Merge pull request #99 from Ciela-Institute/dev

Dev

.github/workflows/coverage.yaml

@@ -57,4 +57,4 @@ jobs:
       uses: codecov/codecov-action@v3
       with:
         files: ${{ github.workspace }}/coverage.xml
-        fail_ci_if_error: true
+        fail_ci_if_error: false

README.md

@@ -1,4 +1,5 @@
 [![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
@@ -28,6 +29,9 @@ pip install -e ".[dev]"
 ```
 This creates an editable install and installs the dev dependencies.
 
-Please use `isort` and `black` to format your code. Open up issues for bugs/missing
-features. Use pull requests for additions to the code. Write tests that can be run
-by [`pytest`](https://docs.pytest.org/).
+Some guidelines:
+- Please use `isort` and `black` to format your code.
+- Use `CamelCase` for class names and `snake_case` for variable and method names.
+- Open up issues for bugs/missing features.
+- Use pull requests for additions to the code.
+- Write tests that can be run by [`pytest`](https://docs.pytest.org/).

caustic/parametrized.py

@@ -6,6 +6,7 @@
 
 import torch
 import re
+import keyword
 from torch import Tensor
 
 from .packed import Packed
@@ -14,6 +15,13 @@
 
 __all__ = ("Parametrized","unpack")
 
+
+def check_valid_name(name):
+    if keyword.iskeyword(name) or not bool(re.match("^[a-zA-Z_][a-zA-Z0-9_]*$", name)):
+        raise NameError(f"The string {name} contains illegal characters (like space or '-'). "\
+                        "Please use snake case or another valid python variable naming style.")
+
+
 class Parametrized:
     """
     Represents a class with Param and Parametrized attributes, typically used to construct parts of a simulator
@@ -40,6 +48,7 @@ class Parametrized:
     def __init__(self, name: str = None):
         if name is None:
             name = self._default_name()
+        check_valid_name(name)
         if not isinstance(name, str):
             raise ValueError(f"name must be a string (received {name})")
         self._name = name
@@ -87,6 +96,7 @@ def name(self) -> str:
 
     @name.setter
     def name(self, new_name: str):
+        check_valid_name(new_name)
         old_name = self.name
         for parent in self._parents.values():
             del parent._childs[old_name]

test/test_cosmology.py

@@ -5,7 +5,9 @@
 from astropy.cosmology import Cosmology as Cosmology_AP
 from astropy.cosmology import FlatLambdaCDM as AstropyFlatLambdaCDM
 
-from caustic.cosmology import Cosmology, FlatLambdaCDM as CausticFlatLambdaCDM, Om0_default, h0_default
+from caustic.cosmology import Cosmology
+from caustic.cosmology import FlatLambdaCDM as CausticFlatLambdaCDM
+from caustic.cosmology import Om0_default, h0_default
 
 
 def get_cosmologies() -> List[Tuple[Cosmology, Cosmology_AP]]:

test/test_jacobian_lens_equation.py

@@ -41,7 +41,7 @@ def test_multiplane_jacobian():
     x = torch.tensor([p for _xs in xs for p in _xs], dtype=torch.float32)
 
     lens = Multiplane(
-        name="multiplane", cosmology=cosmology, lenses=[SIE(name=f"sie-{i}", cosmology=cosmology) for i in range(len(xs))]
+        name="multiplane", cosmology=cosmology, lenses=[SIE(name=f"sie_{i}", cosmology=cosmology) for i in range(len(xs))]
     )
     thx, thy = get_meshgrid(0.1, 10, 10)
 
@@ -66,7 +66,7 @@ def test_multiplane_jacobian_autograd_vs_finitediff():
     x = torch.tensor([p for _xs in xs for p in _xs], dtype=torch.float32)
 
     lens = Multiplane(
-        name="multiplane", cosmology=cosmology, lenses=[SIE(name=f"sie-{i}", cosmology=cosmology) for i in range(len(xs))]
+        name="multiplane", cosmology=cosmology, lenses=[SIE(name=f"sie_{i}", cosmology=cosmology) for i in range(len(xs))]
     )
     thx, thy = get_meshgrid(0.01, 10, 10)
 
@@ -96,7 +96,7 @@ def test_multiplane_effective_convergence():
     x = torch.tensor([p for _xs in xs for p in _xs], dtype=torch.float32)
 
     lens = Multiplane(
-        name="multiplane", cosmology=cosmology, lenses=[SIE(name=f"sie-{i}", cosmology=cosmology) for i in range(len(xs))]
+        name="multiplane", cosmology=cosmology, lenses=[SIE(name=f"sie_{i}", cosmology=cosmology) for i in range(len(xs))]
     )
     thx, thy = get_meshgrid(0.1, 10, 10)
 

test/test_multiplane.py

@@ -30,7 +30,7 @@ def test():
     x = torch.tensor([p for _xs in xs for p in _xs], dtype=torch.float32)
 
     lens = Multiplane(
-        name="multiplane", cosmology=cosmology, lenses=[SIE(name=f"sie-{i}", cosmology=cosmology) for i in range(len(xs))]
+        name="multiplane", cosmology=cosmology, lenses=[SIE(name=f"sie_{i}", cosmology=cosmology) for i in range(len(xs))]
     )
     #lens.effective_reduced_deflection_angle = lens.raytrace
 

test/test_parametrized.py

@@ -1,5 +1,6 @@
 import torch
 from torch import vmap
+import pytest
 import numpy as np
 from caustic.sims import Simulator
 from caustic.parameter import Parameter
@@ -103,11 +104,22 @@ def __init__(self):
     assert sim.name == "Test"
 
     # Check that DAG in SIM is being update updated
-    sim.lens.name = "Test Lens"
-    assert sim.lens.name == "Test Lens"
-    assert "Test Lens" in sim.params.dynamic.keys()
-    assert "Test Lens" in sim.cosmo._parents.keys()
-
+    sim.lens.name = "test_lens"
+    assert sim.lens.name == "test_lens"
+    assert "test_lens" in sim.params.dynamic.keys()
+    assert "test_lens" in sim.cosmo._parents.keys()
+
+
+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:
+        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):
+            module = Sersic(name=name)
 
 def test_parametrized_name_collision():
     # Case 1: Name collision in children of simulator

test/utils.py

@@ -2,6 +2,7 @@
 
 import torch
 import numpy as np
+from astropy.cosmology import FlatLambdaCDM as FlatLambdaCDM_AP
 from lenstronomy.Data.pixel_grid import PixelGrid
 from lenstronomy.LensModel.lens_model import LensModel
 
@@ -121,6 +122,14 @@ def forward(self, params):
     return Sim(), (cosmo_params, lens_params, [kappa], [source])
 
 
+def get_default_cosmologies():
+    cosmology = FlatLambdaCDM("cosmo")
+    cosmology_ap = FlatLambdaCDM_AP(
+        100 * cosmology.h0.value, cosmology.Om0.value, Tcmb0=0
+    )
+    return cosmology, cosmology_ap
+
+
 def setup_grids(res=0.05, n_pix=100):
     # Caustic setup
     thx, thy = get_meshgrid(res, n_pix, n_pix)