diff --git a/changelog.md b/changelog.md
index 2e2d892faa..3afa9961f1 100644
--- a/changelog.md
+++ b/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/
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+++ b/docs/scientific/animal.aux
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\@setckpt{animal}{
-\setcounter{page}{124}
+\setcounter{page}{120}
\setcounter{equation}{0}
\setcounter{enumi}{3}
\setcounter{enumii}{0}
@@ -386,7 +386,7 @@
\setcounter{enumiv}{0}
\setcounter{footnote}{0}
\setcounter{mpfootnote}{0}
-\setcounter{part}{2}
+\setcounter{part}{1}
\setcounter{section}{5}
\setcounter{subsection}{0}
\setcounter{subsubsection}{0}
@@ -399,7 +399,7 @@
\setcounter{section@level}{0}
\setcounter{Item}{37}
\setcounter{Hfootnote}{0}
-\setcounter{bookmark@seq@number}{20}
+\setcounter{bookmark@seq@number}{24}
\setcounter{tcbbreakpart}{1}
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@@ -425,7 +425,7 @@
\setcounter{citetotal}{0}
\setcounter{multicitecount}{0}
\setcounter{multicitetotal}{0}
-\setcounter{instcount}{75}
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@@ -439,8 +439,8 @@
\setcounter{refsegment}{0}
\setcounter{maxextratitle}{0}
\setcounter{maxextratitleyear}{0}
-\setcounter{maxextraname}{2}
-\setcounter{maxextradate}{2}
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\setcounter{abbrvpenalty}{50}
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@@ -530,6 +530,6 @@
\setcounter{smartand}{1}
\setcounter{bbx:relatedcount}{0}
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}
diff --git a/docs/scientific/animal.tex b/docs/scientific/animal.tex
index 72f2508d5f..58d6deda49 100644
--- a/docs/scientific/animal.tex
+++ b/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}
diff --git a/docs/scientific/animalmoddoc.aux b/docs/scientific/animalmoddoc.aux
index 2e0909cff4..6e61f9c449 100644
--- a/docs/scientific/animalmoddoc.aux
+++ b/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}
@@ -202,7 +200,7 @@
\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}
@@ -210,6 +208,7 @@
\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}
diff --git a/docs/scientific/animalmoddoc.bcf b/docs/scientific/animalmoddoc.bcf
index 29188b64d0..f4fb66e9cc 100644
--- a/docs/scientific/animalmoddoc.bcf
+++ b/docs/scientific/animalmoddoc.bcf
@@ -2424,13 +2424,12 @@
Niu2018
Pattanaik2003
Pattanaik2003
- Niu2018
- Niu2018
- Mills2003
- Niu2018
- Mills2003
- Niu2018
- Kebreab2023
+ Niu2018
+ Mills2003
+ Niu2018
+ Mills2003
+ Niu2018
+ Kebreab2023
diff --git a/docs/scientific/animalmoddoc.blg b/docs/scientific/animalmoddoc.blg
index 8fb9b831cb..4d5ed050e5 100644
--- a/docs/scientific/animalmoddoc.blg
+++ b/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
diff --git a/docs/scientific/animalmoddoc.fdb_latexmk b/docs/scientific/animalmoddoc.fdb_latexmk
index 9772cfa100..0f6fd8b400 100644
--- a/docs/scientific/animalmoddoc.fdb_latexmk
+++ b/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 ""
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@@ -270,17 +270,17 @@
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- "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"
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- "resources/animal1.png" 1773835015 204760 63ad4e90063ffaed258c1eb7fc2a7889 ""
+ "animal.aux" 1774467145 40043 aca414875a6883809fb068beca4d81ae "pdflatex"
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+ "animalmoddoc.bbl" 1774467132 58386 3dfad22d6024395a171e9fb63bf83d65 "biber animalmoddoc"
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+ "animalmoddoc.toc" 1774467145 14327 fa5bc811de5a8acabf5746799c5aedbd "pdflatex"
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+ "preamble.tex" 1774442779 4428 2ef0341e8930c3026632d61f45471d7e ""
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"resources/animalgroups.png" 1773235466 99003 12ad61c91b0f8e47e62249e2fdb458b9 ""
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diff --git a/docs/scientific/animalmoddoc.pdf b/docs/scientific/animalmoddoc.pdf
index 768089beaa..74f8c42279 100644
Binary files a/docs/scientific/animalmoddoc.pdf and b/docs/scientific/animalmoddoc.pdf differ
diff --git a/docs/scientific/animalmoddoc.synctex.gz b/docs/scientific/animalmoddoc.synctex.gz
index badc9b2320..4aaf12b03d 100644
Binary files a/docs/scientific/animalmoddoc.synctex.gz and b/docs/scientific/animalmoddoc.synctex.gz differ
diff --git a/docs/scientific/crop_and_soil.aux b/docs/scientific/crop_and_soil.aux
index 70d48649d7..5dac4fe31e 100644
--- a/docs/scientific/crop_and_soil.aux
+++ b/docs/scientific/crop_and_soil.aux
@@ -154,7 +154,7 @@
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diff --git a/docs/scientific/feed_storage.aux b/docs/scientific/feed_storage.aux
index 87facf0c99..10d066a32d 100644
--- a/docs/scientific/feed_storage.aux
+++ b/docs/scientific/feed_storage.aux
@@ -71,7 +71,7 @@
\setcounter{citetotal}{0}
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diff --git a/docs/scientific/main.aux b/docs/scientific/main.aux
index 005adbb605..c4717a5fa5 100644
--- a/docs/scientific/main.aux
+++ b/docs/scientific/main.aux
@@ -173,22 +173,20 @@
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\abx@aux@cite{1}{Mills2003}
\abx@aux@segm{1}{0}{Mills2003}
\abx@aux@page{44}{117}
+\abx@aux@page{45}{117}
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\abx@aux@segm{1}{0}{Niu2018}
\abx@aux@cite{1}{Mills2003}
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\abx@aux@page{46}{118}
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@@ -209,7 +207,7 @@
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@@ -217,6 +215,7 @@
\abx@aux@page{73}{123}
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\@input{manure.aux}
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@@ -235,41 +234,41 @@
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\abx@aux@page{78}{145}
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\abx@aux@page{80}{147}
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-\abx@aux@page{87}{162}
\abx@aux@page{88}{162}
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\abx@aux@segm{2}{0}{Sommer2004}
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@@ -282,12 +281,12 @@
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\abx@aux@page{93}{168}
\abx@aux@page{94}{168}
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@@ -296,24 +295,24 @@
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\abx@aux@segm{2}{0}{Sommer2004}
\abx@aux@cite{2}{Sommer2022}
@@ -326,94 +325,93 @@
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\abx@aux@page{111}{180}
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@@ -432,22 +430,23 @@
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\abx@aux@page{154}{224}
-\abx@aux@page{155}{225}
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\abx@aux@page{156}{225}
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+\abx@aux@page{158}{225}
\@input{crop_and_soil.aux}
\abx@aux@cite{0}{vadas2007}
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\abx@aux@segm{0}{0}{vadas2007}
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+\abx@aux@page{160}{242}
\abx@aux@cite{0}{vadas2007}
\abx@aux@segm{0}{0}{vadas2007}
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\abx@aux@cite{0}{vadas2007}
\abx@aux@segm{0}{0}{vadas2007}
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\abx@aux@cite{0}{hargreaves1985}
\abx@aux@segm{0}{0}{hargreaves1985}
\abx@aux@cite{0}{mu-extsoil}
@@ -456,19 +455,19 @@
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\abx@aux@segm{0}{0}{vadas2007}
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\abx@aux@segm{0}{0}{vadas2007}
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\abx@aux@segm{0}{0}{vadas2007}
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\abx@aux@segm{0}{0}{vadas2007}
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\abx@aux@segm{0}{0}{vadas2007}
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\abx@aux@segm{0}{0}{parton1987analysis}
\abx@aux@cite{0}{parton1987analysis}
@@ -508,11 +507,11 @@
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\abx@aux@page{169}{326}
-\abx@aux@page{170}{330}
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\abx@aux@page{171}{330}
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\gdef \LT@liii {\LT@entry
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diff --git a/docs/scientific/main.bcf b/docs/scientific/main.bcf
index f190b65fa6..a13009d06c 100644
--- a/docs/scientific/main.bcf
+++ b/docs/scientific/main.bcf
@@ -2424,13 +2424,12 @@
Niu2018
Pattanaik2003
Pattanaik2003
- Niu2018
- Niu2018
- Mills2003
- Niu2018
- Mills2003
- Niu2018
- Kebreab2023
+ Niu2018
+ Mills2003
+ Niu2018
+ Mills2003
+ Niu2018
+ Kebreab2023
diff --git a/docs/scientific/main.blg b/docs/scientific/main.blg
index dcc3194b6d..e024851173 100644
--- a/docs/scientific/main.blg
+++ b/docs/scientific/main.blg
@@ -1,53 +1,53 @@
-[0] Config.pm:307> INFO - This is Biber 2.19
-[0] Config.pm:310> INFO - Logfile is 'main.blg'
-[135] biber-MSWIN64:340> INFO - ===
-[180] Biber.pm:419> INFO - Reading 'main.bcf'
-[329] Biber.pm:979> INFO - Found 0 citekeys in bib section 0
-[332] Biber.pm:979> INFO - Found 29 citekeys in bib section 1
-[332] Biber.pm:979> INFO - Found 0 citekeys in bib section 0
-[335] Biber.pm:979> INFO - Found 28 citekeys in bib section 2
-[336] Biber.pm:979> INFO - Found 6 citekeys in bib section 0
-[336] Biber.pm:979> INFO - Found 0 citekeys in bib section 3
-[336] Biber.pm:979> INFO - Found 0 citekeys in bib section 0
-[336] Biber.pm:979> INFO - Found 2 citekeys in bib section 4
-[336] Biber.pm:979> INFO - Found 0 citekeys in bib section 0
-[376] Biber.pm:4419> INFO - Processing section 0
-[391] Biber.pm:4610> INFO - Looking for bibtex file 'resources/animal.bib' for section 0
-[442] bibtex.pm:1713> INFO - LaTeX decoding ...
-[524] bibtex.pm:1519> INFO - Found BibTeX data source 'resources/animal.bib'
-[572] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable'
-[572] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized'
-[572] Biber.pm:4239> INFO - Sorting list 'nyt/global//global/global' of type 'entry' with template 'nyt' and locale 'en-US'
-[572] Biber.pm:4245> INFO - No sort tailoring available for locale 'en-US'
-[574] Biber.pm:4419> INFO - Processing section 1
-[574] Biber.pm:4610> INFO - Looking for bibtex file 'resources/animal.bib' for section 1
-[792] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized'
-[792] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable'
-[792] Biber.pm:4239> INFO - Sorting list 'nyt/global//global/global' of type 'entry' with template 'nyt' and locale 'en-US'
-[792] Biber.pm:4245> INFO - No sort tailoring available for locale 'en-US'
-[837] Biber.pm:4419> INFO - Processing section 2
-[838] Biber.pm:4610> INFO - Looking for bibtex file 'resources/animal.bib' for section 2
-[1031] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable'
-[1031] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized'
-[1031] Biber.pm:4239> INFO - Sorting list 'nyt/global//global/global' of type 'entry' with template 'nyt' and locale 'en-US'
-[1031] Biber.pm:4245> INFO - No sort tailoring available for locale 'en-US'
-[1066] Biber.pm:4419> INFO - Processing section 4
-[1067] Biber.pm:4610> INFO - Looking for bibtex file 'resources/animal.bib' for section 4
-[1119] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized'
-[1119] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable'
-[1119] Biber.pm:4239> INFO - Sorting list 'nyt/global//global/global' of type 'entry' with template 'nyt' and locale 'en-US'
-[1119] Biber.pm:4245> INFO - No sort tailoring available for locale 'en-US'
-[1122] bbl.pm:660> INFO - Writing 'main.bbl' with encoding 'UTF-8'
-[1183] bbl.pm:763> INFO - Output to main.bbl
-[1185] Biber.pm:131> WARN - I didn't find a database entry for 'hargreaves1985' (section 0)
-[1186] Biber.pm:131> WARN - I didn't find a database entry for 'mu-extsoil' (section 0)
-[1186] Biber.pm:131> WARN - I didn't find a database entry for 'hayes2020vindication' (section 0)
-[1186] Biber.pm:131> WARN - I didn't find a database entry for 'parton1987analysis' (section 0)
-[1186] Biber.pm:131> WARN - I didn't find a database entry for 'fan2016root' (section 0)
-[1186] Biber.pm:131> WARN - I didn't find a database entry for 'gomez2010time' (section 2)
-[1186] Biber.pm:131> WARN - I didn't find a database entry for 'espejo2007herd' (section 2)
-[1186] Biber.pm:131> WARN - I didn't find a database entry for 'jewell2019prevalence' (section 2)
-[1186] Biber.pm:131> WARN - I didn't find a database entry for 'meyer2019contract' (section 2)
-[1186] Biber.pm:131> WARN - I didn't find a database entry for 'endres2007behavior' (section 2)
-[1186] Biber.pm:131> WARN - I didn't find a database entry for 'wallaceDMI' (section 2)
-[1186] Biber.pm:133> INFO - WARNINGS: 11
+[1] Config.pm:307> INFO - This is Biber 2.19
+[1] Config.pm:310> INFO - Logfile is 'main.blg'
+[297] biber-MSWIN64:340> INFO - ===
+[385] Biber.pm:419> INFO - Reading 'main.bcf'
+[648] Biber.pm:979> INFO - Found 0 citekeys in bib section 0
+[652] Biber.pm:979> INFO - Found 29 citekeys in bib section 1
+[652] Biber.pm:979> INFO - Found 0 citekeys in bib section 0
+[656] Biber.pm:979> INFO - Found 28 citekeys in bib section 2
+[657] Biber.pm:979> INFO - Found 6 citekeys in bib section 0
+[657] Biber.pm:979> INFO - Found 0 citekeys in bib section 3
+[657] Biber.pm:979> INFO - Found 0 citekeys in bib section 0
+[658] Biber.pm:979> INFO - Found 2 citekeys in bib section 4
+[658] Biber.pm:979> INFO - Found 0 citekeys in bib section 0
+[716] Biber.pm:4419> INFO - Processing section 0
+[736] Biber.pm:4610> INFO - Looking for bibtex file 'resources/animal.bib' for section 0
+[836] bibtex.pm:1713> INFO - LaTeX decoding ...
+[932] bibtex.pm:1519> INFO - Found BibTeX data source 'resources/animal.bib'
+[995] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized'
+[995] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable'
+[995] Biber.pm:4239> INFO - Sorting list 'nyt/global//global/global' of type 'entry' with template 'nyt' and locale 'en-US'
+[995] Biber.pm:4245> INFO - No sort tailoring available for locale 'en-US'
+[998] Biber.pm:4419> INFO - Processing section 1
+[998] Biber.pm:4610> INFO - Looking for bibtex file 'resources/animal.bib' for section 1
+[1283] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized'
+[1283] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable'
+[1283] Biber.pm:4239> INFO - Sorting list 'nyt/global//global/global' of type 'entry' with template 'nyt' and locale 'en-US'
+[1283] Biber.pm:4245> INFO - No sort tailoring available for locale 'en-US'
+[1336] Biber.pm:4419> INFO - Processing section 2
+[1337] Biber.pm:4610> INFO - Looking for bibtex file 'resources/animal.bib' for section 2
+[1541] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized'
+[1542] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable'
+[1542] Biber.pm:4239> INFO - Sorting list 'nyt/global//global/global' of type 'entry' with template 'nyt' and locale 'en-US'
+[1542] Biber.pm:4245> INFO - No sort tailoring available for locale 'en-US'
+[1574] Biber.pm:4419> INFO - Processing section 4
+[1575] Biber.pm:4610> INFO - Looking for bibtex file 'resources/animal.bib' for section 4
+[1630] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable'
+[1631] UCollate.pm:68> INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized'
+[1631] Biber.pm:4239> INFO - Sorting list 'nyt/global//global/global' of type 'entry' with template 'nyt' and locale 'en-US'
+[1631] Biber.pm:4245> INFO - No sort tailoring available for locale 'en-US'
+[1634] bbl.pm:660> INFO - Writing 'main.bbl' with encoding 'UTF-8'
+[1692] bbl.pm:763> INFO - Output to main.bbl
+[1694] Biber.pm:131> WARN - I didn't find a database entry for 'hargreaves1985' (section 0)
+[1694] Biber.pm:131> WARN - I didn't find a database entry for 'mu-extsoil' (section 0)
+[1694] Biber.pm:131> WARN - I didn't find a database entry for 'hayes2020vindication' (section 0)
+[1694] Biber.pm:131> WARN - I didn't find a database entry for 'parton1987analysis' (section 0)
+[1694] Biber.pm:131> WARN - I didn't find a database entry for 'fan2016root' (section 0)
+[1694] Biber.pm:131> WARN - I didn't find a database entry for 'gomez2010time' (section 2)
+[1694] Biber.pm:131> WARN - I didn't find a database entry for 'espejo2007herd' (section 2)
+[1694] Biber.pm:131> WARN - I didn't find a database entry for 'jewell2019prevalence' (section 2)
+[1694] Biber.pm:131> WARN - I didn't find a database entry for 'meyer2019contract' (section 2)
+[1694] Biber.pm:131> WARN - I didn't find a database entry for 'endres2007behavior' (section 2)
+[1694] Biber.pm:131> WARN - I didn't find a database entry for 'wallaceDMI' (section 2)
+[1694] Biber.pm:133> INFO - WARNINGS: 11
diff --git a/docs/scientific/main.fdb_latexmk b/docs/scientific/main.fdb_latexmk
index c594b67914..3e62f1d34a 100644
--- a/docs/scientific/main.fdb_latexmk
+++ b/docs/scientific/main.fdb_latexmk
@@ -1,14 +1,14 @@
# Fdb version 4
-["biber main"] 1773836238.10959 "main.bcf" "main.bbl" "main" 1773836265.77658 0
- "main.bcf" 1773836264 120814 10a9c52fee9bb7676941633b64307201 "pdflatex"
+["biber main"] 1774443119.31534 "main.bcf" "main.bbl" "main" 1774443701.60089 0
+ "main.bcf" 1774443700 120749 31b83e732f8d735eabeec19b303c9ad8 "pdflatex"
"resources/animal.bib" 1773235466 19843 003ce6dc3163a9c1fd885dbc082d404e ""
(generated)
"main.bbl"
"main.blg"
(rewritten before read)
-["pdflatex"] 1773836253.44213 "c:/Users/gmg228/Documents/RuFaS/RuFaS/docs/scientific/main.tex" "main.pdf" "main" 1773836265.77837 0
+["pdflatex"] 1774443691.09685 "c:/Users/gmg228/Documents/RuFaS/RuFaS/docs/scientific/main.tex" "main.pdf" "main" 1774443701.60202 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/ecbx0800.pk" 1772649927 19872 988dfcfb7ecc9f1e0f030b9237c8ba09 ""
@@ -282,23 +282,23 @@
"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" 1773836259 40063 6cae32312defadfc17ce9a72522a0c71 "pdflatex"
- "animal.tex" 1773836205 266447 88be983bc824fdd69b4fcb1bf89be974 ""
- "c:/Users/gmg228/Documents/RuFaS/RuFaS/docs/scientific/main.tex" 1773836220 11418 d6eb4a5fa79e1c1c32fb1c9016e06424 ""
- "crop_and_soil.aux" 1773836263 15928 f6082a192edd9270ae2c2e93f203269b "pdflatex"
- "crop_and_soil.tex" 1773835015 250282 4247930dead3c0560cdd65275d64e942 ""
- "feed_storage.aux" 1773836264 7336 057a56eaf4eb345c068b9f2fd432f100 "pdflatex"
- "feed_storage.tex" 1773835015 23048 c0dad4e42b8676496e377074486e2f99 ""
- "main.aux" 1773836264 19698 8b60a9df0f7d82740ac3d516e0a1f09e "pdflatex"
- "main.bbl" 1773836241 110821 0ad2d42f335dd24d7a8c06b3d176a504 "biber main"
- "main.out" 1773836264 15689 9e5fefbe15f6566391db859ccbb182a4 "pdflatex"
- "main.run.xml" 1773836264 2351 84a8d70dbc8c0b04e3a63b2da8d46186 "pdflatex"
- "main.tex" 1773836220 11418 d6eb4a5fa79e1c1c32fb1c9016e06424 ""
- "main.toc" 1773836264 34219 4ad306310ac397920a7f7df181523840 "pdflatex"
- "manure.aux" 1773836261 28459 1880a907ea4376c9ffcc99c485081545 "pdflatex"
- "manure.tex" 1773835015 276471 ef74d91440de03982e6753ae48ab944e ""
- "preamble.tex" 1773835015 4428 2ef0341e8930c3026632d61f45471d7e ""
- "resources/animal1.png" 1773835015 204760 63ad4e90063ffaed258c1eb7fc2a7889 ""
+ "animal.aux" 1774443696 40063 8a2759fd44a7420249c0727be0011857 "pdflatex"
+ "animal.tex" 1774443682 266445 ddff3369a8cecf234b296740b3edcfaf ""
+ "c:/Users/gmg228/Documents/RuFaS/RuFaS/docs/scientific/main.tex" 1774442779 11418 d6eb4a5fa79e1c1c32fb1c9016e06424 ""
+ "crop_and_soil.aux" 1774443699 15928 d33b3dc38fb9d40205fe3ce0225893ea "pdflatex"
+ "crop_and_soil.tex" 1774442779 250282 4247930dead3c0560cdd65275d64e942 ""
+ "feed_storage.aux" 1774443700 7336 f67690afc7ded46ee08552adbe3e416d "pdflatex"
+ "feed_storage.tex" 1774442779 23048 c0dad4e42b8676496e377074486e2f99 ""
+ "main.aux" 1774443700 19667 f2c5f1beb369ea63d25b3f398239bd1b "pdflatex"
+ "main.bbl" 1774443123 110821 0ad2d42f335dd24d7a8c06b3d176a504 "biber main"
+ "main.out" 1774443700 15689 9e5fefbe15f6566391db859ccbb182a4 "pdflatex"
+ "main.run.xml" 1774443700 2351 84a8d70dbc8c0b04e3a63b2da8d46186 "pdflatex"
+ "main.tex" 1774442779 11418 d6eb4a5fa79e1c1c32fb1c9016e06424 ""
+ "main.toc" 1774443700 34219 4ad306310ac397920a7f7df181523840 "pdflatex"
+ "manure.aux" 1774443698 28459 a3e2769439e6b754b536992ffdaf32d2 "pdflatex"
+ "manure.tex" 1774442779 276471 ef74d91440de03982e6753ae48ab944e ""
+ "preamble.tex" 1774442779 4428 2ef0341e8930c3026632d61f45471d7e ""
+ "resources/animal1.png" 1774442779 204760 63ad4e90063ffaed258c1eb7fc2a7889 ""
"resources/animalgroups.png" 1773235466 99003 12ad61c91b0f8e47e62249e2fdb458b9 ""
"resources/cowbreedmethod.png" 1773235466 249475 26a2153096ad61f7889191c615bffca3 ""
"resources/feedallocation.png" 1773235466 105788 1023adaeffc24f37a9d77f67fdbf994e ""
@@ -310,7 +310,7 @@
"resources/overviewmanure.png" 1773235466 156533 7afabb7e5de5a3d11e63c292e200d962 ""
"resources/repromethod.png" 1773235466 166346 83938a0f852e12d18691536eda26ff67 ""
"resources/rufas.png" 1773235466 73887 efe95f7052122fdf4f1c6ca21cd30e7f ""
- "resources/rufastitlepgimg.png" 1773835015 180386 5943eec5093b0d3c77d4467b45c3826f ""
+ "resources/rufastitlepgimg.png" 1774279830 180386 5943eec5093b0d3c77d4467b45c3826f ""
(generated)
"animal.aux"
"crop_and_soil.aux"
diff --git a/docs/scientific/main.pdf b/docs/scientific/main.pdf
index 9665812467..58bb8dde6c 100644
Binary files a/docs/scientific/main.pdf and b/docs/scientific/main.pdf differ
diff --git a/docs/scientific/main.synctex.gz b/docs/scientific/main.synctex.gz
index 30cacae4da..f14310236f 100644
Binary files a/docs/scientific/main.synctex.gz and b/docs/scientific/main.synctex.gz differ
diff --git a/docs/scientific/manure.aux b/docs/scientific/manure.aux
index cd3727be7e..572a5407ae 100644
--- a/docs/scientific/manure.aux
+++ b/docs/scientific/manure.aux
@@ -235,7 +235,7 @@
\setcounter{citetotal}{0}
\setcounter{multicitecount}{0}
\setcounter{multicitetotal}{0}
-\setcounter{instcount}{157}
+\setcounter{instcount}{158}
\setcounter{maxnames}{3}
\setcounter{minnames}{1}
\setcounter{maxitems}{3}
diff --git a/docs/scientific/rufas.bib b/docs/scientific/rufas.bib
index 8fa94ffc3f..c94204de0d 100644
--- a/docs/scientific/rufas.bib
+++ b/docs/scientific/rufas.bib
@@ -1,3 +1,14 @@
+@article{Niu2018,
+ author = {Niu, M. and Kebreab, E. and Hristov, A.N. and Oh, J. and Arndt, C. and Bannink, A. and Bayat, A.R. and Brito, A.F. and Boland, T. and Casper, D. and Crompton, L.A. and Dijkstra, J. and Eug{\`e}ne, M.A. and Garnsworthy, P.C. and Haque, M.N. and Hellwing, A.L. F. and Huhtanen, P. and Kreuzer, M. and Kuhla, B. and Lund, P. and Madsen, J. and Martin, C. and McClelland, S.C. and McGee, M. and Moate, P.J. and Muetzel, S. and Mu{\~n}oz, C. and O'Kiely, P. and Peiren, N. and Reynolds, C.K. and Schwarm, A. and Shingfield, K.J. and Storlien, T.M. and Weisbjerg, M.R. and Y{\'a}{\~n}ez-Ruiz, D.R. and Yu, Z.},
+ title = {Prediction of enteric methane production, yield, and intensity in dairy cattle using an intercontinental database},
+ journal = {Global Change Biology},
+ year = {2018},
+ volume = {24},
+ number = {8},
+ pages = {3368--3389},
+ doi = {10.1111/gcb.14094}
+}
+
@book{kalantari2015using,
title={Using mathematical modeling techniques for optimized dairy herd management and decision making},
author={Kalantari, Afshin Samia},
@@ -335,17 +346,6 @@ @article{Moraes2014
}
-@article{Niu2018,
- author = {Niu, M. and Kebreab, E. and Hristov, A.N. and others},
- title = {Prediction of enteric methane production, yield, and intensity in dairy cattle using an intercontinental database},
- journal = {Global Change Biology},
- year = {2018},
- volume = {24},
- pages = {3368--3389},
- doi = {10.1111/gcb.14094}
-}
-
-
@misc{IPCC2006,
author = {{IPCC}},
title = {Guidelines for National Greenhouse Gas Inventories},
diff --git a/input/task_manager_metadata.json b/input/task_manager_metadata.json
index 5674a5fcdc..015e442268 100644
--- a/input/task_manager_metadata.json
+++ b/input/task_manager_metadata.json
@@ -6,6 +6,6 @@
"path": "input/data/tasks/example_freestall_task.json",
"type": "json",
"properties": "tasks_properties"
- }
}
}
+}
\ No newline at end of file