Fix race condition

[EmilyBourne]

The race condition is occurring on Macosx because Pyccel occasionally thinks that the source files in the stdlib folder have been modified. This then creates the following series of concurrent events:

Thread 1	Thread 2
Starts compilation process	Still translating
Acquires ndarrays folder lock	Still translating
Checks ndarrays folder	Starts compilation process
All ok	Fails to acquire ndarrays folder lock. Waiting
Releases ndarrays folder lock	Waiting
Acquires locks to compile ndarrays.o (ndarrays.o.lock)	Acquires ndarrays folder lock
Compilation in progress	Reads contents of ndarrays folder (may see ndarrays.o.tmp file created by compilation)
Finished compilation. Released locks	Checks access dates for __pyccel__/ndarrays folder and stdlib/ndarrays folder. Incorrectly determines folder needs updating
Prints wrapper file	Acquires locks to copy ndarrays folder (ndarrays.h.lock, ndarrays.c.lock, ndarrays.o.lock)
Attempts to acquire locks to compile wrapper (including dependencies: ndarrays.o, (ndarrays.h, ndarrays.c)	deletes all files in ndarrays folder
Waiting	Copies ndarrays folder contents back (only ndarrays.h, ndarrays.c)
Waiting	Releases ndarrays locks
Acquires locks	Starts to check if compilation of ndarrays is necessary
Tries to compile generated file but ndarrays.o is missing	Tries to acquire ndarrys.c.lock

The error is therefore not due to a race condition where 2 threads try to do the same thing, but rather due to a bad update condition. I think this is because we are checking when the files were accessed rather than when they were modified.

Additionally the compilation of ndarrays.o does not lock ndarrays.c. This is corrected in this PR but is not strictly necessary as the ndarrays.o.lock is always acquired if ndarrays.c.lock is acquired.

Commit Summary

• Make CompileObj a context manager (with methods __enter__ and __exit__)
• Use with compile_obj: constructs to handle locks more compactly
• Ensure the source file is locked during compilation
• Check the modification time not the access time to decide whether a file should be updated
• Don't raise an error if temporary files are found in a folder being updated
• Add detailed flags which are activated when the tests are rerun with debug logging
  
• Improve the definition of the min/max bounds on a test that failed. The logic now only needs touching in a single place if the bounds need narrowing

Testing
It is quite difficult to test this kind of error, however I have run the full suite of tests with assert False in the code which updates the std libraries and macosx no longer seems to go into this section of the code. (Linux triggers the assertion in the test designed to test this mechanism)

[github-actions]

Hello again! Thank you for this new pull request 🤩.

Don't forget to let me know when it is complete with the command /bot mark as ready.

Here is your checklist:

• Write a clear PR description
• Add tests to check your code works as expected
• Update documentation if necessary
• Update Changelog
• Ensure any relevant issues are linked
• Ensure new tests are passing

[github-actions]

Ran tests on commit 0e78192, for more details see here

• ❌ docs / Documentation Format
• 🚫 macosx / Unit tests
• 🚫 linux / Unit tests
• 🚫 windows / Unit tests
• 🚫 lint / Best practices
• ❌ spelling / Documentation spellcheck
• ✔️ pylint / Python best practices
• 🚫 coverage

[github-actions]

Unfortunately your PR is not passing the tests so it is not quite ready for review yet. Let me know when it is fixed with /bot mark as ready.

The failing tests are:

• docs / Documentation Format
• macosx / Unit tests
• linux / Unit tests
• windows / Unit tests
• lint / Best practices
• spelling / Documentation spellcheck
• coverage

[EmilyBourne]

/bot run spelling docs

[github-actions]

Ran tests on commit a893ebd, for more details see here

• ❌ docs / Documentation Format
• ✔️ spelling / Documentation spellcheck

[github-actions]

Ran tests on commit 9af773b, for more details see here

• ❌ docs / Documentation Format
• 🚫 macosx / Unit tests
• 🚫 linux / Unit tests
• ✔️ pylint / Python best practices
• 🚫 windows / Unit tests
• 🚫 lint / Best practices
• ✔️ spelling / Documentation spellcheck
• 🚫 coverage

[github-actions]

Unfortunately your PR is not passing the tests so it is not quite ready for review yet. Let me know when it is fixed with /bot mark as ready.

The failing tests are:

• docs / Documentation Format
• macosx / Unit tests
• linux / Unit tests
• windows / Unit tests
• lint / Best practices
• coverage

[github-actions]

Running tests on commit 03e00f9, for more details see here

• ⏳ pylint
• ⏳ coverage
• ⏳ docs
• ⏳ spelling
• ⏳ macosx
• ⏳ linux
• ⏳ windows
• ⏳ lint

[github-actions]

Ran tests on commit 03e00f9, for more details see here

• ✔️ docs / Documentation Format
• ✔️ linux / Unit tests
• ✔️ windows / Unit tests
• ✔️ pylint / Python best practices
• ✔️ macosx / Unit tests
• ✔️ lint / Best practices
• ✔️ spelling / Documentation spellcheck
• ❌ coverage / Unit tests

[github-actions]

Hey @pyccel/pyccel-dev ! @EmilyBourne has just created this great new pull request! Check it out and let me know what you think!

[EmilyBourne]

/bot run pr_tests

[github-actions]

Ran tests on commit fb3b1f4, for more details see here

• ✔️ windows / Unit tests
• ✔️ linux / Unit tests
• ✔️ docs / Documentation Format
• ✔️ macosx / Unit tests
• ✔️ lint / Best practices
• ✔️ spelling / Documentation spellcheck
• ✔️ pylint / Python best practices
• ❌ coverage / Unit tests

[yguclu]

I am so glad that you finally found the cause of the macOS failures!

The fix looks good and elegant to me. Great job!

I have a few minor comments.

[github-actions]

@EmilyBourne, @yguclu has a few questions/comments about your code. Can you go through and see if you agree with them. If not go ahead and explain why. Once you've adressed all the comments let me know with /bot mark as ready and we will see if we can get approval.

[EmilyBourne]

/bot run docs

[github-actions]

Ran tests on commit 892a6ad, for more details see here

• ✔️ docs / Documentation Format

[github-actions]

Ran tests on commit 892a6ad, for more details see here

• ✔️ linux / Unit tests
• ✔️ macosx / Unit tests
• ✔️ windows / Unit tests
• ✔️ docs / Documentation Format
• ✔️ lint / Best practices
• ✔️ spelling / Documentation spellcheck
• ✔️ pylint / Python best practices
• ❌ coverage / Unit tests