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Set up Cursor Cloud dev environment (Julia) + AGENTS.md - #5
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Co-authored-by: Demetrios Chiuratto Agourakis <demetrios@agourakis.med.br>
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Summary
Sets up the development environment for the Darwin Operator Symmetry Atlas (DOSA) so the Julia package (Layers 0+1) can be tested, built, and run. Adds
AGENTS.mdwith Cursor Cloud–specific instructions. No existing code is modified.Environment
juliaup(~/.juliaup/bin, onPATHin all shell types).julia --project=julia -e 'using Pkg; Pkg.instantiate(); Pkg.precompile()'.demetrios/kernels need thedc/souccompiler (not installed); relatedmaketargets already no-op gracefully. No Python is used.Verification
julia --project=julia -e 'using Pkg; Pkg.instantiate(); Pkg.precompile()'— 73 deps precompiled.make test-julia— 38/38 tests pass.julia --project=julia julia/scripts/run_pipeline.jl --skip-download— technical validation PASSED, tables generated.verified_double_cover/double_cover_verifiedtrue.The hello-world run exercises the core science (operators, exact/approx symmetry, quaternion double-cover, CSV table generation):
dosa_pipeline_run.log
Notes
make pipeline/fetch_ncbidownloads from NCBI; the assembly-summary fetch works but some sampled genome FASTA URLs return NCBI HTML error pages (logged + skipped, no crash). Network and core science are otherwise fully functional.To show artifacts inline, enable in settings.