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2022-12-02py-nilearn: fix dependency version (#34284)Manuela Kuhn1-1/+1
2022-12-02patch command: add concretizer args (#34282)Greg Becker2-1/+2
* patch command: add concretizer args * tab completion
2022-12-02ROOT: add math/gsl conflict and change version-dependent features to ↵Seth R. Johnson1-10/+7
conditional variants (#34244) * ROOT: add GSL/math dependency * ROOT: use conditional variants instead of conflicts
2022-12-02py-neurokit2: add 0.2.2 (#34267)Manuela Kuhn1-0/+2
2022-12-02feat(Hermes): update version to 0.9.0-beta. (#34243)H. Joe Lee1-3/+3
* feat(Hermes): update version to 0.9.0-beta. This is the latest release. * feat(Hermes): fix checksum. Credit: @tldahlgren
2022-12-02Docs: Minor change 'several'->'over a dozen' (#34274)Tamara Dahlgren1-1/+1
2022-12-02concretizer: use only `attr()` for Spec attributes (#31202)Todd Gamblin4-430/+409
All Spec attributes are now represented as `attr(attribute_name, ... args ...)`, e.g. `attr(node, "hdf5")` instead of `node("hdf5")`, as we *have* to maintain the `attr()` form anyway, and it simplifies the encoding to just maintain one form of the Spec information. Background ---------- In #20644, we unified the way conditionals are done in the concretizer, but this introduced a nasty aspect to the encoding: we have to maintain everything we want in general conditions in two forms: `predicate(...)` and `attr("predicate", ...)`. For example, here's the start of the table of spec attributes we had to maintain: ```prolog node(Package) :- attr("node", Package). virtual_node(Virtual) :- attr("virtual_node", Virtual). hash(Package, Hash) :- attr("hash", Package, Hash). version(Package, Version) :- attr("version", Package, Version). ... ``` ```prolog attr("node", Package) :- node(Package). attr("virtual_node", Virtual) :- virtual_node(Virtual). attr("hash", Package, Hash) :- hash(Package, Hash). attr("version", Package, Version) :- version(Package, Version). ... ``` This adds cognitive load to understanding how the concretizer works, as you have to understand the equivalence between the two forms of spec attributes. It also makes the general condition logic in #20644 hard to explain, and it's easy to forget to add a new equivalence to this list when adding new spec attributes (at least two people have been bitten by this). Solution -------- - [x] remove the equivalence list from `concretize.lp` - [x] simplify `spec_clauses()`, `condition()`, and other functions in `asp.py` that need to deal with `Spec` attributes. - [x] Convert all old-form spec attributes in `concretize.lp` to the `attr()` form - [x] Simplify `display.lp`, where we also had to maintain a list of spec attributes. Now we only need to show `attr/2`, `attr/3`, and `attr/4`. - [x] Simplify model extraction logic in `asp.py`. Performance ----------- This seems to result in a smaller grounded problem (as there are no longer duplicated `attr("foo", ...)` / `foo(...)` predicates in the program), but it also adds a slight performance overhead vs. develop. Ultimately, simplifying the encoding will be a win, particularly for improving error messages. Notes ----- This will simplify future node refactors in `concretize.lp` (e.g., not identifying nodes by package name, which we need for separate build dependencies). I'm still not entirely used to reading `attr()` notation, but I thnk it's ultimately clearer than what we did before. We need more uniform naming, and it's now clear what is part of a solution. We should probably continue making the encoding of `concretize.lp` simpler and more self-explanatory. It may make sense to rename `attr` to something like `node_attr` and to simplify the names of node attributes. It also might make sense to do something similar for other types of predicates in `concretize.lp`.
2022-12-02py-keyrings-alt: add 4.2.0 (#34262)Manuela Kuhn1-0/+5
* py-keyrings-alt: add 4.2.0 * Add missing py-jaraco-classes dependency
2022-12-02Add checksum for py-hatchling 1.8.1 (#34260)iarspider1-0/+1
2022-12-02Bugfix: Fetch should not force use of curl to check url existence (#34225)Tamara Dahlgren1-3/+3
* Bugfix: Fetch should not force use of curl to check url existence * Switch type hints from comments to actual hints
2022-12-01py-flask: add 2.2.2 and fix dependencies for py-werkzeug and py-markupsafe ↵Manuela Kuhn3-5/+13
(#32849) * py-flask: add 2.2.2, py-werkzeug: add 2.2.2, py-markupsafe: add 2.1.1 * Remove py-dataclasses dependency
2022-12-01Herwig3: make njet, vbfnlo dependencies optional... (#33941)iarspider1-8/+17
* Herwig3: make njet, vbfnlo dependencies optional... also drop openloops dependency when building on PowerPC * Update package.py
2022-12-01py-twine: add 4.0.1, py-readme-renderer: add 37.3 (#34203)Manuela Kuhn2-3/+22
* py-twine: add 4.0.1 * Remove py-setuptools as run dependency
2022-12-01acfl: add post-installation check by running examples (#34172)Annop Wongwathanarat1-0/+9
2022-12-01Add py-python-lsp-server and dependencies (#34149)Alec Scott3-0/+66
* Add py-python-lsp-server and dependencies * Update var/spack/repos/builtin/packages/py-python-lsp-server/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Relax version range constraints on py-python-lsp-jsonrpc and add missing dep * Add runtime dependency flag to setuptools dependencies * Remove unused python@3.6: dependency and move setuptools-scm to build dep only Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-12-01gnuplot: make readline optional (#34179)iarspider1-2/+4
* gnuplot: make readline optional * Update package.py Co-authored-by: iarspider <iarspider@users.noreply.github.com>
2022-12-01conditional variant values: allow boolean (#33939)Greg Becker3-17/+46
2022-11-30py-scipy: hardcode to use blis.pc (#34171)Adam J. Stewart1-10/+5
2022-11-30Add HDF5 version 1.13.3. (#34165)Larry Knox1-3/+1
* Add HDF5 version 1.13.3. * Remove maintainers no longer with The HDFGroup. * Fix indentation.
2022-11-30redis-plus-plus: newer version and added TLS support (#34197)Loïc Pottier1-1/+7
Signed-off-by: Loïc Pottier <pottier1@llnl.gov>
2022-11-30py-segmentation-models-pytorch: add v0.3.1 (#34214)Adam J. Stewart1-1/+1
2022-11-30new w3emc version (#34219)Edward Hartnett1-0/+1
* updated version of w3emc package * fixed sha
2022-11-30Add py-yt 4.x versions (#30418)Sam Grayson4-45/+124
* Add py-yt 4.x versions * Fix spelling * Add yt dependencies * Refine cython dependency * Tweak depends_on for py-yt 4.x * Apply suggestions from code review Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Fix comments from code review * Fix formatting * Fix stuff * Fix constraints * Update py-yt to 4.1.2 * Updated packages * Fix py-tomli checksum * Remove `expand` from `py-tomli/package.py` * Respond to Adam's comments * Update checksums * Update checksusm * Respond to comments Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-11-30e4s ci: use 2022-12-01 runner images (#34212)eugeneswalker2-4/+4
2022-11-30e4s ci: hpx: set max_cpu_count=512 (#33977)eugeneswalker2-4/+4
2022-11-30Add checksum for py-kiwisolver 1.4.4 (#34121)iarspider1-0/+5
2022-11-30Fix recipe for py-onnx-runtime (#34130)iarspider1-3/+8
* Fix recipe * Update package.py * Update recipe following review * Update var/spack/repos/builtin/packages/py-onnx-runtime/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * remove unused imports * Update package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-11-30PMIx: enable python bindings (#34107)Sajid Ali1-0/+6
2022-11-30Deduplicate code to propagate module changes across MRO (#34157)Massimiliano Culpo2-50/+22
2022-11-30Single pass text replacement (#34180)Harmen Stoppels2-34/+88
2022-11-29py-bidscoin, py-multiecho: add new packages (#34168)Manuela Kuhn2-0/+55
2022-11-29debug: move "nonexistent config path" message to much higher verbosity level ↵Todd Gamblin1-2/+2
(#34201) We currently report that searched config paths don't exist at debug level 1, which clutters the output quite a bit: ```console > spack -d solve --fresh --show asp hdf5 > hdf5.lp ==> [2022-11-29-14:18:21.035133] Skipping nonexistent config path /Users/gamblin2/src/spack/etc/spack/darwin/concretizer.yaml ==> [2022-11-29-14:18:21.035151] Skipping nonexistent config path /Users/gamblin2/.spack/concretizer.yaml ==> [2022-11-29-14:18:21.035169] Skipping nonexistent config path /Users/gamblin2/.spack/darwin/concretizer.yaml ==> [2022-11-29-14:18:21.035238] Reading config from file /Users/gamblin2/src/spack/etc/spack/defaults/repos.yaml ==> [2022-11-29-14:18:21.035996] Skipping nonexistent config path /Users/gamblin2/src/spack/etc/spack/defaults/darwin/repos.yaml ==> [2022-11-29-14:18:21.036021] Skipping nonexistent config path /etc/spack/repos.yaml ==> [2022-11-29-14:18:21.036039] Skipping nonexistent config path /etc/spack/darwin/repos.yaml ==> [2022-11-29-14:18:21.036057] Skipping nonexistent config path /Users/gamblin2/src/spack/etc/spack/repos.yaml ==> [2022-11-29-14:18:21.036072] Skipping nonexistent config path /Users/gamblin2/src/spack/etc/spack/darwin/repos.yaml ==> [2022-11-29-14:18:21.036088] Skipping nonexistent config path /Users/gamblin2/.spack/repos.yaml ==> [2022-11-29-14:18:21.036105] Skipping nonexistent config path /Users/gamblin2/.spack/darwin/repos.yaml ==> [2022-11-29-14:18:21.071828] Reading config from file /Users/gamblin2/src/spack/etc/spack/defaults/config.yaml ==> [2022-11-29-14:18:21.081628] Skipping nonexistent config path /Users/gamblin2/src/spack/etc/spack/defaults/darwin/config.yaml ==> [2022-11-29-14:18:21.081669] Skipping nonexistent config path /etc/spack/config.yaml ==> [2022-11-29-14:18:21.081692] Skipping nonexistent config path /etc/spack/darwin/config.yaml ==> [2022-11-29-14:18:21.081712] Skipping nonexistent config path /Users/gamblin2/src/spack/etc/spack/config.yaml ==> [2022-11-29-14:18:21.081731] Skipping nonexistent config path /Users/gamblin2/src/spack/etc/spack/darwin/config.yaml ==> [2022-11-29-14:18:21.081748] Skipping nonexistent config path /Users/gamblin2/.spack/config.yaml ==> [2022-11-29-14:18:21.081764] Skipping nonexistent config path /Users/gamblin2/.spack/darwin/config.yaml ==> [2022-11-29-14:18:21.134909] Reading config from file /Users/gamblin2/src/spack/etc/spack/defaults/packages.yaml ==> [2022-11-29-14:18:21.148695] Reading config from file /Users/gamblin2/src/spack/etc/spack/defaults/darwin/packages.yaml ==> [2022-11-29-14:18:21.152555] Skipping nonexistent config path /etc/spack/packages.yaml ==> [2022-11-29-14:18:21.152582] Skipping nonexistent config path /etc/spack/darwin/packages.yaml ==> [2022-11-29-14:18:21.152601] Skipping nonexistent config path /Users/gamblin2/src/spack/etc/spack/packages.yaml ==> [2022-11-29-14:18:21.152620] Skipping nonexistent config path /Users/gamblin2/src/spack/etc/spack/darwin/packages.yaml ==> [2022-11-29-14:18:21.152637] Skipping nonexistent config path /Users/gamblin2/.spack/packages.yaml ==> [2022-11-29-14:18:21.152654] Skipping nonexistent config path /Users/gamblin2/.spack/darwin/packages.yaml ==> [2022-11-29-14:18:21.853915] Skipping nonexistent config path /Users/gamblin2/src/spack/etc/spack/defaults/compilers.yaml ==> [2022-11-29-14:18:21.853962] Skipping nonexistent config path /Users/gamblin2/src/spack/etc/spack/defaults/darwin/compilers.yaml ==> [2022-11-29-14:18:21.853987] Skipping nonexistent config path /etc/spack/compilers.yaml ==> [2022-11-29-14:18:21.854007] Skipping nonexistent config path /etc/spack/darwin/compilers.yaml ==> [2022-11-29-14:18:21.854025] Skipping nonexistent config path /Users/gamblin2/src/spack/etc/spack/compilers.yaml ==> [2022-11-29-14:18:21.854043] Skipping nonexistent config path /Users/gamblin2/src/spack/etc/spack/darwin/compilers.yaml ==> [2022-11-29-14:18:21.854060] Skipping nonexistent config path /Users/gamblin2/.spack/compilers.yaml ==> [2022-11-29-14:18:21.854093] Reading config from file /Users/gamblin2/.spack/darwin/compilers.yaml ``` It is very rare that I want to know this much information about config search, so I've moved this to level 3. Now at level 1, we can see much more clearly what configs were actually found: ```console > spack -d solve --fresh --show asp hdf5 > hdf5.lp ==> [2022-11-29-14:19:04.035457] Imported solve from built-in commands ==> [2022-11-29-14:19:04.035818] Imported solve from built-in commands ==> [2022-11-29-14:19:04.037626] Reading config from file /Users/gamblin2/src/spack/etc/spack/defaults/concretizer.yaml ==> [2022-11-29-14:19:04.040033] Reading config from file /Users/gamblin2/src/spack/etc/spack/defaults/repos.yaml ==> [2022-11-29-14:19:04.080852] Reading config from file /Users/gamblin2/src/spack/etc/spack/defaults/config.yaml ==> [2022-11-29-14:19:04.133241] Reading config from file /Users/gamblin2/src/spack/etc/spack/defaults/packages.yaml ==> [2022-11-29-14:19:04.147175] Reading config from file /Users/gamblin2/src/spack/etc/spack/defaults/darwin/packages.yaml ==> [2022-11-29-14:19:05.157896] Reading config from file /Users/gamblin2/.spack/darwin/compilers.yaml ``` You can still get the old messages with `spack -ddd` (to activate debug level 3).
2022-11-29add 15.0.5, 15.0.6 (#34194)Paul R. C. Kent1-0/+2
2022-11-29CI: Update Data and Vis SDK Stack (#34009)kwryankrattiger3-77/+107
* CI: Update Data and Vis SDK Stack * Update image to match target deployments (E4S) * Enable all packages * Test supported variants of ParaView and VisIt * Sensei: Update Python hint for newer cmake * Sensei: add Python3 hint
2022-11-29icc@2021.6.0 does not support gcc@12 headers (#34191)Stephen Sachs1-0/+3
Error message: ``` /shared/spack/opt/spack/linux-amzn2-x86_64_v3/gcc-7.3.1/gcc-12.2.0-4tairupdxg2tg2yhvjdlbs7xbd7wudl3/bin/../include/c++/12.2.0/bits/random.h(104): error: expected a declaration { extension using type = unsigned __int128; }; ^ ``` Co-authored-by: Stephen Sachs <stesachs@amazon.com>
2022-11-29Dav sdk catalyst (#34010)kwryankrattiger2-2/+5
* SDK: Add Catalyst 1 and 2 support to the SDK * LibCatalyst: Remove unused python3 variant from package
2022-11-29evtgen: add v02.02.00 (#34187)Valentin Volkl1-1/+12
* evtgen: add v02.02.00 * format
2022-11-29Fix libxc cflag (#34000)Cristian Le1-1/+3
Using standard c99 should not be specific to intel compilers.
2022-11-29hiredis: updated package definition to use CMake (#33949)Loïc Pottier1-14/+45
2022-11-28Add maintainer to Exawind stack and Trilinos (#34174)psakievich4-4/+4
* Add maintainer to Nalu-Wind and Trilinos * Add to trilinos * Exawind too * amr-wind too
2022-11-28genfit: add v02-00-01 (#34159)Valentin Volkl1-0/+1
2022-11-28fix typo in path for sanity check (#34117)Hans Fangohr1-1/+1
- typo breaks install
2022-11-28Add new version of snakemake (#34041)Sam Grayson5-7/+116
* Add new version of snakemake * Add myself as a maintainer * py-retry -> py-reretry * Added snakemake variants for storage systems * Updated comments * Responded to Adam's comments * Fixed spack style * Add build/run dependency types
2022-11-28New package: py-statmorph (#34158)Benjamin Meyers4-1/+100
* New package py-statmorph w/ dependecies. Add py-astropy@5.1 * [@spackbot] updating style on behalf of meyersbs * [py-statmorph,py-astropy,py-pyerfa] minor fixes
2022-11-28New package: py-stui (#34156)Benjamin Meyers1-0/+22
* New package py-stui * [py-stui] add maintainer * [@spackbot] updating style on behalf of meyersbs * [py-stui] fix deps
2022-11-28Add checksum for py-rsa 4.9 (#34115)iarspider1-2/+5
* Add checksum for py-rsa 4.9 * Update package.py * Update var/spack/repos/builtin/packages/py-rsa/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-11-28omegah: new scorec version, fix cuda flags (#34169)Cameron Smith1-1/+9
2022-11-28e4s ci: add hdf5-vol-async; remove expired comments (#34110)eugeneswalker1-4/+1
2022-11-28petsc, py-petsc4py: add 3.18.2 (#34161)Satish Balay2-0/+2
2022-11-28py-bidskit: new package and dcm2niix: add 1.0.20220720 (#34162)Manuela Kuhn2-1/+31
* py-bidskit: new package and dcm2niix: add 1.0.20220720 * Remove list_url
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