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Feature/special handling for b09#5

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jedwards4b wants to merge 2438 commits intoclimbfuji:developfrom
jedwards4b:feature/special_handling_for_b09
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Feature/special handling for b09#5
jedwards4b wants to merge 2438 commits intoclimbfuji:developfrom
jedwards4b:feature/special_handling_for_b09

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Although I didn't find an easy way to list all of the 8.3.0 beta tags, I think that this is a cleaner way to handle 8.3.0b09.

tgamblin and others added 30 commits July 31, 2022 13:29
- [x] remove alignment spaces from tempaltes
- [x] replace single with double quotes
- [x] Makefile template now generates parsable code
      (function body is `pass` instead of just a comment)
- [x] template checks now run black to check output
`spack style` tests were annoyingly brittle because we could not easily be
specific about which tools to run (we had to use `--no-black`, `--no-isort`,
`--no-flake8`, and `--no-mypy`). We should be able to specify what to run OR
what to skip.

Now you can run, e.g.:

    spack style --tool black,flake8

or:

    spack style --skip black,isort

- [x] Remove  `--no-black`, `--no-isort`, `--no-flake8`, and `--no-mypy` args.
- [x] Add `--tool TOOL` argument.
- [x] Add `--skip TOOL` argument.
- [x] Allow either `--tool black --tool flake8` or `--tool black,flake8` syntax.
A GitHub rebase merge seems to rewrite commits even if it would be a
fast-forward, which means that the commit merged from spack#24718 is wrong.

- [x] update `.git-blame-ignore-revs` with real commit from `develop`
This test relied on an old version of the `flake8_package` fixture that modified
the spack repository, but it doesn't do that anymore. There are other tests for
`changed_files()` that do a better job of mocking up a git repository with
changes, so we can just delete this one.
* wi4mpi: New version 3.6.0
ROOT also needs updating for downstream macOS packages
…31841)

* kokkos@develop: set CMAKE_CXX_STANDARD instead of Kokkos_CXX_STANDARD

* use CMAKE_CXX_STANDARD regardless of kokkos version
…aml (spack#31864)

Resurrect Known issues, since users ask frequently about that.
adamjstewart and others added 27 commits August 16, 2022 10:55
)

Spack doesn't have an easy way to say something like "If I build
package X, then I *need* version Y":

* If you specify something on the command line, then you ensure
  that the constraints are applied, but the package is always built
* Likewise if you `spack add X...`` to your environment, the
  constraints are guaranteed to hold, but the environment always
  builds the package
* You can add preferences to packages.yaml, but these are not
  guaranteed to hold (Spack can choose other settings)

This commit adds a 'require' subsection to packages.yaml: the
specs added there are guaranteed to hold. The commit includes
documentation for the feature.

Co-authored-by: Massimiliano Culpo <[email protected]>
`requirement_policy/3` is generated and may not be in Spack's inputs to Clingo.
Currently this is causing warnings like:

```
$ spack spec zlib
/global/u2/t/tgamblin/src/spack/lib/spack/spack/solver/concretize.lp:510:3-43: info: atom does not occur in any rule head:
  requirement_policy(Package,X,"one_of")

/global/u2/t/tgamblin/src/spack/lib/spack/spack/solver/concretize.lp:517:3-43: info: atom does not occur in any rule head:
  requirement_policy(Package,X,"one_of")

/global/u2/t/tgamblin/src/spack/lib/spack/spack/solver/concretize.lp:523:3-43: info: atom does not occur in any rule head:
  requirement_policy(Package,X,"any_of")

/global/u2/t/tgamblin/src/spack/lib/spack/spack/solver/concretize.lp:534:3-43: info: atom does not occur in any rule head:
  requirement_policy(Package,X,"any_of")

Input spec
--------------------------------
zlib

Concretized
--------------------------------
[email protected]%[email protected]+optimize+pic+shared arch=cray-sles15-haswell
```

- [x] Silence warning with `#defined requirement_policy/3`
)

* filesystem: use lstat in recursive mtime

When a `develop` path contains a dead symlink, the `os.stat` in the recursive `mtime` determination trips up over it.

Closes spack#32165.
We're seeing errors pop up with older versions of Kokkos and newer versions of
`oneapi`, specifically:

    error: no member named 'ONEAPI' in namespace 'sycl'

This hapens because `sycl::ONEAPI` is `sycl::ext::oneapi` since oneapi `2022.0.0`.
`[email protected]:` uses the new namespace. A conflict was present for this, but it was too
specific -- both to `dpcpp` and to the `2022.0.0` version.

- [x] Expand version ranges in `kokkos` conflict
- [x] Add conflict for `oneapi` in addition to `dpcpp`
…#32179)

* CI: reduce the amount of tests run in the original concretizer
* Don't test Python 3.6 on the original concretizer
…31841)

* kokkos@develop: set CMAKE_CXX_STANDARD instead of Kokkos_CXX_STANDARD

* use CMAKE_CXX_STANDARD regardless of kokkos version
* Adding 36.3.8h_2020-05-04

* [@spackbot] updating style on behalf of mikerenfro

Co-authored-by: mikerenfro <[email protected]>
* Add version 1.4.0

- override build variant with explicit variant instead of __init__ workaround

* Update package.py
* [py-bitshuffle] New package

* [py-bitshuffle] compiling against spack hdf5

* [py-bitshuffle] flake8

* [py-bitshuffle] update import ine

* [@spackbot] updating style on behalf of qwertos

Co-authored-by: James A Zilberman <[email protected]>
Co-authored-by: qwertos <[email protected]>
- [x] Rework `headers` to search a sequence of directories and to display all searched
      locations on error, as opposed to handling each directory with a variable

- [x] Make `headers` and `libs` do the same type of search and raise the same sort of
      errors.

Co-authored-by: Todd Gamblin <[email protected]>
The Python that comes with XCode command line tools is a bit weird.

This fixes two issues that were preventing it from bootstrapping:

- [x] CommandLineTools python does not come with a `python-config` executable. If you
      don't have one of these, CMake's FindPython will, for some reason, assume that you
      want Python 2, so you need to set `CLINGO_PYTHON_VERSION` to ensure that clingo
      tells `find_package(Python <VERSION>)` the right thing.

- [x] We weren't setting `PYTHONHOME` correctly in Python's `package.py`. We were
      setting it to the `prefix` from Python `sysconfig`, but `prefix` tells you where
      the executable lives. CommandLineTools python reports its prefix as

          /Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8

      but that doesn't exist. It looks like Apple builds the full python and just copies
      pieces of it into command line tools. PYTHONHOME is supposed to tell you where the
      default python library location is. So you have to look at the `base`, which
      `sysconfig` reports as

          /Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.8

      On most systems this is probably the same as `prefix`, but not with
      CommandLineTools, which has its system library in a different place.

The second change here was cherry-picked to 0d981a0 before merging and doesn't show
up here.

Co-authored-by: Adam J. Stewart <[email protected]>
Create a package for riscv-gnu-toolchain, a cross-compilation tool.
@jedwards4b
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oops

@jedwards4b jedwards4b closed this Aug 19, 2022
climbfuji pushed a commit that referenced this pull request Apr 28, 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 [email protected]
$ 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 spack#10: MCMCRandomTest ...................   Passed    0.02 sec
      Start 12: Deriv1dTest
 9/31 Test spack#12: Deriv1dTest ......................   Passed    0.01 sec
      Start 13: SecondDeriv1dTest
10/31 Test spack#13: SecondDeriv1dTest ................   Passed    0.01 sec
      Start 14: GradHessianTest
11/31 Test spack#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  spack#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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