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Workspace Restructure (Math Foundations) - Phases 1 & 2#25

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AronT-TLV merged 9 commits into
mainfrom
refactor/contextual-copilot-instructions
May 31, 2026
Merged

Workspace Restructure (Math Foundations) - Phases 1 & 2#25
AronT-TLV merged 9 commits into
mainfrom
refactor/contextual-copilot-instructions

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@AronT-TLV AronT-TLV commented May 31, 2026 •
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Summary

Restructures Math_Foundations to use Julia 1.10+ workspace layout with separate test, docs, and notebook environments. Also upgrades CI actions and opts into Node.js 24.

Phase 1 — Dependency cleanup and workspace setup

  • Add [workspace] and [compat] sections to root Project.toml
  • Move test-only deps to test/Project.toml
  • Move docs-only deps to docs/Project.toml
  • Move notebook/visualization deps to notebooks/Project.toml
  • Remove DrWatson from test/runtests.jl and docs/make.jl
  • Update docs/make.jl to self-activate the docs environment
  • Ignore all Manifest.toml files via .gitignore

Phase 2 — CI workflow updates

  • Test job uses Pkg.instantiate() + Pkg.test() (workspace-aware)
  • Docs build and deploy jobs use --project=docs command path
  • Cache key tightened to workspace Project.toml files only

CI actions upgrade

  • Upgrade actions/checkout@v4 → @v5 in all three CI jobs (natively targets Node.js 24)
  • Remove FORCE_JAVASCRIPT_ACTIONS_TO_NODE24 env var (no longer needed)

Closes

Closes FOU-13, FOU-14, FOU-15, FOU-16, FOU-17, FOU-18, FOU-19, FOU-20, FOU-21, FOU-22, FOU-24, FOU-25, FOU-27, FOU-23, FOU-26, FOU-28, FOU-30, FOU-42

@AronT-TLV
refactor: split copilot-instructions into contextual instruction files
9b9bfdb 
Move domain-specific instructions into .github/instructions/ with applyTo
front matter so they load only when editing relevant files:

- docs.instructions.md (docs/**): LaTeX conventions, MathWorld links, doc structure
- testing.instructions.md (test/**): CI strategy, plotting patterns, test organization
- source.instructions.md (src/**): module structure, coding standards, function signatures, dependencies
- notebooks.instructions.md (notebooks/**): notebook setup and guidelines

Main copilot-instructions.md trimmed from 394 to 126 lines, keeping only
universal content: project overview, workflows, git/PR conventions,
communication patterns, Azure integration.
@AronT-TLV
align: synchronize instruction files with Linear_Algebra
5b188c2 
Add missing shared content to instruction files for cross-project consistency:

docs.instructions.md:
- Add extra bullet point examples for bullet point style (item 1)
- Add MathJax3 Configuration section (item 2)
- Add 'follow existing pattern' line (item 3)
- Add Cross-Document Section Links section (item 4)
- Add project-specific grouping example (item 7)

testing.instructions.md:
- Add CI-Compatible Plotting with ENV detection pattern (item 8)
- Add smarter catch block with rethrow for non-plotting errors (item 9)
- Add atol=1e-10 numerical precision guidance (item 10)

source.instructions.md:
- Add Documentation & Comments subsection (item 15)
- Add Code Organization subsection (item 16)
@AronT-TLV
docs: add instruction to notify user when files cannot be read
2f79abc
@AronT-TLV
docs: add Julia kernel gotchas to notebooks instructions
368061f 
Add three Julia kernel gotchas learned while working on Linear_Algebra:
- Stale variable slot after failed assignment (restart kernel to fix)
- Building matrix from row vectors (use v' not v for stacking)
- Stale cell state from mutated variables across cells (re-run from top)
@AronT-TLV
Make manifests local-only and complete phase 1 setup
58b811c
@AronT-TLV
Update CI jobs for workspace-based phase 2 flow
9ae8918
@AronT-TLV
Resolve conflict: revert notebooks instructions to main; opt into Nod…
f1bb3ba 
…e.js 24 for Actions

- Revert .github/instructions/notebooks.instructions.md to main's version
  (draft content saved locally at _research/notebooks-instructions-draft.md
   for a dedicated instructions pass after merge)
- Add FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true workflow-level env var to address
  actions/checkout@v4 Node.js 20 deprecation before the June 16 2026 deadline
@AronT-TLV
Upgrade actions/checkout from v4 to v5; remove Node.js 24 env var bridge
111e92b 
- Replace actions/checkout@v4 with @v5 in all three CI jobs (test,
  docs-build, deploy-docs)
- Remove FORCE_JAVASCRIPT_ACTIONS_TO_NODE24 workflow-level env var
  (no longer needed since @v5 natively targets Node.js 24)

Closes FOU-42
@AronT-TLV
Upgrade remaining CI actions to Node.js 24 compatible versions
e0a0d3d 
- julia-actions/setup-julia@v1 → @V3 (v3 natively requires Node.js 24)
- julia-actions/cache@v1 → @V3 (pure JS rewrite; drops pyTooling composite
  dependency that was also flagged as Node.js 20)
- actions/cache@v4 → @v5 in deploy-docs explicit cache step

Closes FOU-42
@AronT-TLV AronT-TLV marked this pull request as ready for review May 31, 2026 12:22
@AronT-TLV AronT-TLV merged commit 4917850 into main May 31, 2026
5 checks passed
@AronT-TLV AronT-TLV deleted the refactor/contextual-copilot-instructions branch May 31, 2026 13:13
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