pdf to svg, pptx to pdf, and timing fixes by rebeccamccabe · Pull Request #133 · symbiotic-engineering/MDOcean

rebeccamccabe · 2025-12-19T18:35:49Z

No description provided.

…n into ezra-slides

Copilot

Pull request overview

Adds a small Python-based conversion toolchain to the publications workflow (PPTX→PDF and PDF→SVG) and wires it into the Calkit/DVC pipeline so the Ezra seminar slides and derived figure assets can be built reproducibly.

Changes:

Add py-convert Calkit environment plus dependency specs/lock for conversion utilities.
Introduce pptx_to_pdf.py and pdf_to_svg.py scripts and new pipeline stages to generate PDFs/SVGs for pubs/ezra_seminar_slides/.
Add DVC tracking/ignores for the seminar PPTX and generated SVG outputs.

Reviewed changes

Copilot reviewed 9 out of 11 changed files in this pull request and generated 11 comments.

Show a summary per file

File	Description
requirements.txt	Defines pip requirements for the new `py-convert` environment.
pubs/pptx_to_pdf.py	Adds a CLI script to convert a slides directory from PPTX to PDF.
mdocean/plots/util/pdf_to_svg.py	Adds a CLI script to convert PDFs in a folder to SVGs.
calkit.yaml	Adds `py-convert` env, new conversion stages, and registers the generated seminar PDF as a publication.
dvc.yaml	Adds DVC stages for the conversion steps.
.calkit/env-locks/py-convert.txt	Locks Python dependencies for the conversion environment.
environment.yml	Adds a conda environment definition for conversion dependencies.
pubs/ezra_seminar_slides/.gitignore	Ignores the DVC-tracked PPTX in Git.
pubs/ezra_seminar_slides/figs/.gitignore	Ignores generated SVG outputs in Git.
pubs/ezra_seminar_slides/ezra_emerging_scholar_seminar.pptx.dvc	Adds DVC metadata to track the seminar PPTX artifact.

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Copilot · 2026-04-27T05:05:11Z

        - path: pubs/renewable-energy-mdo/mdocean.synctex.gz
-          storage: null
+          storage:
        - path: pubs/renewable-energy-mdo/aux/
-          storage: null
+          storage:


These storage: keys have empty values. Elsewhere in this file, storage: null is used explicitly; leaving the value blank can be confusing and may be treated differently by some tooling/formatters. Consider reverting to storage: null (or an explicit storage value) for consistency.

Copilot · 2026-04-27T05:05:12Z

+  - path: pubs/ezra_seminar_slides/ezra_emerging_scholar_seminar.pdf
+    kind: presentation
+    title: Ezra emerging scholar seminar
+    description: Slides for the Cornell systems engineering Erza 


Typo in the publication description: "Erza" should be "Ezra".

Suggested change

description: Slides for the Cornell systems engineering Erza

description: Slides for the Cornell systems engineering Ezra

Copilot · 2026-04-27T05:05:12Z

+        file_out = folder_out + os.path.splitext(base)[0]
+        with open(file_out + ".svg", "w", encoding="utf-8") as f:


Output path concatenation assumes folder_out ends with a path separator (file_out = folder_out + ...). Use os.path.join(folder_out, stem) / pathlib so the output path is correct regardless of whether folder_out ends with /.

Suggested change

file_out = folder_out + os.path.splitext(base)[0]

with open(file_out + ".svg", "w", encoding="utf-8") as f:

stem = os.path.splitext(base)[0]

file_out = os.path.join(folder_out, stem + ".svg")

with open(file_out, "w", encoding="utf-8") as f:

Copilot · 2026-04-27T05:05:12Z

+args = sys.argv[1:]
+pdf_to_svg(args[0],args[1])


This CLI entrypoint uses args[0]/args[1] without validating argument count, which will raise IndexError on misuse. Add argument validation (and ideally an if __name__ == "__main__": guard) so importing this module doesn’t execute conversion as a side effect.

Suggested change

args = sys.argv[1:]

pdf_to_svg(args[0],args[1])

if __name__ == "__main__":

args = sys.argv[1:]

if len(args) != 2:

print(

"Usage: python mdocean/plots/util/pdf_to_svg.py <input_pdf_folder/> <output_svg_folder/>",

file=sys.stderr,

)

sys.exit(1)

pdf_to_svg(args[0], args[1])

Copilot · 2026-04-27T05:05:12Z

+name: mdocean-py-convert
+channels:
+  - conda-forge
+dependencies:
+  - pip
+  - pip:
+      - pptxtopdf
+      - pymupdf


This conda environment file appears to be unused in the repo (the new py-convert Calkit environment points at requirements.txt and no references to environment.yml were found). Consider removing it to avoid confusion, or wire it into the pipeline/docs if it’s intended to be supported.

Copilot · 2026-04-27T05:05:13Z

+      args: [pubs/ezra_seminar_slides/figs/pdf/ 
+            pubs/ezra_seminar_slides/figs/svg/]


args is written as a flow-style YAML list but is missing a comma separator between the two paths, which will make calkit.yaml fail to parse. Use a comma-separated flow list or switch to block list syntax (- ...).

Suggested change

args: [pubs/ezra_seminar_slides/figs/pdf/

pubs/ezra_seminar_slides/figs/svg/]

args:

- pubs/ezra_seminar_slides/figs/pdf/

- pubs/ezra_seminar_slides/figs/svg/

Copilot · 2026-04-27T05:05:13Z

+      - mdocean/plots/util/pdf_to_svg.py
+      - pubs/ezra_seminar_slides/figs/pdf/
+      - .calkit/env-locks/py-convert


dvc.yaml depends on .calkit/env-locks/py-convert, but the lock file added in this PR is .calkit/env-locks/py-convert.txt. As-is, dvc repro will treat the dependency path as missing. Update this dependency to point at the actual lock file (or rename the lock file to match the expected path).

Copilot · 2026-04-27T05:05:13Z

+      - pubs/ezra_seminar_slides/ezra_emerging_scholar_seminar.pptx
+      - pubs/ezra_seminar_slides/figs/
+      - .calkit/env-locks/py-convert


dvc.yaml depends on .calkit/env-locks/py-convert, but the lock file added in this PR is .calkit/env-locks/py-convert.txt. As-is, dvc repro will treat the dependency path as missing. Update this dependency to point at the actual lock file (or rename the lock file to match the expected path).

Copilot · 2026-04-27T05:05:14Z

+args = sys.argv[1]
+convert(args, args)


This script assumes at least one CLI argument (sys.argv[1]) and will raise IndexError if called without it. Add a small --help/usage message and validate argument count before calling convert (ideally under an if __name__ == "__main__": guard).

Suggested change

args = sys.argv[1]

convert(args, args)

def main():

if len(sys.argv) != 2 or sys.argv[1] in ("-h", "--help"):

print("Usage: python pubs/pptx_to_pdf.py <input_path>")

return 0 if len(sys.argv) == 2 and sys.argv[1] in ("-h", "--help") else 1

args = sys.argv[1]

convert(args, args)

return 0

if __name__ == "__main__":

sys.exit(main())

Copilot · 2026-04-27T05:05:14Z

+def pdf_to_svg(folder_in,folder_out):
+    files_in = glob.glob(folder_in + '*.pdf')
+    for file in files_in:


Path handling here relies on folder_in ending with a path separator (glob(folder_in + "*.pdf")). Use os.path.join(folder_in, "*.pdf") (or pathlib.Path(folder_in).glob("*.pdf")) to avoid silently producing no matches when the caller passes a path without a trailing /.

review-notebook-app · 2026-04-27T05:46:02Z

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rebeccamccabe and others added 11 commits December 3, 2025 04:44

create blank ezra slides and calkit pub for them

72f6ee3

line ending rebuild index

2987728

add pdf to svg script and insert link to svg in ppt

13907ef

calkit python stages

363aae9

Add uv venv py-convert

b212b91

adjust pdf_to_svg to convert all pdfs in folder; run pipeline

c0ebb6a

update useage comment for pdf_to_svg.py

f166116

fix env lock slash direction

87b74f8

replace profile with timeit for benchmarking

6e60585

Merge branch 'ezra-slides' of github.com:symbiotic-engineering/MDOcea…

fea7785

…n into ezra-slides

Merge remote-tracking branch 'origin/main' into ezra-slides

06d70b4

Copilot AI review requested due to automatic review settings April 27, 2026 04:59

Copilot started reviewing on behalf of rebeccamccabe April 27, 2026 05:00 View session

Copilot AI reviewed Apr 27, 2026

View reviewed changes

rebeccamccabe and others added 3 commits April 27, 2026 01:06

combine py-convert and pubs python environments

903dab9

add ezra slides as calkit target

78f5ea5

Run pipeline

42491f9

Provide feedback

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pdf to svg, pptx to pdf, and timing fixes#133

pdf to svg, pptx to pdf, and timing fixes#133
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	description: Slides for the Cornell systems engineering Erza
	description: Slides for the Cornell systems engineering Ezra

		file_out = folder_out + os.path.splitext(base)[0]
		with open(file_out + ".svg", "w", encoding="utf-8") as f:

-        file_out = folder_out + os.path.splitext(base)[0]
-        with open(file_out + ".svg", "w", encoding="utf-8") as f:
+        stem = os.path.splitext(base)[0]
+        file_out = os.path.join(folder_out, stem + ".svg")
+        with open(file_out, "w", encoding="utf-8") as f:

		args = sys.argv[1:]
		pdf_to_svg(args[0],args[1]) No newline at end of file

-args = sys.argv[1:]
-pdf_to_svg(args[0],args[1])
+if __name__ == "__main__":
+    args = sys.argv[1:]
+    if len(args) != 2:
+        print(
+            "Usage: python mdocean/plots/util/pdf_to_svg.py <input_pdf_folder/> <output_svg_folder/>",
+            file=sys.stderr,
+        )
+        sys.exit(1)
+    pdf_to_svg(args[0], args[1])

		args: [pubs/ezra_seminar_slides/figs/pdf/
		pubs/ezra_seminar_slides/figs/svg/]

-args = sys.argv[1]
-convert(args, args)
+def main():
+    if len(sys.argv) != 2 or sys.argv[1] in ("-h", "--help"):
+        print("Usage: python pubs/pptx_to_pdf.py <input_path>")
+        return 0 if len(sys.argv) == 2 and sys.argv[1] in ("-h", "--help") else 1
+    args = sys.argv[1]
+    convert(args, args)
+    return 0
+if __name__ == "__main__":
+    sys.exit(main())

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