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2023-05-01heaptrack: add v1.3.0 (#37327)Alec Scott1-0/+1
2023-05-01mixcr: add v4.3.2 (#37336)Alec Scott1-0/+1
2023-05-01c-blosc: add v1.21.2 (#37317)Alec Scott1-0/+1
2023-05-01nginx: add v1.24.0 (#37339)Alec Scott1-0/+1
2023-05-01alembic: add v1.8.5 (#37315)Alec Scott1-0/+1
2023-05-01tippecanoe: add v1.36.0 (#37313)Alec Scott1-0/+1
2023-05-01mpi-bash: add v1.3 (#37337)Alec Scott1-0/+1
2023-05-01petsc, py-petsc4py: add v3.19.1 (#37356)Satish Balay2-0/+2
2023-05-01Update py-editdistance@0.6.2 (#37365)Benjamin Meyers1-0/+8
* Update py-editdistance@0.6.2 * [@spackbot] updating style on behalf of meyersbs
2023-05-01console-bridge: add v1.0.2 (#37321)Alec Scott1-0/+1
2023-05-01dropwatch: add v1.5.4 (#37322)Alec Scott1-0/+1
2023-05-01flibcpp: add v1.0.2 (#37323)Alec Scott1-0/+1
2023-05-01helib: add v2.2.2 (#37328)Alec Scott1-0/+1
2023-05-01hunspell: add v1.7.2 (#37329)Alec Scott1-0/+1
2023-05-01procenv: add v0.60 (#37343)Alec Scott1-0/+1
2023-05-01restic: add v0.15.2 (#37345)Alec Scott1-0/+1
2023-05-01shapeit4: add v4.2.2 (#37347)Alec Scott1-0/+1
2023-05-01py-sphinx: add v7.0.0 (#37352)Adam J. Stewart1-0/+2
2023-05-01scons: add v4.5.2 (#37346)Alec Scott1-0/+1
2023-05-01Factor YAML manifest manipulation out of the Environment class (#36927)Massimiliano Culpo14-502/+978
Change the signature of the Environment.__init__ method to have a single argument, i.e. the directory where the environment manifest is located. Initializing that directory is now delegated to a function taking care of all the error handling upfront. Environment objects require a "spack.yaml" to be available to be constructed. Add a class to manage the environment manifest file. The environment now delegates to an attribute of that class the responsibility of keeping track of changes modifying the manifest. This allows simplifying the updates of the manifest file, and helps keeping in sync the spec lists in memory with the spack.yaml on disk.
2023-05-01Revert "new package: roentdek (#37265)" (#37355)eugeneswalker1-33/+0
This reverts commit fec20bb567af73fee6a796447fc19af65a0fc52f.
2023-04-29Feature/topiary (#37157)snehring13-0/+339
* generax: adding new package generax * muscle5: adding new package muscle5 * py-custom-inherit: adding new package py-custom-inherit * py-ete3: adding new package py-ete3 * py-itolapi: adding new package py-itolapi * py-opentree: adding new package py-opentree * py-pypng: adding new package py-pypng * py-toyplot: adding new package py-toyplot * py-toytree: adding new package py-toytree * py-pastml: adding new package py-pastml * raxml-ng: adding new version 1.1.0 * py-topiary: adding new package py-topiary * generax: adding master branch version generax: adding version 2.0.1 generax: add mpi variant * py-topiary: add main * generax: correcting commit for 2.0.1 * Update var/spack/repos/builtin/packages/py-itolapi/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-opentree/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * py-topiary-asr: rename package, requested changes. * Update var/spack/repos/builtin/packages/py-topiary-asr/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-04-29py-nipype: add 1.8.6 (#37279)Manuela Kuhn1-2/+4
* py-nipype: add 1.8.6 * Exchange test dep with skip_modules
2023-04-28Spec.format: fix bug in dependency hash formatting (#37073)Greg Becker2-60/+58
Co-authored-by: becker33 <becker33@users.noreply.github.com>
2023-04-28new package: py-amityping (#37262)eugeneswalker1-0/+21
2023-04-28libmaxminddb: add v1.7.1 (#37185)Alec Scott1-0/+1
2023-04-28superlu-dist: do not discard cflags from Spack (#37260)Victor Brunini1-11/+14
Make sure to append additional flags needed for specific compilers in the flag_handler instead of adding them as separate cmake define lines that override the main spack cflags.
2023-04-28Reduce the number of stat calls in "spack verify" (#37251)Harmen Stoppels2-66/+47
Spack comes to a crawl post-install of nvhpc, which is partly thanks to this post install hook which has a lot of redundancy, and isn't correct. 1. There's no need to store "type" because that _is_ "mode". 2. There are more file types than "symlink", "dir", "file". 3. Don't checksum device type things 4. Don't run 3 stat calls (exists, stat, isdir/islink), but one lstat call 5. Don't read entire files into memory I also don't know why `spack.crypto` wasn't used for checksumming, but I guess it's too late for that now. Finally md5 would've been the faster algorithm, which would've been fine given that a non cryptographicall checksum was used anyways.
2023-04-28Fixing patch version constraint for llvm external ncurses patch (#37145)dale-mittleman1-2/+2
2023-04-28libxml2: fix test method (#37242)Massimiliano Culpo1-1/+1
This was discovered using #34236
2023-04-28new package: roentdek (#37265)eugeneswalker1-0/+33
2023-04-28new package: py-pyabel (#37264)eugeneswalker1-0/+22
2023-04-28new package: xtcdata (#37261)eugeneswalker1-0/+19
2023-04-28sentieon-genomics: adding new version 20211207. (#37223)snehring1-0/+1
2023-04-28Add container images supporting RHEL alternatives (#36713)Jonathon Anderson8-1/+267
Add container support for AlmaLinux, Fedora 37 and 38 and Rocky Linux
2023-04-28kicad: new version 7.0.2 (#37228)Andrew W Elble3-1/+25
2023-04-28slurm: add version 22-05-8-1 and 23-02-1-1 (#37238)Richard Berger1-0/+2
2023-04-28py-psycopg2: add v2.9.6 (#37235)Adam J. Stewart1-5/+17
2023-04-28bricks: Fix package to properly find spack opencl-clhpp (#37239)John Jolly2-2/+22
The bricks package uses header from the opencl-clhpp package when built with the cuda variant activated. In order to find the header files, the bricks CMakeLists.txt uses the `find_package(OpenCL 2.0)` statement. The CMake FindOpenCL module searches several paths to find the header files. Eventually it will search for header files in the local /usr/include directories. If OpenCL headers are found, but CUDA is not installed locally, then the build will fail. One of the CMake variables searched for a path to the OpenCL headers is OCL_ROOT. This fix utilizes the OCL_ROOT variable to identify the correct path to the install opencl-clhpp package within Spack. Also, if the cuda variant is not used, then the OpenCL build is disabled to prevent a build failure due to improperly-identified locally-installed OpenCL header files. The default behavior of the build process has not changed. An external variable definitions must be made to activate these features. Specifically, to disable the OpenCL build, this flag must be provided to CMake: -DBRICK_USE_OPENCL=OFF The Spack build process explicitly uses this option unless the cuda variant is specified. If the cuda variant is specified, then the BRICK_USE_OPENCL variable is set to ON and the OCL_ROOT variable is set to the path of the opencl-clhpp include directory.
2023-04-28apfel: add v3.0.6 (#37267)Alec Scott1-0/+1
2023-04-28cmor: add v3.7.2 (#37268)Alec Scott1-0/+1
2023-04-28figtree: add v1.4.4 (#37269)Alec Scott1-0/+1
2023-04-28fping: add v5.1 (#37270)Alec Scott1-0/+1
2023-04-28gapbs: add v1.4 (#37271)Alec Scott1-0/+1
2023-04-28glfw: add v3.3.8 (#37272)Alec Scott1-0/+1
2023-04-28jemalloc: add v5.3.0 (#37273)Alec Scott1-0/+1
2023-04-28sandbox: add v2.25 (#37274)Alec Scott1-0/+1
2023-04-28snap-berkeley: add v2.0.3 (#37275)Alec Scott1-0/+1
2023-04-28tcpdump: add v4.99.4 (#37276)Alec Scott1-0/+1
2023-04-28wps: add v4.5 (#37277)Alec Scott1-0/+1