[Scientific Documentation] - Update to rufas.bib

changelog.md

@@ -24,7 +24,7 @@ A **changelog** is a structured record of changes made to the codebase over time
 v1.0.0
 
 ### Next Version Updates
-- [2865](https://github.com/RuminantFarmSystems/RuFaS/pull/2865) - [minor change] [NoInputChange] [NoOutputChange] Update to tables and formatting in scientific documentation.
+
 - [2727](https://github.com/RuminantFarmSystems/RuFaS/pull/2727) - [minor change] [NoInputChange] [NoOutputChange] Update the TaskType in Wiki, and fix the broken Sphinx action.
 - [2728](https://github.com/RuminantFarmSystems/RuFaS/pull/2728) - [minor change] [InputManager] [NoInputChange] [NoOutputChange] Enforces the required file blobs.
 - [2743](https://github.com/RuminantFarmSystems/RuFaS/pull/2743) - [minor change] [NoInputChange] [NoOutputChange] Fix broken IM unit test.
@@ -46,11 +46,17 @@ v1.0.0
 - [2848](https://github.com/RuminantFarmSystems/MASM/pull/2848) - [minor change] [NoInputChange] [NoOutputChange] Justify `deepcopy()` usage.
 - [2843](https://github.com/RuminantFarmSystems/MASM/pull/2843) - [minor change] [NoInputChange] [NoOutputChange] Fix Simple `#noqa`s in codebase.
 - [2852](https://github.com/RuminantFarmSystems/MASM/pull/2852) - [minor change] [NoInputChange] [NoOutputChange] Fix AssertionError on `dev`.
+- [2865](https://github.com/RuminantFarmSystems/RuFaS/pull/2865) - [minor change] [NoInputChange] [NoOutputChange] Update to tables and formatting in scientific documentation.
 - [2866](https://github.com/RuminantFarmSystems/MASM/pull/2866) - [minor change] [NoInputChange] [NoOutputChange] Clears all mypy errors in test_field_manager.py.
 - [2863](https://github.com/RuminantFarmSystems/MASM/pull/2863) - [minor change] [NoInputChange] [NoOutputChange] Updates TaskManager to avoid using multiprocessing when running single tasks.
 - [2867](https://github.com/RuminantFarmSystems/MASM/pull/2867) - [minor change] [NoInputChange] [NoOutputChange] Updates expand_data_temporally() util function to offer options of full simulation expansion and front-padding data.
 - [2854](https://github.com/RuminantFarmSystems/MASM/pull/2854) - [minor change] [Emissions][OutputManager] [NoInputChange] [NoOutputChange] Update `emissions.py` filtering process and remove `use_filter_key_name` option in the OM filter.
 - [2872](https://github.com/RuminantFarmSystems/RuFaS/pull/2872) - [minor change] [NoInputChange] [NoOutputChange] Adds information and links for onboarding videos.
+- [2876](https://github.com/RuminantFarmSystems/RuFaS/pull/2876) - [minor change] [DieselConsumption][OutputManager] [NoInputChange] [NoOutputChange] Removes `use_name` output filter option and updates `DieselConsumption` to filter properly without it.
+- [2880](https://github.com/RuminantFarmSystems/RuFaS/pull/2880) - [minor change] [NoInputChange] [NoOutputChange] Add warning message for e2e filter updates
+- [2869](https://github.com/RuminantFarmSystems/RuFaS/pull/2869) - [minor change] [InputChange] [NoOutputChange] Removes `properties` and `cross-validation` file path definitions from metadata JSON files. Properties file paths are now defined as a module-level constant in `input_manager.py`, and cross-validation file paths are moved to the task configuration JSON files.
+- [2850](https://github.com/RuminantFarmSystems/MASM/pull/2850) - [minor change] [NoInputChange] [NoOutputChange] Refactor `Pen.get_manure_stream()`.
+- [2897](https://github.com/RuminantFarmSystems/RuFaS/pull/2897) - [minor change] [NoInputChange] [NoOutputChange] Update references in scientific documentation and proposal of workflow.
 - [2850](https://github.com/RuminantFarmSystems/RuFaS/pull/2850) - [minor change] [NoInputChange] [NoOutputChange] Refactor `Pen.get_manure_stream()`.
 - [2902](https://github.com/RuminantFarmSystems/RuFaS/pull/2902) - [minor change] [NoInputChange] [NoOutputChange] Add v1.0.0 release notes.
 - [2740](https://github.com/RuminantFarmSystems/RuFaS/pull/2740) - [minor change] [NoInputChange] [NoOutputChange] Added warnings for feed purchases exceeding advance purchase allowance/

docs/scientific/animal.tex

@@ -6073,10 +6073,11 @@ \subsection{Enteric Methane Emission}
 
         \item \textbf{Lactating Cow Methane Emissions (calculate\_cow\_methane)}
 
-For lactating cows, the Mutian, Mills, or IPCC model is applied. \nocite{Niu2018}
+For lactating cows, the Mutian, Mills, or IPCC model is applied. 
             \vspace{0.5cm}
 
-\paragraph{Mutian Model}\nocite{Niu2018}
+\paragraph{Mutian Model}
+
 \vspace{-0.25cm}
 
     \begin{center}
@@ -6085,6 +6086,9 @@ \subsection{Enteric Methane Emission}
         \vspace{0.5cm} 
 
             {\raggedleft \textbf{[AN.MET.6]}\par}
+            \vspace{0.15cm}
+
+            {\raggedleft\parencite{Niu2018}\par}
             \vspace{0.5cm}
 
 \paragraph{Mills Model}

docs/scientific/animalmoddoc.aux

@@ -166,22 +166,20 @@
 \abx@aux@segm{1}{0}{Pattanaik2003}
 \abx@aux@cite{1}{Niu2018}
 \abx@aux@segm{1}{0}{Niu2018}
-\abx@aux@cite{1}{Niu2018}
-\abx@aux@segm{1}{0}{Niu2018}
 \abx@aux@cite{1}{Mills2003}
 \abx@aux@segm{1}{0}{Mills2003}
 \abx@aux@page{44}{113}
+\abx@aux@page{45}{113}
 \abx@aux@cite{1}{Niu2018}
 \abx@aux@segm{1}{0}{Niu2018}
 \abx@aux@cite{1}{Mills2003}
 \abx@aux@segm{1}{0}{Mills2003}
 \abx@aux@cite{1}{Niu2018}
 \abx@aux@segm{1}{0}{Niu2018}
-\abx@aux@page{45}{114}
 \abx@aux@page{46}{114}
+\abx@aux@page{47}{114}
 \abx@aux@cite{1}{Kebreab2023}
 \abx@aux@segm{1}{0}{Kebreab2023}
-\abx@aux@page{47}{118}
 \abx@aux@page{48}{118}
 \abx@aux@page{49}{118}
 \abx@aux@page{50}{118}
@@ -202,14 +200,15 @@
 \abx@aux@page{65}{118}
 \abx@aux@page{66}{118}
 \abx@aux@page{67}{118}
-\abx@aux@page{68}{119}
+\abx@aux@page{68}{118}
 \abx@aux@page{69}{119}
 \abx@aux@page{70}{119}
 \abx@aux@page{71}{119}
 \abx@aux@page{72}{119}
 \abx@aux@page{73}{119}
 \abx@aux@page{74}{119}
 \abx@aux@page{75}{119}
+\abx@aux@page{76}{119}
 \abx@aux@read@bbl@mdfivesum{CC895D968E19D8818F4DCC6BF3DD33CD}
 \abx@aux@defaultrefcontext{1}{appuhamy2014}{nyt/global//global/global}
 \abx@aux@defaultrefcontext{1}{appuhamy2018}{nyt/global//global/global}

docs/scientific/animalmoddoc.bcf

@@ -2424,13 +2424,12 @@
     <bcf:citekey order="54" intorder="1">Niu2018</bcf:citekey>
     <bcf:citekey order="55" intorder="1">Pattanaik2003</bcf:citekey>
     <bcf:citekey order="56" intorder="1">Pattanaik2003</bcf:citekey>
-    <bcf:citekey order="57" intorder="14">Niu2018</bcf:citekey>
-    <bcf:citekey order="58" intorder="15">Niu2018</bcf:citekey>
-    <bcf:citekey order="59" intorder="1">Mills2003</bcf:citekey>
-    <bcf:citekey order="60" intorder="16">Niu2018</bcf:citekey>
-    <bcf:citekey order="61" intorder="1">Mills2003</bcf:citekey>
-    <bcf:citekey order="62" intorder="17">Niu2018</bcf:citekey>
-    <bcf:citekey order="63" intorder="14" nocite="1">Kebreab2023</bcf:citekey>
+    <bcf:citekey order="57" intorder="1">Niu2018</bcf:citekey>
+    <bcf:citekey order="58" intorder="1">Mills2003</bcf:citekey>
+    <bcf:citekey order="59" intorder="14">Niu2018</bcf:citekey>
+    <bcf:citekey order="60" intorder="1">Mills2003</bcf:citekey>
+    <bcf:citekey order="61" intorder="15">Niu2018</bcf:citekey>
+    <bcf:citekey order="62" intorder="14" nocite="1">Kebreab2023</bcf:citekey>
   </bcf:section>
   <!-- SECTION 0 (cont.) -->
   <bcf:section number="0">

docs/scientific/animalmoddoc.blg

@@ -1,17 +1,17 @@
 [0] Config.pm:307> INFO - This is Biber 2.19
 [0] Config.pm:310> INFO - Logfile is 'animalmoddoc.blg'
-[137] biber-MSWIN64:340> INFO - === 
-[179] Biber.pm:419> INFO - Reading 'animalmoddoc.bcf'
-[305] Biber.pm:979> INFO - Found 0 citekeys in bib section 0
-[316] Biber.pm:979> INFO - Found 29 citekeys in bib section 1
-[316] Biber.pm:979> INFO - Found 0 citekeys in bib section 0
-[338] Biber.pm:4419> INFO - Processing section 1
-[353] Biber.pm:4610> INFO - Looking for bibtex file 'resources/animal.bib' for section 1
-[401] bibtex.pm:1713> INFO - LaTeX decoding ...
-[480] bibtex.pm:1519> INFO - Found BibTeX data source 'resources/animal.bib'
-[718] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized'
-[719] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable'
-[719] Biber.pm:4239> INFO - Sorting list 'nyt/global//global/global' of type 'entry' with template 'nyt' and locale 'en-US'
-[719] Biber.pm:4245> INFO - No sort tailoring available for locale 'en-US'
-[764] bbl.pm:660> INFO - Writing 'animalmoddoc.bbl' with encoding 'UTF-8'
-[794] bbl.pm:763> INFO - Output to animalmoddoc.bbl
+[171] biber-MSWIN64:340> INFO - === 
+[226] Biber.pm:419> INFO - Reading 'animalmoddoc.bcf'
+[417] Biber.pm:979> INFO - Found 0 citekeys in bib section 0
+[420] Biber.pm:979> INFO - Found 29 citekeys in bib section 1
+[420] Biber.pm:979> INFO - Found 0 citekeys in bib section 0
+[454] Biber.pm:4419> INFO - Processing section 1
+[474] Biber.pm:4610> INFO - Looking for bibtex file 'resources/animal.bib' for section 1
+[535] bibtex.pm:1713> INFO - LaTeX decoding ...
+[630] bibtex.pm:1519> INFO - Found BibTeX data source 'resources/animal.bib'
+[904] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized'
+[904] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable'
+[904] Biber.pm:4239> INFO - Sorting list 'nyt/global//global/global' of type 'entry' with template 'nyt' and locale 'en-US'
+[904] Biber.pm:4245> INFO - No sort tailoring available for locale 'en-US'
+[953] bbl.pm:660> INFO - Writing 'animalmoddoc.bbl' with encoding 'UTF-8'
+[983] bbl.pm:763> INFO - Output to animalmoddoc.bbl

docs/scientific/animalmoddoc.fdb_latexmk

@@ -1,14 +1,14 @@
 # Fdb version 4
-["biber animalmoddoc"] 1773835560.74045 "animalmoddoc.bcf" "animalmoddoc.bbl" "animalmoddoc" 1773836218.08485 0
-  "animalmoddoc.bcf" 1773836216 112259 a9526a3fa13d06622e8c4a1f0455c20c "pdflatex"
+["biber animalmoddoc"] 1774467128.73376 "animalmoddoc.bcf" "animalmoddoc.bbl" "animalmoddoc" 1774467146.70023 0
+  "animalmoddoc.bcf" 1774467145 112194 72c43d110da38474e319f62b9067eddf "pdflatex"
   "resources/animal.bib" 1773235466 19843 003ce6dc3163a9c1fd885dbc082d404e ""
   (generated)
   "animalmoddoc.bbl"
   "animalmoddoc.blg"
   (rewritten before read)
-["pdflatex"] 1773836210.18723 "c:/Users/gmg228/Documents/RuFaS/RuFaS/docs/scientific/animalmoddoc.tex" "animalmoddoc.pdf" "animalmoddoc" 1773836218.08629 0
+["pdflatex"] 1774467140.30855 "c:/Users/gmg228/Documents/RuFaS/RuFaS/docs/scientific/animalmoddoc.tex" "animalmoddoc.pdf" "animalmoddoc" 1774467146.70145 0
   "C:/Program Files/MiKTeX/tex/latex/listings/lstpatch.sty" 1763898348 353 9024412f43e92cd5b21fe9ded82d0610 ""
-  "C:/Users/gmg228/AppData/Local/MiKTeX/fonts/map/pdftex/pdftex.map" 1772637374 82507 a9eef8696c92627b87e9975edea03b2a ""
+  "C:/Users/gmg228/AppData/Local/MiKTeX/fonts/map/pdftex/pdftex.map" 1773946257 83609 ebbc432e6cbbb238d39535255db2c8bd ""
   "C:/Users/gmg228/AppData/Local/MiKTeX/fonts/pk/ljfour/jknappen/ec/dpi600/ecbi1000.pk" 1772637453 34112 54862e108df8d433db242fb093842b53 ""
   "C:/Users/gmg228/AppData/Local/MiKTeX/fonts/pk/ljfour/jknappen/ec/dpi600/ecbx0700.pk" 1772637444 17380 be101539a19ecb433571ddcd4b4463c8 ""
   "C:/Users/gmg228/AppData/Local/MiKTeX/fonts/pk/ljfour/jknappen/ec/dpi600/ecbx1000.pk" 1772637467 25420 fe3092a866f84fb0ab9aeb0748b0ba18 ""
@@ -270,17 +270,17 @@
   "C:/Users/gmg228/AppData/Local/Programs/MiKTeX/tex/latex/url/url.sty" 1388490452 12796 8edb7d69a20b857904dd0ea757c14ec9 ""
   "C:/Users/gmg228/AppData/Local/Programs/MiKTeX/tex/latex/xcolor/xcolor.sty" 1700127522 55487 80a65caedd3722f4c20a14a69e785d8f ""
   "C:/Users/gmg228/AppData/Local/Programs/MiKTeX/tex/latex/xurl/xurl.sty" 1641733940 4675 e4b8c405820368c2dfb03526e16d725a ""
-  "animal.aux" 1773836216 40043 755bfadf5fbf0353c98167e764fbe0aa "pdflatex"
-  "animal.tex" 1773836205 266447 88be983bc824fdd69b4fcb1bf89be974 ""
-  "animalmoddoc.aux" 1773836216 7986 9228d355014ad0137b098bb0d7495673 "pdflatex"
-  "animalmoddoc.bbl" 1773835564 58386 3dfad22d6024395a171e9fb63bf83d65 "biber animalmoddoc"
-  "animalmoddoc.out" 1773836216 4493 549ea7cd37b333b963d30b88592a3938 "pdflatex"
-  "animalmoddoc.run.xml" 1773836216 2407 5735db26526a7c8c171c357b53dd5a9b "pdflatex"
-  "animalmoddoc.tex" 1773835015 574 086e450d70a56906aa4eeebcce58437f ""
-  "animalmoddoc.toc" 1773836216 14327 fa5bc811de5a8acabf5746799c5aedbd "pdflatex"
-  "c:/Users/gmg228/Documents/RuFaS/RuFaS/docs/scientific/animalmoddoc.tex" 1773835015 574 086e450d70a56906aa4eeebcce58437f ""
-  "preamble.tex" 1773835015 4428 2ef0341e8930c3026632d61f45471d7e ""
-  "resources/animal1.png" 1773835015 204760 63ad4e90063ffaed258c1eb7fc2a7889 ""
+  "animal.aux" 1774467145 40043 aca414875a6883809fb068beca4d81ae "pdflatex"
+  "animal.tex" 1774467137 266498 abd392cc3c6d6a10a6acf1d6553ebb11 ""
+  "animalmoddoc.aux" 1774467145 7954 fb2ed8807c79012a6678b0c81e16d262 "pdflatex"
+  "animalmoddoc.bbl" 1774467132 58386 3dfad22d6024395a171e9fb63bf83d65 "biber animalmoddoc"
+  "animalmoddoc.out" 1774467145 4493 549ea7cd37b333b963d30b88592a3938 "pdflatex"
+  "animalmoddoc.run.xml" 1774467145 2407 5735db26526a7c8c171c357b53dd5a9b "pdflatex"
+  "animalmoddoc.tex" 1774279829 574 086e450d70a56906aa4eeebcce58437f ""
+  "animalmoddoc.toc" 1774467145 14327 fa5bc811de5a8acabf5746799c5aedbd "pdflatex"
+  "c:/Users/gmg228/Documents/RuFaS/RuFaS/docs/scientific/animalmoddoc.tex" 1774279829 574 086e450d70a56906aa4eeebcce58437f ""
+  "preamble.tex" 1774442779 4428 2ef0341e8930c3026632d61f45471d7e ""
+  "resources/animal1.png" 1774442779 204760 63ad4e90063ffaed258c1eb7fc2a7889 ""
   "resources/animalgroups.png" 1773235466 99003 12ad61c91b0f8e47e62249e2fdb458b9 ""
   "resources/cowbreedmethod.png" 1773235466 249475 26a2153096ad61f7889191c615bffca3 ""
   "resources/milkrationform.png" 1773235466 181549 021e5e317dfffb2742f68e1379dd4b6a ""

docs/scientific/crop_and_soil.aux

@@ -154,7 +154,7 @@
 \setcounter{citetotal}{0}
 \setcounter{multicitecount}{0}
 \setcounter{multicitetotal}{0}
-\setcounter{instcount}{166}
+\setcounter{instcount}{167}
 \setcounter{maxnames}{3}
 \setcounter{minnames}{1}
 \setcounter{maxitems}{3}

docs/scientific/feed_storage.aux

@@ -71,7 +71,7 @@
 \setcounter{citetotal}{0}
 \setcounter{multicitecount}{0}
 \setcounter{multicitetotal}{0}
-\setcounter{instcount}{171}
+\setcounter{instcount}{172}
 \setcounter{maxnames}{3}
 \setcounter{minnames}{1}
 \setcounter{maxitems}{3}