mirror of
https://gitea.psi.ch/APOG/acsmnode.git
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Add poster with figures
This commit is contained in:
20
docs/Makefile
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20
docs/Makefile
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# Minimal makefile for Sphinx documentation
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#
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# You can set these variables from the command line, and also
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# from the environment for the first two.
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|
SPHINXOPTS ?=
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|
SPHINXBUILD ?= sphinx-build
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SOURCEDIR = source
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|
BUILDDIR = build
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|
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# Put it first so that "make" without argument is like "make help".
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|
help:
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|
@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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|
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.PHONY: help Makefile
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|
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|
# Catch-all target: route all unknown targets to Sphinx using the new
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|
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
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|
%: Makefile
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|
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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35
docs/make.bat
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docs/make.bat
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|
@ECHO OFF
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pushd %~dp0
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REM Command file for Sphinx documentation
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if "%SPHINXBUILD%" == "" (
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set SPHINXBUILD=sphinx-build
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)
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set SOURCEDIR=source
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set BUILDDIR=build
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|
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%SPHINXBUILD% >NUL 2>NUL
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|
if errorlevel 9009 (
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|
echo.
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|
echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
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|
echo.installed, then set the SPHINXBUILD environment variable to point
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|
echo.to the full path of the 'sphinx-build' executable. Alternatively you
|
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|
echo.may add the Sphinx directory to PATH.
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|
echo.
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|
echo.If you don't have Sphinx installed, grab it from
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|
echo.https://www.sphinx-doc.org/
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|
exit /b 1
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|
)
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|
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|
if "%1" == "" goto help
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|
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%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
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|
goto end
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|
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:help
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%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
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|
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|
:end
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|
popd
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2
docs/poster/.latexmkrc
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docs/poster/.latexmkrc
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$bibtex_use = 2;
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$clean_ext = "nav snm";
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docs/poster/LICENSE.md
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docs/poster/LICENSE.md
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The MIT License (MIT)
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|
=====================
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**Copyright (c) 2018-2022 Anish Athalye (me@anishathalye.com)**
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Permission is hereby granted, free of charge, to any person obtaining a copy of
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|
this software and associated documentation files (the "Software"), to deal in
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|
the Software without restriction, including without limitation the rights to
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|
use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
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|
of the Software, and to permit persons to whom the Software is furnished to do
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|
so, subject to the following conditions:
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|
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|
The above copyright notice and this permission notice shall be included in all
|
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|
copies or substantial portions of the Software.
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|
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|
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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|
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
|
||||||
|
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
|
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|
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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|
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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|
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
|
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|
SOFTWARE.
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92
docs/poster/README.md
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docs/poster/README.md
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|
# Gemini [](https://github.com/anishathalye/gemini/actions?query=workflow%3ACI)
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Gemini is a modern LaTeX [beamerposter] theme.
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<p align="center">
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<a href="https://raw.githubusercontent.com/anishathalye/assets/master/gemini/poster-gemini.pdf">
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<img src="https://raw.githubusercontent.com/anishathalye/assets/master/gemini/poster-gemini-small.png">
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</a>
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</p>
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If you're looking for a beamer presentation theme, take a look at [Auriga].
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|
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## Dependencies
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|
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* A TeX installation that includes [LuaTeX]
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|
* You also need `latexmk` if you want to use the provided `Makefile`
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* LaTeX package dependencies including beamerposter (these usually come with
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|
your TeX installation, but if not, you can get them from [CTAN])
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* [Raleway] and [Lato], which are both available under Open Font License
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## Usage
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1. Copy the files in this repository (or clone the repository)
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1. In `poster.tex`, set up your paper size, column layout, and scale the
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content as necessary
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1. Make a copy of `beamercolorthemegemini.sty`, update the `\usecolortheme`
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line in `poster.tex`, and theme the poster to your liking (optional, but
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highly recommended)
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1. Run `make` to build your poster
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## FAQ
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See the [FAQ] in the Wiki for answers to frequently asked questions such as how
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to add an institution logo to the poster.
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## Themes
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Gemini currently includes three color themes:
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* `gemini` (default)
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* `mit`
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|
* `labsix`
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|
The alternative themes are intended to be inspiration for you to make your own
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|
color theme. You're highly recommended to make your own color theme (it's
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|
really easy!) or use the default Gemini theme.
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|
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|
### MIT theme
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<p align="center">
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<a href="https://raw.githubusercontent.com/anishathalye/assets/master/gemini/poster-mit.pdf">
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<img src="https://raw.githubusercontent.com/anishathalye/assets/master/gemini/poster-mit-small.png">
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||||||
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</a>
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</p>
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|
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### LabSix theme
|
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<p align="center">
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<a href="https://raw.githubusercontent.com/anishathalye/assets/master/gemini/poster-labsix.pdf">
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||||||
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<img src="https://raw.githubusercontent.com/anishathalye/assets/master/gemini/poster-labsix-small.png">
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||||||
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</a>
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</p>
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## Design goals
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||||||
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* **Minimal**: clean and easy to read, so that the emphasis is on the content
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* **Batteries included**: works and looks good out of the box
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* **Easy theming**: easy to create and use a new color theme
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||||||
|
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## Contributing
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Contributions to Gemini such as bug reports, new themes, and new poster
|
||||||
|
components are greatly appreciated! Given the subjective nature of design,
|
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|
you're encouraged to open an issue or pull request early to get feedback before
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|
investing a lot of time in implementing a new feature.
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|
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|
## License
|
||||||
|
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Copyright (c) 2018-2022 Anish Athalye. Released under the MIT License. See
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|
[LICENSE.md][license] for details.
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|
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|
[beamerposter]: https://github.com/deselaers/latex-beamerposter
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|
[Auriga]: https://github.com/anishathalye/auriga
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[LuaTeX]: http://www.luatex.org/
|
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|
[CTAN]: https://ctan.org/
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|
[Raleway]: https://www.fontsquirrel.com/fonts/raleway
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|
[Lato]: https://www.fontsquirrel.com/fonts/lato
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|
[license]: LICENSE.md
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|
[FAQ]: https://github.com/anishathalye/gemini/wiki/FAQ
|
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58
docs/poster/beamercolorthemegemini.sty
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58
docs/poster/beamercolorthemegemini.sty
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|
% Gemini theme
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% https://github.com/anishathalye/gemini
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% ====================
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|
% Definitions
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||||||
|
% ====================
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||||||
|
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\definecolor{lightgray}{RGB}{245, 246, 250}
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\definecolor{blue}{RGB}{64, 115, 158}
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\definecolor{darkblue}{RGB}{39, 60, 117}
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||||||
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\definecolor{lightblue}{RGB}{232, 244, 255}
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||||||
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% ====================
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||||||
|
% Theme
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||||||
|
% ====================
|
||||||
|
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||||||
|
% Basic colors
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||||||
|
\setbeamercolor{palette primary}{fg=black,bg=white}
|
||||||
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\setbeamercolor{palette secondary}{fg=black,bg=white}
|
||||||
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\setbeamercolor{palette tertiary}{bg=black,fg=white}
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||||||
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\setbeamercolor{palette quaternary}{fg=black,bg=white}
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||||||
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\setbeamercolor{structure}{fg=darkblue}
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|
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% Headline
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||||||
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\setbeamercolor{headline}{fg=lightgray,bg=blue}
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\setbeamercolor{headline rule}{bg=darkblue}
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% Block
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\setbeamercolor{block title}{fg=blue,bg=white}
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\setbeamercolor{block separator}{bg=black}
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||||||
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\setbeamercolor{block body}{fg=black,bg=white}
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||||||
|
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||||||
|
% Alert Block
|
||||||
|
\setbeamercolor{block alerted title}{fg=blue,bg=lightblue}
|
||||||
|
\setbeamercolor{block alerted separator}{bg=black}
|
||||||
|
\setbeamercolor{block alerted body}{fg=black,bg=lightblue}
|
||||||
|
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||||||
|
% Example Block
|
||||||
|
\setbeamercolor{block example title}{fg=blue,bg=lightgray}
|
||||||
|
\setbeamercolor{block example separator}{bg=black}
|
||||||
|
\setbeamercolor{block example body}{fg=black,bg=lightgray}
|
||||||
|
|
||||||
|
% Heading
|
||||||
|
\setbeamercolor{heading}{fg=black}
|
||||||
|
|
||||||
|
% Itemize
|
||||||
|
\setbeamercolor{item}{fg=darkblue}
|
||||||
|
|
||||||
|
% Bibliography
|
||||||
|
\setbeamercolor{bibliography item}{fg=black}
|
||||||
|
\setbeamercolor{bibliography entry author}{fg=black}
|
||||||
|
\setbeamercolor{bibliography entry title}{fg=black}
|
||||||
|
\setbeamercolor{bibliography entry location}{fg=black}
|
||||||
|
\setbeamercolor{bibliography entry note}{fg=black}
|
||||||
|
\setbeamertemplate{bibliography entry article}{}
|
||||||
|
\setbeamertemplate{bibliography entry title}{}
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||||||
|
\setbeamertemplate{bibliography entry location}{}
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||||||
|
\setbeamertemplate{bibliography entry note}{}
|
||||||
65
docs/poster/beamercolorthememsu.sty
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65
docs/poster/beamercolorthememsu.sty
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|
% Gemini theme
|
||||||
|
% https://github.com/anishathalye/gemini
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||||||
|
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||||||
|
% UTA colors added
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||||||
|
% primiary HEX: #0064B1
|
||||||
|
|
||||||
|
% ====================
|
||||||
|
% Definitions
|
||||||
|
% ====================
|
||||||
|
|
||||||
|
%\definecolor{camblue}{RGB}{0, 62, 114}
|
||||||
|
% \definecolor{lightnyupurple}{RGB}{159, 120, 184}
|
||||||
|
% \definecolor{msugreen}{HTML}{18453B}
|
||||||
|
% \definecolor{umichblue}{HTML}{00274C}
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||||||
|
% \definecolor{yaleblue}{HTML}{00356B}
|
||||||
|
% \definecolor{ualbertagreen}{HTML}{1F4D2A}
|
||||||
|
% \definecolor{ualbertagold}{HTML}{EDC40A}
|
||||||
|
% \definecolor{utaBluePrimary}{HTML}{003C77}
|
||||||
|
% \definecolor{ulethgold}{HTML}{FFCF01}
|
||||||
|
\definecolor{utaBluePrimary}{HTML}{0064B1}
|
||||||
|
% Extra colors
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||||||
|
\definecolor{lightgray}{RGB}{240, 240, 240}
|
||||||
|
\definecolor{lightorange}{RGB}{255, 245, 242}
|
||||||
|
|
||||||
|
% ====================
|
||||||
|
% Theme
|
||||||
|
% ====================
|
||||||
|
|
||||||
|
% Basic colors
|
||||||
|
\setbeamercolor{palette primary}{fg=black,bg=white}
|
||||||
|
\setbeamercolor{palette secondary}{fg=black,bg=white}
|
||||||
|
\setbeamercolor{palette tertiary}{bg=black,fg=white}
|
||||||
|
\setbeamercolor{palette quaternary}{fg=black,bg=white}
|
||||||
|
\setbeamercolor{structure}{fg=utaBluePrimary}
|
||||||
|
|
||||||
|
% Headline
|
||||||
|
\setbeamercolor{headline}{fg=white,bg=utaBluePrimary}
|
||||||
|
|
||||||
|
% Block
|
||||||
|
\setbeamercolor{block title}{fg=utaBluePrimary,bg=white}
|
||||||
|
\setbeamercolor{block separator}{bg=black}
|
||||||
|
\setbeamercolor{block body}{fg=black,bg=white}
|
||||||
|
|
||||||
|
% Alert Block
|
||||||
|
\setbeamercolor{block alerted title}{fg=utaBluePrimary,bg=lightorange}
|
||||||
|
\setbeamercolor{block alerted separator}{bg=black}
|
||||||
|
\setbeamercolor{block alerted body}{fg=black,bg=lightorange}
|
||||||
|
|
||||||
|
% Example Block
|
||||||
|
\setbeamercolor{block example title}{fg=utaBluePrimary,bg=lightgray}
|
||||||
|
\setbeamercolor{block example separator}{bg=black}
|
||||||
|
\setbeamercolor{block example body}{fg=black,bg=lightgray}
|
||||||
|
|
||||||
|
% Heading
|
||||||
|
\setbeamercolor{heading}{fg=black}
|
||||||
|
|
||||||
|
% Itemize
|
||||||
|
\setbeamercolor{item}{fg=utaBluePrimary}
|
||||||
|
|
||||||
|
% Bibliography
|
||||||
|
\setbeamercolor{bibliography item}{fg=black}
|
||||||
|
\setbeamercolor{bibliography entry author}{fg=black}
|
||||||
|
\setbeamercolor{bibliography entry title}{fg=black}
|
||||||
|
\setbeamercolor{bibliography entry location}{fg=black}
|
||||||
|
\setbeamercolor{bibliography entry note}{fg=black}
|
||||||
257
docs/poster/beamerthemegemini.sty
Normal file
257
docs/poster/beamerthemegemini.sty
Normal file
@ -0,0 +1,257 @@
|
|||||||
|
% Gemini theme
|
||||||
|
% https://github.com/anishathalye/gemini
|
||||||
|
|
||||||
|
% ====================
|
||||||
|
% Dependencies
|
||||||
|
% ====================
|
||||||
|
|
||||||
|
\RequirePackage{exscale}
|
||||||
|
\RequirePackage{ragged2e}
|
||||||
|
\RequirePackage{changepage}
|
||||||
|
\RequirePackage{fontspec}
|
||||||
|
\RequirePackage{calc}
|
||||||
|
|
||||||
|
% ====================
|
||||||
|
% Fonts
|
||||||
|
% ====================
|
||||||
|
|
||||||
|
\newfontfamily\Raleway[Ligatures=TeX]{Raleway}
|
||||||
|
\newfontfamily\Lato[Ligatures=TeX]{Lato}
|
||||||
|
|
||||||
|
\usefonttheme{professionalfonts}
|
||||||
|
|
||||||
|
\setsansfont{Lato}[
|
||||||
|
UprightFont=*-Light,
|
||||||
|
ItalicFont=*-LightItalic,
|
||||||
|
BoldFont=*-Regular,
|
||||||
|
BoldItalicFont=*-Italic
|
||||||
|
]
|
||||||
|
|
||||||
|
\setbeamerfont{headline}{family=\Raleway}
|
||||||
|
\setbeamerfont{headline title}{size=\Huge,series=\bfseries}
|
||||||
|
\setbeamerfont{headline author}{size=\Large}
|
||||||
|
\setbeamerfont{headline institute}{size=\normalsize}
|
||||||
|
\setbeamerfont{block title}{family=\Raleway,size=\large,series=\bfseries}
|
||||||
|
\setbeamerfont{heading}{family=\Lato,series=\bfseries}
|
||||||
|
\setbeamerfont{caption}{size=\small}
|
||||||
|
\setbeamerfont{footline}{family=\Raleway,size=\normalsize}
|
||||||
|
|
||||||
|
% ====================
|
||||||
|
% Macros
|
||||||
|
% ====================
|
||||||
|
|
||||||
|
\newcommand{\samelineand}{\qquad}
|
||||||
|
|
||||||
|
% ====================
|
||||||
|
% Elements
|
||||||
|
% ====================
|
||||||
|
|
||||||
|
% List
|
||||||
|
\def\@listi{\leftmargin\leftmarginii
|
||||||
|
\topsep 1ex % spacing before
|
||||||
|
\parsep 0\p@ \@plus\p@
|
||||||
|
\itemsep 0.5ex} % spacing between
|
||||||
|
|
||||||
|
% Itemize
|
||||||
|
|
||||||
|
\setbeamertemplate{itemize item}{\raise0.5ex \hbox{\vrule width 0.5ex height 0.5ex}}
|
||||||
|
\setbeamertemplate{itemize subitem}{\raise0.3ex \hbox{\vrule width 0.5ex height 0.5ex}}
|
||||||
|
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<!-- data/collection_JFJ_2024_2025-06-10_2025-06-10.h5->generate_flags_cpc -->
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<!-- generate_flags_species -->
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<g id="node15" class="node">
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<title>generate_flags_species</title>
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<text text-anchor="middle" x="3213" y="-702.42" font-family="Times New Roman,serif" font-size="48.00">generate_flags_species</text>
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<!-- data/collection_JFJ_2024_2025-06-10_2025-06-10.h5->generate_flags_species -->
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<g id="edge16" class="edge">
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<title>data/collection_JFJ_2024_2025-06-10_2025-06-10.h5->generate_flags_species</title>
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<!-- pipelines/params/calibration_factors.yaml -->
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<g id="node4" class="node">
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<title>pipelines/params/calibration_factors.yaml</title>
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<g id="a_node4"><a xlink:title="pipelines/params/calibration_factors.yaml">
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<!-- pipelines/params/calibration_factors.yaml->apply_calibration_factors -->
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<g id="edge3" class="edge">
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<title>pipelines/params/calibration_factors.yaml->apply_calibration_factors</title>
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<!-- campaignDescriptor.yaml -->
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<g id="node5" class="node">
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<title>campaignDescriptor.yaml</title>
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|
<g id="a_node5"><a xlink:title="campaignDescriptor.yaml">
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|
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</a>
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</g>
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|
<!-- campaignDescriptor.yaml->apply_calibration_factors -->
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<g id="edge4" class="edge">
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<title>campaignDescriptor.yaml->apply_calibration_factors</title>
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<!-- prepare_ebas_submission -->
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<title>prepare_ebas_submission</title>
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<!-- data/.../2024/ACSM_JFJ_2024_timeseries_calibrated.csv->prepare_ebas_submission -->
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|
<g id="edge26" class="edge">
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<title>data/.../2024/ACSM_JFJ_2024_timeseries_calibrated.csv->prepare_ebas_submission</title>
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<!-- data/.../2024/ACSM_JFJ_2024_timeseries_calibrated_err.csv->prepare_ebas_submission -->
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<g id="edge27" class="edge">
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<title>data/.../2024/ACSM_JFJ_2024_timeseries_calibrated_err.csv->prepare_ebas_submission</title>
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<!-- data/.../2024/ACSM_JFJ_2024_timeseries_calibration_factors.csv->prepare_ebas_submission -->
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|
<g id="edge28" class="edge">
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<title>data/.../2024/ACSM_JFJ_2024_timeseries_calibration_factors.csv->prepare_ebas_submission</title>
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<!-- data/.../2024/ACSM_JFJ_2024_meta_flags.csv -->
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<g id="node12" class="node">
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<title>data/.../2024/ACSM_JFJ_2024_meta_flags.csv</title>
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|
<g id="a_node12"><a xlink:title="data/.../2024/ACSM_JFJ_2024_meta_flags.csv">
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<text text-anchor="middle" x="2450.21" y="-438.42" font-family="Times New Roman,serif" font-size="48.00">ACSM_JFJ_2024_meta_flags.csv</text>
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|
</a>
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|
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|
<!-- generate_flags_diagnostics->data/.../2024/ACSM_JFJ_2024_meta_flags.csv -->
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<g id="edge11" class="edge">
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<title>generate_flags_diagnostics->data/.../2024/ACSM_JFJ_2024_meta_flags.csv</title>
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<!-- pipelines/steps/generate_flags.py -->
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|
<g id="node10" class="node">
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<title>pipelines/steps/generate_flags.py</title>
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|
<g id="a_node10"><a xlink:title="pipelines/steps/generate_flags.py">
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</a>
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</g>
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<!-- pipelines/steps/generate_flags.py->generate_flags_diagnostics -->
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<g id="edge8" class="edge">
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<title>pipelines/steps/generate_flags.py->generate_flags_diagnostics</title>
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<!-- pipelines/steps/generate_flags.py->generate_flags_cpc -->
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|
<g id="edge12" class="edge">
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<title>pipelines/steps/generate_flags.py->generate_flags_cpc</title>
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<!-- pipelines/steps/generate_flags.py->generate_flags_species -->
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<g id="edge15" class="edge">
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<title>pipelines/steps/generate_flags.py->generate_flags_species</title>
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<!-- pipelines/params/validity_thresholds.yaml -->
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<g id="node11" class="node">
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|
<title>pipelines/params/validity_thresholds.yaml</title>
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|
<g id="a_node11"><a xlink:title="pipelines/params/validity_thresholds.yaml">
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<!-- pipelines/params/validity_thresholds.yaml->generate_flags_diagnostics -->
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<title>pipelines/params/validity_thresholds.yaml->generate_flags_diagnostics</title>
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<!-- data/.../2024/ACSM_JFJ_2024_meta_flags.csv->generate_flags_species -->
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<g id="edge18" class="edge">
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<title>data/.../2024/ACSM_JFJ_2024_meta_flags.csv->generate_flags_species</title>
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<!-- data/.../2024/CPC.lev1_flags.csv -->
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|
<g id="node14" class="node">
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|
<title>data/.../2024/CPC.lev1_flags.csv</title>
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|
<g id="a_node14"><a xlink:title="data/.../2024/CPC.lev1_flags.csv">
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<ellipse fill="lightgreen" stroke="black" cx="2450.21" cy="-302.02" rx="279.13" ry="82.02"/>
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<text text-anchor="middle" x="2450.21" y="-310.42" font-family="Times New Roman,serif" font-size="48.00">data/.../2024/</text>
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<text text-anchor="middle" x="2450.21" y="-256.42" font-family="Times New Roman,serif" font-size="48.00">CPC.lev1_flags.csv</text>
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|
<!-- generate_flags_cpc->data/.../2024/CPC.lev1_flags.csv -->
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<g id="edge14" class="edge">
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<title>generate_flags_cpc->data/.../2024/CPC.lev1_flags.csv</title>
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<!-- data/.../2024/CPC.lev1_flags.csv->generate_flags_species -->
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<g id="edge19" class="edge">
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<title>data/.../2024/CPC.lev1_flags.csv->generate_flags_species</title>
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<!-- data/.../2024/ACSM_JFJ_2024_timeseries_flags.csv -->
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<g id="node21" class="node">
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<title>data/.../2024/ACSM_JFJ_2024_timeseries_flags.csv</title>
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|
<g id="a_node21"><a xlink:title="data/.../2024/ACSM_JFJ_2024_timeseries_flags.csv">
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<text text-anchor="middle" x="4235.12" y="-1037.42" font-family="Times New Roman,serif" font-size="48.00">ACSM_JFJ_2024_timeseries_flags.csv</text>
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</a>
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<!-- generate_flags_species->data/.../2024/ACSM_JFJ_2024_timeseries_flags.csv -->
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<g id="edge24" class="edge">
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<title>generate_flags_species->data/.../2024/ACSM_JFJ_2024_timeseries_flags.csv</title>
|
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|
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<title>data/.../2024/flag_14_Org_11000.json</title>
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|
<!-- data/.../2024/ACSM_JFJ_2024_timeseries_flags.csv->prepare_ebas_submission -->
|
||||||
|
<g id="edge29" class="edge">
|
||||||
|
<title>data/.../2024/ACSM_JFJ_2024_timeseries_flags.csv->prepare_ebas_submission</title>
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<!-- data/JFJ_ACSM-017_2024.txt -->
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<title>data/JFJ_ACSM-017_2024.txt</title>
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</g>
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<!-- prepare_ebas_submission->data/JFJ_ACSM-017_2024.txt -->
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<title>prepare_ebas_submission->data/JFJ_ACSM-017_2024.txt</title>
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<!-- data/JFJ_ACSM-017_FLAGS_2024.txt -->
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<g id="node27" class="node">
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<title>data/JFJ_ACSM-017_FLAGS_2024.txt</title>
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<text text-anchor="middle" x="6035.24" y="-946.42" font-family="Times New Roman,serif" font-size="48.00">JFJ_ACSM-017_FLAGS_2024.txt</text>
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<!-- prepare_ebas_submission->data/JFJ_ACSM-017_FLAGS_2024.txt -->
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<g id="edge33" class="edge">
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<g id="node23" class="node">
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<title>pipelines/params/"limits_of_detection.yaml->prepare_ebas_submission</title>
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<title>pipelines/params/"station_params.yaml</title>
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|
After Width: | Height: | Size: 30 KiB |
38
docs/poster/poster.bib
Normal file
38
docs/poster/poster.bib
Normal file
@ -0,0 +1,38 @@
|
|||||||
|
@book{chacon2014pro,
|
||||||
|
title={Pro git},
|
||||||
|
author={Chacon, Scott and Straub, Ben},
|
||||||
|
year={2014},
|
||||||
|
publisher={Springer Nature}
|
||||||
|
}
|
||||||
|
|
||||||
|
@article{wilkinson2016fair,
|
||||||
|
title={The FAIR Guiding Principles for scientific data management and stewardship},
|
||||||
|
author={Wilkinson, Mark D and Dumontier, Michel and Aalbersberg, IJsbrand Jan and Appleton, Gabrielle and Axton, Myles and Baak, Arie and Blomberg, Niklas and Boiten, Jan-Willem and da Silva Santos, Luiz Bonino and Bourne, Philip E and others},
|
||||||
|
journal={Scientific data},
|
||||||
|
volume={3},
|
||||||
|
number={1},
|
||||||
|
pages={1--9},
|
||||||
|
year={2016},
|
||||||
|
publisher={Nature Publishing Group}
|
||||||
|
}
|
||||||
|
|
||||||
|
@article{konnecke2015nexus,
|
||||||
|
title={The NeXus data format},
|
||||||
|
author={K{\"o}nnecke, Mark and Akeroyd, Frederick A and Bernstein, Herbert J and Brewster, Aaron S and Campbell, Stuart I and Clausen, Bj{\"o}rn and Cottrell, Stephen and Hoffmann, Jens Uwe and Jemian, Pete R and M{\"a}nnicke, David and others},
|
||||||
|
journal={Journal of applied crystallography},
|
||||||
|
volume={48},
|
||||||
|
number={1},
|
||||||
|
pages={301--305},
|
||||||
|
year={2015},
|
||||||
|
publisher={International Union of Crystallography}
|
||||||
|
}
|
||||||
|
|
||||||
|
@article{bartels2023time,
|
||||||
|
title={It is Time to Introduce the Next Generation of Chemists to FAIR and Open Science: Chemical Education},
|
||||||
|
author={Bartels-Rausch, Thorsten and Ammann, Markus},
|
||||||
|
journal={Chimia},
|
||||||
|
volume={77},
|
||||||
|
number={10},
|
||||||
|
pages={694--696},
|
||||||
|
year={2023}
|
||||||
|
}
|
||||||
313
docs/poster/poster.tex
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313
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Normal file
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|
|||||||
|
% Unofficial University of Texas at Arlington Math Poster template:
|
||||||
|
|
||||||
|
% A fork of the unofficial University of Lethbridge Poster template: https://www.overleaf.com/latex/templates/university-of-lethbridge-unofficial-poster-template/nddfzgvqvfwf
|
||||||
|
% which is a fork of unofficial University of Alberta Poster template:
|
||||||
|
% which is a fork of Yale template: https://www.overleaf.com/latex/templates/yale-poster-template/rjpgqfgvsjcv
|
||||||
|
% which is a fork of the UMich template https://www.overleaf.com/latex/templates/university-of-michigan-umich-poster-template/xpnqzzxwbjzc
|
||||||
|
% which is fork of the MSU template https://www.overleaf.com/latex/templates/an-unofficial-poster-template-for-michigan-state-university/wnymbgpxnnwd
|
||||||
|
% which is a fork of https://www.overleaf.com/latex/templates/an-unofficial-poster-template-for-new-york-university/krgqtqmzdqhg
|
||||||
|
% which is a fork of https://github.com/anishathalye/gemini
|
||||||
|
% also refer to https://github.com/k4rtik/uchicago-poster
|
||||||
|
|
||||||
|
|
||||||
|
\documentclass[final]{beamer}
|
||||||
|
|
||||||
|
% ====================
|
||||||
|
% Packages
|
||||||
|
% ====================
|
||||||
|
|
||||||
|
\usepackage[T1]{fontenc}
|
||||||
|
\usepackage[utf8]{luainputenc}
|
||||||
|
\usepackage{lmodern}
|
||||||
|
%\usepackage[size=custom, width=122,height=91, scale=1.2]{beamerposter}
|
||||||
|
\usepackage[orientation=portrait, size=a0, scale=1.25]{beamerposter}
|
||||||
|
\usetheme{gemini}
|
||||||
|
\usecolortheme{msu}
|
||||||
|
\usepackage{graphicx}
|
||||||
|
\usepackage{booktabs}
|
||||||
|
\usepackage{tikz}
|
||||||
|
\usepackage{pgfplots}
|
||||||
|
\pgfplotsset{compat=1.14}
|
||||||
|
\usepackage{anyfontsize}
|
||||||
|
\usepackage{multirow}
|
||||||
|
\usepackage{listings}
|
||||||
|
\usepackage[dvipsnames]{xcolor}
|
||||||
|
% ====================
|
||||||
|
% Lengths
|
||||||
|
% ====================
|
||||||
|
|
||||||
|
% If you have N columns, choose \sepwidth and \colwidth such that
|
||||||
|
% (N+1)*\sepwidth + N*\colwidth = \paperwidth
|
||||||
|
\newlength{\sepwidth}
|
||||||
|
\newlength{\colwidth}
|
||||||
|
\setlength{\sepwidth}{0.025\paperwidth}
|
||||||
|
\setlength{\colwidth}{0.3\paperwidth}
|
||||||
|
|
||||||
|
\newcommand{\separatorcolumn}{\begin{column}{\sepwidth}\end{column}}
|
||||||
|
|
||||||
|
% ====================
|
||||||
|
% Title
|
||||||
|
% ====================
|
||||||
|
|
||||||
|
\title{Implementing FAIR Data Exchange in ACTRIS Switzerland : An Expert-Driven Approach}
|
||||||
|
%\setbeamerfont{title}{size=\huge}
|
||||||
|
|
||||||
|
\author{Juan F. Fl\'orez-Ospina, Leïla H. Simon, Nora K. Nowak, Benjamin T. Brem, \\ Martin Gysel-Beer, and Robin L. Modini}
|
||||||
|
|
||||||
|
%\author{Juan F. Florez-Ospina$^{1}$, Natasha M. Garner$^{1}$, Lucia Iezzi$^{1}$, David Bell$^{1}$,\\ Imad El Haddad$^{1}$, Julia Schmale$^{2}$, and Thorsten Bartels-Rausch$^{1}$}
|
||||||
|
% add following line if you have co-author(s)
|
||||||
|
% Coauthor One$^{2}$, Coauthor Two$^{3}$
|
||||||
|
|
||||||
|
\institute[shortinst]{PSI Center for Energy and Environmental Sciences, 5232 Villigen PSI, Switzerland}
|
||||||
|
|
||||||
|
% ====================
|
||||||
|
% Footer (optional)
|
||||||
|
% ====================
|
||||||
|
\footercontent{\hfill
|
||||||
|
\href{mailto:juan.florez-ospina@psi.ch}{juan.florez-ospina@psi.ch, juanflo16@gmail.com,} \href{robin.modini@psi.ch}{robin.modini@psi.ch}}
|
||||||
|
% (can be left out to remove footer)
|
||||||
|
%\footercontent{22-Nov-2023, Swiss Data Science Conference, Bern \hfill
|
||||||
|
% \href{mailto:juan.florez-ospina@psi.ch}{juan.florez-ospina@psi.ch} \href{thorsten.bartels-rausch@psi.ch}{thorsten.bartels-rausch@psi.ch}}
|
||||||
|
% (can be left out to remove footer)
|
||||||
|
|
||||||
|
% ====================
|
||||||
|
% Logo
|
||||||
|
%\logoleft{\includegraphics[height=5.5cm]{logos/psi_01_sn.png}}
|
||||||
|
% ====================
|
||||||
|
|
||||||
|
% use this to include logos on the left and/or right side of the header:
|
||||||
|
% Left: institution
|
||||||
|
% \logoright{\includegraphics[height=5cm]{logos/logo-wordmark-variations.png}}
|
||||||
|
% Right: funding agencies and other affilations
|
||||||
|
%\logoright{\includegraphics[height=7cm]{logos/NSF.eps}}
|
||||||
|
|
||||||
|
% ====================
|
||||||
|
% Body
|
||||||
|
% ====================
|
||||||
|
|
||||||
|
|
||||||
|
\begin{document}
|
||||||
|
|
||||||
|
\begin{frame}[t]
|
||||||
|
|
||||||
|
\begin{columns}[t]
|
||||||
|
\separatorcolumn
|
||||||
|
|
||||||
|
|
||||||
|
\begin{column}{1.5\colwidth}
|
||||||
|
|
||||||
|
\begin{block}{Motivation}
|
||||||
|
|
||||||
|
%Given an \textit{allocated time frame},
|
||||||
|
|
||||||
|
\textbf{Problem.} Scientific datasets in atmospheric science are often large, complex and highly specialized, making them hard to reuse across users, tools, and time.
|
||||||
|
\textcolor{white}{insert line here :)}
|
||||||
|
|
||||||
|
Adhering to the FAIR data principles promises to resolve long term reuse of data by machines and humans.
|
||||||
|
\textcolor{white}{insert line here :)}
|
||||||
|
|
||||||
|
\textbf{Yet in practice,} implementations often have the following configuration,
|
||||||
|
\vspace{1em} % Add some space before next block
|
||||||
|
|
||||||
|
\begin{figure}
|
||||||
|
\centering
|
||||||
|
\includegraphics[width=0.75\textwidth]{figures/styled_typical_exchange.pdf}
|
||||||
|
\caption{Diagram of tightly coupled system for integration, processing and ingestion of scientific data into ORD repositories.}
|
||||||
|
\end{figure}
|
||||||
|
which in turn exhibits the following
|
||||||
|
\vspace{1em}
|
||||||
|
\begin{exampleblock}{System drawbacks:}
|
||||||
|
\begin{itemize}
|
||||||
|
\item
|
||||||
|
Task-specific outputs, limiting adaptability to new needs or use cases.
|
||||||
|
\item
|
||||||
|
Monolithic design, making the system hard to maintain, reuse or understand internally.
|
||||||
|
\item
|
||||||
|
Embedded domain knowledge in hard-coded parameters, reducing transparency and flexibility.
|
||||||
|
|
||||||
|
\end{itemize}
|
||||||
|
|
||||||
|
\end{exampleblock}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
%\begin{itemize}
|
||||||
|
% \item
|
||||||
|
|
||||||
|
% Convey the idea about fragmented heterogeneous data (highly collaborative, plenty of coordination, planning)
|
||||||
|
%\item
|
||||||
|
% Data analysis, also heterogeneous (but highly independent)
|
||||||
|
%\end{itemize}
|
||||||
|
|
||||||
|
|
||||||
|
\begin{block}{Expert-driven FAIR data exchange systems}
|
||||||
|
|
||||||
|
\textbf{Therefore.} \textit{We aim to explore and prototype an expert-driven data exchange system, as conceptualized below.}
|
||||||
|
|
||||||
|
\begin{figure}[H]
|
||||||
|
\centering
|
||||||
|
\includegraphics[width=\textwidth]{figures/extended_data_flow_dag_with_actris.pdf}
|
||||||
|
\caption{Diagram of the expert-driven FAIR data exchange system.}
|
||||||
|
\end{figure}
|
||||||
|
|
||||||
|
|
||||||
|
This system, unlike the above implementation, exhibits the following:
|
||||||
|
|
||||||
|
\end{block}
|
||||||
|
|
||||||
|
\vspace{1em} % Add some space before next block
|
||||||
|
|
||||||
|
|
||||||
|
\begin{exampleblock}{System characteristics:}
|
||||||
|
\begin{enumerate}
|
||||||
|
\item
|
||||||
|
Adaptable to new needs, making it interoperable across users and systems.
|
||||||
|
\item
|
||||||
|
Modular, allowing components to be reused, replaced, or maintained independently.
|
||||||
|
\item
|
||||||
|
Configurable with domain knowledge supplied externally, supporting expert feedback loops.
|
||||||
|
\item
|
||||||
|
Transparent, enabling monitoring of data flows and tracking of data provenance through a clear, structured design.
|
||||||
|
\end{enumerate}
|
||||||
|
\end{exampleblock}
|
||||||
|
|
||||||
|
\textbf{Practical implementation (Technical stack)}
|
||||||
|
|
||||||
|
\begin{figure}[H]
|
||||||
|
\centering
|
||||||
|
\includegraphics[width=0.5\textwidth]{figures/layered_stack.pdf}
|
||||||
|
%\caption{Diagram of the expert-driven FAIR data exchange system.}
|
||||||
|
\end{figure}
|
||||||
|
|
||||||
|
\vspace{0.5em}
|
||||||
|
\colorbox{lightgray}{
|
||||||
|
\parbox{0.95\linewidth}{
|
||||||
|
\textbf{Code Repository:} \url{https://gitea.psi.ch/APOG_public/acsmnode.git}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
\vspace{0.5em}
|
||||||
|
|
||||||
|
\end{block}
|
||||||
|
|
||||||
|
\end{column}
|
||||||
|
|
||||||
|
%\end{columns}
|
||||||
|
|
||||||
|
%\begin{columns}[t]
|
||||||
|
|
||||||
|
\separatorcolumn
|
||||||
|
|
||||||
|
\begin{column}{1.5\colwidth}
|
||||||
|
|
||||||
|
\begin{block}{FAIR data chains in ACTRIS Switzerland---Use case}
|
||||||
|
|
||||||
|
|
||||||
|
\textbf{Challenge: }Standardized annual submission of aerosol composition observations from field stations (\textbf{Payerne} and \textbf{Jungfraujoch}) to the \textbf{EBAS database}.
|
||||||
|
|
||||||
|
\textcolor{white}{ }
|
||||||
|
We consider raw data described in the Table below.
|
||||||
|
\textcolor{white}{white}
|
||||||
|
\begin{table}[!ht]
|
||||||
|
\resizebox{0.75\textwidth}{!}{%
|
||||||
|
\centering
|
||||||
|
\begin{tabular}{|c|c|c|}
|
||||||
|
\hline
|
||||||
|
\textbf{Data Source} & \textbf{File Formats} & \textbf{Submission Date} \\
|
||||||
|
\hline
|
||||||
|
Aerodyne & TXT, CSV & \multirow{3}{*}{May 31, 2025} \\
|
||||||
|
Aerosol Chemical Speciation Monitor & NAS & \\
|
||||||
|
(ACSM) & YAML & \\
|
||||||
|
%PTR-TOF MS & NetCDF \\
|
||||||
|
\hline
|
||||||
|
\end{tabular}
|
||||||
|
}
|
||||||
|
\end{table}
|
||||||
|
|
||||||
|
\end{block}
|
||||||
|
%\begin{comment}
|
||||||
|
%\begin{exampleblock}{General data chain properties:}
|
||||||
|
%\begin{itemize}
|
||||||
|
% \item
|
||||||
|
% Standards Compliance: CF convention metadata + EBAS database rules for quality control (flagging)
|
||||||
|
% \item
|
||||||
|
% \textbf{Docker} ensures consistent processing across stations and %time periods
|
||||||
|
%\end{itemize}
|
||||||
|
%\end{exampleblock}
|
||||||
|
%\end{comment}
|
||||||
|
%\textcolor{white}{white}
|
||||||
|
\begin{block}{Configurable Data Integration using YAML files}
|
||||||
|
|
||||||
|
\textbf{Goal:} Search, Retrieve, and Integrate Raw Data in HDF5 format
|
||||||
|
|
||||||
|
\begin{figure}
|
||||||
|
\centering
|
||||||
|
%\includegraphics[width=0.65\textwidth]{figures/EarthObservation_HSI.pdf}
|
||||||
|
\includegraphics[width=0.7\textwidth]{figures/data_integration_step.pdf}
|
||||||
|
\end{figure}
|
||||||
|
\colorbox{lightgray}{
|
||||||
|
\parbox{0.95\linewidth}{
|
||||||
|
\textbf{Code Repository:} \url{https://gitea.psi.ch/5505-public/dima.git}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
\end{block}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
\begin{block}{Interactive Data Annotation for Quality Control} % Quality Control Workflow}
|
||||||
|
|
||||||
|
\textbf{Goal:} Apply time-dependent correction factors to observations and generate quality control flags with expert validation, complying with EBAS database.
|
||||||
|
|
||||||
|
\begin{figure}
|
||||||
|
\includegraphics[width=0.6\textwidth]{figures/quality_control_workflow.pdf}
|
||||||
|
\end{figure}
|
||||||
|
Enables reconciliation of \textbf{Automatic Diagnostic Flags}, \textbf{Station-specific Flags}, and \textbf{Manual Review Flags}.
|
||||||
|
%%\textbf{Features:} Enable reconciliation
|
||||||
|
%\begin{itemize}
|
||||||
|
% \item \textbf{Automatic Diagnostic Flags}: threshold-based detection of instrument malfunctions.
|
||||||
|
% \item
|
||||||
|
% \textbf{Expert Knowledge Flags:} Station operator insights on local conditions and maintenance events and calibration periods.
|
||||||
|
% \item
|
||||||
|
% \textbf{Manual Review Flags:} Visual inspection of time series anomalies.
|
||||||
|
%\end{itemize}
|
||||||
|
|
||||||
|
\end{block}
|
||||||
|
|
||||||
|
\begin{block}{Accessible Data Products for Domain-Agnostic Reuse}
|
||||||
|
|
||||||
|
\textbf{Primary Product:} EBAS-ready files conforming to ACTRIS Level 2 quality standards.
|
||||||
|
|
||||||
|
\textbf{Secondary Product:} A comprehensive, self-describing file that integrates:
|
||||||
|
\begin{itemize}
|
||||||
|
\item Original and intermediate data products with rich contextual and provenance metadata, as shown below.
|
||||||
|
|
||||||
|
\begin{figure}
|
||||||
|
\includegraphics[width=0.9\textwidth]{figures/hdf5_before_after.pdf}
|
||||||
|
%\caption{Initial integrated file (left) and enhanced HDF5 file (right)}
|
||||||
|
\end{figure}
|
||||||
|
\item An auto-generated prospective provenance graph in Renku workflow format, visualized as below
|
||||||
|
|
||||||
|
\begin{figure}
|
||||||
|
\includegraphics[width=\textwidth]{figures/workflow_acsm_data_JFJ_2024.pdf}
|
||||||
|
|
||||||
|
\end{figure}
|
||||||
|
\end{itemize}
|
||||||
|
\end{block}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
%\begin{block}{References}
|
||||||
|
|
||||||
|
% \nocite{*}
|
||||||
|
% \footnotesize{\bibliographystyle{ieeetr}\bibliography{poster}}
|
||||||
|
|
||||||
|
%\end{block}
|
||||||
|
|
||||||
|
\end{column}
|
||||||
|
|
||||||
|
\separatorcolumn
|
||||||
|
\end{columns}
|
||||||
|
\end{frame}
|
||||||
|
|
||||||
|
\end{document}
|
||||||
28
docs/source/conf.py
Normal file
28
docs/source/conf.py
Normal file
@ -0,0 +1,28 @@
|
|||||||
|
# Configuration file for the Sphinx documentation builder.
|
||||||
|
#
|
||||||
|
# For the full list of built-in configuration values, see the documentation:
|
||||||
|
# https://www.sphinx-doc.org/en/master/usage/configuration.html
|
||||||
|
|
||||||
|
# -- Project information -----------------------------------------------------
|
||||||
|
# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
|
||||||
|
|
||||||
|
project = 'ACSM FAIRifier Tool'
|
||||||
|
copyright = '2025, Juan F. Flórez-Ospina, Leïla H. Simon, Nora K. Nowak, Benjamin T. Brem, Martin Gysel-Beer, and Robin L. Modini'
|
||||||
|
author = 'Juan F. Flórez-Ospina, Leïla H. Simon, Nora K. Nowak, Benjamin T. Brem, Martin Gysel-Beer, and Robin L. Modini'
|
||||||
|
release = '0.0.1'
|
||||||
|
|
||||||
|
# -- General configuration ---------------------------------------------------
|
||||||
|
# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
|
||||||
|
|
||||||
|
extensions = []
|
||||||
|
|
||||||
|
templates_path = ['_templates']
|
||||||
|
exclude_patterns = []
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
# -- Options for HTML output -------------------------------------------------
|
||||||
|
# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
|
||||||
|
|
||||||
|
html_theme = 'alabaster'
|
||||||
|
html_static_path = ['_static']
|
||||||
20
docs/source/index.rst
Normal file
20
docs/source/index.rst
Normal file
@ -0,0 +1,20 @@
|
|||||||
|
.. ACSM FAIRifier Tool documentation master file, created by
|
||||||
|
sphinx-quickstart on Tue Jun 17 16:17:43 2025.
|
||||||
|
You can adapt this file completely to your liking, but it should at least
|
||||||
|
contain the root `toctree` directive.
|
||||||
|
|
||||||
|
Welcome to ACSM FAIRifier Tool's documentation!
|
||||||
|
===============================================
|
||||||
|
|
||||||
|
.. toctree::
|
||||||
|
:maxdepth: 2
|
||||||
|
:caption: Contents:
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
Indices and tables
|
||||||
|
==================
|
||||||
|
|
||||||
|
* :ref:`genindex`
|
||||||
|
* :ref:`modindex`
|
||||||
|
* :ref:`search`
|
||||||
Reference in New Issue
Block a user