vschac · vschac · Jun 23, 2025 · Dec 15, 2023 · Dec 15, 2023 · Mar 1, 2024
diff --git a/.DS_Store b/.DS_Store
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -0,0 +1,36 @@
+name: FAST-PT CI
+
+on:
+  push:
+    branches:
+      - beta-fpt
+  pull_request:
+    branches:
+      - beta-fpt
+  workflow_dispatch:
+
+jobs:
+  test:
+    runs-on: macos-latest
+
+    strategy:
+      matrix:
+        python-version: ["3.13", "3.11"]
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e .
+          pip install pytest
+
+      - name: Run unit/benchmark tests
+        run: pytest tests/ --disable-warnings
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,8 @@
 examples/*.pdf
 examples/*.npy
+examples/output/*
+examples/outputs/*
 *.pyc
+build/
+plot_test_outputs/
+fastpt/core/outputs/
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -0,0 +1,15 @@
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.8"
+
+python:
+   install:
+     - method: pip
+       path: .
+     - requirements: docs/requirements.txt
+
+sphinx:
+  configuration: docs/conf.py
diff --git a/README.md b/README.md
@@ -1,5 +1,11 @@
 # FAST-PT
 
+[![Documentation Status](https://readthedocs.org/projects/fast-pt/badge/?version=latest)](https://fast-pt.readthedocs.io/en/latest/?badge=latest)
+[![arXiv:1603.04826](https://img.shields.io/badge/arXiv-1603.04826-b31b1b.svg)](https://arxiv.org/abs/1603.04826)
+[![arXiv:1609.05978](https://img.shields.io/badge/arXiv-1609.05978-b31b1b.svg)](https://arxiv.org/abs/1609.05978)
+[![arXiv:1708.09247](https://img.shields.io/badge/arXiv-1708.09247-b31b1b.svg)](https://arxiv.org/abs/1708.09247)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
 FAST-PT is a code to calculate quantities in cosmological perturbation theory
 at 1-loop (including, e.g., corrections to the matter power spectrum). The code
 utilizes Fourier methods combined with analytic expressions to reduce the
@@ -22,17 +28,17 @@ Full installation with examples:
 * Make sure you have current version of numpy, scipy, and matplotlib
 * download the latest FAST-PT release (or clone the repo)
 * install the repo: `python -m pip install .`
-* run the example: `cd examples && python fastpt_example.py`
+* run the most recent example: `cd examples && python3 hello_fastpt.py`
 * hopefully you get a plot!
-
-See the [user manual](docs/usr_manual.pdf) for more details.
+* for a more in-depth example of new features:  `cd examples && python3 v4_example.py`
+* for older examples see the 'examples' folder
 
 Our papers (JCAP 2016, 9, 15; arXiv:1603.04826) and (JCAP 2017, 2, 30; arXiv:1609.05978)
 describe the FAST-PT algorithm and implementation. Please cite these papers
 when using FAST-PT in your research. For the intrinsic alignment
-implementation, cite arXiv:1708.09247.
+implementation, cite PRD 100, 103506 (arXiv:1708.09247).
 
 FAST-PT is under continued development and should be considered research in
 progress. FAST-PT is open source and distributed with the
 [MIT license](https://opensource.org/licenses/mit). If you have comments,
-questions, or feedback, please file an [issue](https://github.com/JoeMcEwen/FAST-PT/issues).
+questions, or feedback, please file an [issue](https://github.com/jablazek/FAST-PT/issues).
diff --git a/dist/fast_pt-4.0.0b1-py3-none-any.whl b/dist/fast_pt-4.0.0b1-py3-none-any.whl
diff --git a/dist/fast_pt-4.0.0b1.tar.gz b/dist/fast_pt-4.0.0b1.tar.gz
diff --git a/docs/.DS_Store b/docs/.DS_Store
diff --git a/docs/_build/.DS_Store b/docs/_build/.DS_Store
diff --git a/docs/_build/doctrees/api.doctree b/docs/_build/doctrees/api.doctree
diff --git a/docs/_build/doctrees/changelog.doctree b/docs/_build/doctrees/changelog.doctree
diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
diff --git a/docs/_build/doctrees/examples.doctree b/docs/_build/doctrees/examples.doctree
diff --git a/docs/_build/doctrees/index.doctree b/docs/_build/doctrees/index.doctree
diff --git a/docs/_build/doctrees/installation.doctree b/docs/_build/doctrees/installation.doctree
diff --git a/docs/_build/doctrees/quickstart.doctree b/docs/_build/doctrees/quickstart.doctree
diff --git a/docs/_build/doctrees/theory.doctree b/docs/_build/doctrees/theory.doctree
diff --git a/docs/_build/html/.DS_Store b/docs/_build/html/.DS_Store
diff --git a/docs/_build/html/.buildinfo b/docs/_build/html/.buildinfo
@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 43eb43198a4eba09a90caefeb185ff84
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_build/html/.buildinfo.bak b/docs/_build/html/.buildinfo.bak
@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: b2cf89ef06e9ad64bee162009c2d4eca
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_build/html/.doctrees/api.doctree b/docs/_build/html/.doctrees/api.doctree
diff --git a/docs/_build/html/.doctrees/changelog.doctree b/docs/_build/html/.doctrees/changelog.doctree
diff --git a/docs/_build/html/.doctrees/environment.pickle b/docs/_build/html/.doctrees/environment.pickle
diff --git a/docs/_build/html/.doctrees/examples.doctree b/docs/_build/html/.doctrees/examples.doctree
diff --git a/docs/_build/html/.doctrees/index.doctree b/docs/_build/html/.doctrees/index.doctree
diff --git a/docs/_build/html/.doctrees/installation.doctree b/docs/_build/html/.doctrees/installation.doctree
diff --git a/docs/_build/html/.doctrees/quickstart.doctree b/docs/_build/html/.doctrees/quickstart.doctree
diff --git a/docs/_build/html/.doctrees/theory.doctree b/docs/_build/html/.doctrees/theory.doctree
diff --git a/docs/_build/html/_downloads/1abe55494b10c89f9d07e5e5009d7c70/usr_manual.pdf b/docs/_build/html/_downloads/1abe55494b10c89f9d07e5e5009d7c70/usr_manual.pdf
diff --git a/docs/_build/html/_modules/fastpt/FASTPT.html b/docs/_build/html/_modules/fastpt/FASTPT.html
diff --git a/docs/_build/html/_modules/fastpt/FPTHandler.html b/docs/_build/html/_modules/fastpt/FPTHandler.html
diff --git a/docs/_build/html/_modules/fastpt/core/FASTPT.html b/docs/_build/html/_modules/fastpt/core/FASTPT.html
diff --git a/docs/_build/html/_modules/fastpt/core/FPTHandler.html b/docs/_build/html/_modules/fastpt/core/FPTHandler.html
diff --git a/docs/_build/html/_modules/index.html b/docs/_build/html/_modules/index.html
@@ -0,0 +1,107 @@
+
+
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" data-content_root="../">
+<head>
+  <meta charset="utf-8" />
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>Overview: module code &mdash; FAST-PT 4.0.0 documentation</title>
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=b86133f3" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=e59714d7" />
+
+
+      <script src="../_static/jquery.js?v=5d32c60e"></script>
+      <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+      <script src="../_static/documentation_options.js?v=3304f9e4"></script>
+      <script src="../_static/doctools.js?v=9bcbadda"></script>
+      <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+    <script src="../_static/js/theme.js"></script>
+    <link rel="index" title="Index" href="../genindex.html" />
+    <link rel="search" title="Search" href="../search.html" /> 
+</head>
+
+<body class="wy-body-for-nav"> 
+  <div class="wy-grid-for-nav">
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-scroll">
+        <div class="wy-side-nav-search" >
+
+
+
+          <a href="../index.html" class="icon icon-home">
+            FAST-PT
+          </a>
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+        </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+              <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../quickstart.html">Quick Start Guide</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../api.html">API Reference</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../examples.html">Examples</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../theory.html">Theory</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog / Migration Guide</a></li>
+</ul>
+
+        </div>
+      </div>
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
+          <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+          <a href="../index.html">FAST-PT</a>
+      </nav>
+
+      <div class="wy-nav-content">
+        <div class="rst-content">
+          <div role="navigation" aria-label="Page navigation">
+  <ul class="wy-breadcrumbs">
+      <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
+      <li class="breadcrumb-item active">Overview: module code</li>
+      <li class="wy-breadcrumbs-aside">
+      </li>
+  </ul>
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+
+  <h1>All modules for which code is available</h1>
+<ul><li><a href="fastpt/core/FASTPT.html">fastpt.core.FASTPT</a></li>
+<li><a href="fastpt/core/FPTHandler.html">fastpt.core.FPTHandler</a></li>
+</ul>
+
+           </div>
+          </div>
+          <footer>
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>&#169; Copyright 2016-2025, FAST-PT developers.</p>
+  </div>
+
+  Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+    <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
+    provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
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+        </div>
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+          SphinxRtdTheme.Navigation.enable(true);
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+
+</body>
+</html>
diff --git a/docs/_build/html/_sources/api.rst.txt b/docs/_build/html/_sources/api.rst.txt
@@ -0,0 +1,16 @@
+.. _api:
+
+API Reference
+=============
+
+FASTPT Class
+------------
+
+.. autoclass:: fastpt.FASTPT
+   :members:
+
+FPTHandler Class
+----------------
+
+.. autoclass:: fastpt.FPTHandler
+   :members:
diff --git a/docs/_build/html/_sources/changelog.rst.txt b/docs/_build/html/_sources/changelog.rst.txt
@@ -0,0 +1,64 @@
+.. _changelog:
+
+Changelog / Migration Guide
+===========================
+
+This document details the changes between the original FAST-PT implementation and the current version.
+
+For previous versions' changes, see the :download:`complete changelog history </usr_manual.pdf>`.
+
+NOTE: FAST-PT 4.0 is completely backwards compatible with FAST-PT 3.0. However, adjustments to your code may be required to take advantage of the new features and performance improvements.
+
+Major Changes
+-------------
+
+* Caching: FAST-PT now caches individual terms and intermediate calculations to speed up computation. 
+* FPTHandler: The handler class has been introduced to improve the the user's ability to manage FAST-PT and provide many new convenience features that compliment the FAST-PT class. NOTE: the FPTHandler class is not a replacement for the FAST-PT class, but rather a wrapper that provides additional functionality. It is not necessary for computation.
+* To_do list: The to_do list is no longer needed to initialize FAST-PT. The terms will now be calculated as needed and stored as a property of the FAST-PT class.
+
+
+Minor Changes
+-------------
+
+* Simple flag: A new "simple" kwarg has been added to FAST-PT which will instead initialize an instance of FAST-PT simple.
+* Private k: The input k is now "private" after initialization via Python's name mangling. This means that the user cannot change the value of k after initialization but can still access the value of k.
+* Gamma functions cache: A separate (and simpler) caching system has been implemented to cache gamma functions and save time on the calculation of the X terms.
+* Parameter validation: The parameters P, P_window, and C_window are now validated at every function call to ensure that they have the proper traits needed for the calculation. This is done to prevent errors from propagating through the code and causing issues later on.
+* N_pad default: If no n_pad is provided during initialization, the default value is now set to 0.5 * len(k).
+* Nu deprecation: The nu parameter is now deprecated as it is no longer needed for initialization. It will default to -2 unless a different nu value is needed in which case it will be calculated internally.
+* One_loop_dd return: One_loop_dd will only return P_1loop, Ps. Previously returned the dd_bias terms as well however this was contingent on the to_do list which is being deprecated. 
+* Cleft_QR: The Cleft_QR function has been removed due to missing internal functions.
+
+
+Performance Improvements
+------------------------
+
+The improvement in performance of FAST-PT is going to varry largely with your use case. However, about half of the calculation done for most terms was redundant granting a two times speedup do to the new caching system.
+FAST-PT also now calculates terms in a modular format. This means that the user can now choose to calculate only the terms they need, rather than all of the terms grouped into one FAST-PT function. 
+This is done by using the FPTHandler class and the get method, or by calling compute_term with the necessary parameters for each term. 
+This will greatly improve the performance of each FAST-PT function if your use case only requires a select few terms.
+
+
+Description of Caching System
+-----------------------------
+
+Caching in Fast-PT is done via a CacheManager_ object that is initialized with the FAST-PT class. This cache tracks various different "layers" of the calculation of Fast-PT terms. These layers include:
+
+* Individual Power Spectra: Fast-PT functions return a tuple of multiple power spectra, each of which is cached individually.
+* Jk Scalar and Tensor Calculations: Most Fast-PT terms require the calculation of the Jk scalar or tensor functions. Some terms have identical parameters that are passed to these functions, so they are cached individually as well.
+* Fourier Coefficients: Fourier coefficients of the user provided power spectra are cached and then used in the Jk functions.
+* Convolutions: This is the convolution of the power spectrum fourier coefficients and the relevant k grid quantities (X terms). The convolution function is called with fourier coefficients and k grid quantities, which are dependent on the user provided k and P and cached individually.
+
+There is also a separate form of caching used for the k grid quantities (X terms) and the gamma functions used to calculate them. The gamma functions are cached outside the Fast-PT object as they will not be frequently changed, while the k grid quantities are cached as properties of the Fast-PT object and can be accessed via `fastpt_instance.X_IA_A` for example.
+In total, there are three forms of caching used in Fast-PT 4.0, two of which are stored within the object. The gamma functions cache will persist as long as the program runs.
+
+This multi-tiered caching system allows Fast-PT to avoid redundant calculations both on individual power spectra terms and the intermediate calculations that are needed to compute them. 
+To avoid the cache from growing too large, a "dump_cache" flag is provided in initialization that, when True, will clear the cache when a new power spectra is inputted by the user. The user is also able to specify (during Fast-PT initialization) a maximum cache size in mb. This will evict cached items randomly (in linear time) to avoid slowing down the total computation time. However, the cache size limit is meant as a safeguard and should not be treated as a form of memory management for the program. 
+
+.. _CacheManager: https://github.com/jablazek/FAST-PT/tree/master/fastpt/core/CacheManager.py
+
+
+Additional Notes
+------------------
+
+* The 1loop term (one_loop_dd[0]) currently does not pass np.allclose due to numerical noise when compared with FAST-PT 3 when a C_window of 0.63 or less is provided. This only occurs at the very low k end and is negligible. This issue is currently being investigated and will be fixed in a future release.
diff --git a/docs/_build/html/_sources/examples.rst.txt b/docs/_build/html/_sources/examples.rst.txt
@@ -0,0 +1,64 @@
+.. _examples:
+
+Examples
+=======
+
+More examples can be found `here <https://github.com/jablazek/FAST-PT/tree/master/examples>`_.
+
+One-loop Matter Power Spectrum
+----------------------------
+
+.. code-block:: python
+
+   from fastpt import FASTPT
+   import numpy as np
+   import matplotlib.pyplot as plt
+
+   # Load data
+   data = np.loadtxt('Pk_test.dat')
+   k = data[:, 0]
+   P = data[:, 1]
+
+   # Initialize FASTPT
+   fpt = FASTPT(k, low_extrap=-5, high_extrap=3, n_pad=int(0.5*len(k)))
+
+   # Calculate corrections
+   P_1loop, P_components = fpt.one_loop_dd(P, C_window=0.75)
+
+   # Plot
+   plt.figure(figsize=(10, 7))
+   plt.loglog(k, P, label='Linear P(k)')
+   plt.loglog(k, P_1loop, label='1-loop P(k)')
+   plt.xlabel('k [h/Mpc]')
+   plt.ylabel('P(k) [(Mpc/h)³]')
+   plt.legend()
+   plt.tight_layout()
+   plt.show()
+
+Using the FPTHandler
+-----------------
+
+.. code-block:: python
+
+   import numpy as np
+   from fastpt import FASTPT, FPTHandler
+
+   # Initialize with default parameters
+   k_values = np.logspace(-3, 1, 1000)
+
+   fastpt_instance = FASTPT(k_values)
+   handler = FPTHandler(fastpt_instance, P_window=np.array([0.2, 0.2]), C_window=0.75)
+
+   # Generate and store a power spectrum
+   P = handler.generate_power_spectra()
+   handler.update_default_params(P=P)
+
+   # Get the 1-loop power spectrum, using the default parameters
+   result = handler.get("P_1loop")
+
+   #Plot the results
+   handler.plot(data=result)
+
+   # Save the results and your parameters
+   handler.save_output(result, "one_loop_dd")
+   handler.save_params("params.npz")
diff --git a/docs/_build/html/_sources/index.rst.txt b/docs/_build/html/_sources/index.rst.txt
@@ -0,0 +1,26 @@
+.. FAST-PT documentation master file
+
+FAST-PT Documentation
+====================
+
+FAST-PT is a code to calculate quantities in cosmological perturbation theory at 1-loop (including, e.g., corrections to the matter power spectrum). The code utilizes Fourier methods combined with analytic expressions to reduce the computation time to scale as N log N, where N is the number of grid points in the input linear power spectrum.
+
+FASTPT is a numerical algorithm to calculate 1-loop contributions to the matter power spectrum and other integrals of a similar type. The method is presented in papers arXiv:1603.04826 and arXiv:1609.05978. Please cite these papers if you are using FASTPT in your research.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   installation
+   quickstart
+   api
+   examples
+   theory
+   changelog
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`