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merge with upstream #7

Merged
merged 41 commits into from
Oct 17, 2022
Merged

merge with upstream #7

merged 41 commits into from
Oct 17, 2022

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luke-dt
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@luke-dt luke-dt commented Oct 17, 2022

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haampie and others added 30 commits October 13, 2022 14:22
* py-execnet: 1.9.0

* bounds
When a pipeline generation job is automatically failed because it
generated jobs for specs known to be broken on develop, print better
information about the broken specs that were encountered.  Include
at a minimum the hash and the url of the job whose failure caused it
to be put on the broken specs list in the first place.
* Add checksum for py-gitpython 3.1.27

* Update package.py

* Update var/spack/repos/builtin/packages/py-gitpython/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* gasnet: Add new release hash
* upcxx: Add new release hash
* gasnet: misc updates
* upcxx: misc updates
* hip-set-prefix-rocm5.2.0-onwards

* Update var/spack/repos/builtin/packages/hip/package.py

Update description

Co-authored-by: Satish Balay <balay@mcs.anl.gov>
* petsc,py-petsc4py,slepc,py-slepc4py: add version 3.18.0

* workaround for dealii build failure [with petsc version check]

* pism: add compatibility fix to for petsc@3.18

* add in hipsolver dependency
* commit updating py-libensemble package for 0.9.3

* removed commented-out lines
* Add checksum for py-oauthlib 3.2.1

* Update package.py

* [@spackbot] updating style on behalf of iarspider

* Update package.py

* Update package.py

Co-authored-by: iarspider <iarspider@users.noreply.github.com>
Add checksum for latest tag/release
* gptl: new version 8.1.1; use the correct `mpifc`
* add `F90` and `$F77`
* Add checksum for py-seaborn 0.12.0

* Update package.py

* Update package.py

* [@spackbot] updating style on behalf of iarspider

* Update package.py

Co-authored-by: iarspider <iarspider@users.noreply.github.com>
Currently "spack ci generate" chooses the first matching entry in
gitlab-ci:mappings to fill attributes for a generated build-job,
requiring that the entire configuration matrix is listed out
explicitly. This unfortunately causes significant problems in
environments with large configuration spaces, for example the
environment in #31598 (spack.yaml) supports 5 operating systems,
3 architectures and 130 packages with explicit size requirements,
resulting in 1300 lines of configuration YAML.

This patch adds a configuraiton option to the gitlab-ci schema called
"match_behavior"; when it is set to "merge", all matching entries
are applied in order to the final build-job, allowing a few entries
to cover an entire matrix of configurations.

The default for "match_behavior" is "first", which behaves as before
this commit (only the runner attributes of the first match are used).

In addition, match entries may now include a "remove-attributes"
configuration, which allows matches to remove tags that have been
aggregated by prior matches. This only makes sense to use with
"match_behavior:merge". You can combine "runner-attributes" with
"remove-attributes" to effectively override prior tags.
* py-tensorflow: fix zlib

* [@spackbot] updating style on behalf of haampie

Co-authored-by: haampie <haampie@users.noreply.github.com>
michaelkuhn and others added 11 commits October 17, 2022 09:53
…#33278)

* py-jupyterlab-pygments: avoid cyclic dependency

* Fix style

* Update package.py

* Update package.py

* [@spackbot] updating style on behalf of iarspider

* Update package.py

* Flake-8

* fix

Co-authored-by: iarspider <iarspider@users.noreply.github.com>
Print a message of the form
```
Fetch mm:ss.  Build: mm:ss.  Total: mm:ss
```
when installing from buildcache. 

Previously this only happened for source builds.
… 62.6.0, py-wrapt 1.14.1, py-pylint 2.15.0 (#32976)

* Add checksum for py-astroid 2.12.7, py-setuptools 62.6.0

* Also add checksum for py-wrapt

* Update package.py

* Update package.py (#57)

* Update package.py

* Update package.py

* Update package.py
Fixing an oversight in #32537

`get_deptypes` should depend on new `package/dependencies_cache_only`
props.
@luke-dt luke-dt merged commit e552c78 into dantaslab:package/py-bakta Oct 17, 2022
luke-dt pushed a commit that referenced this pull request Jun 6, 2023
1. support version 3.1.3, which now depends on sundials@6

2. support version 3.1.2:, which broke the two patch files and
   therefore the two patch files have been replaced by more flexible
   filter_file() commands inside a patch() function.

3. rename the variant for python extension from using the package name
   "+pyuqtk" to the more standard "+python"

4. add maintainers @omsai and the upstream developer @bjdebus who
   offered to help with the spack packaging.

5. swig should only be a build-time dependency.  swig is only
   necessary until @:3.1.0

6. confirmed python dependencies are correct by inspecting imports,
   subset python dependencies type to build, run, and confirmed all
   31 build-time tests pass including the 9 python tests:

```console
$ spack env create uqtk-dev
$ spack add uqtk@3.1.3
$ spack install --test root && cat $(spack location -i uqtk)/.spack/install-time-test-log.txt
==> Testing package uqtk-3.1.3-nok6fut
==> [2023-04-19-14:56:25.005361] Running build-time tests
==> [2023-04-19-14:56:25.005536] RUN-TESTS: build-time tests [check]
==> [2023-04-19-14:56:25.009543] '/home/omsai/src/spack/opt/spack/linux-pureos10-skylake/gcc-10.2.1/gmake-4.4.1-b6g4apmfvxz3bn4eabh37dehcrg65fj7/bin/make' '-j4' '-n' 'test'
==> [2023-04-19-14:56:25.014903] '/home/omsai/src/spack/opt/spack/linux-pureos10-skylake/gcc-10.2.1/gmake-4.4.1-b6g4apmfvxz3bn4eabh37dehcrg65fj7/bin/make' '-j4' 'test'
Running tests...
/home/omsai/src/spack/opt/spack/linux-pureos10-skylake/gcc-10.2.1/cmake-3.26.3-zjmsfz23j5l4ytniz26uzvxonlu5qebr/bin/ctest --force-new-ctest-process
Test project /tmp/omsai/spack-stage/spack-stage-uqtk-3.1.3-nok6fut47h42cnaau7wkoohgqy5f2qqa/spack-build-nok6fut
      Start  1: ArrayReadAndWrite
      Start  2: ArrayDelColumn
      Start  3: Array1DMiscTest
      Start  4: Array2DMiscTest
 1/31 Test  #1: ArrayReadAndWrite ................   Passed    0.01 sec
      Start  5: ArraySortTest
 2/31 Test  #2: ArrayDelColumn ...................   Passed    0.01 sec
      Start  6: MultiIndexTest
 3/31 Test  #3: Array1DMiscTest ..................   Passed    0.01 sec
      Start  7: CorrTest
 4/31 Test  #4: Array2DMiscTest ..................   Passed    0.01 sec
      Start  8: QuadLUTest
 5/31 Test  #5: ArraySortTest ....................   Passed    0.02 sec
      Start  9: MCMC2dTest
 6/31 Test  #6: MultiIndexTest ...................   Passed    0.01 sec
      Start 10: MCMCRandomTest
 7/31 Test  #8: QuadLUTest .......................   Passed    0.02 sec
      Start 11: MCMCNestedTest
 8/31 Test #10: MCMCRandomTest ...................   Passed    0.02 sec
      Start 12: Deriv1dTest
 9/31 Test #12: Deriv1dTest ......................   Passed    0.01 sec
      Start 13: SecondDeriv1dTest
10/31 Test #13: SecondDeriv1dTest ................   Passed    0.01 sec
      Start 14: GradHessianTest
11/31 Test #11: MCMCNestedTest ...................   Passed    0.03 sec
      Start 15: GradientPCETest
12/31 Test spack#14: GradHessianTest ..................   Passed    0.01 sec
      Start 16: PCE1dTest
13/31 Test spack#15: GradientPCETest ..................   Passed    0.01 sec
      Start 17: PCEImplTest
14/31 Test spack#16: PCE1dTest ........................   Passed    0.01 sec
      Start 18: PCELogTest
15/31 Test spack#18: PCELogTest .......................   Passed    0.01 sec
      Start 19: Hessian2dTest
16/31 Test spack#19: Hessian2dTest ....................   Passed    0.01 sec
      Start 20: BCS1dTest
17/31 Test spack#20: BCS1dTest ........................   Passed    0.01 sec
      Start 21: BCS2dTest
18/31 Test spack#21: BCS2dTest ........................   Passed    0.01 sec
      Start 22: LowRankRegrTest
19/31 Test spack#22: LowRankRegrTest ..................   Passed    0.01 sec
      Start 23: PyModTest
20/31 Test spack#17: PCEImplTest ......................   Passed    0.07 sec
      Start 24: PyArrayTest
21/31 Test spack#23: PyModTest ........................   Passed    0.08 sec
      Start 25: PyArrayTest2
22/31 Test spack#25: PyArrayTest2 .....................   Passed    0.30 sec
      Start 26: PyQuadTest
23/31 Test spack#24: PyArrayTest ......................   Passed    1.44 sec
      Start 27: PyBCSTest1D
24/31 Test spack#26: PyQuadTest .......................   Passed    1.68 sec
      Start 28: PyBCSTest2D
25/31 Test spack#27: PyBCSTest1D ......................   Passed    1.66 sec
      Start 29: PyBADPTest
26/31 Test  #7: CorrTest .........................   Passed    3.43 sec
      Start 30: PyRegressionTest
27/31 Test spack#28: PyBCSTest2D ......................   Passed    1.50 sec
      Start 31: PyGalerkinTest
28/31 Test  #9: MCMC2dTest .......................   Passed    3.90 sec
29/31 Test spack#29: PyBADPTest .......................   Passed    1.66 sec
30/31 Test spack#30: PyRegressionTest .................   Passed    1.72 sec
31/31 Test spack#31: PyGalerkinTest ...................   Passed    1.63 sec

100% tests passed, 0 tests failed out of 31

Total Test time (real) =   5.35 sec
==> [2023-04-19-14:56:30.382797] '/home/omsai/src/spack/opt/spack/linux-pureos10-skylake/gcc-10.2.1/gmake-4.4.1-b6g4apmfvxz3bn4eabh37dehcrg65fj7/bin/make' '-j4' '-n' 'check'
==> [2023-04-19-14:56:30.385983] Target 'check' not found in Makefile
```
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