bug fixes and checks

README.md

@@ -3,11 +3,11 @@
 ### Designed for LISA data analysis of Massive Black Hole Binaries.
 
 
-This package implements GPU/CPU agnostic Massive Black Hole Binary waveforms and likelihood computations from [arXiv:2005.01827](https://arxiv.org/abs/2005.01827) and [arXiv:2111.01064](https://arxiv.org/abs/2111.01064). The various parts of this package are arranged to be modular as waveform or response changes or improvements are made. Generally, the modules fall into four categories: waveforms, response, waveform building, and utilities. Please see the [documentation](https://mikekatz04.github.io/BBHx/) for further information on these modules. The code can be found on Github [here](https://github.com/mikekatz04/BBHx). The data necessary for various modules in this package will automatically download the first time it is needed. If you would like to view the data, it can be found on [Zenodo](https://zenodo.org/record/3981654#.XzS_KRNKjlw).
+This package implements GPU/CPU agnostic Massive Black Hole Binary waveforms and likelihood computations from [arXiv:2005.01827](https://arxiv.org/abs/2005.01827) and [arXiv:2111.01064](https://arxiv.org/abs/2111.01064). The various parts of this package are arranged to be modular as waveform or response changes or improvements are made. Generally, the modules fall into four categories: waveforms, response, waveform building, and utilities. Please see the [documentation](https://mikekatz04.github.io/BBHx/) for further information on these modules. The code can be found on Github [here](https://github.com/mikekatz04/BBHx).
 
 This package is a part of the LISA Analysis Tools environment.
 
-If you use all or any parts of this code, please cite [arXiv:2005.01827](https://arxiv.org/abs/2005.01827) and [arXiv:2111.01064](https://arxiv.org/abs/2111.01064). See the [documentation](https://bhptoolkit.org/FastEMRIWaveforms/) to properly cite specific modules.
+If you use this software please cite [arXiv:2005.01827](https://arxiv.org/abs/2005.01827), [arXiv:2111.01064](https://arxiv.org/abs/2111.01064), and the associated [Zenodo page](https://zenodo.org/record/5730688#.YaFvRkJKhTY) Please also cite any consituent parts used like the response function or waveforms. See the `citation` attribute for each class or docstring for functions for more information. 
 
 ## Getting Started
 
@@ -135,7 +135,7 @@ Please read [CONTRIBUTING.md](CONTRIBUTING.md) for details on our code of conduc
 
 ## Versioning
 
-We use [SemVer](http://semver.org/) for versioning. For the versions available, see the [tags on this repository](https://github.com/BlackHolePerturbationToolkit/FastEMRIWaveforms/tags).
+We use [SemVer](http://semver.org/) for versioning. For the versions available, see the [tags on this repository](https://github.com/mikekatz04/BBHx/tags).
 
 Current Version: 1.0.0
 

bbhx/likelihood.py

@@ -135,7 +135,7 @@ def __init__(
 
     @property
     def citation(self):
-        return katz_1 + katz_2
+        return katz_citations
 
     def get_ll(
         self,
@@ -361,7 +361,7 @@ def __init__(
     @property
     def citation(self):
         """Citations for this class"""
-        return katz_1 + katz_2 + Cornish_Heterodyning + Rel_Bin_citation
+        return katz_citations + Cornish_Heterodyning + Rel_Bin_citation
 
     def init_heterodyne_info(
         self,

bbhx/response/fastfdresponse.py

@@ -102,7 +102,7 @@ def __init__(self, TDItag="AET", order_fresnel_stencil=0, use_gpu=False):
     @property
     def citation(self):
         """Return citations for this class"""
-        return katz_1 + katz_2 + marsat_1 + marsat_2
+        return katz_citations + marsat_1 + marsat_2
 
     def _sanity_check_modes(self, ells, mms):
         """Make sure modes are allowed"""

bbhx/utils/citations.py

@@ -23,7 +23,7 @@
 attribute.
 """
 
-katz_1 = """
+katz_citations = """
 @article{Katz:2020hku,
     author = "Katz, Michael L. and Marsat, Sylvain and Chua, Alvin J. K. and Babak, Stanislav and Larson, Shane L.",
     title = "{GPU-accelerated massive black hole binary parameter estimation with LISA}",
@@ -37,9 +37,7 @@
     pages = "023033",
     year = "2020"
 }
-"""
 
-katz_2 = """
 @article{Katz:2021uax,
     author = "Katz, Michael L.",
     title = "{A fully-automated end-to-end pipeline for massive black hole binary signal extraction from LISA data}",
@@ -49,6 +47,16 @@
     month = "11",
     year = "2021"
 }
+
+@article{michael katz_2021,
+    title={mikekatz04/BBHx: First official public release},
+    DOI={10.5281/zenodo.5730688},
+    abstractNote={No description provided.},
+    publisher={Zenodo},
+    author={Michael Katz},
+    year={2021},
+    month={Nov}
+}
 """
 
 marsat_1 = """

bbhx/utils/interpolate.py

@@ -21,14 +21,13 @@
 try:
     import cupy as xp
     from pyInterpolate import interpolate_wrap as interpolate_wrap_gpu
-    from pyInterpolate import interpolate_TD_wrap as interpolate_TD_wrap_gpu
+
 
 except (ImportError, ModuleNotFoundError) as e:
     print("No CuPy or GPU interpolation available.")
     import numpy as xp
 
 from pyInterpolate_cpu import interpolate_wrap as interpolate_wrap_cpu
-from pyInterpolate_cpu import interpolate_TD_wrap as interpolate_TD_wrap_cpu
 
 from bbhx.utils.constants import *
 

bbhx/waveformbuild.py

@@ -85,7 +85,7 @@ def template_channels(self):
     @property
     def citation(self):
         """citations for this class"""
-        return katz_1 + katz_2
+        return katz_citations
 
     def __call__(
         self,
@@ -299,12 +299,7 @@ def __init__(
     def citation(self):
         """Citations for this class"""
         return (
-            katz_1
-            + katz_2
-            + marsat_1
-            + marsat_2
-            + phenomhm_citation
-            + phenomd_citations
+            katz_citations + marsat_1 + marsat_2 + phenomhm_citation + phenomd_citations
         )
 
     def __call__(

bbhx/waveforms/phenomhm.py

@@ -140,7 +140,7 @@ def __init__(self, use_gpu=False, run_phenomd=False, mf_min=1e-4, mf_max=0.6):
     @property
     def citation(self):
         """Return citations for this class"""
-        return katz_1 + katz_2 + phenomhm_citation + phenomd_citations
+        return katz_citations + phenomhm_citation + phenomd_citations
 
     def _init_phenomd_fring_spline(self):
         """Prepare PhenomD fring and fdamp splines"""

docs/doctrees/nbsphinx/bbhx_tutorial.ipynb

@@ -13,7 +13,7 @@
    "source": [
     "`bbhx` is a software package that produces black hole binary waveforms. It focuses on LISA and provides the proper LISA response function for MBHBs ([arXiv:1806.10734](https://arxiv.org/abs/1806.10734), [arXiv:2003.00357](https://arxiv.org/abs/2003.00357)). `bbhx` also provides fast likelihood functions. The package is GPU-accelerated for fast analysis. \n",
     "\n",
-    "If you use this software please cite [arXiv:2005.01827](https://arxiv.org/abs/2005.01827) and [arXiv:2111.01064](https://arxiv.org/abs/2111.01064) any parts within the package that you use (like waveforms and response functions). See the `citation` attribute for each class. "
+    "If you use this software please cite [arXiv:2005.01827](https://arxiv.org/abs/2005.01827), [arXiv:2111.01064](https://arxiv.org/abs/2111.01064), and the associated [Zenodo page](https://zenodo.org/record/5730688#.YaFvRkJKhTY) Please also cite any consituent parts used like the response function or waveforms. See the `citation` attribute for each class or docstring for functions for more information. "
    ]
   },
   {
@@ -857,7 +857,7 @@
     {
      "data": {
       "text/plain": [
-       "<matplotlib.legend.Legend at 0x7fd2d4ae4150>"
+       "<matplotlib.legend.Legend at 0x7ffe90dcbc90>"
       ]
      },
      "execution_count": 17,
@@ -1482,7 +1482,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 30,
+   "execution_count": 27,
    "metadata": {},
    "outputs": [
     {
@@ -1524,7 +1524,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 31,
+   "execution_count": 28,
    "metadata": {},
    "outputs": [
     {
@@ -1553,7 +1553,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 32,
+   "execution_count": 29,
    "metadata": {},
    "outputs": [
     {
@@ -1588,7 +1588,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 33,
+   "execution_count": 30,
    "metadata": {},
    "outputs": [
     {
@@ -1654,7 +1654,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 27,
+   "execution_count": 31,
    "metadata": {},
    "outputs": [
     {
@@ -1686,6 +1686,16 @@
       "    year = \"2021\"\n",
       "}\n",
       "\n",
+      "@article{michael katz_2021,\n",
+      "    title={mikekatz04/BBHx: First official public release},\n",
+      "    DOI={10.5281/zenodo.5730688},\n",
+      "    abstractNote={No description provided.},\n",
+      "    publisher={Zenodo},\n",
+      "    author={Michael Katz},\n",
+      "    year={2021},\n",
+      "    month={Nov}\n",
+      "}\n",
+      "\n",
       "@article{Marsat:2018oam,\n",
       "    author = \"Marsat, Sylvain and Baker, John G.\",\n",
       "    title = \"{Fourier-domain modulations and delays of gravitational-wave signals}\",\n",