flipcosmo 1.0.0__tar.gz → 1.2.1__tar.gz

flipcosmo-1.2.1/PKG-INFO

@@ -0,0 +1,78 @@
+Metadata-Version: 2.4
+Name: flipcosmo
+Version: 1.2.1
+Summary:  Field Level Inference Package
+Author-email: Corentin Ravoux <corentin.ravoux.research@gmail.com>, Bastien Carreres <bastien.carreres@duke.edu>
+License-Expression: MIT
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pandas
+Requires-Dist: numpy
+Requires-Dist: scipy>=1.12
+Requires-Dist: matplotlib
+Requires-Dist: importlib-metadata
+Requires-Dist: emcee
+Requires-Dist: iminuit
+Requires-Dist: astropy
+Requires-Dist: mpmath
+Provides-Extra: docs
+Requires-Dist: markdown; extra == "docs"
+Requires-Dist: sphinx>=5.2.3; extra == "docs"
+Requires-Dist: sphinx-markdown-tables>=0.0.15; extra == "docs"
+Requires-Dist: numpydoc; extra == "docs"
+Requires-Dist: sphinx_book_theme; extra == "docs"
+Requires-Dist: myst-parser; extra == "docs"
+Requires-Dist: sphinx-copybutton; extra == "docs"
+Requires-Dist: sphinx-design; extra == "docs"
+Requires-Dist: sphinx-inline-tabs; extra == "docs"
+Requires-Dist: sphinx-tabs; extra == "docs"
+Requires-Dist: sphinx-autoapi; extra == "docs"
+Dynamic: license-file
+
+<img src="docs/_static/flip_logo.webp" width=350>
+
+# flip: Field Level Inference Package
+
+flip is a Python package that uses the maximum likelihood method to fit the growth rate based on the velocity and density fields. The first part of the software is the computation of a covariance matrix from a model power spectrum and the considered coordinates. This part is generalized to work for any linear power spectrum models, both for velocities, densities, and cross-terms, and it is optimized with Hankel transform for any model. In the second part, the covariance is used to create a likelihood by multiplying it by velocities or densities. Finally, this package includes some integrated fitters such as Minuit and MCMC (with emcee) to fit the growth rate of structures.
+
+
+[![Documentation Status](https://readthedocs.org/projects/flip/badge/?version=latest)](https://flip.readthedocs.io/en/latest/?badge=latest)
+
+## Quick install
+```bash
+git clone https://github.com/corentinravoux/flip.git
+cd flip
+pip install .
+```
+For now, the package requires you to install manually cosmoprimo: pip install git+https://github.com/cosmodesi/cosmoprimo
+
+
+## Required packages
+
+Mandatory: numpy, scipy, matplotlib, [cosmoprimo](https://github.com/adematti/cosmoprimo), iminuit, emcee, sympy
+
+Optional: classy, pyccl, pypower, GPy, tensorflow 
+
+## Examples
+
+For an example with velocity fit check out: <a target="_blank" href="https://colab.research.google.com/github/corentinravoux/flip/blob/main/notebook/fit_velocity.ipynb">
+  <img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/>
+</a>
+
+For density only: <a target="_blank" href="https://colab.research.google.com/github/corentinravoux/flip/blob/main/notebook/fit_density.ipynb">
+  <img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/>
+</a>
+
+For a joint fit: <a target="_blank" href="https://colab.research.google.com/github/corentinravoux/flip/blob/main/notebook/fit_joint.ipynb">
+  <img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/>
+</a>
+
+## Need help?
+Documentation available on [ReadTheDoc](https://flip.readthedocs.io/) 
+
+## How to cite
+
+The full description of the core concepts of this package is given [here](https://arxiv.org/abs/2501.16852).
+This package was started on the previous work of [@bastiencarreres](https://github.com/bastiencarreres), detail in [this article](https://arxiv.org/abs/2303.01198).
+Please cite both paper when using the package.

flipcosmo-1.2.1/docs/conf.py

@@ -0,0 +1,154 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+import sys
+import os
+import numpy
+sys.path.insert(0, os.path.abspath('..'))
+import flip 
+
+project = 'flip'
+copyright = '2023, C. Ravoux, B. Carreres'
+author = 'C. Ravoux, B. Carreres'
+
+# The full version, including alpha/beta/rc tags
+release = flip.__version__
+
+intersphinx_mapping = {
+    'python': ('https://docs.python.org/3/', None),
+    'numpy': ('https://docs.scipy.org/doc/numpy/', None),
+    'scipy': ('https://docs.scipy.org/doc/scipy/reference/', None),
+    'astropy': ('http://docs.astropy.org/en/stable/', None),
+    'sncosmo': ('https://sncosmo.readthedocs.io/en/stable/', None),
+    'pandas': ('https://pandas.pydata.org/docs/', None)}
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+
+extensions = ['myst_parser', 'sphinx.ext.napoleon', 'sphinx_markdown_tables', 'sphinx.ext.autosectionlabel',
+              'sphinx.ext.linkcode', 'sphinx.ext.intersphinx', 'sphinx.ext.autodoc', 'sphinx.ext.autosummary']
+extensions.append('autoapi.extension')
+
+# Auto-API config
+autoapi_dirs = ['../flip', '../flip/covariance']
+
+def skip_util_classes(app, what, name, obj, skip, options):
+    if name == "__init__":
+       skip = False
+    return skip
+
+def setup(sphinx):
+   sphinx.connect("autoapi-skip-member", skip_util_classes)
+   
+   
+
+napoleon_google_docstring = True
+myst_enable_extensions = ["dollarmath"]
+myst_dmath_double_inline = True
+
+
+autosectionlabel_prefix_document = True
+# Add any paths that contain templates here, relative to this directory.
+autosummary_generate = True
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', '_templates']
+
+source_suffix = {
+    '.rst': 'restructuredtext',
+    '.txt': 'markdown',
+    '.md': 'markdown',
+}
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_book_theme"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+html_logo = "_static/flip_logo.webp"
+html_title = "FLIP"
+html_theme_options = {
+    "icon_links": [
+        {
+            # Label for this link
+            "name": "GitHub",
+            # URL where the link will redirect
+            "url": "https://github.com/corentinravoux/flip",  # required
+            # Icon class (if "type": "fontawesome"), or path to local image (if "type": "local")
+            "icon": "fa-brands fa-github",
+            # The type of image to be used (see below for details)
+            "type": "fontawesome",
+        }
+    ]
+}
+
+import inspect
+from os.path import relpath
+
+
+# Copied on sncosmo documentation
+def linkcode_resolve(domain, info):
+    """Determine the URL corresponding to Python object."""
+    if domain != 'py':
+        return None
+
+    modname = info['module']
+    fullname = info['fullname']
+
+    submod = sys.modules.get(modname)
+    if submod is None:
+        return None
+
+    obj = submod
+    for part in fullname.split('.'):
+        try:
+            obj = getattr(obj, part)
+        except:
+            return None
+
+    try:
+        fn = inspect.getsourcefile(obj)
+    except:
+        fn = None
+    if not fn:
+        return None
+
+    try:
+        source, lineno = inspect.findsource(obj)
+    except:
+        lineno = None
+
+    if lineno:
+        linespec = "#L%d" % (lineno + 1)
+    else:
+        linespec = ""
+
+    fn = relpath(fn, start=flip.__flip_dir_path__)
+    
+    return "https://github.com/corentinravoux/flip/tree/main/flip/%s%s" % (fn, linespec)

{flipcosmo-1.0.0 → flipcosmo-1.2.1}/flip/__init__.py

@@ -5,16 +5,8 @@ import os
 from flip.utils import create_log
 
 log = create_log()
-from . import (
-    covariance,
-    data_vector,
-    fisher,
-    fitter,
-    gridding,
-    likelihood,
-    power_spectra,
-    utils,
-)
+from . import covariance, data, data_vector, power_spectra, utils
+from .utils import __secret_logo__
 
 try:
     import jax
@@ -23,5 +15,6 @@ try:
 except:
     log.add("Jax is not available, loading numpy and scipy instead")
 
-__version__ = "1.0.0"
 __flip_dir_path__ = os.path.dirname(__file__)
+
+__version__ = "1.2.1"

flipcosmo-1.2.1/flip/covariance/__init__.py

@@ -0,0 +1,14 @@
+"""Init file of the flip.covariance package."""
+
+from . import (
+    analytical,
+    contraction,
+    cov_utils,
+    emulators,
+    fisher,
+    fitter,
+    generator,
+    likelihood,
+    symbolic,
+)
+from .covariance import CovMatrix

{flipcosmo-1.0.0/flip/covariance → flipcosmo-1.2.1/flip/covariance/analytical}/__init__.py

@@ -1,15 +1,11 @@
-"""Init file of the flip.covariance package."""
-
 from . import (
     adamsblake17,
     adamsblake17plane,
     adamsblake20,
     carreres23,
-    cov_utils,
-    emulators,
+    genericzdep,
     lai22,
     ravouxcarreres,
     ravouxnoanchor25,
     rcrk24,
 )
-from .covariance import CovMatrix

{flipcosmo-1.0.0/flip/covariance/adamsblake17plane → flipcosmo-1.2.1/flip/covariance/analytical/adamsblake17}/coefficients.py

@@ -2,7 +2,7 @@ def get_coefficients(
     parameter_values_dict,
     model_kind,
     variant=None,
-    redshift_dict=None,
+    covariance_prefactor_dict=None,
 ):
     coefficients_dict = {}
     if model_kind in ["density", "full", "density_velocity"]:

{flipcosmo-1.0.0/flip/covariance → flipcosmo-1.2.1/flip/covariance/analytical}/adamsblake17/fisher_terms.py

@@ -5,7 +5,7 @@ def get_partial_derivative_coefficients(
     model_kind,
     parameter_values_dict,
     variant=None,
-    redshift_dict=None,
+    covariance_prefactor_dict=None,
 ):
     if model_kind == "density":
         return get_partial_derivative_coefficients_density(

{flipcosmo-1.0.0/flip/covariance → flipcosmo-1.2.1/flip/covariance/analytical}/adamsblake17/flip_terms.py

@@ -74,5 +74,4 @@ dictionary_subterms = {
     "vv_0_2": 1,
 }
 multi_index_model = False
-redshift_dependent_model = False
 regularize_M_terms = None

{flipcosmo-1.0.0/flip/covariance/adamsblake17 → flipcosmo-1.2.1/flip/covariance/analytical/adamsblake17plane}/coefficients.py

@@ -2,7 +2,7 @@ def get_coefficients(
     parameter_values_dict,
     model_kind,
     variant=None,
-    redshift_dict=None,
+    covariance_prefactor_dict=None,
 ):
     coefficients_dict = {}
     if model_kind in ["density", "full", "density_velocity"]:

{flipcosmo-1.0.0/flip/covariance → flipcosmo-1.2.1/flip/covariance/analytical}/adamsblake17plane/fisher_terms.py

@@ -5,7 +5,7 @@ def get_partial_derivative_coefficients(
     model_kind,
     parameter_values_dict,
     variant=None,
-    redshift_dict=None,
+    covariance_prefactor_dict=None,
 ):
     if model_kind == "density":
         return get_partial_derivative_coefficients_density(

{flipcosmo-1.0.0/flip/covariance → flipcosmo-1.2.1/flip/covariance/analytical}/adamsblake17plane/flip_terms.py

@@ -71,5 +71,4 @@ dictionary_subterms = {
     "vv_0_2": 1,
 }
 multi_index_model = False
-redshift_dependent_model = False
 regularize_M_terms = None

{flipcosmo-1.0.0/flip/covariance → flipcosmo-1.2.1/flip/covariance/analytical}/adamsblake17plane/generator.py

@@ -8,7 +8,17 @@ from flip.covariance import cov_utils
 
 
 def angle_between(ra_0, ra_1, dec_0, dec_1):
-    """Compute cos of the angle between r0 and r1."""
+    """Compute cos of the angle between two sky directions.
+
+    Args:
+        ra_0: Right ascension of first object (radians).
+        ra_1: Right ascension of second object (radians).
+        dec_0: Declination of first object (radians).
+        dec_1: Declination of second object (radians).
+
+    Returns:
+        Cosine of the angular separation.
+    """
     cos_alpha = np.cos(ra_1 - ra_0) * np.cos(dec_0) * np.cos(dec_1) + np.sin(
         dec_0
     ) * np.sin(dec_1)
@@ -16,12 +26,31 @@ def angle_between(ra_0, ra_1, dec_0, dec_1):
 
 
 def separation(r_0, r_1, cos_alpha):
-    """Compute separation between r_0 and r_1."""
+    """Compute comoving separation given distances and angular cosine.
+
+    Args:
+        r_0: Comoving distance of first object.
+        r_1: Comoving distance of second object.
+        cos_alpha: Cosine of angular separation.
+
+    Returns:
+        Scalar separation between points.
+    """
     return np.sqrt(r_0**2 + r_1**2 - 2 * r_0 * r_1 * cos_alpha)
 
 
 def window_vv(r_0, r_1, cos_alpha, sep, j0kr, j2kr):
-    """Note: here, the bisector angle definition is used to compute"""
+    """Wide-angle window for vv using bisector definition.
+
+    Args:
+        r_0, r_1: Comoving distances of the two objects.
+        cos_alpha: Cosine of angle between directions.
+        sep: Comoving separation.
+        j0kr, j2kr: Spherical Bessel terms evaluated on ``k*sep``.
+
+    Returns:
+        Window values per k contributing to vv covariance integral.
+    """
     win = 1 / 3 * (j0kr + j2kr)
     alpha = np.arccos(np.clip(cos_alpha, -1.0, 1.0))
     phi = cov_utils.compute_phi_bisector_theorem(sep, alpha, r_0, r_1)
@@ -30,7 +59,17 @@ def window_vv(r_0, r_1, cos_alpha, sep, j0kr, j2kr):
 
 
 def window_vg(r_0, r_1, cos_alpha, sep, j1kr):
-    """Note: here, the bisector angle definition is used to compute"""
+    """Wide-angle window for gv using bisector definition.
+
+    Args:
+        r_0, r_1: Comoving distances of the two objects.
+        cos_alpha: Cosine of angle between directions.
+        sep: Comoving separation.
+        j1kr: Spherical Bessel term ``j_1(k*sep)``.
+
+    Returns:
+        Window values per k contributing to gv covariance integral.
+    """
     alpha = np.arccos(np.clip(cos_alpha, -1.0, 1.0))
     phi = cov_utils.compute_phi_bisector_theorem(sep, alpha, r_0, r_1)
     win = j1kr * np.cos(phi)
@@ -38,11 +77,31 @@ def window_vg(r_0, r_1, cos_alpha, sep, j1kr):
 
 
 def intp(win, k, pk):
+    """Integrate window times spectrum over k using trapezoidal rule.
+
+    Args:
+        win: Window array per k.
+        k: Wavenumber grid.
+        pk: Spectrum values at k.
+
+    Returns:
+        Scalar integral value.
+    """
     pint = win.T * pk
     return np.trapz(pint, x=k)
 
 
 def compute_coef_gg(k, pk, coord):
+    """Coefficient contributing to gg covariance for a single pair.
+
+    Args:
+        k: Wavenumber grid.
+        pk: Matter spectrum values at k.
+        coord: Tuple/list ``(ra_i, ra_j, dec_i, dec_j, r_i, r_j)``.
+
+    Returns:
+        Scalar integral value for gg.
+    """
     cos = angle_between(coord[0], coord[1], coord[2], coord[3])
     sep = separation(coord[4], coord[5], cos)
     ksep = np.outer(k, sep)
@@ -52,6 +111,13 @@ def compute_coef_gg(k, pk, coord):
 
 
 def compute_coef_gv(k, pk, coord):
+    """Coefficient contributing to gv covariance for a single pair.
+
+    Args mirror those of ``compute_coef_gg`` but using cross-spectrum and window.
+
+    Returns:
+        Scalar integral value for gv.
+    """
     cos = angle_between(coord[0], coord[1], coord[2], coord[3])
     sep = separation(coord[4], coord[5], cos)
     ksep = np.outer(k, sep)
@@ -62,6 +128,13 @@ def compute_coef_gv(k, pk, coord):
 
 
 def compute_coef_vv(k, pk, coord):
+    """Coefficient contributing to vv covariance for a single pair.
+
+    Args mirror those of ``compute_coef_gg`` but using velocity spectrum and window.
+
+    Returns:
+        Scalar integral value for vv.
+    """
     cos = angle_between(coord[0], coord[1], coord[2], coord[3])
     sep = separation(coord[4], coord[5], cos)
     ksep = np.outer(k, sep)
@@ -81,6 +154,18 @@ def covariance_vv(
     size_batch=100_000,
     number_worker=8,
 ):
+    """Compute velocity-velocity covariance (plane-parallel wide-angle bisector).
+
+    Args:
+        ra_v, dec_v, rcomov_v: Velocity tracer coordinates and distances.
+        wavenumber: Wavenumber grid for velocity spectrum.
+        power_spectrum: Spectrum values at wavenumber.
+        size_batch: Number of pairs per batch.
+        number_worker: Number of parallel workers.
+
+    Returns:
+        Flattened covariance vector with variance at index 0.
+    """
     N = len(ra_v)
     n_task = int((N * (N + 1)) / 2) - N
     batches = []
@@ -114,6 +199,10 @@ def covariance_gv(
     size_batch=100_000,
     number_worker=8,
 ):
+    """Compute density-velocity covariance (plane-parallel wide-angle bisector).
+
+    Returns flattened covariance vector with variance at index 0.
+    """
     number_objects_g = len(ra_g)
     number_objects_v = len(ra_v)
 
@@ -147,6 +236,7 @@ def covariance_gg(
     size_batch=100_000,
     number_worker=8,
 ):
+    """Compute density-density covariance (plane-parallel)."""
     N = len(ra_g)
     n_task = int((N * (N + 1)) / 2) - N
     batches = []
@@ -176,23 +266,19 @@ def generate_covariance(
     coordinates_density=None,
     **kwargs,
 ):
-    """
-    The generate_covariance function generates the covariance matrix for a given model type, power spectrum, and coordinates.
+    """Generate covariance blocks using Adams & Blake (2017) plane approximation.
+
+    Wide-angle definition uses the bisector. Supports ``gg``, ``vv``, and ``gv``.
 
     Args:
-        model_kind: Determine which covariance matrices are generated, and the coordinates_density and coordinates_velocity parameters are used to generate the covariance matrices
-        power_spectrum_dict: Pass the power spectrum to the function
-        coordinates_velocity: Define the coordinates of the velocity field
-        coordinates_density: Define the coordinates of the density field
-        **kwargs: Pass keyword arguments to the function
-        : Generate the covariance matrix for a given model
-        The wide angle definition is bisector.
+        model_kind: One of ``"density"``, ``"velocity"``, ``"full"``, ``"density_velocity"``.
+        power_spectrum_dict: Dict providing required spectra grids and values.
+        coordinates_velocity: Tuple ``(ra, dec, rcom)`` for velocity tracers.
+        coordinates_density: Tuple ``(ra, dec, rcom)`` for density tracers.
+        **kwargs: Forwarded to low-level covariance functions (batch/workers).
 
     Returns:
-        A dictionary of covariance matrices
-
-    Doc Author:
-        Trelent
+        Tuple ``(covariance_dict, number_densities, number_velocities, los_definition)``.
     """
     cov_utils.check_generator_need(
         model_kind,
@@ -253,11 +339,9 @@ def generate_covariance(
         )
 
     los_definition = "bisector"
-    redshift_dict = None
     return (
         covariance_dict,
         number_densities,
         number_velocities,
         los_definition,
-        redshift_dict,
     )

{flipcosmo-1.0.0/flip/covariance → flipcosmo-1.2.1/flip/covariance/analytical}/adamsblake20/coefficients.py

@@ -2,7 +2,7 @@ def get_coefficients(
     parameter_values_dict,
     model_kind,
     variant=None,
-    redshift_dict=None,
+    covariance_prefactor_dict=None,
 ):
     coefficients_dict = {}
     if model_kind in ["density", "full", "density_velocity"]:

{flipcosmo-1.0.0/flip/covariance/ravouxcarreres → flipcosmo-1.2.1/flip/covariance/analytical/adamsblake20}/fisher_terms.py

@@ -5,7 +5,7 @@ def get_partial_derivative_coefficients(
     model_kind,
     parameter_values_dict,
     variant=None,
-    redshift_dict=None,
+    covariance_prefactor_dict=None,
 ):
     if model_kind == "density":
         return get_partial_derivative_coefficients_density(

{flipcosmo-1.0.0/flip/covariance → flipcosmo-1.2.1/flip/covariance/analytical}/adamsblake20/flip_terms.py

@@ -342,5 +342,4 @@ dictionary_subterms = {
     "vv_0_2": 1,
 }
 multi_index_model = False
-redshift_dependent_model = False
 regularize_M_terms = {"gg": "mpmath", "gv": "mpmath", "vv": None}

{flipcosmo-1.0.0/flip/covariance → flipcosmo-1.2.1/flip/covariance/analytical}/carreres23/coefficients.py

@@ -1,11 +1,8 @@
-import numpy as np
-
-
 def get_coefficients(
     parameter_values_dict,
     model_kind,
     variant=None,
-    redshift_dict=None,
+    covariance_prefactor_dict=None,
 ):
     coefficients_dict = {}
     coefficients_dict["vv"] = [parameter_values_dict["fs8"] ** 2]

{flipcosmo-1.0.0/flip/covariance → flipcosmo-1.2.1/flip/covariance/analytical}/carreres23/fisher_terms.py

@@ -5,7 +5,7 @@ def get_partial_derivative_coefficients(
     model_kind,
     parameter_values_dict,
     variant=None,
-    redshift_dict=None,
+    covariance_prefactor_dict=None,
 ):
     if variant == "growth_index":
         partial_coefficients_dict = {

{flipcosmo-1.0.0/flip/covariance → flipcosmo-1.2.1/flip/covariance/analytical}/carreres23/flip_terms.py

@@ -42,5 +42,4 @@ dictionary_terms = {"vv": ["0"]}
 dictionary_lmax = {"vv": [2]}
 dictionary_subterms = {"vv_0_0": 1, "vv_0_1": 0, "vv_0_2": 1}
 multi_index_model = False
-redshift_dependent_model = False
 regularize_M_terms = None