Merge branch 'main' into module/power_spectrum

Author: rrjbca

.github/workflows/compatibility.yaml

@@ -9,8 +9,8 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python: ['3.10']
-        toxenv: [py310-test, py310-test-dev]
+        python: ['3.11']
+        toxenv: [py311-test, py311-test-dev]
         release: [main, latest]
     steps:
     - name: Checkout Repository

.github/workflows/tests.yaml

@@ -19,8 +19,8 @@ jobs:
 
           - name: latest supported versions
             os: ubuntu-latest
-            python: '3.10'
-            toxenv: py310-test-all-latest-cov
+            python: '3.11'
+            toxenv: py311-test-all-latest-cov
             toxposargs: --cov-report=xml:${GITHUB_WORKSPACE}/coverage.xml
 
           - name: oldest supported versions
@@ -30,13 +30,13 @@ jobs:
 
           - name: macOS latest supported
             os: macos-latest
-            python: '3.10'
-            toxenv: py310-test-latest
+            python: '3.11'
+            toxenv: py311-test-latest
 
           - name: Windows latest supported
             os: windows-latest
-            python: '3.10'
-            toxenv: py310-test-latest
+            python: '3.11'
+            toxenv: py311-test-latest
 
     steps:
     - name: Checkout Repository

.zenodo.json

@@ -43,6 +43,11 @@
             "affiliation": "University of Manchester",
             "name": "Juan Pablo Cordero"
         },
+        {
+            "orcid": "0000-0003-1560-7959",
+            "affiliation": "University of Portsmouth",
+            "name": "Fox Davidson"
+        },
         {
             "orcid": "0000-0002-8218-563X",
             "affiliation": "University of Portsmouth",

CONTRIBUTING.rst

@@ -1,6 +1,45 @@
 Contributor Guidelines
 ======================
 
+How to contribute
+-----------------
+We love contributions! SkyPy is open source,
+built on open source, and we'd love to have you hang out in our community.
+Whether you would like to contribute to SkyPy with your own piece of code or
+helping develop a concrete feature in SkyPy:
+
+1. Read through our `Discussions Page`_ to start a new conversation and share your
+ideas or follow up an existing conversation on a particular feature.
+
+2. Following the discussions, when you have a good idea of the specifics 
+of the feature you wish to contribute, open an `Issue`_ describing the feature. 
+
+3. Then follow the `Contributor Guidelines`_ on the rest of this page to open
+a `Pull Request`_ to contribute the code implementing the new feature.
+
+Members vs External contributions
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+SkyPy allows contributions from two types of contributor: *Members* and *External Contributors*.
+These two categories are intended to allow contributions both from those who are willing and
+able to commit to being part of the SkyPy community and actively involved in the steering of the project,
+and those who wish to simply contribute code where a need has been identified.
+
+1. SkyPy *Members* go through a simple onboarding process where their expertise and expected contributions
+are discussed and defined. Members have access to internal communication channels, they are involved in
+SkyPy decision making processes and attend quarterly meetings.
+Members are listed as a separate tier in author lists for SkyPy publications,
+with the classification of "Creators" in the Zenodo DoI.
+
+2. *External Contributors* are able to develop, discuss and commit code in the same way as *Members*,
+but do not have the same responsibilities and opportunities for contributing to the guidance and management
+of SkyPy as a project. *External Contributors* are listed as a separate tier in author lists for SkyPy publications,
+with the classification of "Others" in the Zenodo DoI.
+
+ .. _Discussions Page: https://github.com/skypyproject/skypy/discussions
+ .. _Issue: https://github.com/skypyproject/skypy/issues
+ .. _Pull Request: https://github.com/skypyproject/skypy/pulls
+
 GitHub Workflow
 ---------------
 

README.rst

@@ -63,28 +63,66 @@ Examples_ that demonstrate how to use it.
 .. _Examples: https://skypy.readthedocs.io/en/stable/examples/index.html
 
 
-Get in Touch
+Contributing
 ------------
 
-You are welcome to talk about the SkyPy package and code using our
-`Discussions Page`_. For any other questions about the project in general,
-please get in touch with the `SkyPy Co-ordinators`_.
+We love contributions! 
+SkyPy is open source,
+built on open source, and we'd love to have you hang out in our community.
 
- .. _Discussions Page: https://github.com/skypyproject/skypy/discussions
- .. _SkyPy Co-ordinators: mailto:skypy-coordinators@googlegroups.com
+How to contribute
+^^^^^^^^^^^^^^^^^
 
-Contributing
-------------
+Whether you would like to contribute to SkyPy with your own piece of code or
+helping develop a concrete feature in SkyPy:
 
-We love contributions! SkyPy is open source,
-built on open source, and we'd love to have you hang out in our community.
-For information on how to contribute see our `Contributor Guidelines`_.
+1. Read through our `Discussions Page`_ to start a new conversation and share your
+ideas or follow up an existing conversation on a particular feature.
+
+2. Following the discussions, when you have a good idea of the specifics 
+of the feature you wish to contribute, open an `Issue`_ describing the feature. 
+
+3. Then follow the `Contributor Guidelines`_ to open a `Pull Request`_ to contribute
+the code implementing the new feature.
+
+For further information on how to contribute see our `Contributor Guidelines`_.
 All communication relating to The SkyPy Project must meet the standards set out
 in the `Code of Conduct`_.
 
+.. _Issue: https://github.com/skypyproject/skypy/issues
+.. _Pull Request: https://github.com/skypyproject/skypy/pulls
 .. _Contributor Guidelines: https://skypy.readthedocs.io/en/latest/developer/contributing.html
 .. _Code of Conduct: https://skypy.readthedocs.io/en/stable/project/code_of_conduct.html
 
+Members vs External contributions
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+SkyPy allows contributions from two types of contributor: *Members* and *External Contributors*.
+These two categories are intended to allow contributions both from those who are willing and
+able to commit to being part of the SkyPy community and actively involved in the steering of the project,
+and those who wish to simply contribute code where a need has been identified.
+
+1. SkyPy *Members* go through a simple onboarding process where their expertise and expected contributions
+are discussed and defined. Members have access to internal communication channels, they are involved in
+SkyPy decision making processes and attend quarterly meetings.
+Members are listed as a separate tier in author lists for SkyPy publications,
+with the classification of "Project Members" in the Zenodo DoI.
+
+2. *External Contributors* are able to develop, discuss and commit code in the same way as *Members*,
+but do not have the same responsibilities and opportunities for contributing to the guidance and management
+of SkyPy as a project. *External Contributors* are listed as a separate tier in author lists for SkyPy publications,
+with the classification of "Others" in the Zenodo version DoI.
+
+Get in Touch
+------------
+
+You are welcome to talk about the SkyPy package and code using our
+`Discussions Page`_. For any other questions about the project in general,
+please get in touch with the `SkyPy Co-ordinators`_.
+
+ .. _Discussions Page: https://github.com/skypyproject/skypy/discussions
+ .. _SkyPy Co-ordinators: mailto:skypy-coordinators@googlegroups.com
+
 .. |PyPI| image:: https://img.shields.io/pypi/v/skypy?label=PyPI&logo=pypi
     :target: https://pypi.python.org/pypi/skypy
 

docs/galaxies.rst

@@ -91,6 +91,18 @@ The following models are found in the `skypy.galaxies.stellar_mass` package.
   schechter_smf_mass
 
 
+Velocity dispersion
+-------------------
+
+The following models are found in the `skypy.galaxies.velocity_dispersion` package.
+
+.. currentmodule:: skypy.galaxies.velocity_dispersion
+.. autosummary::
+  :nosignatures:
+
+  schechter_vdf
+
+
 Reference/API
 =============
 
@@ -103,3 +115,4 @@ Reference/API
 .. automodapi:: skypy.galaxies.spectrum
    :include-all-objects:
 .. automodapi:: skypy.galaxies.stellar_mass
+.. automodapi:: skypy.galaxies.velocity_dispersion

docs/utils/index.rst

@@ -143,6 +143,8 @@ create their own named `speclite.filters.FilterResponse`.
    luminosity_in_band
    mag_ab
    SpectrumTemplates
+   magnitude_error_rykoff
+   logistic_completeness_function
 
 
 Random sampling (`skypy.utils.random`)

skypy/galaxies/__init__.py

@@ -5,13 +5,15 @@
 
 __all__ = [
     'schechter_lf',
+    'schechter_smf',
 ]
 
 from . import luminosity  # noqa F401,F403
 from . import morphology  # noqa F401,F403
 from . import redshift  # noqa F401,F403
 from . import spectrum  # noqa F401,F403
 from . import stellar_mass  # noqa F401,F403
+from . import velocity_dispersion  # noqa F401,F403
 
 from ._schechter import schechter_lf  # noqa
 from ._schechter import schechter_smf  # noqa

skypy/galaxies/spectrum.py

@@ -143,6 +143,28 @@ def stellar_mass(self, coefficients, magnitudes, filter):
         Mt = self.absolute_magnitudes(coefficients, filter)
         return np.power(10, 0.4*(Mt-magnitudes))
 
+    def stellar_mass_remain(self, coefficients, magnitudes, filter):
+        r'''Compute total surviving stellar mass from absolute magnitudes.
+
+        Parameters
+        ----------
+        coefficients : (ng, nt) array_like
+            Array of template coefficients.
+        magnitudes : (ng,) array_like
+            The magnitudes to match in the reference bandpass.
+        filter : str
+            A single reference bandpass filter specification for
+            `~speclite.filters.load_filters`.
+
+        Returns
+        -------
+        stellar_mass : (ng,) array_like
+            Total surviving stellar mass of each galaxy in template units.
+        '''
+        m = self.stellar_mass(coefficients, magnitudes, filter)
+        m *= np.dot(coefficients, self.mremain)
+        return m
+
     def metallicity(self, coefficients):
         r'''Galaxy metallicities from kcorrect templates.
 

skypy/galaxies/stellar_mass.py

@@ -4,13 +4,16 @@
 import numpy as np
 
 from ..utils.random import schechter
+from ..utils import dependent_argument
 
 
 __all__ = [
     'schechter_smf_mass',
 ]
 
 
+@dependent_argument('m_star', 'redshift')
+@dependent_argument('alpha', 'redshift')
 def schechter_smf_mass(redshift, alpha, m_star, m_min, m_max, size=None,
                        resolution=1000):
     r""" Stellar masses following the Schechter mass function [1]_.
@@ -19,9 +22,10 @@ def schechter_smf_mass(redshift, alpha, m_star, m_min, m_max, size=None,
     ----------
     redshift : array_like
         Galaxy redshifts for which to sample magnitudes.
-    alpha : float
-        The alpha parameter in the Schechter stellar mass function.
-    m_star : (nm,) array-like
+    alpha : float or function
+        The alpha parameter in the Schechter stellar mass function. If function,
+        it must return a scalar value.
+    m_star : (nm,) array-like or function
         Characteristic stellar mass m_*.
     size: int, optional
          Output shape of stellar mass samples. If size is None and m_star