[showyourwork] first commit

.github/workflows/build-pull-request.yml

@@ -0,0 +1,25 @@
+name: build pull request
+
+on:
+  pull_request:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    name: Build the article PDF
+    concurrency: showyourwork-${{ github.ref }}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Build the article PDF
+        id: build
+        uses: showyourwork/showyourwork-action@v1
+        with:
+          showyourwork-spec: git+https://github.com/showyourwork/showyourwork.git@7fb81ba4571da2aa335efd48a3f97392ee508ee4#egg=showyourwork
+        env:
+          SANDBOX_TOKEN: ${{ secrets.SANDBOX_TOKEN }}
+          OVERLEAF_EMAIL: ${{ secrets.OVERLEAF_EMAIL }}
+          OVERLEAF_PASSWORD: ${{ secrets.OVERLEAF_PASSWORD }}

.github/workflows/build.yml

@@ -0,0 +1,25 @@
+name: build
+
+on:
+  push:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    name: Build the article PDF
+    concurrency: showyourwork-${{ github.ref }}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Build the article PDF
+        id: build
+        uses: showyourwork/showyourwork-action@v1
+        with:
+          showyourwork-spec: git+https://github.com/showyourwork/showyourwork.git@7fb81ba4571da2aa335efd48a3f97392ee508ee4#egg=showyourwork
+        env:
+          SANDBOX_TOKEN: ${{ secrets.SANDBOX_TOKEN }}
+          OVERLEAF_EMAIL: ${{ secrets.OVERLEAF_EMAIL }}
+          OVERLEAF_PASSWORD: ${{ secrets.OVERLEAF_PASSWORD }}

.github/workflows/process-pull-request.yml

@@ -0,0 +1,14 @@
+name: process pull request
+
+on:
+  workflow_run:
+    workflows: [build pull request]
+    types: [completed]
+
+jobs:
+  process-pr:
+    runs-on: ubuntu-latest
+    name: Process pull request
+    steps:
+      - name: Process pull request
+        uses: showyourwork/showyourwork-action/process-pull-request@v1

.gitignore

@@ -0,0 +1,15 @@
+# Snakemake and showyourwork temporaries
+**/.snakemake
+**/.showyourwork*
+
+# Showyourwork output files
+/*.pdf
+report.html
+arxiv.tar.gz
+
+# Figure output
+src/tex/figures/*
+
+# Miscellaneous
+__pycache__
+*.synctex.gz

.vscode/settings.json

@@ -0,0 +1,6 @@
+{
+    "latex-workshop.latex.external.build.command": "showyourwork",
+    "latex-workshop.latex.external.build.args": [],
+    "latex-workshop.view.pdf.viewer": "tab",
+    "latex-workshop.latex.outDir": "%WORKSPACE_FOLDER%"
+}

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2023 @showyourwork
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -0,0 +1,18 @@
+<p align="center">
+<a href="https://github.com/showyourwork/showyourwork">
+<img width = "450" src="https://raw.githubusercontent.com/showyourwork/.github/main/images/showyourwork.png" alt="showyourwork"/>
+</a>
+<br>
+<br>
+<a href="https://github.com/showyourwork/test-dir-cache/actions/workflows/build.yml">
+<img src="https://github.com/showyourwork/test-dir-cache/actions/workflows/build.yml/badge.svg?branch=main" alt="Article status"/>
+</a>
+<a href="https://github.com/showyourwork/test-dir-cache/raw/main-pdf/arxiv.tar.gz">
+<img src="https://img.shields.io/badge/article-tarball-blue.svg?style=flat" alt="Article tarball"/>
+</a>
+<a href="https://github.com/showyourwork/test-dir-cache/raw/main-pdf/ms.pdf">
+<img src="https://img.shields.io/badge/article-pdf-blue.svg?style=flat" alt="Read the article"/>
+</a>
+</p>
+
+An open source scientific article created using the [showyourwork](https://github.com/showyourwork/showyourwork) workflow.

environment.yml

@@ -0,0 +1,6 @@
+dependencies:
+  - conda-forge::numpy=1.19.2
+  - conda-forge::pip=21.0.1
+  - conda-forge::python=3.9
+  - pip:
+      - matplotlib==3.4.3

showyourwork.yml

@@ -0,0 +1,99 @@
+# 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
+  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
+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
+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
+  pull:
+    - src/tex/ms.tex
+    - src/tex/bib.bib
+
+# Always require all input files to be present on disk for workflow to pass?
+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
+  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
+tectonic_args: []
+
+# Enable verbose output?
+verbose: false
+
+# Version of `showyourwork` used to create this workflow
+version: 0.4.3rc3.dev16+g7fb81ba

src/data/.gitignore

@@ -0,0 +1,3 @@
+# Nothing in this folder should be tracked by git
+*
+!.gitignore

src/scripts/.gitignore

@@ -0,0 +1,9 @@
+# Don't track figure output
+*.pdf
+*.eps
+*.png
+*.jpeg
+*.jpg
+*.tiff
+*.gif
+*.svg

src/scripts/matplotlibrc

@@ -0,0 +1,2 @@
+# Enforce a non-interactive backend
+backend: agg

src/scripts/paths.py

@@ -0,0 +1,29 @@
+"""
+Exposes common paths useful for manipulating datasets and generating figures.
+
+"""
+from pathlib import Path
+
+# Absolute path to the top level of the repository
+root = Path(__file__).resolve().parents[2].absolute()
+
+# Absolute path to the `src` folder
+src = root / "src"
+
+# Absolute path to the `src/data` folder (contains datasets)
+data = src / "data"
+
+# Absolute path to the `src/static` folder (contains static images)
+static = src / "static"
+
+# Absolute path to the `src/scripts` folder (contains figure/pipeline scripts)
+scripts = src / "scripts"
+
+# Absolute path to the `src/tex` folder (contains the manuscript)
+tex = src / "tex"
+
+# Absolute path to the `src/tex/figures` folder (contains figure output)
+figures = tex / "figures"
+
+# Absolute path to the `src/tex/output` folder (contains other user-defined output)
+output = tex / "output"

src/static/.gitignore

@@ -0,0 +1,2 @@
+# Anything is game in this folder
+!*

src/tex/.gitignore

@@ -0,0 +1,2 @@
+# Don't track TeX temporaries
+*latexindent*