Merge branch 'dev' into improve-book

.github/workflows/contributors/update_contributors.py

@@ -1,10 +1,10 @@
-import hashlib
-import json
 import os
+import json
 import random
+import hashlib
 
-import pandas as pd
 import requests
+import pandas as pd
 from absl import app
 from absl import logging
 
@@ -87,6 +87,7 @@ def main(_):
     next_page = res.links.get("next", {}).get("url", None)
     last_page = res.links.get("last", {}).get("url", None)
 
+  usernames = set()
   commit_data = []
   for node in data:
     commit_message = node.get("commit", {}).get("message", pd.NA)
@@ -111,6 +112,14 @@ def main(_):
     elif committer_login_info:
       username = committer_login_info["login"]
 
+    try:
+        if username:
+            usernames.add(username)
+    except Exception as e:
+        logging.error(f"Error parsing username: {username}")
+
+
+
     commit_data.append(
         {
             "commit_message": commit_message,
@@ -119,6 +128,12 @@ def main(_):
         }
     )
   commit_data_df = pd.DataFrame(commit_data)
+
+  username_to_fullname = {}
+  for username in usernames:
+      user_data = get_user_data_from_username(username)
+      username_to_fullname[username] = user_data['user_full_name']
+
   co_authors_list = [get_co_authors_from_commit_message(row["commit_message"])
                      for index, row in commit_data_df.iterrows()]
   co_authors_df = pd.concat(co_authors_list, ignore_index=True)
@@ -194,6 +209,11 @@ def main(_):
       lambda row: row['username'] if '@' in row['user_full_name'] else row[
         'user_full_name'],
       axis=1)
+
+  commit_data_df['user_full_name'] = commit_data_df.apply(
+  lambda row: username_to_fullname[row['username']] if row['username'] in username_to_fullname else row['user_full_name'], axis=1
+  )
+
 
   def generate_gravatar_url(name):
     random.seed(name)

_extensions/nmfs-opensci/titlepage/_author-affiliation-themes.tex

@@ -0,0 +1,95 @@
+$if(false)$
+% This sectrion defines the author block and affiliation blocks
+% based on the author and affiliation theme
+$endif$
+\newcommand{\authorstyle}[1]{{$if(titlepage-theme.author-fontsize)$\fontsize{$titlepage-theme.author-fontsize$}{$titlepage-theme.author-spacing$}\selectfont
+$endif$$for(titlepage-theme.author-fontstyle)$\$titlepage-theme.author-fontstyle${$endfor$#1$for(titlepage-theme.author-fontstyle)$}$endfor$}}
+
+\newcommand{\affiliationstyle}[1]{{$if(titlepage-theme.affiliation-fontsize)$\fontsize{$titlepage-theme.affiliation-fontsize$}{$titlepage-theme.affiliation-spacing$}\selectfont
+$endif$$for(titlepage-theme.affiliation-fontstyle)$\$titlepage-theme.affiliation-fontstyle${$endfor$#1$for(titlepage-theme.affiliation-fontstyle)$}$endfor$}}
+
+$if(titlepage-style-code.author.none)$
+\newcommand{\titlepageauthorblock}{}
+$endif$
+$if(titlepage-style-code.author.plain)$
+\newcommand{\titlepageauthorblock}{
+$if(titlepage-theme.author-color)$\textcolor{$titlepage-theme.author-color$}$endif${\authorstyle{$for(by-author)$\nohyphens{$by-author.name.literal$}$sep$$titlepage-theme.author-sep$$if(titlepage-theme.author-space-between)$~\\ \vspace{$titlepage-theme.author-space-between$}$endif$$endfor$\\}}
+}
+$endif$
+$if(titlepage-style-code.author.plain-with-and)$
+\newcommand{\titlepageauthorblock}{
+$if(titlepage-theme.author-color)$\textcolor{$titlepage-theme.author-color$}$endif${\authorstyle{$if(by-author/allbutlast)$$for(by-author/allbutlast)$\nohyphens{$by-author.name.literal$}$sep$$titlepage-theme.author-sep$ $if(titlepage-theme.author-space-between)$~\\ \vspace{$titlepage-theme.author-space-between$}$endif$$endfor$$for(by-author/last)$ and \nohyphens{$by-author.name.literal$}$endfor$$else$$for(by-author/last)$\nohyphens{$by-author.name.literal$}$if(titlepage-theme.author-space-between)$~\\ \vspace{$titlepage-theme.author-space-between$}$endif$$endfor$$endif$}}
+}
+$endif$
+$if(titlepage-style-code.author.superscript)$
+\newcommand{\titlepageauthorblock}{
+$if(titlepage-theme.author-color)$\textcolor{$titlepage-theme.author-color$}$endif${\authorstyle{$for(by-author)$\nohyphens{$by-author.name.literal$}$for(by-author.affiliations)${\textsuperscript{$it.number$}}$sep${\textsuperscript{,}}$endfor$$if(by-author.email)$$if(by-author.affiliations)$\textsuperscript{,}$endif${\textsuperscript{*}}$endif$$sep$$titlepage-theme.author-sep$  $if(titlepage-theme.author-space-between)$~\\ \vspace{$titlepage-theme.author-space-between$}$endif$$endfor$}}
+}
+$endif$
+$if(titlepage-style-code.author.superscript-with-and)$
+\newcommand{\titlepageauthorblock}{
+$if(titlepage-theme.author-color)$\textcolor{$titlepage-theme.author-color$}$endif${\authorstyle{$if(by-author/allbutlast)$$for(by-author/allbutlast)$\nohyphens{$by-author.name.literal$}$for(by-author.affiliations)${\textsuperscript{$it.number$}}$sep$\textsuperscript{,}$endfor$$if(by-author.email)$$if(by-author.affiliations)$\textsuperscript{,}$endif${\textsuperscript{*}}$endif$$sep$$titlepage-theme.author-sep$ $if(titlepage-theme.author-space-between)$~\\ \vspace{$titlepage-theme.author-space-between$}$endif$$endfor$$for(by-author/last)$ and $if(titlepage-theme.author-space-between)$~\\ \vspace{$titlepage-theme.author-space-between$}$endif$\nohyphens{$by-author.name.literal$}$for(by-author.affiliations)${\textsuperscript{$it.number$}}$sep$\textsuperscript{,}$endfor$$if(by-author.email)$$if(by-author.affiliations)$\textsuperscript{,}$endif${\textsuperscript{*}}$endif$$endfor$$else$$for(by-author/last)$\nohyphens{$by-author.name.literal$}$for(by-author.affiliations)${\textsuperscript{$it.number$}}$sep$\textsuperscript{,}$endfor$$if(by-author.email)$$if(by-author.affiliations)$\textsuperscript{,}$endif${\textsuperscript{,*}}$endif$$endfor$$endif$}}}
+$endif$
+$if(titlepage-style-code.author.author-address)$
+\newcommand{\titlepageauthorblock}{
+$if(titlepage-theme.author-color)$\textcolor{$titlepage-theme.author-color$}$endif${\authorstyle{
+$for(by-author)$$by-author.name.literal$$if(by-author.affiliations)$$titlepage-theme.affiliation-sep$$for(by-author.affiliations)$$by-author.affiliations.name$$if(by-author.affiliations.department)$$titlepage-theme.affiliation-sep$$by-author.affiliations.department$$endif$$if(by-author.affiliations.address)$$titlepage-theme.affiliation-sep$$for(by-author.affiliations.address)$$by-author.affiliations.address$$sep$$titlepage-theme.affiliation-sep$$endfor$$endif$$sep$$titlepage-theme.affiliation-sep$$endfor$$endif$$if(by-author.email)$$titlepage-theme.affiliation-sep$$by-author.email$$endif$$sep$\\
+$if(titlepage-theme.author-space-between)$\vspace{$titlepage-theme.author-space-between$}$endif$$endfor$}}}
+$endif$
+$if(titlepage-style-code.author.two-column)$
+\newcommand{\titlepageauthorblock}{
+\newlength{\miniA}
+\setlength{\miniA}{0pt}
+\newlength{\namelen}
+$for(by-author)$\settowidth{\namelen}{$by-author.name.literal$}\setlength{\miniA}{\maxof{\miniA}{\namelen}}$endfor$
+\setlength{\miniA}{\miniA+0.05\textwidth}
+\newlength{\miniB}
+\setlength{\miniB}{0.99\textwidth - \miniA}
+\begin{minipage}{\miniA}
+\begin{flushleft}
+$if(titlepage-theme.author-color)$\textcolor{$titlepage-theme.author-color$}$endif${\authorstyle{$for(by-author)$$by-author.name.literal$$sep$\\ $if(titlepage-theme.author-space-between)$
+\vspace{$titlepage-theme.author-space-between$}$endif$$endfor$}}
+\end{flushleft}
+\end{minipage}
+\begin{minipage}{\miniB}
+\begin{flushright}
+$if(titlepage-theme.affiliation-color)$\textcolor{$titlepage-theme.affiliation-color$}$endif${\affiliationstyle{$for(by-author)$$for(by-author.affiliations/first)$$by-author.affiliations.name$
+$endfor$$sep$\\
+$if(titlepage-theme.affiliation-space-between)$\vspace{$titlepage-theme.affiliation-space-between$}
+$endif$$endfor$\\}}
+\end{flushright}
+\end{minipage}}
+$endif$
+
+$if(titlepage-style-code.affiliation.none)$
+\newcommand{\titlepageaffiliationblock}{}
+$endif$
+$if(titlepage-style-code.affiliation.numbered-list)$
+\newcommand{\titlepageaffiliationblock}{
+\hangindent=1em
+\hangafter=1
+\affiliationstyle{$for(by-affiliation)${$it.number$}.~$if(by-affiliation.name)$$it.name$$endif$$if(by-affiliation.department)$$if(by-affiliation.name)$$titlepage-theme.affiliation-sep$$endif$$it.department$$endif$$if(by-affiliation.address)$$if(by-affiliation.name)$$titlepage-theme.affiliation-sep$$else$$if(by-affiliation.department)$$titlepage-theme.affiliation-sep$$endif$$endif$$it.address$$endif$%
+$sep$\par\hangindent=1em\hangafter=1$if(titlepage-theme.affiliation-space-between)$
+\vspace{$titlepage-theme.affiliation-space-between$}$endif$
+$endfor$
+}}
+$endif$
+$if(titlepage-style-code.affiliation.numbered-list-with-correspondence)$
+\newcommand{\titlepageaffiliationblock}{
+\hangindent=1em
+\hangafter=1
+{\affiliationstyle{
+$for(by-affiliation)${$it.number$}.~$if(by-affiliation.name)$$it.name$$endif$$if(by-affiliation.department)$$if(by-affiliation.name)$$titlepage-theme.affiliation-sep$$endif$$it.department$$endif$$if(by-affiliation.address)$$if(by-affiliation.name)$$titlepage-theme.affiliation-sep$$else$$if(by-affiliation.department)$$titlepage-theme.affiliation-sep$$endif$$endif$$it.address$$endif$
+$sep$\par\hangindent=1em\hangafter=1$if(titlepage-theme.affiliation-space-between)$
+\vspace{$titlepage-theme.affiliation-space-between$}$endif$
+$endfor$
+
+\vspace{1\baselineskip} 
+$if(author)$
+$for(by-author)$
+$if(by-author.email)$
+* \textit{Correspondence:}~$by-author.name.literal$~$by-author.email$
+$endif$$endfor$$endif$
+}}
+}
+$endif$

_extensions/nmfs-opensci/titlepage/_coverpage.tex

@@ -0,0 +1,121 @@
+% This is a combination of Pandoc templating and LaTeX
+% Pandoc templating https://pandoc.org/MANUAL.html#templates
+% See the README for help
+
+\thispagestyle{empty}
+
+$if(coverpage-geometry)$
+\newgeometry{$for(coverpage-geometry)$$coverpage-geometry$$sep$,$endfor$}
+$else$
+\newgeometry{top=-100in}
+$endif$
+
+% Page color
+$if(coverpage-theme.page-html-color)$
+\definecolor{pgcolor}{HTML}{$coverpage-theme.page-html-color$}
+\pagecolor{pgcolor}\afterpage{\nopagecolor}
+$endif$
+
+\newcommand{\coverauthorstyle}[1]{{$if(coverpage-theme.author-fontsize)$\fontsize{$coverpage-theme.author-fontsize$}{$coverpage-theme.author-spacing$}\selectfont
+$endif$$for(coverpage-theme.author-fontstyle)$\$coverpage-theme.author-fontstyle${$endfor$#1$for(coverpage-theme.author-fontstyle)$}$endfor$}}
+
+\begin{tikzpicture}[remember picture, overlay, inner sep=0pt, outer sep=0pt]
+
+$if(coverpage-bg-image)$
+\tikzfading[name=fadeout, inner color=transparent!0,outer color=transparent!100]
+\tikzfading[name=fadein, inner color=transparent!100,outer color=transparent!0]
+\node[$if(coverpage-theme.bg-image-fading)$ scope fading=$coverpage-theme.bg-image-fading$, $endif$anchor=south west$if(coverpage-theme.bg-image-rotate)$, rotate=$coverpage-theme.bg-image-rotate$$endif$$if(coverpage-theme.bg-image-opacity)$, opacity=$coverpage-theme.bg-image-opacity$$endif$] at ($$(current page.south west)+($if(coverpage-theme.bg-image-left)$$coverpage-theme.bg-image-left$$else$0cm$endif$, $if(coverpage-theme.bg-image-bottom)$$coverpage-theme.bg-image-bottom$$else$0cm$endif$)$$) {
+\includegraphics[width=$coverpage-theme.bg-image-size$, keepaspectratio]{$coverpage-bg-image$}};
+$endif$
+
+$if(coverpage-style-code.title.plain)$
+$if(coverpage-title)$
+% Title
+\newcommand{\titlelocationleft}{$coverpage-theme.title-left$}
+\newcommand{\titlelocationbottom}{$coverpage-theme.title-bottom$}
+\newcommand{\titlealign}{$coverpage-theme.title-align$}
+
+\begin{scope}{%
+$if(coverpage-theme.title-fontsize)$\fontsize{$coverpage-theme.title-fontsize$}{$coverpage-theme.title-spacing$}\selectfont
+$endif$$if(coverpage-theme.title-fontfamily)$\coverpagetitlefont
+$endif$\node[anchor=$coverpage-theme.title-anchor$, align=$coverpage-theme.title-align$, rotate=$coverpage-theme.title-rotate$] (Title1) at ($$(current page.south west)+(\titlelocationleft,\titlelocationbottom)$$)  [text width = $coverpage-theme.title-width$$if(coverpage-theme.title-node-spec)$, $coverpage-theme.title-node-spec$$endif$]  {$if(coverpage-theme.title-color)$\textcolor{$coverpage-theme.title-color$}$endif${$for(coverpage-theme.title-fontstyle)$\$coverpage-theme.title-fontstyle${$endfor$\nohyphens{$coverpage-title$}$for(coverpage-theme.title-fontstyle)$}$endfor$}};
+}
+\end{scope}
+$endif$
+$endif$
+$if(coverpage-style-code.author.plain)$
+$if(coverpage-author)$
+
+% Author
+\newcommand{\authorlocationleft}{$coverpage-theme.author-left$}
+\newcommand{\authorlocationbottom}{$coverpage-theme.author-bottom$}
+\newcommand{\authoralign}{$coverpage-theme.author-align$}
+
+\begin{scope}
+{%
+$if(coverpage-theme.author-fontsize)$\fontsize{$coverpage-theme.author-fontsize$}{$coverpage-theme.author-spacing$}\selectfont
+$endif$$if(coverpage-theme.author-fontfamily)$\coverpageauthorfont
+$endif$\node[anchor=$coverpage-theme.author-anchor$, align=$coverpage-theme.author-align$, rotate=$coverpage-theme.author-rotate$] (Author1) at ($$(current page.south west)+(\authorlocationleft,\authorlocationbottom)$$)  [text width = $coverpage-theme.author-width$$if(coverpage-theme.author-node-spec)$, $coverpage-theme.author-node-spec$$endif$]  {
+$if(coverpage-theme.author-color)$\textcolor{$coverpage-theme.author-color$}$endif$\coverauthorstyle{$for(coverpage-author)$$coverpage-author$$sep$$coverpage-theme.author-sep$$endfor$\\}};
+}
+\end{scope}
+$endif$
+$endif$
+$if(coverpage-style-code.header.plain)$
+$if(coverpage-header)$
+
+% Header
+\newcommand{\headerlocationleft}{$coverpage-theme.header-left$}
+\newcommand{\headerlocationbottom}{$coverpage-theme.header-bottom$}
+\newcommand{\headerlocationalign}{$coverpage-theme.header-align$}
+
+\begin{scope}
+{%
+$if(coverpage-theme.header-fontsize)$\fontsize{$coverpage-theme.header-fontsize$}{$coverpage-theme.header-spacing$}\selectfont
+$endif$ $if(coverpage-theme.header-fontfamily)$\coverpageheaderfont
+$endif$\node[anchor=$coverpage-theme.header-anchor$, align=$coverpage-theme.header-align$, rotate=$coverpage-theme.header-rotate$] (Header1) at %
+($$(current page.south west)+(\headerlocationleft,\headerlocationbottom)$$)  [text width = $coverpage-theme.header-width$$if(coverpage-theme.header-node-spec)$, $coverpage-theme.header-node-spec$$endif$]  {$if(coverpage-theme.header-color)$\textcolor{$coverpage-theme.header-color$}$endif${$for(coverpage-theme.header-fontstyle)$\$coverpage-theme.header-fontstyle${$endfor$\nohyphens{$coverpage-header$}$for(coverpage-theme.header-fontstyle)$}$endfor$}};
+}
+\end{scope}
+$endif$
+$endif$
+$if(coverpage-style-code.footer.plain)$
+$if(coverpage-footer)$
+
+% Footer
+\newcommand{\footerlocationleft}{$coverpage-theme.footer-left$}
+\newcommand{\footerlocationbottom}{$coverpage-theme.footer-bottom$}
+\newcommand{\footerlocationalign}{$coverpage-theme.footer-align$}
+
+\begin{scope}
+{%
+$if(coverpage-theme.footer-fontsize)$\fontsize{$coverpage-theme.footer-fontsize$}{$coverpage-theme.footer-spacing$}\selectfont
+$endif$ $if(coverpage-theme.footer-fontfamily)$\coverpagefooterfont
+$endif$\node[anchor=$coverpage-theme.footer-anchor$, align=$coverpage-theme.footer-align$, rotate=$coverpage-theme.footer-rotate$] (Footer1) at %
+($$(current page.south west)+(\footerlocationleft,\footerlocationbottom)$$)  [text width = $coverpage-theme.footer-width$$if(coverpage-theme.footer-node-spec)$, $coverpage-theme.footer-node-spec$$endif$]  {$if(coverpage-theme.footer-color)$\textcolor{$coverpage-theme.footer-color$}$endif${$for(coverpage-theme.footer-fontstyle)$\$coverpage-theme.footer-fontstyle${$endfor$\nohyphens{$coverpage-footer$}$for(coverpage-theme.footer-fontstyle)$}$endfor$}};
+}
+\end{scope}
+$endif$
+$endif$
+$if(coverpage-style-code.date.plain)$
+$if(coverpage-date)$
+
+% Date
+\newcommand{\datelocationleft}{$coverpage-theme.date-left$}
+\newcommand{\datelocationbottom}{$coverpage-theme.date-bottom$}
+\newcommand{\datelocationalign}{$coverpage-theme.date-align$}
+
+\begin{scope}
+{%
+$if(coverpage-theme.date-fontsize)$\fontsize{$coverpage-theme.date-fontsize$}{$coverpage-theme.date-spacing$}\selectfont
+$endif$ $if(coverpage-theme.date-fontfamily)$\coverpagedatefont
+$endif$\node[anchor=$coverpage-theme.date-anchor$, align=$coverpage-theme.date-align$, rotate=$coverpage-theme.date-rotate$] (Date1) at %
+($$(current page.south west)+(\datelocationleft,\datelocationbottom)$$)  [text width = $coverpage-theme.date-width$$if(coverpage-theme.date-node-spec)$, $coverpage-theme.date-node-spec$$endif$]  {$if(coverpage-theme.date-color)$\textcolor{$coverpage-theme.date-color$}$endif${$for(coverpage-theme.date-fontstyle)$\$coverpage-theme.date-fontstyle${$endfor$\nohyphens{$coverpage-date$}$for(coverpage-theme.date-fontstyle)$}$endfor$}};
+}
+\end{scope}
+$endif$
+$endif$
+
+\end{tikzpicture}
+\clearpage
+\restoregeometry

_extensions/nmfs-opensci/titlepage/_extension.yml

@@ -0,0 +1,20 @@
+title: titlepage
+author: Eli Holmes
+quarto-required: ">=1.1.0"
+version: 3.3.10
+contributes:
+  format:
+    pdf:
+      filters:
+        - titlepage-theme.lua
+        - coverpage-theme.lua
+      template-partials:
+        - "_coverpage.tex"
+        - "_author-affiliation-themes.tex"
+        - "_header-footer-date-themes.tex"
+        - "_title-themes.tex"
+        - "_titlepage.tex"
+        - "before-body.tex"
+        - "pandoc.tex"
+      format-resources:
+        - "fonts/qualitype/opentype/QTDublinIrish.otf"