auto commit from showyourwork tests

README.md

@@ -15,4 +15,6 @@
 </a>
 </p>
 
-An open source scientific article created using the [showyourwork](https://github.com/showyourwork/showyourwork) workflow.
+*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).*
+
+Test a repo that downloads data from Zenodo.

showyourwork.yml

@@ -1,105 +1,67 @@
-# Enable rule caching on Zenodo?
 cache_on_zenodo: true
-
-# Workflow graph (DAG) generation
 dag:
-  # Generate `dag.pdf` on each build?
-  render: false
-  # Graphviz layout engine
   engine: sfdp
-  # Group files by type into plates?
-  group_by_type: false
-  # Custom graph attributes
   graph_attr:
-    ranksep: "1"
-    nodesep: "0.65"
-  # Custom node attributes
+    nodesep: '0.65'
+    ranksep: '1'
+  group_by_type: false
   node_attr:
-    shape: "box"
-    penwidth: "2"
-    width: "1"
-  # Files and glob patterns to ignore
-  # ignore_files:
-  #  - src/tex/orcid-ID.png
-
-
-# Externally-hosted datasets, e.g. on Zenodo
+    penwidth: '2'
+    shape: box
+    width: '1'
+  render: false
 datasets:
-  # 10.5281/zenodo.6468327:
-  #   contents:
-  #     TOI640b.json: src/data/TOI640b.json
-
-# Custom file dependencies
+  10.5281/zenodo.6515864:
+    contents:
+      README.md: null
+      TOI640b.json: src/data/TOI640/planet.json
+      images.tar.gz:
+        README.md: null
+        S06:
+          image.json: src/data/TOI640/S06.json
+        S07:
+          image.json: src/data/TOI640/S07.json
+      lightcurves.zip:
+        lightcurves:
+          README.md: null
+          S06:
+            lc.txt: src/data/TOI640/S06.txt
+          S07:
+            lc.txt: src/data/TOI640/S07.txt
+    destination: src/data/TOI640
 dependencies:
-  # src/scripts/my_script.py:
-  #   - src/data/dataset_for_my_script.dat
-  # src/tex/ms.tex:
-  #   - src/tex/stylesheet.tex
-
-# Name of the `.tex` manuscript and corresponding `.pdf` article
+  src/scripts/test_figure.py:
+  - src/data/TOI640/planet.json
+  - src/data/TOI640/S06.txt
+  - src/data/TOI640/S06.json
+  - src/data/TOI640/S07.txt
+  - src/data/TOI640/S07.json
 ms_name: ms
-
-# Optimize DAG by removing unnecessary jobs upstream of cache hits?
 optimize_caching: false
-
-# Overleaf sync settings
 overleaf:
-  # Overleaf project ID (blank = disabled)
-  id: 
-  # Perform sync on GitHub Actions?
   gh_actions_sync: true
-  # List of files to push to Overleaf
-  push:
-    - src/tex/figures
-    - src/tex/output
-  # List of files to pull from Overleaf
+  id: null
   pull:
-    - src/tex/ms.tex
-    - src/tex/bib.bib
-
-# Always require all input files to be present on disk for workflow to pass?
+  - src/tex/ms.tex
+  - src/tex/bib.bib
+  push:
+  - src/tex/figures
+  - src/tex/output
 require_inputs: true
-
-# Allow cacheable rules to run on GitHub Actions?
 run_cache_rules_on_ci: false
-
-# Mapping of script file extensions to instructions for executing them
 scripts:
   py: python {script}
-
-# Display of the `showyourwork` stamp on first page
 stamp:
-  # Show the stamp?
-  enabled: true
-  # Stamp angle in degrees
   angle: -20.0
-  # Stamp size in inches
+  enabled: true
   size: 0.75
-  # Horizontal position in inches from right edge of paper
-  xpos: 0.50
-  # Vertical position in inches from top edge of paper
-  ypos: 0.50
-  # Display of the repo URL in the stamp
   url:
-    # Show the URL?
     enabled: true
-    # Maximum URL length to display
     maxlen: 40
-
-# Enable SyncTeX?
-synctex: True
-
-# Command-line options to be passed to tectonic when building the manuscript
+  xpos: 0.5
+  ypos: 0.5
+synctex: true
 tectonic_args: []
-
-# Preprocessing script for arXiv tarball
-# (such as to switch `minted` from `finalizecache` to `frozencache`)
-# The script will be passed a directory containing the manuscript source
-# as input, and should modify the contents of that directory in-place.
-# preprocess_arxiv_script: my_preprocess_script.sh
-
-# Enable verbose output?
 verbose: false
-
-# Version of `showyourwork` used to create this workflow
 version: 0.4.4.dev54+g2662d4d
+

src/scripts/test_figure.py

@@ -0,0 +1,64 @@
+
+import matplotlib.pyplot as plt
+import numpy as np
+import json
+import paths
+
+# Set up the figure
+fig = plt.figure(figsize=(7, 6))
+ax = fig.subplot_mosaic(
+    '''
+    AB
+    CC
+    '''
+)
+fig.subplots_adjust(wspace=0.1, hspace=0.15)
+
+# Images
+for n, dataset in zip(["A", "B"], ["S06", "S07"]):
+    with open(paths.data / "TOI640" / f"{dataset}.json", "r") as f:
+        image_data = json.load(f)
+    aperture = np.array(image_data["aperture"])
+    image = np.array(image_data["image"]) / 1e3
+    im = ax[n].imshow(image, origin="lower", vmin=0, vmax=4)
+    ax[n].set_xticks([])
+    ax[n].set_yticks([])
+    ax[n].set_title(dataset)
+    ax[n].set_aspect("auto")
+fig.colorbar(im, ax=[ax["A"], ax["B"]], shrink=1, label="flux [ke$^-$/s]")
+
+# Dummy colorbar to get the spacing right
+cbar = fig.colorbar(im, ax=ax["C"], shrink=1)
+cbar.ax.set_visible(False)
+
+# Load planet data
+with open(paths.data / "TOI640" / "planet.json", "r") as f:
+    planet_data = json.load(f)
+phase = planet_data["phase"]
+period = planet_data["period"]
+
+# Photometry
+for dataset in ["S06", "S07"]:
+
+    # Load the data
+    time, flux, *_ = np.loadtxt(paths.data / "TOI640" / f"{dataset}.txt").T
+
+    # Divide out the rolling 1-day median baseline
+    dt = np.median(np.diff(time))
+    w = int(1 / dt)
+    baseline = [np.median(flux[a : a + w]) for a in range(len(flux))]
+    flux /= baseline
+
+    # Fold the data
+    time = (time % period) / period + phase
+
+    # Plot it
+    ax["C"].plot(time, flux, ".", label=dataset)
+
+# Format the figure
+ax["C"].legend()
+ax["C"].set_xlim(-0.1, 0.1)
+ax["C"].set_xlabel("orbital phase")
+ax["C"].set_ylabel("normalized flux")
+fig.savefig(paths.figures / "test_figure.pdf", bbox_inches="tight", dpi=300)
+

src/tex/ms.tex

@@ -54,4 +54,14 @@ \section{Introduction}
 
 \bibliography{bib}
 
+\begin{figure}[ht!]
+\script{test_figure.py}
+\begin{centering}
+\includegraphics[width=\linewidth]{figures/test_figure.pdf}
+\caption{A test figure.}
+\label{fig:test_figure}
+\end{centering}
+\end{figure}
+
 \end{document}
+