com/NanoComp/meep",
   "issueTracker": "https://github.com/NanoComp/issues",
@@ -87,8 +88,12 @@
   ],
   "developmentStatus": "active",
   "downloadUrl": "https://github.com/NanoComp/releases",
-  "version":"1.11",
-  "dateCreated":"2003-02-12",
-  "datePublished":"2006-04-01",
-  "programmingLanguage": ["C++", "Python", "Scheme"]
+  "version": "1.11",
+  "dateCreated": "2003-02-12",
+  "datePublished": "2006-04-01",
+  "programmingLanguage": [
+    "C++",
+    "Python",
+    "Scheme"
+  ]
 }

doc/_api_snippets/class_template.md

@@ -12,4 +12,3 @@ class {class_name}({base_classes}):
 {docstring}
 
 </div>
-

doc/_api_snippets/function_template.md

@@ -9,4 +9,4 @@ def {function_name}{parameters}:{other_signatures}
 
 {docstring}
 
-</div>
+</div>

doc/_api_snippets/method_template.md

@@ -13,4 +13,4 @@ def {method_name}{parameters}:{other_signatures}
 
 </div>
 
-</div>
+</div>

doc/docs/2d_Cell_Special_kz.md

@@ -100,4 +100,4 @@ The Meep results are identical to within six decimal digits and agree well with
 
 ```
 refl:, 0.3272338236967464 (real/imag), 0.3272338244372344 (complex), 0.3272330216564413 (3d), 0.3293821216165117 (analytic)
-```
+```

doc/docs/C++_Tutorial.md

@@ -86,7 +86,7 @@ const double half_cavity_width = d2;
 const int N = 5;
 ```
 
-Meep supports perfectly matching layers (PML) as absorbing boundary conditions. The PML begins at the edge of the computational volume and works inwards. Hence, we specify the size of the cell as follows: 
+Meep supports perfectly matching layers (PML) as absorbing boundary conditions. The PML begins at the edge of the computational volume and works inwards. Hence, we specify the size of the cell as follows:
 
 ```c++
 const double pml_thickness = 1.0;

doc/docs/Developer_Codes/Makefile.manual

@@ -15,5 +15,5 @@ LIBS = -lmeepgeom -lmeep -lctlgeom
 WriteChunkInfo:  	WriteChunkInfo.o
 			$(CXX) $(LDFLAGS) -o $@ $^ $(LIBS)
 
-clean:	
+clean:
 		rm *.o *.a

doc/docs/Developer_Codes/WriteChunkInfo.cpp

@@ -123,8 +123,9 @@ structure create_structure(double resolution, int symmetries) {
   geometry_lattice.size.z = 0.0;
   grid_volume gv = voltwo(sx, sy, resolution);
   gv.center_origin();
-  symmetry S = (symmetries == 1 ? mirror(Y, gv)
-                                : symmetries == 2 ? mirror(X, gv) + mirror(Y, gv) : symmetry());
+  symmetry S = (symmetries == 1   ? mirror(Y, gv)
+                : symmetries == 2 ? mirror(X, gv) + mirror(Y, gv)
+                                  : symmetry());
   structure the_structure(gv, dummy_eps, pml(dpml), S);
 
   vector3 e1 = v3(1.0, 0.0, 0.0);

doc/docs/Download.md

@@ -28,4 +28,4 @@ You will also be able to install the [parallel version of Meep](https://packages
 sudo apt-get install python3-meep-openmpi
 ```
 
-These upcoming Meep packages for Ubuntu 21.04 are derived from the Debian 11 ("Bullseye") packages ([serial](https://packages.debian.org/bullseye/python3-meep) and [parallel](https://packages.debian.org/bullseye/python3-meep-openmpi)). Debian 11 is currently the testing distribution.
+These upcoming Meep packages for Ubuntu 21.04 are derived from the Debian 11 ("Bullseye") packages ([serial](https://packages.debian.org/bullseye/python3-meep) and [parallel](https://packages.debian.org/bullseye/python3-meep-openmpi)). Debian 11 is currently the testing distribution.

doc/docs/FAQ.md

@@ -320,7 +320,7 @@ Only the [harmonic mean](https://en.wikipedia.org/wiki/Harmonic_mean) of eigenva
 
 ### How do I model graphene or other 2d materials with single-atom thickness?
 
-Typically, graphene and similar "2d" materials are mathematically represented as a [delta function](https://en.wikipedia.org/wiki/Dirac_delta_function) conductivity in Maxwell's equations because their thickness is negligible compared to the wavelength, where the conductivity is furthermore usually anisotropic (producing surface-parallel currents in response to the surface-parallel components of the electric field). In a discretized computer model like Meep, this is approximated by an anisotropic volume conductivity (or other polarizable dispersive material) whose thickness is proportional to (`1/resolution`) *and* whose amplitude is proportional `resolution`. For example, this could be represented by a one-pixel-thick [conductor](Materials.md#conductivity-and-complex) can be represented by e.g. a [`Block`](Python_User_Interface.md#block) with `size=meep.Vector3(x,y,1/resolution)` in a 3d cell, with the value of the conductivity explicitly multiplied by `resolution`. 
+Typically, graphene and similar "2d" materials are mathematically represented as a [delta function](https://en.wikipedia.org/wiki/Dirac_delta_function) conductivity in Maxwell's equations because their thickness is negligible compared to the wavelength, where the conductivity is furthermore usually anisotropic (producing surface-parallel currents in response to the surface-parallel components of the electric field). In a discretized computer model like Meep, this is approximated by an anisotropic volume conductivity (or other polarizable dispersive material) whose thickness is proportional to (`1/resolution`) *and* whose amplitude is proportional `resolution`. For example, this could be represented by a one-pixel-thick [conductor](Materials.md#conductivity-and-complex) can be represented by e.g. a [`Block`](Python_User_Interface.md#block) with `size=meep.Vector3(x,y,1/resolution)` in a 3d cell, with the value of the conductivity explicitly multiplied by `resolution`.
 ### How do I model a continuously varying permittivity?
 
 You can use a [material function](Python_User_Interface.md#medium) to model any arbitrary, position-dependent permittivity/permeability function $\varepsilon(\vec{r})$/$\mu(\vec{r})$ including anisotropic, [dispersive](Materials.md#material-dispersion), and [nonlinear](Materials.md#nonlinearity) media. For an example involving a non-dispersive, anisotropic material, see [Tutorial/Mode Decomposition/Diffraction Spectrum of Liquid-Crystal Polarization Gratings](Python_Tutorials/Mode_Decomposition.md#diffraction-spectrum-of-liquid-crystal-polarization-gratings). The material function construct can also be used to specify arbitrary *shapes* (e.g., curves such as parabolas, sinusoids, etc.) within: (1) the interior boundary of a [`GeometricObject`](Python_User_Interface.md#geometricobject) (e.g., `Block`, `Sphere`, `Cylinder`, etc.), (2) the entire cell via the [`material_function`](Python_User_Interface.md#material-function) parameter of the `Simulation` constructor, or (3) a combination of the two.

doc/docs/Installation.md

@@ -123,7 +123,7 @@ There are upcoming packages for [Meep version 1.17.1](https://github.com/NanoCom
 
 In the meantime, the following dependencies are already available as precompiled packages: BLAS and LAPACK possibly as part of a package for [Atlas BLAS](https://en.wikipedia.org/wiki/Automatically_Tuned_Linear_Algebra_Software), Guile, MPI, and HDF5. One thing to be careful of is that many distributions split packages into two parts: one main package for the libraries and programs, and a **devel** package for [header files](https://en.wikipedia.org/wiki/Header_file) and other things needed to compile software using those libraries. You will need to install **both**. So, for example, you will probably need both a `guile` package (probably installed by default) and a `guile-dev` or `guile-devel` package (probably *not* installed by default), and similarly for HDF5 etcetera. You will probably also want to install a `libpng-dev` or `libpng-devel` package in order to compile the `h5topng` utility in [h5utils](https://github.com/NanoComp/h5utils/blob/master/README.md).
 
-Installation from source on macOS 
+Installation from source on macOS
 ---------------------------------
 Most macOS users will probably want to install via the Conda packages as described above.  It is also possible to compile Meep from source, however.
 

doc/docs/Materials.md

@@ -188,7 +188,7 @@ Similar relationships can be found for systems with more than two atomic levels
 ### Natural Units for Saturable Media
 
 A conversion chart for different choices of parameter nomenclature for the saturable medium.
-	
+
 There is no standard convention in the literature on lasers and saturable gain media for defining the various constants in the equations above. The following are the relationships among these constants for the three different groups of work discussed in this section:
 
 $$ \omega_n \; (\textrm{Meep}) = \omega_{ba} \; (\textrm{Boyd}) = \omega_a \; (\textrm{SALT}) $$