From a29b2af43d86b93f881bc198bea0fe4e8a97c674 Mon Sep 17 00:00:00 2001
From: Michael DeWitt <me.dewitt.jr@gmail.com>
Date: Tue, 31 Mar 2026 19:49:01 -0400
Subject: [PATCH 1/3] update latest

---
 .gitignore                 | 2 +-
 Cargo.lock                 | 2 +-
 Cargo.toml                 | 2 +-
 src/templates/Taskfile.yml | 5 +++++
 4 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/.gitignore b/.gitignore
index 23f5f27..98d9fd1 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,7 +2,7 @@
 # will have compiled files and executables
 debug
 target
-
+md-notes.md
 # These are backup files generated by rustfmt
 **/*.rs.bk
 
diff --git a/Cargo.lock b/Cargo.lock
index 9cee2e9..7bc5444 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -773,7 +773,7 @@ dependencies = [
 
 [[package]]
 name = "ptmp"
-version = "0.1.3"
+version = "1.1.2"
 dependencies = [
  "anyhow",
  "chrono",
diff --git a/Cargo.toml b/Cargo.toml
index adfee8b..fc74b8c 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -1,7 +1,7 @@
 
 [package]
 name = "ptmp"
-version = "0.1.3"
+version = "1.1.2"
 edition = "2021"
 authors = ["Michael DeWitt <michael.dewitt@wfusm.edu>"]
 description = "Copy a template directory and render Tera placeholders via a TUI."
diff --git a/src/templates/Taskfile.yml b/src/templates/Taskfile.yml
index 51a8ee4..da340de 100644
--- a/src/templates/Taskfile.yml
+++ b/src/templates/Taskfile.yml
@@ -90,4 +90,9 @@ tasks:
     deps: [latex]
     cmds:
       - open {{.OUTDIR}}/{{.MAIN}}
+
+  bib:
+    desc: Format references.bib
+    cmds:
+      - bibfmt references.bib
 {% endraw %}

From 71162e2b0a1b1b6221ddc53023972b6e748b4ca7 Mon Sep 17 00:00:00 2001
From: Michael DeWitt <me.dewitt.jr@gmail.com>
Date: Thu, 21 May 2026 11:19:49 -0400
Subject: [PATCH 2/3] updates

---
 README.Md                                     |  13 ++
 src/cli.rs                                    |  12 ++
 src/components.rs                             |  75 ++++++-
 src/config.rs                                 | 115 +++++++++++
 src/main.rs                                   |  36 ++++
 src/templates.rs                              |   5 +
 src/templates/Taskfile.yml                    |  11 +
 src/templates/example.R                       |   3 +-
 src/templates/example.slurm                   |   4 +
 src/templates/justfile                        |  24 +++
 src/templates/nature.csl                      | 189 ++++++++++++++++++
 .../pandoc-reference-arial11-0p5in.docx       | Bin 0 -> 26430 bytes
 src/templates/review-taskfile.yml             |  53 +++++
 13 files changed, 534 insertions(+), 6 deletions(-)
 create mode 100644 src/config.rs
 create mode 100644 src/templates/justfile
 create mode 100644 src/templates/nature.csl
 create mode 100644 src/templates/pandoc-reference-arial11-0p5in.docx
 create mode 100644 src/templates/review-taskfile.yml

diff --git a/README.Md b/README.Md
index c8e262f..ab49a74 100644
--- a/README.Md
+++ b/README.Md
@@ -29,6 +29,17 @@ ptmp new \
   --destination ~/projects/WNV-modeling
 ```
 
+### Set personal defaults
+
+Run once to save your name, email, ORCID, and other fields.
+These become the pre-filled defaults whenever ptmp prompts you.
+
+```bash
+ptmp config
+```
+
+Defaults are stored in `~/.config/ptmp/defaults.toml`.
+
 ### Emit a single component
 
 Write one file into the current working directory, prompting only for the fields that file needs.
@@ -48,6 +59,8 @@ ptmp citation       # CITATION.cff
 ptmp license        # LICENSE (MIT)
 ptmp quarto         # report.qmd
 ptmp slides         # slides.qmd
+ptmp docx           # templates/ (pandoc reference docx + CSL)
+ptmp justfile       # justfile (pandoc rendering tasks)
 ```
 
 ## Template rendering
diff --git a/src/cli.rs b/src/cli.rs
index 4ccd78b..0eb833e 100644
--- a/src/cli.rs
+++ b/src/cli.rs
@@ -79,4 +79,16 @@ pub enum Commands {
 
     /// Emit a Quarto revealjs slide deck (slides.qmd) into the current directory
     Slides,
+
+    /// Emit a review Taskfile.yml for academic peer review
+    Review,
+
+    /// Emit pandoc reference docx and CSL into templates/
+    Docx,
+
+    /// Emit a justfile with pandoc rendering tasks
+    Justfile,
+
+    /// Set personal defaults (author, email, ORCID, etc.)
+    Config,
 }
diff --git a/src/components.rs b/src/components.rs
index eb74fa0..022a234 100644
--- a/src/components.rs
+++ b/src/components.rs
@@ -45,21 +45,39 @@ pub static KNOWN_FIELDS: &[FieldDef] = &[
     FieldDef {
         name: "slurm_account",
         prompt: "SLURM account/group",
-        default: "",
+        default: "kortessisGrp",
         required: true,
     },
     FieldDef {
         name: "slurm_email",
         prompt: "Email for SLURM notifications",
-        default: "",
+        default: "dewime23@wfu.edu",
         required: true,
     },
+    FieldDef {
+        name: "email",
+        prompt: "Email address",
+        default: "michael.dewitt@wfusm.edu",
+        required: false,
+    },
     FieldDef {
         name: "orcid",
-        prompt: "ORCID identifier (e.g., 0000-0001-2345-6789)",
-        default: "",
+        prompt: "ORCID identifier (e.g., 0000-0001-8940-1967)",
+        default: "0000-0001-8940-1967",
         required: false,
     },
+    FieldDef {
+        name: "pdf_path",
+        prompt: "Path to the PDF to review",
+        default: "",
+        required: true,
+    },
+    FieldDef {
+        name: "reviewer_name",
+        prompt: "Reviewer name",
+        default: "",
+        required: true,
+    },
 ];
 
 pub struct Component {
@@ -184,6 +202,33 @@ pub static COMPONENTS: &[Component] = &[
         extra_text: &[("reveal-theme.scss", templates::REVEAL_THEME)],
         extra_binary: &[("assets/logo-wide.png", templates::LOGO_WIDE)],
     },
+    Component {
+        name: "review",
+        output_path: "Taskfile.yml",
+        template: templates::REVIEW_TASKFILE,
+        fields: &["pdf_path", "reviewer_name"],
+        extra_text: &[],
+        extra_binary: &[],
+    },
+    Component {
+        name: "docx",
+        output_path: "templates/nature.csl",
+        template: templates::NATURE_CSL,
+        fields: &["title"],
+        extra_text: &[],
+        extra_binary: &[(
+            "templates/pandoc-reference-arial11-0p5in.docx",
+            templates::PANDOC_REFERENCE_DOCX,
+        )],
+    },
+    Component {
+        name: "justfile",
+        output_path: "justfile",
+        template: templates::JUSTFILE,
+        fields: &["title"],
+        extra_text: &[],
+        extra_binary: &[],
+    },
 ];
 
 /// Map a CLI command variant to its registered [`Component`], if applicable.
@@ -205,13 +250,28 @@ pub fn component_for_command(cmd: &Commands) -> Option<&'static Component> {
         Commands::License => "license",
         Commands::Quarto => "quarto",
         Commands::Slides => "slides",
+        Commands::Review => "review",
+        Commands::Docx => "docx",
+        Commands::Justfile => "justfile",
         _ => return None,
     };
     COMPONENTS.iter().find(|c| c.name == name)
 }
 
 /// Prompt only for the fields required by a component.
+///
+/// User defaults from `~/.config/ptmp/defaults.toml` override
+/// hardcoded defaults so the user can just press Enter.
 pub fn collect_fields_for_component(component: &Component) -> Result<HashMap<String, String>> {
+    collect_fields_with_defaults(component, &crate::config::load_user_defaults()?)
+}
+
+/// Inner implementation that accepts explicit user defaults
+/// (makes unit-testing possible without touching the filesystem).
+pub fn collect_fields_with_defaults(
+    component: &Component,
+    user_defaults: &HashMap<String, String>,
+) -> Result<HashMap<String, String>> {
     let mut values = HashMap::new();
     for &needed in component.fields {
         let def = KNOWN_FIELDS
@@ -219,7 +279,9 @@ pub fn collect_fields_for_component(component: &Component) -> Result<HashMap<Str
             .find(|f| f.name == needed)
             .unwrap_or_else(|| panic!("Unknown field '{needed}' in component registry"));
         let mut prompt = Text::new(def.prompt);
-        if !def.default.is_empty() {
+        if let Some(user_val) = user_defaults.get(needed) {
+            prompt = prompt.with_default(user_val);
+        } else if !def.default.is_empty() {
             prompt = prompt.with_default(def.default);
         }
         if def.required {
@@ -267,6 +329,9 @@ mod tests {
             (Commands::License, "license"),
             (Commands::Quarto, "quarto"),
             (Commands::Slides, "slides"),
+            (Commands::Review, "review"),
+            (Commands::Docx, "docx"),
+            (Commands::Justfile, "justfile"),
         ];
         for (cmd, expected_name) in cases {
             let comp = component_for_command(cmd)
diff --git a/src/config.rs b/src/config.rs
new file mode 100644
index 0000000..b635540
--- /dev/null
+++ b/src/config.rs
@@ -0,0 +1,115 @@
+use anyhow::{Context, Result};
+use std::collections::HashMap;
+use std::fs;
+use std::path::PathBuf;
+
+/// Path to the user defaults file.
+pub fn config_path() -> PathBuf {
+    dirs_fallback().join("defaults.toml")
+}
+
+/// Best-effort XDG / macOS config directory.
+fn dirs_fallback() -> PathBuf {
+    if let Ok(xdg) = std::env::var("XDG_CONFIG_HOME") {
+        PathBuf::from(xdg).join("ptmp")
+    } else if let Some(home) = home_dir() {
+        home.join(".config").join("ptmp")
+    } else {
+        PathBuf::from(".config").join("ptmp")
+    }
+}
+
+fn home_dir() -> Option<PathBuf> {
+    std::env::var("HOME").ok().map(PathBuf::from)
+}
+
+/// Load user defaults from `~/.config/ptmp/defaults.toml`.
+///
+/// Returns an empty map if the file does not exist.
+pub fn load_user_defaults() -> Result<HashMap<String, String>> {
+    load_defaults_from(&config_path())
+}
+
+/// Load defaults from an arbitrary path (used by tests).
+pub fn load_defaults_from(path: &std::path::Path) -> Result<HashMap<String, String>> {
+    if !path.exists() {
+        return Ok(HashMap::new());
+    }
+    let content = fs::read_to_string(path)
+        .with_context(|| format!("Failed to read config: {}", path.display()))?;
+    let table: toml::Table = content
+        .parse()
+        .with_context(|| format!("Failed to parse config: {}", path.display()))?;
+    let mut map = HashMap::new();
+    for (key, val) in table {
+        if let toml::Value::String(s) = val {
+            if !s.is_empty() {
+                map.insert(key, s);
+            }
+        }
+    }
+    Ok(map)
+}
+
+/// Save user defaults to `~/.config/ptmp/defaults.toml`.
+pub fn save_user_defaults(values: &HashMap<String, String>) -> Result<()> {
+    save_defaults_to(values, &config_path())
+}
+
+/// Save defaults to an arbitrary path (used by tests).
+pub fn save_defaults_to(values: &HashMap<String, String>, path: &std::path::Path) -> Result<()> {
+    if let Some(parent) = path.parent() {
+        fs::create_dir_all(parent)?;
+    }
+    let mut table = toml::Table::new();
+    let mut keys: Vec<&String> = values.keys().collect();
+    keys.sort();
+    for key in keys {
+        table.insert(
+            key.clone(),
+            toml::Value::String(values.get(key).cloned().unwrap_or_default()),
+        );
+    }
+    let content = toml::to_string_pretty(&table).context("Failed to serialise config")?;
+    fs::write(path, content)
+        .with_context(|| format!("Failed to write config: {}", path.display()))?;
+    println!("Saved config to {}", path.display());
+    Ok(())
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+    use tempfile::tempdir;
+
+    #[test]
+    fn load_missing_file_returns_empty() {
+        let dir = tempdir().unwrap();
+        let path = dir.path().join("nope.toml");
+        let defaults = load_defaults_from(&path).unwrap();
+        assert!(defaults.is_empty());
+    }
+
+    #[test]
+    fn round_trip_save_load() {
+        let dir = tempdir().unwrap();
+        let path = dir.path().join("defaults.toml");
+
+        let mut vals = HashMap::new();
+        vals.insert("author".to_string(), "Test Author".to_string());
+        vals.insert("email".to_string(), "test@example.com".to_string());
+        save_defaults_to(&vals, &path).unwrap();
+
+        assert!(path.exists());
+
+        let loaded = load_defaults_from(&path).unwrap();
+        assert_eq!(
+            loaded.get("author").map(|s| s.as_str()),
+            Some("Test Author")
+        );
+        assert_eq!(
+            loaded.get("email").map(|s| s.as_str()),
+            Some("test@example.com")
+        );
+    }
+}
diff --git a/src/main.rs b/src/main.rs
index a8da712..89be46a 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -32,6 +32,7 @@ use std::collections::HashMap;
 mod cli;
 mod commands;
 mod components;
+mod config;
 mod manifest;
 mod render;
 mod templates;
@@ -102,6 +103,9 @@ fn main() -> Result<()> {
                 destination.display()
             );
         }
+        Commands::Config => {
+            run_config()?;
+        }
         cmd => {
             let component = component_for_command(cmd).expect("Unhandled command variant");
             emit_component(component)?;
@@ -110,3 +114,35 @@ fn main() -> Result<()> {
 
     Ok(())
 }
+
+/// Interactive config: prompt for every known field and save
+/// to `~/.config/ptmp/defaults.toml`.
+fn run_config() -> Result<()> {
+    use components::KNOWN_FIELDS;
+    use config::{load_user_defaults, save_user_defaults};
+    use inquire::Text;
+
+    let existing = load_user_defaults()?;
+    let mut values = HashMap::new();
+
+    println!(
+        "Set your personal defaults (press Enter to keep \
+         current value).\n"
+    );
+
+    for field in KNOWN_FIELDS {
+        let current = existing
+            .get(field.name)
+            .map(|s| s.as_str())
+            .unwrap_or(field.default);
+        let mut prompt = Text::new(field.prompt);
+        if !current.is_empty() {
+            prompt = prompt.with_default(current);
+        }
+        let val = prompt.prompt().unwrap_or_default();
+        values.insert(field.name.to_string(), val);
+    }
+
+    save_user_defaults(&values)?;
+    Ok(())
+}
diff --git a/src/templates.rs b/src/templates.rs
index b9abcc8..f04e234 100644
--- a/src/templates.rs
+++ b/src/templates.rs
@@ -16,3 +16,8 @@ pub const QUARTO: &str = include_str!("templates/report.qmd");
 pub const SLIDES: &str = include_str!("templates/slides.qmd");
 pub const REVEAL_THEME: &str = include_str!("templates/reveal-theme.scss");
 pub const LOGO_WIDE: &[u8] = include_bytes!("templates/logo-wide.png");
+pub const REVIEW_TASKFILE: &str = include_str!("templates/review-taskfile.yml");
+pub const NATURE_CSL: &str = include_str!("templates/nature.csl");
+pub const PANDOC_REFERENCE_DOCX: &[u8] =
+    include_bytes!("templates/pandoc-reference-arial11-0p5in.docx");
+pub const JUSTFILE: &str = include_str!("templates/justfile");
diff --git a/src/templates/Taskfile.yml b/src/templates/Taskfile.yml
index da340de..00650b3 100644
--- a/src/templates/Taskfile.yml
+++ b/src/templates/Taskfile.yml
@@ -95,4 +95,15 @@ tasks:
     desc: Format references.bib
     cmds:
       - bibfmt references.bib
+
+  docx:
+    desc: Render Markdown to Word via pandoc
+    cmds:
+      - mkdir -p {{.OUTDIR}}
+      - >-
+        pandoc report.md
+        --reference-doc=templates/pandoc-reference-arial11-0p5in.docx
+        --citeproc --csl=templates/nature.csl
+        --bibliography=references.bib
+        -o {{.OUTDIR}}/report.docx
 {% endraw %}
diff --git a/src/templates/example.R b/src/templates/example.R
index 68940d8..c40ad5c 100644
--- a/src/templates/example.R
+++ b/src/templates/example.R
@@ -1,4 +1,3 @@
-# Example R script
 # Project: {{ title }}
 # Author: {{ author }}
 # Date: {{ today }}
@@ -11,3 +10,5 @@ library(here)
 # library(officer)
 
 message(paste("Project root is:", here::here()))
+
+# Data import -----------------------------------------------------------------
diff --git a/src/templates/example.slurm b/src/templates/example.slurm
index 3f9ba74..2fbdfe6 100644
--- a/src/templates/example.slurm
+++ b/src/templates/example.slurm
@@ -10,3 +10,7 @@
 #SBATCH --time=00-14:00:00
 
 echo "Running {{ title }}"
+
+# module load apps/python/3.11.8
+# module load apps/julia/1.10.2
+# module load apps/r/4.3.2
\ No newline at end of file
diff --git a/src/templates/justfile b/src/templates/justfile
new file mode 100644
index 0000000..7572f31
--- /dev/null
+++ b/src/templates/justfile
@@ -0,0 +1,24 @@
+# Justfile for {{ title }}
+
+main_file := "report.md"
+outdir := "output"
+template := "templates/pandoc-reference-arial11-0p5in.docx"
+csl := "templates/nature.csl"
+bib := "references.bib"
+
+{% raw %}
+default: render
+
+# Render Markdown to Word via pandoc
+render:
+    mkdir -p {{outdir}}
+    pandoc {{main_file}} \
+        --reference-doc={{template}} \
+        --citeproc --csl={{csl}} \
+        --bibliography={{bib}} \
+        -o {{outdir}}/report.docx
+
+# Clean generated output
+clean:
+    rm -rf {{outdir}}
+{% endraw %}
diff --git a/src/templates/nature.csl b/src/templates/nature.csl
new file mode 100644
index 0000000..8e7c5f4
--- /dev/null
+++ b/src/templates/nature.csl
@@ -0,0 +1,189 @@
+<?xml version="1.0" encoding="utf-8"?>
+<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="sort-only" default-locale="en-GB">
+  <info>
+    <title>Nature</title>
+    <id>http://www.zotero.org/styles/nature</id>
+    <link href="http://www.zotero.org/styles/nature" rel="self"/>
+    <link href="https://www.nature.com/nature/for-authors/formatting-guide" rel="documentation"/>
+    <author>
+      <name>Michael Berkowitz</name>
+      <email>mberkowi@gmu.edu</email>
+    </author>
+    <contributor>
+      <name>Patrick O'Brien</name>
+      <email>citationstyler@gmail.com</email>
+    </contributor>
+    <category citation-format="numeric"/>
+    <category field="science"/>
+    <category field="generic-base"/>
+    <issn>0028-0836</issn>
+    <eissn>1476-4687</eissn>
+    <updated>2025-09-10T18:26:21+00:00</updated>
+    <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
+  </info>
+  <macro name="title">
+    <choose>
+      <if type="bill book graphic legal_case legislation motion_picture report song" match="any">
+        <text variable="title" font-style="italic" text-case="title"/>
+      </if>
+      <else>
+        <text variable="title"/>
+      </else>
+    </choose>
+  </macro>
+  <macro name="author">
+    <names variable="author">
+      <name sort-separator=", " delimiter=", " and="symbol" initialize-with=". " delimiter-precedes-last="never" name-as-sort-order="all"/>
+      <label form="short" prefix=", "/>
+      <et-al font-style="italic"/>
+    </names>
+  </macro>
+  <macro name="access">
+    <choose>
+      <if variable="volume" type="article dataset software" match="any"/>
+      <else-if variable="DOI">
+        <text variable="DOI" prefix="doi:"/>
+      </else-if>
+    </choose>
+  </macro>
+  <macro name="access-data">
+    <choose>
+      <if type="dataset software" match="any">
+        <text variable="DOI" prefix="https://doi.org/"/>
+      </if>
+    </choose>
+  </macro>
+  <macro name="issuance">
+    <choose>
+      <if type="bill book graphic legal_case legislation motion_picture song thesis chapter paper-conference" match="any">
+        <group delimiter="; " suffix=".">
+          <group delimiter=", " prefix="(" suffix=")">
+            <text variable="publisher" form="long"/>
+            <text variable="publisher-place"/>
+            <date variable="issued">
+              <date-part name="year"/>
+            </date>
+          </group>
+        </group>
+      </if>
+      <else-if type="article">
+        <group delimiter=" ">
+          <choose>
+            <if variable="genre" match="any">
+              <text variable="genre" text-case="capitalize-first"/>
+            </if>
+            <else>
+              <text term="preprint" text-case="capitalize-first"/>
+            </else>
+          </choose>
+          <text term="at"/>
+          <choose>
+            <if variable="DOI" match="any">
+              <text variable="DOI" prefix="https://doi.org/"/>
+            </if>
+            <else>
+              <text variable="URL"/>
+            </else>
+          </choose>
+          <date date-parts="year" form="text" variable="issued" prefix="(" suffix=")"/>
+        </group>
+      </else-if>
+      <else-if type="dataset software" match="any">
+        <group delimiter=" ">
+          <text variable="publisher"/>
+          <text macro="access-data"/>
+          <date date-parts="year" form="text" variable="issued" prefix="(" suffix=")"/>
+        </group>
+      </else-if>
+      <else-if type="report webpage post post-weblog" match="any">
+        <group delimiter=" ">
+          <text variable="URL"/>
+          <date date-parts="year" form="text" variable="issued" prefix="(" suffix=")"/>
+        </group>
+      </else-if>
+      <else-if type="article-journal" match="any">
+        <group delimiter=" ">
+          <choose>
+            <if match="none" variable="volume page">
+              <choose>
+                <if match="any" variable="DOI">
+                  <text variable="DOI" prefix="https://doi.org/"/>
+                </if>
+                <else>
+                  <text variable="URL"/>
+                </else>
+              </choose>
+            </if>
+          </choose>
+          <date date-parts="year" form="text" variable="issued" prefix="(" suffix=")"/>
+        </group>
+      </else-if>
+      <else>
+        <date variable="issued" prefix="(" suffix=")">
+          <date-part name="year"/>
+        </date>
+      </else>
+    </choose>
+  </macro>
+  <macro name="container-title">
+    <choose>
+      <if type="article-journal">
+        <text variable="container-title" font-style="italic" form="short"/>
+      </if>
+      <else>
+        <text variable="container-title" font-style="italic"/>
+      </else>
+    </choose>
+  </macro>
+  <macro name="editor">
+    <choose>
+      <if type="chapter paper-conference" match="any">
+        <names variable="editor" prefix="(" suffix=")">
+          <label form="short" suffix=" "/>
+          <name and="symbol" delimiter-precedes-last="never" initialize-with=". " name-as-sort-order="all"/>
+        </names>
+      </if>
+    </choose>
+  </macro>
+  <macro name="volume">
+    <choose>
+      <if type="article-journal" match="any">
+        <text variable="volume" font-weight="bold" suffix=","/>
+      </if>
+      <else>
+        <group delimiter=" ">
+          <label variable="volume" form="short"/>
+          <text variable="volume"/>
+        </group>
+      </else>
+    </choose>
+  </macro>
+  <citation collapse="citation-number">
+    <sort>
+      <key variable="citation-number"/>
+    </sort>
+    <layout vertical-align="sup" delimiter=",">
+      <text variable="citation-number"/>
+    </layout>
+  </citation>
+  <bibliography et-al-min="6" et-al-use-first="1" second-field-align="flush" entry-spacing="0" line-spacing="2">
+    <layout suffix=".">
+      <text variable="citation-number" suffix="."/>
+      <group delimiter=" ">
+        <text macro="author" suffix="."/>
+        <text macro="title" suffix="."/>
+        <choose>
+          <if type="chapter paper-conference" match="any">
+            <text term="in"/>
+          </if>
+        </choose>
+        <text macro="container-title"/>
+        <text macro="editor"/>
+        <text macro="volume"/>
+        <text variable="page"/>
+        <text macro="issuance"/>
+        <text macro="access"/>
+      </group>
+    </layout>
+  </bibliography>
+</style>
\ No newline at end of file
diff --git a/src/templates/pandoc-reference-arial11-0p5in.docx b/src/templates/pandoc-reference-arial11-0p5in.docx
new file mode 100644
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diff --git a/src/templates/review-taskfile.yml b/src/templates/review-taskfile.yml
new file mode 100644
index 0000000..c2102ac
--- /dev/null
+++ b/src/templates/review-taskfile.yml
@@ -0,0 +1,53 @@
+# Taskfile for academic peer review
+# Reviewer: {{ reviewer_name }}
+# https://taskfile.dev
+version: "3"
+
+vars:
+  PDF: "{{ pdf_path }}"
+  REVIEWER: "{{ reviewer_name }}"
+  OUTDIR: .
+
+{% raw %}
+tasks:
+  default:
+    desc: Run the full review pipeline
+    deps: [review]
+
+  review:
+    desc: Extract annotations and generate review template
+    cmds:
+      - >-
+        academic-review {{.PDF}}
+        -f markdown
+        -o {{.OUTDIR}}
+
+  review-all:
+    desc: Generate review in all formats (md, tex, docx)
+    cmds:
+      - >-
+        academic-review {{.PDF}}
+        -f markdown latex docx
+        -o {{.OUTDIR}}
+
+  review-zotero:
+    desc: Generate review with live Zotero lookup
+    cmds:
+      - >-
+        academic-review {{.PDF}}
+        -f markdown
+        -o {{.OUTDIR}}
+        --no-zotero-stub
+
+  clean:
+    desc: Remove generated review files
+    vars:
+      STEM:
+        sh: basename "{{.PDF}}" .pdf
+    cmds:
+      - rm -f {{.OUTDIR}}/{{.STEM}}_review.md
+      - rm -f {{.OUTDIR}}/{{.STEM}}_review.tex
+      - rm -f {{.OUTDIR}}/{{.STEM}}_review.docx
+      - rm -f {{.OUTDIR}}/{{.STEM}}_citations.md
+      - rm -f {{.OUTDIR}}/{{.STEM}}_context.json
+{% endraw %}

From 15a12547be1e3101dad4ff541cc320836fe1c3e6 Mon Sep 17 00:00:00 2001
From: Michael DeWitt <me.dewitt.jr@gmail.com>
Date: Sun, 5 Jul 2026 15:47:54 -0400
Subject: [PATCH 3/3] tweaks and updates

---
 README.Md                    |  2 +-
 src/components.rs            |  4 +-
 src/render.rs                | 36 ++++++++++++++
 src/templates/main.tex       | 92 +++++++++++++++++++++++++++++-------
 src/templates/references.bib | 15 +++++-
 5 files changed, 128 insertions(+), 21 deletions(-)

diff --git a/README.Md b/README.Md
index ab49a74..fbc30d5 100644
--- a/README.Md
+++ b/README.Md
@@ -46,7 +46,7 @@ Write one file into the current working directory, prompting only for the fields
 
 ```bash
 ptmp taskfile       # Taskfile.yml
-ptmp latex          # main.tex
+ptmp latex          # main.tex + references.bib (Nature-style manuscript)
 ptmp makefile       # Makefile
 ptmp readme         # README.md
 ptmp r              # R/example.R
diff --git a/src/components.rs b/src/components.rs
index 022a234..c94e936 100644
--- a/src/components.rs
+++ b/src/components.rs
@@ -102,8 +102,8 @@ pub static COMPONENTS: &[Component] = &[
         name: "latex",
         output_path: "main.tex",
         template: templates::MAIN_TEX,
-        fields: &["title", "author", "affiliation"],
-        extra_text: &[],
+        fields: &["title", "author", "affiliation", "email"],
+        extra_text: &[("references.bib", templates::REFERENCES_BIB)],
         extra_binary: &[],
     },
     Component {
diff --git a/src/render.rs b/src/render.rs
index 6eb78c2..7d99ec9 100644
--- a/src/render.rs
+++ b/src/render.rs
@@ -217,6 +217,42 @@ mod tests {
         assert_eq!(copied, bytes);
     }
 
+    // --- MAIN_TEX template ---
+
+    #[test]
+    fn main_tex_renders_with_all_fields() {
+        let mut vals = HashMap::new();
+        vals.insert("title".to_string(), "My Paper".to_string());
+        vals.insert("author".to_string(), "Jane Doe".to_string());
+        vals.insert("affiliation".to_string(), "Some Lab".to_string());
+        vals.insert("email".to_string(), "jane@example.com".to_string());
+        let ctx = make_tera_context(vals, "proj");
+
+        let out = Tera::one_off(crate::templates::MAIN_TEX, &ctx, false).unwrap();
+
+        assert!(out.contains("\\documentclass[11pt,letterpaper]{article}"));
+        assert!(out.contains("My Paper"));
+        assert!(out.contains("\\thanks{Correspondence:"));
+        assert!(out.contains("\\href{mailto:jane@example.com}{jane@example.com}"));
+        assert!(out.contains("\\itshape Some Lab"));
+        assert!(out.contains("\\bibliographystyle{unsrtnat}"));
+    }
+
+    #[test]
+    fn main_tex_omits_optional_fields_when_empty() {
+        let mut vals = HashMap::new();
+        vals.insert("title".to_string(), "My Paper".to_string());
+        vals.insert("author".to_string(), "Jane Doe".to_string());
+        vals.insert("affiliation".to_string(), String::new());
+        vals.insert("email".to_string(), String::new());
+        let ctx = make_tera_context(vals, "proj");
+
+        let out = Tera::one_off(crate::templates::MAIN_TEX, &ctx, false).unwrap();
+
+        assert!(!out.contains("\\thanks{"));
+        assert!(!out.contains("\\itshape"));
+    }
+
     // --- copy_template ---
 
     #[test]
diff --git a/src/templates/main.tex b/src/templates/main.tex
index da22d03..764f83e 100644
--- a/src/templates/main.tex
+++ b/src/templates/main.tex
@@ -1,34 +1,94 @@
-\documentclass[12pt,letterpaper]{article}
-\usepackage{setspace}
-% Packages
-\usepackage[margin=1in]{geometry}
-\usepackage{graphicx} % Required for inserting images
-\usepackage{comment}
+% !TEX program = pdflatex
+% Modern single-column manuscript in a Nature-like style.
+% Citations render as sorted, superscript numbers ordered by appearance.
+\documentclass[11pt,letterpaper]{article}
+
+% --- Encoding and fonts ----------------------------------------------------
 \usepackage[T1]{fontenc}
 \usepackage[utf8]{inputenc}
+% lmodern is universal; for a Times look swap in: newtxtext,newtxmath
 \usepackage{lmodern}
-\usepackage{natbib}
+\usepackage{microtype} % subtle protrusion/expansion for cleaner justification
+
+% --- Page layout -----------------------------------------------------------
+\usepackage[margin=1in]{geometry}
+\usepackage{setspace}
+\onehalfspacing
+\usepackage{parskip} % vertical space between paragraphs, no first-line indent
+
+% --- Figures, tables, and math ---------------------------------------------
+\usepackage{graphicx}
+{% raw %}\graphicspath{{figures/}}{% endraw %}
+\usepackage[font=small,labelfont=bf]{caption}
+\usepackage{booktabs} % \toprule \midrule \bottomrule for clean tables
+\usepackage{siunitx}  % \num{1.2e3}, \qty{5}{\micro\liter}
+\usepackage{amsmath}
+\usepackage{amssymb}
+
+% --- Colour and bibliography -----------------------------------------------
+\usepackage{xcolor}
+% Nature-style: numeric, sorted, compressed, superscript citations.
+\usepackage[numbers,sort&compress,super]{natbib}
+% unsrtnat ships with natbib and always compiles; if you have naturemag.bst,
+% swap the next line for \bibliographystyle{naturemag}.
+\bibliographystyle{unsrtnat}
 
-\title{ {{ title }} }
-\author{ {{ author }} \\ {{ affiliation }} }
+% --- Hyperlinks and smart cross-references (load these last) ---------------
+\usepackage[colorlinks=true,allcolors=blue!55!black]{hyperref}
+\usepackage{cleveref} % \cref{fig:x} -> "Fig. 1", \Cref{...} -> "Figure 1"
+
+% --- Metadata --------------------------------------------------------------
+\title{\bfseries {{ title }}}
+\author{
+{{- author -}}
+{%- if email -%}
+\thanks{Correspondence: \href{mailto:{{ email }}}{ {{- email -}} }}
+{%- endif -%}
+{%- if affiliation -%}
+\\[0.4em]\normalsize\itshape {{ affiliation }}
+{%- endif -%}
+}
 \date{ {{ today }} }
 
 \begin{document}
 \maketitle
 
-\section{Introduction}
-Write your introduction here.
+\begin{abstract}
+\noindent
+State the question, what you did, and the main result in a few sentences.
+Keep the abstract self-contained and free of citations.
+\end{abstract}
 
-\section{Methods}
-Describe your methods here.
+\section{Introduction}
+Motivate the problem and state your contribution.
+Cite prior work with \verb|\cite{key}|, which renders as a superscript
+number\cite{example2024}.
 
 \section{Results}
-Present results here. Figures can be stored in `figures/`.
+Present the findings.
+Reference figures with \verb|\cref{fig:label}| and keep sources in
+\texttt{figures/}, one figure per file.
 
 \section{Discussion}
-Discuss findings here.
+Interpret the results, state the limitations, and give the outlook.
+
+\section*{Methods}
+Describe the data, models, and analysis in enough detail to reproduce.
+Report uncertainty, not just point estimates.
+
+% --- Back matter -----------------------------------------------------------
+\section*{Data and code availability}
+State where the data and analysis code can be found.
+
+\section*{Acknowledgements}
+Funding sources and thanks.
+
+\section*{Author contributions}
+Summarise each author's contribution by initials.
+
+\section*{Competing interests}
+The authors declare no competing interests.
 
-\bibliographystyle{plain}
 \bibliography{references}
 
 \end{document}
diff --git a/src/templates/references.bib b/src/templates/references.bib
index d31bb9b..1ca0389 100644
--- a/src/templates/references.bib
+++ b/src/templates/references.bib
@@ -1,2 +1,13 @@
-% Bibliography for {{ title }}
-% Add BibTeX entries below
+% Bibliography. Add BibTeX entries below.
+% Format with `bibfmt` before committing.
+
+@article{example2024,
+  author  = {Doe, Jane and Roe, Richard},
+  title   = {An example reference},
+  journal = {Journal of Examples},
+  year    = {2024},
+  volume  = {1},
+  number  = {1},
+  pages   = {1--10},
+  doi     = {10.1000/example},
+}