# Inspecting manuscripts in `LaTeX` This vignette walks through some utilities to inspect manuscripts compiled from `LaTeX` ([https://github.com/lsys/texCheckmate/](https://github.com/lsys/texCheckmate/)). Examples of inspection include retrieving text with hardcoded numbers (so that they can checked by hand), finding unreferenced labels, or finding dead links. Much of this is adapted directly from Jonathan Dingel's project template ([https://github.com/jdingel/projecttemplate/](https://github.com/jdingel/projecttemplate/)) which includes a `Makefile` to inspect ("review") a manuscript in `LaTeX`. ## Repeated strings To find repeated strings (one of the most common example being "... the the ..."), use the extended `grep` ```bash $ egrep "\b([a-zA-Z]+) \1\b" paper.tex -n ``` ```text # Example output 243:the the ``` which grabs repeated words and report the line number (`-n`). This can be adapted to more than just single words (thanks ChatGPT): ```bash $ egrep "\b(\S+) (\S+) \1 \2\b" paper.tex -n ``` ```text # Example output 246:flag this flag this ``` A simple shell script for this would look like this: ```bash # inspecting/repeated-strings.sh #!/bin/bash SRC_TEX="paper.tex" echo "Repeated unigrams:" egrep "\b([a-zA-Z]+) \1\b" "$SRC_TEX" -n echo "Repeated bigrams:" egrep "\b(\S+) (\S+) \1 \2\b" "$SRC_TEX" -n echo "Repeated trigrams:" egrep "\b(\S+) (\S+) (\S+) \1 \2 \3\b" "$SRC_TEX" -n ``` and the `Make` recipe would be: ```makefile # Makefile REPEATED_STRINGS_SRC = ./inspecting/repeated-strings.sh .PHONY: repeated_strings repeated_strings: ## Check for repeated words @echo "==> $@" @echo "Check for repeated words (e.g. 'the the table shows...')" -$(REPEATED_STRINGS_SRC) ``` ```{admonition} Regex nuance :class: note `[a-zA-Z]` and `\S` are not the same. `\S` includes digits. So a repeated "Fig 3 Fig 3" is flagged with `\S` but not with `[a-zA-Z]`. ``` ## Duplicated labels To check for duplicated labels (`TeX` does warn for this too), e.g., having used the same `\label{tab:summary}` more than once in all the `*.tex` files, `grep` all such labels ```bash $ grep -o '\\label{[^}]*}' paper.tex | uniq -cd ``` Unpacking the above: * `grep -o '\\label{[^}]*}' paper.tex` finds all "\label{**}" in the source. * `sort` sorts the labels so that repeats can be detected. * `uniq` (assumes results have been sorted, hence `sort`) then finds duplicates. * `c` prefix lines by number of occurences. * `d` reports only duplicated lines, one for each group. A `Make` recipe can then be defined as: ```makefile # Makefile .PHONY: duplicated_labels duplicated_labels: ## Check for duplicated labels @echo "==> $@" @echo "Check for duplicated labels" grep -o '\\label{[^}]*}' paper.tex | sort | uniq -cd ``` ## Unreferenced labels To find unreferenced labels in the `tex` files, use the `diff` to compare the labels defined from `\label{**}` and labels used in all the `\*ref*{**}` A simple shell script would look like: ```bash # unreferenced-labels.sh #!/bin/bash SRC_TEX="paper.tex" diff \ --side-by-side \ --suppress-common-lines \ <(grep -o --no-filename 'ref{[A-Za-z0-9:_]*}' "$SRC_TEX" | sed 's/ref//' | sort | uniq) \ <(grep -o --no-filename 'label{[A-Za-z0-9:_]*}' "$SRC_TEX" | sed 's/label//' | sort | uniq) ``` ```text # Example output > {fig:un} > {sec:intro} > {sm:results} ``` A `Make` recipe would look like: ```makefile # Makefile .PHONY: unreferenced_labels unreferenced_labels: ## Check for label referencing @echo "==> $@" @echo "Check for unreferenced labels" ./inspecting/unreferenced-labels.sh ``` ## Hardcoded numbers One of the things to check with a manuscript is whether hardcoded numbers are correct (e.g., "...sample size of 42..."). A quick way to grab all lines of a `tex` file that contains some hardcoded number is using `grep` (again). For example, a simple shell script would be: ```bash # hardcoded-numbers.sh #!/bin/bash do cat paper.tex | sed -n '/\\begin{document}/,$p' | # Skip lines until \begin{document} sed '/\\begin{table}/,/\\end{table}/d' | # Remove lines within table environments sed 's/\\cite{[A-Za-z0-9:,\-]*}//g' | #Drop citations with \cite{} that may contain numbers grep '[0-9]' done ``` which excludes lines before `\begin{document}`, lines within `table` environments, and lines where numbers come only from the `\cite{}` command. The last line `grep '[0-9]'` then extracts lines with numbers and prints them. ```text # Example output Hello world! The tex also, contains error of \emph{gramar and and spelling}. or use this text too see an few of of the problems that LanguageTool can detecd. What do you thinks of grammar checkers? Please not that they are not perfect. Style ssues get a blue marker: It's 5 P.M. in the afternoon. LanguageTool 3.8 was released on Thursday, 27 June 2017. Here,I forget to put a space after a comma. I refer to \ref{fig:thisfig1} in the text, but I do not refer to the second one. \\ const seedUrl = "http://127.0.0.1:8080/"; \email{asdfgh.zxcvbnm@123.12345678.ca} ``` using the `example.tex` from [textidote](#textidote-grammar-and-latex-checker). Amongst other numbers, I can then, for example, check that the "5 P.M." is correct or that the `LanguageTool` version is correct, and if not, make the necessary amendments. The `hardcoded-numbers.sh` (fully adapted to omit lines from certain environments at [the end](#all-together)) can be called with a `Make` recipe: ```makefile # Makefile .PHONY: hardcodednumbers hardcodednumbers: ## Find hardcoded numbers @echo "==> $@" ./inspecting/hardcoded-numbers.sh ``` ## Acronyms A shell one-liner to find all the acronyms in the file with a tally of count usage is ```bash $ cat *.tex | grep -wo "[A-Z]\+\{2,10\}" | sort | uniq -c | sort -gr ``` * `grep -wo "[A-Z]\+\{2,10\}"` matches upper case words between 2 to 10 characters long * `sort | uniq -c` sorts the results (like in [Duplicated labels](#duplicated-labels)) before creating a counter (`-c`) * `sort -gr` then sorts the results numerically (`-g`) in descending order (`-r`) ```text # Example output 167 PFAS 123 PFBS 59 GUSTO 30 SD ... ``` This can be adapted to exclude certain parts of a `tex` file (like [Harcoded numbers](#hardcoded-numbers)) ```bash # acronyms.sh #!/bin/bash do cat paper.tex | sed -n '/\\begin{document}/,$p' | # Skip lines until \begin{document} sed '/\\begin{table}/,/\\end{table}/d' | # Remove lines within table environments sed 's/\\cite{[A-Za-z0-9:,\-]*}//g' | #Drop citations with \cite{} that may contain numbers grep -wo "[A-Z]\+\{2,10\}" | sort | uniq -c | sort -gr done ``` which can then be called from the `Makefile`: ```makefile # Makefile .PHONY: acronyms acronyms: ## Find and tally acronyms @echo "==> $@" ./inspecting/acronyms.sh ``` **Resource:** * [https://doofussoftware.blogspot.com/2012/09/a-linux-one-liner-to-find-all-acronyms.html](https://doofussoftware.blogspot.com/2012/09/a-linux-one-liner-to-find-all-acronyms.html) ## Check URLs Another thing to check is that the URLs referenced in the manuscripts are live and working. This can be done by combining the use of `grep` to find all URLs specified in the `\url{}` and `\href{}{}` commands before using `wget` to check that the link works: ```bash # urls.sh #!/bin/bash HREF_LIST=$(grep -o 'href{[A-Za-z0-9:/\._?#=]*}' paper.tex | sed 's/.*href{//' | sed 's/}//;s/\\#/#/') for URL in $HREF_LIST; do wget --spider --no-verbose "$URL" done ``` to get output that looks like: ```text 2023-09-29 14:42:49 URL: https://en.wikipedia.org/wiki/ 200 OK 2023-09-29 14:42:49 URL: https://developers.google.com/maps/documentation/javascript 200 OK wget: unable to resolve host address ‘www.this-should-not-work.com’ ... ... ``` ```{admonition} fake.com :class: attention I tried using [www.fake.com](www.fake.com) as an example of a failure but apparently that's a real website.. ``` The `Make` recipe would then be: ```makefile # Makefile .PHONY: checkURLs checkURLs: @echo "==> $@" ./inspecting/urls.sh ``` ## Wordcount To count words, `TeXcount` comes in handy. The basic `TeXcount` command-line syntax is: ```bash $ texcount paper.tex [opts] ``` ```text # Example output File: paper.tex Encoding: utf8 Words in text: 4382 Words in headers: 47 Words outside text (captions, etc.): 266 Number of headers: 20 Number of floats/tables/figures: 6 Number of math inlines: 32 Number of math displayed: 3 Subcounts: text+headers+captions (#headers/#floats/#inlines/#displayed) 1+0+3 (1/0/0/0) _top_ 442+1+0 (1/0/0/0) Section: Introduction}\label{sec:intro ... ... ``` A simple `.sh` file can be made to log the wordcount. The `-nobib` option exclude bibliography and `-quiet` suppresses error messages. ```bash # wordcount.sh #!/bin/bash DETAILED_OUTPUT_FILE="inspecting/wordcount-detailed.txt" STORE=$(texcount \ -nobib \ -quiet \ paper.tex ) echo "$STORE" > "$DETAILED_OUTPUT_FILE" ``` which can then be called from a Makefile: ```makefile # Makefile .PHONY: wordcount wordcount: ## Wordcount via texcount @echo "==> $@" @echo "Check word count using texcount" ./inspecting/wordcount.sh ``` ```{admonition} Ignore text count from within tex :class: note Within the `tex` file(s), use `%TC:ignore` to start ignoring text and end it with `%TC:endignore`. ``` ```{admonition} Commented text are ignored :class: caution Apparently `TeXcount` intelligently ignores text (including notes to self) that are commented out in the `*.tex` files. ``` **Resources:** * [Texcount document](https://app.uio.no/ifi/texcount/download.php?doc=QuickReference_3_2.pdf) ## Textidote: Grammar and `LaTeX` checker A helpful tool to check for both `LaTeX` and language (using [LanguageTool](https://languagetool.org/)) is [textidote](https://github.com/sylvainhalle/textidote). `textidote` can take a pre-specified dictionary of ignores (using `--dict` `path_to_dict`) and output a HTML file with detected errors. ```bash $ textidote --check en paper.tex ``` ![[https://github.com/sylvainhalle/textidote](https://github.com/sylvainhalle/textidote)](textidote.png) (*Source:* [https://github.com/PatrBal/vim-textidote](https://github.com/PatrBal/vim-textidote)) ```{admonition} Installation :class: tip I had issues installing textidote. But turns out it's available via [`brew`](https://formulae.brew.sh/formula/textidote) (although undocumented). ``` The `Make` recipe would look something like: ```makefile # Makefile .PHONY: textidote textidote: ./inspecting/textidote_dict.txt @echo "==> $@" @echo "Check doc with textidote" textidote --check en --dict $< --output ../paper.tex > inspecting/textidote.html ``` which outputs the results like in the image above to `inspecting/textidote.html`. It looks like the distinct colors indicate types of error but the colors cannot be configured. ![[https://sylvainhalle.github.io/textidote/](https://sylvainhalle.github.io/textidote/)](textidote2.png) (Source: [https://sylvainhalle.github.io/textidote/](https://sylvainhalle.github.io/textidote/)) Color meanings: * Red: Spelling errors * Orange: Grammar errors * Yellow: `TeX` syntax style suggestions **Resources** * [https://github.com/sylvainhalle/textidote](https://github.com/sylvainhalle/textidote) * [https://formulae.brew.sh/formula/textidote](https://formulae.brew.sh/formula/textidote) ## Bonus: "Due to" All it takes to find *bureaucratese* like "due to" (`Elements of Style` by Strunk and White) is: ```bash $ grep -n 'due to' paper.tex ``` which then spits out lines containing "due to" that can then be nuked. The corresponding `Make` recipe is: ```makefile # Makefile .PHONY: dueto dueto: ## Find "due to"s; Did you mean "because of", "owing to", or "from"? @echo "==> $@" @echo "Find all the 'due to's in writing" grep -n 'due to' paper.tex ``` **Resources** * Strunk, William, and E. B. White. The Elements of Style. 4th ed., Pearson, 2000. ## All together All together, the directory containing the `tex` files, the `Makefile`, and the shell scripts would look something like ```console . ├── inspecting │ ├── logs │ ├── acronyms.sh │ ├── ay2numeric.sh │ ├── hardcoded-numbers.sh │ ├── linkchecker.sh │ ├── numeric2ay.sh │ ├── repeated-strings.sh │ ├── textidote_dict.txt │ ├── unreferenced-labels.sh │ ├── wordcount.sh ├── Makefile ├── paper.tex ├── paper.pdf └── references.bib ``` `./inspecting/logs` contains the log files for reference. `ay2numeric.sh` and `numeric2ay.sh` swaps citations from author-year to numeric, and vice versa. *Click to expand and see the full `.sh` scripts ([https://github.com/lsys/texCheckmate/](https://github.com/lsys/texCheckmate/)) that logs the output:* ````{dropdown} acronyms.sh ```bash #!/bin/bash SRC_TEX="paper.tex" LOG_DIR="./inspecting/logs" LOG_FILE="$LOG_DIR/acronyms.log" # Ensure the log directory exists mkdir -p "$LOG_DIR" # Overwrite the log file at the start > "$LOG_FILE" # Function to process files, renamed to "acronyms" acronyms() { local file="$1" # Check if file exists if [[ ! -f "$file" ]]; then echo "Error: $file not found" | tee -a "$LOG_FILE" return 1 fi echo "Checking file: $file" | tee -a "$LOG_FILE" # Output file marker echo '===' "$file" '===' | tee -a "$LOG_FILE" cat "$file" | # Process the file content and log results # ======================================================================= # Ignore lines relating to environment sed -n '/\\begin{document}/,$p' | # Skip lines until \begin{document} grep -Ev '^\\newcommand' | # Ignore lines starting with \newcommand (e.g., \newcommand{\nc}{} ) grep -Ev '^\\setcounter' | # Ignore lines starting with \setcounter grep -Ev '^\\vspace' | grep -Ev '^\\hspace' | grep -Ev '^\\usepackage' | grep -Ev '^\\setlength' | # ======================================================================= # Ignore math, tables, figures sed '/begin{equation}/,/end{equation}/d' | sed '/begin{equation\*}/,/end{equation\*}/d' | sed '/begin{align}/,/end{align}/d' | sed '/begin{align\*}/,/end{align\*}/d' | # Remove equation environments sed 's/\\input{[A-Za-z0-9_\/\.]*}//g' | # Drop input files that might contain numbers grep -v 'includegraphics' | # Drop lines that are graphics filepaths or numbers setting the figure size sed 's/[0-9\.]*\\textwidth//g' | sed 's/\$[A-Za-z0-9+=_{}\ ]*\$//g' | # Drop inline equations that may contain numbers sed '/\\begin{figure}/,/\\end{figure}/d' | # Remove lines within figure environments sed '/\\begin{table}/,/\\end{table}/d' | # Remove lines within table environments # ======================================================================= # Ignore commented-out lines sed '/\\iffalse/,/\\fi/d' | # Remove lines between \iffalse and \fi sed '/^%/d' | # Remove lines beginning with % # ======================================================================= # Ignore citations sed 's/\\cite{[A-Za-z0-9:,\-]*}//g' | # Drop citations with \cite{} that may contain numbers sed 's/\\citealt{[^}]*}//g' | # Drop citations with \citealt{} that may contain numbers sed 's/\\citep{[^}]*}//g' | # This seems to work for \citep and not line 16.. sed 's/\\citet{[^}]*}//g' | # This seems to work for \citep and not line 16.. # ======================================================================= grep -wo "[A-Z]\+\{2,20\}" | sort | uniq -c | sort -gr | tee -a "$LOG_FILE" # Log results to file } # Main loop to find and process all files named $SRC_TEX find . -name "$SRC_TEX" | while IFS= read -r file; do acronyms "$file" done ``` ```` ````{dropdown} hardcoded-numbers.sh ```bash #!/bin/bash #This script allow you to review hardcoded numbers appearing in the manuscript #From https://github.com/jdingel/projecttemplate/blob/master/paper/reviewing/hardcodednumbers.sh SRC_TEX="paper.tex" LOG_DIR="./inspecting/logs" LOG_FILE="$LOG_DIR/hardcoded-numbers.log" for file in $(find -name $SRC_TEX) do echo '===' ${file} '===' cat ${file} | # ======================================================================= # Ignore lines relating to environment sed -n '/\\begin{document}/,$p' | # Skip lines until \begin{document} grep -Ev '^\\newcommand' | # Ignore lines starting with \newcommand (e.g., \newcommand{\nc}{}) grep -Ev '^\\setcounter' | # Ignore lines starting with \setcounter grep -Ev '^\\vspace' | grep -Ev '^\\hspace' | grep -Ev '^\\usepackage' | grep -Ev '^\\setlength' | # ======================================================================= # Ignore math, tables, figures sed '/begin{equation}/,/end{equation}/d' | sed '/begin{equation\*}/,/end{equation\*}/d' | sed '/begin{align}/,/end{align}/d' | sed '/begin{align\*}/,/end{align\*}/d' | #Remove equation environments sed 's/\\input{[A-Za-z0-9_\/\.]*}//g' | # Drop input files that might contain numbers grep -v 'includegraphics' | #Drop lines that are graphics filepaths or numbers setting the figure size sed 's/[0-9\.]*\\textwidth//g' | sed 's/\$[A-Za-z0-9+=_{}\ ]*\$//g' | #Drop inline equations that may contain numbers sed '/\\begin{figure}/,/\\end{figure}/d' | # Remove lines within figure environments sed '/\\begin{table}/,/\\end{table}/d' | # Remove lines within table environments # ======================================================================= # Ignore commented-out lines sed '/\\iffalse/,/\\fi/d' | # Remove lines between \iffalse and \fi sed '/^%/d' | # Remove lines beginning with % # ======================================================================= # Ignore internal links sed 's/\\cref{[^}]*}//g' | # Ignore numbers from \cref{} sed 's/\\ref{[^}]*}//g' | # Ignore numbers from \ref{} sed 's/\\nameref{[^}]*}//g' | # Ignore numbers from \nameref{} sed 's/\\crefrange{[^}]*}//g' | # Ignore numbers from \nameref{} # ======================================================================= # Ignore citations sed 's/\\cite{[A-Za-z0-9:,\-]*}//g' | #Drop citations with \cite{} that may contain numbers sed 's/\\citealt{[^}]*}//g' | #Drop citations with \citealt{} that may contain numbers sed 's/\\citep{[^}]*}//g' | # This seems to work for \citep and not line 16.. sed 's/\\citet{[^}]*}//g' | # This seems to work for \citep and not line 16.. sed 's/\\cite{[^}]*}//g' | grep '[0-9]' -n done > $LOG_FILE cat $LOG_FILE ``` ```` ````{dropdown} linkchecker.sh ```bash #!/bin/bash SRC_TEX="paper.tex" LOG_DIR="./inspecting/logs" LOG_FILE="$LOG_DIR/linkchecker.log" # Ensure the log directory exists mkdir -p "$LOG_DIR" # Overwrite the log file at the beginning > "$LOG_FILE" # Log and output both stdout and stderr { echo "---> Retrieving URL(s) in \href{}{}:" # This one reverses the escaping of \# in the URL HREF_LIST=$(grep -o 'href{[A-Za-z0-9:/\._?#=]*}' "$SRC_TEX" | sed 's/.*href{//' | sed 's/}//;s/\\#/#/') echo "---> Retrieving URL(s) in \url{}:" URL_LIST=$(grep -o '\\url{[^}]*}' "$SRC_TEX" | sed 's/\\url{//;s/}//;s/\\#/#/g') echo "---> Retrieving all other URLs" GLOBAL_LIST=$(cat "$SRC_TEX" | egrep -o "(http|https)://[a-zA-Z0-9./?=_%:-]*" | sort -u) ALL_URLS=$(echo "$HREF_LIST $URL_LIST $GLOBAL_LIST" | tr ' ' '\n' | sort -u) for URL in $ALL_URLS; do echo "Checking URL: $URL" wget --spider --no-verbose "$URL" done } 2>&1 | tee -a "$LOG_FILE" ``` ```` ````{dropdown} repeated-strings.sh ```bash #!/bin/bash SRC_TEX="paper.tex" LOG_DIR="./inspecting/logs" LOG_FILE="$LOG_DIR/repeated-strings.log" # Overwrite the log file at the beginning > "$LOG_FILE" { echo "Repeated unigrams:" egrep "\b([a-zA-Z]+) \1\b" "$SRC_TEX" -n echo "Repeated bigrams:" egrep "\b(\S+) (\S+) \1 \2\b" "$SRC_TEX" -n echo "Repeated trigrams:" egrep "\b(\S+) (\S+) (\S+) \1 \2 \3\b" "$SRC_TEX" -n } 2>&1 | tee -a "$LOG_FILE" ``` ```` ````{dropdown} unreferenced-labels.sh ```bash #!/bin/bash # From https://github.com/jdingel/projecttemplate/blob/master/paper/reviewing/Makefile SRC_TEX="paper.tex" LOG_DIR="./inspecting/logs" LOG_FILE="$LOG_DIR/unreferenced-labels.log" diff \ --side-by-side \ --suppress-common-lines \ <(grep -o --no-filename 'ref{[A-Za-z0-9:_]*}' "$SRC_TEX" | sed 's/ref//' | sort | uniq) \ <(grep -o --no-filename 'label{[A-Za-z0-9:_]*}' "$SRC_TEX" | sed 's/label//' | sort | uniq) | tee "$LOG_FILE" ``` ```` ````{dropdown} wordcount.sh ```bash #!/bin/bash SRC_TEX="paper.tex" LOG_DIR="./inspecting/logs" # total: Do not give sums per file, only total sum. # nobib: Do not include bibliography in count (default). # sum Make sum of all word and equation counts. May also use # -sum=#[,#] with up to 7 numbers to indicate how each of the # counts (text words, header words, caption words, #headers, # #floats, #inlined formulae, #displayed formulae) are summed. # The default sum (if only -sum is used) is the same as # -sum=1,1,1,0,0,1,1. # sub: Generate subcounts. Option values are none, part, chapter, # section or subsection. Default (-sub) is set to subsection, # whereas unset is none. (Alternative option name is -subcount.) # inc: Parse included TeX files (as separate file). # quiet: Quiet mode, no error messages. Use is discouraged! TEXCOUNT_OUTPUT=$(texcount \ -total \ -nobib \ -sum \ -sub \ -inc \ -quiet \ "$SRC_TEX" ) echo "Word count report for $SRC_TEX: $TEXCOUNT_OUTPUT" # Store total word count OUTPUT_FILE="$LOG_DIR/wordcount.txt" STORE=$(texcount \ -1 \ -nobib \ -nosum \ -quiet \ "$SRC_TEX") echo "$STORE" > "$OUTPUT_FILE" # Store detailed word count DETAILED_OUTPUT_FILE="$LOG_DIR/wordcount-detailed.txt" STORE=$(texcount \ -nobib \ -quiet \ "$SRC_TEX") echo "$STORE" > "$DETAILED_OUTPUT_FILE" ``` ```` The `Makefile` with all the recipes would be ````{dropdown} Makefile ```makefile # .SUFFIXES: .pdf .tex .DEFAULT_GOAL := help #============================================================================== # Inspecting #============================================================================== WORDCOUNT_SCR := ./inspecting/wordcount.sh .PHONY: wordcount wordcount: ## Wordcount via texcount @echo "==> $@" @echo "Check word count using texcount" dos2unix $(WORDCOUNT_SCR) chmod +x $(WORDCOUNT_SCR) $(WORDCOUNT_SCR) ACRONYMS_SRC = ./inspecting/acronyms.sh .PHONY: acronyms acronyms: ## Find and tally acronyms @echo "==> $@" @echo "Check for acronyms" dos2unix $(ACRONYMS_SRC) chmod +x $(ACRONYMS_SRC) $(ACRONYMS_SRC) .PHONY: dueto dueto: ## Find "due to"s; Did you mean "because of", "owing to", or "from"? @echo "==> $@" @echo "Find all the 'due to's in writing" grep -n "due to" $(SRC_TEX) > inspecting/logs/duetos.log .PHONY: duplicated_labels duplicated_labels: ## Check for duplicated labels @echo "==> $@" @echo "Check for duplicated labels" grep -o '\\label{[^}]*}' $(SRC_TEX) | sort | uniq -cd | tee ./inspecting/logs/duplicated-labels.log HARDCODEDNUMBERS_SRC = ./inspecting/hardcoded-numbers.sh .PHONY: hardcodednumbers hardcodednumbers: ## Find hardcoded numbers @echo "==> $@" @echo "Check for hardcoded numbers" dos2unix $(HARDCODEDNUMBERS_SRC) chmod +x $(HARDCODEDNUMBERS_SRC) $(HARDCODEDNUMBERS_SRC) LINKCHECKER_SRC = ./inspecting/linkchecker.sh .PHONY: linkchecker linkchecker: ## Check URLs @echo "==> $@" @echo "Check that URLs work" dos2unix $(LINKCHECKER_SRC) chmod +x $(LINKCHECKER_SRC) $(LINKCHECKER_SRC) REPEATED_STRINGS_SRC = ./inspecting/repeated-strings.sh .PHONY: repeated_strings repeated_strings: ## Check for repeated words @echo "==> $@" @echo "Check for repeated words (e.g. 'the the table shows...')" dos2unix $(REPEATED_STRINGS_SRC) chmod +x $(REPEATED_STRINGS_SRC) -$(REPEATED_STRINGS_SRC) .PHONY: textidote textidote: ## Check with textidote textidote: ./inspecting/textidote_dict.txt @echo "==> $@" @echo "Check doc with textidote" -textidote --check en --dict $< --output html $(SRC_TEX) > inspecting/logs/textidote.html UNREFERENCED_LABELS_SRC = ./inspecting/unreferenced-labels.sh .PHONY: unreferenced_labels unreferenced_labels: ## Check for label referencing @echo "==> $@" @echo "Check for unreferenced labels" dos2unix $(UNREFERENCED_LABELS_SRC) chmod +x $(UNREFERENCED_LABELS_SRC) -$(UNREFERENCED_LABELS_SRC) .PHONY: inspect inspect: ## Do all inspections of manuscript inspect: duplicated_labels \ repeated_strings \ unreferenced_labels \ hardcodednumbers \ acronyms \ linkchecker \ textidote \ dueto \ wordcount #============================================================================== # Additional utilities #============================================================================== AY2NUMERIC_SRC = ./inspecting/ay2numeric.sh .PHONY: aynumeric aynumeric: ## Change author-year to numeric citation @echo "==> $@" @echo "Change author-year to numeric citations" dos2unix $(AY2NUMERIC_SRC) chmod +x $(AY2NUMERIC_SRC) $(AY2NUMERIC_SRC) NUMERICAY_SRC = ./inspecting/numeric2ay.sh .PHONY: numericay numericay: ## Change author-year to numeric citation @echo "==> $@" @echo "Change numeric to author-year citations" dos2unix $(NUMERICAY_SRC) chmod +x $(NUMERICAY_SRC) $(NUMERICAY_SRC) #============================================================================== # Help #============================================================================== .PHONY: help help: ## Show this help message and exit @grep -E '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | sort | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-16s\033[0m %s\n", $$1, $$2}' ``` ```` Then, to run all inspections, just do: ```bash $ make inspect ``` Some shell scripts like the `diff` to check unreferenced labels can return non-`0` status codes and might (annoyingly) turn up as a `Make` error (`make: *** [Makefile: ... Error 1`) even if there are no errors. ```text # Example output ... ... ==> unreferenced_labels Check for unreferenced labels dos2unix ./inspecting/unreferenced-labels.sh dos2unix: converting file ./inspecting/unreferenced-labels.sh to Unix format... ./inspecting/unreferenced-labels.sh ... ... make: *** [Makefile:93: unreferenced_labels] Error 1 ``` To make `Make` ignore this, do a `make inspect -k` (where the `-k` prevents `Make` from stopping). ```bash $ make inspect -k ``` Or, add a `-` before the command that would return non-zero status codes (e.g., `-./inspecting/unreferenced-labels.sh` instead of `./inspecting/unreferenced-labels.sh`). ## Summary And this, in summary, is how to procrastinate on submitting a manuscript.
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