* Set pubkey trust to ultimate during `gpg trust`
Tries to solve the same problem as #24760 without surpressing stderr
from gpg commands.
This PR makes every imported key trusted in the gpg database.
Note: I've outlined
[here](https://github.com/spack/spack/pull/24760#issuecomment-883183175)
that gpg's trust model makes sense, since how can we trust a random
public key we download from a binary cache?
* Fix test
Fixes#25603
This commit adds a new context manager to temporarily
deactivate active environments. This context manager
is used when setting up bootstrapping configuration to
make sure that the current environment is not affected
by operations on the bootstrap store.
* Preserve exit code 1 if nothing is found
* Use context manager for the environment
This commit adds a regression test for version selection
with preferences in `packages.yaml`. Before PR 25585 we
used negative weights in a minimization to select the
optimal version. This may lead to situations where a
dependency may make the version score of dependents
"better" if it is preferred in packages.yaml.
PackageInstaller and Package.installed disagree over what it means
for a package to be installed: PackageInstaller believes it should be
enough for a database entry to exist, whereas Package.installed
requires a database entry & a prefix directory.
This leads to the following niche issue:
* a develop spec in an environment is successfully installed
* then somehow its install prefix is removed (e.g. through a bug fixed
in #25583)
* you modify the sources and reinstall the environment
1. spack checks pkg.installed and realizes the develop spec is NOT
installed, therefore it doesn't need to have 'overwrite: true'
2. the installer gets the build task and checks the database and
realizes the spec IS installed, hence it doesn't have to install it.
3. the develop spec is not rebuilt.
The solution is to make PackageInstaller and pkg.installed agree over
what it means to be installed, and this PR does that by dropping the
prefix directory check from pkg.installed, so that it only checks the
database.
As a result, spack will create a build task with overwrite: true for
the develop spec, and the installer in fact handles overwrite requests
fine even if the install prefix doesn't exist (it just does a normal
install).
see #25563
When we have a concrete environment and we ask to install a
concrete spec from a file, currently Spack returns a list of
specs that are all the one that match the argument DAG hash.
Instead we want to compare build hashes, which also account
for build-only dependencies.
#25303 filtered padding from build output, but it's still there in binary install/relocate output,
so our CI logs are still quite long and frequently hit the limit.
- [x] add context handler from #25303 to buildcache installation as well
This allows you to run `spack graph --installed` from within an environment and get a dot graph of
its concrete specs.
- [x] make `spack graph -i` environment-aware
- [x] add code to the generated dot graph to ensure roots have min rank (i.e., they're all at the
top or left of the DAG)
Bootstrapping clingo on macOS on `develop` gives errors like this:
```
==> Error: RuntimeError: Unable to locate python command in /System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/bin
/Users/gamblin2/Workspace/spack/var/spack/repos/builtin/packages/python/package.py:662, in command:
659 return Executable(path)
660 else:
661 msg = 'Unable to locate {0} command in {1}'
>> 662 raise RuntimeError(msg.format(self.name, self.prefix.bin))
```
On macOS, `python` is laid out differently. In particular, `sys.executable` is here:
```console
Python 2.7.16 (default, May 8 2021, 11:48:02)
[GCC Apple LLVM 12.0.5 (clang-1205.0.19.59.6) [+internal-os, ptrauth-isa=deploy on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import sys
>>> sys.executable
'/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python'
```
Based on that, you'd think that
`/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents` would be
where you'd look for a `bin` directory, but you (and Spack) would be wrong:
```console
$ ls /System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/
Info.plist MacOS/ PkgInfo Resources/ _CodeSignature/ version.plist
```
You need to look in `sys.exec_prefix`
```
>>> sys.exec_prefix
'/System/Library/Frameworks/Python.framework/Versions/2.7'
```
Which looks much more like a standard prefix, with understandable `bin`, `lib`, and `include`
directories:
```console
$ ls /System/Library/Frameworks/Python.framework/Versions/2.7
Extras/ Mac/ Resources/ bin/ lib/
Headers@ Python* _CodeSignature/ include/
$ ls -l /System/Library/Frameworks/Python.framework/Versions/2.7/bin/python
lrwxr-xr-x 1 root wheel 7B Jan 1 2020 /System/Library/Frameworks/Python.framework/Versions/2.7/bin/python@ -> python2
```
- [x] change `bootstrap.py` to use the `sys.exec_prefix` as the external prefix, instead of just
getting the parent directory of the executable.
This adds lockfile tracking to Spack's lock mechanism, so that we ensure that there
is only one open file descriptor per inode.
The `fcntl` locks that Spack uses are associated with an inode and a process.
This is convenient, because if a process exits, it releases its locks.
Unfortunately, this also means that if you close a file, *all* locks associated
with that file's inode are released, regardless of whether the process has any
other open file descriptors on it.
Because of this, we need to track open lock files so that we only close them when
a process no longer needs them. We do this by tracking each lockfile by its
inode and process id. This has several nice properties:
1. Tracking by pid ensures that, if we fork, we don't inadvertently track the parent
process's lockfiles. `fcntl` locks are not inherited across forks, so we'll
just track new lockfiles in the child.
2. Tracking by inode ensures that referencs are counted per inode, and that we don't
inadvertently close a file whose inode still has open locks.
3. Tracking by both pid and inode ensures that we only open lockfiles the minimum
number of times necessary for the locks we have.
Note: as mentioned elsewhere, these locks aren't thread safe -- they're designed to
work in Python and assume the GIL.
Tasks:
- [x] Introduce an `OpenFileTracker` class to track open file descriptors by inode.
- [x] Reference-count open file descriptors and only close them if they're no longer
needed (this avoids inadvertently releasing locks that should not be released).
This commit rework version facts so that:
1. All the information on versions is collected
before emitting the facts
2. The same kind of atom is emitted for versions
stemming from different origins (package.py
vs. packages.yaml)
In the end all the possible versions for a given
package are totally ordered and they are given
different and increasing weights staring from zero.
This refactor allow us to avoid using negative
weights, which in some configurations may make
parent node score "better" and lead to unexpected
"optimal" results.
Once PR binary graduation is deployed, the shared PR mirror will
contain binaries just built by a merged PR, before the subsequent
develop pipeline has had time to finish. Using the shared PR mirror
as a source of binaries will reduce the number of times we have to
rebuild the same full hash.
* Refactor active environment getters
- Make `spack.environment.active_environment` a trivial getter for the active
environment, replacing `spack.environment.get_env` when the arguments are
not needed
- New method `spack.cmd.require_active_environment(cmd_name)` for
commands that require an environment (rather than abusing
get_env/active_environment)
- Clean up calling code to call spack.environment.active_environment or
spack.cmd.require_active_environment as appropriate
- Remove the `-e` parsing from `active_environment`, because `main.py` is
responsible for processing `-e` and already activates the environment.
- Move `spack.environment.find_environment` to
`spack.cmd.find_environment`, to avoid having spack.environment aware
of argparse.
- Refactor `spack install` command so argument parsing is all handled in the
command, no argparse in spack.environment or spack.installer
- Update documentation
* Python 2: toplevel import errors only with 'as ev'
In two files, `import spack.environment as ev` leads to errors
These errors are not well understood ("'module' object has no attribute
'environment'"). All other files standardize on the above syntax.
* 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
Spack is internally using a patched version of `argparse` mainly to backport Python 3 functionality
into Python 2. This PR makes it such that for the supported Python 3 versions we use `argparse`
from the standard Python library. This PR has been extracted from #25371 where it was needed
to be able to use recent versions of `pytest`.
* Fixed formatting issues when using a pristine argparse.py
* Fix error message for Python 3.X when missing positional arguments
* Account for the change of API in Python 3.7
* Layout multi-valued args into columns in error messages
* Seamless transition in develop if argparse.pyc is in external
* Be more defensive in case we can't remove the file.
Add link type to spack.yaml format
Add tests to verify link behavior is correct for installed files
for all three view types
Co-authored-by: vsoch <vsoch@users.noreply.github.com>
The commands have been deprecated in #7098, and have
been failing with an error message since then.
Cleaning the code since it is unlikely that somebody
is still using them.
Preferred providers had a non-zero weight because in an earlier formulation of the logic program that was needed to prefer external providers over default providers. With the current formulation for externals this is not needed anymore, so we can give a weight of zero to both default choices and providers that are externals. _Using zero ensures that we don't introduce any drift towards having less providers, which was happening when minimizing positive weights_.
Modifications:
- [x] Default weight for providers starts at 0 (instead of 10, needed before to prefer externals)
- [x] Rules to compute the `provider_weight` have been refactored. There are multiple possible weights for a given `Virtual`. Only one gets selected by the solver (the one that minimizes the objective function).
- [x] `provider_weight` are now accounting for each different `Virtual`. Before there was a single weight per provider, even if the package was providing multiple virtuals.
* Give preferred providers a weight of zero
Preferred providers had a non-zero weight because in an earlier
formulation of the logic program that was needed to prefer
external providers over default providers.
With the current formulation for externals this is not needed anymore,
so we can give a weight of zero to default choices. Using zero
ensures that we don't introduce any drift towards having
less providers, which was happening when minimizing positive weights.
* Simplify how we compute weights for providers
Rewrite rules so that specific events (i.e. being
an external) unlock the possibility to use certain
weights. The weight being considered is then selected
by the minimization process to be the one that gives
the best score.
* Allow providers to have different weights for different virtuals
Before this change we didn't differentiate providers based on
the virtual they provide, which meant that packages providing
more than one virtual had nonetheless a single weight.
With this change there will be a weight per virtual.
This is both a bugfix and a generalization of #25168. In #25168, we attempted to filter padding
*just* from the debug output of `spack.util.executable.Executable` objects. It turns out we got it
wrong -- filtering the command line string instead of the arg list resulted in output like this:
```
==> [2021-08-05-21:34:19.918576] ["'", '/', 'b', 'i', 'n', '/', 't', 'a', 'r', "'", ' ', "'", '-', 'o', 'x', 'f', "'", ' ', "'", '/', 't', 'm', 'p', '/', 'r', 'o', 'o', 't', '/', 's', 'p', 'a', 'c', 'k', '-', 's', 't', 'a', 'g', 'e', '/', 's', 'p', 'a', 'c', 'k', '-', 's', 't', 'a', 'g', 'e', '-', 'p', 'a', 't', 'c', 'h', 'e', 'l', 'f', '-', '0', '.', '1', '3', '-', 'w', 'p', 'h', 'p', 't', 'l', 'h', 'w', 'u', 's', 'e', 'i', 'a', '4', 'k', 'p', 'g', 'y', 'd', 'q', 'l', 'l', 'i', '2', '4', 'q', 'b', '5', '5', 'q', 'u', '4', '/', 'p', 'a', 't', 'c', 'h', 'e', 'l', 'f', '-', '0', '.', '1', '3', '.', 't', 'a', 'r', '.', 'b', 'z', '2', "'"]
```
Additionally, plenty of builds output padded paths in other plcaes -- e.g., not just command
arguments, but in other `tty` messages via `llnl.util.filesystem` and other places. `Executable`
isn't really the right place for this.
This PR reverts the changes to `Executable` and moves the filtering into `llnl.util.tty`. There is
now a context manager there that you can use to install a filter for all output.
`spack.installer.build_process()` now uses this context manager to make `tty` do path filtering
when padding is enabled.
- [x] revert filtering in `Executable`
- [x] add ability for `tty` to filter output
- [x] install output filter in `build_process()`
- [x] tests
`compare_specs()` had a `colorful` keyword argument, but everything else in
spack uses `color` for this.
- [x] rename the argument
- [x] make the default follow spack's `--color=always/never/auto` setting
Add a workflow to test bootstrapping clingo on
different platforms so that we can detect changes
that break it.
Compute `site_packages_dir` in `bootstrap.py` as it was
before #24095, until we figure a better way to override
that attribute.
Long, padded install paths can get to be very long in the verbose install
output. This has to be filtered out by the Executable class, as it
generates these debug messages.
- [x] add ability to filter paths from Executable output.
- [x] add a context manager that can enable path filtering
- [x] make `build_process` in `installer.py`
This should hopefully allow us to see most of the build output in
Gitlab pipeline builds again.
`build_process` has been around a long time but it's become a very large,
unwieldy method. It's hard to work with because it has a lot of local
variables that need to persist across all of the code.
- [x] To address this, convert it its own `BuildInfoProcess` class.
- [x] Start breaking the method apart by factoring out the main
installation logic into its own function.
When context managers are used to save and restore values, we need to remember
to use try/finally around the yield in case an exception is thrown. Otherwise,
the cleanup will be skipped.
