Merge branch 'pre-commit-ci-update-config' of github.com:Ciela-Instit…

…ute/caustics into pre-commit-ci-update-config

.github/workflows/ci.yml

@@ -71,4 +71,12 @@ jobs:
           pytest -vvv --cov=${{ env.PROJECT_NAME }} --cov-report=xml --cov-report=term tests/
 
       - name: Upload coverage reports to Codecov with GitHub Action
+        if:
+          ${{ matrix.python-version == '3.10' && matrix.os == 'ubuntu-latest'}}
         uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          flags: unittests
+          name: codecov-umbrella
+          fail_ci_if_error: true

.github/workflows/image_ci.yml

@@ -98,7 +98,7 @@ jobs:
         uses: docker/setup-buildx-action@v3
 
       - name: Build and export to Docker
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v6
         with:
           context: .
           file: ./resources/docker/Dockerfile

.pre-commit-config.yaml

@@ -9,12 +9,12 @@ ci:
 
 repos:
   - repo: https://github.com/psf/black
-    rev: "24.4.2"
+    rev: "24.8.0"
     hooks:
       - id: black-jupyter
 
   - repo: https://github.com/asottile/blacken-docs
-    rev: "1.16.0"
+    rev: "1.18.0"
     hooks:
       - id: blacken-docs
         additional_dependencies: [black==23.7.0]
@@ -23,6 +23,7 @@ repos:
     rev: "v4.6.0"
     hooks:
       - id: check-added-large-files
+        args: ["--maxkb=1000"]
       - id: check-case-conflict
       - id: check-merge-conflict
       - id: check-symlinks
@@ -50,13 +51,13 @@ repos:
         args: [--prose-wrap=always]
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.4.10"
+    rev: "v0.5.6"
     hooks:
       - id: ruff
         args: ["--fix", "--show-fixes"]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.10.0"
+    rev: "v1.11.1"
     hooks:
       - id: mypy
         files: src
@@ -70,11 +71,20 @@ repos:
       - id: codespell
         args: ["--write-changes", "--ignore-words", ".codespell-whitelist"]
 
-  - repo: https://github.com/kynan/nbstripout
-    rev: 0.7.1
+  #- repo: https://github.com/kynan/nbstripout
+  #rev: 0.7.1
+  #hooks:
+  #- id: nbstripout
+  #args: [--extra-keys=metadata.kernelspec metadata.language_info.version]
+
+  - repo: local
     hooks:
-      - id: nbstripout
-        args: [--extra-keys=metadata.kernelspec metadata.language_info.version]
+      - id: strip-output-keep-html
+        name: Strip Jupyter Notebook output but keep HTML
+        entry: python strip_output_keep_html.py
+        language: python
+        additional_dependencies: [nbformat]
+        files: \.ipynb$
 
   - repo: local
     hooks:

README.md

@@ -10,7 +10,9 @@
 [![Documentation Status](https://readthedocs.org/projects/caustics/badge/?version=latest)](https://caustics.readthedocs.io/en/latest/?badge=latest)
 [![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)
-[![DOI](https://zenodo.org/badge/521722463.svg)](https://zenodo.org/doi/10.5281/zenodo.10806382)
+[![status](https://joss.theoj.org/papers/995fa98462eb534a32952549ef2244f8/status.svg)](https://joss.theoj.org/papers/995fa98462eb534a32952549ef2244f8)
+[![Zenodo](https://zenodo.org/badge/521722463.svg)](https://zenodo.org/doi/10.5281/zenodo.10806382)
+[![arXiv](https://img.shields.io/badge/arXiv-2406.15542-b31b1b.svg)](https://arxiv.org/abs/2406.15542)
 
 # caustics
 
@@ -45,7 +47,7 @@ x = torch.tensor([
     5.0, -0.2, 0.0, 0.8, 0.0, 1., 1.0, 10.0
 ])  # fmt: skip
 
-minisim = caustics.Lens_Source(
+minisim = caustics.LensSource(
     lens=sie, source=src, lens_light=lnslt, pixelscale=0.05, pixels_x=100
 )
 plt.imshow(minisim(x, quad_level=3), origin="lower")

docs/source/_toc.yml

@@ -9,11 +9,12 @@ chapters:
   - file: websim
   - file: tutorials/index
     sections:
-      - file: basicindex
+      - file: tutorials/Introduction
+      - file: interfaceindex
         sections:
-          - file: tutorials/BasicIntroduction_yaml
-          - file: tutorials/BasicIntroduction_oop
-          - file: tutorials/BasicIntroduction_func
+          - file: tutorials/InterfaceIntroduction_yaml
+          - file: tutorials/InterfaceIntroduction_oop
+          - file: tutorials/InterfaceIntroduction_func
       - file: tutorials/LensZoo
       - file: tutorials/VisualizeCaustics
       - file: tutorials/MultiplaneDemo

docs/source/citation.rst

@@ -3,4 +3,23 @@
 Citation
 ========
 
-Paper coming soon! We will put all the citation information here when its ready.
+Paper is submitted to JOSS, in the meantime please cite the `arXiv version <https://arxiv.org/abs/2406.15542>`_ of the paper:
+
+.. code-block:: bibtex
+
+    @ARTICLE{2024arXiv240615542S,
+        author = {{Stone}, Connor and {Adam}, Alexandre and {Coogan}, Adam and {Yantovski-Barth}, M.~J. and {Filipp}, Andreas and {Setiawan}, Landung and {Core}, Cordero and {Legin}, Ronan and {Wilson}, Charles and {Missael Barco}, Gabriel and {Hezaveh}, Yashar and {Perreault-Levasseur}, Laurence},
+            title = "{Caustics: A Python Package for Accelerated Strong Gravitational Lensing Simulations}",
+        journal = {arXiv e-prints},
+        keywords = {Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Cosmology and Nongalactic Astrophysics},
+            year = 2024,
+            month = jun,
+            eid = {arXiv:2406.15542},
+            pages = {arXiv:2406.15542},
+            doi = {10.48550/arXiv.2406.15542},
+    archivePrefix = {arXiv},
+        eprint = {2406.15542},
+    primaryClass = {astro-ph.IM},
+        adsurl = {https://ui.adsabs.harvard.edu/abs/2024arXiv240615542S},
+        adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+    }

docs/source/examples/Example_ImageFit_LM.ipynb

@@ -56,10 +56,9 @@
     "cosmology.to(dtype=torch.float32)\n",
     "\n",
     "upsample_factor = 1\n",
-    "thx, thy = caustics.utils.get_meshgrid(\n",
+    "thx, thy = caustics.utils.meshgrid(\n",
     "    pixelscale / upsample_factor,\n",
     "    upsample_factor * numPix,\n",
-    "    upsample_factor * numPix,\n",
     "    dtype=torch.float32,\n",
     ")\n",
     "z_l = torch.tensor(0.5, dtype=torch.float32)\n",
@@ -110,7 +109,7 @@
     ")\n",
     "\n",
     "# Image plane simulator\n",
-    "sim = caustics.Lens_Source(\n",
+    "sim = caustics.LensSource(\n",
     "    lens=lens_mass_model,\n",
     "    lens_light=lens_light_model,\n",
     "    source=source_light_model,\n",

docs/source/examples/Example_ImageFit_NUTS.ipynb

@@ -61,10 +61,9 @@
     "cosmology.to(dtype=torch.float32)\n",
     "\n",
     "upsample_factor = 1\n",
-    "thx, thy = caustics.utils.get_meshgrid(\n",
+    "thx, thy = caustics.utils.meshgrid(\n",
     "    pixelscale / upsample_factor,\n",
     "    upsample_factor * numPix,\n",
-    "    upsample_factor * numPix,\n",
     "    dtype=torch.float32,\n",
     ")\n",
     "z_l = torch.tensor(0.5, dtype=torch.float32)\n",
@@ -115,7 +114,7 @@
     ")\n",
     "\n",
     "# Image plane simulator\n",
-    "sim = caustics.Lens_Source(\n",
+    "sim = caustics.LensSource(\n",
     "    lens=lens_mass_model,\n",
     "    lens_light=lens_light_model,\n",
     "    source=source_light_model,\n",

docs/source/examples/Example_QSOLensFit.ipynb

@@ -103,10 +103,9 @@
     "res = 0.05\n",
     "upsample_factor = 1\n",
     "fov = res * n_pix\n",
-    "thx, thy = caustics.utils.get_meshgrid(\n",
+    "thx, thy = caustics.utils.meshgrid(\n",
     "    res / upsample_factor,\n",
     "    upsample_factor * n_pix,\n",
-    "    upsample_factor * n_pix,\n",
     "    dtype=torch.float32,\n",
     ")\n",
     "\n",

docs/source/basicindex.rst → docs/source/interfaceindex.rst

@@ -1,5 +1,5 @@
-Basic Introduction
-==================
+The three interfaces to Caustics
+================================
 
 There are three user interfaces to Caustics: configuration file, object-oriented, and functional.
 Here we have built the same tutorial three times over so you can see how the three interfaces compare.

docs/source/intro.md

@@ -39,7 +39,7 @@ x = torch.tensor([
     5.0, -0.2, 0.0, 0.8, 0.0, 1., 1.0, 10.0
 ])  # fmt: skip
 
-minisim = caustics.Lens_Source(
+minisim = caustics.LensSource(
     lens=sie, source=src, lens_light=lnslt, pixelscale=0.05, pixels_x=100
 )
 plt.imshow(minisim(x, quad_level=3), origin="lower")

docs/source/tutorials/BasicIntroduction_func.ipynb → docs/source/tutorials/InterfaceIntroduction_func.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Welcome to Caustics! Functional\n",
+    "# Caustics Interface: Functional\n",
     "\n",
     "Caustics is a powerful gravitational lensing simulator that can support users from beginner to highly advanced. In this tutorial we will cover the basics of the caustics functional interface. This one is a bit different from the other two since we are building from the ground up."
    ]
@@ -59,7 +59,7 @@
     "# First lets define the sampling grid\n",
     "npix = 100\n",
     "pixelscale = 0.05\n",
-    "thx, thy = caustics.utils.get_meshgrid(pixelscale, npix, npix)\n",
+    "thx, thy = caustics.utils.meshgrid(pixelscale, npix, npix)\n",
     "gqx, gqy, gqW = caustics.utils.gaussian_quadrature_grid(\n",
     "    pixelscale, thx, thy, quad_level=3\n",
     ")"

docs/source/tutorials/BasicIntroduction_oop.ipynb → docs/source/tutorials/InterfaceIntroduction_oop.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Welcome to Caustics! Object Oriented\n",
+    "# Caustics Interface: Object Oriented\n",
     "\n",
     "Caustics is a powerful gravitational lensing simulator that can support users from beginner to highly advanced. In this tutorial we will cover the basics of the caustics object oriented programming interface."
    ]
@@ -128,7 +128,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sim = caustics.Lens_Source(\n",
+    "sim = caustics.LensSource(\n",
     "    lens=sie, source=src, lens_light=lnslt, pixelscale=0.05, pixels_x=100\n",
     ")"
    ]
@@ -244,7 +244,7 @@
    "source": [
     "### The Simulator Graph\n",
     "\n",
-    "Here we take a quick look at the simulator graph for the image we have produced. You will learn much more about what this means in the `Simulators` tutorial notebook, but let's cover the basics here. First, note that this is a Directed Acyclic Graph (DAG), this is how all simulator parameters are represented in Caustics. At the top of the graph is the `Lens_Source` object, you can see in brackets it has a name `sim` which is used as the identifier for it's node in the graph. At the next level is the `z_s` parameter for the redshift of the source. Next are the `SIE` lens, `Sersic` source, and `Sersic` lenslight objects which themselves each hold parameters. You will notice that all the parameters are in white boxes right now, this is because they are `dynamic` parameters which need values to be passed, grey boxes are used for parameters with fixed values."
+    "Here we take a quick look at the simulator graph for the image we have produced. You will learn much more about what this means in the `Simulators` tutorial notebook, but let's cover the basics here. First, note that this is a Directed Acyclic Graph (DAG), this is how all simulator parameters are represented in Caustics. At the top of the graph is the `LensSource` object, you can see in brackets it has a name `sim` which is used as the identifier for it's node in the graph. At the next level is the `z_s` parameter for the redshift of the source. Next are the `SIE` lens, `Sersic` source, and `Sersic` lenslight objects which themselves each hold parameters. You will notice that all the parameters are in white boxes right now, this is because they are `dynamic` parameters which need values to be passed, grey boxes are used for parameters with fixed values."
    ]
   },
   {
@@ -254,7 +254,7 @@
    "outputs": [],
    "source": [
     "# Substitute sim with sim for the yaml method\n",
-    "sim.get_graph(True, True)"
+    "sim.graph(True, True)"
    ]
   },
   {

docs/source/tutorials/BasicIntroduction_yaml.ipynb → docs/source/tutorials/InterfaceIntroduction_yaml.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Welcome to Caustics! YAML\n",
+    "# Caustics Interface: YAML\n",
     "\n",
     "Caustics is a powerful gravitational lensing simulator that can support users from beginner to highly advanced. In this tutorial we will cover the basics of the caustics `yaml` interface."
    ]
@@ -181,7 +181,7 @@
    "source": [
     "### The Simulator Graph\n",
     "\n",
-    "Here we take a quick look at the simulator graph for the image we have produced. You will learn much more about what this means in the `Simulators` tutorial notebook, but let's cover the basics here. First, note that this is a Directed Acyclic Graph (DAG), this is how all simulator parameters are represented in Caustics. At the top of the graph is the `Lens_Source` object, you can see in brackets it has a name `sim` which is used as the identifier for it's node in the graph. At the next level is the `z_s` parameter for the redshift of the source. Next are the `SIE` lens, `Sersic` source, and `Sersic` lenslight objects which themselves each hold parameters. You will notice that all the parameters are in white boxes right now, this is because they are `dynamic` parameters which need values to be passed, grey boxes are used for parameters with fixed values."
+    "Here we take a quick look at the simulator graph for the image we have produced. You will learn much more about what this means in the `Simulators` tutorial notebook, but let's cover the basics here. First, note that this is a Directed Acyclic Graph (DAG), this is how all simulator parameters are represented in Caustics. At the top of the graph is the `LensSource` object, you can see in brackets it has a name `sim` which is used as the identifier for it's node in the graph. At the next level is the `z_s` parameter for the redshift of the source. Next are the `SIE` lens, `Sersic` source, and `Sersic` lenslight objects which themselves each hold parameters. You will notice that all the parameters are in white boxes right now, this is because they are `dynamic` parameters which need values to be passed, grey boxes are used for parameters with fixed values."
    ]
   },
   {
@@ -191,7 +191,7 @@
    "outputs": [],
    "source": [
     "# The simulator is internally represented as a directed acyclic graph of operations\n",
-    "sim.get_graph(True, True)"
+    "sim.graph(True, True)"
    ]
   },
   {
@@ -336,7 +336,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Lens_Source Simulator\n",
+    "### LensSource Simulator\n",
     "\n",
     "Next we pass our configuration to a `Simulator` in caustics, simulators perform the work of forward modelling various configurations and producing the desired outputs. Here we are interested in a common scenario of producing an image of a background source through a lens distribution. It is possible to make your own simulator to represent all sorts of situations. First, we pass the `lens` model and the `source` model defined above. Next we use `pixelscale` and `pixels_x` to define the grid of pixels that will be sampled. Finally, we pass the `z_s` redshift at which the source (`Sersic`) model should be placed; recall that light models don't use the cosmology model and so aren't aware of their placement in space.\n",
     "\n",
@@ -347,7 +347,7 @@
     "```yaml\n",
     "simulator:\n",
     "    name: minisim\n",
-    "    kind: Lens_Source\n",
+    "    kind: LensSource\n",
     "    init_kwargs:\n",
     "        lens: *lens\n",
     "        source: *src\n",
@@ -359,7 +359,7 @@
     "In this section:\n",
     "-  `simulator:` is the key that starts the definition of the simulator.\n",
     "- `name: minisim` sets the name of the simulator to 'minisim'.\n",
-    "- `kind: Lens_Source` sets the kind of the simulator to 'Lens_Source', which indicates that this simulator will simulate a lens and a source.\n",
+    "- `kind: LensSource` sets the kind of the simulator to 'LensSource', which indicates that this simulator will simulate a lens and a source.\n",
     "- `init_kwargs:` is a key for additional parameters required for the simulator.\n",
     "- `lens: *lens` sets the lens for the simulator to the lens defined earlier in the YAML file.\n",
     "- `source: *src` sets the source for the simulator to the source defined earlier in the YAML file.\n",
@@ -369,16 +369,14 @@
     "\n",
     "This section defines the `simulator` that will be used to perform the simulation. It references the lens, source, and lens light definitions from earlier in the YAML file and sets additional parameters for the simulator."
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
+  "kernelspec": {
+   "display_name": "caustic",
+   "language": "python",
+   "name": "python3"
+  },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
@@ -388,7 +386,8 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.9.18"
   }
  },
  "nbformat": 4,