Non-expanded resources were being deleted from the cache on account
of two behaviors:
* ResourceStage was moving files rather than copying them, and uses
"os.path.realpath" to resolve symlinks
* CacheFetchStrategy creates a symlink to a cached resource rather
than copying it
This alters the first behavior: ResourceStage now copies the file
rather than moving it.
"mirror create" was invoking a package's do_patch method in order to
retrieve and archive URL patches. If a package implements a "patch"
method, this is also called as part of do_patch; this failed when the
package-specific implementation referred to environment variables
that are only available at the time the package is built
(e.g. "spack_cc").
This change introduces fetch and clean methods for patches. They are
no-ops for FilePatch but perform the appropriate actions for
UrlPatch. This allows "mirror create" to invoke do_fetch, which does
not call the package's patch method.
- in many files, regular strings were used in places where raw strings
should've been used.
- convert these to raw strings and get rid of new flake8 errors
This PR improves the validation of `modules.yaml` by introducing a custom validator that checks if an attribute listed in `properties` or `patternProperties` is a valid spec. This new check applied to the test case in #9857 gives:
```console
$ spack install szip
==> Error: /home/mculpo/.spack/linux/modules.yaml:5: "^python@2.7@" is an invalid spec [Invalid version specifier]
```
Details:
* Moved the set-up of a custom validator class to spack.schema
* In Spack we use `jsonschema` to validate configuration files
against a schema. We also need custom validators to enforce
writing default values within "properties" or "patternProperties"
attributes.
* Currently, validators were customized at the place of use and with the
recent introduction of environments that meant we were setting-up and
using 2 different validator classes in two different modules.
* This commit moves the set-up of a custom validator class in the
`spack.schema` module and refactors the code in `spack.config` and
`spack.environments` to use it.
* Added a custom validator to check if an attribute is a valid spec
* Added a custom validator that can be used on objects, which yields an
error if the attribute is not a valid spec.
* Updated the schema for modules.yaml
* Updated modules.yaml to fix a few inconsistencies:
- a few attributes were not tested properly using 'anyOf'
- suffixes has been updated to also check that the attribute is a spec
- hierarchical_scheme has been updated to hierarchy
* Removed $ref from every schema
* $ref is not composable or particularly legible
* Use python dicts and regular old variables instead.
- The nested directive implementation was broken for python 3
- directive results were not properly removed from the directive list
when it was processed in the DirectiveMeta metaclass.
- the issue was that remove_directives only descended into a list or
tuple, but in Python3, the initial value passed to the function is a
view of dictionary values.
- make it a list to fix things, and add a regression test.
- currently just looks at patches
- allows you to find out which package applied a patch to a spec
- intended to work with tarballs and resources in the future.
- add tab completion for `spack resource` and subcommands
- previously, if a concrete sub-DAG with patched specs was written out
and read back in, its patches would not be found because the dependent
that patched it was no longer in the DAG.
- Add a test to ensure that the PatchCache handles this case.
- Also add tests to ensure that patch objects are properly created from
Specs -- previously we only checked that the patches were on the Spec.
- this fixes a bug where if we save a concretized sug-DAG where a package
had been patched by a dependent, and the dependent was not in the DAG,
we would not read in all patches correctly.
- Rather than looking up patches in the DAG, we look them up globally
from an index created from the entire repository.
- The patch cache is a bit tricky for several reasons:
- we have to cache information from packages, specifically, the patch
level and working directory.
- FilePatches need to know which package owns them, so that they can
figure out where the patch lives. The repo can change locations from
run to run, so we have to store relative paths and restore them when
the cache is reloaded.
- Patch files can change underneath the cache, because repo indexes
only update on package changes. We currently punt on this -- there
are stub methods for needs_update() that will need to check patch
files when packages are loaded. There isn't an easy way to do this
at global indexing time without making the FastPackageChecker a lot
slower. This is TBD for a future commit.
- Currently, the same patch can only be used one way in a package. That
is, if it appears twice with different level/working_dir settings,
bad things will happen. There's no package that current uses the
same patch two different ways, so we've punted on this as well, but
we may need to fix this in the future by moving a lot of the metdata
(level, working dir) to the spec, and *only* caching sha256sums in
the PatchCache. That would require some much more complicated tweaks
to the Spec, so we're holding off on that til later.
- This required patches to be refactored somewhat -- the difference
between a UrlPatch and a FilePatch is still not particularly clean.
- indexes should use json, not YAML, to optimize for speed
- only use YAML in human-editable files
- this makes ProviderIndex consistent with other indexes
- virtual provider cache and tags were previously generated by nearly
identical but separate methods.
- factor out an Indexer interface for updating repository caches, and
provide implementations for each type of index (TagIndex,
ProviderIndex) so that more can be added if needed.
- Among other things, this allows all indexes to be updated at once.
This is an advantage because loading package files is the real
overhead, and building the indexes once the packages are loaded is
trivial. We avoid extra bulk read-ins by generating all package indexes
at once.
- This can be extended for dependents (reverse dependencies) and patches
later.
- cleanup patch.py:
- make patch.py constructors more understandable
- loosen coupling of patch.py with package
- in Package: make package_dir, module, and namespace class properties
- These were previously instance properties and couldn't be called from
directives, e.g. in patch.create()
- make them class properties so that they can be used in class definition
- also add some instance properties to delegate to class properties so
that prior usage on Package objects still works
- When returning string output, use text_type and decode utf-8 in Python
2 instead of using `str`
- This properly handles unicode, whereas before we would pass bad strings
to colify in `spack blame` when reading git output
- add a test that round-trips some unicode through an Executable object
* Remove /nfs/tmp2 from default configuration
* /nfs/tmp2 is going away from LC... and doesn’t exist for the rest of the world.
* update documentation to remove /nfs/tmp2 as well
* Record build output as an array of lines rather than concatenating to a
single large string.
* Use string.find to avoid running re.search on every line of output.
- some commands were missed in the rollout of spack environments
- this makes all commands that need to disambiguate specs restrict the
disambiguation to installed packages in the active environment, as
users would expect
* This fixes a number of bugs:
* Patches were not properly downloaded and added to mirrors.
* Mirror create didn't respect `list_url` in packages
* Update the `spack mirror` command to add all packages in the
concretized DAG (where originally it only added the package specified
by the user). This is required in order to collect patches that are specified
by dependents. Example:
* if X->Y and X requires a patch on Y called Pxy, then Pxy will only
be discovered if you create a mirror with X.
* replace confusing --one-version-per-spec option for `spack mirror create`
with --versions-per-spec; support retrieving multiple versions for
concrete specs
* Implementation details:
* `spack mirror create` now uses regular staging logic to download files
into a mirror, instead of reimplementing it in `add_single_spec`.
* use a separate resource caching object to keep track of new
resources and already-existing resources; also accepts storing
resources retrieved from a cache (unlike the local cache)
* mirror cache object now stores resources that are considered
non-cachable, like (e.g. the tip of a branch);
* the 'create' function of the mirror module no longer traverses
dependencies since this was already handled by the 'mirror' command;
* Change handling of `--no-checksum`:
* now that 'mirror create' uses stages, the mirror tests disable
checksums when creating the mirror
* remove `no_checksum` argument from library functions - this is now
handled at the Spack-command-level (like for 'spack install')
- all multimethod tests are now run for both `multimethod` and
`multimethod-inheritor`
- do this with a parameterized fixture (pkg_name) that runs the same
tests on both
- Since early Spack versions, the SpecParser has (weirdly) been
responsible for initializing Spec fields.
- This refactors initialization to take place in Spec.__init__, as it
probably should have originally.
- This makes the code easier to read, the parser easier to understand,
and removes the use of __new__ in the parser to initialize the Spec.
- This also makes it possible to make a completely empty Spec with
`Spec()` -- this is an abstract Spec that will match anything.
* "spack install" now uses cache by default, update examples accordingly
* Replace some example packages with others
* Packing tutorial reference to "spack env" replaced with "spack build-env"
* Command line prompts in examples are shortened
* Example output (including paths) are updated to be more relevant to training environment
Update all examples that need an MPI provider to build with MPICH; reorganize so that fixing MPICH (as part of environment section) comes first in the tutorial (most examples in the tutorial use an MPI provider).
- previously, uninstall would complain if a spec was needed by an
environment.
- Now, we analyze dependents and dependent environments and simply remove
(not uninstall) specs that are needed by environments
- with no arguments, these commands will now edit or dump the
environment's `spack.yaml` file.
- users may not know where named environments live
- this makes it convenient for users to get to the spack.yaml
configuration file for their named environment.
* Update Makefile to use property methods ("build_targets"/"install_targets")
to demonstrate their usage
* Fix highlighting
* Change cbench example to ESMF:
CBench package file was changed and no longer uses the example shown in
the old docs
Scopes added with -C are now referred to as "custom scopes"
rather than "command line scopes". "command line scope" now refers
to specific config options that are set on the command line (like
"--insecure")
- default is still to use the cache, but we've added back the
`--use-cache` argument so that scripts that used it are still correct.
- `--no-cache` is stil present and is mutually exclusive with `--use-cache`
* Introduce FFTW2 and FFT3 providers for Intel-MKL and FFTW Spack packages.
* make fftw default package for fftw-api virtual package
* virtual package test assertion now provides location of default virtual packages.
* Change name of virtual package to fftw-api and used versioned interface.
- all commands (except `spack find`, through `ConstraintAction`) now go
through get_env() to get the active environment
- ev.active was hard to read -- and the name wasn't descriptive.
- rename it to _active_environment to be more descriptive and to strongly
indicate that spack.environment manages it
- to aovid changing spec hashes drastically, only add this attribute to
differentiated abstract specs.
- othherwise assume that read-in specs are concrete
- spack.yaml files in the current directory were picked up inconsistently
-- make this a sure thing by moving that logic into find_environment()
and moving find_environment() to main()
- simplify arguments to Spack command:
- remove short args for infrequently used commands (--pdb/-D, -P, -s)
- `spack -D` now forces an env with a directory
- The `Spec` class maintains a special `_patches_in_order_of_appearance`
attribute on patch variants, but it is was preserved when specs are
copied.
- This caused issues for some builds
- Add special logic to `Spec` to preserve this variant on copy
- TODO: in the long term we should get rid of the special variant and
make it the responsibility of one of the variant classes.
- split 'environment' section into 'environments' and 'modules'
- move location to 'query packages' section
- move cd to developer section
- --env-dir no longer has a short optino (was -E)
- -E now means "run without an environment" (no longer same as --env-dir)
- -D now means "run with this directory environment"
- remove short options for may infrequently used top-level commands
- `spack env status` used to show install status; consolidate that into
`spack find`.
- `spack env status` will still print out whether there is an active
environment
- uninstall now:
- restricts its spec search to the current environment
- removes uninstalled specs from the current environment
- reports envs that still need specs you're trying to uninstall
- removed spack env uninstall command
- updated tests
- moved get_env from cmd/env.py to environment.py
- spack install will now install into the active environment when no
arguments are provided. It looks:
1. at the command line
2. for a local spack.yaml file
3. for any currently activated environment
- `spack env create <name>` works as before
- `spack env create <path>` now works as well -- environments can be
created in their own directories outside of Spack.
- `spack install` will look for a `spack.yaml` file in the current
directory, and will install the entire project from the environment
- The Environment class has been refactored so that it does not depend on
the internal Spack environment root; it just takes a path and operates
on an environment in that path (so internal and external envs are
handled the same)
- The named environment interface has been hoisted to the
spack.environment module level.
- env.yaml is now spack.yaml in all places. It was easier to go with one
name for these files than to try to handle logic for both env.yaml and
spack.yaml.
- `spack env activate foo`: sets SPACK_ENV to the current active env name
- `spack env deactivate`: unsets SPACK_ENV, deactivates the environment
- added support to setup_env.sh and setup_env.csh
- other env commands work properly with SPACK_ENV, as with an environment
arguments.
- command-line --env arguments take precedence over the active
environment, if given.
- env.yaml is now meaningful; it contains authoritative user specs
- concretize diffs user specs in env.yaml and env.json to allow user to
add/remove by simply updating env.yaml
- comments are preserved when env.yaml is updated by add/unadd
- env.yaml can contain configuration and include external configuration
either from merged files or from config scopes
- there is only one file format to remember (env.yaml, no separate init
format)
- env.json is now env.lock, and it stores the *last* user specs to be
concretized, along with full provenance.
- internal structure was modified slightly for readability
- env.lock contains a _meta section with metadata, in case needed
- added more tests for environments
- env commands follow Spack conventions; no more `spack env foo install`
- add `SingleFileScope` to configuration, which allows us to pull config
sections from a single file.
- update `env.yaml` and tests to ensure that the env.yaml schema works
when pulling configurtion from the env file.
- Each schema now has a top-level `properties` and `schema` attribute.
- The `properties` is a fragment that can be included in other
jsonschemas, via Python, not via '$ref'
- Th `schema` is a complete `jsonschema` with `title` and `$schema`
properties.
- add a common argument for `-e/--env`
- modify the database to support queries on subsets of hashes
- allow `spack find` to be filtered by hashes in an environment
- logic used in `spack find` was hiding duplicate installations if their
hashes were different
- short hash doesn't work in this scenario, since specs are structurally
identical
- ConstraintAction always works on a DB query, so use the DAG hash to
ensure uniqueness
- `spack.environment` is now the home for most of the infrastructure
around Spack environments
- refactor `cmd/env.py` to use everything from spack.environment
- refactor the cmd/env test to use pytest and fixtures
- `spack.util.environment` is the new home for routines that modify
environment variables.
- This is to make room for `spack.environment` to contain new routines
for dealing with spack environments
- Instead of one method with all parsers, each subcommand gets two
functions: `setup_<cmd>_parser()` and `environment_<cmd>()`
- the `setup_parser()` and `env()` functions now generate the parser
based on these and a list of subcommands.
- it is now easier to associate the arguments with the subcommand.
* modified tutorial packages
* update hint in hdf5 tutorial file (typo for suggested argument)
* add repo.yaml to tutorial repository
* update tutorial docs to refer user to tutorial package repository
* flake edits
* recommend site scope vs. defaults
* you don't specify the repo's name when adding a repo, just the path
* omit symlinks and create file copies when making a binary cache of a package
* unrelated flake edits involving regexes that recent flake is now angry about
* Record stdout for packages without errors
Previously our reporter only stored stdout if something went wrong
while installing a package. This prevented us from properly reporting
on steps where everything went as expected.
* More robustly report all phases to CDash
Previously if a phase generated no output it would not be reported to CDash.
For example, consider the following output:
==> Executing phase: 'configure'
==> Executing phase: 'build'
This would not generate a report for the configure phase. Now it does.
* Add test case for CDash reporting clean builds
* Fix default directory for CDash reports
The default 'cdash_report' directory name was getting overwritten
by 'junit-report'.
* Upload the build phase first to CDash
Older versions of CDash expect Build.xml to be the first file uploaded
for any given build.
* Define cdash_phase before referring to it
fixes#9739
The non-daemonic pool relies heavily on implementation details of the
multiprocessing package. In this commit we provide an implementation
that fits recent python versions.
This allows installing software on a namespace basis by including ${NAMESPACE} in `install_path_scheme`. e.g.,
```
cat ~/.spack/config.yaml
config:
install_path_scheme:
"${ARCHITECTURE}/${NAMESPACE}/${COMPILERNAME}-${COMPILERVER}/${PACKAGE}-${VERSION}-${HASH}"
```
The 'static_to_shared_library' function takes a compiler Executable,
which is intended to be invoked with a list of arguments; the
arguments must be separated from their values in the list, given
the way that 'Executable.__call__' invokes the underlying executable.
'static_to_shared_library' was not doing this, which this commit fixes.
Clang has support for using different fortran compilers with the Clang executable.
Spack includes logic to select a compiler wrapper symlink which refers to the fortran executable (since some build systems depend on the name of the compiler, e.g. 'gfortran' or 'flang').
This selection was previously based on the architecture, and chose incorrectly in some situations (e.g. for clang/gfortran on Linux). This replaces architecture-based wrapper selection with a selection that is based on the name of the Fortran compiler executable.
* Unite Dockerfiles - add build/run/push scripts
* update docker documentation
* update .travis.yml
* switch to using a preprocessor on Dockerfiles
* skip building docker images on pull requests
* update files with copyright info
* tweak when travis builds for docker files are done
fixes#9624
merge_config_rules was using `strict=False` to check if a spec
satisfies a constraint, which loosely translates to "this spec has
no conflict with the constraint, so I can potentially add it to the
spec". We want instead `strict=True` which means "the spec satisfies
the constraint right now".
- #8773 made the default mode 0o777, which is what's documented but
mkdirp actually takes the OS default or umask by default
- revert to the Python default by default, and only set the mode when
asked explicitly.
#9100 added a warning message when a path extracted from a module file
did not appear to be a valid filesystem path. This check was applied
to a variable which could be a list of paths, which would erroneously
trigger the warning. This commit updates the check to run at the
actual point where the path has been extracted.
* Add a build_language config.yaml option which controls the language
of compiler messages
* build_language defaults to "C", in which case the compiler messages
will be in English. This allows Spack log parsing to detect and
highlight error messages (since the regular expressions to find
error messages are in English)
* The user can use the default language in their environment by setting
the build_language config variable to null or ''
- `spack license list-files`: list all files that should have license headers
- `spack license list-lgpl`: list files still under LGPL-2.1
- `spack license verify`: check that license headers are correct
- Added `spack license verify` to style tests
- remove the old LGPL license headers from all files in Spack
- add SPDX headers to all files
- core and most packages are (Apache-2.0 OR MIT)
- a very small number of remaining packages are LGPL-2.1-only
compilers.yaml can track a module that is needed for a compiler, but
Spack does not fill this in automatically. This adds a note to the
documentation informing the user how to do this.
If we do not specify libdir explicitly, Meson chooses something like
lib/x86_64-linux-gnu, which causes problems when trying to find libraries
and pkg-config files.
Spack packages installed using spack buildcache were not running
post-install hooks, which create module files and manage licenses
(if necessary).
This was already occurring for Spack packages installed with
spack install --use-cache
Spack can now be configured to assign permissions to the files installed by a package.
In the `packages.yaml` file under `permissions`, the attributes `read`, `write`, and `group` control the package permissions. These attributes can be set per-package, or for all packages under `all`. If permissions are set under `all` and for a specific package, the package-specific settings take precedence. The `read` and `write` attributes take one of `user`, `group`, and `world`.
packages:
all:
permissions:
write: group
group: spack
my_app:
permissions:
read: group
group: my_team
* Better default CLI arguments for CDash reporting
--log-format=cdash is now implied if you specify the --cdash-upload-url
option to spack install.
We also now default to writing CTest XML files to cdash_report/ when using
the CDash reporter if no --log-file argument was specified.
* Improved documentation on how to use the CDash reporter
* Push default flag handlers into module scope
* Preserve backwards compatibility of builtin flag handler names
Ensure Spack continues to work for packages using the `Package.env_flags` idiom and equivalent.
* update docs and tests to match
* Update packages to match new syntax
Fix two bugs with module file parsing:
* Detection of the CRAY_LD_LIBRARY_PATH variable was broken by #9100.
This fixes it and adds a test for it.
* For module names like "foo-bar/1.0", the associated PACKAGE_DIR
environment variable name would be "FOO_BAR_DIR", but Spack was not
parsing the components and not converting "-" to "_"
Fixes#9166
This is intended to reduce errors related to lock timeouts by making
the following changes:
* Improves error reporting when acquiring a lock fails (addressing
#9166) - there is no longer an attempt to release the lock if an
acquire fails
* By default locks taken on individual packages no longer have a
timeout. This allows multiple spack instances to install overlapping
dependency DAGs. For debugging purposes, a timeout can be added by
setting 'package_lock_timeout' in config.yaml
* Reduces the polling frequency when trying to acquire a lock, to
reduce impact in the case where NFS is overtaxed. A simple
adaptive strategy is implemented, which starts with a polling
interval of .1 seconds and quickly increases to .5 seconds
(originally it would poll up to 10^5 times per second).
A test is added to check the polling interval generation logic.
* The timeout for Spack's whole-database lock (e.g. for managing
information about installed packages) is increased from 60s to
120s
* Users can configure the whole-database lock timeout using the
'db_lock_timout' setting in config.yaml
Generally, Spack locks (those created using spack.llnl.util.lock.Lock)
now have no timeout by default
This does not address implementations of NFS that do not support file
locking, or detect cases where services that may be required
(nfslock/statd) aren't running.
Users may want to be able to more-aggressively release locks when
they know they are the only one using their Spack instance, and they
encounter lock errors after a crash (e.g. a remote terminal disconnect
mentioned in #8915).
When a Spack Executable was configured to capture stderr and the
process failed, the error messages of the process were discarded.
This made it difficult to understand why the process failed. The
exception is now updated to include the stderr of the process when
the Executable captures stderr.
Adds 'code' to the list of suffixes that are excluded from version
parsing of URLs, such that if a URL contains the string
'cistem-1.0.0-beta-source-code', a version X will substitute in to
produce a URL with cistem-X-source-code ('source' was already excluded).
The 'cistem' package version is updated to make use of this (and fix
a fetching bug with the cistem package). A unit test is added to check
this parsing case.
Improve Spack's parsing of module show to eliminate some false
positives (e.g. accepting MODULEPATH when it is in fact looking for
PATH). This makes the following changes:
* Updates the pattern searching for several paths to avoid the case
where they are prefixes of unwanted paths
* Adds a warning message when an extracted path doesn't exist (which
may help catch future module parsing bugs faster)
* Adds a test with the content mentioned in #9083
Spack originally handled environment modifications in the following
order:
1. clear environment variables
(unless Spack was invoked with --dirty)
2. apply spack-specific environment variable updates,
including variables set by Spack core like CC/PKG_CONFIG_PATH
and those set by installed dependencies (e.g. in
setup_dependent_environment)
3. load all external/compiler modules
1 and 2 were done together. This splits 1 into its own function and
imposes the following order for environment modifications:
1. clear environment variables
2. load all external/compiler modules
3. apply spack-specific environment variable updates
As a result, prepend-path actions taken by Spack (or installed Spack
dependencies) take precedence over prepend-path actions from compiler
and external modules. Additionally, when Spack (or a package
dependency) sets/unsets an environment variable, that will override
the actions of external/compiler modules.
* Add 'extra_env' argument to Executable.__call__: this will be added
to the environment but does not affect whether the current
environment is reused. If 'env' is not set, then the current
environment is copied and the variables from 'extra_env' are added
to it.
* MakeExecutable can take a 'jobs_env' parameter that specifies the
name of an environment variable used to set the level of parallelism.
This is added to 'extra_env' (so does not affect whether the current
environment is reused).
* CMake-based Spack packages set 'jobs_env' when executing the 'test'
target for make and ninja (which does not use -j)
Consolidate prefix calculation logic for intel packages into the
IntelPackage class.
Add documentation on installing Intel packages with Spack an
(alternatively) adding them as external packages in Spack.
The functions returning the default scope to be modified or listed
have been moved from spack.cmd to spack.config.
Lmod now writes the guessed core compiler in the default modify scope
instead of the 'site' scope.
closes#8916
Currently Spack ends with an error if asked to write lmod modules files
and the 'core_compilers' entry is not found in `modules.yaml`. After
this PR an attempt will be made to guess that entry and the site
configuration file will be updated accordingly.
This is similar to what Spack already does to guess compilers on first
run.
- Support for Python 3.3 isn't really needed, as nothing uses it as the
default system Python, and nearly everyone will have a newer Python 3
version installed.
#8223 replaced regex-based makefile target parsing with an invocation of
"make -q". #8818 discovered that "make -q" can result in an error for some
packages.
Also, the "make -q" strategy relied on interpreting the error code, which only
worked for GNU Make and not BSD Make (which was deemed acceptable at
the time). As an added bonus, this implementation ignores the exit code and
instead parses STDERR for any indications that the target does not exist; this
works for both GNU Make and BSD Make.
#8223 also updated ninja target detection to use "ninja -t targets". This does
not change that behavior but makes it more-explicit with "ninja -t targets all"
This also adds tests for detection of "make" and "ninja" targets.
Fixes#9001#8289 added support for install_tree and copy_tree to merge into an existing
directory structure. However, it did not properly handle relative symlinks and
also removed support for the 'ignore' keyword. Additionally, some of the tests
were overly-strict when checking the permissions on the copied files.
This updates the install_tree/copy_tree methods and their tests:
* copy_tree/install_tree now preserve relative link targets (if the symlink in the
source directory structure is relative, the symlink created in the destination
will be relative)
* Added support for 'ignore' argument back to copy_tree/install_tree (removed
in #8289). It is no longer the object output by shutil.ignore_patterns: you pass a
function that accepts a path relative to the source and returns whether that
path should be copied.
* The openfoam packages (currently the only ones making use of the 'ignore'
argument) are updated for the new API
* When a symlink target is absolute, copy_tree and install_tree now rewrite the
source prefix to be the destination prefix
* copy_tree tests no longer check permissions: copy_tree doesn't enforce
anything about permissions so its tests don't check for that
* install_tree tests no longer check for exact permission matching since it can add
file permissions
- `imp` is deprecated and seems to have started having some weird
issues on certain Linux versions.
- In particular, the file argument to `load_source` is ignored on
arch linux with Python 3.7.
- `imp` is the only way to do imports in 2.6, so we'll keep it around for
now and use it if importlib won't work.
- `importlib` is the new import system, and it allows us to get
lower-level access to the import implementation.
- This consolidates all import logic into `spack.util.imp`, and make it
use `importlib` if it's avialable.
Replace use of `shutil.copytree` with `copy_tree` and `install_tree` functions in `llnl.util.filesystem`.
- `copy_tree` copies without setting permissions. It should be used to copy files around in the build directory.
- `install_tree` copies files and sets permissions. It should be used to copy files into the installation directory.
- `install` and `copy` are analogous single-file functions.
- add more extensive tests for these functions
- update packages to use these functions.
- dependency patching test didn't attempt to apply patches; just to see
whether they were on the spec.
- it applies the patch now and verifies that that patch was applied.
* Branch with the meson build-system
* Fix build_environment for dual loads and add create code
* Add documentation
* Fixed option list
* Update build_system_guess for meson
* Fixed documentation errors
* Added meson to build and configure and updated documentation
* fix typos
- cc cleanup caused a parsing regression in flag handling
- We added proper quoting to array expansions, but flag variables were
never actually converted to arrays. Old code relied on this.
This commit:
- Adds reads to convert flags to arrays.
- Makes the cc test check for improper space handling to prevent future
regressions.
- flags were prepended in reverse order to args, but this makes it hard
to see what order they'll be in on the final command line.
- add them in the order they'll appear to make cc easier to maintain.
- simplify code for assembling the command line
- fix separator used in SPACK_SYSTEM_DIRS test
- This corrects most of the issues found by shellcheck
- This also uses ':' as the delimiter for SPACK_SYSTEM_DIRS, for
consistency with other variables.
- filtering using sed causes most builds to slow down quite a bit, as the
compiler wrapper has to run sed many times, and *it* runs many times
- do the system directory parsing directly in bash
- Add tests to ensure that RPATHs are not added in cc mode, which can
cause some builds to fail.
- Change cc.py to use pytest style
- Instead of writing out all the flags, break the flags down into
variables so that it's easy to read what each test is supposed to
check. This should make cc.py more maintainable in the future.
- Adding -L and -Wl,-rpath to compile-only command lines ("cc mode" or
"-c") causes clang (if not also other compilers) to emit warnings that
confuse configure systems.
- Clang will print warnings about unused command-line arguments.
- This fix ensures that -L and -Wl,-rpath are not added if the compile
line is just building an object file with -c
- This also cleans up the cc script in several places.
Spack currently prepends include paths, library paths, and rpaths to the
compile line. This causes problems when a header or library in the package
has the same name as one exported by one of its dependencies. The
*dependency's* header will be preferred over the package's, which is not
what most builds expect. This also breaks some of our production codes.
This restores the original cc behavior (from *very* early Spack) of parsing
compiler arguments out by type (`-L`, `-I`, `-Wl,-rpath`) and reconstituting
the full command at the end.
`<includes> <other_args> <library dirs> <rpaths>`
This differs from the original behavior in one significant way, though: it
*appends* the library arguments so that dependency libraries do not shadow
those in the build.
This is safe because semantics aren't affected by *interleaving* `-I`, `-L`,
and `-Wl,-rpath` arguments with others, only with each other (so the order of
two `-L` args affects the search path, but we search for all libraries on the
command line using the same search path).
We preserve the following:
1. Any system directory in the paths will be listed last.
2. The root package's include/library/RPATH flags come before flags of the
same type for any dependency.
3. Order will be preserved within flags passed by the build (except system
paths, which are moved to be last)
4. Flags for dependencies will appear between the root flags and the system
flags, and the flags for any dependency will come before those for *its*
dependencies (this is for completeness -- we already guarantee this in
`build_environment.py`)
* Fix performance issue when compiling.
Spack was doing active wait when compiling, spoiling one core.
My fix consists in not setting any timeout for select, instead of
the previous 0 second.
* Fix comments about select.select timeout
- This was a nasty workaround due to the way our compiler wrappers used
to work. We don't want to have to modify our elfutils installation to
install libdwarf.
- Since cd9691de5, we no longer need this because the package will always
come before dependencies in our include order.
Spack currently prepends include paths, library paths, and rpaths to the compile line. This causes problems when a header or library in the package has the same name as one exported by one of its dependencies. The *dependency's* header will be preferred over the package's, which is not what most builds expect. This also breaks some of our production codes.
This restores the original cc behavior (from *very* early Spack) of parsing compiler arguments out by type (`-L`, `-I`, `-Wl,-rpath`) and reconstituting the full command at the end.
`<includes> <other_args> <library dirs> <rpaths>`
This differs from the original behavior in one significant way, though: it *appends* the library arguments so that dependency libraries do not shadow those in the build.
This is safe because semantics aren't affected by *interleaving* `-I`, `-L`, and `-Wl,-rpath` arguments with others, only with each other (so the order fo two `-L` args affects the search path, but we search for all libraries on the command line using the same search path).
We preserve the following:
1. Any system directory in the paths will be listed last.
2. The root package's include/library/RPATH flags come before flags of the same type for any dependency.
3. Order will be preserved within flags passed by the build (except system paths, which are moved to be last)
4. Flags for dependencies will appear between the root flags and the system flags, and the flags for any dependency will come before those for *its* dependencies (this is for completeness -- we already guarantee this in `build_environment.py`)
- previously, output could be confusing when deptypes were only shown for
one dependent when a node had *multiple* dependents
- also fix default coverage of `Spec.tree()`: it previously defaulted to
cover only build and link dependencies, but this is a holdover from
when those were the only types.
- Previously, Spack didn't check the arguments you put in version()
directives.
- So, you could do something like this, where there are arguments for a
URL fetcher AND for a git fetcher:
version('1.0', md5='abc123', git='https://foo.bar', commit='feda2343')
- Now, we check the arguments before constructing a fetcher, to ensure
that each package has *only* arguments for a single type of fetcher.
- Also added `test_package_version_consistency()` to the `package_sanity`
test, so that all builtin packages are required to have valid
`version()` directives.
- packagers can specify two top-level fetch URLs if one is `url`
- e.g., `url` and `git` or `url` and `svn`
- allow only one VCS fetcher so we can differentiate between URL and VCS.
- also clean up fetcher logic and class structure
- Packages can remove the top-level `url` attribute and still work
- These are now legal:
- Packages with *only* version-specific URLs (even with gaps)
- Packages with a top-level git/hg/svn attribute and `version`
directives for that.
- If a package has both a top-level hg/git/svn attribute AND a top-level
url attribute, the url attribute takes precedence.
Some packages do not have a `url` and are instead downloaded via `git`,
`hg`, or `svn`. Some packages like `spectrum-mpi` cannot be downloaded at
all, and are placeholder packages for system installations. Previously,
`__init__()` in `PackageBase` crashed if a package did not have a `url`
attribute defined.
I hacked this section of code out, but I have no idea what the
repercussions of that are.
- This hard-codes the hash lengths rather than computing them on import.
- Also cleans up the code in `spack.util.crypto` to make it easier to
understand.
Fix this output error:
```
$ spack -m module loads mpileaks
==> Error: `spack module loads -m t -m c -m l ...` has been moved. Try this instead:
$ spack module t loads mpileaks
$ spack module c loads mpileaks
$ spack module l loads mpileaks
```
In case a deprecated form of the module command is used, the program
will exit non-zero and print an informative error message suggesting
which command should be used instead.
As requested in the review all the commands meant to manage module
files have been grouped under the `spack module` command.
Unit tests have been refactored to match the new command structure.
fixes#2215fixes#2570fixes#6676fixes#7281closes#3827
This PR reverts the use of `spack module loads` in favor of
`spack module find` when loading module files via Spack. After this PR
`spack load` will accept a single spec at a time, and will be able
to interpret correctly the `--dependencies` option.
fixes#4400
The feature requested in #4400 was already part of the module file
configuration, but it was neither tested nor documented. This
commit takes care of adding a few lines in the documentation and a
regression test.
This just because the fixture has been moved one level above the one
it was originally defined. In this more general context there's more
than one configuration file that could be patched for tests.
'spack module' has been split into multiple commands, each one tied to a
specific module type. This permits the specialization of the new
commands with features that are module type specific (e.g. set the
default module file in lmod when multiple versions of the same package
are installed at the same time).
- repo membership test was broken by the refactor of spack/__init__.py
- refactor singleton so that 'spec in repo' works again for `spack.repo.path`
- fix spec command and add basic tests for `spack spec` and `spack spec --yaml`
- There was a lot of documentation in `PackageBase` dating back to the
very first versions of Spack.
- It was repetitive and out of date, and the docs at spack.readthedocs.io
are better.
- Remove the outdated specifics, and leave the minimal useful set of
developer docs in `package.py`.
- This changes `get_checksums_for_versions` to generate code that uses an
explicit `sha256` argument instead if the bare `md5` hash we used to
generate.
- also use a generic digest parameter for the `version` directive, rather
than a specific `md5` parameter.
- Add command-line scope option to Spack
- Rework structure of main to allow configuration system to raise
errors more naturally
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
- Fixes a bug in `llnl.util.lock`
- Locks in the current directory would fail because the parent directory
was the empty string.
- Fix this and return '.' for the parent of locks in the current
directory.
Replace regex-based target detection for Makefiles with a preliminary "make -q"
to check if a target exists. This does not work for NetBSD make; additional work
is required to detect if NetBSD make is present and to use a regex in that case.
The affected makefile target checks are only performed when the "--test" flag is
added to a "spack install" invocation.
Fixes#8036
Before this PR Package.installed was returning True if the spec prefix
existed, without checking the DB. This is wrong for external packages,
whose prefix exists before being registered into the DB. Now the property
checks for both the prefix and a DB entry.
Spack provides a number of classes based on commonly-used build systems
that users can extend when writing packages; the classes provide functionality
to perform the actions relevant to the build system (e.g. running "configure" for
an Autotools-based package). This adds documentation for classes supporting the
following build systems:
* Makefile
* Autotools
* CMake
* QMake
* SCons
* Waf
This includes build systems for managing extensions of the following packages:
* Perl
* Python
* R
* Octave
This also adds documentation on implementing packages that use a custom build
system (e.g. Perl/CMake).
Spack also provides extendable classes which aggregate functionality for related
sets of packages, e.g. those using CUDA. Documentation is added for
CudaPackage.
- The setup-env.sh script currently makes two calls to spack, but it
should only need to make one.
- Add a fast-path shell setup routine in `main.py` to allow the shell
setup to happen in a single, fast call that doesn't load more than it
needs to.
- This simplifies setup code, as it has to eval what Spack prints
- TODO: consider eventually making the whole setup script the output of a
spack command
* update help of `clean --all` to include `-p`
* remove old orphaned `.pyc` removal
* restrict removal or orphaned pyc files to `lib/spack` and `var/spack`
- Clean up error messages for when a lock can't be created, or when an
exclusive (write) lock can't be taken on a file.
- Add a number of subclasses of LockError to distinguish timeouts from
permission issues.
- Add an explicit check to prevent the user from taking a write lock on a
read-only file.
- We had a check for this for when we try to *upgrade* a lock on an RO
file, but not for an initial write lock attempt.
- Add more tests for different lock permission scenarios.
- write locks previously wrote information about the lock holder (host
and pid), and read locks woudl read this in.
- This is really only for debugging, so only enable it then
- add some tests that target debug info, and improve multiproc lock test
output
When a user specifies a URL for a specific version of a package, Spack originally
would use that URL for all newer versions of the package. This behavior has
proven to be generally more harmful than useful, so this PR removes the feature
such that a version-specific URL override affects only that version.
If the user sets "ccache: true" in spack's config.yaml, Spack will use an available
ccache executable when compiling c/c++ code. This feature is disabled by default
(i.e. "ccache: false") and the documentation is updated with how to enable
ccache support
Functional updates:
- `python` now creates a copy of the `python` binaries when it is added
to a view
- Python extensions (packages which subclass `PythonPackage`) rewrite
their shebang lines to refer to python in the view
- Python packages in the same namespace will not generate conflicts if
both have `...lib/site-packages/namespace-example/__init__.py`
- These `__init__` files will also remain when removing any package in
the namespace until the last package in the namespace is removed
Generally (Updated 2/16):
- Any package can define `add_files_to_view` to customize how it is added
to a view (and at the moment custom definitions are included for
`python` and `PythonPackage`)
- Likewise any package can define `remove_files_from_view` to customize
which files are removed (e.g. you don't always want to remove the
namespace `__init__`)
- Any package can define `view_file_conflicts` to customize what it
considers a merge conflict
- Global activations are handled like views (where the view root is the
spec prefix of the extendee)
- Benefit: filesystem-management aspects of activating extensions are
now placed in views (e.g. now one can hardlink a global activation)
- Benefit: overriding `Package.activate` is more straightforward (see
`Python.activate`)
- Complication: extension packages which have special-purpose logic
*only* when activated outside of the extendee prefix must check for
this in their `add_files_to_view` method (see `PythonPackage`)
- `LinkTree` is refactored to have separate methods for copying a
directory structure and for copying files (since it was found that
generally packages may want to alter how files are copied but still
wanted to copy directories in the same way)
TODOs (updated 2/20):
- [x] additional testing (there is some unit testing added at this point
but more would be useful)
- [x] refactor or reorganize `LinkTree` methods: currently there is a
separate set of methods for replicating just the directory structure
without the files, and a set for replicating everything
- [x] Right now external views (i.e. those not used for global
activations) call `view.add_extension`, but global activations do not
to avoid some extra work that goes into maintaining external views. I'm
not sure if addressing that needs to be done here but I'd like to
clarify it in the comments (UPDATE: for now I have added a TODO and in
my opinion this can be merged now and the refactor handled later)
- [x] Several method descriptions (e.g. for `Package.activate`) are out
of date and reference a distinction between global activations and
views, they need to be updated
- [x] Update aspell package activations
- Spack was assuming that a group with gid == current uid would always exist.
- This was breaking the travis build for macos.
- also fix issue with the DB tarball test finding coverage filesx
- pytest was not reporing the correct version from pytest.__version__.
It reported 'unknown'
- this fixes issues on some systems where system-installed pytest plugins
would try to use the version and convert it to an int
The following improvements are made to cxx standard support
(e.g. compiler.cxxNN_flag functions) in compilers:
* Add cxx98_flag property
* Add support for throwing an exception when a flag is not supported (previously
if a flag was not supported the application was terminated with tty.die)
* The name of the flag associated with e.g. c++14 standard support changes for
different compiler versions (e.g. c++1y vs c++14). This makes a few corrections
on what flag to return for which version.
* Added tests to confirm that versions report expected flags for various c++
standards (or raise an exception for versions that don't provide a given cxx
standard)
Note that if a given cxx standard is the default, the associated flag property will
return ""; cxx98 is assumed to be the default standard so this is the behavior for
the associated property in the base compiler class.
Package changes:
* Improvements to the boost spec to take advantage of the improved standard
flag facility.
* Update the clingo spec to catch the new exception rather than look for an
empty flag to indicate non-support (which is not part of the compiler flag API)
Fixes#7885#7193 added the patches_to_apply function to collect patches which are then
applied in Package.do_patch. However this only collects patches that are
associated with the Package object and does not include Spec-related patches
(which are applied by dependents, added in #5476).
Spec.patches already collects patches from the package as well as those applied
by dependents, so the Package.patches_to_apply function isn't necessary. All
uses of Package.patches_to_apply are replaced with Package.spec.patches.
This also updates Package.content_hash to require the associated spec to be
concrete: Spec.patches is only set after concretization. Before this PR, it was
possible for Package.content_hash to be valid before concretizing the associated
Spec if all patches were associated with the Package (vs. being applied by
dependents). This behavior was unreliable though so the change is unlikely to
be disruptive.
Fixes#8345
Spack environment modifications are applied before modules are loaded; this
includes settings to CC, FC, F77, and CXX, which point to the Spack compiler
wrappers. If the loaded modules set CC, this overrides the Spack compiler
wrappers. This PR adds a context manager to preserve the values of CC etc. that
are set by Spack: any effects on the CC, FC, F77, and CXX variables from modules
are undone and their original values are restored.
* pybind11: test support
Add a test functionality to pybind11.
* CMake: test also on "make check"
Some projects use non-CTest manual targets for tests.
* extend Prefix class with join() member to support dynamic directories
* add more tests for Prefix.join()
* more tests for Prefix.join()
* add docstring
* add example to docstring of Prefix class
* cleanup Prefix.join() tests
* use Prefix.join() in Packaging Guide
Fixes#8217
Trying to relocate a distribution when the new and old paths are
equal leads to failure, because the test that ensures that no
unrelocated bits are left over always fails. As an example, this
occurs if a user installs a package, generates a binary with it
using 'spack buildcache', uninstalls it, and then attempts to
reinstall into the same spack installation using the generated
binary package.
This updates the relocation check to accept the presence of the
old prefix in binaries if the package is being reinstalled into
its original location.
* allow user to constrain dependencies that are added conditionally
* remove check for not-visited deps from normalize, move it to concretize. The check now runs after the concretization loop completes (so an error is only reported if the user-mentioned spec doesnt appear anywhere in the dag)
* remove separate full_spec_deps variable; rename spec_deps to all_spec_deps to clarify that it merges user-specified dependencies with derived dependencies
* add unit test to confirm new functionality
- `spack config blame` is similar to `spack config get`, but it prints
out the config file and line number that each line of the merged
configuration came from.
- This is a debugging tool for understanding where Spack config settings
come from.
- add tests for config blame
Fixes: #8258#8090 altered import behavior so that import spack no longer
provides access to many other Spack modules. This addresses
a case which depended on the prior behavior and was not
updated as part of #8090. This particular import error only
came up when users were setting compiler flags on specs.
See also: #8194
- there were some leftover spack.* names being used after we removed
globals and moved everything in the top-level namespace to spack.pkgkit
- point those references to their new homes
- remove most `import spack` statements, except for files that need
`spack_version`
- import spack is no longer sufficient to use submodules
(e.g. spack.directives).
- these submodules must be imported directly. Update references
accordingly.
- Spack packages were originally expected to call `from spack import *`
themselves, but it has become difficult to manage imports in the
Spack core.
- the top-level namespace polluted by package symbols, and it's not
possible to avoid circular dependencies and unnecessary module loads in
the core, given all the stuff the packages need.
- This makes the top-level `spack` package essentially empty, save for a
version tuple and a version string, and `from spack import *` is now
essentially a no-op.
- The common routines and directives that packages need are now in
`spack.pkgkit`, and the import system forces packages to automatically
include this so that old packages that call `from spack import *`
will continue to work without modification.
- Since `from spack import *` is no longer required, we could consider
removing ``from spack import *`` from packages in the future and
shifting to ``from spack.pkgkit import *``, but we can wait a while to
do this.
- spack.util.lock behaves the same as llnl.util.lock, but Lock._lock and
Lock._unlock do nothing.
- can be disabled with a control variable.
- configuration options can enable/disable locking:
- `locks` option in spack configuration controls whether Spack will use filesystem locks or not.
- `-l` and `-L` command-line options can force-disable or force-enable locking.
- Spack will check for group- and world-writability before disabling
locks, and it will not allow a group- or world-writable instance to
have locks disabled.
- update documentation
- Spack core has long used llnl.util.filesystem.join_path, but
os.path.join is pretty much the same thing, and is more efficient.
- Use os.path.join in the core Spack code from now on.
- simplify the singleton pattern across the codebase
- reduce lines of code needed for crufty initialization
- reduce functions that need to mess with a global
- Singletons whose semantics changed:
- spack.store.store() -> spack.store
- spack.repo.path() -> spack.repo.path
- spack.config.config() -> spack.config.config
- spack.caches.fetch_cache() -> spack.caches.fetch_cache
- spack.caches.misc_cache() -> spack.caches.misc_cache
- `spack.cmd.all_commands` does a directory listing on
`lib/spack/spack/cmd`, regardless of whether it is needed
- make this lazy so that the directory listing won't happen unless it's
necessary.
- It turns out that jsonschema is one of the more expensive imports.
- move imports of jsonschema into functions to avoid the performance hits
for calls that don't need config.
- spack.store was previously initialized at the spack.store module level,
but this means the store has to be initialized on every spack call.
- this moves the state in spack.store to a singleton so that the store is
only initialized when needed.
- spack.repository module is now spack.repo
- `spack.repo` is now `spack.repo.path()` and loaded lazily
- Added `spack.repo.get()` and `spack.repo.all_package_names()` as
convenience functions to simplify the new lazy interface.
- updated tests and code
- no longer require `spack_version` to be a Version (it isn't used that
way anyway)
- use a simple tuple `spack_version_info` with major, minor, patch
versions
- generate `spack_version` from the tuple
- replace `spack.config.get_configuration()` with `spack.config.config()`
- replace `get_config`/`update_config` with `get`, `set`
- add a path syntax that can be used to refer to specific config options
without firt getting the entire configuration dict
- update usages of `get_config` and `update_config` to use `get` and `set`
- Current configuration code forces the config system to be initialized
at module scope, so configs are parsed on every Spack run, essentially
before anything else.
- We need more control over configuration init order, so move the config
scopes into a class and reduce global state in config.py
Fixes#2781
This PR introduces a new attribute for packages called
`archive_files`, which designates files that should be saved from
a package build (e.g. the config.log generated during autotools
builds).
The attribute contains a list of glob expressions; Any file that
matches will be archived in the `<prefix>/.spack/archived-files`
directory. Errors that occur when archiving files are collected and
reported in a file named `<prefix>/.spack/archived-files/errors.txt`.
`AutotoolsPackage` and `CMakePackage` provide a sensible default
override for this attribute.
fixes#7941
Modified string representation of Specs to add a space before deps
Unit-tests have been modified accordingly
Added a test for regression on #7941
Fixes#7924
Spack's yaml schema validator was initializing all instances of
unspecified properties with the same object, so that updating the
property for one entry was updating it for others (e.g. updating
versions for one package would update it for other packages).
This updates the schema validator to instantiate defaults with
separate object instances and adds a test to confirm this behavior
(and also confirms #7924 without this change).
* Use reported version of IBM XL Fortran compiler for compiler versions >= 16.0.
Starting with the April 2018 release, the IBM XL C and Fortran compilers report the same version, 16.0. Consequently, there is no need to downgrade the Fortran compiler version to match that of the C compiler.
* Use GitLab's API endpoint for fetching a git snapshot.
* More GitLab packages use the API.
* find_list_url for GitLab's API URLs.
* Flake8
* Url for 'hacckernels'.
* Check GitLab API regexps before the non-API ones.
Activating a package that is already activated now sends a `tty.msg`
and returns.
```
-bash-4.2$ ~/spack/bin/spack activate aspell6-en
==> Package aspell6-en/lc4v24f is already activated.
```
* Better error message for spack providers
fixes#1355
`spack providers` now outputs a sensible error message if non-virtual
specs are provided as arguments:
```
$ spack providers mpi zlib petsc
==> Error: non-virtual specs cannot be part of the query [zlib, petsc]
```
Formatting of the output changed slightly.
* Calling 'spack providers' without arguments print the virtual pkg list
Also, the error message in case of a wrong parameter has been improved
to show the list of valid packages.
* Avoid printing headers if stdout is not a tty
* The provider list is formatted with colify if not in a tty
* Added a test to check the list of providers returned from the command
Popping the when spec from kwargs in the extends directive breaks
class inheritance. Inheriting classes do not find their when spec.
We now get the when spec from kwargs instead, leaving it to be found
by any downstream package classes.
fixes#7705
Package.provides now checks constraints to ensure that a spec provides
a given virtual package. Note that 'strict=True' is not passed to
satisfies as this function is also used during concretization.
Fixes#7548
This updates the "spack view" command to use the same parsing logic
as "spack install" on the user-provided specs. For example you can
provide a DAG hash to refer to an exact installed spec instead of
specifying name, compiler, etc.
This fixes a check that decides when to skip buildcache relocation.
Originally the check was flawed in two ways: it would skip if the
source prefix matched the destination prefix, which no longer
matters since the source prefix is replaced with a placeholder
(so it always needs to be updated); it also would skip relocation
if the rpaths were not relative, when in fact it should be the
opposite (binaries without relative rpaths *should* be relocated,
and those without don't need it).
