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2021-08-28Add a __reduce__ method to Spec (#25658)Massimiliano Culpo1-22/+38
* Add a __reduce__ method to Spec fixes #23892 The recursion limit seems to be due to the default way in which a Spec is serialized, following all the attributes. It's still not clear to me why this is related to being in an environment, but in any case we already have methods to serialize Specs to disk in JSON and YAML format. Here we use them to pickle a Spec instance too. * Downgrade to build-hash Hopefully nothing will change the package in between serializing the spec and sending it to the child process. * Add support for Python 2
2021-08-28recorder: add v2.2.1, v2.2.0, "master" and "pilgrim" (#25674)Chen Wang1-0/+5
2021-08-27Add zstd support to libarchive (#25659)Harmen Stoppels1-7/+6
2021-08-27py-flit: add maintainer (#25667)Adam J. Stewart2-3/+2
2021-08-27add py-flameprof (#25539)Harmen Stoppels1-0/+19
2021-08-27Fix: --overwrite backs up old install dir, but it gets destroyed anyways ↵Harmen Stoppels3-5/+30
(#25583) * Make sure PackageInstaller does not remove the just-restored install dir after failure in spack install --overwrite * Remove cryptic error message and rethrow actual error
2021-08-27Load package environment prior to stand-alone/smoke test execution (#25619)Tamara Dahlgren1-0/+9
2021-08-27Add missing link dep for py-uwsgi (#25654)Harmen Stoppels1-0/+1
2021-08-27py-psycopg2: add version 2.9.1 (#25646)Adam J. Stewart1-3/+6
2021-08-27py-pathlib: prevent conflicts with standard library (#25631)Adam J. Stewart3-2/+10
2021-08-27New package: py-flit (#25630)Adam J. Stewart2-0/+48
2021-08-27FEniCSx packages: add version 0.3.0 (#25627)Chris Richardson5-8/+33
2021-08-27py-pyinstrument: add version 4.0.3 (#25632)Adam J. Stewart1-6/+9
* Swap github download link for pypi * Versions >= 4 dont need npm
2021-08-27r-irkernel: add version 1.2; update version 0.7 (#25644)Dylan Simon1-1/+2
Use a commit hash instead of a tag for 0.7
2021-08-27figlet: Fix figlet font dir (#25662)Jordan Galby1-0/+4
By default, figlet looks for fonts in `/usr/local/share/figlet`, and if it doesn't exist you get `figlet: standard: Unable to open font file`. This fix changes the default font dir to the one installed in the install prefix.
2021-08-27ESMF package: add version 8.1.1 (#25590)Timothy Brown1-5/+5
Also build with internal lapack library by default.
2021-08-27meson: add 0.59.1 and 0.58.2 (#25661)Michael Kuhn1-0/+2
2021-08-27glib: add 2.68.4 (#25660)Michael Kuhn1-0/+1
2021-08-27Add ld.gold and ld.lld compiler wrapper (#25626)Jordan Galby4-1/+4
The gcc compiler can be configured to use `ld.gold` by default. It will then call `ld.gold` explicitly when linking. When so, spack need to have a ld.gold wrapper in PATH to inject rpaths link flags etc... Also I wouldn't be surprised to see some package calling `ld.gold` directly. As for ld.gold, the argument could be made that we want to support any package that could call ld.lld.
2021-08-27Make `SpecBuildInterface` pickleable (#25628)Massimiliano Culpo2-1/+10
* Add a __reduce__ method to SpecBuildInterface This class was confusing pickle when being serialized, due to its scary nature of being an object that disguise as another type. * Add more MacOS tests, switch them to clingo * Fix condition syntax * Remove Python v3.6 and v3.9 with macOS
2021-08-27Fix fish test "framework" (#25242)Harmen Stoppels1-34/+16
Remove broken test, see #21699
2021-08-27adding remainder of issues from repology problems (#25653)Vanessasaurus144-145/+147
some of these are not resolvable in that there is only an http page available, or a page reported as broken is actually ok, or a page has an SSL error that does not prevent one from visiting (and no good replacement) Signed-off-by: vsoch <vsoch@users.noreply.github.com> Co-authored-by: vsoch <vsoch@users.noreply.github.com>
2021-08-27Add ReFrame 3.8.0 (#25648)Vasileios Karakasis1-0/+1
2021-08-26Incorporate intel-tbb-oneapi package into intel-tbb package (#25613)Patrick Gartung1-6/+39
* Add intel-tbb-oneapi package that does the cmake configure and build. Compare too the intel-oneapi-tbb package which only downloads a script that contains prebuilt binaries. * Rename package intel-tbb-cmake * Incorporate intel-tbb-cmake into intel-tbb package
2021-08-26Make env (de)activate error with -e, -E, -D flags (#25625)Harmen Stoppels2-0/+33
* Make sure that spack -e. env activate b and spack -e. env deactivate error * Add a test
2021-08-26py-black: add new version, missing dep (#25629)Adam J. Stewart2-2/+31
2021-08-26activeharmony: Switch to https (#25641)Tamara Dahlgren1-2/+2
2021-08-26acl: Switch to https (#25640)Tamara Dahlgren1-1/+1
2021-08-26ACE: Switch to https (#25638)Tamara Dahlgren1-2/+2
2021-08-26adlbx: switch url to https (#25642)Tamara Dahlgren1-1/+1
2021-08-26py-vermin: add latest version 1.2.2 (#25643)Morten Kristensen1-1/+2
2021-08-26New package: reprimand (#25364)Erik Schnetter2-0/+89
2021-08-26Conditionally remove 'context' from kwargs in _urlopen (#25316)Paul Kuberry1-3/+9
* Conditionally remove 'context' from kwargs in _urlopen Previously, 'context' is purged from kwargs in _urlopen to conform to varying support for 'context' in different versions of urllib. This fix tries to use 'context', and then removes it if an exception is thrown and tries again. * Specify error type in try statement in _urlopen Specify TypeError when checking if 'context' is in kwargs for _urlopen. Also, if try fails, check that 'context' is in the error message before removing from kwargs.
2021-08-26Speedup environment activation, part 2 (#25633)Adam J. Stewart5-113/+90
This is a direct followup to #13557 which caches additional attributes that were added in #24095 that are expensive to compute. I had to reopen #25556 in another PR to invalidate the GitLab CI cache, but see #25556 for prior discussion. ### Before ```console $ time spack env activate . real 2m13.037s user 1m25.584s sys 0m43.654s $ time spack env view regenerate ==> Updating view at /Users/Adam/.spack/.spack-env/view real 16m3.541s user 10m28.892s sys 4m57.816s $ time spack env deactivate real 2m30.974s user 1m38.090s sys 0m49.781s ``` ### After ```console $ time spack env activate . real 0m8.937s user 0m7.323s sys 0m1.074s $ time spack env view regenerate ==> Updating view at /Users/Adam/.spack/.spack-env/view real 2m22.024s user 1m44.739s sys 0m30.717s $ time spack env deactivate real 0m10.398s user 0m8.414s sys 0m1.630s ``` Fixes #25555 Fixes #25541 * Speedup environment activation, part 2 * Only query distutils a single time * Fix KeyError bug * Make vermin happy * Manual memoize * Add comment on cross-compiling * Use platform-specific include directory * Fix multiple bugs * Fix python_inc discrepancy * Fix import tests
2021-08-26aws-parallelcluster: add v2.11.2 (#25635)Enrico Usai1-1/+2
Signed-off-by: Rex <shuningc@amazon.com>
2021-08-26fixing "problems in speck" as identified by repology (#25491)Vanessasaurus378-393/+394
Most of these are perl packages that need to point to the meta docs site, and then a fair amount of http addresses that need to be https, and then the rest are usually documentation sites that no longer exist or were otherwise changes Signed-off-by: vsoch <vsoch@users.noreply.github.com> Co-authored-by: vsoch <vsoch@users.noreply.github.com>
2021-08-26Set pubkey trust to ultimate during `gpg trust` (#24976)Harmen Stoppels1-3/+42
* Set pubkey trust to ultimate during `gpg trust` Tries to solve the same problem as #24760 without surpressing stderr from gpg commands. This PR makes every imported key trusted in the gpg database. Note: I've outlined [here](https://github.com/spack/spack/pull/24760#issuecomment-883183175) that gpg's trust model makes sense, since how can we trust a random public key we download from a binary cache? * Fix test
2021-08-26Ensure environment are deactivated when bootstrapping (#25607)Massimiliano Culpo5-23/+52
Fixes #25603 This commit adds a new context manager to temporarily deactivate active environments. This context manager is used when setting up bootstrapping configuration to make sure that the current environment is not affected by operations on the bootstrap store. * Preserve exit code 1 if nothing is found * Use context manager for the environment
2021-08-26opencl-c-headers and opencl-clhpp: add new versions (#25576)lorddavidiii2-0/+4
2021-08-26py-omegaconf: add missing dependency (#25589)Adam J. Stewart1-0/+1
2021-08-26opium package: add version 4.1 and update blas/lapack dependencies (#25591)Glenn Johnson1-12/+17
- remove unneeded dependency on blas - create external-lapack variant - patch makefile to not build lapack if `+external-lapack` Also: - fix homepage link - set parallel = False - make references to `spec` consistent - remove unneeded `build` method
2021-08-26Remove references to self.install_test_root from packaging guide (#25238)Tamara Dahlgren1-27/+19
2021-08-26Avoid double loop in subprocess_context.store_patches (#25621)Massimiliano Culpo1-10/+9
fixes #21643 As far as I can see the double loop is not needed, since "patch" is never used and the items in the list are tuples of three values.
2021-08-26Remove fork_context from llnl.util.lang (#25620)Massimiliano Culpo1-18/+0
This object was introduced in #18124, and was later superseded by #18205 and removed any use if the object.
2021-08-26Regression test for version selection with preferences (#25602)Massimiliano Culpo5-0/+60
This commit adds a regression test for version selection with preferences in `packages.yaml`. Before PR 25585 we used negative weights in a minimization to select the optimal version. This may lead to situations where a dependency may make the version score of dependents "better" if it is preferred in packages.yaml.
2021-08-26zstd package: use make instead of CMake (#25610)Harmen Stoppels2-32/+17
zstd doesn't use -pthread for the static lib anymore, so gcc should be fine
2021-08-26VTK: add version 9.0.3 (#25609)Rémi Lacroix1-0/+1
2021-08-26fixing bugs with new package updates for samtools and abi-dum (#25615)Vanessasaurus2-0/+3
samtools needed more constraints for htslib, and abi-dumper was missing pkg-config on the dependency universal ctags Signed-off-by: vsoch <vsoch@users.noreply.github.com> Co-authored-by: vsoch <vsoch@users.noreply.github.com>
2021-08-25Bugfix: reinstalling updated develop specs (#25579)Harmen Stoppels1-6/+2
PackageInstaller and Package.installed disagree over what it means for a package to be installed: PackageInstaller believes it should be enough for a database entry to exist, whereas Package.installed requires a database entry & a prefix directory. This leads to the following niche issue: * a develop spec in an environment is successfully installed * then somehow its install prefix is removed (e.g. through a bug fixed in #25583) * you modify the sources and reinstall the environment 1. spack checks pkg.installed and realizes the develop spec is NOT installed, therefore it doesn't need to have 'overwrite: true' 2. the installer gets the build task and checks the database and realizes the spec IS installed, hence it doesn't have to install it. 3. the develop spec is not rebuilt. The solution is to make PackageInstaller and pkg.installed agree over what it means to be installed, and this PR does that by dropping the prefix directory check from pkg.installed, so that it only checks the database. As a result, spack will create a build task with overwrite: true for the develop spec, and the installer in fact handles overwrite requests fine even if the install prefix doesn't exist (it just does a normal install).
2021-08-26py-grpcio: set parallel build jobs (#25616)Xiao-Yong1-0/+3
By default the number of parellel compiler processes launched by py-grpcio equals the number of threads. This commit limit it to spack config build_jobs.
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