Fix inline cite problem and add bibliography page (#1137)

* fix cite rendering problem

* fix bib file

* add bibliography file

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

docs/source/_config.yml

@@ -47,7 +47,7 @@ sphinx:
     'sphinxcontrib.mermaid'
   ]
   config:
-    bibtex_reference_style: author_year
+    bibtex_reference_style: label
   #   # https://github.com/executablebooks/jupyter-book/issues/1186
   #   # https://sphinx-book-theme.readthedocs.io/en/latest/customize/sidebar-secondary.html
   #   html_theme_options:

docs/source/_toc.yml

@@ -26,10 +26,11 @@ parts:
   - file: viz
   - file: processing-levels
     title: Processing levels
-- caption: Help & reference
+- caption: Help & references
   chapters:
-  - file: api
   - file: whats-new
-  - file: roadmap
   - file: contributing
+  - file: api
+  - file: zbibliography
+  - file: roadmap
   - file: resources

docs/source/data-proc-func.ipynb

@@ -403,7 +403,7 @@
         "When custom environmental values are supplied, echopype calculates sound speed and absorption coefficients based on the following:\n",
         "- EK60 and EK80:\n",
         "    - sound speed: {cite}`MacKenzie1981`\n",
-        "    - absorption coefficients: {cite}`MacKenzie1981`\n",
+        "    - absorption coefficients: {cite}`Ainslie1998`\n",
         "- AZFP: formulae provided in the AZFP Operator's Manual from ASL Environmental Sciences"
       ]
     },

docs/source/references.bib

@@ -1,22 +1,19 @@
 @article{DeRobertis2007_noise,
 	title = {A post-processing technique to estimate the signal-to-noise ratio and remove echosounder background noise},
 	volume = {64},
-	url = {http://icesjms.oxfordjournals.org.libproxy.mit.edu/cgi/content/abstract/64/6/1282},
 	doi = {10.1093/icesjms/fsm112},
 	number = {6},
-	urldate = {2009-08-03},
 	journal = {ICES J. Mar. Sci.},
 	author = {De Robertis, Alex and Higginbottom, Ian},
-	month = sep,
 	year = {2007},
 	pages = {1282--1291},
 }
 @techreport{Demer2015,
-	title = {Calibration of acoustic instruments. {ICES} {Cooperative} {Research} {Report} {No}.326},
+	title = {Calibration of acoustic instruments},
 	institution = {ICES Cooperative Research Report, No. 326},
 	author = {Demer, D.A. and Berger, L. and Bernasconi, M. and Bethke, E. and Boswell, Kevin M. and Chu, D. and Domokos, R. and Dunford, A. and Fassler, Sascha and Gauthier, S. and Hufnagle, L. and Jech, J. and Bouffant, N. and Lebourges-Dhaaussy, A. and Lurton, X. and Macaulay, G. and Perrot, Y. and Ryan, T. and Parker-Stetter, Sandra L. and Stienessen, S. and Weber, Tom and Williamson, Neal},
 	year = {2015},
-	note = {ISBN: 9788774821670},
+	doi = {10.17895/ices.pub.5494},
 	pages = {133 pp},
 }
 @article{MacKenzie1981,
@@ -27,18 +24,17 @@ @article{MacKenzie1981
 	author = {MacKenzie, Kenneth V},
 	year = {1981},
 	pages = {807--812},
+	doi = {10.1121/1.386920},
 }
-@article{ainslie_simplified_1998,
+@article{Ainslie1998,
 	title = {A simplified formula for viscous and chemical absorption in sea water},
 	volume = {103},
 	issn = {0001-4966},
-	url = {https://asa.scitation.org/doi/10.1121/1.421258},
 	doi = {10.1121/1.421258},
 	number = {3},
 	urldate = {2022-01-14},
 	journal = {The Journal of the Acoustical Society of America},
 	author = {Ainslie, Michael A. and McColm, James G.},
-	month = mar,
 	year = {1998},
 	note = {Publisher: Acoustical Society of America},
 	pages = {1671--1672},

docs/source/zbibliography.md

@@ -0,0 +1,4 @@
+# Bibliography
+
+```{bibliography} references.bib
+```