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‎README.md‎

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</a>
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</p>
2020

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An open source scientific article created using the [showyourwork](https://github.com/showyourwork/showyourwork) workflow.
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*This is an automatically generated test for [showyourwork](https://github.com/showyourwork/showyourwork) generated from the file [test_zenodo.py](https://github.com/showyourwork/showyourwork/blob/main/tests/integration/test_zenodo.py).*
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Test a repo that downloads data from Zenodo.

‎showyourwork.yml‎

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# Enable rule caching on Zenodo?
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cache_on_zenodo: true
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# Workflow graph (DAG) generation
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dag:
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# Generate `dag.pdf` on each build?
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render: false
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# Graphviz layout engine
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engine: sfdp
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# Group files by type into plates?
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group_by_type: false
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# Custom graph attributes
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graph_attr:
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ranksep: "1"
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nodesep: "0.65"
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# Custom node attributes
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nodesep: '0.65'
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ranksep: '1'
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group_by_type: false
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node_attr:
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shape: "box"
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penwidth: "2"
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width: "1"
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# Files and glob patterns to ignore
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# ignore_files:
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# - src/tex/orcid-ID.png
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# Externally-hosted datasets, e.g. on Zenodo
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penwidth: '2'
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shape: box
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width: '1'
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render: false
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datasets:
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# 10.5281/zenodo.6468327:
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# contents:
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# TOI640b.json: src/data/TOI640b.json
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# Custom file dependencies
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10.5281/zenodo.6515864:
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contents:
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README.md: null
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TOI640b.json: src/data/TOI640/planet.json
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images.tar.gz:
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README.md: null
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S06:
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image.json: src/data/TOI640/S06.json
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S07:
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image.json: src/data/TOI640/S07.json
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lightcurves.zip:
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lightcurves:
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README.md: null
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S06:
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lc.txt: src/data/TOI640/S06.txt
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S07:
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lc.txt: src/data/TOI640/S07.txt
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destination: src/data/TOI640
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dependencies:
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# src/scripts/my_script.py:
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# - src/data/dataset_for_my_script.dat
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# src/tex/ms.tex:
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# - src/tex/stylesheet.tex
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# Name of the `.tex` manuscript and corresponding `.pdf` article
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src/scripts/test_figure.py:
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- src/data/TOI640/planet.json
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- src/data/TOI640/S06.txt
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- src/data/TOI640/S06.json
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- src/data/TOI640/S07.txt
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- src/data/TOI640/S07.json
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ms_name: ms
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# Optimize DAG by removing unnecessary jobs upstream of cache hits?
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optimize_caching: false
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# Overleaf sync settings
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overleaf:
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# Overleaf project ID (blank = disabled)
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id:
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# Perform sync on GitHub Actions?
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gh_actions_sync: true
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# List of files to push to Overleaf
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push:
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- src/tex/figures
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- src/tex/output
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# List of files to pull from Overleaf
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id: null
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pull:
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- src/tex/ms.tex
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- src/tex/bib.bib
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# Always require all input files to be present on disk for workflow to pass?
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- src/tex/ms.tex
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- src/tex/bib.bib
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push:
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- src/tex/figures
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- src/tex/output
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require_inputs: true
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# Allow cacheable rules to run on GitHub Actions?
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run_cache_rules_on_ci: false
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# Mapping of script file extensions to instructions for executing them
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scripts:
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py: python {script}
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# Display of the `showyourwork` stamp on first page
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stamp:
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# Show the stamp?
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enabled: true
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# Stamp angle in degrees
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angle: -20.0
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# Stamp size in inches
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enabled: true
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size: 0.75
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# Horizontal position in inches from right edge of paper
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xpos: 0.50
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# Vertical position in inches from top edge of paper
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ypos: 0.50
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# Display of the repo URL in the stamp
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url:
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# Show the URL?
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enabled: true
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# Maximum URL length to display
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maxlen: 40
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# Enable SyncTeX?
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synctex: True
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# Command-line options to be passed to tectonic when building the manuscript
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xpos: 0.5
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ypos: 0.5
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synctex: true
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tectonic_args: []
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# Preprocessing script for arXiv tarball
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# (such as to switch `minted` from `finalizecache` to `frozencache`)
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# The script will be passed a directory containing the manuscript source
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# as input, and should modify the contents of that directory in-place.
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# preprocess_arxiv_script: my_preprocess_script.sh
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# Enable verbose output?
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verbose: false
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# Version of `showyourwork` used to create this workflow
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version: 0.4.4.dev261+g098a369e9
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‎src/scripts/test_figure.py‎

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import matplotlib.pyplot as plt
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import numpy as np
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import json
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import paths
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# Set up the figure
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fig = plt.figure(figsize=(7, 6))
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ax = fig.subplot_mosaic(
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'''
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AB
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CC
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'''
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)
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fig.subplots_adjust(wspace=0.1, hspace=0.15)
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# Images
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for n, dataset in zip(["A", "B"], ["S06", "S07"]):
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with open(paths.data / "TOI640" / f"{dataset}.json", "r") as f:
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image_data = json.load(f)
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aperture = np.array(image_data["aperture"])
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image = np.array(image_data["image"]) / 1e3
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im = ax[n].imshow(image, origin="lower", vmin=0, vmax=4)
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ax[n].set_xticks([])
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ax[n].set_yticks([])
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ax[n].set_title(dataset)
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ax[n].set_aspect("auto")
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fig.colorbar(im, ax=[ax["A"], ax["B"]], shrink=1, label="flux [ke$^-$/s]")
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# Dummy colorbar to get the spacing right
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cbar = fig.colorbar(im, ax=ax["C"], shrink=1)
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cbar.ax.set_visible(False)
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# Load planet data
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with open(paths.data / "TOI640" / "planet.json", "r") as f:
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planet_data = json.load(f)
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phase = planet_data["phase"]
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period = planet_data["period"]
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# Photometry
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for dataset in ["S06", "S07"]:
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# Load the data
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time, flux, *_ = np.loadtxt(paths.data / "TOI640" / f"{dataset}.txt").T
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# Divide out the rolling 1-day median baseline
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dt = np.median(np.diff(time))
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w = int(1 / dt)
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baseline = [np.median(flux[a : a + w]) for a in range(len(flux))]
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flux /= baseline
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# Fold the data
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time = (time % period) / period + phase
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# Plot it
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ax["C"].plot(time, flux, ".", label=dataset)
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# Format the figure
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ax["C"].legend()
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ax["C"].set_xlim(-0.1, 0.1)
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ax["C"].set_xlabel("orbital phase")
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ax["C"].set_ylabel("normalized flux")
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fig.savefig(paths.figures / "test_figure.pdf", bbox_inches="tight", dpi=300)
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‎src/tex/ms.tex‎

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\bibliography{bib}
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\begin{figure}[ht!]
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\script{test_figure.py}
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\begin{centering}
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\includegraphics[width=\linewidth]{figures/test_figure.pdf}
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\caption{A test figure.}
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\label{fig:test_figure}
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\end{centering}
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\end{figure}
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\end{document}

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