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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
2023-05-01Revert "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
2023-04-28new 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.
2023-04-28Fixing 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
2023-04-28kicad: 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
2023-04-28py-subword-nmt (#37161)Sangu Mbekelu1-0/+19
* "new py-subword-nmt package" * [@spackbot] updating style on behalf of Sangu-Mbekelu * Update package.py updating package based on review * [@spackbot] updating style on behalf of Sangu-Mbekelu --------- Co-authored-by: Sangu Mbekelu <s.mbekelu9@gmail.com>
2023-04-27py-virtualenv: add 20.22.0 (#37259)Manuela Kuhn4-29/+55
* py-virtualenv: add 20.22.0 * [@spackbot] updating style on behalf of manuelakuhn * Fix dependency versions for release 20.22.0 * Remove python version restrictions * [@spackbot] updating style on behalf of manuelakuhn * py-platformdirs: add 3.5.0 * py-filelock: add 3.12.0 * Fix dependency bound for py-platformdirs * py-importlib-metadata: add 6.6.0
2023-04-27macOS: use Apple GL/GLU by default (#36618)Adam J. Stewart2-21/+7
* macOS: use Apple GL/GLU by default * Use CLT instead * Use CLT instead * Undo change to libuuid
2023-04-27legion: add versions up to 23.03.0 (#37257)eugeneswalker1-1/+9
* legion: add versions up to 23.03.0 * add maintainer
2023-04-27[py-breathe] New version 4.35.0 (#37233)Chris Green1-1/+3
* [py-breathe] New version 4.35.0 * Update var/spack/repos/builtin/packages/py-breathe/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-04-27fixes #29350 by enabling headers variant in binutils when compiling llvm ↵Thomas-Ulrich1-1/+1
with gold (#37245)
2023-04-27py-memory-profiler: add 0.61.0 (#37248)Manuela Kuhn1-0/+2
2023-04-27[py-sphinx-design] New versions 0.4.0, 0.4.1 (#37234)Chris Green1-1/+4
* [py-sphinx-design] New versions 0.4.0, 0.4.1 * conflicts() -> depends_on() Per @adamjstewart Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-04-27gcc: add v13.1.0 (#37230)Massimiliano Culpo1-1/+6
version 13.1 builds with apple-clang@14.0.3
2023-04-27gcc: no need to special case macos/linux wrt rpaths (#37243)Harmen Stoppels1-6/+1
2023-04-27Fix pkgconfig dependencies (#37236)Michael Kuhn7-7/+7
Packages shouldn't typically depend on pkg-config or pkgconf but on the virtual provider pkgconfig.
2023-04-27r-covr: add v3.6.2 (#37194)Alec Scott1-0/+1
2023-04-26py-gssapi: depends_on krb5 (#37227)Wouter Deconinck1-0/+1
This dependency was somehow overlooked (but is pretty crucial) because it doesn't appear in the python requirements...
2023-04-26py-bidscoin: add 4.0.0 and py-pydeface as new deb package (#37231)Manuela Kuhn2-0/+28
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