Update paper.md: fixed references

Author: bnord

paper/paper.md

@@ -94,7 +94,7 @@ The full package workflow is demonstrated in \autoref{fig:workflow}.
 
 The `DeepCMBsim` package combines physical processes and sources of noise in a software framework that enables fast and realistic simulation of the CMB in which key cosmological parameters can be varied. `DeepCMBSim` simulates correlations of temperatures and polarization signals from the CMB, including large-scale gravitational lensing and BB polarization caused by non-zero tensor-to-scalar ratios.
 
-DeepCMBSim’s primary physics module is `camb_power_spectrum`, which defines the `CAMBPowerSpectrum` class. This calls `CAMB` [@Lewis:1999bs; @Howlett:2012mh]. The power spectrum of the noise follows the form in [@Hu:2001kj], assuming statistical independence in the Stokes parameters [@Knox:1995dq; @Zaldarriaga:1996xe].
+DeepCMBSim’s primary physics module is `camb_power_spectrum`, which defines the `CAMBPowerSpectrum` class. This calls `CAMB` [@Lewis:1999bs; @Howlett:2012mh]. The power spectrum of the noise follows the form in @\Hu:2001kj, assuming statistical independence in the Stokes parameters [@Knox:1995dq; @Zaldarriaga:1996xe].
 This software allows the user to specify cosmological parameters (e.g., omega matter, omega baryon, the lensing scale, the tensor-to-scalar ratio, which are inputs to CAMB) and experiment parameters (e.g., white noise level, beam size) in a  `yaml` configuration file to permit a user-friendly interface to permit reproducible simulations. The default parameters reproduce the Planck 2018 cosmology [@Planck:2018vyg]. 
 
 ![Example output angular spectra for the `DeepCMBsim` package for a set of tensor-to-scalar ratios r and lens scaling factors A_lens.\label{fig:cmb}](figures/CMBSpectra_Examples.png)
@@ -105,9 +105,9 @@ We present examples of the primary outputs from `DeepCMBSim` in  \autoref{fig:cm
 
 ## SZ Cluster Simulation
 
-`DeepSZsim` includes code for producing fast simulations of the thermal SZ effect for galaxy halos of varying mass and redshift, based on average thermal pressure profile fits from Battaglia et al. 2012 [@Battaglia:2012]. The output is an array of simulated submaps of the tSZ effect associated with galaxy halos, which can include simulated CMB, instrument beam convolution, and/or white noise. 
+`DeepSZsim` includes code for producing fast simulations of the thermal SZ effect for galaxy halos of varying mass and redshift, based on average thermal pressure profile fits from @\Battaglia:2012. The output is an array of simulated submaps of the tSZ effect associated with galaxy halos, which can include simulated CMB, instrument beam convolution, and/or white noise. 
 
-The user provides inputs to generate an array of redshift and mass ($M_{200}$) for dark matter halos, the desired pixel and submap size for the output submaps, and inputs such as experiment properties (observation frequency, noise level, beam size) and a cosmological model. These inputs are easily customizable, or the user can run defaults based on the Atacama Cosmology Telescope [@ACT:2021] and Planck cosmology [@Planck:2019]. Cosmology computations depend on `colossus` [@Colossus:2018] and `astropy` [@Astropy:2013].
+The user provides inputs to generate an array of redshift and mass ($M_{200}$) for dark matter halos, the desired pixel and submap size for the output submaps, and inputs such as experiment properties (observation frequency, noise level, beam size) and a cosmological model. These inputs are easily customizable, or the user can run defaults based on the Atacama Cosmology Telescope [@ACT:2021] and Planck cosmology [@Planck:2018vyg]. Cosmology computations depend on `colossus` [@Colossus:2018] and `astropy` [@Astropy:2013].
 
 From these inputs, pressure profiles, Compton-y profiles, and tSZ signal maps are generated for the dark matter halo array [@Kaiser:1986; @Arnaud:2010; @Battaglia:2012]. Simulated CMB primary anisotropy maps can be generated through a dependency on `DeepCMBSim`. Final simulated submaps can include instrument beam convolution and white noise [@actnotebooks:2015]. Plotting functions for the simulations and an aperture photometry filter are included as tools. The submap handling functions rely on `pixell` [@pixell:2024].