andrewheiss/hikmah-academic-quarto

A set of nice Quarto templates

hikmah-academic-quarto's Issues

Spacing for tables with lists leads to overcrowding of text

I absolutely love this template!

I did want to bring to your attention, though, that the environment created for tables with lists in them can overcrowd the text in the lists, particularly if the text for the list item wraps to the next line.

include-in-header.tex


% Remove left margin in lists inside longtables
% https://tex.stackexchange.com/a/378190/11851
\AtBeginEnvironment{longtable}{\setlist[itemize]{nosep, wide=0pt, leftmargin=*, before=\vspace*{-\baselineskip}, after=\vspace*{-\baselineskip}}}

Issues with rendering the template?

Thank you for creating this great template!

I cloned the repository and tried to render the template file as a basic check, but it isn't working. It looks like Quarto can't find the generated .tex file from the second pass through XeLaTeX, but I'm not sure what's causing this. I haven't had a similar issue with other templates.

Below is the error message I receive:

Error

❯ quarto render hikmah-testing-default.qmd


processing file: hikmah-testing-default.qmd
1/5
2/5 [unnamed-chunk-1]
3/5
4/5 [fig-n-lights]
5/5
output file: hikmah-testing-default.knit.md

pandoc
  to: latex
  output-file: hikmah-testing-default.tex
  standalone: true
  pdf-engine: xelatex
  variables:
    graphics: true
    tables: true
  default-image-extension: pdf
  cite-method: biblatex

metadata
  block-headings: false
  date-format: full
  geometry:
    - top=10pc
    - bottom=10pc
    - left=11pc
    - right=11pc
    - heightrounded
  colorlinks: true
  linkcolor: DarkSlateBlue
  urlcolor: DarkSlateBlue
  citecolor: DarkSlateBlue
  link-citations: true
  biblio-title: References
  biblio-config: false
  biblatex-chicago: false
  biblio-style: apa
  biblatexoptions:
    - backend=biber
  indent: true
  title: |-
    On the Surgical Removal of \
    Cardassian Cranial Implants
  subtitle: A case study of a Cardassian patient
  short-title: Cranial Implants
  published: Under review at *Starfleet Medical Journal*
  code-repo: 'Access the code, data, and analysis at <https://git.starfleet.ufp/bashir/cranial-implants>'
  correspondence-prefix: Correspondence concerning this article should be addressed to
  author:
    - name: Julian Bashir
      email: [email protected]
      orcid: 0000-0002-3948-3914
      title: Chief Medical Officer
      affiliations:
        - id: ds9
          name: Starbase Deep Space Nine
          department: Sick Bay
          address: 1234 Main Street
          city: Anytown
          region: NY
          country: USA
          postal-code: 90210
      attributes:
        corresponding: true
    - name: Elim Garak
      email: [email protected]
      title: Shopkeeper and Tailor
      affiliations:
        - id: terok
          name: Terok Nor
          department: Promenade
        - ref: ds9
  abstract: |
    Space: the final frontier. These are the voyages of the starship *Enterprise*. Its continuing mission: to explore strange new worlds. To seek out new life and new civilizations. To boldly go where no one has gone before!
  thanks: 'Placeholder text generated at <https://vlad-saling.github.io/star-trek-ipsum/>.'
  additional-info: We have no known conflict of interest to disclose.
  keywords:
    - surgery
    - espionage
    - brains
  date: 'August 24, 2022'
  epigraph:
    - text: War is good for business.
      source: Ferengi Rule of Acquisition 34
    - text: Peace is good for business.
      source: Ferengi Rule of Acquisition 35
  bibliography:
    - references.bib



processing file: hikmah-testing-default.qmd
1/5
2/5 [unnamed-chunk-1]
3/5
4/5 [fig-n-lights]
5/5
output file: hikmah-testing-default.knit.md

pandoc
  to: docx
  output-file: hikmah-testing-default.docx
  default-image-extension: png
  reference-doc: _extensions/hikmah-manuscript/styles/reference.docx

metadata
  date-format: full
  knitr:
    opts_chunk:
      dev: ragg_png
      dpi: 300
      out.width: 80%
  title: |-
    On the Surgical Removal of \
    Cardassian Cranial Implants
  subtitle: A case study of a Cardassian patient
  short-title: Cranial Implants
  published: Under review at *Starfleet Medical Journal*
  code-repo: 'Access the code, data, and analysis at <https://git.starfleet.ufp/bashir/cranial-implants>'
  correspondence-prefix: Correspondence concerning this article should be addressed to
  author:
    - name: Julian Bashir
      email: [email protected]
      orcid: 0000-0002-3948-3914
      title: Chief Medical Officer
      affiliations:
        - id: ds9
          name: Starbase Deep Space Nine
          department: Sick Bay
          address: 1234 Main Street
          city: Anytown
          region: NY
          country: USA
          postal-code: 90210
      attributes:
        corresponding: true
    - name: Elim Garak
      email: [email protected]
      title: Shopkeeper and Tailor
      affiliations:
        - id: terok
          name: Terok Nor
          department: Promenade
        - ref: ds9
  abstract: |
    Space: the final frontier. These are the voyages of the starship *Enterprise*. Its continuing mission: to explore strange new worlds. To seek out new life and new civilizations. To boldly go where no one has gone before!
  thanks: 'Placeholder text generated at <https://vlad-saling.github.io/star-trek-ipsum/>.'
  additional-info: We have no known conflict of interest to disclose.
  keywords:
    - surgery
    - espionage
    - brains
  date: 'August 24, 2022'
  epigraph:
    - text: War is good for business.
      source: Ferengi Rule of Acquisition 34
    - text: Peace is good for business.
      source: Ferengi Rule of Acquisition 35
  bibliography:
    - references.bib



processing file: hikmah-testing-default.qmd
1/5
2/5 [unnamed-chunk-1]
3/5
4/5 [fig-n-lights]
5/5
output file: hikmah-testing-default.knit.md

pandoc
  to: odt
  output-file: hikmah-testing-default.odt
  template: _extensions/hikmah-manuscript/templates/odt-manuscript.odt
  default-image-extension: png
  reference-doc: _extensions/hikmah-manuscript/styles/reference.odt

metadata
  date-format: full
  knitr:
    opts_chunk:
      dev: ragg_png
      dpi: 300
      out.width: 80%
  title: |-
    On the Surgical Removal of \
    Cardassian Cranial Implants
  subtitle: A case study of a Cardassian patient
  short-title: Cranial Implants
  published: Under review at *Starfleet Medical Journal*
  code-repo: 'Access the code, data, and analysis at <https://git.starfleet.ufp/bashir/cranial-implants>'
  correspondence-prefix: Correspondence concerning this article should be addressed to
  author:
    - name: Julian Bashir
      email: [email protected]
      orcid: 0000-0002-3948-3914
      title: Chief Medical Officer
      affiliations:
        - id: ds9
          name: Starbase Deep Space Nine
          department: Sick Bay
          address: 1234 Main Street
          city: Anytown
          region: NY
          country: USA
          postal-code: 90210
      attributes:
        corresponding: true
    - name: Elim Garak
      email: [email protected]
      title: Shopkeeper and Tailor
      affiliations:
        - id: terok
          name: Terok Nor
          department: Promenade
        - ref: ds9
  abstract: |
    Space: the final frontier. These are the voyages of the starship *Enterprise*. Its continuing mission: to explore strange new worlds. To seek out new life and new civilizations. To boldly go where no one has gone before!
  thanks: 'Placeholder text generated at <https://vlad-saling.github.io/star-trek-ipsum/>.'
  additional-info: We have no known conflict of interest to disclose.
  keywords:
    - surgery
    - espionage
    - brains
  date: 'August 24, 2022'
  epigraph:
    - text: War is good for business.
      source: Ferengi Rule of Acquisition 34
    - text: Peace is good for business.
      source: Ferengi Rule of Acquisition 35
  bibliography:
    - references.bib



processing file: hikmah-testing-default.qmd
1/5
2/5 [unnamed-chunk-1]
3/5
4/5 [fig-n-lights]
5/5
output file: hikmah-testing-default.knit.md

pandoc
  to: latex
  output-file: hikmah-testing-default.tex
  standalone: true
  pdf-engine: xelatex
  variables:
    graphics: true
    tables: true
  default-image-extension: pdf
  cite-method: biblatex

metadata
  block-headings: false
  date-format: full
  documentclass: article
  papersize: letter
  fontsize: 12pt
  linestretch: 2
  geometry:
    - top=1in
    - bottom=1in
    - left=1in
    - right=1in
  colorlinks: true
  linkcolor: DarkSlateBlue
  urlcolor: DarkSlateBlue
  citecolor: DarkSlateBlue
  link-citations: true
  biblio-title: References
  biblio-config: false
  biblatex-chicago: false
  biblio-style: apa
  biblatexoptions:
    - backend=biber
  indent: true
  title: |-
    On the Surgical Removal of \
    Cardassian Cranial Implants
  subtitle: A case study of a Cardassian patient
  short-title: Cranial Implants
  published: Under review at *Starfleet Medical Journal*
  code-repo: 'Access the code, data, and analysis at <https://git.starfleet.ufp/bashir/cranial-implants>'
  correspondence-prefix: Correspondence concerning this article should be addressed to
  author:
    - name: Julian Bashir
      email: [email protected]
      orcid: 0000-0002-3948-3914
      title: Chief Medical Officer
      affiliations:
        - id: ds9
          name: Starbase Deep Space Nine
          department: Sick Bay
          address: 1234 Main Street
          city: Anytown
          region: NY
          country: USA
          postal-code: 90210
      attributes:
        corresponding: true
    - name: Elim Garak
      email: [email protected]
      title: Shopkeeper and Tailor
      affiliations:
        - id: terok
          name: Terok Nor
          department: Promenade
        - ref: ds9
  abstract: |
    Space: the final frontier. These are the voyages of the starship *Enterprise*. Its continuing mission: to explore strange new worlds. To seek out new life and new civilizations. To boldly go where no one has gone before!
  thanks: 'Placeholder text generated at <https://vlad-saling.github.io/star-trek-ipsum/>.'
  additional-info: We have no known conflict of interest to disclose.
  keywords:
    - surgery
    - espionage
    - brains
  date: 'August 24, 2022'
  epigraph:
    - text: War is good for business.
      source: Ferengi Rule of Acquisition 34
    - text: Peace is good for business.
      source: Ferengi Rule of Acquisition 35
  bibliography:
    - references.bib

running xelatex - 1
  This is XeTeX, Version 3.141592653-2.6-0.999995 (TeX Live 2023) (preloaded format=xelatex)
   restricted \write18 enabled.
  entering extended mode

generating bibliography
  INFO - This is Biber 2.19
  INFO - Logfile is 'hikmah-testing-default.blg'
  INFO - Reading 'hikmah-testing-default.bcf'
  INFO - Found 3 citekeys in bib section 0
  INFO - Processing section 0
  INFO - Looking for bibtex file 'references.bib' for section 0
  INFO - LaTeX decoding ...
  INFO - Found BibTeX data source 'references.bib'
  INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable'
  INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized'
  INFO - Sorting list 'apa/apasortcite//global/global' of type 'entry' with template 'apa' and locale 'en-US'
  INFO - No sort tailoring available for locale 'en-US'
  INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized'
  INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable'
  INFO - Sorting list 'apa/global//global/global' of type 'entry' with template 'apa' and locale 'en-US'
  INFO - No sort tailoring available for locale 'en-US'
  INFO - Writing 'hikmah-testing-default.bbl' with encoding 'UTF-8'
  INFO - Output to hikmah-testing-default.bbl

running xelatex - 2
  This is XeTeX, Version 3.141592653-2.6-0.999995 (TeX Live 2023) (preloaded format=xelatex)
   restricted \write18 enabled.
  entering extended mode


ERROR: NotFound: No such file or directory (os error 2), open '/Users/max/hikmah-academic-quarto/hikmah-testing-default.tex'

NotFound: No such file or directory (os error 2), open '/Users/max/hikmah-academic-quarto/hikmah-testing-default.tex'
    at async Object.open (deno:runtime/js/40_files.js:55:17)
    at async processLines (file:///Applications/quarto/bin/quarto.js:81521:18)
    at async file:///Applications/quarto/bin/quarto.js:81500:9
    at async Object.complete (file:///Applications/quarto/bin/quarto.js:81077:21)
    at async Object.onPostProcess (file:///Applications/quarto/bin/quarto.js:86678:36)
    at async renderFiles (file:///Applications/quarto/bin/quarto.js:86649:13)
    at async renderProject (file:///Applications/quarto/bin/quarto.js:86800:25)
    at async Command.fn (file:///Applications/quarto/bin/quarto.js:90856:32)
    at async Command.execute (file:///Applications/quarto/bin/quarto.js:8437:13)
    at async quarto (file:///Applications/quarto/bin/quarto.js:127545:5)

Usage

Might it help to include some usage instructions, e.g. for the YAML header:

format:
  hikmah-pdf: default

Or for the terminal:

quarto render article.qmd --to hikmah-pdf

(I think)

Installation instructions

Cool templates! For installation, to get the templates into an existing repo, I found that this worked:

quarto install extension andrewheiss/hikmah-academic-quarto

In your instructions, you said to do this:

quarto add andrewheiss/hikmah-academic-quarto

(but that didn't work for me)

Quarto template page misspelling

Not an issue with your templates, but FYI on the Quarto site, your extension is listed as hikmax rather than hikmah.