Add tests for the Nix build #791

wd15 · 2021-03-22T21:54:14Z

Seems to be possible to run completely independent configurations on Travis with the jobs / include syntax.

Allow a Nixpkgs version tag to be passed at the command line. Update the version of Nix to 20.09.

Seems to be possible to run completely separate configurations using the jobs -> include syntax. Trying with a Nix build.

wd15 · 2021-03-23T13:00:12Z

Only seems to be running a single version of the Travis osx tests

wd15 · 2021-03-24T13:10:12Z

The following is failing on the Nix build so need to fix that. Also failing locally. Might be to do with the Gmsh version. Should be able to get to the bottom of this one.

======================================================================
FAIL: circleQuad (examples.diffusion)
Doctest: examples.diffusion.circleQuad
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/nix/store/z65l1jqvxa58zzwwa3bvglb6asj4y8cv-python3-3.8.5/lib/python3.8/doctest.py", line 2204, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for examples.diffusion.circleQuad
  File "/home/travis/build/usnistgov/fipy/examples/diffusion/circleQuad.py", line 0, in circleQuad
----------------------------------------------------------------------
File "/home/travis/build/usnistgov/fipy/examples/diffusion/circleQuad.py", line 159, in examples.diffusion.circleQuad
Failed example:
    print(phi.allclose(x, atol = 0.035)) # doctest: +GMSH
Expected:
    1
Got:
    False

The other failures on Travis aren't to do with these changes, but VTK. Getting

numpy.dtype(numpy.character): vtkConstants.VTK_UNSIGNED_CHAR,
    DeprecationWarning: Converting `np.character` to a dtype is deprecated. The current result is `np.dtype(np.str_)` which is not strictly correct. Note that `np.character` is generally deprecated and 'S1' should be used.

guyer · 2021-03-24T19:13:31Z

Can you tell if it's a different version of Gmsh or something?

wd15 · 2021-03-24T20:15:26Z

Can you tell if it's a different version of Gmsh or something?

It's giving

$ gmsh --version      
4.6.0

Is that supported?

guyer · 2021-03-24T21:20:01Z

$ gmsh --version      
4.6.0
Is that supported?

It looks like it stopped working between Gmsh 4.4 and 4.5.

I think that failure shouldn't stop you from merging this PR.

wd15 · 2021-03-24T22:48:15Z

It looks like it stopped working between Gmsh 4.4 and 4.5.

I think that failure shouldn't stop you from merging this PR.

I'll try and fix it. This is an issue that arose from introducing a newer version of Gmsh than Conda's (or whatever FIPy conda recipe is using) version so should be fixed. Is Gmsh fixed in FiPy's conda recipe? At least one of the conda tests is using 3.06.

guyer · 2021-03-25T14:18:52Z

I think the "fix" is just to relax the tolerance of the test. We definitely should support Gmsh 4.x and, largely, we do.¹ I've often seen we get sporadic failures when different versions of Gmsh tweak their meshing algorithms. We either need to find a more robust metric to test, or just (continue to) drop the tolerances.

¹ Remaining issues with Gmsh 4.x

Some earlier versions of Gmsh 4.x did not properly record ghost cells in msh2 meshes, but that's been fixed for awhile.
We should support newer MSH formats
Our conda-forge feedstock pulls in a really old Gmsh 3.0.6 sometimes
Our conda-forge feedstock feedstock doesn't pull in Gmsh at all sometimes (recent Py3k, at least on some platforms (I don't think any of our CIs exhibit this, but they're all still using Python 3.6, which also needs to be updated)).

review-notebook-app · 2022-11-09T17:58:01Z

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Also, add sanitize file for nbval

wd15 · 2022-11-09T19:18:53Z

@guyer, @tkphd: please review this when you get a chance. Running Jupyter using Nix on macos should work now.

tkphd · 2022-12-08T16:35:26Z

shell.nix

+  pkgs = import (builtins.fetchTarball "https://github.com/NixOS/nixpkgs/archive/${tag}.tar.gz") {};
+  pypkgs = pkgs.python3Packages;
+
+  nixes_src = builtins.fetchTarball "https://github.com/wd15/nixes/archive/9a757526887dfd56c6665290b902f93c422fd6b1.zip";


What is this magic ~~tarball~~ zip file, and is a user account the proper source for it?

Good catch. It's a bunch of Jupyter dependencies, here. I don't know why I thought that was a good idea. They can just be listed directly here.

[TODO]: check if nixpkgs has some sort of built in jupyter-complete expression with all Jupyter add ons.

Stop using remote repository for Jupyter install with Nix.

wd15 · 2022-12-14T19:49:15Z

@tkphd should be better now

tkphd

LGTM!

guyer · 2023-01-10T15:14:00Z

Remaining CI failure is due to PETSc 3.18 or some CI glitch (for example, why is the Test log blank, when it can be seen along the way that the tests run successfully to completion?). Regardless, it fails on master, too, so no reason to hold up this PR.

wd15 added 3 commits March 22, 2021 17:49

build(nix): command line version tag

ca1cfd8

Allow a Nixpkgs version tag to be passed at the command line. Update the version of Nix to 20.09.

ci(travis): add nix build

01516f0

Seems to be possible to run completely separate configurations using the jobs -> include syntax. Trying with a Nix build.

ci(travis): remove unused yaml file

72a94d6

guyer mentioned this pull request Mar 22, 2021

fix: stop divide by zero warning in LU solvers #790

Merged

build(nix): add comment for building docs

9b33b9c

wd15 added 2 commits March 23, 2021 09:09

fiddling

3bf7ff2

include a name for the build and use linux

1b1aa9a

guyer added installation CI labels Mar 24, 2021

guyer mentioned this pull request Mar 24, 2021

circleQuad example fails with Gmsh > 4.4 #792

Closed

Merge branch 'master' into update-nix

375c80d

wd15 marked this pull request as ready for review November 8, 2022 21:04

wd15 changed the title ~~Add Nix build to Travis~~ Add tests for the Nix build Nov 9, 2022

wd15 added 3 commits November 9, 2022 14:00

build(nix): jupyter should work on all platforms

c71e488

ci(github): add nix recipe

e038b2d

tests: rerun test notebook for pytest

c147b45

Also, add sanitize file for nbval

wd15 force-pushed the update-nix branch from 1cba87d to c147b45 Compare November 9, 2022 19:01

wd15 requested review from tkphd and guyer November 9, 2022 19:17

tkphd reviewed Dec 8, 2022

View reviewed changes

ci(actions): stop using remote repository

b272c85

Stop using remote repository for Jupyter install with Nix.

wd15 requested a review from tkphd December 14, 2022 19:48

tkphd approved these changes Dec 15, 2022

View reviewed changes

guyer merged commit db5292d into usnistgov:master Jan 10, 2023

wd15 deleted the update-nix branch August 7, 2023 15:31

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Add tests for the Nix build #791

Add tests for the Nix build #791

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Add tests for the Nix build #791

Add tests for the Nix build #791

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