Duplicate entries in bibliography and footnotes

[Sieboldianus]

I am not sure what is causing this, but I updated to the latest mkdocs-bibtex and I am seeing duplicate entries of references. Have a look here:
lbsn.vgiscience.org mkdocs material docs

If the same citation is references several times, it will appear the same number of times duplicates in the bibliography.

Here's our mkdocs.yml:

site_name: LBSN Structure
site_url: https://lbsn.vgiscience.org/
site_author: Alexander Dunkel, Marc Löchner, Filip Krumpe
copyright: CC BY 4.0, 2022 Alexander Dunkel, Marc Löchner, Filip Krumpe, vgiscience.org and contributors
site_dir: site

plugins:
  - search
  - git-revision-date-localized
  - minify:
      minify_html: true
  - bibtex:
      bib_file: 'docs/references.bib'
      csl_file: 'apa.csl'

theme:
    name: 'material'
    custom_dir: overrides/
    palette:
      primary: 'Light Blue' #43C3F5
      accent: 'Orange' #F8A610
    logo: 'img/logo-white.svg'
    favicon: 'img/favicon.png'
    features:
      - navigation.instant
      - navigation.expand
      - navigation.top

...

markdown_extensions:
  - markdown.extensions.codehilite:
      guess_lang: false
  - markdown_include.include:
      base_path: docs
  - admonition
  - codehilite
  - extra
  - tables
  - sane_lists
  - pymdownx.superfences
  - pymdownx.details
  - pymdownx.tabbed:
      alternate_style: true 
  - footnotes

Here is some more testing:

• also happens with default csl_file (parameter set to none)
• mkdocs 1.2.3 and mkdocs-material 8.2.5 (both latest), mkdocs-bibtex 2.0.2
• also happens with the test files provided in this repository
• as you can see in the exmaple docs above, there are ::: characters added beyond each bibliography ending. This is independent of the csl file uses. I don't know where these are coming from.
• I have a feeling that this may be related to pandoc, or the way it is installed, or the version. Running pandoc 2.17.1.1 locally, installed with conda,
• in Debian Docker I observe the same behavior (same pandoc version, but installed with *.deb)

[shyamd]

Super weird. I don't see anything wrong with your mkdocs.yml file. I'll take a look at it this coming weekend. Any chance you could attach a snippet of the markdown that gets a duplicate citation and corresponding bibtex?

[Sieboldianus]

I know. Thanks for looking at this @shyamd

This is probably easiest: I've set the project to public.

• mkdocs.yml
• Example markdown file: metrics.md that gets processed to this result structure/metrics/ (with duplicates)
• the corresponding references.bib (it is only one file)

I know it is not your job to look through other people's repositories. I am happy to help wherever I can. I would not have asked in the first place if I hadn't tried already to solve this.

[Sieboldianus]

Here is the way to setup/test the repository (conda):

git clone https://gitlab.vgiscience.de/lbsn/lbsn.vgiscience.org.git
conda create -n mkdocs
conda activate mkdocs
conda install -c conda-forge mkdocs mkdocs-material-extensions mkdocs-material mkdocs-git-revision-date-plugin pandoc
pip install mkdocs-bibtex
pip install markdown-include
pip install mkdocs-git-revision-date-localized-plugin
pip install mkdocs-minify-plugin
pip install mkdocs-rtd-dropdown
mkdocs serve

Without conda (this is taken from the Docker setup, but modified for WSL/Linux):

PANDOC_VERSION=2.17.1.1
PANDOC_DOWNLOAD_URL=https://github.com/jgm/pandoc/releases/download/$PANDOC_VERSION/pandoc-$PANDOC_VERSION-1-amd64.deb

curl -fsSL "$PANDOC_DOWNLOAD_URL" -o pandoc.deb \
 && dpkg -i pandoc.deb \
 && rm pandoc.deb

# install mkdocs
apt-get install python3-venv
python3 -m venv mkdocs_env
source ./mkdocs_env/bin/activate
pip install --no-cache-dir mkdocs && \
    pip install --no-cache-dir mkdocs-material && \
    pip install --no-cache-dir mkdocs-material-extensions && \
    pip install --no-cache-dir markdown-include && \
    pip install --no-cache-dir pygments && \
    pip install --no-cache-dir pymdown-extensions && \
    pip install --no-cache-dir mkdocs-minify-plugin && \
    pip install --no-cache-dir mkdocs-git-revision-date-localized-plugin && \
    pip install --no-cache-dir mkdocs-bibtex
mkdocs serve
# remove venv
rm -rf mkdocs_env

Both setups result in the same issue.

[reumar]

Hi! I'm having the same issue. Any updates?

[shyamd]

Should be fixed in PR #116 . Download v2.0.3 for the fix

[Sieboldianus]

Awesome, thanks so much @shyamd ! Solved. Closed.