Merge branch 'master' into image

.readthedocs.yml

@@ -1,5 +1,9 @@
+version: 2
+sphinx:
+  configuration: docs/source/conf.py
+formats: all
 python:
+  version: 3.7
   install:
     - requirements: docs/requirements.txt
-    - method: pip
-      path: .
+    - path: .

CHANGELOG.md

@@ -15,10 +15,26 @@ Types of changes:
 
 ## [Unreleased]
 
+## [0.6.2] - 2020-08-11
+
 ### Changed
 
 - Use setup.cfg for setuptools, and pyproject.toml (and setup.cfg) for config of tools.
 - Version is set in setup.cfg and imported into plonk via importlib_metadata.
+- Changed API documentation.
+- Moved sph module from utils sub-package to analysis.
+
+### Deprecated
+
+- plonk.particle_plot will be removed.
+- plonk.plot will change from image plots to particle plots, and plonk.image and plonk.vector will be added to replace plonk.plot.
+- Default units will change from cgs to SI.
+
+### Fixed
+
+- Fixed bug in Profile with getting number of mixture dust species.
+- Fixed bugs in animation functions (due to making physical units on by default).
+- Fixed issues with colorbar size matching height of plots.
 
 ## [0.6.1] - 2020-08-09
 

CONTRIBUTING.md

@@ -160,7 +160,7 @@ New releases and PyPI and Conda packages
 
 ### Make a release
 
-First, increase the version number in `__init__.py`, and update the `CHANGELOG.md` adding a heading like `[v0.3.1] - yyyy-mm-dd` under "Unreleased" heading. Then commit the change with a message like "Bump version to v0.3.1".
+First, increase the version number in `setup.cfg`, and update the `CHANGELOG.md` adding a heading like `[v0.3.1] - yyyy-mm-dd` under "Unreleased" heading. Then commit the change with a message like "Bump version to v0.3.1".
 
 Then, make a new release on GitHub at <https://github.com/dmentipl/plonk/releases>. The title and tag should both be like "v0.3.1" which corresponds to the Plonk version number. Copy in the changes from the `CHANGELOG.md`. This creates a git tag for the commit, and generates a GitHub release with downloadable source as a tar.gz file.
 

docs/source/api/analysis.rst

@@ -7,9 +7,9 @@ Smoothed particle hydrodynamics analysis tools.
 .. toctree::
 
     analysis/profile
+    analysis/filters
     analysis/particles
     analysis/total
     analysis/sinks
     analysis/discs
-    analysis/filters
     analysis/sph

docs/source/api/miscellaneous.rst

@@ -4,15 +4,30 @@ Miscellaneous
 
 Here are some useful utility functions.
 
-.. autofunction:: plonk.utils.geometry.cartesian_to_polar
-.. autofunction:: plonk.utils.math.average
-.. autofunction:: plonk.utils.math.cross
-.. autofunction:: plonk.utils.math.norm
-.. autofunction:: plonk.utils.utils.is_documented_by
-.. autofunction:: plonk.utils.utils.time_string
-.. autofunction:: plonk.utils.kernels.kernel_cubic
-.. autofunction:: plonk.utils.kernels.kernel_quintic
-.. autofunction:: plonk.utils.kernels.kernel_wendland_c4
-.. autofunction:: plonk.utils.kernels.kernel_gradient_cubic
-.. autofunction:: plonk.utils.kernels.kernel_gradient_quintic
-.. autofunction:: plonk.utils.kernels.kernel_gradient_wendland_c4
+~~~~~~~~
+Geometry
+~~~~~~~~
+
+.. automodule:: plonk.utils.geometry
+    :members:
+
+~~~~
+Math
+~~~~
+
+.. automodule:: plonk.utils.math
+    :members:
+
+~~~~~
+Utils
+~~~~~
+
+.. automodule:: plonk.utils.utils
+    :members:
+
+~~~~~~~
+Kernels
+~~~~~~~
+
+.. automodule:: plonk.utils.kernels
+    :members:

docs/source/api/visualization.rst

@@ -9,4 +9,4 @@ Visualize smoothed particle hydrodynamics data.
     visualization/plots
     visualization/animations
     visualization/interpolation
-    visualization/utility
+    visualization/utils

docs/source/api/visualization/utility.rst → docs/source/api/visualization/utils.rst

@@ -1,6 +1,6 @@
-~~~~~~~
-Utility
-~~~~~~~
+~~~~~
+Utils
+~~~~~
 
 The following are utility functions for visualization.
 

docs/source/conf.py

@@ -13,12 +13,11 @@
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
 import configparser
-import os
 import sys
+from pathlib import Path
 
-import importlib_metadata
-
-sys.path.insert(0, os.path.abspath('../..'))
+path = (Path(__file__) / '../../..').resolve()
+sys.path.insert(0, str(path))
 
 # -- Project information -----------------------------------------------------
 

docs/source/examples/dust-profiles.rst

@@ -0,0 +1,33 @@
+-------------
+Dust profiles
+-------------
+
+Plot the dust density profile per species.
+
+.. code-block:: python
+
+    import plonk
+
+    snap = plonk.load_snap('dstau2mj_00130.h5')
+
+    prof = plonk.load_profile(snap)
+
+    # The line below produces a list of strings like:
+    #   ['dust_density_001',
+    #    'dust_density_002',
+    #    'dust_density_003',
+    #    'dust_density_004',
+    #    'dust_density_005',
+    #    'dust_density_006']
+    y = [f'dust_density_{n+1:03}' for n in range(snap.num_dust_species)]
+
+    ax = prof.plot(x='radius', y=y, units={'x': 'au'})
+    ax.set_yscale('log')
+
+.. figure:: ../_static/dust_profiles.png
+
+.. note::
+
+    The data is from a Phantom snapshot with multiple dust species using the
+    mixture (or "1-fluid") method. I.e., the particles carry a mixture of dust
+    and gas.

plonk/_units.py

@@ -1,7 +1,13 @@
 """Units."""
 
+import warnings
+
 import pint
 
+warnings.warn(
+    'In Plonk v0.7.0 default units will change from cgs to SI.', DeprecationWarning,
+)
+
 units = pint.UnitRegistry(system='cgs')
 Quantity = units.Quantity
 

plonk/analysis/filters.py

@@ -68,7 +68,7 @@ def cylinder(
     Returns
     -------
     SubSnap
-        The SubSnap with particles in the box.
+        The SubSnap with particles in the cylinder.
     """
     dh = height / 2
     R = radial_distance(snap=snap, origin=center, coordinates='cylindrical')
@@ -106,7 +106,7 @@ def annulus(
     Returns
     -------
     SubSnap
-        The SubSnap with particles in the box.
+        The SubSnap with particles in the annulus.
     """
     dh = height / 2
     R = radial_distance(snap=snap, origin=center, coordinates='cylindrical')
@@ -135,7 +135,7 @@ def sphere(snap: SnapLike, radius: Quantity, center: Quantity = CENTER) -> SubSn
     Returns
     -------
     SubSnap
-        The SubSnap with particles in the box.
+        The SubSnap with particles in the sphere.
     """
     R = radial_distance(snap=snap, origin=center, coordinates='spherical')
     mask = R < radius
@@ -165,7 +165,7 @@ def shell(
     Returns
     -------
     SubSnap
-        The SubSnap with particles in the box.
+        The SubSnap with particles in the shell.
     """
     R = radial_distance(snap=snap, origin=center, coordinates='spherical')
     mask = (R > radius_min) & (R < radius_max)

plonk/analysis/profile.py

@@ -171,9 +171,11 @@ def __init__(
             self._x.magnitude, self.bin_edges.magnitude
         )[0]
 
-        num_mixture_dust_species = self.snap.num_dust_species - len(
-            self.snap.num_particles_of_type['dust']
-        )
+        try:
+            num_separate_dust = len(self.snap.num_particles_of_type['dust'])
+        except KeyError:
+            num_separate_dust = 0
+        num_mixture_dust_species = self.snap.num_dust_species - num_separate_dust
         _generate_profiles(num_mixture_dust_species)
 
     def _setup_particle_mask(self, ignore_accreted: bool) -> ndarray: