Fix: undefined behavior in C++ implementation (Issue #236)

[GaneshPatil7517]

Summary

Fixes critical undefined behavior and cross-platform compatibility issues in concore.hpp as reported in Issue #236.

Changes

Bug A — Destructor UB (CRITICAL)

• Initialized shmId_create and shmId_get to -1
• Initialized sharedData_create and sharedData_get to nullptr
• Added guards in destructor to prevent calling shmdt()/shmctl() on uninitialized pointers

Bug B — POSIX-only headers

• Wrapped <sys/ipc.h>, <sys/shm.h>, <unistd.h> with #ifdef __linux__
• Guarded shared memory logic to allow Windows compilation

Bug C — mapParser() crash on empty port file

• Added early return if portstr is empty to prevent index -1 access

Bug D — Empty map iterator dereference

• Added !iport.empty() and !oport.empty() guards before accessing begin()

Bug E — Infinite loop in read_FM(), read_SM(), getSharedMemory()

• Added MAX_RETRY = 100 limit to all retry loops

Testing

• Verified no compile errors on Windows
• Linux shared memory functionality preserved
• File-based communication unaffected

Closes #236

[pradeeban]

@GaneshPatil7517 Please pay extra-attention when you create a PR. We need to test and create PRs against the dev branch. That way, your effort is not wasted (and also avoids the risk of the PR being mistakenly merged into the main branch).

[GaneshPatil7517]

hey @pradeeban i immedatly switched to dev branch......

[Copilot]

Pull request overview

This PR addresses correctness and portability issues in the core concore runtimes (notably the C++ shared-memory implementation), while also introducing a new Python CLI + packaging/CI/test scaffolding and migrating many scripts from print() to logging.

Changes:

• Fixes multiple undefined-behavior and infinite-loop risks in concore.hpp (Linux shared-memory guarded, destructor safety, retry limits, empty-file guards).
• Adds a new concore CLI (init/run/validate/inspect/status/stop) with packaging metadata and GitHub Actions CI/tests.
• Updates Python/Docker runtimes and several tools/ scripts (logging, parameter parsing, ZMQ support, test coverage).

Reviewed changes

Copilot reviewed 1 out of 1 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
tools/shannon.py	Replace print() with logging calls.
tools/pwrap.py	Replace print() with logging calls (includes request-loop diagnostics).
tools/plotymlag.py	Replace print() with logging calls.
tools/plotym.py	Replace print() with logging calls.
tools/plotu.py	Replace print() with logging calls.
tools/pidsig.py	Replace print() with logging calls for errors/info.
tools/pidmayuresh.py	Replace print() with logging calls.
tools/pid2.py	Replace print() with logging calls.
tools/learn.py	Replace print() with logging calls.
tools/cwrap.py	Replace print() with logging calls + minor URL logging formatting.
tools/cardiac_pm.py	Replace print() with logging calls + startup log.
tools/bangbang.py	Replace print() with logging calls + startup log.
tests/test_graph.py	Adds CLI validation tests for GraphML workflows.
tests/test_concoredocker.py	Adds tests for concoredocker.py I/O helpers and semantics.
tests/test_concore.py	Adds tests for concore.py helpers and param parsing.
tests/test_cli.py	Adds CLI smoke tests for init/run/validate/status.
tests/conftest.py	Adds pytest temp-dir fixture + path setup for tests.
tests/init.py	Marks tests as a package (empty).
startserver.bat	Adds Windows helper to start fri/server.
startserver	Adds POSIX helper to start fri/server.
setup.py	Adds setuptools packaging for CLI distribution.
requirements.txt	Adds CLI/runtime deps (e.g., pyzmq, click, rich, psutil).
requirements-dev.txt	Adds pytest tooling for development.
requirements-ci.txt	Adds minimal dependency set for CI.
pytest.ini	Adds pytest discovery/config defaults.
pyproject.toml	Adds PEP 517/518 + project metadata and console script entry point.
mkconcore.py	Adds input validation, safer file handling, and shell escaping in generated scripts.
contribute.py	Removes hardcoded token; uses env var for GitHub auth.
concoredocker.py	Adds logging, ZMQ support, param parsing, numpy conversion, and retry limits.
concoredocker.java	Expands Java runtime: parsing, retry limits, simtime double, Python-literal serialization.
concoredocker.hpp	Adds parsing helpers and simtime handling for Docker C++ runtime.
concore_read.m	Adds retry limit to prevent infinite loop on empty reads.
concore_cli/commands/validate.py	Implements workflow validation (XML/GraphML/node/edge checks).
concore_cli/commands/stop.py	Implements process stopping via psutil/taskkill/terminate.
concore_cli/commands/status.py	Implements process listing/status via psutil.
concore_cli/commands/run.py	Implements workflow generation and optional build execution.
concore_cli/commands/inspect.py	Adds workflow inspection (rich output + JSON output).
concore_cli/commands/init.py	Adds project scaffolding generation.
concore_cli/commands/init.py	Exposes command entry points.
concore_cli/cli.py	Adds Click-based CLI and command wiring.
concore_cli/init.py	Exposes CLI package entry.
concore_cli/README.md	Documents CLI usage and workflow format.
concore.py	Adds logging/ZMQ cleanup handling, param parsing, numpy conversion, and I/O changes.
concore.hpp	Fixes Linux shared-memory safety, retry limits, and empty-file guards.
TestLiteralEval.java	Adds standalone tests for the Java Python-literal parser.
README.md	Adds top-level CLI documentation section.
Dockerfile.java	Updates base image and adjusts jar copy logic.
.gitignore	Expands ignore rules for Python/IDE/testing artifacts.
.github/workflows/tests.yml	Adds Python test matrix workflow.
.github/workflows/ci.yml	Adds CI workflow (ruff + pytest + optional docker build).
.github/workflows/PR-review.yaml	Adds Gemini-based AI PR review workflow trigger.

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[pradeeban]

@GaneshPatil7517 yes, I noticed. It was one of those rarest moments when I am online and reviewing the PRs when someone is actively creating them! Good work.

[GaneshPatil7517]

@GaneshPatil7517 yes, I noticed. It was one of those rarest moments when I am online and reviewing the PRs when someone is actively creating them! Good work.

Thank you @pradeeban! It's my pleasure to contribute to this project.

I'm committed to staying consistent and would love to continue collaborating with you on future improvements. From now on, I'll try to be more active and available for reviews.
Previously I didn't know your timezone, so I was creating PRs based on Indian Standard Time (IST). If you could share your preferred timezone or review hours, I'll try to align my contributions accordingly for better collaboration.
Looking forward to working together!
lets Connect: https://www.linkedin.com/in/ganesh-patil-9b74bb30b/
Happy to connet with you.....

[pradeeban]

@GaneshPatil7517 my timezone is AKST. I work 6:15 am - 6:15 pm during Tues - Fri. I do not look at GitHub on Mondays usually and I do not work on weekends usually.

[pradeeban]

Most of our mentors are based in Alaska. Some in EST (Atlanta or Lehigh) and many others in IST (India). A few other locations too (UK for one).

[GaneshPatil7517]

@pradeeban yahh i see from today on wards ill come online at your time.....