docs, docstrings and bug fixes

BlackHolePerturbationToolkit · Dec 18, 2024 · e917408 · e917408
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Showing 219 changed files with 11,407 additions and 7,451 deletions.
diff --git a/docs/.DS_Store b/docs/.DS_Store
diff --git a/docs/doctrees/README.doctree b/docs/doctrees/README.doctree
diff --git a/docs/doctrees/environment.pickle b/docs/doctrees/environment.pickle
diff --git a/docs/doctrees/general/docs_main.doctree b/docs/doctrees/general/docs_main.doctree
diff --git a/docs/doctrees/index.doctree b/docs/doctrees/index.doctree
diff --git a/docs/doctrees/nbsphinx/tutorial/FastEMRIWaveforms_tutorial.ipynb b/docs/doctrees/nbsphinx/tutorial/FastEMRIWaveforms_tutorial.ipynb
diff --git a/docs/doctrees/nbsphinx/tutorial/Trajectory_tutorial.ipynb b/docs/doctrees/nbsphinx/tutorial/Trajectory_tutorial.ipynb
diff --git a/docs/doctrees/nbsphinx/tutorial/Tutorial_FD_construction_single_mode.ipynb b/docs/doctrees/nbsphinx/tutorial/Tutorial_FD_construction_single_mode.ipynb
diff --git a/docs/doctrees/nbsphinx/tutorial/Tutorial_FrequencyDomain_Waveforms.ipynb b/docs/doctrees/nbsphinx/tutorial/Tutorial_FrequencyDomain_Waveforms.ipynb
@@ -19,10 +19,22 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 2,
    "id": "348daf55",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "ename": "ModuleNotFoundError",
+     "evalue": "No module named 'lisatools.diagnostic'",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mModuleNotFoundError\u001b[0m                       Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[2], line 6\u001b[0m\n\u001b[1;32m      3\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mmatplotlib\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mpyplot\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m \u001b[38;5;21;01mplt\u001b[39;00m\n\u001b[1;32m      4\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mmatplotlib\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m \u001b[38;5;21;01mmpl\u001b[39;00m\n\u001b[0;32m----> 6\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mlisatools\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mdiagnostic\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;241m*\u001b[39m\n\u001b[1;32m      7\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mlisatools\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01msensitivity\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m get_sensitivity\n\u001b[1;32m      9\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mfew\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mwaveform\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m GenerateEMRIWaveform\n",
+      "\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'lisatools.diagnostic'"
+     ]
+    }
+   ],
    "source": [
     "import time\n",
     "import numpy as np\n",
@@ -36,7 +48,9 @@
     "from few.utils.constants import *\n",
     "from few.utils.utility import *\n",
     "from few.trajectory.inspiral import EMRIInspiral\n",
-    "traj_module = EMRIInspiral(func=\"SchwarzEccFlux\")\n",
+    "from few.trajectory.ode.flux import SchwarzEccFlux\n",
+    "\n",
+    "traj_module = EMRIInspiral(func=SchwarzEccFlux)\n",
     "\n",
     "from scipy.signal.windows import tukey, hann, boxcar, nuttall, blackman\n",
     "from few.utils.fdutils import *\n",
@@ -707,7 +721,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "few-tf",
    "language": "python",
    "name": "python3"
   },
@@ -721,7 +735,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.12"
+   "version": "3.11.10"
   }
  },
  "nbformat": 4,

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diff --git a/docs/doctrees/tutorial/FastEMRIWaveforms_tutorial.doctree b/docs/doctrees/tutorial/FastEMRIWaveforms_tutorial.doctree
diff --git a/docs/doctrees/tutorial/Trajectory_tutorial.doctree b/docs/doctrees/tutorial/Trajectory_tutorial.doctree
diff --git a/docs/doctrees/tutorial/Tutorial_FD_construction_single_mode.doctree b/docs/doctrees/tutorial/Tutorial_FD_construction_single_mode.doctree
diff --git a/docs/doctrees/tutorial/Tutorial_FrequencyDomain_Waveforms.doctree b/docs/doctrees/tutorial/Tutorial_FrequencyDomain_Waveforms.doctree
diff --git a/docs/doctrees/user/amp.doctree b/docs/doctrees/user/amp.doctree
diff --git a/docs/doctrees/user/cite.doctree b/docs/doctrees/user/cite.doctree
diff --git a/docs/doctrees/user/main.doctree b/docs/doctrees/user/main.doctree
diff --git a/docs/doctrees/user/pointer.doctree b/docs/doctrees/user/pointer.doctree
diff --git a/docs/doctrees/user/sum.doctree b/docs/doctrees/user/sum.doctree
diff --git a/docs/doctrees/user/traj.doctree b/docs/doctrees/user/traj.doctree
diff --git a/docs/doctrees/user/util.doctree b/docs/doctrees/user/util.doctree
diff --git a/docs/html/.buildinfo b/docs/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
-# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 1abcea7d474198d107de3ce8b98d87f5
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: d03aa64e5c7fd96c736dedc673aa6f3e
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/html/.buildinfo.bak b/docs/html/.buildinfo.bak
@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 1abcea7d474198d107de3ce8b98d87f5
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/html/README.html b/docs/html/README.html
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diff --git a/docs/html/_images/tutorial_Tutorial_FD_construction_single_mode_9_0.png b/docs/html/_images/tutorial_Tutorial_FD_construction_single_mode_9_0.png
diff --git a/docs/html/_sources/README.rst.txt b/docs/html/_sources/README.rst.txt
@@ -50,8 +50,7 @@ notebook <https://github.com/BlackHolePerturbationToolkit/FastEMRIWaveforms/blob
 Prerequisites
 ~~~~~~~~~~~~~
 
-To install this software for CPU usage, you need `gsl
->2.0 <https://www.gnu.org/software/gsl/>`__ , `lapack
+To install this software for CPU usage, you need `lapack
 (3.6.1) <https://www.netlib.org/lapack/lug/node14.html>`__, Python >3.4,
 wget, and NumPy. If you install lapack with conda, the new version (3.9)
 seems to not install the correct header files. Therefore, the lapack
@@ -76,7 +75,8 @@ will download automatically the first time they are needed. Files are
 generally under 10MB. However, there is a 100MB file needed for the slow
 waveform and the bicubic amplitude interpolation. This larger file will
 only download if you run either of those two modules. The files are
-hosted on `Zenodo <https://zenodo.org/record/3981654#.XzS_KRNKjlw>`__.
+hosted on the `Black Hole Perturbation Toolkit Download
+Server <https://download.bhptoolkit.org/few/data>`__.
 
 Installing
 ~~~~~~~~~~
@@ -146,14 +146,17 @@ More Customized Installation (legacy)
 
 ::
 
-   conda create -n few_env -c conda-forge gcc_linux-64 gxx_linux-64 wget gsl lapack=3.6.1 hdf5 numpy Cython scipy tqdm jupyter ipython h5py requests matplotlib python=3.7
+   conda create -n few_env -c conda-forge gcc_linux-64 gxx_linux-64 wget lapack=3.6.1 hdf5 numpy Cython scipy tqdm jupyter ipython h5py requests rich matplotlib numba python=3.7
    conda activate few_env
 
-::
-
-   If on MACOSX, substitute `gcc_linux-64` and `gxx_linus-64` with `clang_osx-64` and `clangxx_osx-64`.
-
-   If you want a faster install, you can install the python packages (numpy, Cython, scipy, tqdm, jupyter, ipython, h5py, requests, matplotlib) with pip.
+- If you want a faster install, you can install the python packages
+  (numpy, Cython, scipy, tqdm, jupyter, ipython, h5py, requests, rich,
+  numba, matplotlib) with pip.
+- If on MACOSX with an Intel CPU, substitute ``gcc_linux-64`` and
+  ``gxx_linux-64`` with ``clang_osx-64`` and ``clangxx_osx-64``.
+- For an ARM CPU (Apple Silicon) substitute these arguments with
+  ``clang_osx-arm64`` and ``clangxx_osx-arm64`` instead, and replace
+  ``lapack=3.6.1`` with ``liblapacke``, ``lapack`` and ``openblas``.
 
 2) Clone the repository.
 
@@ -170,23 +173,29 @@ More Customized Installation (legacy)
 
    pip install cupy-cuda92
 
-4) Run install.
+4) Copy the prebuild script to the top-level directory of the repository
+   and run it (simply running it will not work!):
+
+::
+
+   python scripts/prebuild.py
+
+5) Run install.
 
 ::
 
    python setup.py install
 
-When installing lapack and gsl, the setup file will default to assuming
-lib and include for both are in installed within the conda environment.
-To provide other lib and include directories you can provide command
-line options when installing. You can also remove usage of OpenMP.
+When installing lapack, the setup file will default to assuming lib and
+include for both are in installed within the conda environment. To
+provide other lib and include directories you can provide command line
+options when installing. You can also remove usage of OpenMP.
 
 ::
 
    python setup.py --help
    usage: setup.py [-h] [--lapack_lib LAPACK_LIB]
                    [--lapack_include LAPACK_INCLUDE] [--lapack LAPACK]
-                   [--gsl_lib GSL_LIB] [--gsl_include GSL_INCLUDE] [--gsl GSL]
                    [--ccbin CCBIN]
 
    optional arguments:
@@ -199,13 +208,6 @@ line options when installing. You can also remove usage of OpenMP.
                            includ, must also add lapack lib.
      --lapack LAPACK       Directory of both lapack lib and include. '/include'
                            and '/lib' will be added to the end of this string.
-     --gsl_lib GSL_LIB     Directory of the gsl lib. If you add gsl lib, must
-                           also add gsl include.
-     --gsl_include GSL_INCLUDE
-                           Directory of the gsl include. If you add gsl include,
-                           must also add gsl lib.
-     --gsl GSL             Directory of both gsl lib and include. '/include' and
-                           '/lib' will be added to the end of this string.
      --ccbin CCBIN         path/to/compiler to link with nvcc when installing
                            with CUDA.
 
@@ -233,6 +235,7 @@ In the main directory of the package run in the terminal (if you run
 
 ::
 
+   cd tests/
    python -m unittest discover
 
 Contributing
@@ -265,20 +268,20 @@ Current Version: 1.5.5
 Authors/Developers
 ------------------
 
--  **Michael Katz**
--  Lorenzo Speri
--  Christian Chapman-Bird
--  Alvin J. K. Chua
--  Niels Warburton
--  Scott Hughes
+- **Michael Katz**
+- Lorenzo Speri
+- Christian Chapman-Bird
+- Alvin J. K. Chua
+- Niels Warburton
+- Scott Hughes
 
 Contibutors
 ~~~~~~~~~~~
 
--  Philip Lynch
--  Soichiro Isoyama
--  Ryuichi Fujita
--  Monica Rizzo
+- Philip Lynch
+- Soichiro Isoyama
+- Ryuichi Fujita
+- Monica Rizzo
 
 License
 -------
@@ -433,10 +436,10 @@ development of FEW.
 Acknowledgments
 ---------------
 
--  This research resulting in this code was supported by National
-   Science Foundation under grant DGE-0948017 and the Chateaubriand
-   Fellowship from the Office for Science & Technology of the Embassy of
-   France in the United States.
--  It was also supported in part through the computational resources and
-   staff contributions provided for the Quest/Grail high performance
-   computing facility at Northwestern University.
+- This research resulting in this code was supported by National Science
+  Foundation under grant DGE-0948017 and the Chateaubriand Fellowship
+  from the Office for Science & Technology of the Embassy of France in
+  the United States.
+- It was also supported in part through the computational resources and
+  staff contributions provided for the Quest/Grail high performance
+  computing facility at Northwestern University.
diff --git a/docs/html/_sources/index.rst.txt b/docs/html/_sources/index.rst.txt
@@ -16,6 +16,7 @@
    :maxdepth: 4
    :caption: Tutorial:
 
+   tutorial/Trajectory_tutorial
    tutorial/FastEMRIWaveforms_tutorial
    tutorial/Tutorial_FD_construction_single_mode
    tutorial/Tutorial_FrequencyDomain_Waveforms

diff --git a/docs/html/_sources/tutorial/FastEMRIWaveforms_tutorial.ipynb.txt b/docs/html/_sources/tutorial/FastEMRIWaveforms_tutorial.ipynb.txt