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2018-08-17install_tree: symlink handling and add 'ignore' option (#9019)scheibelp2-19/+86
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
2018-08-16imports: spack uses importlib instead of imp when availableTodd Gamblin7-39/+199
- `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.
2018-08-16Fix spack versions behavior when no URL (#8967)Adam J. Stewart3-12/+45
* Fix spack versions behavior when no URL * Unit test packages without URLs or safe versions
2018-08-15install_tree, copy_tree can install into existing directory structures (#8289)Adam J. Stewart3-73/+294
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.
2018-08-14tests: make the dependency patching test more completeTodd Gamblin2-3/+21
- 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.
2018-08-10Branch with the meson build-system (#8467)Tom Merrick9-0/+309
* 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
2018-08-09spec: make full_hash look like dag_hash (#8911)Scott Wittenburg1-2/+7
2018-08-09bugfix: cc handles spaces in flag variables properlyTodd Gamblin2-90/+82
- 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.
2018-08-08cc: refactor flag adding so that it's not in reverse orderTodd Gamblin2-29/+56
- 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
2018-08-08cc: restore ccache support in the wrapper, add a regression testTodd Gamblin2-2/+38
- Add back ccache support to the wrapper. - Add a regression test to make sure ccache is working properly.
2018-08-08cc: run shellcheck linter on the cc compiler script, minor cleanupTodd Gamblin2-12/+14
- This corrects most of the issues found by shellcheck - This also uses ':' as the delimiter for SPACK_SYSTEM_DIRS, for consistency with other variables.
2018-08-08cc: don't use sed to filter system directoriesTodd Gamblin2-42/+93
- 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
2018-08-08refactor: clean up and fix the cc testTodd Gamblin2-414/+503
- 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.
2018-08-08bugfix: cc should not add -L or -Wl,-rpath in compile-only modeTodd Gamblin1-80/+108
- 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.
2018-08-08Restore cc: package search paths come before dependency paths (#4692)Gregory Becker4-158/+330
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`)
2018-08-07Fix performance issue when compiling. (#8828)cedricchevalier191-4/+3
* 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
2018-08-06libstdc++ detection uses os.path.realpath instead of os.readlink (#8865)Paul Chelarescu1-1/+1
2018-08-06Remove default variant bug from list of known issues (#8900)Adam J. Stewart1-32/+0
2018-08-06Docstring typo: builing -> building (#8896)George Hartzell1-1/+1
2018-08-04revert cd9691de5 (#4692) while we work on a fix.Todd Gamblin4-330/+158
2018-08-03spack spec: no extra newline with --yaml; error with no specsTodd Gamblin2-1/+16
- `spack spec` now returns an error if given no specs - removed superfluous trailing newline from `spack spec --yaml` output (only one newline now)
2018-08-03Add spack arch --operating-system and --target flagsAdam J. Stewart3-6/+40
2018-08-02libdwarf: remove use of hide_files()Todd Gamblin1-13/+0
- 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.
2018-08-01cc: package search paths come before dependency paths (#4692)becker334-158/+330
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`)
2018-08-01docs: minor text changes (#8858)Holly3-13/+13
2018-08-01lmod: fix use of custom separator in prepend_path etc. (#8737)Stephen Herbein2-0/+19
fixes #8736
2018-07-31docs: update `spack view` argument synatx (#8839)Stephen Herbein1-2/+2
The `--dependencies` and `--exclude` flags are now arguments to the `spack view` comand rather than the `spack view symlink` command.
2018-07-29spec: `Spec.tree()` merges deptypes when only covering nodes (#8821)Todd Gamblin2-8/+56
- 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.
2018-07-27Fixed a typo in the docs (the docker image to pull was wrong) (#8814)Massimiliano Culpo1-1/+1
2018-07-25Add docs on new top-level VCS attributesAdam J. Stewart1-108/+181
2018-07-25tests: convert mirror test to pytest with free functions.Todd Gamblin1-44/+47
2018-07-25tests: add checks and tests for consistent version() argumentsTodd Gamblin3-2/+60
- 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.
2018-07-25tests: correct name of `check_db` to `check_repo`Todd Gamblin1-7/+6
- this test is checking the package *repository*, not the database.
2018-07-25core: differentiate package-level fetch URLs by args to `version()`Todd Gamblin2-84/+186
- 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
2018-07-25core: add check for conflicting top-level fetch attributes in packagesTodd Gamblin4-6/+35
- ensure that packages can't have more than one of git, hg, svn, or url
2018-07-25style: clean up exception definitions in package.pyTodd Gamblin1-7/+2
2018-07-25core: fixes and tests for handling of fetcher attributes in packagesTodd Gamblin3-40/+174
- 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.
2018-07-25core: quick fix for packages without URLsAdam J. Stewart1-11/+0
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.
2018-07-24Fix order of regexes reported by spack url summaryAdam J. Stewart1-2/+2
2018-07-24core: make `spack.util.crypto` initialization less expensive.Todd Gamblin2-38/+54
- 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.
2018-07-24bugfix: `spack module -m` error message (#8794)Todd Gamblin1-3/+2
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 ```
2018-07-24Die with a meaningful error if a deprecated command is usedMassimiliano Culpo2-3/+57
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.
2018-07-24Grouped all the module commands under `spack module`Massimiliano Culpo13-390/+266
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.
2018-07-24module file tutorial: rebuilt docker image and updated the scriptMassimiliano Culpo1-170/+216
2018-07-24Added --dependencies to the help text of spack loadMassimiliano Culpo2-3/+5
fixes #6321
2018-07-24spack load exits with 1 if module does not exist or is not installedMassimiliano Culpo2-7/+68
fixes #2215 fixes #2570 fixes #6676 fixes #7281 closes #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.
2018-07-24Added blacklisting of implicit modules in docs + regression testsMassimiliano Culpo5-1/+52
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.
2018-07-24Renamed 'patch_configuration' fixture to 'module_configuration'Massimiliano Culpo5-78/+79
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.
2018-07-24Added a unit test for 'spack lmod setdefault'Massimiliano Culpo4-12/+101
2018-07-24Updated references to `spack module` in the documentation.Massimiliano Culpo5-55/+46