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).
- FastPackageChecker was being called at startup every time Spack runs,
which takes a long time on networked filesystems. Startup was taking
5-7 seconds due to this call.
- The checker was intended to avaoid importing all packages (which is
really expensive) when all it needs is to stat them. So it's only
"fast" for parts of the code that *need* it.
- This commit makes repositories instantiate the checker lazily, so it's
only constructed when needed.
- This was needed when we transitioned to all lowercase packages because
git didn't handle case changes well on case-insensitive filesystems.
- Now it just adds extra stat calls to startup, and we check for
all-lowercase package names in tests, so we'll remove it.
- people using really old versions of Spack can re-clone.
* Create unload_module method
Extract code from load_module into unload_module.
* Unload modules to create a clean env on Cray
removes cray-libsci, cray-mpich and darshan to prevent any silent
linking with those packages.
* Add format to separate target and os for path
spec format can now handle separations of target and os for setting
up the path.
* Added ${PLATFORM} et al to spec.format()
${PLATFORM}, ${OS}, ${TARGET}
* Update tests
Updated tests and got rid of unnecessary code.
* Also update documentation to reflect this new ability.
* Add default path scheme to config.yaml
Added default path scheme to config.yaml. Users can overwrite this
section if they want.
* Speedup the default 'libs' property search - important for external
packages.
* As advised by @alalazo, use tuples instead of lists inside
_libs_default_handler.
* Added installation date and time to the database
Information on the date and time of installation of a spec is recorded
into the database. The information is retained on reindexing.
* Expose the possibility to query for installation date
The DB can now be queried for specs that have been installed in a given
time window. This query possibility is exposed to command line via two
new options of the `find` command.
* Extended docstring for Database._add
* Use timestamps since the epoch instead of formatted date in the DB
* Allow 'pretty date' formats from command line
* Substituted kwargs with explicit arguments
* Simplified regex for pretty date strings. Added unit tests.
This updates architecture concretization to
* Search for the nearest parent in the DAG for architecture information
rather than defaulting to the root of the DAG
* Propagate architecture settings transitively, such that if for
example the target is set at the root of the dag it will set the
same target on indirect dependencies (assuming no intermediate
dependency specifies a separate target). Previously this occurred
in general but under some conditions did not, for example if an
intermediate dependency specified some subset of architecture
properties.
* Create mirror for system with different compilers
Spack concretizes the spec provided by the user in
"spack mirror create" to ensure downloading the right
dependencies. Under normal circumstances concretization
requires that the chosen compiler exists on the system,
but this is not required when creating download mirrors
for other systems, so this requirement is removed in that
case.
* Add test for disabling compiler existence check
* Update compiler existence checking logic
* improve test for disabling compiler existence check
* make py-setuptools a run-time-only dep for py-basemap and patch python package to only apply setuptools flag for build deps
* py-qtconsole does not require setuptools
* This allows Spack to work with MD5 hashes on machines with openssl in FIPS mode.
* We are still using MD5 for validation in many places, and a later PR will replace all uses of MD5 with SHA256.
* This is a quick fix until that happens.
- transitive dependencies were not being handled correctly
- restructure code to do recursion and mark visited packages properly
- add `-V` option to *not* expand virtuals in spack dependencies
This re-adds the option to create and install unsigned tarballs, now
with the -u option (--unsigned) rather than the -y option.
This also changes the "keys" command, replacing the -y/--yes-to-all
option with the -t/--trust option (which has the same effect but is
more-clearly named).
Fixes#7130
shutil.move expects a source path like "/x/y/" to be a directory and
fails if "/x/y" is a symlink. This invokes realpath on the source
path to avoid the issue.
Fixes#7356
In some cases OperatingSystem (e.g. LinuxDistro) was getting
instantiated with a version that contains dashes. This breaks because
the concretizer later converts this value to a string and re-parses
it, and the '-' character is used to separate architecture components.
This adds a guard in the initializer to convert '-' to '_'.
Fixes#7237Fixes#6404Fixes#6418Fixes#6369
Identify when binary relocation fails to remove all instances of the
source prefix (and report an error to the user unless they specify
-a to allow the old root to appear). This check occurs at two stages:
during "bincache create" all instances of the root are replaced with
a special placeholder string ("@@@@..."), and a failure occurs if the
root is detected at this point; when the binary package is extracted
there is a second check. This addresses #7237 and #6418.
This is intended to be compatible with previously-created binary
packages.
This also adds:
* Better error messages for "spack install --use-cache" (#6404)
* Faster relocation on Mac OS (using a single call to
install_name_tool for all files rather than a call for each file)
* Clean up when "buildcache create" fails (addresses #6369)
* Explicit error message when the spack instance extracting the binary
package uses a different install layout than the spack instance that
created the binary package (since this is currently not supported)
* Remove the option to create unsigned binary packages with -y
This updates Cray.setup_platform_environment to use cray-specific
pkgconfig paths so that all providers of 'pkgconfig' have access
to them (previously the 'pkg-config' provider had this but the
'pkgconf' provider did not).
* [SPACK/spec.py] When a query through ForwardQueryToPackage returns
'None', treat that as query failure and raise RuntimeError with
suitable message. This overrides the current behavior to raise an
AttributeError which is now triggered only when no suitable query
property is found and there is no default handler.
* [spack/spec.py] Fix style.
* [SPACK/spec.py] In case of query failure, i.e. property returning
'None', raise AttributeError instead of RuntimeError in order to
pass the unit test. Also, small update in the logic distinguishing
query failure and lack of relevant property/attribute handling.
This updates the fix_darwin_install_name function to use the Spack
Executable object to run install_name_tool, which ensures that
process output is formatted as a 'str' for python2 and python3.
Originally fix_darwin_install_name was invoking subprocess.Popen
directly.
Fixes#5189
When working with non-normalized paths containing ".." on some
file systems, Spack was found to encounter a permission error when
writing to the path. This normalizes a path written by the
intel-parallel-studio package and also normalizes all paths
written by the license install hook (for all packages) to avoid
this issue for intel-parallel-studio.
Following the discussion with Todd and Adam, find has been modified to
accept glob expressions. This should not affect performance as every
glob implementation I inspected has 3 cases (no wildcard, wildcard but
no directories involved, wildcard and directories involved) and uses
fnmatch underneath.
Mixins have been changed to do by default a non-recursive search (but
a recursive search can still be triggered using the recursive keyword).
Following a comment from Todd, the search path for the files listed in
`filter_compiler_wrappers` can now be narrowed. Anyhow, the function
implementation still makes use of `find`, the rationale being that we
have already seen packages that install artifacts in e.g. architecture
dependent folders. The possibility to have a relative search path might
be a good compromise between the previous approach and the one suggested
in the review.
Also: 'ignore_absent' and 'backup' keyword arguments can be optionally
forwarded to `filter_file`.
Following comments from Todd:
- the call to tty.debug has been moved deeper, to log the filtering of each file
- the shadowing on the name "kwargs" is avoided
Implemented a declarative syntax for the additional behavior that can
get attached to classes. Implemented a function to filter compiler
wrappers that uses the mechanism above.
- command reference now includes usage for all Spack commands as output
by `spack help`. Each command usage links to any related section in
the docs.
- added `spack commands` command which can list command names,
subcommands, and generate RST docs for commands.
- added `llnl.util.argparsewriter`, which analyzes an argparse parser and
calls hooks for description, usage, options, and subcommands
- Shorten Spack command usage for short options. Short options are now
shown as [-abc] instead of as [-a] [-b] [-c]
- fix bug that mixed long and short options for top-level `spack help`
- Add proper help for `spack buildcache` subcommands
- Reorganize the help categories of Spack commands so that buildcache is
in packaging and diy and setup are now in build.
- previously commands with this argument showed a long list of choices
that were platform specific.
- use a better metavar: {defaults,system,site,user}[/PLATFORM]
Fixes#7159
When activating extensions in external views, the --ignore-conflicts
option was being ignored. In this particular issue the conflict was
for the duplicate __init__ file for multiple python packages in the
same namespace, but in general any conflict for extensions would
cause an error whether or not --ignore-conflicts was set.
This also renames the 'force' option of do_activate to
'with_dependencies' and updates views to call do_activate with this
set to False (since it traverses the dependency dag anyway). This
isn't strictly required, it just avoids redundant calls.
This reorganizes most sections and rewords a significant portion of
the content (including all introductions) but keeps all the examples.
* Remove section 'What happens at subscript time' from tutorial:
it is too detailed for a tutorial
* Move the 'Extra query parameters' and 'Attach attributes to other
packages' sections into a separate grouping 'Other packaging topics'
* move the 'Set variables at build time yourself' section after
'Set environment variables in dependents' section since the latter
is more motivating
* start the 'set environment variables at build-time for yourself'
section with qt as an example
* renamed section 'specs build interface' to 'retrieving library
information' and updated section introduction
* renamed section 'a motivating example' to 'accessing library
dependencies'; split out the material which deals with implementing
.libs for netlib-lapack into a separate section called 'providing
libraries to dependents'. consolidated in material from the section
'single package providing multiple virtual specs' since
netlib-lapack is an example of this (this removes the material
about intel-parallel studio)
* Allow dashes in command names and fix command name handling
- Command should allow dashes in their names like the reest of spack,
e.g. `spack log-parse`
- It might be too late for `spack build-cache` (since it is already
called `spack buildcache`), but we should try a bit to avoid
inconsistencies in naming conventions
- The code was inconsistent about where commands should be called by
their python module name (e.g. `log_parse`) and where the actual
command name should be used (e.g. `log-parse`).
- This made it hard to make a command with a dash in the name, and it
made `SpackCommand` fail to recognize commands with dashes.
- The code now uses the user-facing name with dashes for function
parameters, then converts that the module name when needed.
* Improve performance of log parsing
- A number of regular expressions from ctest_log_parser have really poor
performance, most due to untethered expressions with * or + (i.e., they
don't start with ^, so the repetition has to be checked for every
position in the string with Python's backtracking regex implementation)
- I can't verify that CTest's regexes work with an added ^, so I don't
really want to touch them. I tried adding this and found that it
caused some tests to break.
- Instead of using only "efficient" regular expressions, Added a
prefilter() class that allows the parser to quickly check a
precondition before evaluating any of the expensive regexes.
- Preconditions do things like check whether the string contains "error"
or "warning" (linear time things) before evaluating regexes that would
require them. It's sad that Python doesn't use Thompson string
matching (see https://swtch.com/~rsc/regexp/regexp1.html)
- Even with Python's slow implementation, this makes the parser ~200x
faster on the input we tried it on.
* Add `spack log-parse` command and improve the display of parsed logs
- Add better coloring and line wrapping to the log parse output. This
makes nasty build output look better with the line numbers.
- `spack log-parse` allows the log parsing logic used at the end of
builds to be executed on arbitrary files, which is handy even outside
of spack.
- Also provides a profile option -- we can profile arbitrary files and
show which regular expressions in the magic CTest parser take the most
time.
* Parallelize log parsing
- Log parsing now uses multiple threads for long logs
- Lines from logs are divided into chnks and farmed out to <ncpus>
- Add -j option to `spack log-parse`
* Marking database tests as slow
* Marking url command tests as slow
* Marking every test that uses database as slow
* Marking tests that import files as slow
* Marking gpg tests as slow
* Marking all versions and one list tests as slow
* Added more markers to unit tests + cli option to skip slow tests
Following a discussion with Axel, the generic 'slowtest' marker has been
split into 'db', 'network' and 'maybeslow'. A brief description of the
meaning of each marker has been added to pytest.ini.
A command line option to run only fast tests has been added to
'spack test'
* Don't use classes to group tests together
Reverted grouping tests under a class, as required in the review
* Minor style changes
This attempts to address one of the complaints at #5996 (comment):
> Repo currently caches package instances by Spec, and those Package instances have a Spec.
> This is unnecessary and causes confusion. I think I thought that we'd need to cache instances
> after loading package classes, but really just caching the classes is fine.
With this update, Repo's package cache is removed and Specs cache the package reference themselves. One consequence is that Specs which compare as equal will store separate instances of a Package class (not doing this creates issues for #4595 (comment)).
There were several references to Spec.package that could be replaced with Spec.package_class without any additional modifications. There are still a couple remaining references to Spec.package in Spec that would require adding functionality before replacing (e.g. calling Package.provides and Package.installed).
Note this makes it difficult to mock fetchers for tests which invokes code that reconstructs specs. test_packaging was one example of this where the updates caused a failure (in that case the error was avoided by not making an unnecessary call).
Details:
* Replace instances of spec.package with spec.package_class where a class method is being called
* Remove instances of Repo.get where Spec.package_class can be used in its place
* remove Repo.get caching instances of Package class for specs
* remove redundant check (which is also incorrect now that each spec stores its own copy of its package)
* avoid creating mirror with specs because it copies specs and those copies dont refer to the mocked fetcher (and it is also not required for the test)
* remove checks that are no longer necessary since repo doesn't cache specs
* Cleaned up JUnit report generation on install
The generation of a JUnit report was previously part of the install
command. This commit factors the logic into its own module, and uses
a template for the generation of the report.
It also improves report generation, that now can deal with multiple
specs installed at once. Finally, extending the list of supported
formats is much easier than before, as it entails just writing a
new template.
* Polished report generation + added tests for failures and errors
The generation of a JUnit report has been polished, so that the
stacktrace is correctly displayed with Jenkins JUnit plugin. Standard
error is still not used.
Added unit tests to cover for installation failures and installation
errors.
Avoid adding an "outside" (local home's) python user site directory
during python package installs.
Implements #6611
Fixes packages with auto-find side effects such as `py-setuptools`
that cause `py-matplotlib` to fail to build #6558
The flag_handlers method was being set as a bound method, but when
reset in the package.py file it was being set as an unbound method
(all python2 issues). This gets the underlying function information,
which is the same in either case.
The bug was uncovered for parmetis in #6858. This is a partial fix.
Included are changes to the parmetis package.py file to make use of
flag_handlers.
The feature added in #4611 is currently broken. This commit fixes the
behavior of the command and adds unit tests to ensure the basic semantic
is maintained.
It also changes slightly the behavior of Spec.concretized to avoid
copying caches before the concretization (as this may result in a
wrong hash computation for the DAG).
- Generating the HTML from for >2300 packages from RST in Sphinx seems to
take forever.
- Add an option to `spack list` to generate straight HTML instead.
- This reduces the doc build time to about a minute (from 5 minutes on a mac laptop).
* Vendor ordereddict for python2.6 only
This commit substitutes the custom module 'ordereddict_backport' with
the more known 'ordereddict' and vendors it only for python 2.6. Other
supported versions of python will use 'collections.OrderedDict'.
* Use absolute imports also for python 2.6
See PEP-328 for more information on the subject
* Added provenance of vendored ordereddict
See #6794
This fixes cases where test-only dependencies were omitted from
consideration when modifying the environment at build time. This
includes an update to the python package definition to add
testing-related python extensions to its specialized environment
setup.
This updates the conflict-checking logic to require that the conflict
spec matches exactly and that all fields mentioned in the conflict
spec are present in the concretized spec in order to report a
conflict. This will automatically skip all conflict checks for
dependencies of externals (since externals strip dependencies). This
will not affect non-external packages since all fields and
dependencies are fully specified for such packages.
* Keep track of source and versions for external libraries
* Note source of more obscure libraries
* We aren't upgrading jsonschema after all
* Add note on modifications made to pytest
* add OctavePackage
1. remove import CudaPackage which is not needed anymore
2. mention CudaPackage and OctavePackage in packaging guide
3. adjust OctavePackageTemplate
4. add clue file for Octave build
5. sanity check on self.prefix
* use setup_environment
* Only specify a file as needing relocation if it contains the spack
root as a text string (this constraint also applies to binaries)
* Don't fail if there is an error retrieving RPATH information from a
binary (even if it is specified as requiring relocation)
This adds the ability for packages to apply compiler flags in one of
three ways: by injecting them into the compiler wrapper calls (the
default in this PR and previously the only automated choice);
exporting environment variable definitions for variables with
corresponding names (e.g. CPPFLAGS=...); providing them as arguments
to the build system (e.g. configure).
When applying compiler flags using build system arguments, a package
must implement the 'flags_to_build_system_args" function. This is
provided for CMake and autotools packages, so for packages which
subclass those build systems, they need only update their flag
handler method specify which compiler flags should be specified as
arguments to the build system.
Convenience methods are provided to specify that all flags be applied
in one of the 3 available ways, so a custom implementation is only
required if more than one method of applying compiler flags is
needed.
This also removes redundant build system definitions from tutorial
examples
Fixes#5940
This PR changes the option '--restage' of 'spack install' to
'--dont-restage', inverting its meaning and the default behavior
of the command.
Fixes#6200
For compilers that successfully run a version detection script but
don't actually return a version, Spack was keeping track of the
empty version and then failing when attempting to construct a
compiler spec. This skips any attempt to add a compiler entry when
no version is reported (but logs when a compiler fails to report
a version).
* Support pruning of vars with Env from_sourcing_file (issue #6501)
- Blacklist string literals or regular expressions of environment
variables that are to be removed from consideration as being affect
by the sourcing of the file. Conversely, whitelist modifications
that should not ignored. Whitelisted variables have priority over
blacklisting.
Eg,
EnvironmentModifications.from_sourcing_file
(
bashrc
blacklist=['JUNK_ENV', 'OPTIONAL_.*'],
whitelist=['OPTIONAL_REQUIRED.*']
)
This modification can be used to eliminate environment variables that
are not generalized for modules (eg, user-specific variables).
* BUG: module prepend-path in wrong order (fixes#6501)
* STYLE: module variables in sorted order (issue #6501)
- looks nicer and also helps when comparing the contents of different
module files.
* ENH: remove duplicates from env paths when creating modules (issue #6501)
- this makes for a cleaner module environment and helps avoid some
unnecessary changes to the environment that are only provoked by
redundancies in the PATH.
eg,
before PATH=/usr/bin
after PATH=/usr/bin:/usr/bin:/my/application/bin
should only result in /my/application/bin being added to the PATH
and not /usr/bin:/my/application/bin
Activate via the 'clean' flag (default: False):
EnvironmentModifications.from_sourcing_file(bashrc, clean=True,..
Fixes#2440
The "Getting started" guide should be short and sweet. This commit
simplifies the "Environment-Modules" section pruning:
- outdated / wrong suggestions as noted in #2440
- uncommon setups that are better treated in a reference guide
According to the documentation here:
http://www.sphinx-doc.org/en/stable/ext/autodoc.html
"For module data members and class attributes, documentation can either
be put into a comment with special formatting (using a #: to start the
comment instead of just #), or in a docstring after the definition."
* Updated function which checks if a binary file needs relocation.
Previously this was incorrectly identifying ELF binaries as symbolic
links (so they were being excluded from relocation). Added test to
check that ELF binaries are not considered symlinks.
* relocate_text was not replacing paths in text files. Added test to
check that text files are relocated properly (i.e. paths in the file
are converted to the new prefix).
* Exclude backup files created by filter_file when installing from
binary cache.
* Update write_buildinfo_file method signature to distinguish between
the spec prefix and the working directory for the binary cache
package.
"spack spec" was providing helpful error information about conflicts
that was missing from "spack install", this updates "spack install"
to provide the same information.
The original docstring had confusing wording re: what is going to
symlinked and where when using the `extend` directive, and how exactly
the symlinking is performed (not automatically on install, but using
`spack activate`). See #5559.
Showing "Normalize" on output doesn't give users additional information,
as this step is essentially an implementation detail of concretization.
This PR skips it and shows just the input spec and the concretized one.
Printing partial hashes for input spec has been disabled.
* First draft for SC17 build systems portion
Added tutorial_buildsystems.rst file as well as example files under
the tutorial/ directory.
* Remove floating `
* Add requested changes, and examples of subclasses
Added in the requested changes to the documentation. Also added in
information about the subclasses and the defaults that they provide.
Also fixed some phrasing issues, formatting and punctuation.
* Flake8 fixes and new files for classes
Made flake8 fixes to pass tests and also added files to demonstrate code
in the classes.
* Minor edits
Edits in formatting and made some sentence changes
* Flake8 fixes
More flake8 fixes
* Flake8 fix
* Change section order on tutorial and minor edits
Placed the section at the appropriate section for the tutorial and then
added some minor edits that were requested.
* Add requested changes and more details
Added more details to Cmake, Makefile and Python Packages.
* Fixed formatting and minor edits
* Fix doc build error
* Allow types and 'any' in variant definitions.
- Previously variant values had to be a tuple or a callable predicate.
- This allows 'any' as shorthand for `lambda x: True` and type objects
as shorthand for "any value of this type".
- Makes variant definitions more readable, keeps lambdas out of
packages for common cases.
* Update packaging tutorial
* Fix bad file reference in packaging tutorial
* First draft of the advanced packaging tutorial
* advanced packaging tutorial: improved phrasing
Thanks Denis and Hartzell!
* Fixed typos + reworded a couple of sentences
* Reworked module file tutorial section
First draft for the SC17 update. This includes:
- adding an introduction on module files + Spack's module
generation blueprints
- adding a set-up section and provide a docker image for easy set-up
- updating all the relevant snippets
- extending a bit some of the concepts that were already touched
* Added reference to #5582 + committed Dockerfiles
Also fixed a couple of typos spotted by Denis.
* module file tutorial: added section on template customization
* module file tutorial: fixed minor typos + rephrased a sentence
* module file tutorial: made explicit that Docker image comes with software
* module file tutorial: improved phrasing and layout.
Thanks Hartzell!
* module file tutorial: added vim and nano to editors
* module file tutorial: fixed typo
* Fixed typos
Thanks Adam!
* module file tutorial: updated Dockerfile + minor changes in introduction
Fixes#6154
For compiler options which set values using the syntax "-flag value"
(with a space between the flag and the flag's value) the flag and
value were treated as separate and reordered. This updates Spack's
logic to treat the flag and value as a single unit, even if there is
a space between them. It assumes that all flags are prefixed with
"-" and that all flag values are not.
