Merge pull request #286 from nkhadka21/test_fix

Fixed some testing functions and bug in Lens class.
LSST-strong-lensing · Nov 22, 2024 · 94bf863 · 94bf863
2 parents 70f6a07 + 4ed9aea
commit 94bf863
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,8 +1,7 @@
 ci:
     autofix_commit_msg: |
-        [pre-commit.ci] auto fixes from pre-commit.com hooks
+        Autofix formatting from pre-commit.com hooks
 
-        for more information, see https://pre-commit.ci
     autofix_prs: true
     autoupdate_branch: ''
     autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
@@ -13,18 +12,18 @@ ci:
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.5.6
+    rev: v0.7.4
     hooks:
       - id: ruff
         exclude: docs/.*
         args: ["--line-length=88"]
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.8.7
+    rev: 1.9.1
     hooks:
       - id: nbqa-ruff
         args: ["--line-length=120"]
   - repo: https://github.com/psf/black
-    rev: 24.8.0
+    rev: 24.10.0
     hooks:
       - id: black
         # It is recommended to specify the latest version of Python
@@ -33,13 +32,20 @@ repos:
         # https://pre-commit.com/#top_level-default_language_version
         language_version: python3
   - repo: https://github.com/psf/black
-    rev: 24.8.0
+    rev: 24.10.0
     hooks:
       - id: black-jupyter
         language_version: python3
-  - repo: https://github.com/PyCQA/docformatter
-    rev: v1.7.5
+  - repo: local
     hooks:
       - id: docformatter
-        additional_dependencies: [tomli]
-        args: [-r, --black, --in-place]
+        name: docformatter
+        description: Formats docstrings to follow PEP 257.
+        entry: python -Im docformatter
+        additional_dependencies:
+          - docformatter == 1.7.5
+        args:
+          - --in-place
+        language: python
+        types:
+          - python
diff --git a/notebooks/Opsim_supernovae_plus_extended_source_tutorial.ipynb b/notebooks/Opsim_supernovae_plus_extended_source_tutorial.ipynb
@@ -135,7 +135,7 @@
     "    deflector_population=lens_galaxies,\n",
     "    source_population=source_galaxies,\n",
     "    cosmo=cosmo,\n",
-    "    sky_area=sky_area\n",
+    "    sky_area=sky_area,\n",
     ")\n",
     "kwargs_lens_cut = {}\n",
     "supernova_lens_class = supernova_lens_pop.select_lens_at_random(**kwargs_lens_cut)\n",

diff --git a/notebooks/lensed_quasar_population_with_variability.ipynb b/notebooks/lensed_quasar_population_with_variability.ipynb
@@ -63,10 +63,7 @@
    "source": [
     "# generate galaxy population using skypy pipeline.\n",
     "galaxy_simulation_pipeline = pipelines.SkyPyPipeline(\n",
-    "    skypy_config=None,\n",
-    "    sky_area=galaxy_sky_area,\n",
-    "    filters=None,\n",
-    "    cosmo=cosmo\n",
+    "    skypy_config=None, sky_area=galaxy_sky_area, filters=None, cosmo=cosmo\n",
     ")"
    ]
   },

diff --git a/notebooks/supernovae_injection_to_opsim_data.ipynb b/notebooks/supernovae_injection_to_opsim_data.ipynb
@@ -10,7 +10,6 @@
     "from astropy.units import Quantity\n",
     "from slsim.lens_pop import LensPop\n",
     "import numpy as np\n",
-    "from astropy.units import Quantity\n",
     "import slsim.Sources as sources\n",
     "import slsim.Deflectors as deflectors\n",
     "import slsim.Pipelines as pipelines\n",
@@ -20,8 +19,7 @@
     "import astropy.coordinates as coord\n",
     "import astropy.units as u\n",
     "from slsim.LsstSciencePipeline import opsim_pipeline\n",
-    "from slsim.LsstSciencePipeline.util_lsst import opsim_variable_lens_injection\n",
-    "from slsim.Plots.plot_functions import create_image_montage_from_image_list"
+    "from slsim.LsstSciencePipeline.util_lsst import opsim_variable_lens_injection"
    ]
   },
   {
@@ -68,7 +66,7 @@
     "kwargs_deflector_cut = {\"band\": \"g\", \"band_max\": 24, \"z_min\": 0.01, \"z_max\": 2.5}\n",
     "kwargs_source_cut = {\"z_min\": 0.1, \"z_max\": 5.0}\n",
     "\n",
-    "time_range = np.linspace(-50, 100, 500)\n"
+    "time_range = np.linspace(-50, 100, 500)"
    ]
   },
   {
@@ -185,7 +183,7 @@
     "    deflector_population=lens_galaxies,\n",
     "    source_population=supernovae_sourece,\n",
     "    sky_area=sky_area_full,\n",
-    "    cosmo=cosmo\n",
+    "    cosmo=cosmo,\n",
     ")"
    ]
   },
@@ -315,7 +313,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#np.random.seed(1)\n",
+    "# np.random.seed(1)\n",
     "N = 10\n",
     "\n",
     "ra_points = coord.Angle(np.random.uniform(low=0, high=360, size=N) * u.degree)\n",
@@ -345,16 +343,16 @@
     }
    ],
    "source": [
-    "# opsim_path is a path for opsim summary data. One need to download baseline_v3.4_10yrs.db \n",
-    "# to run this pipeline. Please download this data from and replace opsim_path with your path: \n",
+    "# opsim_path is a path for opsim summary data. One need to download baseline_v3.4_10yrs.db\n",
+    "# to run this pipeline. Please download this data from and replace opsim_path with your path:\n",
     "# https://epyc.astro.washington.edu/~lynnej/opsim_downloads/fbs_3.4/initial/initial_v3.4_10yrs.db\n",
     "exposure_data = opsim_pipeline.opsim_time_series_images_data(\n",
     "    ra_points,\n",
     "    dec_points,\n",
     "    \"baseline_v3.0_10yrs\",\n",
     "    print_warning=True,\n",
     "    num_pix=63,\n",
-    "    opsim_path=\"/Users/narayankhadka/downloads/baseline_v3.4_10yrs.db\"\n",
+    "    opsim_path=\"/Users/narayankhadka/downloads/baseline_v3.4_10yrs.db\",\n",
     ")"
    ]
   },
@@ -371,7 +369,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#There are multiple time series datasets, so I chose the first one.\n",
+    "# There are multiple time series datasets, so I chose the first one.\n",
     "index = 0\n",
     "bands = [\"i\"]\n",
     "num_pix = 63\n",
@@ -401,8 +399,11 @@
    "source": [
     "## Plot first 10 images. One can plot any number of images\n",
     "plot_montage = create_image_montage_from_image_list(\n",
-    "    num_rows=2, num_cols=5, images=images[\"injected_lens\"][:10], image_center=[pix_coord[0][0], pix_coord[1][0]],\n",
-    "    time=images[\"obs_time\"][:10]\n",
+    "    num_rows=2,\n",
+    "    num_cols=5,\n",
+    "    images=images[\"injected_lens\"][:10],\n",
+    "    image_center=[pix_coord[0][0], pix_coord[1][0]],\n",
+    "    time=images[\"obs_time\"][:10],\n",
     ")"
    ]
   },

diff --git a/notebooks/supernovae_plus_extended_source_tutorial.ipynb b/notebooks/supernovae_plus_extended_source_tutorial.ipynb
@@ -70,7 +70,7 @@
     "kwargs_deflector_cut = {\"band\": \"g\", \"band_max\": 23, \"z_min\": 0.01, \"z_max\": 2.5}\n",
     "kwargs_source_cut = {\"z_min\": 0.1, \"z_max\": 5.0}\n",
     "\n",
-    "# This file can be downloaded from here: https://github.com/LSST-strong-lensing/data_public . \n",
+    "# This file can be downloaded from here: https://github.com/LSST-strong-lensing/data_public .\n",
     "# Please download this file and replace the path with your path.\n",
     "sn_modeldir = \"/Users/narayankhadka/downloads/sncosmo_sn_models/SALT3.NIR_WAVEEXT\""
    ]

diff --git a/slsim/Deflectors/DeflectorTypes/deflector_base.py b/slsim/Deflectors/DeflectorTypes/deflector_base.py
@@ -6,8 +6,8 @@
 
 
 class DeflectorBase(ABC):
-    """Class of a single deflector with quantities only related to the deflector
-    (independent of the source)"""
+    """Class of a single deflector with quantities only related to the
+    deflector (independent of the source)"""
 
     def __init__(self, deflector_dict):
         """
@@ -100,7 +100,8 @@ def mass_ellipticity(self):
 
     @abstractmethod
     def mass_model_lenstronomy(self, lens_cosmo):
-        """Returns lens model instance and parameters in lenstronomy conventions.
+        """Returns lens model instance and parameters in lenstronomy
+        conventions.
 
         :param lens_cosmo: lens cosmology model
         :type lens_cosmo: ~lenstronomy.Cosmo.LensCosmo instance
@@ -110,7 +111,8 @@ def mass_model_lenstronomy(self, lens_cosmo):
 
     @abstractmethod
     def light_model_lenstronomy(self, band=None):
-        """Returns lens model instance and parameters in lenstronomy conventions.
+        """Returns lens model instance and parameters in lenstronomy
+        conventions.
 
         :param band: imaging band
         :type band: str

diff --git a/slsim/Deflectors/DeflectorTypes/epl_sersic.py b/slsim/Deflectors/DeflectorTypes/epl_sersic.py
@@ -38,7 +38,8 @@ def light_ellipticity(self):
         return e1_light, e2_light
 
     def mass_model_lenstronomy(self, lens_cosmo):
-        """Returns lens model instance and parameters in lenstronomy conventions.
+        """Returns lens model instance and parameters in lenstronomy
+        conventions.
 
         :param lens_cosmo: lens cosmology model
         :type lens_cosmo: ~lenstronomy.Cosmo.LensCosmo instance
@@ -73,7 +74,8 @@ def mass_model_lenstronomy(self, lens_cosmo):
         return lens_mass_model_list, kwargs_lens_mass
 
     def light_model_lenstronomy(self, band=None):
-        """Returns lens model instance and parameters in lenstronomy conventions.
+        """Returns lens model instance and parameters in lenstronomy
+        conventions.
 
         :param band: imaging band
         :type band: str

diff --git a/slsim/Deflectors/DeflectorTypes/nfw_cluster.py b/slsim/Deflectors/DeflectorTypes/nfw_cluster.py
@@ -6,8 +6,8 @@
 
 
 class NFWCluster(DeflectorBase):
-    """Class of a NFW halo lens model with subhalos. Each subhalo is a EPLSersic
-    instance with its own mass and light.
+    """Class of a NFW halo lens model with subhalos. Each subhalo is a
+    EPLSersic instance with its own mass and light.
 
     required quantities in dictionary:
     - 'halo_mass': halo mass in physical M_sol
@@ -29,8 +29,8 @@ def __init__(self, deflector_dict):
         super(NFWCluster, self).__init__(deflector_dict)
 
     def velocity_dispersion(self, cosmo=None):
-        """Velocity dispersion of deflector. Simplified assumptions on anisotropy and
-        averaged over the characteristic radius.
+        """Velocity dispersion of deflector. Simplified assumptions on
+        anisotropy and averaged over the characteristic radius.
 
         :param cosmo: cosmology
         :type cosmo: ~astropy.cosmology class
@@ -40,7 +40,8 @@ def velocity_dispersion(self, cosmo=None):
         return vel_disp_nfw(m_halo, c_halo, cosmo, self.redshift)
 
     def mass_model_lenstronomy(self, lens_cosmo):
-        """Returns lens model instance and parameters in lenstronomy conventions.
+        """Returns lens model instance and parameters in lenstronomy
+        conventions.
 
         :param lens_cosmo: lens cosmology model
         :type lens_cosmo: ~lenstronomy.Cosmo.LensCosmo instance
@@ -58,8 +59,8 @@ def mass_model_lenstronomy(self, lens_cosmo):
         return lens_mass_model_list, kwargs_lens_mass
 
     def _halo_mass_model_lenstronomy(self, lens_cosmo):
-        """Returns lens model instance and parameters in lenstronomy conventions for the
-        main halo.
+        """Returns lens model instance and parameters in lenstronomy
+        conventions for the main halo.
 
         :param lens_cosmo: lens cosmology model
         :type lens_cosmo: ~lenstronomy.Cosmo.LensCosmo instance
@@ -86,7 +87,8 @@ def _halo_mass_model_lenstronomy(self, lens_cosmo):
         return lens_mass_model_list, kwargs_lens_mass
 
     def light_model_lenstronomy(self, band=None):
-        """Returns lens model instance and parameters in lenstronomy conventions.
+        """Returns lens model instance and parameters in lenstronomy
+        conventions.
 
         :param band: imaging band
         :type band: str

diff --git a/slsim/Deflectors/DeflectorTypes/nfw_hernquist.py b/slsim/Deflectors/DeflectorTypes/nfw_hernquist.py
@@ -20,8 +20,8 @@ class NFWHernquist(DeflectorBase):
     """
 
     def velocity_dispersion(self, cosmo=None):
-        """Velocity dispersion of deflector. Simplified assumptions on anisotropy and
-        averaged over the half-light radius.
+        """Velocity dispersion of deflector. Simplified assumptions on
+        anisotropy and averaged over the half-light radius.
 
         :param cosmo: cosmology
         :type cosmo: ~astropy.cosmology class
@@ -55,7 +55,8 @@ def velocity_dispersion(self, cosmo=None):
             return self._deflector_dict["vel_disp"]
 
     def mass_model_lenstronomy(self, lens_cosmo):
-        """Returns lens model instance and parameters in lenstronomy conventions.
+        """Returns lens model instance and parameters in lenstronomy
+        conventions.
 
         :param lens_cosmo: lens cosmology model
         :type lens_cosmo: ~lenstronomy.Cosmo.LensCosmo instance
@@ -100,7 +101,8 @@ def mass_model_lenstronomy(self, lens_cosmo):
         return lens_mass_model_list, kwargs_lens_mass
 
     def light_model_lenstronomy(self, band=None):
-        """Returns lens model instance and parameters in lenstronomy conventions.
+        """Returns lens model instance and parameters in lenstronomy
+        conventions.
 
         :param band: imaging band
         :type band: str

diff --git a/slsim/Deflectors/all_lens_galaxies.py b/slsim/Deflectors/all_lens_galaxies.py
@@ -40,8 +40,8 @@ def __init__(
         :param sky_area: Sky area over which galaxies are sampled. Must be in units of
             solid angle.
         :param gamma_pl: power law slope in EPL profile.
-        :type gamma_pl: A float or a dictionary with given mean and standard deviation 
-         of a density slope for gaussian distribution or minimum and maximum values of 
+        :type gamma_pl: A float or a dictionary with given mean and standard deviation
+         of a density slope for gaussian distribution or minimum and maximum values of
          gamma for uniform distribution. eg: gamma_pl=2.1, gamma_pl={"mean": a, "std_dev": b},
          gamma_pl={"gamma_min": c, "gamma_max": d}
         :param catalog_type: type of the catalog. If user is using deflector catalog
@@ -72,7 +72,7 @@ def __init__(
             kwargs_cut=kwargs_cut,
             cosmo=cosmo,
             sky_area=sky_area,
-            gamma_pl=gamma_pl
+            gamma_pl=gamma_pl,
         )
 
         n = len(galaxy_list)
@@ -126,8 +126,9 @@ def draw_deflector(self):
             deflector["e2_mass"] = e2_mass
         if deflector["n_sersic"] == -1:
             deflector["n_sersic"] = 4  # TODO make a better estimate with scatter
-        deflector_class = Deflector(deflector_type=self.deflector_profile,
-                                     deflector_dict=deflector)
+        deflector_class = Deflector(
+            deflector_type=self.deflector_profile, deflector_dict=deflector
+        )
         return deflector_class
 
 

diff --git a/slsim/Deflectors/cluster_deflectors.py b/slsim/Deflectors/cluster_deflectors.py
@@ -20,11 +20,13 @@
 
 
 class ClusterDeflectors(DeflectorsBase):
-    """Class describing cluster lens model with a NFW profile for the dark matter halo
-    and EPL profile for the subhalos (cluster members). It makes use of a group/cluster
-    catalog and a group/cluster member catalog (e.g. redMaPPer).
+    """Class describing cluster lens model with a NFW profile for the dark
+    matter halo and EPL profile for the subhalos (cluster members). It makes
+    use of a group/cluster catalog and a group/cluster member catalog (e.g.
+    redMaPPer).
 
-    This class is called by setting deflector_type == "cluster-catalog" in LensPop.
+    This class is called by setting deflector_type == "cluster-catalog"
+    in LensPop.
     """
 
     def __init__(
@@ -121,8 +123,9 @@ def draw_deflector(self):
         deflector = self.draw_cluster(index)
         members = self.draw_members(deflector["cluster_id"], **self.kwargs_draw_members)
         deflector["subhalos"] = members
-        deflector_class = Deflector(deflector_type=self.deflector_profile,
-                                     deflector_dict=deflector)
+        deflector_class = Deflector(
+            deflector_type=self.deflector_profile, deflector_dict=deflector
+        )
         return deflector_class
 
     def draw_cluster(self, index):
@@ -211,10 +214,11 @@ def assign_similar_galaxy(
         bands=("g", "r", "i", "z", "Y"),
         max_gals=10000,
     ):
-        """Assigns a similar galaxy to each member of a group/cluster member catalog by
-        comparing their magnitudes and redshifts.
+        """Assigns a similar galaxy to each member of a group/cluster member
+        catalog by comparing their magnitudes and redshifts.
 
-        :param members_list: astropy table with columns 'mag_{band}', 'z'
+        :param members_list: astropy table with columns 'mag_{band}',
+            'z'
         :type members_list: astropy.table.Table
         :param galaxy_list: astropy table with columns 'mag_{band}', 'z'
         :type galaxy_list: astropy.table.Table
@@ -323,7 +327,8 @@ def preprocess_members(self, cluster_list, members_list, galaxy_list):
         return members_list
 
     def set_cosmo(self):
-        """Set the cosmology in colossus to match the astropy.cosmology instance."""
+        """Set the cosmology in colossus to match the astropy.cosmology
+        instance."""
         params = dict(
             flat=(self.cosmo.Ok0 == 0.0),
             H0=self.cosmo.H0.value,