Add forestclaw IO option #547

mandli · 2016-11-06T01:18:16Z

Included a bit of a refactor for the ASCII output as well so that
forestclaw could reuse as much of that code as possible.

Included a bit of a refactor for the ASCII output as well so that forestclaw could reuse as much of that code as possible.

…ading

mandli · 2017-03-18T01:20:26Z

I am having two issues getting this to work correctly so if anyone has some ideas they would be most welcome:

For reasons I don't understand and am having difficulty debugging some of the tests are importing the new ForestClaw IO routines which lead to errors as the non-ForestClaw Patch class is missing two attributes. This happens in only some of the tests so I am guessing somehow there's an import problem.
The test in clawpack.forestclaw.io.forestclaw is not being found sometimes.

I could make this easier and only add these to the ForestClaw repository itself but I was thinking it would be nice to start to build up the infrastructure for having a Python interface to ForestClaw.

mandli · 2017-03-18T01:20:54Z

Strangely tests are passing on travis beyond the issues with Python 3.x. Still not seeing the test for ForestClaw though.

coveralls · 2017-03-18T01:40:15Z

Coverage decreased (-6.4%) to 39.481% when pulling 158d895 on mandli:add-forestclaw-reading into 986a3d1 on clawpack:master.

coveralls · 2017-03-18T02:15:04Z

Coverage decreased (-6.4%) to 39.481% when pulling 725bcfd on mandli:add-forestclaw-reading into 986a3d1 on clawpack:master.

ketch · 2017-03-18T04:53:52Z

You probably already know this but the test failures on Travis seem like they would be fixed by using range instead of xrange. See http://stackoverflow.com/questions/17192158/nameerror-global-name-xrange-is-not-defined-in-python-3.

ketch · 2017-03-18T05:05:57Z

The test in clawpack.forestclaw.io.forestclaw is not being found sometimes.

I believe nose does not pick up functions with test in the name that are not in a file with test in the name. Running nosetests in forestclaw/io does nothing, but if I rename forestclaw.py to test.py then it runs the test.

ketch · 2017-03-18T05:08:29Z

src/forestclaw/geometry.py

+def test_forestclaw_patch():
+    """Test the simple extension of the pyclaw.Patch class"""
+
+    patch = Patch(pyclaw.geometry.dimension(0.0, 1.0, 10))


When I run this test, I get an error because dimension is not capitalized. Changing it to Dimension (the class name) fixes that and the test passes.

ketch · 2017-03-18T05:12:50Z

The refactor of ascii.py is definitely an improvement. Thanks!

mandli · 2017-03-18T19:04:18Z

I see, I was confused to where the xrange would have come from given that io.ascii was working before but then realized it was my fault. Should be working again.

mandli · 2017-03-18T19:11:44Z

I realized that it would be better to call the io module in the forestclaw package ascii to align better with petclaw and that this is really just a slightly changed ascii format for ForestClaw.

mandli · 2017-03-18T19:43:47Z

I think I may have confused myself. If forestclaw has it's own geometry module then do I need to also import all of the PyClaw versions of the classes I am not overriding or is there a way to do that more simply? It looks like PetClaw does all the classes but tends to modify all of them as well so I am not exactly certain what the right thing to do here is.

Also include an actual test.

mandli · 2017-03-18T19:46:37Z

Note now with the move to have forestclaw be a package at the level of petclaw and pyclaw that the clawpack/clawpack repository will also need an update in the setup.py file so that the link to forestclaw will be taken care of.

coveralls · 2017-03-18T20:16:08Z

Coverage decreased (-0.06%) to 45.783% when pulling c2a91c8 on mandli:add-forestclaw-reading into 986a3d1 on clawpack:master.

ketch · 2017-03-20T18:02:17Z

I think I may have confused myself. If forestclaw has it's own geometry module then do I need to also import all of the PyClaw versions of the classes I am not overriding or is there a way to do that more simply? It looks like PetClaw does all the classes but tends to modify all of them as well so I am not exactly certain what the right thing to do here is.

You need to import them only if you wish to be able to access them under the ForestClaw namespace. For instance, petclaw.geometry does not include a definition of a Grid class, so there is no clawpack.petclaw.Grid. Internally, PetClaw just uses the clawpack.pyclaw.Grid class. Perhaps it would make sense to do from pyclaw import Grid there, but nobody seems to care so far.

mandli · 2017-03-21T00:03:50Z

I kind of want to mimic what is possible with PetClaw as much as possible but I will try some things. I still actually do not have the tests passing on my own machine due to a weird import conflict but I think I have seen something weird like this before. Given that the Travis tests are working maybe this is ready to merge then.

ketch · 2017-03-21T00:32:44Z

Care to post the error you're getting locally?

ketch · 2017-04-16T16:44:33Z

Oops, I was wrong. To fix the current Travis error, you just need to change io -> fileio on line 11 of pyclaw/src/pyclaw/setup.py.

mandli · 2017-04-17T19:59:04Z

I just opened a PR for clawpack/clawpack#110. Still working out the testing issues.

mandli · 2017-04-19T02:30:59Z

Made some incremental changes and bug fixes. I am hoping that this can soon be merged in. @donnacalhoun and @ketch I may need to have you test these things out given that this will be a multi-repository commit.

donnaaboise · 2017-04-19T02:39:50Z

Thanks for all of your work on this! I'll check it out in the next few days.

Rename io -> fileio in pyclaw/src/pyclaw/setup.py.

…-forestclaw-reading

Also fix forestclaw tests

ketch · 2017-04-28T06:50:16Z

Never mind; the issue is that we're getting this when we install pyclaw:

Warning: Subpackage 'clawpack.pyclaw.fileio' configuration returned as 'clawpack.pyclaw.io'

This seems to come from

https://github.com/numpy/numpy/blob/master/numpy/distutils/misc_util.py#L925

but I have no idea why. There must still be a reference to pyclaw.io somewhere...?

I think the only important change here is the one in pyclaw/src/pyclaw/fileio/setup.py.

ketch · 2017-04-28T11:54:37Z

Okay, my latest PR fixes it. I think that with that we are ready to merge.

Annihilate pyclaw.io.

coveralls · 2017-04-28T15:15:51Z

Coverage decreased (-0.05%) to 45.78% when pulling e5f1e9a on mandli:add-forestclaw-reading into 31aa16d on clawpack:master.

ketch · 2017-04-28T16:06:54Z

Yeah, I think this doesn't pass yet because it needs the clawpack/clawpack PR.

mandli · 2017-04-28T17:06:50Z

Does this work for you then?

mandli · 2017-04-29T01:01:45Z

I am a bit concerned that there is still something not working quite right but maybe we can merge this in and see where non-travis testing might give us.

…ading

coveralls · 2017-05-07T17:17:54Z

Coverage decreased (-0.05%) to 45.78% when pulling 33c066a on mandli:add-forestclaw-reading into 047f1c1 on clawpack:master.

donnaaboise · 2017-05-13T22:59:43Z

We are having trouble getting the read function in pyclaw/ascii to use the read_patch_header in forestclaw.fileio.ascii. So either we shouldn't' be in pyclaw.fileio.ascii.read at all, or somewhere, the correct header function is not getting assigned. We have set format='forestclaw' in the setplot file, but this doesn't seem to be enough. In looking at forestclaw.fileio.asii, the only reference to a read function is to the pyclaw version.

mandli · 2017-05-14T21:46:45Z

This might be best in an issue instead. In any case I am in the midst of trying to replicate the problem in the swirl ForestClaw example. Hopefully I can identify what's wrong.

donnaaboise · 2017-05-14T22:09:14Z

I'd be happy to start an issue, it that helps.

mandli · 2017-05-14T22:16:07Z

I think that would be a bit cleaner given that this is already merged.

Add forestclaw IO option

4f58667

Included a bit of a refactor for the ASCII output as well so that forestclaw could reuse as much of that code as possible.

ketch added the in progress label Nov 6, 2016

mandli added 8 commits March 17, 2017 19:08

Merge remote-tracking branch 'clawpack/master' into add-forestclaw-re…

06d15a8

…ading

Remove executable status from ascii and binary

a2f58d0

Move forestclaw support to own package

11e59b0

Remove header from file

624b38b

Corrections to forestclaw support

de892cb

Fix doc-string

f92af37

Fix some inconsistencies

deda406

Add ForestClaw as an option to Solution

158d895

Add test for ForestClaw Patch extension:

725bcfd

ketch reviewed Mar 18, 2017

View reviewed changes

mandli added 2 commits March 18, 2017 14:02

Move tests to separate modules

2669a1b

Remove xrange

5483f06

Move io.forestclaw to io.ascii

c2a91c8

Also include an actual test.

mandli added 2 commits April 18, 2017 22:24

Fix hanging dependencies

5b9f622

Correct rename bugs

f3cad9f

ketch and others added 8 commits April 19, 2017 06:13

Rename io -> fileio in pyclaw/src/pyclaw/setup.py.

4de50b1

Merge pull request #3 from ketch/add-forestclaw-reading

95f85f6

Rename io -> fileio in pyclaw/src/pyclaw/setup.py.

Add other stub modules for ForestClaw

2f73849

Merge remote-tracking branch 'mandli/add-forestclaw-reading' into add…

1f15b0c

…-forestclaw-reading

Fix missing fileio references

d0cf610

Also fix forestclaw tests

Add print_function import

a8bf299

Tweak travis tests

bc2a428

Change way file io imports are handled

c318270

Annihilate pyclaw.io.

7ff8441

I think the only important change here is the one in pyclaw/src/pyclaw/fileio/setup.py.

Merge pull request #4 from ketch/add-forestclaw-reading

e5f1e9a

Annihilate pyclaw.io.

Merge remote-tracking branch 'clawpack/master' into add-forestclaw-re…

33c066a

…ading

mandli merged commit 3f06f91 into clawpack:master May 10, 2017

ketch removed the in progress label May 10, 2017

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Add forestclaw IO option #547

Add forestclaw IO option #547

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Add forestclaw IO option #547

Add forestclaw IO option #547

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