MAINT: merge main into module/halos

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,7 +1,7 @@
 ## Description
 
 ## Checklist
-- [ ] Follow the [Contributor Guidelines](https://github.com/skypyproject/skypy/blob/master/CONTRIBUTING.md)
+- [ ] Follow the [Contributor Guidelines](https://github.com/skypyproject/skypy/blob/main/CONTRIBUTING.rst)
 - [ ] Write unit tests
 - [ ] Write documentation strings
 - [ ] Assign someone from your working team to review this pull request

.github/workflows/codestyle.yaml

@@ -2,11 +2,11 @@ name: Code Style
 on:
   push:
     branches:
-    - master
+    - main
     - module/*
   pull_request:
     branches:
-    - master
+    - main
     - module/*
 jobs:
   flake8:

.github/workflows/compatibility.yaml

@@ -9,15 +9,15 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python: [3.9]
-        toxenv: [py39-test, py39-test-dev]
-        release: [master, latest]
+        python: ['3.10']
+        toxenv: [py310-test, py310-test-dev]
+        release: [main, latest]
     steps:
     - name: Checkout Repository
       uses: actions/checkout@v2
       with:
         fetch-depth: 0
-    - if: matrix.release != 'master'
+    - if: matrix.release != 'main'
       name: Checkout Release
       run: |
         git checkout tags/$(curl -s https://api.github.com/repos/skypyproject/skypy/releases/${{ matrix.release }} | python -c "import sys, json; print(json.load(sys.stdin)['tag_name'])")

.github/workflows/tests.yaml

@@ -2,11 +2,11 @@ name: Tests
 on:
   push:
     branches:
-    - master
+    - main
     - module/*
   pull_request:
     branches:
-    - master
+    - main
     - module/*
 jobs:
   test:
@@ -19,24 +19,24 @@ jobs:
 
           - name: latest supported versions
             os: ubuntu-latest
-            python: 3.9
-            toxenv: py39-test-all-latest-cov
+            python: '3.10'
+            toxenv: py310-test-all-latest-cov
             toxposargs: --cov-report=xml:${GITHUB_WORKSPACE}/coverage.xml
 
           - name: oldest supported versions
             os: ubuntu-latest
-            python: 3.6
-            toxenv: py36-test-oldest
+            python: 3.7
+            toxenv: py37-test-oldest
 
           - name: macOS latest supported
             os: macos-latest
-            python: 3.9
-            toxenv: py39-test-latest
+            python: '3.10'
+            toxenv: py310-test-latest
 
           - name: Windows latest supported
             os: windows-latest
-            python: 3.9
-            toxenv: py39-test-latest
+            python: '3.10'
+            toxenv: py310-test-latest
 
     steps:
     - name: Checkout Repository

.mailmap

@@ -13,5 +13,6 @@
 Adam Amara <[email protected]> adamamara <adamamara@penguin>
 Coleman Krawczyk <[email protected]> CKrawczyk
 Ian Harry <[email protected]> <[email protected]>
+Lucia F. de la Bella <[email protected]>
 Nicolas Tessore <[email protected]> <[email protected]>
 Richard R <[email protected]> <[email protected]>

.readthedocs.yml

@@ -1,17 +1,24 @@
 version: 2
 
 build:
-  image: latest
+  os: ubuntu-20.04
+  apt_packages:
+    - graphviz
+  tools:
+    python: "3.7"
 
 sphinx:
+  builder: html
+  configuration: docs/conf.py
   fail_on_warning: true
 
 python:
-  version: 3.7
+  system_packages: false
   install:
     - method: pip
       path: .
       extra_requirements:
         - docs
+        - all
 
 formats: []

.zenodo.json

@@ -25,7 +25,7 @@
         },
         {
             "orcid": "0000-0002-1064-3400",
-            "affiliation": "University of Manchester",
+            "affiliation": "University of Portsmouth",
             "name": "Lucia F. de la Bella"
         },
         {
@@ -43,21 +43,31 @@
             "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",
             "name": "Ginevra Favole"
         },
         {
             "orcid": "0000-0002-4437-0770",
-            "affiliation": "University of Manchester",
+            "affiliation": "University of Oxford, University of Manchester",
             "name": "Ian Harrison"
         },
         {
             "orcid": "0000-0002-5304-9372",
             "affiliation": "University of Portsmouth",
             "name": "Ian Harry"
         },
+        {
+            "orcid": "0000-0001-9994-1115",
+            "affiliation": "University of Geneva",
+            "name": "William G. Hartley"
+        },
         {
             "orcid": "0000-0001-9233-2341",
             "affiliation": "University of Portsmouth",
@@ -80,14 +90,19 @@
         },
         {
             "orcid": "0000-0003-1291-1023",
-            "affiliation": "University of Manchester",
-            "name": "Richard Rollins"
+            "affiliation": "University of Edinburgh",
+            "name": "Richard P. Rollins"
         },
         {
             "orcid": "0000-0001-8685-2308",
             "affiliation": "University of Portsmouth",
             "name": "Philipp Sudek"
         },
+        {
+            "orcid": "0000-0002-6724-833X",
+            "affiliation": "Institute of Astronomy and Astrophysics Academia Sinica",
+            "name": "Sut-Ieng Tam"
+        },
         {
             "orcid": "0000-0002-9696-7931",
             "affiliation": "UCL",
@@ -98,10 +113,20 @@
             "affiliation": "Institute of Astronomy and Astrophysics Academia Sinica",
             "name": "Keiichi Umetsu"
         },
+        {
+            "orcid": "0000-0001-9841-943X",
+            "affiliation": "University of Portsmouth",
+            "name": "Arthur E. Tolley"
+        },
         {
             "orcid": "0000-0002-7627-8688",
             "affiliation": "University of Portsmouth",
             "name": "Andrew R. Williamson"
+        },
+        {
+            "orcid": "0000-0003-3334-3037",
+            "affiliation": "University of Manchester",
+            "name": "Laura Wolz"
         }
     ],
     "contributors": [

CITATION.rst

@@ -1,13 +1,27 @@
+Citation Guidelines
+===================
+
+|JOSS| |Zenodo|
+
+
 If you use SkyPy for work or research presented in a publication (whether
-directly, or as a dependency to another package) we recommend and encourage
+directly, or as a dependency of another package) we recommend and encourage
 the following acknowledgment:
 
   This research made use of SkyPy, a Python package for forward modeling
-  astronomical surveys (SkyPy Collaboration, 2020).
+  astronomical surveys (Amara et. al., 2021, SkyPy Collaboration, 202x).
+
+where the citations are to our publication in the `Journal of Open Source
+Software`_ and the `Zenodo DOI`_ for the specific version of the software that
+you used. We also encourage citations within the main text wherever
+appropriate. DOIs and BibTeX keys are available through the links above.
+
+.. _Journal of Open Source Software: https://joss.theoj.org/papers/10.21105/joss.03056
+.. _Zenodo DOI: https://zenodo.org/record/3755531
+
 
-where (SkyPy Collaboration, 2020) is a citation to the software DOI for the
-specific version that you used. We also encourage you to cite the software DOI
-in the main text wherever appropriate. DOIs and BibTeX keys for each release
-can be found on Zenodo_.
+.. |JOSS| image:: https://joss.theoj.org/papers/10.21105/joss.03056/status.svg
+    :target: https://doi.org/10.21105/joss.03056
 
-.. _Zenodo: https://zenodo.org/record/3755531
+.. |Zenodo| image:: https://zenodo.org/badge/doi/10.5281/zenodo.4475347.svg
+    :target: https://doi.org/10.5281/zenodo.3755531

CONTRIBUTING.rst

@@ -32,12 +32,12 @@ Finally add the ``skypyproject`` repository as a *remote*. This will allow you t
 Create a branch for your new feature
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Create a *branch* off the ``skypyproject`` master branch. Working on unique branches for each new feature simplifies the development, review and merge processes by maintining logical separation. To create a feature branch:
+Create a *branch* off the ``skypyproject`` main branch. Working on unique branches for each new feature simplifies the development, review and merge processes by maintining logical separation. To create a feature branch:
 
 ::
 
   git fetch skypyproject
-  git checkout -b <your-branch-name> skypyproject/master
+  git checkout -b <your-branch-name> skypyproject/main
 
 
 Hack away!
@@ -73,7 +73,7 @@ When you feel that work on your new feature is complete, you should create a *Pu
   1. Go to `SkyPy Pull Requests <https://github.com/skypyproject/skypy/pulls>`_
   2. Click the green **New pull request** button
   3. Click **compare across forks**
-  4. Confirm that the base fork is ``skypyproject/skypy`` and the base branch is ``master``
+  4. Confirm that the base fork is ``skypyproject/skypy`` and the base branch is ``main``
   5. Confirm the head fork is ``<your-account>/skypy`` and the compare branch is ``<your-branch-name>``
   6. Give your pull request a title and fill out the the template for the description
   7. Click the green **Create pull request** button
@@ -91,22 +91,22 @@ A series of automated checks will be run on your pull request, some of which wil
 Updating your branch
 ^^^^^^^^^^^^^^^^^^^^
 
-As you work on your feature, new commits might be made to the ``skypyproject`` master branch. You will need to update your branch with these new commits before your pull request can be accepted. You can achieve this in a few different ways:
+As you work on your feature, new commits might be made to the ``skypyproject`` main branch. You will need to update your branch with these new commits before your pull request can be accepted. You can achieve this in a few different ways:
 
   - If your pull request has no conflicts, click **Update branch**
   - If your pull request has conflicts, click **Resolve conflicts**, manually resolve the conflicts and click **Mark as resolved**
-  - *merge* the ``skypyproject`` master branch from the command line:
+  - *merge* the ``skypyproject`` main branch from the command line:
 
     ::
 
         git fetch skypyproject
-        git merge skypyproject/master
+        git merge skypyproject/main
 
-  - *rebase* your feature branch onto the ``skypyproject`` master branch from the command line:
+  - *rebase* your feature branch onto the ``skypyproject`` main branch from the command line:
     ::
 
         git fetch skypyproject
-        git rebase skypyproject/master
+        git rebase skypyproject/main
 
 
 **Warning**: It is bad practice to *rebase* commits that have already been pushed to a remote such as your fork. Rebasing creates new copies of your commits that can cause the local and remote branches to diverge. ``git push --force`` will **overwrite** the remote branch with your newly rebased local branch. This is strongly discouraged, particularly when working on a shared branch where you could erase a collaborators commits.
@@ -129,7 +129,7 @@ Before your pull request can be merged into the codebase, it will be reviewed by
 General Guidelines
 ^^^^^^^^^^^^^^^^^^
 
-- SkyPy is compatible with Python>=3.6 (see `setup.cfg <https://github.com/skypyproject/skypy/blob/master/setup.cfg>`_). SkyPy *does not* support backwards compatibility with Python 2.x; `six`, `__future__` and `2to3` should not be used.
+- SkyPy is compatible with Python>=3.7 (see `setup.cfg <https://github.com/skypyproject/skypy/blob/main/setup.cfg>`_). SkyPy *does not* support backwards compatibility with Python 2.x; `six`, `__future__` and `2to3` should not be used.
 - All contributions should follow the `PEP8 Style Guide for Python Code <https://www.python.org/dev/peps/pep-0008/>`_. We recommend using `flake8 <https://flake8.pycqa.org/>`__ to check your code for PEP8 compliance.
 - Importing SkyPy should only depend on having `NumPy <https://www.numpy.org>`_, `SciPy <https://www.scipy.org/>`_ and `Astropy <https://www.astropy.org/>`__ installed.
 - Code is grouped into submodules based on broad science areas e.g. `galaxies <https://skypy.readthedocs.io/en/stable/galaxies.html>`_. There is also a `utils <https://skypy.readthedocs.io/en/stable/utils/index.html>`_ submodule for general utility functions.
@@ -150,7 +150,6 @@ All public classes, methods and functions require docstrings. You can build docu
   - Description
   - Parameters
   - Notes
-  - Examples
   - References
 
 For more information see the Astropy guide to `Writing Documentation <https://docs.astropy.org/en/stable/development/docguide.html>`_.