auto commit from showyourwork tests

README.md

@@ -15,4 +15,10 @@
 </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_cache.py](https://github.com/showyourwork/showyourwork/blob/main/tests/integration/test_cache.py).*
+
+
+Test the Zenodo Sandbox caching feature for a rule that outputs an
+entire directory.
+
+

Snakefile

@@ -0,0 +1,10 @@
+
+
+
+rule generate_data:
+    output:
+        directory('src/data/test_data')
+    cache:
+        True
+    script:
+        'src/scripts/test_data.py'

showyourwork.yml

@@ -1,105 +1,44 @@
-# 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
-datasets:
-  # 10.5281/zenodo.6468327:
-  #   contents:
-  #     TOI640b.json: src/data/TOI640b.json
-
-# Custom file dependencies
+    penwidth: '2'
+    shape: box
+    width: '1'
+  render: false
+datasets: null
 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/test_data
 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.dev12+gbe241a0
+

src/scripts/test_data.py

@@ -0,0 +1,11 @@
+import numpy as np
+import paths
+import os
+if os.getenv('CI', 'false') == 'true' or os.getenv('SYW_NO_RUN', 'false') == 'true':
+    raise Exception('Output should have been downloaded from Zenodo.')
+np.random.seed(0)
+(paths.data / 'test_data').mkdir(exist_ok=True)
+for n in range(50):
+    np.random.seed(n)
+    data = np.random.randn(100)
+    np.savez(paths.data / 'test_data' / f'test_data{n:02d}.npz', data=data)

src/scripts/test_figure.py

@@ -0,0 +1,8 @@
+import matplotlib.pyplot as plt
+import numpy as np
+import paths
+np.random.seed(0)
+data = np.array([np.load(paths.data / 'test_data' / f'test_data{n:02d}.npz')['data'] for n in range(50)])
+fig = plt.figure(figsize=(7, 6))
+plt.plot(data)
+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}
+