refactor: Setup package structure to follow the Scientific Python Library Development Guide

.devcontainer/environment.yml

@@ -9,6 +9,7 @@ dependencies:
   - pandas
   - scipy
   - h5py
+  - nox
   - sphinx
   - myst-parser
   - jupyter-book

.github/workflows/cd.yml

@@ -69,15 +69,15 @@ jobs:
 
           echo "=== Testing wheel file ==="
           # Install wheel to get dependencies and check import
-          python -m pip install --extra-index-url https://test.pypi.org/simple --upgrade --pre caustic
-          python -c "import caustic; print(caustics.__version__)"
+          python -m pip install --extra-index-url https://test.pypi.org/simple --upgrade --pre caustics
+          python -c "import caustics; print(caustics.__version__)"
           echo "=== Done testing wheel file ==="
 
           echo "=== Testing source tar file ==="
           # Install tar gz and check import
-          python -m pip uninstall --yes caustic
-          python -m pip install --extra-index-url https://test.pypi.org/simple --upgrade --pre --no-binary=:all: caustic
-          python -c "import caustic; print(caustics.__version__)"
+          python -m pip uninstall --yes caustics
+          python -m pip install --extra-index-url https://test.pypi.org/simple --upgrade --pre --no-binary=:all: caustics
+          python -c "import caustics; print(caustics.__version__)"
           echo "=== Done testing source tar file ==="
 
   publish:

README.md

@@ -8,7 +8,7 @@
 [![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/caustic)](https://app.codecov.io/gh/Ciela-Institute/caustic)
+[![coverage](https://img.shields.io/codecov/c/github/Ciela-Institute/caustics)](https://app.codecov.io/gh/Ciela-Institute/caustics)
 
 # caustics
 
@@ -26,14 +26,14 @@ pip install caustics
 
 ## Documentation
 
-Please see our [documentation page](Ciela-Institute.github.io/caustics/) for
+Please see our [documentation page](https://caustics.readthedocs.io/en/latest/) for
 more detailed information.
 
 ## Contribution
 
 We welcome contributions from collaborators and researchers interested in our
 work. If you have improvements, suggestions, or new findings to share, please
-submit a pull request. Your contributions help advance our research and analysis
+submit an issue or pull request. Your contributions help advance our research and analysis
 efforts.
 
 To get started with your development (or fork), click the "Open with GitHub

docs/source/conf.py

@@ -12,7 +12,7 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
-
+from caustics import __version__
 # sys.path.insert(0, os.path.abspath('../src'))
 
 
@@ -23,9 +23,9 @@
 author = "Ciela Institute"
 
 # The short X.Y version
-version = "0.5"
+version = __version__
 # The full version, including alpha/beta/rc tags
-release = "v0.5.0"
+release = version
 
 
 # -- General configuration ---------------------------------------------------
@@ -158,7 +158,7 @@
         "caustics Documentation",
         author,
         "caustics",
-        "One line description of project.",
+        "The gravitational lensing pipeline of the future.",
         "Miscellaneous",
     ),
 ]

noxfile.py

@@ -36,7 +36,7 @@ def tests(session: nox.Session) -> None:
     """
     Run the unit and regular tests. Use --cov to activate coverage.
     """
-    session.install(".[test]")
+    session.install(".[dev]")
     session.run("pytest", *session.posargs)
 
 

src/caustics/lenses/pixelated_convergence.py

@@ -287,7 +287,7 @@ def _deflection_angle_conv2d(
         # Use convergence_map as kernel since the kernel is twice as large. Flip since
         # we actually want the cross-correlation.
 
-        2 * self.n_pix
+        pad = 2 * self.n_pix
         convergence_map_flipped = convergence_map.flip((-1, -2))[
             None, None
         ]  # F.pad(, ((pad - self.n_pix)//2, (pad - self.n_pix)//2, (pad - self.n_pix)//2, (pad - self.n_pix)//2), mode = self.padding_mode)

tests/test_parametrized.py

@@ -123,12 +123,12 @@ def test_parametrized_name_setter_bad_names():
     # Make sure bad names are catched by our added method. Bad names are name which cannot be used as class attributes.
     good_names = ["variable", "_variable", "var_iable2"]
     for name in good_names:
-        Sersic(name=name)
+        module = Sersic(name=name)
     bad_names = ["for", "2variable", "variable!", "var-iable", "var iable", "def"]
     for name in bad_names:
         print(name)
         with pytest.raises(NameError):
-            Sersic(name=name)
+            module = Sersic(name=name)
 
 
 def test_parametrized_name_collision():