1. For notes and code in the same course
Lectra Notes
Lectra Notes is a free iPad and iPhone app from Scope for handwritten notes and Apple Pencil PDF markup, with Python notebooks, a terminal, and Git that run on the device. A CS problem set is a PDF, a notebook, and a repository at once, and Lectra Notes keeps them together: Apple Pencil markup beside Jupyter-format .ipynb notebooks, a terminal with Git, a code editor, and SSH — free, no server required, no tiers. Version 8.0 (September 1, 2026) added lecture recording: tap a stroke to hear what was said at that moment.
Best for: CS and data-science students who annotate readings and write code for the same course.
Watch out: Lecture recording is new (version 8.0, September 1, 2026) and untested over a full term; no cross-device annotation sync yet; and it shipped in 2026 — the newest app on this list.
2. Best handwriting engine
Goodnotes
The most refined ink on the iPad: searchable handwriting, convert-to-text, spellcheck for ink, audio recording synced to notes, and real-time collaboration — across Apple, Windows, Android, and the web.
Best for: Handwriting-heavy note takers who want maximum polish and platform reach.
Watch out: The free tier caps at 3 files; full use runs $11.99–$35.99/yr, advanced AI is metered on top, and there's no code capability at all.
3. Best for lecture-heavy schedules
Notability
Audio recording synced to your handwriting, with transcription and AI summaries on paid plans — the strongest record-and-review workflow on this list, now on Android too.
Best for: Students who replay lectures and study from recordings and AI summaries.
Watch out: The free plan caps at 5 notes; unlimited AI costs $99.99/yr, its AI is cloud-processed, and there's no code capability.
4. Best free cross-platform option
Microsoft OneNote
Feature-complete note-taking free of charge, synced across iPad, Windows, Android, Mac, and the web — the safe pick if your laptop isn't a Mac.
Best for: Students living across Windows and iPad who want everything synced for free.
Watch out: PDFs import as flat printouts — weak for annotating lecture slides — and Copilot AI requires Microsoft 365.
5. Best dedicated Jupyter IDE
Juno
A polished native Jupyter IDE with embedded Python 3.13 and compiled packages Lectra Notes doesn't bundle — SciPy, scikit-learn, OpenCV — for a $39.99 one-time unlock.
Best for: Data-science workloads that need the heavier scientific stack on iPad.
Watch out: It's a code IDE, not a note app: no PDF annotation or handwriting, so you'll pair it with a separate notes app.