updates name of main tex file, correctly uses miniforge3

.github/workflows/CI.yml

@@ -27,7 +27,7 @@ jobs:
       - name: Create environment with Mamba
         uses: conda-incubator/setup-miniconda@v2
         with:
-          miniforge-variant: Mambaforge # mamba is faster than base conda
+          miniforge-variant: Miniforge3 # mamba is faster than base conda
           miniforge-version: latest
           channels: conda-forge, bioconda
           auto-activate-base: false

.gitignore

@@ -28,7 +28,7 @@
 *.pyg
 .env
 .snakemake
-thesis.pdf
+*.pdf
 __pycache__/
 .ipynb_checkpoints/
 data/benchmark/data/*

README.md

@@ -9,10 +9,10 @@ This repository holds my preliminary exam document. The style guide comes from t
 The document style must be compiled using `biber`. Doing this from the command line is more reliable than modifying TeXworks or other editor (I have experienced issues with Windows blocking a biber.exe call from TeXworks). **Make sure your LaTeX installation is up-to-date.**
 
 ```bash
-C:\Users\samgd\Research\2025-dotson-dissertation\docs>pdflatex -shell-escape thesis.tex
-C:\Users\samgd\Research\2025-dotson-dissertation\docs>biber thesis  # This is not a typo. Do not include a file extension.
-C:\Users\samgd\Research\2025-dotson-dissertation\docs>pdflatex -shell-escape thesis.tex
-C:\Users\samgd\Research\2025-dotson-dissertation\docs>pdflatex -shell-escape thesis.tex
+C:\Users\samgd\Research\2025-dotson-dissertation\docs>pdflatex -shell-escape 2025-dotson-thesis.tex
+C:\Users\samgd\Research\2025-dotson-dissertation\docs>biber 2025-dotson-thesis  # This is not a typo. Do not include a file extension.
+C:\Users\samgd\Research\2025-dotson-dissertation\docs>pdflatex -shell-escape 2025-dotson-thesis.tex
+C:\Users\samgd\Research\2025-dotson-dissertation\docs>pdflatex -shell-escape 2025-dotson-thesis.tex
 ```
 
 ## Linux

analysis/Snakefile

@@ -7,32 +7,40 @@ latexopt = """
             -halt-on-error
             """
 
+docs_path = "../docs/"
+
+with open(f"{docs_path}Makefile", "r") as file:
+    lines = file.readlines()
+
+output_name = lines[0].strip('\n').replace(' ', '').split('=')[-1]
+
+#============================RULES================================
 rule targets:
     input:
-        thesis = "../docs/thesis.pdf",
+        thesis = f"{docs_path}{output_name}.pdf",
         dag = "dag.png"
 
 if sys.platform == 'Windows':
     rule build_thesis:
         input: 
-            main_tex = "../docs/thesis.tex"
-        output: "../docs/thesis.pdf"
+            main_tex = f"{docs_path}{output_name}.tex"
+        output: f"{docs_path}{output_name}.pdf"
         shell:
             f"""
             cd ../docs && \
-            pdflatex {latexopt} thesis.tex && \
-            biber thesis && \
-            pdflatex {latexopt} thesis.tex && \
-            pdflatex {latexopt} thesis.tex &&
+            pdflatex {latexopt} {output_name}.tex && \
+            biber {output_name} && \
+            pdflatex {latexopt} {output_name}.tex && \
+            pdflatex {latexopt} {output_name}.tex &&
             """
 elif sys.platform in ['darwin', 'linux']:
     rule build_thesis:
         input: 
-            main_tex = "../docs/thesis.tex"
-        output: "../docs/thesis.pdf"
+            main_tex = f"{docs_path}{output_name}.tex"
+        output: f"{docs_path}{output_name}.pdf"
         shell:
-            """
-            (cd ../docs && make)
+            f"""
+            (cd {docs_path} && make)
             """
 
 rule build_dag:

docs/Makefile

@@ -1,4 +1,4 @@
-manuscript = thesis
+manuscript = 2025-dotson-thesis
 references = $(wildcard *.bib)
 latexopt   = -shell-escape -halt-on-error -file-line-error