Merge branch 'LSST-strong-lensing:main' into main

.github/workflows/tests.yml

@@ -16,9 +16,9 @@ jobs:
         python-version: [3.8]
 
     steps:
-      - uses: actions/checkout@v3
+      - 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

.pre-commit-config.yaml

@@ -13,18 +13,18 @@ ci:
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.1.1
+    rev: v0.4.7
     hooks:
       - id: ruff
         exclude: docs/.*
         args: ["--line-length=88"]
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.7.0
+    rev: 1.8.5
     hooks:
       - id: nbqa-ruff
         args: ["--line-length=120"]
   - repo: https://github.com/psf/black
-    rev: 23.10.0
+    rev: 24.4.2
     hooks:
       - id: black
         # It is recommended to specify the latest version of Python
@@ -33,7 +33,7 @@ repos:
         # https://pre-commit.com/#top_level-default_language_version
         language_version: python3
   - repo: https://github.com/psf/black
-    rev: 23.10.0
+    rev: 24.4.2
     hooks:
       - id: black-jupyter
         language_version: python3

CONTRIBUTING.rst

@@ -30,13 +30,14 @@ Finally add the ``slsim-project`` repository as a *remote*. This will allow you
 
 
 Install slsim in development mode
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-To run your own version of slsim and making sure that your own development changes are reflected (as well as switcing branches),
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+To run your own version of slsim and making sure that your own development changes are reflected (as well as switching branches),
 install the slsim package in development mode with
 
 ::
 
   cd slsim
+  pip install -r requirements.txt --user
   python setup.py develop --user
 
 
@@ -163,4 +164,4 @@ All public classes, methods and functions require docstrings. You can build docu
   - Notes
   - References
 
-For more information see the Astropy guide to `Writing Documentation <https://docs.astropy.org/en/stable/development/docguide.html>`_.
+For more information see the Astropy guide to `Writing Documentation <https://docs.astropy.org/en/stable/development/docguide.html>`_.

README.rst

@@ -1,6 +1,6 @@
-============
+==========================================
 SLSim (Strong Lensing Simulation) pipeline
-============
+==========================================
 
 |Read the Docs| |GitHub| |Codecov| |Black| |docformatter| |docstyle|
 

codecov.yml

@@ -1,6 +1,12 @@
+codecov: 
+ token: b297bdac-173f-4244-8986-433e435fee61
 comment:                  # this is a top-level key
   layout: " diff, flags, files"
   behavior: default
   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]
+  require_head: true       # [true :: must have a head report to post]
+ignore:
+  - "slsim/lsst_science_pipeline.py"
+  - "setup.py"
+  - "tests/*"

data/SL-Hammocks/README.md

@@ -0,0 +1,70 @@
+# README.md
+
+## Overview
+
+This README file provides an overview of the CSV file located in the `data/SL-Hammocks` folder. This document aims to help users and contributors understand the structure and the specifics of the data contained within.
+
+## File Description
+
+### `pop_salp_a0001_zl001_to_5_wo_sub.csv`
+
+- **Purpose**: This file provides the deflector population of compound lens model. We set "sky_area= 0.001 [deg^2]", "z_min=0.01", and "z_max=5.0" to generate this population.
+- **Source**: [SL-Hammocks](https://github.com/kta-cosmo/SL-Hammocks) Currently, this is private project
+
+## Column Descriptions
+
+This section details what each column in the CSV file represents. Below is a list of the columns along with a brief description for each.
+
+1. **id**: Original deflector ID before cutting out to create this file (Basically ignore it.)
+
+2. **zl**: redshift of each deflector
+
+3. **m_h**: mass of dark matter halo component in units of Msun/h
+
+4. **m_acc**: mass of subhalo component at the accretion time in units of Msun/h. For host halos, this value becomes 0. Currently, this file does not include subhalos.
+
+5. **e_h**: ellipticily of dark matter halo, which is defined by e=1-b/a, where a,b are major and minor axis of dark matter halo.
+
+6. **p_h**: position angle of dark matter halo in units of degree
+
+7. **con**: concentration parameter of dark matter halo
+
+8. **m_g**: mass of galaxy(stellar) component in units of Msun/h
+
+9. **e_g**: ellipticily of galaxy, which is defined by e=1-b/a, where a,b are major and minor axis of galaxy.
+
+10. **p_g**: position angle of galaxy in units of degree
+
+11. **tb**: the scale radius appreared in Hernquist profile in units of arcsec. This parameter relates to the commonly used galaxy effective (half-mass) radius by t_b = 0.551\*theta_eff.
+
+12. **vel_disp**: the luminosity-weighted averaged value of the line-of-sight
+    velocity dispersion within the galaxy effective radius
+
+## Usage
+
+- **Loading Data**: An example of how to load this CSV file is slsim:
+
+  ```python
+  from astropy.cosmology import FlatLambdaCDM
+  from astropy.units import Quantity
+  from slsim.lens_pop import LensPop
+
+  cosmo = FlatLambdaCDM(H0=70, Om0=0.3)
+  sky_area = Quantity(value=0.001, unit="deg2")
+  kwargs_deflector_cut ={"z_min": 0.01, "z_max": 2.0}
+  kwargs_source_cut = {"band": "g", "band_max": 28, "z_min": 0.1, "z_max": 5.0}
+
+  skypy_config='/your-path-to-slsim/data/SkyPy/lsst-like.yml'
+  slhammocks_config='/your-path-to-slsim/data/SL-Hammocks/pop_salp_a0001_zl001_to_5_wo_sub.csv'
+  gg_lens_pop = LensPop(
+    deflector_type="halo-models",
+    source_type="galaxies",
+    kwargs_deflector_cut=kwargs_deflector_cut,
+    kwargs_source_cut=kwargs_source_cut,
+    kwargs_mass2light=None,
+    skypy_config=skypy_config,
+    slhammocks_config=slhammocks_config,
+    sky_area=sky_area,
+    cosmo=cosmo,
+  )
+  ```