The required hash of a submodule might point to the
non-HEAD commit of the current main branch and hence
would lead to a "no such remote ref" at checkout in
a shallow submodule.
## Motivation
Python installations are both important and unfortunately inconsistent. Depending on the Python version, OS, and the strength of the Earth's magnetic field when it was installed, the name of the Python executable, directory containing its libraries, library names, and the directory containing its headers can vary drastically.
I originally got into this mess with #3274, where I discovered that Boost could not be built with Python 3 because the executable is called `python3` and we were telling it to use `python`. I got deeper into this mess when I started hacking on #3140, where I discovered just how difficult it is to find the location and name of the Python libraries and headers.
Currently, half of the packages that depend on Python and need to know this information jump through hoops to determine the correct information. The other half are hard-coded to use `python`, `spec['python'].prefix.lib`, and `spec['python'].prefix.include`. Obviously, none of these packages would work for Python 3, and there's no reason to duplicate the effort. The Python package itself should contain all of the information necessary to use it properly. This is in line with the recent work by @alalazo and @davydden with respect to `spec['blas'].libs` and friends.
## Prefix
For most packages in Spack, we assume that the installation directory is `spec['python'].prefix`. This generally works for anything installed with Spack, but gets complicated when we include external packages. Python is a commonly used external package (it needs to be installed just to run Spack). If it was installed with Homebrew, `which python` would return `/usr/local/bin/python`, and most users would erroneously assume that `/usr/local` is the installation directory. If you peruse through #2173, you'll immediately see why this is not the case. Homebrew actually installs Python in `/usr/local/Cellar/python/2.7.12_2` and symlinks the executable to `/usr/local/bin/python`. `PYTHONHOME` (and presumably most things that need to know where Python is installed) needs to be set to the actual installation directory, not `/usr/local`.
Normally I would say, "sounds like user error, make sure to use the real installation directory in your `packages.yaml`". But I think we can make a special case for Python. That's what we decided in #2173 anyway. If we change our minds, I would be more than happy to simplify things.
To solve this problem, I created a `spec['python'].home` attribute that works the same way as `spec['python'].prefix` but queries Python to figure out where it was actually installed. @tgamblin Is there any way to overwrite `spec['python'].prefix`? I think it's currently immutable.
## Command
In general, Python 2 comes with both `python` and `python2` commands, while Python 3 only comes with a `python3` command. But this is up to the OS developers. For example, `/usr/bin/python` on Gentoo is actually Python 3. Worse yet, if someone is using an externally installed Python, all 3 commands may exist in the same directory! Here's what I'm thinking:
If the spec is for Python 3, try searching for the `python3` command.
If the spec is for Python 2, try searching for the `python2` command.
If neither are found, try searching for the `python` command.
## Libraries
Spack installs Python libraries in `spec['python'].prefix.lib`. Except on openSUSE 13, where it installs to `spec['python'].prefix.lib64` (see #2295 and #2253). On my CentOS 6 machine, the Python libraries are installed in `/usr/lib64`. Both need to work.
The libraries themselves change name depending on OS and Python version. For Python 2.7 on macOS, I'm seeing:
```
lib/libpython2.7.dylib
```
For Python 3.6 on CentOS 6, I'm seeing:
```
lib/libpython3.so
lib/libpython3.6m.so.1.0
lib/libpython3.6m.so -> lib/libpython3.6m.so.1.0
```
Notice the `m` after the version number. Yeah, that's a thing.
## Headers
In Python 2.7, I'm seeing:
```
include/python2.7/pyconfig.h
```
In Python 3.6, I'm seeing:
```
include/python3.6m/pyconfig.h
```
It looks like all Python 3 installations have this `m`. Tested with Python 3.2 and 3.6 on macOS and CentOS 6
Spack has really nice support for libraries (`find_libraries` and `LibraryList`), but nothing for headers. Fixed.
When a compiler was not found a stacktrace was displayed to user because
there were three arguments to be substituted in a string with only two
substitutions to be done.
Fixes#4026#1167 updated Database.reindex to keep old installation records to
support external packages. However, when a user manually removes a
prefix and reindexes this kept the records so the packages were
still installed according to "spack find" etc. This adds a check
for non-external packages to ensure they are properly installed
according to the directory layout.
- add Version.__format__ to support new-style formatting.
- Python3 doesn't handle this well -- it delegates to
object.__format__(), which raises an error for fancy format strings.
- not sure why it doesn't call str(self).__format__ instead, but that's
hwo things are.
* Properly ignore flake8 F811 redefinition errors
* Add unit tests for flake8 command
* Allow spack flake8 to work on systems with older git
* Skip flake8 unit tests for Python 2.6 and 3.3
* treats correctly a change from `explicit=False` to `explicit=True` in an external package DB entry.
* added unit tests
* fixed issues raised by @tgamblin . In particular the PR is no more hash-changing for packages that are not external.
* added a test to check correctness of a spec/yaml round-trip for things that involve an external
* Don't find external module path at each step of concretization
* it's not necessary.. The paths are retrieved at the end of concretizaion
* Don't find replacements for external packages.
* Test root of the DAG if external
* No reason not to test if the root of the DAG is external when external
packages are now first class citizens!
* Create `external` property for Spec (for external_path and external_module)
* Allow users to specify external package paths relative to spack
* Canonicalize external package paths so that users may specify their
locations relative to spack's directory.
* Update tests to use new external_path and external properly.
* skip license hooks on external
- Spack doesn't need eggs -- it manages its own directories
- Simplify install layout and reduce sys.path searches by installing all
packages flat (eggs are deprecated for wheels, and this is also what
wheels do).
- We now supply the --single-version-externally-managed argument to
`setup.py install` for setuptools packages and setuptools.
- modify packages to only use setuptools args if setuptools is an
immediate dependency
- Remove setuptools from packages that do not need it.
- Some packages use setuptools *only* when certain args (likeb
'develop' or 'bdist') are supplied to setup.py, and they specifically
do not use setuptools for installation.
- Spack never calls setup.py this way, so just removing the setuptools
dependency works for these packages.
* fetch git submodules recursively
This is useful if the submodules have submodules themselves. On
the other hand doing a recursive update doesn't hurt if there
is only one level.
* fetch submodules with depth=1 as well (fix#2190)
* use git submodule with depth only for git>=1.8.4
- Spack install would previously fail if it could not load a package for
the thing being uninstalled.
- This reworks uninstall to handle cases where the package is no longer
known, e.g.:
a) the package has been renamed or is no longer in Spack
b) the repository the package came from is no longer registered in
repos.yaml
- gcc on macOS says it's version 4.2.1, but it's really clang, and it's
actually the *same* clang as the system clang.
- It also doesn't respond with a full path when called with
--print-file-name=libstdc++.dylib, which is expected from gcc in abi.py.
Instead, it gives a relative path and _gcc_compiler_compare doesn't
understand what to do with it. This results in errors like:
```
lib/spack/spack/abi.py, line 71, in _gcc_get_libstdcxx_version
libpath = os.readlink(output.strip())
OSError: [Errno 2] No such file or directory: 'libstdc++.dylib'
```
- This commit does two things:
1. Ignore any gcc that's actually clang in abi.py. We can probably do
better than this, but it's not clear there is a need to, since we
should handle the compiler as clang, not gcc.
2. Don't auto-detect any "gcc" that is actually clang anymore. Ignore
it and expect people to use clang (which is the default macOS
compiler anyway).
Users can still add fake gccs to their compilers.yaml if they want, but
it's discouraged.
* Checksum code wasn't opening binary files as binary.
- Fixes Python 3 issue where files are opened as unicode text by default,
and decoding fails for binary blobs.
* Simplify fetch test parametrization.
* - add tests for URL fetching and checksumming.
- fix coverage on interface functions in FetchStrategy superclass
- add some extra crypto tests.
* Package install remove prior unfinished installs
Depending on how spack is terminated in the middle of building a
package it may leave a partially installed package in the install
prefix. Originally Spack treated the package as being installed if
the prefix was present, in which case the user would have to
manually remove the installation prefix before restarting an
install. This commit adds a more thorough check to ensure that a
package is actually installed. If the installation prefix is present
but Spack determines that the install did not complete, it removes
the installation prefix and starts a new install; if the user has
enabled --keep-prefix, then Spack reverts to its old behavior.
* Added test for partial install handling
* Added test for restoring DB
* Style fixes
* Restoring 2.6 compatibility
* Relocated repair logic to separate function
* If --keep-prefix is set, package installs will continue an install from an existing prefix if one is present
* check metadata consistency when continuing partial install
* Added --force option to make spack reinstall a package (and all dependencies) from scratch
* Updated bash completion; removed '-f' shorthand for '--force' for install command
* dont use multiple write modes for completion file
* Add tests to mercurial package
* Add support for --insecure with mercurial fetching
* Install man pages and tab-completion scripts
* Add tests and latest version for all deps
* Flake8 fix
* Use certifi module to find CA certificate
* Flake8 fix
* Unset PYTHONPATH when running hg
* svn_fetch should use to svn-test, not hg-test
* Drop Python 3 support in Mercurial
Python 3 support is a work in progress and isn't currently
recommended:
https://www.mercurial-scm.org/wiki/SupportedPythonVersions
* Test both secure and insecure hg fetching
* Test both secure and insecure git and svn fetching
`set_executable` now checks if a user/group.other had read permission
on a file and if it does then it sets the corresponding executable
bit.
See #1483.
