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(#22097)
Add output of build- and install-time tests to info command
Enable dependencies, variants, and versions by default (i.e., provide --no*
options; add gcc to test_info_fields to increase coverage for c_names->v_names
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This reverts commit 531b1c5c3dcc9bc7bec27e223608aed477e94dbd.
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Adds `spack external read-cray-manifest`, which reads a json file that describes a set of package DAGs. The parsed results are stored directly in the database. A user can see these installed specs with `spack find` (like any installed spec). The easiest way to use them right now as dependencies is to run `spack spec ... ^/hash-of-external-package`.
Changes include:
* `spack external read-cray-manifest --file <path/to/file>` will add all specs described in the file to Spack's installation DB and will also install described compilers to the compilers configuration (the expected format of the file is described in this PR as well including examples of the file)
* Database records now may include an "origin" (the command added in this PR registers the origin as "external-db"). In the future, it is assumed users may want to be able to treat installs registered with this command differently (e.g. they may want to uninstall all specs added with this command)
* Hash properties are now always preserved when copying specs if the source spec is concrete
* I don't think the hashes of installed-and-concrete specs should change and this was the easiest way to handle that
* also specs that are concrete preserve their `.normal` property when copied (external specs may mention compilers that are not registered, and without this change they would fail in `normalize` when calling `validate_or_raise`)
* it might be this should only be the case if the spec was installed
- [x] Improve testing
- [x] Specifically mark DB records added with this command (so that users can do something like "uninstall all packages added with `spack read-external-db`)
* This is now possible with `spack uninstall --all --origin=external-db` (this will remove all specs added from manifest files)
- [x] Strip variants that are listed in json entries but don't actually exist for the package
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
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Setup Installer CI (#25184), (#25191)
Co-authored-by: Zack Galbreath <zack.galbreath@kitware.com>
Co-authored-by: lou.lawrence@kitware.com <lou.lawrence@kitware.com>
Co-authored-by: Betsy McPhail <betsy.mcphail@kitware.com>
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* Add 'make-installer' command for Windows
* Add '--bat' arg to env activate, env deactivate and unload commands
* An equivalent script to setup-env on linux: spack_cmd.bat. This script
has a wrapper to evaluate cd, load/unload, env activate/deactivate.(#21734)
* Add spacktivate and config editor (#22049)
* spack_cmd: will find python and spack on its own. It preferentially
tries to use python on your PATH (#22414)
* Ignore Windows python installer if found (#23134)
* Bundle git in windows installer (#23597)
* Add Windows section to Getting Started document
(#23131), (#23295), (#24240)
Co-authored-by: Stephen Crowell <stephen.crowell@kitware.com>
Co-authored-by: lou.lawrence@kitware.com <lou.lawrence@kitware.com>
Co-authored-by: Betsy McPhail <betsy.mcphail@kitware.com>
Co-authored-by: Jared Popelar <jpopelar@txcorp.com>
Co-authored-by: Ben Cowan <benc@txcorp.com>
Update Installer CI
Co-authored-by: John Parent <john.parent@kitware.com>
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We can see what is in the bootstrap store with `spack find -b`, and you can clean it with `spack
clean -b`, but we can't do much else with it, and if there are bootstrap issues they can be hard to
debug.
We already have `spack --mock`, which allows you to swap in the mock packages from the command
line. This PR introduces `spack -b` / `spack --bootstrap`, which runs all of spack with
`ensure_bootstrap_configuration()` set. This means that you can run `spack -b find`, `spack -b
install`, `spack -b spec`, etc. to see what *would* happen with bootstrap configuration, to remove
specific bootstrap packages, etc. This will hopefully make developers' lives easier as they deal
with bootstrap packages.
This PR also uses a `nullcontext` context manager. `nullcontext` has been implemented in several
other places in Spack, and this PR consolidates them to `llnl.util.lang`, with a note that we can
delete the function if we ever reqyire a new enough Python.
- [x] introduce `spack --bootstrap` option
- [x] consolidated all `nullcontext` usages to `llnl.util.lang`
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See https://github.com/spack/spack/issues/25353#issuecomment-1041868116
This commit changes the default behavior of
```
$ spack external find
```
from searching all the possible packages Spack knows about to
search only for the ones tagged as being a "build-tool".
It also introduces a `--all` option to restore the old behavior.
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Since Spack does not install external packages, this commit skips them by
default when running stand-alone tests. The assumption is that such packages
have likely undergone an acceptance test process.
However, the tests can be run against installed externals using
```
% spack test run --externals ...
```
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`--reuse` was previously handled individually by each command that
needed it. We are growing more concretization options, and they'll
need their own section for commands that support them.
Now there are two concretization options:
* `--reuse`: Attempt to reuse packages from installs and buildcaches.
* `--fresh`: Opposite of reuse -- traditional spack install.
To handle thes, this PR adds a `ConfigSetAction` for `argparse`, so
that you can write argparse code like this:
```
subgroup.add_argument(
'--reuse', action=ConfigSetAction, dest="concretizer:reuse",
const=True, default=None,
help='reuse installed dependencies/buildcaches when possible'
)
```
With this, you don't need to add logic to pull the argument out and
handle it; the `ConfigSetAction` just does it for you. This can probably
be used to clean up some other commands later, as well.
Code that was previously passing `reuse=True` around everywhere has
been refactored to use config, and config is set from the CLI using
a new `add_concretizer_args()` function in `spack.cmd.common.arguments`.
- [x] Add `ConfigSetAction` to simplify concretizer config on the CLI
- [x] Refactor code so that it does not pass `reuse=True` to every function.
- [x] Refactor commands to use `add_concretizer_args()` and to pass
concretizer config using the config system.
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To make it easier to see how package hashes change and how they are computed, add two
commands:
* `spack pkg source <spec>`: dumps source code for a package to the terminal
* `spack pkg source --canonical <spec>`: dumps canonicalized source code for a
package to the terminal. It strips comments, directives, and known-unused
multimethods from the package. It is used to generate package hashes.
* `spack pkg hash <spec>`: This gives the package hash for a particular spec.
It is generated from the canonical source code for the spec.
- [x] `add spack pkg source` and `spack pkg hash`
- [x] add tests
- [x] fix bug in multimethod resolution with boolean `@when` values
Co-authored-by: Greg Becker <becker33@llnl.gov>
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This command pokes the environment, Python interpreter
and bootstrap store to check if dependencies needed by
Spack are available.
If any are missing, it shows a comprehensible message.
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spack monitor now requires authentication as each build must be associated
with a user, so it does not make sense to allow the --monitor-no-auth flag
and this commit will remove it
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This commit introduces the command
spack module tcl setdefault <package>
similar to the one already available for lmod
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
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performance (#27970)
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
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This PR is meant to move code with "business logic" from `spack.cmd.buildcache` to appropriate core modules[^1].
Modifications:
- [x] Add `spack.binary_distribution.push` to create a binary package from a spec and push it to a mirror
- [x] Add `spack.binary_distribution.install_root_node` to install only the root node of a concrete spec from a buildcache (may check the sha256 sum if it is passed in as input)
- [x] Add `spack.binary_distribution.install_single_spec` to install a single concrete spec from a buildcache
- [x] Add `spack.binary_distribution.download_single_spec` to download a single concrete spec from a buildcache to a local destination
- [x] Add `Spec.from_specfile` that construct a spec given the path of a JSON or YAML spec file
- [x] Removed logic from `spack.cmd.buildcache`
- [x] Removed calls to `spack.cmd.buildcache` in `spack.bootstrap`
- [x] Deprecate `spack buildcache copy` with a message that says it will be removed in v0.19.0
[^1]: The rationale is that commands should be lightweight wrappers of the core API, since that helps with both testing and scripting (easier mocking and no need to invoke `SpackCommand`s in a script).
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The "spack flake8" command wwas deprecated in favor
of "spack style". The deprecation wwarning is in the
0.17.X series, so removing it for v0.18.x
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* Add connection specification to mirror creation
This allows each mirror to contain information about the credentials
used to access it.
Update command and tests based on comments
Switch to only "long form" flags for the s3 connection information.
Use the "any" function instead of checking for an empty list when looking
for s3 connection information.
Split test to use the access token separately from the access id and key.
Use long flag form in test.
Add endpoint_url to available S3 options.
Extend the special parameters for an S3 mirror to accept the
endpoint_url parameter.
Add a test.
* Add connection information per URL not per mirror
Expand the mirror-based connection information to be per-URL.
This will allow a user to specify different S3 connection information
for both the fetch and the push URLs.
Add a parameter for "profile", another way of storing the id/secret pair.
* Switch from "access_profile" to "profile"
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Commands should not reuse option names defined in main.
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See #25249 and https://github.com/spack/spack/pull/27159#issuecomment-958163679.
This adds `spack load --list` as an alias for `spack find --loaded`. The new command is
not as powerful as `spack find --loaded`, as you can't combine it with all the queries or
formats that `spack find` provides. However, it is more intuitively located in the command
structure in that it appears in the output of `spack load --help`.
The idea here is that people can use `spack load --list` for simple stuff but fall back to
`spack find --loaded` if they need more.
- add help to `spack load --list` that references `spack find`
- factor some parts of `spack find` out to be called from `spack load`
- add shell tests
- update docs
Co-authored-by: Peter Josef Scheibel <scheibel1@llnl.gov>
Co-authored-by: Richarda Butler <39577672+RikkiButler20@users.noreply.github.com>
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* GnuPG: allow bootstrapping from buildcache and sources
* Add a test to bootstrap GnuPG from binaries
* Disable bootstrapping in tests
* Add e2e test to bootstrap GnuPG from sources on Ubuntu
* Add e2e test to bootstrap GnuPG on macOS
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The `--generic` argument allows printing the best generic target for the
current machine. This can be quite handy when wanting to find the
generic architecture to use when building a shared software stack for
multiple machines.
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This PR adds a "spack tags" command to output package tags or
(available) packages with those tags. It also ensures each package
is listed in the tag cache ONLY ONCE per tag.
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some cases) (#26120)
Currently spack is a bit of a bad actor as a zsh plugin, and it was my
fault. The autoload and compinit should really be handled by the user,
as was made abundantly clear when I found spack was doing completion
initialization for *all* of my plugins due to a deferred setup that was
getting messed up by it.
Making this conditional took spack load time from 1.5 seconds (with
module loading disabled) to 0.029 seconds. I can actually afford to load
spack by default with this change in.
Hopefully someday we'll do proper zsh completion support, but for now
this helps a lot.
* use zsh hist expansion in place of dirname
* only run (bash)compinit if compdef/complete missing
* add zsh compiled files to .gitignore
* move changes to .in file, because spack
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This PR permits to specify the `url` and `ref` of the Spack instance used in a container recipe simply by expanding the YAML schema as outlined in #20442:
```yaml
container:
images:
os: amazonlinux:2
spack:
ref: develop
resolve_sha: true
```
The `resolve_sha` option, if true, verifies the `ref` by cloning the Spack repository in a temporary directory and transforming any tag or branch name to a commit sha. When this new ability is leveraged an additional "bootstrap" stage is added, which builds an image with Spack setup and ready to install software. The Spack repository to be used can be customized with the `url` keyword under `spack`.
Modifications:
- [x] Permit to pin the version of Spack, either by branch or tag or sha
- [x] Added a few new OSes (centos:8, amazonlinux:2, ubuntu:20.04, alpine:3, cuda:11.2.1)
- [x] Permit to print the bootstrap image as a standalone
- [x] Add documentation on the new part of the schema
- [x] Add unit tests for different use cases
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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
```
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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.
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* 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).
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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>
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* 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
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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>
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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
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* 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
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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
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Add a new "spack audit" command. This command can check for issues
with configuration or with packages and is intended to help a
user debug a failed Spack build.
In some cases the reported issues are always errors but are too
costly to check for (e.g. packages that specify missing variants on
dependencies). In other cases the issues may be legitimate but
uncommon usage of Spack and we want to be sure the user intended the
behavior (e.g. duplicate compiler definitions).
Audits are grouped by theme, and for now the two themes are packages
and configuration. For example you can run all available audits
on packages with "spack audit packages". It is intended that in
the future users will be able to define their own audits.
The package audits are good candidates for running in package_sanity
(i.e. they could catch bugs in user-submitted packages before they
are merged) but that is left for a later PR.
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This should get us most of the way there to support using monitor during a spack container build, for both Singularity and Docker. Some quick notes:
### Docker
Docker works by way of BUILDKIT and being able to specify --secret. What this means is that you can prefix a line with a mount of type secret as follows:
```bash
# Install the software, remove unnecessary deps
RUN --mount=type=secret,id=su --mount=type=secret,id=st cd /opt/spack-environment && spack env activate . && export SPACKMON_USER=$(cat /run/secrets/su) && export SPACKMON_TOKEN=$(cat /run/secrets/st) && spack install --monitor --fail-fast && spack gc -y
```
Where the id for one or more secrets corresponds to the file mounted at `/run/secrets/<name>`. So, for example, to build this container with su (spackmon user) and sv (spackmon token) defined I would export them on my host and do:
```bash
$ DOCKER_BUILDKIT=1 docker build --network="host" --secret id=st,env=SPACKMON_TOKEN --secret id=su,env=SPACKMON_USER -t spack/container .
```
And when we add `env` to the secret definition that tells the build to look for the secret with id "st" in the environment variable `SPACKMON_TOKEN` for example.
If the user is building locally with a local spack monitor, we also need to set the `--network` to be the host, otherwise you can't connect to it (a la isolation of course.)
## Singularity
Singularity doesn't have as nice an ability to clearly specify secrets, so (hoping this eventually gets implemented) what I'm doing now is providing the user instructions to write the credentials to a file, add it to the container to source, and remove when done.
## Tags
Note that the tags PR https://github.com/spack/spack/pull/23712 will need to be merged before `--monitor-tags` will actually work because I'm checking for the attribute (that doesn't exist yet):
```bash
"tags": getattr(args, "monitor_tags", None)
```
So when that PR is merged to update the argument group, it will work here, and I can either update the PR here to not check if the attribute is there (it will be) or open another one in the case this PR is already merged.
Finally, I added a bunch of documetation for how to use monitor with containerize. I say "mostly working" because I can't do a full test run with this new version until the container base is built with the updated spack (the request to the monitor server for an env install was missing so I had to add it here).
Signed-off-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: vsoch <vsoch@users.noreply.github.com>
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this will first support uploads for spack monitor, and eventually could be
used for other kinds of spack uploads
Signed-off-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: vsoch <vsoch@users.noreply.github.com>
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This PR allows users to `--export`, `--export-secret`, or both to export GPG keys
from Spack. The docs are updated that include a warning that this usually does not
need to be done.
This addresses an issue brought up in slack, and also represented in #14721.
Signed-off-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: vsoch <vsoch@users.noreply.github.com>
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