* r-roxygen : dependencies and version updated

* Dependencies updated for condition

* r-rematch2 : new package

* Updating URL

* new version r-ellipsis

* r-ellipsis : R dependency updated

* Adding version conditions for dependencies

* new version r-cli

* r-cli : dependencies updated

* Adding version conditions for dependencies

* new version r-rcurl

* RCurl dependency R version updated

* Adding version conditions

* change print order for variants to avoid zsh parsing bugs

* change tests for new variant parse order

* revbayes: update for 1.1.0

* revbayes: Fix flake8

Modifications:

- [x] Travis now uses `bionic` as a default (`xenial` used for Python 3.5, `trusty` for Python 2.6)
- [x] Shell unit tests have been factored into their own run
- [x] `kcov` is built only for tests that upload coverage results

Overall with this we shave 3-4 mins. on each run and add an additional run of about 3 min. For some reason `kcov` 38 fails forwarding output when used with Python unit tests, so I used v34 for that and v38 (latest) for shell testing. Previously we were using v25.

* r-testthat : dependencies and version updated

* Adding version conditions for dependencies

* r-testthat: Fix dependecies condition

* py-plotly: unfix dependency versions (fixes #16544)

* py-plotly: add missing dependencies for #16546

* py-plotly: match setup.py instead of requirements.txt for #16546

This improves the documentation for `spack external find` in several ways:

* Provide a code example of implementing `determine_spec_details` for a package
* Explain how to define executables to look for (and also e.g. that they are treated as regular expressions and so can pull in unexpected files).
* Add the "why" for a couple of constraints (i.e. explain that this logic only works for build/run deps because it examines `PATH` for executables)
* Spread the docs between build customization and packaging sections
* Add cross-references
* Add a label so that `spack external find` is linked from the command reference.

* r-xml2: new version & updated dependencies

* r-xml2: updated dependencies

Co-authored-by: Lori Pritchett-Sheats <[email protected]>

* Clarify comments about QMCPACK-to-QE converter.

* Allow hdf5=serial with QE 6.4.1 + qmcpack, but apply filter_file.

* Ammend comments about the use of the filter_file.

Add version 1.2.2.
Add conditional python dependency.
Add patch for 1.1.4.1 and python.

* Unify tests for compiler command in the same file

Tests for the "spack compiler" command were previously
scattered among different files.

* Tests should use mutable_config, since they modify the compiler list

* Adding a module for sbml.

* Adding support for all the languages.

* Update var/spack/repos/builtin/packages/sbml/package.py

Co-authored-by: Greg Becker <[email protected]>

* Update var/spack/repos/builtin/packages/sbml/package.py

Co-authored-by: Greg Becker <[email protected]>

Co-authored-by: Robert Blake <[email protected]>
Co-authored-by: Greg Becker <[email protected]>

Fix message 'amber requires cuda version :10.1.243, but spec asked for 10.2.89'

fixes #12527

Mention that specs  can be uninstalled by hash also in
the help message. Reference `spack gc` in case people
are looking for ways to clean the store from build time
dependencies.

Use "spec" instead of "package" to avoid ambiguity in
the error message.

* Implicit rpaths for NAG.

* set up environment when checking for implicit rpaths

* add subcommand `spack view copy/relocate`

* update bash completions

* add copy/relocate commands to view tests

* allow copied views to be removed

…ster (#16935)

* add an --exclude-file option to 'spack mirror create' which allows a user to specify a file of specs to exclude when creating a mirror. this is anticipated to be useful especially when using the '--all' option

* allow specifying number of versions when mirroring all packages

* when mirroring all specs within an environment, include dependencies of root specs

* add '--exclude-specs' option to allow user to specify that specs should be excluded on the command line

* add test for excluding specs

* update darshan-runtime & darshan-util versions

includes up through the current release, 3.2.1

* remove pre-releases, not needed in spack

* gnuplot: Fix for #16928

Dependency for --with-wx flag mistyped (should be wxwidgets)

* Revert "gnuplot: Fix for #16928"

This reverts commit 2b85814.

* gnuplot: Fix for #16928

Dependency spec for --with-wx flag mistyped (should be wxwidgets, not
wx)

* Fix parsing of EvtGen URL

* Flake8 fix

* IPython: fix setuptools dependency

* Remove extra colon

Dropping atomicwrites dependency: pytest-dev/pytest#6147

+ Update maintainers for OPPPY package
+ remove "run" requirement for setuptools and sphynx

Co-authored-by: Cleveland <[email protected]>

Stratimikos is an optional dependency for our project. It depends on
Thyra, and thyra has subpackages that should be enabled based on
tpetra/epetra/epetraext.