blocked cholesky paper replication materials (#1)

* created subdir for blocked cholesky paper replication materials

* gitignore additions for blockedchol

* ignore generated tex files in blockecholesky

* added draft generation material for blockedcholesky

* blockedcholesky: added draft compilation instructions to readme

* fix instantiate command in README

* added instructions to install jupyter cache. Thanks to Sam Ozminkowski for catching this!

* added replication material for JSS submission in blockedcholesky/replication

* added latex temp files to gitignore

* added instructions to render instead of preview in blockedcholesky/REAMDE.md

Author: ajinkya-k

.gitignore

@@ -22,3 +22,41 @@ docs/site/
 # committed for packages, but should be committed for applications that require a static
 # environment.
 Manifest.toml
+
+
+
+**/.cache
+blockedcholesky/BlockedCholeskyMM_files/
+
+
+
+
+_files/
+.cache/
+blockedcholesky/BlockedCholeskyMM.tex
+blockedcholesky/ms.tex
+blockedcholesky/orcidlink.sty
+blockedcholesky/arxiv.sty
+blockedcholesky/jss.bst
+blockedcholesky/jss.cls
+blockedcholesky/jsslogo.jpg
+blockedcholesky/jss-draft.tex
+.jupyter_cache/
+scratch/
+.luarc.json
+BlockedCholeskyMM.quarto_ipynb
+
+/.luarc.json
+blockedcholesky/BlockedCholeskyMM+jss.tex
+blockedcholesky/BlockedCholeskyMM+arxiv.tex
+blockedcholesky/BlockedCholeskyMM+arxiv.pdf
+blockedcholesky/BlockedCholeskyMM+jss.pdf
+
+
+**/*.aux
+**/*.bbl
+**/*.blg
+**/*.fdb_latexmk
+**/*.fls
+**/*.log
+**/*.synctex.gz

blockedcholesky/BlockedCholeskyMM.qmd

@@ -0,0 +1,33 @@
+DOCNAME := BlockedCholeskyMM
+TEMPS := jss.bst jss.cls jsslogo.jpg $(DOCNAME).tex ms.tex arxiv.sty orcidlink.sty
+OUTFILES :=  $(TEMPS) $(DOCNAME).pdf $(DOCNAME)+arxiv.tex $(DOCNAME)+arxiv.pdf $(DOCNAME)+jss.tex $(DOCNAME)+jss.pdf
+
+.PHONY: rbench render-arxiv
+preview:
+	quarto preview $(DOCNAME).qmd
+
+render:
+	quarto render $(DOCNAME).qmd --to jss-pdf+jss
+
+render-arxiv:
+	sed -i'.bak' -e '/city:/d' $(DOCNAME).qmd
+	quarto render $(DOCNAME).qmd --to arxiv-pdf+arxiv
+	mv $(DOCNAME).qmd.bak $(DOCNAME).qmd
+
+clean:
+	./latex-clean.sh && rm -v $(OUTFILES)
+
+clean-temps:
+	./latex-clean.sh && rm -v $(TEMPS)
+
+clean-arxiv:
+	./latex-clean.sh && rm -v ms.tex arxiv.sty orcidlink.sty
+
+clean-replication:
+	rm -rfv replication
+
+rbench:
+	R --quiet --no-restore --file=scripts/benchmark.R > scripts/benchmarkoutput.txt
+
+submit-arxiv: rbench render-arxiv
+	./arxiver.sh

blockedcholesky/Makefile

@@ -0,0 +1,26 @@
+[deps]
+AlgebraOfGraphics = "cbdf2221-f076-402e-a563-3d30da359d67"
+AppleAccelerate = "13e28ba4-7ad8-5781-acae-3021b1ed3924"
+Arrow = "69666777-d1a9-59fb-9406-91d4454c9d45"
+CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
+Chairmarks = "0ca39b1e-fe0b-4e98-acfc-b1656634c4de"
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+MKL = "33e6dc65-8f57-5167-99aa-e5a354878fb2"
+MKL_jll = "856f044c-d86e-5d09-b602-aeab76dc8ba7"
+MixedModels = "ff71e718-51f3-5ec2-a782-8ffcbfa3c316"
+PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
+Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+
+[compat]
+AlgebraOfGraphics = "0.10.4"
+Arrow = "2.8"
+CSV = "0.10"
+CairoMakie = "0.13.4"
+Chairmarks = "1.3"
+DataFrames = "1.7"
+MixedModels = "4.34"
+PrettyTables = "2.4"
+Printf = "1"
+julia = "1.10"

blockedcholesky/Project.toml

@@ -0,0 +1,19 @@
+# Replication Materials for "Mixed-model Log-likelihood Evaluation Via a Blocked Cholesky Factorization"
+
+
+## Steps
+
+- Install `jupyter-cache` using the instructions from the quarto Julia docs [here](https://quarto.org/docs/computations/julia.html#jupyter-cache).
+- Install required `Julia` dependencies by running:
+   ```bash
+    $ julia --project=@. -e "import Pkg; Pkg.instantiate()"
+   ```
+- Generate the JSS formatted preview using:
+    ```bash
+     $ make render
+    ```
+- Generate the arXiv formatted version using:
+    ```bash
+    $ make render-arxiv
+    ```
+    **Note:** this command re-runs the `R` benchmark script which can take a long time.

blockedcholesky/README.md

@@ -0,0 +1,8 @@
+title: Git-Rev
+author: Quarto Docs
+version: 1.0.0
+quarto-required: ">=1.2.222"
+contributes:
+  shortcodes:
+    - git.lua
+

blockedcholesky/_extensions/gitrev/_extension.yml

@@ -0,0 +1,28 @@
+-- from https://quarto.org/docs/extensions/shortcodes.html
+function git(command)
+  local p = io.popen("git " .. command)
+  local output = p:read('*all')
+  p:close()
+  return output
+end
+
+-- return a table containing shortcode definitions
+-- defining shortcodes this way allows us to create helper
+-- functions that are not themselves considered shortcodes
+return {
+  ["git-rev"] = function(args, kwargs)
+    -- command line args
+    local cmdArgs = ""
+    local short = pandoc.utils.stringify(kwargs["short"])
+    if short == "true" then
+      cmdArgs = cmdArgs .. "--short "
+    end
+
+    -- run the command
+    local cmd = "rev-parse " .. cmdArgs .. "HEAD"
+    local rev = git(cmd)
+
+    -- return as string
+    return pandoc.Str(string.gsub(rev, '%s+$', ''))
+  end
+}

blockedcholesky/_extensions/gitrev/git.lua

@@ -0,0 +1,46 @@
+title: ArXiv Template
+author: Mike Mahoney
+version: 0.2.3
+contributes:
+  formats:
+    common:
+      filters:
+        - jss.lua
+      # define below YAML configuration common to all formats
+#      filters:
+        # You can include here Lua filters from your extension format
+      shortcodes:
+        # You can include here Lua filters defining shortcodes from your extension
+        - shortcodes.lua
+      knitr:
+        opts_chunk:
+          echo: false
+      number-sections: true
+    pdf:
+      # define default configuration for the pdf version of your format
+      documentclass: article
+      linenumbers: false
+      doublespacing: false
+      authorcols: false
+      # Content to add in header that your format is using
+      header-includes: |
+        \usepackage{arxiv}
+        \usepackage{orcidlink}
+        \usepackage{amsmath}
+        \usepackage{lmodern}
+        \usepackage[T1]{fontenc}
+        \let\proglang=\texttt
+        \newcommand{\pkg}[1]{{\fontseries{m}\fontseries{b}\selectfont #1}}
+      template-partials: ["partials/_authors.tex", "partials/title.tex", "partials/before-body.tex"]
+      mathfont: "Latin Modern Math"
+      mainfont: "Latin Modern Roman"
+      format-resources:
+        # Add here the resources required for the PDF rendering
+        - arxiv.sty
+        - orcidlink.sty
+      cite-method: natbib
+      natbiboptions: round
+    html:
+      toc: true
+      # Use a CSL file to style (https://www.zotero.org/styles/)
+      csl: https://www.zotero.org/styles/chicago-author-date-16th-edition