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build(deps): bump actions/checkout from 2 to 3#15

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build(deps): bump actions/checkout from 2 to 3#15
dependabot[bot] wants to merge 269 commits intodevelopfrom
dependabot/github_actions/actions/checkout-3

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@dependabot dependabot bot commented on behalf of github Mar 2, 2022

Bumps actions/checkout from 2 to 3.

Release notes

Sourced from actions/checkout's releases.

v3.0.0

  • Update default runtime to node16

v2.4.0

  • Convert SSH URLs like org-<ORG_ID>@github.com: to https://github.com/ - pr

v2.3.5

Update dependencies

v2.3.4

v2.3.3

v2.3.2

Add Third Party License Information to Dist Files

v2.3.1

Fix default branch resolution for .wiki and when using SSH

v2.3.0

Fallback to the default branch

v2.2.0

Fetch all history for all tags and branches when fetch-depth=0

v2.1.1

Changes to support GHES (here and here)

v2.1.0

Changelog

Sourced from actions/checkout's changelog.

Changelog

v2.3.1

v2.3.0

v2.2.0

v2.1.1

  • Changes to support GHES (here and here)

v2.1.0

v2.0.0

v2 (beta)

  • Improved fetch performance
    • The default behavior now fetches only the SHA being checked-out
  • Script authenticated git commands
    • Persists with.token in the local git config
    • Enables your scripts to run authenticated git commands
    • Post-job cleanup removes the token
    • Coming soon: Opt out by setting with.persist-credentials to false
  • Creates a local branch
    • No longer detached HEAD when checking out a branch
    • A local branch is created with the corresponding upstream branch set
  • Improved layout

... (truncated)

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tgamblin and others added 30 commits February 1, 2022 11:42
…ersions

Python 2 and 3 represent string literals differently in the AST. Python 2 requires '\x'
literals, and Python 3 source is always unicode, and allows unicode to be written
directly.  These also unparse differently by default.

- [x] modify unparser to write both out the way `repr` would in Python 2 when
  `py_ver_consistent` is provided.
Some packages use top-level unassigned strings instead of comments, either just after a
docstring on in the body somewhere else. Ignore those strings becasue they have no
effect on package behavior.

- [x] adjust RemoveDocstrings to remove all free-standing strings.
- [x] move tests for util/package_hash.py to test/util/package_hash.py

Co-authored-by: Danny McClanahan <[email protected]>
Previously we used `directives.__all__` to get directive names, but it wasn't
quite right -- it included `DirectiveMeta`, etc.  It's not wrong, but it's also
not the clearest way to do this.

- [x] Refactor `@directive` to track names in `directive_names` global
- [x] Rename `_directive_names` to `_directive_dict_names` in `DirectiveMeta`
- [x] Add a test for `RemoveDirectives`

Co-authored-by: Danny McClanahan <[email protected]>
Package hashing was not properly handling multimethods. In particular, it was removing
any functions that had decorators from the output, so we'd miss things like
`@run_after("install")`, etc.

There were also problems with handling multiple `@when`'s in a single file, and with
handling `@when` functions that *had* to be evaluated dynamically.

- [x] Rework static `@when` resolution for package hash
- [x] Ensure that functions with decorators are not removed from output
- [x] Add tests for many different @when scenarios (multiple @when's,
      combining with other decorators, default/no default, etc.)

Co-authored-by: Danny McClanahan <[email protected]>
Our package hash is supposed to be consistent from python version to python version.
Test this by adding some known unparse inputs and ensuring that they always have the
same canonical hash.  This test relies on the fact that we run Spack's unit tests
across many python versions.  We can't compute for several python versions within the
same test run so we precompute the hashes and check them in CI.
…nparsed

- [x] add option to canonical source to *not* filter multimethods
- [x] add test to unparse every package in builtin
We are planning to switch to using full hashes for Spack specs, which means that the
package hash will be included in the deployment descriptor. This means we need a more
robust package hash than simply dumping the `repr` of the AST.

The AST repr that we previously used for package content is unreliable because it can
vary between python versions (Python's AST actually changes fairly frequently).

- [x] change `package_hash`, `package_ast`, and `canonical_source` to accept a string for
      alternate source instead of a filename.
- [x] consolidate package hash tests in `test/util/package_hash.py`.
- [x] remove old `package_content` method.
- [x] make `package_hash` do what `canonical_source_hash` was doing before.
- [x] modify `content_hash` in `package.py` to use the new `package_hash` function.

Co-authored-by: Danny McClanahan <[email protected]>
To make it easier to see how package hashes change and how they are computed, add two
commands:

* `spack pkg source <spec>`: dumps source code for a package to the terminal

* `spack pkg source --canonical <spec>`: dumps canonicalized source code for a
   package to the terminal. It strips comments, directives, and known-unused
   multimethods from the package. It is used to generate package hashes.

* `spack pkg hash <spec>`: This gives the package hash for a particular spec.
  It is generated from the canonical source code for the spec.

- [x] `add spack pkg source` and `spack pkg hash`
- [x] add tests
- [x] fix bug in multimethod resolution with boolean `@when` values

Co-authored-by: Greg Becker <[email protected]>
We can't tell `print(a, b, c)` and `print((a, b, c))` apart -- both of these expressions
generate different ASTs in Python 2 and Python 3.  However, we can decide that we don't
care.  This commit treats both of them the same when `py_ver_consistent` is set with
`unparse()`.

This means that the package hash won't notice changes from printing a tuple to printing
multiple values, but we don't care, because this is extremely unlikely to affect the build.
More than likely this is just an error message for the user of the package.

- [x] treat `print(a, b, c)` and `print((a, b, c))` the same in py2 and py3
- [x] add another package parsing test -- legion -- that exercises this feature
…ream

These are refactors that have happened in upstream `ast.unparse()`
These refactors have happened in upstream `ast.unparse()`
These are the unit tests from astunparse, converted to pytest, with a few backports from
upstream cpython. These should hopefully keep `unparser.py` well covered as we change it.
Many packages implement logic at the class level to handle complex dependencies and
conflicts. Others have started using `with when("@1.0"):` blocks since we added that
capability. The loops and other control logic can cause some pure directive logic not to
be removed by our package hashing logic -- and in many cases that's a lot of code that
will cause unnecessary rebuilds.

This commit changes the unparser so that it will descend into these blocks. Specifically:

  1. Descend into loops, if statements, and with blocks at the class level.
  2. Don't look inside function definitions (in or outside a class).
  3. Don't look at nested class definitions (they don't have directives)
  4. Add logic to *remove* empty loops/with blocks/if statements if all directives
     in them were removed.

This allows our package hash to ignore a lot of pure metadata that it was not ignoring
before, and makes it less sensitive.

In addition, we add `maintainers` and `tags` to the list of metadata attributes that
Spack should remove from packages when constructing canonoical source for a package
hash.

- [x] Make unparser handle if/for/while/with at class level.
- [x] Add tests for control logic removal.
- [x] Add a test to ensure that all packages are not only unparseable, but also
      that their canonical source is still compilable. This is a test for
      our control logic removal.
- [x] Add another unparse test package that has complex logic.
Charm++ versions below 7.0.0 have build issues on macOS, mainly due to the
pre-7.0.0 `VERSION` file conflicting with other version files on the
system: charmplusplus/charm#2844. Specifically, it
conflicts with LLVM's `<version>` header that was added in [email protected] to
comply with the C++20 standard:
https://en.cppreference.com/w/cpp/header/version. The conflict only occurs
on case-insensitive file systems, as typically used on macOS machines.
spack paths can be long and this overflows (at least) these buffers
inside of the bundled T1lib inside of the grace distribution, leading
to crashes on startup.
Backport a patch for v1.3.4 that fixes an unsigned typedef problem
on macOS: xiph/ogg#64

Also add v1.3.5 that has this issue fixed.
When `spack compiler list` is run without being restricted to a
particular scope, and no compilers are found, say that none are 
available, and hint that the use should run spack compiler find to 
auto detect compilers.

* Improve docs
* Check if stdin is a tty
* add a test
* Add new package to spack.  survey is a lightweight application performance tool that also gathers system information and stores it as metadata.

* Add maintainer and note about source access.

* Update the man path per spack reviewer suggestion.

* Remove redundant settings for PYTHONPATH, PATH, and MANPATH.

* Move to a one mpi collector approach for cce/tce integration.

* Add pyyaml dependency

* Make further spack reviewer changes to python type specs, mpi args, build type variant.

* Add reviewer requested changes.

* Add reviewer docstring requested changes.

* Add more updates from spack reviewer comments.

* Update the versions to use tags, not branches

* Redo dashes to fix issue with spack testing.

Co-authored-by: Jim Galarowicz <[email protected]>
msimberg and others added 22 commits February 1, 2022 11:44
Co-authored-by: Mikael Simberg <[email protected]>
- deprecate versions 2 and 3
- set needed opencv variants
- adjust proj constraint
- patch header path for opencv
…8523)

* rct: update packages (RE, RP, RS, RU) with new versions

* rct: minor version release for RP

* rct: fixed versions for dependencies (RS and RU)
Fixes the following build failure when building with gcc 11:

         478    ../../../../CPP/7zip/Archive/Wim/WimHandler.cpp: In member function 'virtual LONG NArchive::NWim::CHandler::GetArchiveProperty(PROPID, PROPVARIANT*)':
      >> 479    ../../../../CPP/7zip/Archive/Wim/WimHandler.cpp:308:11: error: use of an operand of type 'bool' in 'operator++' is forbidden in C++17
         480      308 |           numMethods++;
         481          |           ^~~~~~~~~~
      >> 482    ../../../../CPP/7zip/Archive/Wim/WimHandler.cpp:318:9: error: use of an operand of type 'bool' in 'operator++' is forbidden in C++17
         483      318 |         numMethods++;
         484          |         ^~~~~~~~~~
Do not silently turn off fortran support based on checking if
a fortran compiler exists. Let the build fail if there is no
working fortran compiler.
[email protected]: is required for the new version of vtkHDFReader
- To retrieve the correct spack version we need to get it from the git
  repo.

- Recommend installing the package with root for production

- Add Tomas as maintainer to sarus' spack package

- Add the option to disable unit tests in latest versions
@dependabot dependabot bot added the dependencies Pull requests that update a dependency file label Mar 2, 2022
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dependabot bot commented on behalf of github Mar 22, 2022

Dependabot tried to update this pull request, but something went wrong. We're looking into it, but in the meantime you can retry the update by commenting @dependabot rebase.

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dependabot bot commented on behalf of github Apr 6, 2022

Dependabot tried to update this pull request, but something went wrong. We're looking into it, but in the meantime you can retry the update by commenting @dependabot rebase.

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dependabot bot commented on behalf of github Apr 15, 2022

Superseded by #23.

@dependabot dependabot bot closed this Apr 15, 2022
@dependabot dependabot bot deleted the dependabot/github_actions/actions/checkout-3 branch April 15, 2022 10:11
RikkiButler20 pushed a commit that referenced this pull request Apr 25, 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 #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 #14: GradHessianTest ..................   Passed    0.01 sec
      Start 16: PCE1dTest
13/31 Test #15: GradientPCETest ..................   Passed    0.01 sec
      Start 17: PCEImplTest
14/31 Test #16: PCE1dTest ........................   Passed    0.01 sec
      Start 18: PCELogTest
15/31 Test #18: PCELogTest .......................   Passed    0.01 sec
      Start 19: Hessian2dTest
16/31 Test #19: Hessian2dTest ....................   Passed    0.01 sec
      Start 20: BCS1dTest
17/31 Test #20: BCS1dTest ........................   Passed    0.01 sec
      Start 21: BCS2dTest
18/31 Test #21: BCS2dTest ........................   Passed    0.01 sec
      Start 22: LowRankRegrTest
19/31 Test #22: LowRankRegrTest ..................   Passed    0.01 sec
      Start 23: PyModTest
20/31 Test #17: PCEImplTest ......................   Passed    0.07 sec
      Start 24: PyArrayTest
21/31 Test #23: PyModTest ........................   Passed    0.08 sec
      Start 25: PyArrayTest2
22/31 Test #25: PyArrayTest2 .....................   Passed    0.30 sec
      Start 26: PyQuadTest
23/31 Test #24: PyArrayTest ......................   Passed    1.44 sec
      Start 27: PyBCSTest1D
24/31 Test #26: PyQuadTest .......................   Passed    1.68 sec
      Start 28: PyBCSTest2D
25/31 Test #27: PyBCSTest1D ......................   Passed    1.66 sec
      Start 29: PyBADPTest
26/31 Test  #7: CorrTest .........................   Passed    3.43 sec
      Start 30: PyRegressionTest
27/31 Test #28: PyBCSTest2D ......................   Passed    1.50 sec
      Start 31: PyGalerkinTest
28/31 Test  #9: MCMC2dTest .......................   Passed    3.90 sec
29/31 Test #29: PyBADPTest .......................   Passed    1.66 sec
30/31 Test #30: PyRegressionTest .................   Passed    1.72 sec
31/31 Test #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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