Creates an environment in a temporary directory and activates it, which
is useful for a quick ephemeral environment:
```
$ spack env activate -p --temp
[spack-1a203lyg] $ spack add zlib
==> Adding zlib to environment /tmp/spack-1a203lyg
==> Updating view at /tmp/spack-1a203lyg/.spack-env/view
```
Modifications:
- Modify the workflow to build container images without pushing when the workflow file itself is modified
- Strip the leading ghcr.io/spack/ from env.container env.versioned to prepare pushing to multiple registries
- Fixed CentOS 7 and Amazon Linux builds
- Login and push to Docker Hub as well as Github Action
- Add a badge to README.md with the status of docker images
Modifications:
- [x] Change `defaults/config.yaml`
- [x] Add a fix for bootstrapping patchelf from sources if `compilers.yaml` is empty
- [x] Make `SPACK_TEST_SOLVER=clingo` the default for unit-tests
- [x] Fix package failures in the e4s pipeline
Caveats:
1. CentOS 6 still uses the original concretizer as it can't connect to the buildcache due to issues with `ssl` (bootstrapping from sources requires a C++14 capable compiler)
1. I had to update the image tag for GitlabCI in e699f14.
1. libtool v2.4.2 has been deprecated and other packages received some update
This is a major rework of Spack's core core `spec.yaml` metadata format. It moves from `spec.yaml` to `spec.json` for speed, and it changes the format in several ways. Specifically:
1. The spec format now has a `_meta` section with a version (now set to version `2`). This will simplify major changes like this one in the future.
2. The node list in spec dictionaries is no longer keyed by name. Instead, it is a list of records with no required key. The name, hash, etc. are fields in the dictionary records like any other.
3. Dependencies can be keyed by any hash (`hash`, `full_hash`, `build_hash`).
4. `build_spec` provenance from #20262 is included in the spec format. This means that, for spliced specs, we preserve the *full* provenance of how to build, and we can reproduce a spliced spec from the original builds that produced it.
**NOTE**: Because we have switched the spec format, this PR changes Spack's hashing algorithm. This means that after this commit, Spack will think a lot of things need rebuilds.
There are two major benefits this PR provides:
* The switch to JSON format speeds up Spack significantly, as Python's builtin JSON implementation is orders of magnitude faster than YAML.
* The new Spec format will soon allow us to represent DAGs with potentially multiple versions of the same dependency -- e.g., for build dependencies or for compilers-as-dependencies. This PR lays the necessary groundwork for those features.
The old `spec.yaml` format continues to be supported, but is now considered a legacy format, and Spack will opportunistically convert these to the new `spec.json` format.
* tests: make `spack url [stats|summary]` work on mock packages
Mock packages have historically had mock hashes, but this means they're also invalid
as far as Spack's hash detection is concerned.
- [x] convert all hashes in mock package to md5 or sha256
- [x] ensure that all mock packages have a URL
- [x] ignore some special cases with multiple VCS fetchers
* url stats: add `--show-issues` option
`spack url stats` tells us how many URLs are using what protocol, type of checksum,
etc., but it previously did not tell us which packages and URLs had the issues. This
adds a `--show-issues` option to show URLs with insecure (`http`) URLs or `md5` hashes
(which are now deprecated by NIST).
This PR will add a new audit, specifically for spack package homepage urls (and eventually
other kinds I suspect) to see if there is an http address that can be changed to https.
Usage is as follows:
```bash
$ spack audit packages-https <package>
```
And in list view:
```bash
$ spack audit list
generic:
Generic checks relying on global variables
configs:
Sanity checks on compilers.yaml
Sanity checks on packages.yaml
packages:
Sanity checks on specs used in directives
packages-https:
Sanity checks on https checks of package urls, etc.
```
I think it would be unwise to include with packages, because when run for all, since we do requests it takes a long time. I also like the idea of more well scoped checks - likely there will be other addresses for http/https within a package that we eventually check. For now, there are two error cases - one is when an https url is tried but there is some SSL error (or other error that means we cannot update to https):
```bash
$ spack audit packages-https zoltan
PKG-HTTPS-DIRECTIVES: 1 issue found
1. Error with attempting https for "zoltan":
<urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: Hostname mismatch, certificate is not valid for 'www.cs.sandia.gov'. (_ssl.c:1125)>
```
This is either not fixable, or could be fixed with a change to the url or (better) contacting the site owners to ask about some certificate or similar.
The second case is when there is an http that needs to be https, which is a huge issue now, but hopefully not after this spack PR.
```bash
$ spack audit packages-https xman
Package "xman" uses http but has a valid https endpoint.
```
And then when a package is fixed:
```bash
$ spack audit packages-https zlib
PKG-HTTPS-DIRECTIVES: 0 issues found.
```
And that's mostly it. :)
Signed-off-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: vsoch <vsoch@users.noreply.github.com>
* Bootstrap clingo from binaries
* Move information on clingo binaries to a JSON file
* Add support to bootstrap on Cray
Bootstrapping on Cray requires, at the moment, to
swap the platform when looking for binaries - due
to #22800.
* Add SHA256 verification for bootstrapped software
Use sha256 verification for binaries necessary to bootstrap
the concretizer and gpg for signature verification
* patchelf: use Spec._old_concretize() to bootstrap
As noted in #24450 we may happen to need the
concretizer when bootstrapping clingo. In that case
only the old concretizer is available.
* Add a schema for bootstrapping methods
Two fields have been added to bootstrap.yaml:
"sources" which lists the methods available for
bootstrapping software
"trusted" which records if a source is trusted or not
A subcommand has been added to "spack bootstrap" to list
the sources currently available.
* Methods used for bootstrapping are configurable from bootstrap:sources
The function that tries to ensure a given Python module
is importable now tries bootstrapping methods in the same
order as they are defined in `bootstrap.yaml`
* Permit to trust/untrust bootstrapping methods
* Add binary tests for MacOS, Ubuntu
* Add documentation
* Add a note on bash
This pull request adds a new workflow to build and deploy Spack Docker containers
from GitHub Actions. In comparison with our current system where we use Dockerhub's
CI to build our Docker containers, this workflow will allow us to now build for multiple
architectures and deploy to multiple registries. (At the moment x86_64 and Arm64 because
ppc64le is throwing an error within archspec.)
As currently set up, the PR will build all of the current containers (minus Centos6 because
those yum repositories are no longer available?) as both x86_64 and Arm64 variants. The
workflow is currently setup to build and deploy containers nightly from develop as well as
on tagged releases. The workflow will also build, but NOT deploy containers on a pull request
for the purposes of testing this PR. At the moment it is setup to deploy the built containers to
GitHub's Container Registry although, support for also uploading to Dockerhub/Quay can be
included easily if we decide to keep releasing on Dockerhub/want to begin releasing on Quay.
Gitlab truncates job trace output (even the complete raw output) at 4MB,
so this change captures it to a file under "user_data" artifacts as well,
to make sure we can debug output from the end of the rebuild job.
A `spack diff` will take two specs, and then use the spack.solver.asp.SpackSolverSetup to generate
lists of facts about each (e.g., nodes, variants, etc.) and then take a set difference between the
two to show the user the differences.
Example output:
$ spack diff python@2.7.8 python@3.8.11
==> Warning: This interface is subject to change.
--- python@2.7.8/tsxdi6gl4lihp25qrm4d6nys3nypufbf
+++ python@3.8.11/yjtseru4nbpllbaxb46q7wfkyxbuvzxx
@@ variant_value @@
- python patches a8c52415a8b03c0e5f28b5d52ae498f7a7e602007db2b9554df28cd5685839b8
+ python patches 0d98e93189bc278fbc37a50ed7f183bd8aaf249a8e1670a465f0db6bb4f8cf87
@@ version @@
- openssl Version(1.0.2u)
+ openssl Version(1.1.1k)
- python Version(2.7.8)
+ python Version(3.8.11)
Currently this uses diff-like output but we will attempt to improve on this in the future.
One use case for `spack diff` is whenever a user has a disambiguate situation and cannot
remember how two different installs are different. The command can also output `--json` in
the case of a more analysis type use case where we want to save complete data with all
diffs and the intersection. However, the command is really more intended for a command
line use case, and we likely will have an analyzer more suited to saving data
Signed-off-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
Modifications:
- Remove the "build tests" workflow from GitHub Actions
- Setup a similar e2e test on Gitlab
In this way we'll reduce load on GitHub Actions workflows and for e2e tests will
benefit from the buildcache reuse granted by pipelines.
`spack style` previously used a Travis CI variable to figure out
what the base branch of a PR was, and this was apparently also set
on `develop`. We switched to `GITHUB_BASE_REF` to support GitHub
Actions, but it looks like this is set to `""` in pushes to develop,
so `spack style` breaks there.
This PR does two things:
- [x] Remove `GITHUB_BASE_REF` knowledge from `spack style` entirely
- [x] Handle `GITHUB_BASE_REF` in style scripts instead, and explicitly
pass the base ref if it is present, but don't otherwise.
This makes `spack style` *not* dependent on the environment and fixes
handling of the base branch in the right place.
This adds a `--root` option so that `spack style` can check style for
a spack instance other than its own.
We also change the inner workings of `spack style` so that `--config FILE`
(and similar options for the various tools) options are used. This ensures
that when `spack style` runs, it always uses the config from the running spack,
and does *not* pick up configuration from the external root.
- [x] add `--root` option to `spack style`
- [x] add `--config` (or similar) option when invoking style tools
- [x] add a test that verifies we can check an external instance
This uses our bootstrapping logic to automatically install dependencies for
`spack style`. Users should no longer have to pre-install all of the tools
(`isort`, `mypy`, `black`, `flake8`). The command will do it for them.
- [x] add logic to bootstrap specs with specific version requirements in `spack style`
- [x] remove style tools from CI requirements (to ensure we test bootstrapping)
- [x] rework dependencies for `mypy` and `py-typed-ast`
- `py-typed-ast` needs to be a link dependency
- it needs to be at 1.4.1 or higher to work with python 3.9
Signed-off-by: vsoch <vsoch@users.noreply.github.com>
* trilinos: rename basker variant
The Basker solver is part of amesos2 but is clearer without the extra
scoping.
* trilinos: automatically enable teuchos and remove variant
Basically everything in trilinos needs teuchos
* trilinos: group top-level dependencies
* trilinos: update dependencies, removing unused
- GLM, X11 are unused (x11 lacks dependency specs too)
- Python variant is more like a TPL so rearrange that
- Gtest internal package shouldn't be compiled or exported
- Add MPI4PY requirement for pytrilinos
* trilinos: remove package meta-options
- XSDK settings and "all opt packages" are not used anywhere
- all optional packages are dangerous
* trilinos: Use hwloc iff kokkos
See #19119, also the HWLOC tpl name was misspelled so this was being ignored before.
* Flake
* Fix trilinos +netcdf~mpi
* trilinos: default to disabling external dependencies
* Remove teuchos from downstream dependencies
* fixup! trilinos: Use hwloc iff kokkos
* Add netcdf requirements to packages with ^trilinos+exodus
* trilinos: disable exodus by default
* fixup! Add netcdf requirements to packages with ^trilinos+exodus
* trilinos: only enable hwloc when @13: +kokkos
* xyce: propagate trilinos dependencies more simply
* dtk: fix missing boost dependency
* trilinos: remove explicit metis dependency
* trilinos: require metis/parmetis for zoltan
Disable zoltan by default to minimize default dependencies
* trilinos: mark mesquite disabled and fix kokkos arch
* xsdk: fix trilinos to also list zoltan [with zoltan2]
* ci: remove nonexistent variant from trilinos
* trilinos: add missing boost dependency
Co-authored-by: Satish Balay <balay@mcs.anl.gov>
* Permit to enable/disable bootstrapping and customize store location
This PR adds configuration handles to allow enabling
and disabling bootstrapping, and to customize the store
location.
* Move bootstrap related configuration into its own YAML file
* Add a bootstrap command to manage configuration
* fix remaining flake8 errors
* imports: sort imports everywhere in Spack
We enabled import order checking in #23947, but fixing things manually drives
people crazy. This used `spack style --fix --all` from #24071 to automatically
sort everything in Spack so PR submitters won't have to deal with it.
This should go in after #24071, as it assumes we're using `isort`, not
`flake8-import-order` to order things. `isort` seems to be more flexible and
allows `llnl` mports to be in their own group before `spack` ones, so this
seems like a good switch.
This consolidates code across tools in `spack style` so that each
`run_<tool>` function can be called indirecty through a dictionary
of handlers, and os that checks like finding the executable for the
tool can be shared across commands.
- [x] rework `spack style` to use decorators to register tools
- [x] define tool order in one place in `spack style`
- [x] fix python 2/3 issues to Get `isort` checks working
- [x] make isort error regex more robust across versions
- [x] remove unused output option
- [x] change vestigial `TRAVIS_BRANCH` to `GITHUB_BASE_REF`
- [x] update completion
