Merge pull request #240 from deepskies/dev

final pre-JOSS merge including docs

deepszsim/io_params.py

@@ -82,7 +82,7 @@ def update_val(self, attr, new_val):
             print("not a valid attribute")
 
 
-    def write_params_yaml_new()
+    def write_params_yaml_new():
         """
         write updated yaml file to disk
         incorporate run id
@@ -92,7 +92,7 @@ def write_params_yaml_new()
             yaml_file.write( dump )
 
 
-     def _generate_run_id(random_digits=6):
+    def _generate_run_id(random_digits=6):
         '''
         '''
 

deepszsim/simclusters.py

@@ -9,48 +9,50 @@
 from datetime import datetime as dt
 
 class simulate_clusters:
+    """
+    class for simulating a distribution of clusters
+    
+    Parameters
+    ----------
+    M200: float or array-like of float
+        the mass contained within R200 in solar masses (same length as z_dist)
+    redshift_z: float or array-like of float
+        the redshift of the cluster (unitless) (same length as M200_dist)
+    num_halos: None or int
+        number of halos to simulate if none supplied
+    halo_params_dict: None or dict
+        parameters from which to sample halos if `num_halos` specified,
+        must contain `zmin`, `zmax`, `m200min_SM`, `m200max_SM`
+    R200_Mpc: None or float or np.ndarray(float)
+        if None, will calculate the R200 values corresponding to a given set of
+        M200 and redshift_z values for the specified cosmology
+    profile: str
+        Name of profile, currently only supports "Battaglia2012"
+    image_size_pixels: None or int
+        image size in pixels (should be odd; if even, will return images whose
+        sides are `image_size_pixels+1` in length)
+    image_size_arcmin: None or float
+        image size in arcmin
+    pixel_size_arcmin: None or float
+        pixel size in arcmin
+    alpha: float
+        fixed to equal 1.0 in Battaglia 2012
+    gamma: float
+        fixed to equal -0.3 in Battaglia 2012
+    load_vars_yaml: None or str
+        path to yaml file with params; if `None`, must explicitly include image specifications
+    seed: None or int
+        random seed value to sample with
+    tqverb: bool
+        whether or not to display tqdm progress bar while making T maps
+    """
     def __init__(self, M200 = None, redshift_z = None, num_halos = None, halo_params_dict = None,
                  R200_Mpc = None, profile = "Battaglia2012",
                  image_size_pixels = None, image_size_arcmin = None, pixel_size_arcmin = None,
                  alpha = 1.0, gamma = -0.3,
                  load_vars_yaml = os.path.join(os.path.dirname(__file__), 'Settings', 'config_simACTDR5.yaml'),
                  seed = None, tqverb = False
                  ):
-        """
-        Parameters
-        ----------
-        M200: float or array-like of float
-            the mass contained within R200 in solar masses (same length as z_dist)
-        redshift_z: float or array-like of float
-            the redshift of the cluster (unitless) (same length as M200_dist)
-        num_halos: None or int
-            number of halos to simulate if none supplied
-        halo_params_dict: None or dict
-            parameters from which to sample halos if `num_halos` specified,
-            must contain `zmin`, `zmax`, `m200min_SM`, `m200max_SM`
-        R200_Mpc: None or float or np.ndarray(float)
-            if None, will calculate the R200 values corresponding to a given set of
-            M200 and redshift_z values for the specified cosmology
-        profile: str
-            Name of profile, currently only supports "Battaglia2012"
-        image_size_pixels: None or int
-            image size in pixels (should be odd; if even, will return images whose
-            sides are `image_size_pixels+1` in length)
-        image_size_arcmin: None or float
-            image size in arcmin
-        pixel_size_arcmin: None or float
-            pixel size in arcmin
-        alpha: float
-            fixed to equal 1.0 in Battaglia 2012
-        gamma: float
-            fixed to equal -0.3 in Battaglia 2012
-        load_vars_yaml: None or str
-            path to yaml file with params; if `None`, must explicitly include image specifications
-        seed: None or int
-            random seed value to sample with
-        tqverb: bool
-            whether or not to display tqdm progress bar while making T maps
-        """
 
         if (M200 is not None) and (redshift_z is not None):
             self.M200, self.redshift_z = M200, redshift_z

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/requirements.txt

@@ -0,0 +1,11 @@
+sphinx==7.1.2
+sphinx-rtd-theme==1.3.0rc1
+numpy
+camb
+h5py
+astropy
+colossus
+tqdm
+pixell
+pandas
+scipy

docs/source/api.rst

@@ -0,0 +1,8 @@
+API
+===
+
+.. autosummary::
+  :toctree::
+  :maxdepth: 2
+
+  deepszsim

docs/source/conf.py

@@ -0,0 +1,39 @@
+# Configuration file for the Sphinx documentation builder.
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../../'))
+
+# -- Project information
+
+project = 'DeepSZSim'
+copyright = '2024, DeepSkies'
+author = 'DeepSkies'
+
+release = '0.1'
+version = '0.1.0'
+
+# -- General configuration
+
+extensions = [
+    'sphinx.ext.duration',
+    'sphinx.ext.doctest',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.intersphinx',
+    # 'autoapi.extension',
+]
+
+intersphinx_mapping = {
+    'python': ('https://docs.python.org/3/', None),
+    'sphinx': ('https://www.sphinx-doc.org/en/master/', None),
+}
+intersphinx_disabled_domains = ['std']
+
+templates_path = ['_templates']
+
+# -- Options for HTML output
+
+html_theme = 'sphinx_rtd_theme'
+
+# -- Options for EPUB output
+epub_show_urls = 'footnote'

docs/source/deepszsim.rst

@@ -0,0 +1,106 @@
+deepszsim package
+=================
+
+Documentation for `DeepSZSim <https://www.github.com/DeepSkies/DeepSZSim/>`_.
+
+To create a simulation of two SZ clusters as quickly as possible, run
+``tc = deepszsim.simulate_clusters(num_halos=2).get_T_maps()``, which will return a dictionary with two entries, accessed by ``tc.clusters``. Each of these entries includes a ``params`` subdirectory and a ``maps`` subdirectory.
+
+Submodules
+----------
+
+deepszsim.dm\_halo\_dist module
+-------------------------------
+
+.. automodule:: deepszsim.dm_halo_dist
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+deepszsim.filters module
+------------------------
+
+.. automodule:: deepszsim.filters
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+deepszsim.io\_params module
+---------------------------
+
+.. automodule:: deepszsim.io_params
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+deepszsim.load\_vars module
+---------------------------
+
+.. automodule:: deepszsim.load_vars
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+deepszsim.make\_sz\_cluster module
+----------------------------------
+
+.. automodule:: deepszsim.make_sz_cluster
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+deepszsim.noise module
+----------------------
+
+.. automodule:: deepszsim.noise
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+deepszsim.read\_yaml module
+---------------------------
+
+.. automodule:: deepszsim.read_yaml
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+deepszsim.simclusters module
+----------------------------
+
+.. automodule:: deepszsim.simclusters
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+deepszsim.simtools module
+-------------------------
+
+.. automodule:: deepszsim.simtools
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+deepszsim.utils module
+----------------------
+
+.. automodule:: deepszsim.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+deepszsim.visualization module
+------------------------------
+
+.. automodule:: deepszsim.visualization
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: deepszsim
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/index.rst

@@ -0,0 +1,12 @@
+Welcome to DeepSZSim's documentation!
+=====================================
+
+**DeepSZSim** offers fast simulation of clusters observed via the Sunyaev-Zel'dovich effect in the CMB.
+
+Check out the `github <https://www.github.com/DeepSkies/DeepSZSim/>`_ for installation and usage examples.
+
+.. toctree::
+   :maxdepth: 3
+   :caption: Contents:
+
+   deepszsim

docs/source/modules.rst

@@ -0,0 +1,7 @@
+deepszsim
+=========
+
+.. toctree::
+   :maxdepth: 3
+
+   deepszsim

pyproject.toml

@@ -4,15 +4,15 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "deepszsim"
-version = "0.1.0"
+version = "0.1.1"
 description = "code for fast simulations of galaxy clusters"
 authors = [{name = "Eve Vavagiakis", email = "[email protected]"}]
 license = {text="LICENSE.txt"}
 requires-python = ">= 3.9, <3.12"
 dependencies = [
   "camb >= 1.4.0",
   "h5py >= 3.8.0",
-  "numpy >= 1.24.3",
+  "numpy >= 1.24.3, <2",
   "astropy >= 6.0",
   "colossus >= 1.3.0",
   "tqdm >= 4.66.0",
@@ -23,5 +23,9 @@ dependencies = [
 pytest = "^7.3.1"
 pytest-cov = "^4.0.0"
 
-[tool.setuptools.packages.find]
-namespaces = false
+[tool.setuptools]
+packages = ["deepszsim"]
+include-package-data = true
+
+[tool.setuptools.package-data]
+"deepszsim" = ["Settings/*.yaml"]

readthedocs.yaml

@@ -0,0 +1,13 @@
+version: "2"
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.11"
+
+python:
+  install:
+    - requirements: docs/requirements.txt
+
+sphinx:
+  configuration: docs/source/conf.py