JOSS manuscript second draft

paper/README.md

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+# $Y_0$ Manuscript
+
+This folder contains source material for a
+[Journal of Open Source Software](https://joss.theoj.org/) submission:
+
+1. [paper.md](paper.md): the main manuscript
+2. [paper.bib](paper.bib): BibTex citations for the manuscript
+
+Target submission date: June 20th, 2025.
+
+## TODO
+
+- mention HCM data structure from `[@weinstein2024hierarchicalcausalmodels]`,
+  _only after_ https://github.com/y0-causal-inference/y0/pull/236 is finished
+  and merged
+- @Jeremy reference other PNNL use cases (even if they're not published)
+- @Jeremy there's a note for you to fill in a sentence in the future work
+  paragraph
+- Get Richard and Pruthvi's ORCIDs
+
+## Linting
+
+The markdown files here are linted with:
+
+```shell
+npx prettier --prose-wrap always --check "**/*.md" --write
+```
+
+## Build
+
+Follow the instructions at
+https://joss.readthedocs.io/en/latest/submitting.html#docker:
+
+```shell
+sh build.sh
+```
+
+## Submission
+
+Follow the instructions at https://joss.theoj.org/papers/new.
+
+## Authorship Concept
+
+- All material contributors to the $Y_0$ package are eligible for authorship.
+- Lead authorship will be shared between Charles Tapley Hoyt and Jeremy Zucker
+- Remaining authors will be listed alphabetically by last name
+- JOSS's
+  [authorship policy](https://joss.readthedocs.io/en/latest/submitting.html#authorship)
+  states:
+
+  > Purely financial (such as being named on an award) and organizational (such
+  > as general supervision of a research group) contributions are not considered
+  > sufficient for co-authorship of JOSS submissions, but active project
+  > direction and other forms of non-code contributions are.
+
+## Extras
+
+Some references that didn't make it into the manuscript:
+
+- Good and bad controls [@cinelli2022crash] (could go in future work)

paper/build.sh

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+# old way
+# see https://joss.readthedocs.io/en/latest/submitting.html#docker
+# docker run --rm \
+#  --volume $PWD:/data \
+#  --user $(id -u):$(id -g) \
+#  --env JOURNAL=joss \
+#  openjournals/paperdraft
+
+# new way using `inara`, not documented by JOSS yet
+# see https://github.com/openjournals/inara/tree/main
+docker run --rm \
+  --volume $PWD:/data \
+  --user $(id -u):$(id -g) \
+  --env JOURNAL=joss \
+  openjournals/inara \
+  -o pdf,preprint \
+  paper.md
+
+latexmk -pdf paper.preprint.tex
+rm paper.preprint.aux
+rm paper.preprint.fdb_latexmk
+rm paper.preprint.fls
+rm paper.preprint.log
+rm paper.preprint.tex

paper/figures/figure_1.py

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+"""Generate Figure 1 for the JOSS manuscript."""
+
+import matplotlib.pyplot as plt
+
+from y0.dsl import Variable
+from y0.graph import NxMixedGraph
+
+Cancer = Variable("Cancer")
+Smoking = Variable("Smoking")
+Tar = Variable("Tar")
+
+layout = {
+    Smoking: [-5, 0],
+    Tar: [0, 0.5],
+    Cancer: [5, 0],
+}
+
+cancer_graph_initial = NxMixedGraph.from_edges(
+    directed=[(Smoking, Tar), (Tar, Cancer), (Smoking, Cancer)]
+)
+cancer_graph = NxMixedGraph.from_edges(
+    directed=[(Smoking, Tar), (Tar, Cancer), (Smoking, Cancer)], undirected=[(Smoking, Tar)]
+)
+
+fig, (lax, rax) = plt.subplots(1, 2, figsize=(10, 3))
+
+fontdict = {"fontsize": 20, "fontweight": "bold"}
+lax.text(-6.55, 0.56, "A", fontdict=fontdict)
+rax.text(-6.55, 0.56, "B", fontdict=fontdict)
+
+cancer_graph_initial.draw(ax=lax, layout=layout, font_size=15, node_size=5000)
+cancer_graph.draw(ax=rax, layout=layout, font_size=15, node_size=5000, radius=-0.7)
+
+fig.tight_layout(pad=0.0)
+fig.savefig("cancer_tar.pdf")