moja-global · ayush78781 · Mar 29, 2023 · Mar 29, 2023 · Mar 29, 2023 · Mar 29, 2023
diff --git a/Chapter1/section_one.rst b/Chapter1/section_one.rst
@@ -16,10 +16,11 @@ Scientists extremely knowledgeable in climate science review these data reports
 
 - Working Group III(WGIII): The IPCC WGII focuses on how to mitigate climate change. It takes a solution-oriented approach but refrains from advocating for any specific climate change mitigation approach.
 
+For more information refer to IPCC :footcite:t:`2023:IPCC`.
 
 **What is the UNFCCC?**
 
-Established in 1992, the United Nations Framework Convention on Climate Change, also known as UNFCCC, constitutes the foundational climate agreement that has provided the platform for most subsequent international climate agreements. Signed by 154 states, the UNFCCC created an international treaty to mitigate the effects of "dangerous human interference with the climate system" by stabilizing the greenhouse gas concentrations in the atmosphere. 
+Established in 1992, the United Nations Framework Convention on Climate Change, also known as UNFCCC :footcite:t:`2013:UN`, constitutes the foundational climate agreement that has provided the platform for most subsequent international climate agreements. Signed by 154 states, the UNFCCC created an international treaty to mitigate the effects of "dangerous human interference with the climate system" by stabilizing the greenhouse gas concentrations in the atmosphere. 
 
 The UNFCC uses the framework agreement to develop treaties. This framework agreement begins with the parties signed to UNFCCC acknowledging a problem and committing to take action without taking concrete obligations.
 
@@ -52,4 +53,6 @@ In line with the `UNFCC reporting guidelines <https://unfccc.int/resource/docs/2
 - Completeness: The greenhouse gas report should cover at least all the sources and sinks, and gases. 
 - Accuracy: The report submitted must be correct, that is, neither under nor over true emissions or removals, and those uncertainties are reduced as far as practicable.
 
+.. rubric:: References
 
+.. footbibliography::
diff --git a/Chapter2/index.rst b/Chapter2/index.rst
@@ -1,13 +1,14 @@
 Chapter 2: Introduction to the Full Lands Integration Tool
 ===========================================================
 
-`Full Lands Integration Tool (FLINT) <https://moja.global/flint/>`_ is a modular, flexible, and open-source software that enables users to measure, report, verify and forecast greenhouse gas emissions and removals from forestry, agriculture, and other land users. 
+`Full Lands Integration Tool (FLINT) <https://moja.global/flint/>`_ :footcite:t:`2021:Video` is a modular, flexible, and open-source software that enables users to measure, report, verify and forecast greenhouse gas emissions and removals from forestry, agriculture, and other land users. 
 
 Built primarily on simulating events and processes, FLINT captures, curates, and outputs the data from the simulations in different forms depending on a user's needs.
 
 
+.. rubric:: References
 
-
+.. footbibliography::
 
 .. toctree::
    :hidden:

diff --git a/Chapter3/index.rst b/Chapter3/index.rst
@@ -1,8 +1,10 @@
 Chapter 3: Introduction to Generic Carbon Budget Model
 ==========================================================
-The Generic Carbon Budget Model, also known as the GCBM, is a tool developed to assess and report the cumulative effects of anthropogenic and natural disturbances on our forests. The GCBM is a set of science modules developed by the Canadian Forest Service (CFS) to run with FLINT.
-
+The Generic Carbon Budget Model :footcite:t:`2022:GCBM`, also known as the GCBM, is a tool developed to assess and report the cumulative effects of anthropogenic and natural disturbances on our forests. The GCBM is a set of science modules developed by the Canadian Forest Service (CFS) to run with FLINT.
 
+.. rubric:: References
+.. footbibliography::
+
 .. toctree::
    :hidden:
 

diff --git a/Chapter4/index.rst b/Chapter4/index.rst
@@ -3,7 +3,7 @@ Chapter 4: The Work DVC Plays in the Land Sector Repo
 
 FLINT requires data to run simulations properly, and this data is available in the `Land Sector Dataset repository <https://github.com/moja-global/Land_Sector_Datasets>`__.
 
-`Data Version Control (DVC) <https://dvc.org/>`__ is a data and Machine
+According to :footcite:t:`2023:DVC`, `Data Version Control (DVC) <https://dvc.org/>`__ is a data and Machine
 Learning management tool that leverages tools like Git and CI/CD to
 track and save data and simulation results models. DVC allows us to
 create and switch between different versions of data/models and adopt
@@ -24,9 +24,11 @@ The Land Sector Dataset repository is built using DVC to verify that the
 data inputs and the resulting outputs to a simulation are the same -
 which is essential when talking about scientific models. DVC can cache
 preprocessed data on publicly available remote storage, making sharing
-datasets ready for FLINT analysis easier.
+datasets ready for FLINT analysis easier. Learn more here :footcite:t:`2020:DVCorg`. 
 
+.. rubric:: References
 
+.. footbibliography::
 
 .. toctree::
    :hidden:

diff --git a/Chapter4/section_one.rst b/Chapter4/section_one.rst
@@ -5,7 +5,7 @@ To add datasets to the Land sector
 `repository <https://github.com/moja-global/Land_Sector_Datasets>`__, we
 start by cloning this repository. Check out `this
 article <https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository>`__
-to understand how to clone a repository on GitHub.
+to understand how to clone a repository on GitHub. Learn more :footcite:t:`2020:VCS`.
 
 Next, we go through the library and find the raw dataset that we want to
 process, in this case, the ``HarmonizedWorldSoilDatabase`` dataset. It
@@ -118,4 +118,8 @@ responsible for recreating this DVC pipeline.
 
 
 It is important to note that GitHub Actions only runs when there is a
-change in the python script, producing a different data output.
+change in the python script, producing a different data output.
+
+.. rubric:: References
+
+.. footbibliography::
diff --git a/Chapter5/index.rst b/Chapter5/index.rst
@@ -1,6 +1,6 @@
 Chapter 5: Running a GCBM Simulation
 =====================================
-The Generic Carbon Budget Model, also known as the GCBM, is a tool
+The Generic Carbon Budget Model :footcite:t:`2022:GCBMFlint`, also known as the GCBM, is a tool
 developed to assess and report the cumulative effects of anthropogenic
 and natural disturbances on our forests.
 
@@ -12,7 +12,10 @@ Standalone Project. The Standalone Project is a collection of individual
 pre - and post-processing tools organized into a workflow for getting
 started with GCBM quickly.
 
+.. rubric:: References
 
+.. footbibliography::
+
 .. toctree::
    :hidden:
 

diff --git a/Chapter5/section_one.rst b/Chapter5/section_one.rst
@@ -12,7 +12,7 @@ To run a GCBM simulation, we have to complete the following processes:
    -  Familiar ecosystem indicators (NPP, etc.) in database format
    -  Convert raw spatial output to final layers
 
-This document discusses these steps in detail to help us run a GCBM
+This document :footcite:t:`2022:GCBMbelize` discusses these steps in detail to help us run a GCBM
 simulation successfully.
 
 **Project Structure** 
@@ -55,3 +55,6 @@ information:
 -  ``readme.txt``: This file contains the GCBM setup information
 -  ``run_all.bat``: This file runs the project from start to finish 
 
+.. rubric:: References
+
+.. footbibliography::
diff --git a/Chapter6/section_one.rst b/Chapter6/section_one.rst
@@ -1,8 +1,7 @@
 How do we expect our world to change?
 =====================================
 
-According to `UCAR Center for Science
-Education <https://scied.ucar.edu/learning-zone/climate-change-impacts/predictions-future-global-climate>`__,
+According to :footcite:t:`2023:UCAR`,
 an increase in carbon dioxide and greenhouse gases in the atmosphere
 births a warmer world. This warmth can be felt in the increase of the
 earth’s average temperature and sea level, change in precipitation, etc.
@@ -58,4 +57,8 @@ Multiple studies have revealed that climate change has already caused an
 increase in the frequency, season length, and affected areas of
 wildfires. The lengthened wildfire season can be attributed to different
 reasons, including more extended summer dry seasons, drier soils and
-vegetation, and predominantly increased temperatures and drought.
+vegetation, and predominantly increased temperatures and drought.
+
+.. rubric:: References
+
+.. footbibliography::
diff --git a/Chapter6/section_two.rst b/Chapter6/section_two.rst
@@ -14,4 +14,8 @@ change results in high atmospheric CO2, it also brings about warming,
 which can cause plants to use a lot more water and photosynthesize less.
 The survival of the plants largely depends on whether the benefits
 gained from high atmospheric CO2 are significant enough to compensate
-for the stress experienced due to high temperatures.
+for the stress experienced due to high temperatures. Learn more here :footcite:t:`2019:PNAS`.
+
+.. rubric:: References
+
+.. footbibliography::
diff --git a/conf.py b/conf.py
@@ -27,8 +27,10 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = [
-]
+extensions = ['sphinxcontrib.bibtex']
+
+# adding the BibTeX file here
+bibtex_bibfiles = ['refs.bib']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -49,4 +51,6 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ['_static']
+
+
diff --git a/refs.bib b/refs.bib
@@ -0,0 +1,108 @@
+// Chapter 1 Citations
+@Article{2023:IPCC,
+  title={The Intergovernmental Panel on Climate Change, IPCC},
+  author={Secretariat, I.P.C.C},
+  journal={https://www.ipcc.ch/},
+  year={2023}
+},
+
+@Article{2013:UN,
+  title={Report of the Conference of the Parties on its nineteenth  session, held in Warsaw from 11 to 23 November 2013},
+  author={United Nations},
+  journal={https://undocs.org/Home/Mobile?FinalSymbol=FCCC%2FCP%2F2013%2F10%2FAdd.3&amp;Language=E&amp;DeviceType=Mobile&amp;LangRequested=False},
+  year={2013}
+},Moja Global.
+
+@Article{2021:Moja,
+  title={Flint - moja global},
+  author={Moja Global},
+  journal={https://moja.global/flint/},
+  year={2021}
+},
+
+//Chapter 2 Citations
+
+@Article{2021:Video,
+  title={About moja global - FLINT},
+  author={Moja Global FLINT},
+  journal={https://www.youtube.com/watch?v=eUa9ficyOPg},
+  year={2021}
+},
+
+@Article{2022:documentation,
+  title={Moja FLINT - moja global Technical Guide documentation},
+  author={Moja Global},
+  journal={https://docs.moja.global/en/master/FLINT/UnderstandingFLINT/MojaFlint/index.html},
+  year={2022}
+},
+
+// Chapter 3
+
+@Article{2022:GCBM,
+  title={Understanding GCBM},
+  author={Moja Global GCBM},
+  journal={https://docs.google.com/document/d/1wKhmnXvP4mom1vaKz2gbVFzE_npyEDdmBtOTVinXX6Y/edit#heading=h.c7wb49aw32we},
+  year={2022}
+},
+
+// Chapter 4
+
+@Article{2023:DVC,
+  title={Data Version Control (software)},
+  author={Dmitry Petrov},
+  journal={https://en.wikipedia.org/wiki/Data_Version_Control_(software)},
+  year={2023}
+},
+
+@Article{2020:DVCorg,
+  title={Version Control for Data Science Explained in 5 Minutes (No Code!)},
+  author={DVCorg},
+  journal={https://www.youtube.com/watch?v=UbL7VUpv1Bs},
+  year={2020}
+},
+
+@Article{2020:VCS,
+  title={Version Control for Data Science Explained in 5 Minutes (No Code!)},
+  author={DVCorg},
+  journal={https://www.youtube.com/watch?v=UbL7VUpv1Bs},
+  year={2020}
+},
+
+// Chapter 5
+
+@Article{2022:GCBMFlint,
+  title={Introduction to the Generic Carbon Budget Model (GCBM): 1.The FLINT explained},
+  author={Moja Global GCBM},
+  journal={https://www.youtube.com/watch?v=G9T805eQGBQ&amp;list=PL_WECUlMWiUmZYoPHNn6RnMSia5Naj5gE},
+  year={2022}
+},
+
+@Article{2022:GCBMbelize,
+  title={Gcbm.belize/STANDALONE_GCBM/documentation at master · Moja-Global/gcbm.belize},
+  author={Moja Global GCBMBelize},
+  journal={ https://github.com/moja-global/GCBM.Belize/tree/master/Standalone_GCBM/documentation},
+  year={2022}
+},
+
+// Chapter 6
+
+@Article{2023:UCAR,
+  title={Predictions of Future Global Climate},
+  author={UCAR},
+  journal={https://scied.ucar.edu/learning-zone/climate-change-impacts/predictions-future-global-climate},
+  year={2023}
+},
+
+@Article{2019:PNAS,
+  title={The impact of rising CO2 and acclimation on the response of US forests to global warming},
+  author={John S. Sperry},
+  journal={ https://www.pnas.org/doi/10.1073/pnas.1913072116},
+  year={2019}
+}
+
+
+
+
+
+
+