Revisions to abstract and introduction

.github/workflows/CI.yml

@@ -74,11 +74,29 @@ jobs:
             initexmf --mklinks
             initexmf --mklangs
           fi
+
+      - name: Debug conda environment
+        shell: bash -l {0}
+        run: |
+          echo "Conda info:"
+          conda info
+          echo "Conda envs:"
+          conda env list
+          echo "Current PATH:"
+          echo $PATH
+          echo "Which python:"
+          which python
+          echo "Which snakemake:"
+          which snakemake || echo "snakemake not found"
 
       # Execute the Snakemake workflow
       - name: Run Snakemake workflow
+        shell: bash -l {0}  # Explicitly use login shell
         run: |
-          cd analysis && snakemake -j2
+          conda activate 2025-dotson-thesis
+          which python
+          which snakemake
+          cd analysis && snakemake -j2 --force
 
       # Upload the generated PDF as an artifact
       - name: Upload PDF artifact

analysis/Snakefile

@@ -270,8 +270,8 @@ rule benchmark_chapter:
         done
         """
 #============================EXAMPLES CHAPTER================================
-app_d_url = "https://fuelcycleevaluation.inl.gov/Shared%20Documents/ES%20Appendix%20D.pdf"
-app_c_url = "https://fuelcycleevaluation.inl.gov/Shared%20Documents/ES%20Appendix%20C.pdf"
+app_d_url = "https://sai.inl.gov/content/uploads/29/2024/11/es_appendix_d.pdf"
+app_c_url = "https://sai.inl.gov/content/uploads/29/2024/11/es_appendix_c.pdf"
 atbe_url = "https://oedi-data-lake.s3.amazonaws.com/ATB/electricity/csv/2024/v3.0.0/ATBe.csv"
 
 rule retrieve_fuel_cycles_report_D:

analysis/scripts/05-examples-scripts/solve_datacenter.py

@@ -37,10 +37,11 @@
     with open(snakemake.input.dc_problem, "rb") as file:
         problem = pickle.load(file)
 
+    use_checkpoints = False
 
     checkpoint_list = glob("checkpoint_*.pkl")
     checkpoint_list.sort()
-    if len(checkpoint_list) > 0:
+    if (len(checkpoint_list) > 0) and use_checkpoints:
         with open(checkpoint_list[-1], 'rb') as f:
             algorithm = pickle.load(f)
             algorithm.termination = MaximumGenerationTermination(200)

docs/00-outline.tex

@@ -2,26 +2,26 @@ \chapter{Introduction}
 \label{chapter:introduction}
 \input{1-introduction/1-introduction.tex}
 
-% \chapter{Literature Review}
-% \label{chapter:lit-review}
-% \input{2-literature/20-literature}
+\chapter{Literature Review}
+\label{chapter:lit-review}
+\input{2-literature/20-literature}
 
-% \chapter{\acf{osier}}
-% \label{chapter:osier}
-% \input{3-osier/30-intro}
+\chapter{\acf{osier}}
+\label{chapter:osier}
+\input{3-osier/30-intro}
 
-% \chapter{Benchmark Results}
-% \label{chapter:benchmark-results}
-% \input{4-benchmark-results/40-benchmark.tex}
+\chapter{Benchmark Results}
+\label{chapter:benchmark-results}
+\input{4-benchmark-results/40-benchmark.tex}
 
-% \chapter{Examples with \acs{osier}}
-% \label{chapter:examples}
-% \input{5-examples/50-intro.tex}
+\chapter{Examples with \acs{osier}}
+\label{chapter:examples}
+\input{5-examples/50-intro.tex}
 
-% \chapter{Energy modeling, planning, and justice}
-% \label{chapter:communities}
-% \input{7-interviews/70-outline}
+\chapter{Energy modeling, planning, and justice}
+\label{chapter:communities}
+\input{7-interviews/70-outline}
 
-% \chapter{Conclusions}
-% \label{chapter:conclusions}
-% \input{8-conclusion/80-conclusion.tex}
+\chapter{Conclusions}
+\label{chapter:conclusions}
+\input{8-conclusion/80-conclusion.tex}

docs/02-acks.tex

@@ -0,0 +1,43 @@
+Writing a thesis can often feel like a solitary experience. Despite appearances,
+such an endeavor is only possible through the collective support of mentors,
+colleagues, friends, and family (and those friends who became family).
+
+I am profoundly indebted to my advisor and mentor, Professor Kathryn D. Huff,
+who set me on this path. Her uncompromising standards for excellence are matched
+only by the care and attention she affords her students. I only hope I can live
+up to her example. I would also like to thank my co-advisor, Professor Madicken
+Munk, for encouraging me to pursue my curiosity, which led to this sprawling
+multi-disciplinary work.
+
+I thank the other members of my committee, James Stubbins, Clifford Singer,
+McKenzie Johnson, and Denia Djoki\'c. I am particularly grateful to Professor
+Johnson for her patience and humor while mentoring me through the nuances of
+interacting with and writing about real people (gasp!). I am also deeply
+appreciative of the time and effort Dr. Djoki\'c put into guiding myself and
+Haley Williams (UC Berkeley) through the philosophy of science literature in
+weekly meetings of the ``Nuclear Contextualizers."
+
+Of course, I thank my colleagues, past and present, from the Advanced Reactors
+and Fuel Cycles (ARFC) group: Gwendolyn Chee, Sun Myung Park, Amanda Bachmann,
+Nathan Ryan, Olek Yardas, Zo\"e Richter, and Luke Seifert. Their feedback and
+code reviews were indispensable. 
+
+I would like to extend a special thanks to the following people. Shannon
+Anderson, thank you for helping me navigate the challenges of social science and
+engaging with the energy justice literature. Roberto Fairhurst, thanks for being
+a great friend and roommate. I miss interrupting you at work (and I appreciate
+your patience with my interruptions). Jeremy Mettler, although I credit
+Professor Huff with officially starting my journey, I truly would not be here
+without your persistent, friendly nudges. Thank you for always inviting me, for
+being a trusted confidant, and a dear friend. Nataly Panczyk, I adore your
+curiosity, kindness, and infectious enthusiasm. I am perpetually in awe of you. 
+
+I would also like to acknowledge the many incredible professors at the
+University of Illinois and at the College of Lake County. In particular, I
+acknowledge Drs. Ryan Stock, Ana Mazilu, Josephine Faulk, Kristi Dameron, and
+Steve Chamberlin for encouraging me to pursue graduate studies.
+
+Finally, I received financial support for this work from the Nuclear Regulatory
+Commission Fellowship Program, the Felix T. Adler Fellowship from the NPRE
+Department at UIUC, and the Union of Concerned Scientists Professional
+Development Fund.