Prepare for 1.25 release (#2311)

* prepare for 1.25 release * add bug fix to NEWS.md and refresh documentation from docstrings * link fixes Co-authored-by: Steven G. Johnson <[email protected]>
NanoComp · Nov 17, 2022 · 78b6411 · 78b6411
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diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,21 @@
 # Meep Release Notes
 
+## Meep 1.25.0
+
+11/17/2022
+
+* Support for connectivity constraints in adjoint solver ([#2207]).
+
+* Support for animation in topology optimization ([#2186]).
+
+* Support for `load_minus_flux` in adjoint solver ([#2271]).
+
+* Support colorbars in `plot2D` ([#2289]).
+
+* Support for `plot3D` ([#2305]).
+
+* Various improvements and bug fixes ([#2176], [#2179], [#2190], [#2194], [#2202], [#2203], [#2208], [#2251], [#2253], [#2264], [#2290]), and additional unit tests and documentation.
+
 ## Meep 1.24.0
 
 7/21/2022
@@ -1053,6 +1069,7 @@ Meep 1.0.1
 [#1830]: https://github.com/NanoComp/meep/issues/1830
 [#1839]: https://github.com/NanoComp/meep/issues/1839
 [#1849]: https://github.com/NanoComp/meep/issues/1849
+[#1855]: https://github.com/NanoComp/meep/issues/1855
 [#1860]: https://github.com/NanoComp/meep/issues/1860
 [#1871]: https://github.com/NanoComp/meep/issues/1871
 [#1872]: https://github.com/NanoComp/meep/issues/1872
@@ -1061,8 +1078,38 @@ Meep 1.0.1
 [#1895]: https://github.com/NanoComp/meep/issues/1895
 [#1919]: https://github.com/NanoComp/meep/issues/1919
 [#1955]: https://github.com/NanoComp/meep/issues/1955
+[#1959]: https://github.com/NanoComp/meep/issues/1959
 [#1968]: https://github.com/NanoComp/meep/issues/1968
 [#2005]: https://github.com/NanoComp/meep/issues/2005
 [#2016]: https://github.com/NanoComp/meep/issues/2016
 [#2021]: https://github.com/NanoComp/meep/issues/2021
 [#2027]: https://github.com/NanoComp/meep/issues/2027
+[#2032]: https://github.com/NanoComp/meep/issues/2032
+[#2044]: https://github.com/NanoComp/meep/issues/2044
+[#2049]: https://github.com/NanoComp/meep/issues/2049
+[#2053]: https://github.com/NanoComp/meep/issues/2053
+[#2066]: https://github.com/NanoComp/meep/issues/2066
+[#2073]: https://github.com/NanoComp/meep/issues/2073
+[#2076]: https://github.com/NanoComp/meep/issues/2076
+[#2077]: https://github.com/NanoComp/meep/issues/2077
+[#2079]: https://github.com/NanoComp/meep/issues/2079
+[#2082]: https://github.com/NanoComp/meep/issues/2082
+[#2091]: https://github.com/NanoComp/meep/issues/2091
+[#2095]: https://github.com/NanoComp/meep/issues/2095
+[#2114]: https://github.com/NanoComp/meep/issues/2114
+[#2176]: https://github.com/NanoComp/meep/issues/2176
+[#2179]: https://github.com/NanoComp/meep/issues/2179
+[#2186]: https://github.com/NanoComp/meep/issues/2186
+[#2190]: https://github.com/NanoComp/meep/issues/2190
+[#2194]: https://github.com/NanoComp/meep/issues/2194
+[#2202]: https://github.com/NanoComp/meep/issues/2202
+[#2203]: https://github.com/NanoComp/meep/issues/2203
+[#2207]: https://github.com/NanoComp/meep/issues/2207
+[#2208]: https://github.com/NanoComp/meep/issues/2208
+[#2251]: https://github.com/NanoComp/meep/issues/2251
+[#2253]: https://github.com/NanoComp/meep/issues/2253
+[#2264]: https://github.com/NanoComp/meep/issues/2264
+[#2271]: https://github.com/NanoComp/meep/issues/2271
+[#2289]: https://github.com/NanoComp/meep/issues/2289
+[#2290]: https://github.com/NanoComp/meep/issues/2290
+[#2305]: https://github.com/NanoComp/meep/issues/2305
diff --git a/configure.ac b/configure.ac
@@ -1,13 +1,13 @@
 # Process this file with autoconf to produce a configure script.
 
-AC_INIT([meep],[m4_esyscmd(./version.sh 1.25.0-beta)])
+AC_INIT([meep],[m4_esyscmd(./version.sh 1.25.0)])
 AC_CONFIG_SRCDIR(src/step.cpp)
 
 # Shared-library version number; indicates api compatibility, and is
 # not the same as the "public" version number.  (Don't worry about this
 # except for public releases.) Note that any change to a C++ class
 # definition (in the .hpp file) generally breaks binary compatibility.
-SHARED_VERSION_INFO="29:0:0" # CURRENT:REVISION:AGE
+SHARED_VERSION_INFO="30:0:0" # CURRENT:REVISION:AGE
 
 AM_INIT_AUTOMAKE([foreign color-tests parallel-tests silent-rules 1.11])
 AM_SILENT_RULES(yes)

diff --git a/doc/docs/Python_User_Interface.md b/doc/docs/Python_User_Interface.md
@@ -2745,20 +2745,22 @@ This module provides basic visualization functionality for the simulation domain
 
 ```python
 def plot2D(self,
-           ax=None,
-           output_plane=None,
-           fields=None,
-           labels=False,
-           eps_parameters=None,
-           boundary_parameters=None,
-           source_parameters=None,
-           monitor_parameters=None,
-           field_parameters=None,
-           frequency=None,
-           plot_eps_flag=True,
-           plot_sources_flag=True,
-           plot_monitors_flag=True,
-           plot_boundaries_flag=True,
+           ax: Optional[matplotlib.axes._axes.Axes] = None,
+           output_plane: Optional[meep.simulation.Volume] = None,
+           fields: Optional = None,
+           labels: Optional[bool] = False,
+           eps_parameters: Optional[dict] = None,
+           boundary_parameters: Optional[dict] = None,
+           source_parameters: Optional[dict] = None,
+           monitor_parameters: Optional[dict] = None,
+           field_parameters: Optional[dict] = None,
+           colorbar_parameters: Optional[dict] = None,
+           frequency: Optional[float] = None,
+           plot_eps_flag: bool = True,
+           plot_sources_flag: bool = True,
+           plot_monitors_flag: bool = True,
+           plot_boundaries_flag: bool = True,
+           nb: bool = False,
            **kwargs):
 ```
 
@@ -2814,6 +2816,7 @@ to be called on all processes, but only generates a plot on the master process.
       plot. Defaults to the `frequency` parameter of the [Source](#source) object.
     - `resolution=None`: the resolution of the $\varepsilon$ grid. Defaults to the
       `resolution` of the `Simulation` object.
+    - `colorbar=False`: whether to add a colorbar to the plot's parent Figure based on epsilon values.
 * `boundary_parameters`: a `dict` of optional plotting parameters that override
   the default parameters for the boundary layers.
     - `alpha=1.0`: transparency of boundary layers
@@ -2850,6 +2853,21 @@ to be called on all processes, but only generates a plot on the master process.
     - `alpha=0.6`: transparency of fields
     - `post_process=np.real`: post processing function to apply to fields (must be
       a function object)
+    - `colorbar=False`: whether to add a colorbar to the plot's parent Figure based on field values.
+* `colorbar_parameters`:  a `dict` of optional plotting parameters that override the default parameters for
+  the colorbar.
+    - `label=None`: an optional label for the colorbar, defaults to '$\epsilon_r$' for epsilon and
+    'field values' for fields.
+    - `orientation='vertical'`: the orientation of the colorbar gradient
+    - `extend=None`: make pointed end(s) for out-of-range values. Allowed values are:
+    ['neither', 'both', 'min', 'max']
+    - `format=None`: formatter for tick labels. Can be an fstring (i.e. "{x:.2e}") or a
+    [matplotlib.ticker.ScalarFormatter](https://matplotlib.org/stable/api/ticker_api.html#matplotlib.ticker.ScalarFormatter).
+    - `position='right'`: position of the colorbar with respect to the Axes
+    - `size='5%'`: size of the colorbar in the dimension perpendicular to its `orientation`
+    - `pad='2%'`: fraction of original axes between colorbar and image axes
+* `nb`: set this to True if plotting in a Jupyter notebook to use ipympl for plotting. Note: this requires
+ipympl to be installed.
 
 </div>
 
@@ -6241,7 +6259,7 @@ def __init__(self,
              side: int = -1,
              R_asymptotic: float = 1e-15,
              mean_stretch: float = 1.0,
-             pml_profile: Callable[[float], float] = <function <lambda> at 0x7f0880782ca0>):
+             pml_profile: Callable[[float], float] = <function <lambda> at 0x7f41474eeb00>):
 ```
 
 <div class="method_docstring" markdown="1">
@@ -7147,14 +7165,12 @@ class Animate2D(object):
 <div class="class_docstring" markdown="1">
 
 A class used to record the fields during timestepping (i.e., a [`run`](#run-functions)
-function). The object is initialized prior to timestepping by specifying the
-simulation object and the field component. The object can then be passed to any
-[step-function modifier](#step-function-modifiers). For example, one can record the
-$E_z$ fields at every one time unit using:
+function). The object is initialized prior to timestepping by specifying the field component.
+The object can then be passed to any [step-function modifier](#step-function-modifiers).
+For example, one can record the $E_z$ fields at every one time unit using:
 
 ```py
-animate = mp.Animate2D(sim,
-                       fields=mp.Ez,
+animate = mp.Animate2D(fields=mp.Ez,
                        realtime=True,
                        field_parameters={'alpha':0.8, 'cmap':'RdBu', 'interpolation':'none'},
                        boundary_parameters={'hatch':'o', 'linewidth':1.5, 'facecolor':'y', 'edgecolor':'b', 'alpha':0.3})
@@ -7183,7 +7199,9 @@ track different volume locations (using `mp.in_volume`) or field components.
 <div class="class_members" markdown="1">
 
 ```python
-def __call__(self, sim, todo):
+def __call__(self,
+             sim: meep.simulation.Simulation,
+             todo: str):
 ```
 
 <div class="method_docstring" markdown="1">
@@ -7201,12 +7219,12 @@ Call self as a function.
 
 ```python
 def __init__(self,
-             fields,
-             sim=None,
-             f=None,
-             realtime=False,
-             normalize=False,
-             plot_modifiers=None,
+             sim: Optional[meep.simulation.Simulation] = None,
+             fields: Optional = None,
+             f: Optional[matplotlib.figure.Figure] = None,
+             realtime: bool = False,
+             normalize: bool = False,
+             plot_modifiers: Optional[list] = None,
              update_epsilon: bool = False,
              nb: bool = False,
              **customization_args):
@@ -7216,9 +7234,9 @@ def __init__(self,
 
 Construct an `Animate2D` object.
 
-+ **`sim`** — Simulation object.
++ **`sim=None`** — Optional Simulation object (this has no effect, and is included for backwards compatibility).
 
-+ **`fields`** — Field component to record at each time instant.
++ **`fields=None`** — Optional Field component to record at each time instant.
 
 + **`f=None`** — Optional `matplotlib` figure object that the routine will update
   on each call. If not supplied, then a new one will be created upon
@@ -7261,7 +7279,7 @@ Construct an `Animate2D` object.
 <div class="class_members" markdown="1">
 
 ```python
-def to_gif(self, fps, filename):
+def to_gif(self, fps: int, filename: str) -> None:
 ```
 
 <div class="method_docstring" markdown="1">
@@ -7282,7 +7300,8 @@ format only supports 256 colors from a _predefined_ color palette. Requires
 <div class="class_members" markdown="1">
 
 ```python
-def to_jshtml(self, fps):
+def to_jshtml(self,
+              fps: int):
 ```
 
 <div class="method_docstring" markdown="1">
@@ -7301,7 +7320,7 @@ playback. User must specify a frame rate `fps` in frames per second.
 <div class="class_members" markdown="1">
 
 ```python
-def to_mp4(self, fps, filename):
+def to_mp4(self, fps: int, filename: str) -> None:
 ```
 
 <div class="method_docstring" markdown="1">