Merge pull request Ciela-Institute#101 from Ciela-Institute/logo

add caustics Logo
uw-ssec · Nov 21, 2023 · d122818 · d122818
2 parents 22ad60e + 0732333
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diff --git a/.github/workflows/coverage.yaml b/.github/workflows/coverage.yaml
@@ -15,7 +15,7 @@ jobs:
   coverage:
     runs-on: ubuntu-latest
     steps:
-    - name: Checkout caustic
+    - name: Checkout caustics
       uses: actions/checkout@v3
 
     - name: Set up Python 3.10
@@ -40,17 +40,17 @@ jobs:
         pip install -r requirements.txt
       shell: bash
 
-    - name: Install Caustic
+    - name: Install Caustics
       run: |
         cd $GITHUB_WORKSPACE
         pip install -e .[dev]
-        pip show caustic
+        pip show caustics
       shell: bash
     - name: Test with pytest
       run: |
         cd $GITHUB_WORKSPACE
         pwd
-        pytest --cov-report=xml --cov=caustic test/
+        pytest --cov-report=xml --cov=caustics test/
         cat coverage.xml
       shell: bash
     - name: Upload coverage report to Codecov

diff --git a/.github/workflows/documentation.yaml b/.github/workflows/documentation.yaml
@@ -24,11 +24,11 @@ jobs:
           sudo apt-get install -y pandoc
           pip install sphinx sphinx_rtd_theme nbsphinx
           
-      - name: Install Caustic
+      - name: Install Caustics
         run: |
           cd $GITHUB_WORKSPACE
           pip install -e .[dev]
-          pip show caustic
+          pip show caustics
         shell: bash
 
       - name: Clone external Jupyter Notebook repository
@@ -38,7 +38,7 @@ jobs:
           
       - name: Sphinx build
         run: |
-          sphinx-apidoc -f -o docs/ caustic/
+          sphinx-apidoc -f -o docs/ caustics/
           sphinx-build docs _build
           
       - name: Deploy

diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
@@ -24,7 +24,7 @@ jobs:
         os: [ubuntu-latest, windows-latest, macOS-latest]
 
     steps:
-    - name: Checkout caustic
+    - name: Checkout caustics
       uses: actions/checkout@v3
 
     - name: Set up Python ${{ matrix.python-version }}
@@ -49,11 +49,11 @@ jobs:
         pip install -r requirements.txt
       shell: bash
 
-    - name: Install Caustic
+    - name: Install Caustics
       run: |
         cd $GITHUB_WORKSPACE
         pip install -e .[dev]
-        pip show caustic
+        pip show caustics
       shell: bash
 
     - name: Test with pytest

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -0,0 +1,48 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+    # You can also specify other tool versions:
+    # nodejs: "19"
+    # rust: "1.64"
+    # golang: "1.19"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#    - pdf
+#    - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+# Specify dependencies to be installed
+# Define the system dependencies
+build:
+  os: "ubuntu-20.04"
+  tools:
+    python: "3.9"
+  apt_packages:
+    - pandoc  # Specify pandoc to be installed via apt-get
+
+python:
+  install:
+    - requirements: requirements.txt  # Path to your requirements.txt file
+    - requirements: docs/requirements.txt  # Path to your requirements.txt file
+    - method: pip
+      path: .  # Install the package itself
+
+# python:
+#    install:
+#    - requirements: docs/requirements.txt
diff --git a/README.md b/README.md
@@ -1,23 +1,30 @@
-[![tests](https://github.com/Ciela-Institute/caustic/actions/workflows/python-app.yml/badge.svg?branch=main)](https://github.com/Ciela-Institute/caustic/actions)
-[![Docs](https://github.com/Ciela-Institute/caustic/actions/workflows/documentation.yaml/badge.svg)](https://github.com/Ciela-Institute/caustic/actions/workflows/documentation.yaml)
-[![PyPI version](https://badge.fury.io/py/caustic.svg)](https://pypi.org/project/caustic/)
-[![coverage](https://img.shields.io/codecov/c/github/Ciela-Institute/caustic)](https://app.codecov.io/gh/Ciela-Institute/caustic)
-# caustic
+<picture>
+  <source media="(prefers-color-scheme: dark)" srcset="https://github.com/Ciela-Institute/caustics/blob/main/media/caustics_logo.png?raw=true">
+  <source media="(prefers-color-scheme: light)" srcset="https://github.com/Ciela-Institute/caustics/blob/main/media/caustics_logo_white.png?raw=true">
+  <img alt="caustics logo" src="media/caustics_logo.png" width="70%">
+</picture>
+
+
+[![tests](https://github.com/Ciela-Institute/caustics/actions/workflows/python-app.yml/badge.svg?branch=main)](https://github.com/Ciela-Institute/caustics/actions)
+[![Docs](https://github.com/Ciela-Institute/caustics/actions/workflows/documentation.yaml/badge.svg)](https://github.com/Ciela-Institute/caustics/actions/workflows/documentation.yaml)
+[![PyPI version](https://badge.fury.io/py/caustics.svg)](https://pypi.org/project/caustics/)
+[![coverage](https://img.shields.io/codecov/c/github/Ciela-Institute/caustics)](https://app.codecov.io/gh/Ciela-Institute/caustics)
+# caustics
 
 The lensing pipeline of the future: GPU-accelerated, automatically-differentiable,
 highly modular. Currently under heavy development: expect interface changes and
 some imprecise/untested calculations.
 
 ## Installation 
 
-Simply install caustic from PyPI:
+Simply install caustics from PyPI:
 ```bash
-pip install caustic
+pip install caustics
 ```
 
 ## Documentation
 
-Please see our [documentation page](Ciela-Institute.github.io/caustic/) for more detailed information.
+Please see our [documentation page](Ciela-Institute.github.io/caustics/) for more detailed information.
 
 ## Contributing
 

diff --git a/caustic/__init__.py → caustics/__init__.py b/caustic/__init__.py → caustics/__init__.py
@@ -1,4 +1,4 @@
-__version__ = '0.4.10'
+__version__ = '0.5.0'
 __author__ = "Ciela"
 
 from .constants import *

diff --git a/caustic/constants.py → caustics/constants.py b/caustic/constants.py → caustics/constants.py
diff --git a/caustic/cosmology.py → caustics/cosmology.py b/caustic/cosmology.py → caustics/cosmology.py
diff --git a/caustic/data/__init__.py → caustics/data/__init__.py b/caustic/data/__init__.py → caustics/data/__init__.py
diff --git a/caustic/data/hdf5dataset.py → caustics/data/hdf5dataset.py b/caustic/data/hdf5dataset.py → caustics/data/hdf5dataset.py
diff --git a/caustic/data/illustris_kappa.py → caustics/data/illustris_kappa.py b/caustic/data/illustris_kappa.py → caustics/data/illustris_kappa.py
diff --git a/caustic/data/probes.py → caustics/data/probes.py b/caustic/data/probes.py → caustics/data/probes.py
diff --git a/caustic/lenses/__init__.py → caustics/lenses/__init__.py b/caustic/lenses/__init__.py → caustics/lenses/__init__.py
diff --git a/caustic/lenses/base.py → caustics/lenses/base.py b/caustic/lenses/base.py → caustics/lenses/base.py
diff --git a/caustic/lenses/epl.py → caustics/lenses/epl.py b/caustic/lenses/epl.py → caustics/lenses/epl.py
diff --git a/caustic/lenses/external_shear.py → caustics/lenses/external_shear.py b/caustic/lenses/external_shear.py → caustics/lenses/external_shear.py
diff --git a/caustic/lenses/mass_sheet.py → caustics/lenses/mass_sheet.py b/caustic/lenses/mass_sheet.py → caustics/lenses/mass_sheet.py
diff --git a/caustic/lenses/multiplane.py → caustics/lenses/multiplane.py b/caustic/lenses/multiplane.py → caustics/lenses/multiplane.py
diff --git a/caustic/lenses/nfw.py → caustics/lenses/nfw.py b/caustic/lenses/nfw.py → caustics/lenses/nfw.py
diff --git a/caustic/lenses/pixelated_convergence.py → caustics/lenses/pixelated_convergence.py b/caustic/lenses/pixelated_convergence.py → caustics/lenses/pixelated_convergence.py
diff --git a/caustic/lenses/point.py → caustics/lenses/point.py b/caustic/lenses/point.py → caustics/lenses/point.py
diff --git a/caustic/lenses/pseudo_jaffe.py → caustics/lenses/pseudo_jaffe.py b/caustic/lenses/pseudo_jaffe.py → caustics/lenses/pseudo_jaffe.py
diff --git a/caustic/lenses/sie.py → caustics/lenses/sie.py b/caustic/lenses/sie.py → caustics/lenses/sie.py
diff --git a/caustic/lenses/singleplane.py → caustics/lenses/singleplane.py b/caustic/lenses/singleplane.py → caustics/lenses/singleplane.py
diff --git a/caustic/lenses/sis.py → caustics/lenses/sis.py b/caustic/lenses/sis.py → caustics/lenses/sis.py
diff --git a/caustic/lenses/tnfw.py → caustics/lenses/tnfw.py b/caustic/lenses/tnfw.py → caustics/lenses/tnfw.py
diff --git a/caustic/lenses/utils.py → caustics/lenses/utils.py b/caustic/lenses/utils.py → caustics/lenses/utils.py
diff --git a/caustic/light/__init__.py → caustics/light/__init__.py b/caustic/light/__init__.py → caustics/light/__init__.py
diff --git a/caustic/light/base.py → caustics/light/base.py b/caustic/light/base.py → caustics/light/base.py
diff --git a/caustic/light/pixelated.py → caustics/light/pixelated.py b/caustic/light/pixelated.py → caustics/light/pixelated.py
diff --git a/caustic/light/probes.py → caustics/light/probes.py b/caustic/light/probes.py → caustics/light/probes.py
diff --git a/caustic/light/sersic.py → caustics/light/sersic.py b/caustic/light/sersic.py → caustics/light/sersic.py
diff --git a/caustic/namespace_dict.py → caustics/namespace_dict.py b/caustic/namespace_dict.py → caustics/namespace_dict.py
diff --git a/caustic/packed.py → caustics/packed.py b/caustic/packed.py → caustics/packed.py
diff --git a/caustic/parameter.py → caustics/parameter.py b/caustic/parameter.py → caustics/parameter.py
@@ -9,7 +9,7 @@
 
 class Parameter:
     """
-    Represents a static or dynamic parameter used for strong gravitational lensing simulations in the caustic codebase.
+    Represents a static or dynamic parameter used for strong gravitational lensing simulations in the caustics codebase.
 
     A static parameter has a fixed value, while a dynamic parameter must be passed in each time it's required.
 

diff --git a/caustic/parametrized.py → caustics/parametrized.py b/caustic/parametrized.py → caustics/parametrized.py
diff --git a/caustic/sims/__init__.py → caustics/sims/__init__.py b/caustic/sims/__init__.py → caustics/sims/__init__.py
diff --git a/caustic/sims/lens_source.py → caustics/sims/lens_source.py b/caustic/sims/lens_source.py → caustics/sims/lens_source.py
@@ -22,23 +22,23 @@ class Lens_Source(Simulator):
     Example usage::
 
        import matplotlib.pyplot as plt
-       import caustic
+       import caustics
 
-       cosmo = caustic.FlatLambdaCDM()
-       lens = caustic.lenses.SIS(cosmology = cosmo, x0 = 0., y0 = 0., th_ein = 1.)
-       source = caustic.sources.Sersic(x0 = 0., y0 = 0., q = 0.5, phi = 0.4, n = 2., Re = 1., Ie = 1.)
-       sim = caustic.sims.Lens_Source(lens, source, pixelscale = 0.05, gridx = 100, gridy = 100, upsample_factor = 2, z_s = 1.)
+       cosmo = caustics.FlatLambdaCDM()
+       lens = caustics.lenses.SIS(cosmology = cosmo, x0 = 0., y0 = 0., th_ein = 1.)
+       source = caustics.sources.Sersic(x0 = 0., y0 = 0., q = 0.5, phi = 0.4, n = 2., Re = 1., Ie = 1.)
+       sim = caustics.sims.Lens_Source(lens, source, pixelscale = 0.05, gridx = 100, gridy = 100, upsample_factor = 2, z_s = 1.)
        
        img = sim()
        plt.imshow(img, origin = "lower")
        plt.show()
 
     Attributes:
-      lens: caustic lens mass model object
-      source: caustic light object which defines the background source
+      lens: caustics lens mass model object
+      source: caustics light object which defines the background source
       pixelscale: pixelscale of the sampling grid.
       pixels_x: number of pixels on the x-axis for the sampling grid
-      lens_light (optional): caustic light object which defines the lensing object's light
+      lens_light (optional): caustics light object which defines the lensing object's light
       psf (optional): An image to convolve with the scene. Note that if ``upsample_factor > 1`` the psf must also be at the higher resolution.
       pixels_y (optional): number of pixels on the y-axis for the sampling grid. If left as ``None`` then this will simply be equal to ``gridx``
       upsample_factor (default 1): Amount of upsampling to model the image. For example ``upsample_factor = 2`` indicates that the image will be sampled at double the resolution then summed back to the original resolution (given by pixelscale and gridx/y).

diff --git a/caustic/sims/simulator.py → caustics/sims/simulator.py b/caustic/sims/simulator.py → caustics/sims/simulator.py
diff --git a/caustic/utils.py → caustics/utils.py b/caustic/utils.py → caustics/utils.py
diff --git a/docs/conf.py b/docs/conf.py
@@ -19,14 +19,14 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'caustic'
+project = 'caustics'
 copyright = '2023, Ciela Institute'
 author = 'Ciela Institute'
 
 # The short X.Y version
-version = '0.4'
+version = '0.5'
 # The full version, including alpha/beta/rc tags
-release = 'v0.4.10'
+release = 'v0.5.0'
 
 
 # -- General configuration ---------------------------------------------------
@@ -106,13 +106,13 @@
 # 'searchbox.html']``.
 #
 # html_sidebars = {}
-html_favicon = "../media/caustic_favicon.ico"
+html_favicon = "../media/caustics_favicon.ico"
 
 
 # -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'causticdoc'
+htmlhelp_basename = 'causticsdoc'
 
 
 # -- Options for LaTeX output ------------------------------------------------
@@ -139,7 +139,7 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'caustic.tex', 'caustic Documentation',
+    (master_doc, 'caustics.tex', 'caustics Documentation',
      'Ciela Institute', 'manual'),
 ]
 
@@ -149,7 +149,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, 'caustic', 'caustic Documentation',
+    (master_doc, 'caustics', 'caustics Documentation',
      [author], 1)
 ]
 
@@ -160,8 +160,8 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'caustic', 'caustic Documentation',
-     author, 'caustic', 'One line description of project.',
+    (master_doc, 'caustics', 'caustics Documentation',
+     author, 'caustics', 'One line description of project.',
      'Miscellaneous'),
 ]
 

diff --git a/docs/contributing.rst b/docs/contributing.rst
@@ -4,12 +4,12 @@ Contributing
 .. contents:: Table of Contents
    :local:
 
-Thanks for helping make caustic better! Here you will learn the full process needed to contribute to caustic. Following these steps will make the process as painless as possible for everyone.
+Thanks for helping make caustics better! Here you will learn the full process needed to contribute to caustics. Following these steps will make the process as painless as possible for everyone.
 
 Create An Issue
 ---------------
 
-Before actually writing any code, its best to create an issue on the GitHub. Describe the issue in detail and let us know the desired solution. Here it will be possible to address concerns (maybe its aready solved and just not yet documented) and plan out the best solution. We may also assign someone to work on it if that seems better. Note that submitting an issue is a contribution to caustic, we appreciate your ideas! Still, if after discussion it seems that the problem does need some work and you're the person to do it, then we can move on to the next steps.
+Before actually writing any code, its best to create an issue on the GitHub. Describe the issue in detail and let us know the desired solution. Here it will be possible to address concerns (maybe its aready solved and just not yet documented) and plan out the best solution. We may also assign someone to work on it if that seems better. Note that submitting an issue is a contribution to caustics, we appreciate your ideas! Still, if after discussion it seems that the problem does need some work and you're the person to do it, then we can move on to the next steps.
 
 1. Navigate to the **Issues** tab of the GitHub repository.
 2. Click on **New Issue**.
@@ -20,14 +20,14 @@ Before actually writing any code, its best to create an issue on the GitHub. Des
 Install
 -------
 
-Please fork the caustic repo, then follow the developer install instructions at the :doc:`install` page. This will ensure you have a version of caustic that you can tinker with and see the results.
+Please fork the caustics repo, then follow the developer install instructions at the :doc:`install` page. This will ensure you have a version of caustics that you can tinker with and see the results.
 
-The reason you should fork the repo is so that you have full control while making your edits. You will still be able to make a Pull Request later when it is time to merge your code with the main caustic branch. Note that you should keep your fork up to date with the caustic repo to make the merge as smooth as possible.
+The reason you should fork the repo is so that you have full control while making your edits. You will still be able to make a Pull Request later when it is time to merge your code with the main caustics branch. Note that you should keep your fork up to date with the caustics repo to make the merge as smooth as possible.
 
 Notebooks
 ---------
 
-You will likely want to see how your changes affect various features of caustic. A good way to quickly see this is to run the tutorial notebooks which can be found `here <https://github.com/Ciela-Institute/caustic-tutorials>`_. Any change that breaks one of these must be addressed, either by changing the nature of your updates to the code, or by forking and updating the caustic-tutorials repo as well (this is usually pretty easy).
+You will likely want to see how your changes affect various features of caustics. A good way to quickly see this is to run the tutorial notebooks which can be found `here <https://github.com/Ciela-Institute/caustics-tutorials>`_. Any change that breaks one of these must be addressed, either by changing the nature of your updates to the code, or by forking and updating the caustics-tutorials repo as well (this is usually pretty easy).
 
 Resolving the Issue
 -------------------
@@ -43,12 +43,12 @@ As you modify the code, make sure to regularly commit changes and push them to y
 Unit Tests
 ----------
 
-When you think you've solved an issue, please make unit tests related to any code you have added. Any new code added to caustic must have unit tests which match the level of completion of the rest of the code. Generally you should test all cases for the newly added code. Also ensure the previous unit tests run correctly.
+When you think you've solved an issue, please make unit tests related to any code you have added. Any new code added to caustics must have unit tests which match the level of completion of the rest of the code. Generally you should test all cases for the newly added code. Also ensure the previous unit tests run correctly.
 
 Submitting a Pull Request
 -------------------------
 
-Once you think your updates are ready to merge with the rest of caustic you can submit a PR! This should provide a description of what you have changed and if it isn't straightforward, why you made those changes.
+Once you think your updates are ready to merge with the rest of caustics you can submit a PR! This should provide a description of what you have changed and if it isn't straightforward, why you made those changes.
 
 1. Navigate to the **Pull Requests** tab of the original repository.
 2. Click on **New Pull Request**.

diff --git a/docs/getting_started.rst b/docs/getting_started.rst
@@ -11,10 +11,10 @@ Please follow the instructions on the :doc:`install` page. For most users, the b
 Tutorials
 ---------
 
-We have created a repository of tutorial Jupyter notebooks that can help initiate you on the main features of caustic. Please checkout the `tutorials here <https://github.com/Ciela-Institute/caustic-tutorials>`_ to see what caustic can do!
+We have created a repository of tutorial Jupyter notebooks that can help initiate you on the main features of caustics. Please checkout the `tutorials here <https://github.com/Ciela-Institute/caustics-tutorials>`_ to see what caustics can do!
 
 
 Read The Docs
 -------------
 
-Docs for all the main functions in caustic are avaialble at :doc:`caustic` at varying degrees of completeness. Further development of the docs is always ongoing.
+Docs for all the main functions in caustics are avaialble at :doc:`caustics` at varying degrees of completeness. Further development of the docs is always ongoing.
diff --git a/docs/illustrative_examples.rst b/docs/illustrative_examples.rst
@@ -2,4 +2,4 @@
 Examples
 ========
 
-Here we present a few examples of analysis done with caustic. There will hopefully be one that is close to your use case and so can act as a good starting point.
+Here we present a few examples of analysis done with caustics. There will hopefully be one that is close to your use case and so can act as a good starting point.
diff --git a/docs/index.rst b/docs/index.rst
@@ -1,25 +1,31 @@
-.. caustic documentation master file, created by
+.. caustics documentation master file, created by
    sphinx-quickstart on Thu Jun  1 09:33:32 2023.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to Caustic's documentation!
+.. image:: https://github.com/Ciela-Institute/caustics/blob/main/media/AP_logo.png?raw=true
+   :width: 100 %
+   :target: https://github.com/Ciela-Institute/caustics
+
+|br|
+
+Welcome to Caustics' documentation!
 ===================================
 
 The lensing pipeline of the future: GPU-accelerated, automatically-differentiable, highly modular and extensible.
 
 .. note::
 
-    Caustic is in its early development phase. This means the API will change with time. These changes are a good thing, but they can be annoying. Watch the version numbers, when we get to 1.0.0 that will be the first stable release!
+    Caustics is in its early development phase. This means the API will change with time. These changes are a good thing, but they can be annoying. Watch the version numbers, when we get to 1.0.0 that will be the first stable release!
 
 Intallation
 ===========
 
 The easiest way to install is to make a new virtual environment then run::
 
-    pip install caustic
+    pip install caustics
 
-this will install all the required libraries and then install caustic and you are ready to go! You can check out the tutorials afterwards to see some of caustic's capabilities.  If you want to help out with building the caustic code base check out the developer installation instructions instead.
+this will install all the required libraries and then install caustics and you are ready to go! You can check out the tutorials afterwards to see some of caustics's capabilities.  If you want to help out with building the caustics code base check out the developer installation instructions instead.
 
 Read The Docs
 =============