Merge pull request #1 from sibirrer/main

updating main
ajshajib · Jan 4, 2024 · e0bc099 · e0bc099
2 parents f7656e4 + b331dbc
commit e0bc099
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Showing 34 changed files with 1,632 additions and 501 deletions.
diff --git a/.github/workflows/ci_test.yml b/.github/workflows/ci_test.yml
@@ -17,9 +17,9 @@ jobs:
         python-version: [3.8]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -10,7 +10,7 @@ ci:
 
 repos:
   - repo: https://github.com/psf/black
-    rev: 23.11.0
+    rev: 23.12.1
     hooks:
       - id: black
         # It is recommended to specify the latest version of Python
@@ -19,7 +19,7 @@ repos:
         # https://pre-commit.com/#top_level-default_language_version
         language_version: python3
   - repo: https://github.com/psf/black
-    rev: 23.11.0
+    rev: 23.12.1
     hooks:
       - id: black-jupyter
         language_version: python3

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -1,23 +1,35 @@
-# .readthedocs.yml
-# Read the Docs configuration file
+# Read the Docs configuration file for Sphinx projects
 # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
 
 # Required
 version: 2
 
-# Build documentation in the docs/ directory with Sphinx
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+    # You can also specify other tool versions:
+    # nodejs: "20"
+    # rust: "1.70"
+    # golang: "1.20"
+
+# Build documentation in the "docs/" directory with Sphinx
 sphinx:
   configuration: docs/conf.py
-
-# Build documentation with MkDocs
-#mkdocs:
-#  configuration: mkdocs.yml
+  # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
+  # builder: "dirhtml"
+  # Fail on all warnings to avoid broken references
+  # fail_on_warning: true
 
 # Optionally build your docs in additional formats such as PDF and ePub
-formats: all
+# formats:
+#    - pdf
+#    - epub
 
-# Optionally set the version of Python and requirements required to build your docs
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
 python:
-  version: 3.6
-  install:
-    - requirements: requirements.txt
+    install:
+    - requirements: requirements.txt
diff --git a/codecov.yml b/codecov.yml
@@ -4,3 +4,7 @@ comment:                  # this is a top-level key
   require_changes: false  # if true: only post the comment if coverage changes
   require_base: false        # [true :: must have a base report to post]
   require_head: true       # [true :: must have a head report to post]
+ignore:
+  - "setup.py"
+  - "test/*.py"
+  - "test/**/*.py"
diff --git a/hierarc/LensPosterior/base_config.py b/hierarc/LensPosterior/base_config.py
@@ -32,6 +32,7 @@ def __init__(
         num_psf_sampling=100,
         num_kin_sampling=1000,
         multi_observations=False,
+        cosmo_fiducial=None,
     ):
         """
 
@@ -59,6 +60,8 @@ def __init__(
             routine
         :param hernquist_approx: bool, if True, uses the Hernquist approximation for the
             light profile
+        :param cosmo_fiducial: astropy.cosmology instance, if None,
+            uses astropy's default cosmology
         """
         self._z_lens, self._z_source = z_lens, z_source
 
@@ -77,7 +80,7 @@ def __init__(
             z_lens,
             z_source,
             kwargs_model,
-            cosmo_fiducial=None,
+            cosmo_fiducial=cosmo_fiducial,
             lens_model_kinematics_bool=None,
             light_model_kinematics_bool=None,
             kwargs_seeing=kwargs_seeing,

diff --git a/hierarc/LensPosterior/kin_constraints.py b/hierarc/LensPosterior/kin_constraints.py
@@ -35,6 +35,7 @@ def __init__(
         num_psf_sampling=100,
         num_kin_sampling=1000,
         multi_observations=False,
+        cosmo_fiducial=None,
     ):
         """
 
@@ -46,24 +47,36 @@ def __init__(
         :param gamma_error: 1-sigma uncertainty on power-law slope
         :param r_eff: half-light radius of the deflector (arc seconds)
         :param r_eff_error: uncertainty on half-light radius
-        :param sigma_v_measured: numpy array of IFU velocity dispersion of the main deflector in km/s
-        :param sigma_v_error_independent: numpy array of 1-sigma uncertainty in velocity dispersion of the IFU
+        :param sigma_v_measured: numpy array of IFU velocity dispersion of the main
+            deflector in km/s
+        :param sigma_v_error_independent: numpy array of 1-sigma uncertainty in velocity
+            dispersion of the IFU
          observation independent of each other
-        :param sigma_v_error_covariant: covariant error in the measured kinematics shared among all IFU measurements
-        :param sigma_v_error_cov_matrix: error covariance matrix in the sigma_v measurements (km/s)^2
-        :type sigma_v_error_cov_matrix: nxn matrix with n the length of the sigma_v_measured array
-        :param kwargs_aperture: spectroscopic aperture keyword arguments, see lenstronomy.Galkin.aperture for options
-        :param kwargs_seeing: seeing condition of spectroscopic observation, corresponds to kwargs_psf in the GalKin
+        :param sigma_v_error_covariant: covariant error in the measured kinematics
+            shared among all IFU measurements
+        :param sigma_v_error_cov_matrix: error covariance matrix in the sigma_v
+            measurements (km/s)^2
+        :type sigma_v_error_cov_matrix: nxn matrix with n the length of the
+            sigma_v_measured array
+        :param kwargs_aperture: spectroscopic aperture keyword arguments, see
+            lenstronomy.Galkin.aperture for options
+        :param kwargs_seeing: seeing condition of spectroscopic observation, corresponds
+            to kwargs_psf in the GalKin
          module specified in lenstronomy.GalKin.psf
-        :param kwargs_numerics_galkin: numerical settings for the integrated line-of-sight velocity dispersion
-        :param anisotropy_model: type of stellar anisotropy model. See details in MamonLokasAnisotropy() class of
-         lenstronomy.GalKin.anisotropy
+        :param kwargs_numerics_galkin: numerical settings for the integrated
+            line-of-sight velocity dispersion
+        :param anisotropy_model: type of stellar anisotropy model. See details in
+            MamonLokasAnisotropy() class of lenstronomy.GalKin.anisotropy
         :param lens_model_list: keyword argument list of lens model (optional)
         :param kwargs_lens_light: keyword argument list of lens light model (optional)
-        :param kwargs_mge_light: keyword arguments that go into the MGE decomposition routine
-        :param hernquist_approx: bool, if True, uses the Hernquist approximation for the light profile
-        :param multi_observations: bool, if True, interprets kwargs_aperture and kwargs_seeing as lists of multiple
-         observations
+        :param kwargs_mge_light: keyword arguments that go into the MGE decomposition
+            routine
+        :param hernquist_approx: bool, if True, uses the Hernquist approximation for the
+            light profile
+        :param multi_observations: bool, if True, interprets kwargs_aperture and
+            kwargs_seeing as lists of multiple observations
+        :param cosmo_fiducial: astropy.cosmology instance, if None,
+            uses astropy's default
         """
         self._sigma_v_measured = np.array(sigma_v_measured)
         self._sigma_v_error_independent = np.array(sigma_v_error_independent)
@@ -97,6 +110,7 @@ def __init__(
             num_psf_sampling=num_psf_sampling,
             num_kin_sampling=num_kin_sampling,
             multi_observations=multi_observations,
+            cosmo_fiducial=cosmo_fiducial,
         )
 
     def j_kin_draw(self, kwargs_anisotropy, no_error=False):
@@ -165,9 +179,10 @@ def hierarchy_configuration(self, num_sample_model=20):
     def model_marginalization(self, num_sample_model=20):
         """
 
-        :param num_sample_model: number of samples drawn from the lens and light model posterior to compute the
-         dimensionless kinematic component J()
-        :return: J() as array for each measurement prediction, covariance matrix in sqrt(J)
+        :param num_sample_model: number of samples drawn from the lens and light model
+            posterior to compute the dimensionless kinematic component J()
+        :return: J() as array for each measurement prediction, covariance matrix in
+            sqrt(J)
         """
         num_data = len(self._sigma_v_measured)
         j_kin_matrix = np.zeros(