This PR adds a `--format=bash` option to `spack commands` to
auto-generate the Bash programmable tab completion script. It can be
extended to work for other shells.

Progress:

- [x] Fix bug in superclass initialization in `ArgparseWriter`
- [x] Refactor `ArgparseWriter` (see below)
- [x] Ensure that output of old `--format` options remains the same
- [x] Add `ArgparseCompletionWriter` and `BashCompletionWriter`
- [x] Add `--aliases` option to add command aliases
- [x] Standardize positional argument names
- [x] Tests for `spack commands --format=bash` coverage
- [x] Tests to make sure `spack-completion.bash` stays up-to-date
- [x] Tests for `spack-completion.bash` coverage
- [x] Speed up `spack-completion.bash` by caching subroutine calls

This PR also necessitates a significant refactoring of
`ArgparseWriter`. Previously, `ArgparseWriter` was mostly a single
`_write` method which handled everything from extracting the information
we care about from the parser to formatting the output. Now, `_write`
only handles recursion, while the information extraction is split into a
separate `parse` method, and the formatting is handled by `format`. This
allows subclasses to completely redefine how the format will appear
without overriding all of `_write`.

Co-Authored-by: Todd Gamblin <tgamblin@llnl.gov>

The gpg2 command isn't always around; it's sometimes called gpg.  This is
the case with the brew-installed version, and it's breaking our tests.

- [x] Look for both 'gpg2' and 'gpg' when finding the command
- [x] If we find 'gpg', ensure the version is 2 or higher
- [x] Add tests for version detection.

Enable the ADIOS1 backend by default.

- [x] Factored to a common place the fixture `testing_gpg_directory`, renamed it as 
      `mock_gnupghome`
- [x] Removed altogether the function `has_gnupg2`

For `has_gnupg2`, since we were not trying to parse the version from the output of:
```console
$ gpg2 --version
```
this is effectively equivalent to check if `spack.util.gpg.GPG.gpg()` was found. If we need to ensure version is `^2.X` it's probably better to do it in `spack.util.gpg.GPG.gpg()` than in a separate function.

Update the patch to fix builds with NVCC <= 10.2.89 with
the accepted PR for upcoming releases of the library.

Despite trying very hard to keep dicts out of our hash algorithm, we seem
to still accidentally add them in ways that the tests can't catch. This
can cause errors when hashes are not computed deterministically.

This fixes an error we saw with Python 3.5, where dictionary iteration
order is random.  In this instance, we saw a bug when reading Spack
environment lockfiles -- The load would fail like this:

```
...
File "/sw/spack/lib/spack/spack/environment.py", line 1249, in concretized_specs
  yield (s, self.specs_by_hash[h])
KeyError: 'qcttqplkwgxzjlycbs4rfxxladnt423p'
```

This was because the hashes differed depending on whether we wrote `path`
or `module` first when recomputing the build hash as part of reading a
Spack lockfile.  We can fix it by ensuring a determistic iteration order.

- [x] Fix two places (one that caused an issue, and one that did
  not... yet) where our to_node_dict-like methods were using regular python
  dicts.

- [x] Also add a check that statically analyzes our to_node_dict
  functions and flags any that use Python dicts.

The test found the two errors fixed here, specifically:

```
E       AssertionError: assert [] == ['Use syaml_dict instead of ...pack/spack/spec.py:1495:28']
E         Right contains more items, first extra item: 'Use syaml_dict instead of dict at /Users/gamblin2/src/spack/lib/spack/spack/spec.py:1495:28'
E         Full diff:
E         - []
E         + ['Use syaml_dict instead of dict at '
E         +  '/Users/gamblin2/src/spack/lib/spack/spack/spec.py:1495:28']
```

and

```
E       AssertionError: assert [] == ['Use syaml_dict instead of ...ack/architecture.py:359:15']
E         Right contains more items, first extra item: 'Use syaml_dict instead of dict at /Users/gamblin2/src/spack/lib/spack/spack/architecture.py:359:15'
E         Full diff:
E         - []
E         + ['Use syaml_dict instead of dict at '
E         +  '/Users/gamblin2/src/spack/lib/spack/spack/architecture.py:359:15']
```

Rework Spack's continuous integration workflow to be environment-based.

- Add the `spack ci` command, which replaces the many scripts in `bin/`

- `spack ci` decouples the CI workflow from the spack instance:
  - CI is defined in a spack environment
  - environment is in its own (single) git repository, separate from Spack
  - spack instance used to run the pipeline is up to the user
  - A new `gitlab-ci` section in environments allows users to configure how
    specs in the environment should be mapped to runners
  - Compilers can be bootstrapped in the new pipeline workflow

- Add extensive documentation on pipelines (see `pipelines.rst` for further details)
- Add extensive tests for pipeline code

* Update and fix samtools

This PR adds samtools-1.10 and sets the htlib directory so that the
spack built htslib can be used. This PR also arranges the dependencies
so that the htslib sequence is grouped on its own. Finally, the bzip2
dependency is removed and python and perl run dependencies are added.

* Fix samtools when built with ncurses+termlib

* The CI flake8 tests require lowercase variable

Interestingly, this did not show up when I ran `spack flake8` locally.

* Reorder GNU mirrors (#14395)

As @adamjstewart commented in #14395, GNU suggests to use
their mirror. So reorder the mirror to the top.

GNU Doc: https://www.gnu.org/prep/ftp.en.html

* Use spack.util.url.join for URLs in GNU mirrors (#14395)

One should not use os.path.join for URLs. This does only
work on POSIX systems.

Instead use spack.util.url.join.
So every part in spack uses the same url joining method.

Add patch locally to make sure checksum cannot change again.

This PR adds the CudaPackage mixin class to py-theano. This replaces the
`gpu` variant with the `cuda` variant.

* Add new kcov package

* Fix linking error and add test

Signed-off-by: Sean Smith <seaam@amazon.com>

* capnproto: New package.

* capnproto: Fix flake8 errors.

* Remove characters invalid in Python 2.

Unfortunately UCX 1.7.0 is appearing in RPMS before it's officially released.
There's a problem with Open MPI 4.0.x where x < 3 and this version of UCX,
namely that the UCT BTL fails to compile.

See https://github.com/open-mpi/ompi/issues/7128



This patch works around the problem by disabling the build of the UCT BTL
for releases 4.0.0 to 4.0.2.

add hppritcha (me) as maintainer

Signed-off-by: Howard Pritchard <howardp@lanl.gov>

* Added py-spdlog package

* pleasing flake-8

* pleasing flake-8

* addressed some comments from adamjstewart

* changed URL for archive

* replaced with pypi.io url

* Add +cfitsio variant to wcslib dependency

* Replace ncurses dependency with readline dependency

casacore explicitly may depend on readline, not ncurses

* Add workaround for casacore's readline dependency

casacore optionally depends upon readline, but it's CMakeLists.txt provides no
user control over whether or not readline becomes a dependency. As readline is
often present by default on systems, it's better for this package to explicitly
depend on readline in order to prevent linking to whatever system version of the
library happens to be found during the build process. This should be considered
a workaround until casacore's CMakeLists.txt is fixed.

* Apply workaround for casacore's dependency on SOFA

Similar to the issues with casacore's readline dependency, casacore's optional
dependency on SOFA does not provide the user with a means of controlling the
dependency during build time. Unlike the readline library, the SOFA library is
unlikely to exist on most systems by default. As the SOFA dependency is only
optionally used for testing casacore, requiring it by default is not a good
workaround. Until casacore's CMakeLists.txt is fixed, this variant has been
removed to avoid unexpected library dependencies in the installed package.

* Add newer casacore versions

* Add mpokorny to maintainer field

Co-authored-by: mlhardware <57849932+mlhardware@users.noreply.github.com>

- The suite-sparse author publishes new versions starting with 5.5.0 on GitHub, see https://github.com/DrTimothyAldenDavis/SuiteSparse/releases and http://faculty.cse.tamu.edu/davis/SuiteSparse/
  - change spack to download from there
  - updated sha256 checksums from GitHub for all available releases
- For versions 5.4.0, 5.5.0, 5.6.0 there is a slightly different compilation necessary: first `make default` then `make install`.

Summary of the version changes (+ added, -removed [because not available on GitHub]):
```
+ 5.6.0
+ 5.5.0
+ 5.4.0
  5.3.0
  5.2.0
+ 5.1.2
  5.1.0
+ 5.0.0
+ 4.5.6
  4.5.5
- 4.5.4
  4.5.3
- 4.5.1
```

* Added new hashes for the protobuf and py-protobuf packates.

* Fixed flake8

* Fix use of sys.executable for module/env commands

* Fix unit tests

* More consistent quotation, less duplication

* Fix import syntax

This updates the UnifyFS package to account for the latest 0.9.0
version and removes support for version 0.2.0.

to disabled use of libunwind.  Without this mesa fails to build
using recent Cray compilers - cce 9 and higher -  on aarch64 systems.

Signed-off-by: Howard Pritchard <hppritcha@gmail.com>

* add new package : geode

* remove provides for gemfire

This PR adds CudaPackage in order to pick up the cuda/compiler conflicts
defined in CudaPackage.