Merge pull request #711 from dirac-institute/cite_updates

document minor updates and update citation text
dirac-institute · Oct 19, 2023 · afa3b40 · afa3b40
2 parents 3b1f641 + e7f2682
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diff --git a/docs/cite.rst b/docs/cite.rst
@@ -1,14 +1,26 @@
 Citing the Software
 ==========================
 
-Cite our AAS journal software paper and JOS paper. (in prep)
+Built-In Citation Function
+----------------------------
+If you use Sorcha in your research, please do include a citation in your published papers for sorcha and the software packages and resources that sorcha is based on. The simplest way to find this information is to use our built-in citation function. In an interactive python session or a Jupyter notebook::
+
+   import sorcha
+   sorcha.cite()
+
+
+Additional Citation Details
+----------------------------
+
+The main overview of Sorcha is provided in our AAS journal software papers and JOS paper. (in prep)
 
 Please also cite the software and ancillary data files that helps power Sorcha:
 
 * assist https://assist.readthedocs.io/en/latest/
 * astropy https://www.astropy.org/acknowledging.html
 * healpy https://healpy.readthedocs.io/en/latest/
 * matplotlib https://matplotlib.org/stable/users/project/citing.html
+* Minor Planet Center https://www.minorplanetcenter.net/data
 * numba https://numba.pydata.org/ 
 * numpy https://numpy.org/citing-numpy/
 * pandas https://pandas.pydata.org/about/citing.html
@@ -21,5 +33,6 @@ Please also cite the software and ancillary data files that helps power Sorcha:
 * spiceypy https://spiceypy.readthedocs.io/en/main/citation.html
 * tqdm https://tqdm.github.io/
 
-
+.. note::
+   The same information is available from our built-in citation function.
 
diff --git a/docs/contributors.rst b/docs/contributors.rst
@@ -3,5 +3,5 @@ Contributors
 
 The people who contributed to Sorcha include:
 
-Pedro Bernardinelli, Aidan Berres, Colin Orion Chandler, Carl Christofferson, Sam Cornwall, Siegfried Eggl, Grigori Fedorets, Matt Holman, Lynne Jones, Mario Jurić, Jeremy Kubica, Jake Kurlander, Michael S. P. Kelley, Conor MacBride, Shannon Matthews, Steph Merritt, Joachim Moeyens, Shantanu Naidu, Drew Oldag, Brian Rogers, Meg Schwamb, Colin Snodgrass, Max West, Dave Young
+Pedro Bernardinelli, Aidan Berres, Colin Orion Chandler, Carl Christofferson, Sam Cornwall, Siegfried Eggl, Grigori Fedorets, Matt Holman, Lynne Jones, Mario Jurić, Jeremy Kubica, Jake Kurlander, Michael S. P. Kelley, Conor MacBride, Shannon Matthews, Steph Merritt, Joachim Moeyens, Joe Murtagh, Shantanu Naidu, Drew Oldag, Brian Rogers, Meg Schwamb, Colin Snodgrass, Max West, Dave Young
 
diff --git a/docs/installation.rst b/docs/installation.rst
@@ -48,7 +48,7 @@ If using mamba::
 .. tip::
    We recommend using python version 3.9 or higher with Sorcha. The conda command uses python 3.10.
 
-**Step 2** Activate your conda/mamba environment::
+**Step 2** Activate your conda/mamba environment
 
 On conda::
 
@@ -116,7 +116,7 @@ To install the necessary SPICE auxiliary files for ephemeris generation (774 MB
 
     bootstrap_sorcha_data_files
 
-.. info::
+.. note::
    This script will download and store the auxillary files in your computer's local cache directory. 
 
 .. note::

diff --git a/docs/uninstall.rst b/docs/uninstall.rst
@@ -1,6 +1,14 @@
 Uninstalling 
 =================
 
+If you have installed Sorcha using conda, then you can uninstall the package with::
+
+   conda uninstall sorcha
+
+If you have installed Sorcha using mamba, then you can uninstall the package with::
+
+   mamba uninstall sorcha
+
 If you have installed Sorcha using pip, then you can uninstall the package with::
 
    pip uninstall sorcha

diff --git a/src/sorcha/utilities/citation_text.py b/src/sorcha/utilities/citation_text.py
@@ -8,6 +8,8 @@ def cite_sorcha():
     print("\nSorcha: \n")
     print("Merritt et al. (in prep)")
 
+    print("\n")
+
     print("Please also cite the packages that are utilized by Sorcha:")
 
     print("\nAstropy:\n")
@@ -400,7 +402,37 @@ def cite_sorcha():
     print(" adsnote = {Provided by the SAO/NASA Astrophysics Data System}")
     print("}")
 
-    print("\nAssist:\n")
+    print("\nASSIST:\n")
+
+    print("@ARTICLE{2023PSJ.....4...69H,")
+    print(
+        "author = {{Holman}, Matthew J. and {Akmal}, Arya and {Farnocchia},"
+        " Davide and {Rein}, Hanno and {Payne}, Matthew J. and {Weryk}, Robert"
+        " and {Tamayo}, Daniel and {Hernandez}, David M.},"
+    )
+    print('title = "{ASSIST: An Ephemeris-quality Test-particle Integrator}",')
+    print("journal = {\psj},")
+    print(
+        "keywords = {Ephemerides, N-body simulations, Asteroid dynamics, "
+        "Comet dynamics, 464, 1083, 2210, 2213, Astrophysics - Earth and Planetary Astrophysics,"
+        "Astrophysics - Instrumentation and Methods for Astrophysics},"
+    )
+    print("year = 2023,")
+    print("month = apr,")
+    print("volume = {4},")
+    print("number = {4},")
+    print("eid = {69},")
+    print("pages = {69},")
+    print("doi = {10.3847/PSJ/acc9a9},")
+    print("archivePrefix = {arXiv},")
+    print("eprint = {2303.16246},")
+    print("primaryClass = {astro-ph.EP},")
+    print("adsurl = {https://ui.adsabs.harvard.edu/abs/2023PSJ.....4...69H},")
+    print("adsnote = {Provided by the SAO/NASA Astrophysics Data System}")
+    print("}")
+
+    print("\n")
+
     print("@software{hanno_rein_2023_7778017,")
     print("author       = {Hanno Rein and matthewholman and Arya Akmal},")
     print("title        = {matthewholman/assist: v1.1.1},")
@@ -412,7 +444,7 @@ def cite_sorcha():
     print("url          = {https://doi.org/10.5281/zenodo.7778017}")
     print("}")
 
-    print("\nRebound:\n")
+    print("\nREBOUND:\n")
     sim = rebound.Simulation()
     sim.cite()
 
@@ -490,7 +522,13 @@ def cite_sorcha():
     print("}")
 
     print(
-        "Add an acknowledgment statement:  The SPICE Resource files used in this work ere described in \citep{1996P&SS...44...65A, 2018P&SS..150....9A}"
+        "\nAdd an acknowledgment statement:  The SPICE Resource files used in this work ere described in \citep{1996P&SS...44...65A, 2018P&SS..150....9A}"
+    )
+
+    print("\nMinor Planet Center Resources:\n")
+
+    print(
+        "Add an acknowledgment statement: This research has made use of data and/or services provided by the International Astronomical Union's Minor Planet Center. "
     )
 
     print("\nHealpy:\n")
@@ -627,23 +665,31 @@ def cite_sorcha():
 
     print("\n")
     print(
-        "If you are submitting a paper to AAS Journals journals, here's "
-        "the software citation latex command you will need once including "
-        "all the above bibtex references above.\n"
+        "If you are submitting a paper to AAS Journals, here is"
+        " the software citation latex command you will need once you have included "
+        "all of the above  bibtex references above.\n"
     )
 
     print(
-        "\\software{Sorcha, Astropy \citep{2013A&A...558A..33A,2018AJ....156..123A,2022ApJ...935..167A}, "
-        "Numpy \citep{harris2020array}, pandas \citep{mckinney-proc-scipy-2010, reback2020pandas}, "
-        "SciPy \citep{2020SciPy-NMeth}, Numba \citep{2015llvm.confE...1L},  "
-        "sbpy \citep{2019JOSS....4.1426M}, Matplotlib \citep{Hunter:2007}, "
-        "PyTables \citep{pytables}, Assist \citep{hanno_rein_2023_7778017},"
-        "Rebound \citep{rebound,reboundias15}, Pooch \citep{uieda2020}, "
-        "Spiceypy \citep{2020JOSS....5.2050A},  Healpy \citep{Zonca2019,2005ApJ...622..759G}, "
-        "tqdm \citep{casper_da_costa_luis_2023_8233425}, rubin$\_$sim "
-        "\citep{2018Icar..303..181J,peter_yoachim_2022_7087823}, "
+        "\\software{"
+        "Sorcha,"
+        "ASSIST \citep{2023PSJ.....4...69H,hanno_rein_2023_7778017},"
+        "Astropy \citep{2013A&A...558A..33A,2018AJ....156..123A,2022ApJ...935..167A}, "
+        "Healpy \citep{Zonca2019,2005ApJ...622..759G}, "
+        "Matplotlib \citep{Hunter:2007}, "
+        "Numba \citep{2015llvm.confE...1L}, "
+        "Numpy \citep{harris2020array}, "
+        "pandas \citep{mckinney-proc-scipy-2010, reback2020pandas}, "
+        "Pooch \citep{uieda2020}, "
+        "PyTables \citep{pytables}, "
+        "REBOUND \citep{rebound,reboundias15}, "
+        "rubin$\_$sim \citep{2018Icar..303..181J,peter_yoachim_2022_7087823}, "
+        "sbpy \citep{2019JOSS....4.1426M}, "
+        "SciPy \citep{2020SciPy-NMeth}, "
+        "Spiceypy \citep{2020JOSS....5.2050A}, "
         "sqlite (\\url{https://www.sqlite.org/index.html}), "
         "sqlite3 (\\url{https://docs.python.org/3/library/sqlite3.html}), "
+        "tqdm \citep{casper_da_costa_luis_2023_8233425}, "
         "Black (\\url{https://black.readthedocs.io/en/stable/faq.html}), "
         "Jupyter Notebooks \citep{soton403913}}"
     )
Original file line number	Diff line number	Diff line change
Expand Up		@@ -3,5 +3,5 @@ Contributors

		The people who contributed to Sorcha include:

		Pedro Bernardinelli, Aidan Berres, Colin Orion Chandler, Carl Christofferson, Sam Cornwall, Siegfried Eggl, Grigori Fedorets, Matt Holman, Lynne Jones, Mario Jurić, Jeremy Kubica, Jake Kurlander, Michael S. P. Kelley, Conor MacBride, Shannon Matthews, Steph Merritt, Joachim Moeyens, Shantanu Naidu, Drew Oldag, Brian Rogers, Meg Schwamb, Colin Snodgrass, Max West, Dave Young
		Pedro Bernardinelli, Aidan Berres, Colin Orion Chandler, Carl Christofferson, Sam Cornwall, Siegfried Eggl, Grigori Fedorets, Matt Holman, Lynne Jones, Mario Jurić, Jeremy Kubica, Jake Kurlander, Michael S. P. Kelley, Conor MacBride, Shannon Matthews, Steph Merritt, Joachim Moeyens, Joe Murtagh, Shantanu Naidu, Drew Oldag, Brian Rogers, Meg Schwamb, Colin Snodgrass, Max West, Dave Young