…psafe (#32849)

* py-flask: add 2.2.2, py-werkzeug: add 2.2.2, py-markupsafe: add 2.1.1

* Remove py-dataclasses dependency

…4225)

* Bugfix: Fetch should not force use of curl to check url existence

* Switch type hints from comments to actual hints

* py-keyrings-alt: add 4.2.0

* Add missing py-jaraco-classes dependency

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`.

* feat(Hermes): update version to 0.9.0-beta.
   This is the latest release.
* feat(Hermes): fix checksum.
  Credit: @tldahlgren

…conditional variants (#34244)

* ROOT: add GSL/math dependency
* ROOT: use conditional variants instead of conflicts

* patch command: add concretizer args
* tab completion

* py-alphafold: update to 2.2.4, update dependencies

* style

* vecgeom: add new 1.2.1 version
* vecgeom: introduce conflict between gcc/cuda

Recent tests of vecgeom in Spack environments have shown that the build
with +cuda fails with GCC >= 11.3 and CUDA < 11.7 with error

...lib/gcc/x86_64-pc-linux-gnu/11.3.0/include/serializeintrin.h(41):
error: identifier "__builtin_ia32_serialize" is undefined

1 error detected in the compilation of
".../VecGeom/source/BVHManager.cu".

Other GCC/CUDA combinations appear o.k.

Avoid this error in spack, and document it for users, with a conflict
directive to express the restriction.

* doxygen: add build-tool tag
   This allows it to be included automatically as an external. No one links against doxygen so this should be ok.
* doxygen: add self as maintainer

We've stopped supporting Python 2, and contributors are noticing that our CI no longer
allows Python 2.7 comment type hints. They end up having to adapt them, but this adds
extra unrelated work to PRs.

- [x] Move to 3.6 type hints across the entire code base

* py-mne: add 1.2.2 and depencendy packages

* py-mne: add 1.2.3

* Remove unnecessary when statement

We no longer support Python <3.6, so we don't need to check whether Python supports SSL
verification in `spack.util.web`.

- [x] Remove a bunch of logic we needed to appease Python 2

* Add conflicts with [email protected]

* Add more links for reference

Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>

Co-authored-by: sxs-bot <[email protected]>

All the vermin annotations we were using were for optional features introduced in early
Python 3 versions. We no longer need any of them, as we only support Python 3.6+. If we
start optionally using features from newer Pythons than 3.6, we will need more vermin
annotations.

Co-authored-by: Harmen Stoppels <[email protected]>

Co-authored-by: Harmen Stoppels <[email protected]>

* py-nbclassic: add 0.4.8 and new package py-notebook-shim

* Add missing dependencies

* Add the very first version of cernlib
* Update package.py
* Update package.py

Co-authored-by: Andrii Verbytskyi <[email protected]>

See release notes at https://github.com/potassco/clingo/releases/tag/v5.6.2

* epsic: add epsic package to spack

* psrcat: add psrcat to spack

* psrchive: add psarchive to spack

* tempo: add tempo package to spack

The 0.9.0-beta requires yaml-cpp for parsing the configuration file format in YAML.

P.S. I'm using https://www.conventionalcommits.org/en/v1.0.0/#specification for this commit message.

* LAMMPS: Add version 20220803 and 20220623.1

* LAMMPS: Add 20220915, 20221103, and 20220623.2