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Windows Compatibility #1296

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neuromusic opened this issue May 3, 2019 · 1 comment
Closed

Windows Compatibility #1296

neuromusic opened this issue May 3, 2019 · 1 comment
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0.2.0

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@neuromusic
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neuromusic commented May 3, 2019 •
edited by ambrosejcarr
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Objective:

I can't be a user of starfish unless it supports my operating system

ACs:

  • Starfish CI runs on windows

Validation

  • Our windows users tell us they have successfully run starfish on their machines.

Notes

  • The primary operating system of more than half our users is windows.
  • We have WSL support.
  • Some of our users have windows machines that are too old for WSL.
@neuromusic neuromusic added the Epic label May 3, 2019
@shanaxel42 shanaxel42 changed the title Starfish supports Windows, Linux, and OSX, and can be installed through pip or conda Windows Compatibility May 7, 2019
@shanaxel42 shanaxel42 added this to the 0.2.0 milestone May 7, 2019
@neuromusic
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neuromusic commented Jul 13, 2019 •
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If we decide to support Windows, need to...

@ttung ttung mentioned this issue Aug 22, 2019
Merged
ttung pushed a commit that referenced this issue Aug 23, 2019
Bump slicedimage to 4.0.2
02eb143 
Part of #1296
ttung pushed a commit that referenced this issue Aug 26, 2019
Bump slicedimage to 4.0.2 (#1503)
a4c891a 
Part of #1296
ttung pushed a commit to spacetx/slicedimage that referenced this issue Aug 27, 2019
Change 0.0.0.0 to 127.0.0.1
8ec312d 
Windows does not like binding to 0.0.0.0 (all interfaces on POSIX systems).  Bind to 127.0.0.1, which works.

Test plan: pass on Windows.
Part of spacetx/starfish#1296
This was referenced Aug 27, 2019
Merged
Merged
Merged
ttung pushed a commit to spacetx/slicedimage that referenced this issue Aug 27, 2019
[easy] Reverse context unwind
7aab990 
We have a mechanism for tracking multiple context managers for unit test setup and teardown.  For unwinding them context managers, we should unwind them in the reverse order they are created.

On POSIX systems, this does not matter, as we can hold file handles to files that are deleted.  However, on Windows, the ordering is critical as one cannot delete files that are still held open.

In the case where we create a temporary directory, and then spin up a http server to listen to requests at that directory, we need to kill the process _before_ we clean up the temporary directory.

Test plan: works on windows
Part of spacetx/starfish#1296
@ttung ttung mentioned this issue Aug 27, 2019
Merged
ttung pushed a commit to spacetx/slicedimage that referenced this issue Aug 27, 2019
[easy] disable reentrant tests
bd3671a 
It's not possible on Windows, with standard filesystem calls, to open the same file twice.  Reentrant tests on the disk backend requires that behavior, so this disables the test on Windows.

Test plan: Windows!
Part of spacetx/starfish#1296
ttung pushed a commit to spacetx/slicedimage that referenced this issue Aug 27, 2019
[easy] disable reentrant tests
9dcfe7b 
It's not possible on Windows, with standard filesystem calls, to open the same file twice.  Reentrant tests on the disk backend requires that behavior, so this disables the test on Windows.

Test plan: Windows!
Part of spacetx/starfish#1296
This was referenced Aug 27, 2019
Merged
Merged
ttung pushed a commit to spacetx/slicedimage that referenced this issue Aug 29, 2019
[easy] Reverse context unwind (#119)
357abf1 
We have a mechanism for tracking multiple context managers for unit test setup and teardown.  For unwinding them context managers, we should unwind them in the reverse order they are created.

On POSIX systems, this does not matter, as we can hold file handles to files that are deleted.  However, on Windows, the ordering is critical as one cannot delete files that are still held open.

In the case where we create a temporary directory, and then spin up a http server to listen to requests at that directory, we need to kill the process _before_ we clean up the temporary directory.

Test plan: works on windows
Part of spacetx/starfish#1296
ttung pushed a commit to spacetx/slicedimage that referenced this issue Aug 29, 2019
[easy] disable reentrant tests (#120)
db53dfd 
It's not possible on Windows, with standard filesystem calls, to open the same file twice.  Reentrant tests on the disk backend requires that behavior, so this disables the test on Windows.

Test plan: Windows!
Part of spacetx/starfish#1296
ttung pushed a commit to spacetx/slicedimage that referenced this issue Aug 29, 2019
Change 0.0.0.0 to 127.0.0.1 (#115)
810cee7 
Windows does not like binding to 0.0.0.0 (all interfaces on POSIX systems).  Bind to 127.0.0.1, which works.

Test plan: pass on Windows.
Part of spacetx/starfish#1296
ttung pushed a commit to spacetx/slicedimage that referenced this issue Aug 29, 2019
Clean up our usage of DiskCache (#121)
32a55c6 
In our caching tests, we create a temporary directory, and then initialize a cache in that temporary directory.  The issue is that the cache handle holds an open file handle, and on Windows, the cleanup of the temporary directory fails if the cache handle still exists.

The fix is to add a context manager to remove the cache handle.

Test plan: works on windows
Part of spacetx/starfish#1296
ttung pushed a commit to spacetx/slicedimage that referenced this issue Aug 30, 2019
Eliminate string construction of file:// urls. (#117)
4e78b5f 
Use Pathlib's `as_uri()` method, which is cross-platform.

Test plan: `make test`
Part of spacetx/starfish#1296
ttung pushed a commit to spacetx/slicedimage that referenced this issue Aug 30, 2019
Close files before using them in tests (#118)
a0e207d 
It's not possible, using python stdlib, to open a file in Windows for write and read simultaneously.  A common idiom in the test code is to set up a temporary file using `with tempfile.NamedTemporaryFile()`, write some content to it, and then switch to the test code, and then cleaning up the temp file when the `with` statement goes out of scope.

This is incompatible with Windows, so we instead just create the temporary file, write out the necessary contents, and then close it (and not delete it).  We rely on the temporary directory cleanup to ensure that the files eventually get cleaned up.

On the */test_disk_backend.py, we were not using a temporary directory, so we add that.

Test plan: works on windows
Part of spacetx/starfish#1296
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