Martin Weinelt
8c7d490da6
python3Packages.pyslurm: 19-05-0 -> 21.08.4
...
Unbreaks the package.
2022-04-15 03:17:40 +02:00
Martin Weinelt
9a9f7b940b
python3Packages.pytorch-bin: don't build on hydra
...
It won't complete anyhow, as it exceeds the recently increased maximum
output size by another 200 MB.
https://hydra.nixos.org/build/173626214
2022-04-15 03:17:39 +02:00
Martin Weinelt
4e4e4a570f
python3Packages.trytond: fix werkzeug2.1 compat in test suite
2022-04-15 03:17:39 +02:00
Martin Weinelt
8e3fae565c
python3Packages.chalice: relax jmespath constraint
...
48511562f1
2022-04-15 03:17:39 +02:00
Martin Weinelt
2f7893fbf6
python3Packages.sanic: disable test_noisy_exceptions
...
Sometimes the noisy exceptions output is missing, which makes the test flaky.
2022-04-15 03:17:39 +02:00
Martin Weinelt
77e83e985a
python3Packages.scikit-build: fix build
...
Drops code that references non-existant distutils object and then:
- Migrates to pyproject,
- uses pytestCheckHook,
- trims checkInputs.
2022-04-15 03:17:39 +02:00
Martin Weinelt
cc58bb1169
python3Packages.matchpy: 0.5.1 -> 0.5.5
2022-04-15 03:17:39 +02:00
Justinas Stankevičius
2532909462
jellyfin-ffmpeg: init at 4.4.1-4, use as default for jellyfin ( #151617 )
...
Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
2022-04-15 03:04:18 +02:00
Will Dietz
dde5b0ca7a
python3Packages.fenics: fix build, pin to older boost ( #166728 )
...
* python3Packages.fenics: fix build, pin to older boost
Looking at upstream, there are various issues with newer boost.
(At least some of them have been since fixed)
For now, fix the build by using a version of boost that works
with the current version.
Error here was complaining about `std::min_element`,
which is no longer available, apparently, due to newer boost
no longer (transitively) including <algorithm>.
This was added in C++17, so I'm not sure the cmake flag
specifying dolfin built with C++11 makes sense or is used.
Leaving for now :).
* nixos/tests/fenics: fix name of machine/node in script
Still fails for now.
* python3Packages.fenics: fix accidentally changed strings in subst
Looks like in migration to pkg-config this was erroneously
changed from `pkgconfig` (python package, and source string)
to `pkg-config` (nix package name, tool name).
(see 9bb3fccb5b
2022-04-14 19:37:20 -05:00
Martin Weinelt
f65c792154
Merge pull request #168401 from jboyens/bump-ruby
2022-04-15 02:23:26 +02:00
JR Boyens
5bd5ab2410
ruby_3_1: 3.1.1 -> 3.1.2
...
https://www.ruby-lang.org/en/news/2022/04/12/ruby-3-1-2-released/
Fixes: CVE-2022-28738, CVE-2022-28739
2022-04-15 02:22:24 +02:00
JR Boyens
3e995fbb31
ruby_3_0: 3.0.3 -> 3.0.4
...
https://www.ruby-lang.org/en/news/2022/04/12/ruby-3-0-4-released/
Fixes: CVE-2022-28738, CVE-2022-28739
2022-04-15 02:21:54 +02:00
JR Boyens
dd5210d85a
ruby_2_7: 2.7.5 -> 2.7.6
...
https://www.ruby-lang.org/en/news/2022/04/12/ruby-2-7-6-released/
Fixes: CVE-2022-28739
2022-04-15 02:21:06 +02:00
Anderson Torres
ccb9653427
Merge pull request #168648 from AndersonTorres/new-vivarium
...
tomlc99: init at 0.pre+date=2022-04-04
tomlcpp: init at 0.pre+date=2022-05-01
2022-04-14 21:08:20 -03:00
github-actions[bot]
1c0229dbfd
Merge staging-next into staging
2022-04-15 00:03:21 +00:00
github-actions[bot]
faca36d9c0
Merge master into staging-next
2022-04-15 00:02:18 +00:00
Martin Weinelt
60d698f8bf
python3Packages.datasette: relax click & jinja2 constraints
...
Move substituion into postPatch, the canonical place for this kind of
operation.
2022-04-15 01:39:56 +02:00
Martin Weinelt
b08880a4f8
python3Packages.ansible-runner: build requires pbr
2022-04-15 01:39:56 +02:00
Martin Weinelt
50907e3009
python3Packages.kivy-garden: fix source
2022-04-15 01:39:56 +02:00
Frederik Rietdijk
498a4d8feb
python3Packages.jaxlib: set platforms
2022-04-15 01:39:56 +02:00
Martin Weinelt
b95480efb1
fava: 1.19 -> 1.21; fix Werkzeug compat
2022-04-15 01:39:56 +02:00
Martin Weinelt
8e6075b2ac
python3Packages.atom: fix versioning and tests
2022-04-15 01:39:56 +02:00
Martin Weinelt
2dde351eca
python3Packages.glean-parser: relax markupsafe constraint
2022-04-15 01:39:56 +02:00
Martin Weinelt
f6e6d95100
python3Packages.flask-socketio: 5.0.1 -> 5.1.1
2022-04-15 01:39:56 +02:00
Martin Weinelt
5eb123c365
python3Packages.approvaltests: 4.0.0 -> 5.0.0
2022-04-15 01:39:56 +02:00
Martin Weinelt
c0ea8f066e
python3Packages.python3-saml: relax lxml constraint
2022-04-15 01:39:56 +02:00
Martin Weinelt
1ccdd9ad73
python3Packages.starlette: 0.18.0 -> 0.19.0
2022-04-15 01:39:56 +02:00
Martin Weinelt
4584d22ba1
python3Packages.azure-core: propagate typing-extensions
2022-04-15 01:39:56 +02:00
Martin Weinelt
04c0a4b7b6
home-assistant-cli: downgrade click to 8.0.4
...
https://github.com/home-assistant-ecosystem/home-assistant-cli/issues/382
2022-04-15 01:39:55 +02:00
Martin Weinelt
95769fb2c8
octoprint: fix eval
...
Relying on attributes like these to always be available is prone to an
eval error when the overridden package drops them.
2022-04-15 01:39:55 +02:00
Martin Weinelt
3d0ccac7fe
home-assistant: reduce component tests processes
...
Component tests are often of lesser quality, which may lead to spurious
errors when run with high parallelization. Reducing to 4 processes
aligns the setup with what GitHub actions provides, which is what
upstream uses to test.
2022-04-15 01:39:55 +02:00
Martin Weinelt
2d1e788f60
buku: update sqlalchemy hash
2022-04-15 01:39:55 +02:00
Martin Weinelt
69900853ca
mailman: fix build
...
Required an update to the sqlalchemy override due to new hash variable
usage. Also disables tests for sqlalchemy and alembic because neither
can find any, so they error out.
2022-04-15 01:39:55 +02:00
Martin Weinelt
e391e40d02
python3Packages.falcon: fix build; cythonize!
2022-04-15 01:39:55 +02:00
Kirill Radzikhovskyy
7f613bbdb6
awsebcli: fixup, downgrade jmespath
2022-04-15 01:39:55 +02:00
Martin Weinelt
a484235634
grab-site: update sqlalchemy hash
2022-04-15 01:39:55 +02:00
Martin Weinelt
1828ad603b
python3.pkgs.pylint: 2.13.4 -> 2.13.5
...
https://github.com/PyCQA/pylint/releases/tag/v2.13.5
2022-04-15 01:39:55 +02:00
Martin Weinelt
abacec3d0b
python3Packages.pytest-shutil: fix build
...
Propagates six and replaces path.py dependency with path, the new name.
2022-04-15 01:39:55 +02:00
Martin Weinelt
90112c221f
python3Packages.fakeredis: relax redis constraint
2022-04-15 01:39:55 +02:00
Martin Weinelt
1feb33974a
python3Packages.mkdocs-material: 8.2.7 -> 8.2.9
2022-04-15 01:39:55 +02:00
Martin Weinelt
3847540f6d
python3Packages.mkdocs: 1.2.3 -> 1.3.0
...
https://github.com/mkdocs/mkdocs/releases/tag/1.3.0
2022-04-15 01:39:55 +02:00
Martin Weinelt
b4ead6abae
python3Packges.pep257: remove together with pytest-pep257
...
The code apparently was migrated into pycodestyle.
https://github.com/PyCQA/pydocstyle/issues/580
2022-04-15 01:39:54 +02:00
Martin Weinelt
5ee7d17afc
python3Packages.path: rename from path.py; 12.0.1 -> 16.4.0
...
The project had been renamed after 12.5.0 back in 2020, which is why we
didn't receive further updates.
Created an alias and renamed all existing references.
2022-04-15 01:39:54 +02:00
Martin Weinelt
8aaa019221
python3Packages.twisted: 22.2.0 -> 22.4.0
2022-04-15 01:39:54 +02:00
Robert Schütz
d735ed3864
python3Packages.pytest-asyncio: 0.18.1 -> 0.18.3
...
https://github.com/pytest-dev/pytest-asyncio/blob/v0.18.3/CHANGELOG.rst
2022-04-15 01:39:54 +02:00
Robert Schütz
bfcb28e128
python3Packages.async_generator: does not depend on pytest-asyncio
2022-04-15 01:39:54 +02:00
Martin Weinelt
c2d2758147
borgbackup: disable racy test
...
https://github.com/borgbackup/borg/issues/6573
2022-04-15 01:39:54 +02:00
Martin Weinelt
9f340b5bf1
treewide: remove redundant numprocesses pytest-xdist parameter
...
Including the pytest-xdist package automatically configures numprocesses
to $NIX_BUILD_CORES, so specifying these on a package level has become
redundant.
2022-04-15 01:39:54 +02:00
Martin Weinelt
836e3af544
python3Packages.jax: disable test_custom_linear_solve_aux
...
```
______________ CustomLinearSolveTest.test_custom_linear_solve_aux ______________
[gw3] linux -- Python 3.9.11 /nix/store/k1physzalj5vffsvl7ag6h6b6vaqip5x-python3-3.9.11/bin/python3.9
self = <custom_linear_solve_test.CustomLinearSolveTest testMethod=test_custom_linear_solve_aux>
@jtu.skip_on_flag("jax_skip_slow_tests", True)
def test_custom_linear_solve_aux(self):
def explicit_jacobian_solve_aux(matvec, b):
x = lax.stop_gradient(jnp.linalg.solve(jax.jacobian(matvec)(b), b))
return x, array_aux
def matrix_free_solve_aux(matvec, b):
return lax.custom_linear_solve(
matvec, b, explicit_jacobian_solve_aux, explicit_jacobian_solve_aux,
symmetric=True, has_aux=True)
def linear_solve_aux(a, b):
return matrix_free_solve_aux(partial(high_precision_dot, a), b)
# array aux values, to be able to use jtu.check_grads
array_aux = {"converged": np.array(1.), "nfev": np.array(12345.)}
rng = self.rng()
a = rng.randn(3, 3)
a = a + a.T
b = rng.randn(3)
expected = jnp.linalg.solve(a, b)
actual_nojit, nojit_aux = linear_solve_aux(a, b)
actual_jit, jit_aux = jax.jit(linear_solve_aux)(a, b)
self.assertAllClose(expected, actual_nojit)
self.assertAllClose(expected, actual_jit)
# scalar dict equality check
self.assertDictEqual(nojit_aux, array_aux)
self.assertDictEqual(jit_aux, array_aux)
# jvp / vjp test
> jtu.check_grads(linear_solve_aux, (a, b), order=2, rtol=4e-3)
tests/custom_linear_solve_test.py:157:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
jax/_src/test_util.py:372: in check_grads
_check_grads(f, args, order)
jax/_src/test_util.py:361: in _check_grads
_check_grads(partial(api.jvp, f), (args, args), order - 1, fwd_msg)
jax/_src/test_util.py:365: in _check_grads
_check_vjp(f, partial(api.vjp, f), args, err_msg=rev_msg)
jax/_src/test_util.py:325: in check_vjp
check_close(ip, ip_expected, atol=atol, rtol=rtol,
jax/_src/test_util.py:227: in check_close
tree_all(tree_multimap(assert_close, xs, ys))
jax/_src/tree_util.py:180: in tree_map
return treedef.unflatten(f(*xs) for xs in zip(*all_leaves))
jax/_src/tree_util.py:180: in <genexpr>
return treedef.unflatten(f(*xs) for xs in zip(*all_leaves))
jax/_src/test_util.py:217: in _assert_numpy_close
_assert_numpy_allclose(a, b, atol=atol * a.size, rtol=rtol * b.size,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
a = array(1.89683694), b = array(1.88698006), atol = 0.002, rtol = 0.004
err_msg = 'VJP of JVP cotangent projection'
def _assert_numpy_allclose(a, b, atol=None, rtol=None, err_msg=''):
if a.dtype == b.dtype == _dtypes.float0:
np.testing.assert_array_equal(a, b, err_msg=err_msg)
return
a = a.astype(np.float32) if a.dtype == _dtypes.bfloat16 else a
b = b.astype(np.float32) if b.dtype == _dtypes.bfloat16 else b
kw = {}
if atol: kw["atol"] = atol
if rtol: kw["rtol"] = rtol
with np.errstate(invalid='ignore'):
# TODO(phawkins): surprisingly, assert_allclose sometimes reports invalid
# value errors. It should not do that.
> np.testing.assert_allclose(a, b, **kw, err_msg=err_msg)
E AssertionError:
E Not equal to tolerance rtol=0.004, atol=0.002
E VJP of JVP cotangent projection
E Mismatched elements: 1 / 1 (100%)
E Max absolute difference: 0.00985688
E Max relative difference: 0.00522363
E x: array(1.896837)
E y: array(1.88698)
jax/_src/test_util.py:187: AssertionError
```
2022-04-15 01:39:54 +02:00
Sandro Jäckel
84cc0b7449
python310Packages.click: 8.1.1 -> 8.1.2
2022-04-15 01:39:54 +02:00
