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Merge develop#15

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koning merged 26 commits intokoning:developfrom
spack:develop
Nov 27, 2019
Merged

Merge develop#15
koning merged 26 commits intokoning:developfrom
spack:develop

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@koning koning commented Nov 27, 2019

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G-Ragghianti and others added 26 commits November 25, 2019 15:42
…13885)

* Improved library access for lm-sensors and implemented use in papi.

* Fixed comment formatting

* Removed explicit "None" from return of libs().

* Added two new software release versions.
* Add the py-coloredlogs package

* Remove extraneous line.

* Remove dashed line.

* Add version for humanfriendly dep and build to type.

* Change source url to use pypi.
* Added new package libmmtf-cpp required by py-pymol

* Added SPDX-License-Identifier to MIT

*  Updated py-pymol to version 2.3.0

* py-pymol: Added mising py-pmw dependency

* py-pymol: flake8 minor change

* py-pymol: Added patch for apbstools_tcltk8.6

This patch is borrowed from archlinux
https://bugs.archlinux.org/task/39526

* libmmtf-cpp: flake8 compliance

* libmmtf-cpp: flake8 compliance

* libmmtf-cpp: change license to  (Apache-2.0 OR MIT) when refering to the MIT license

* libmmtf-cpp: Added header text about license as in examples

* py-pymol: removed unnecesary dependency mesa-glu

* py-pymol: removed unnecesary patch

* py-pymol: Removed empty line at the end of the file to comply with flake8.
* Add SOLLVE package with Shintaro's help on rebasing.

Co-authored-by: Vivek Kale <[email protected]>

* sollve: reflect suggestions by @adamjstewart

* sollve: update target detection

Copied from llvm/package.py.

* sollve: fix a few things

- url -> git
- remove git in version()
- explicit cmake options in else clauses
- add newlines for better readability
* add variant for enabling testing

* enable tests and clean up other options

* add numbered versions

* updates to avoid enable_tests variant; correct versioning

* fixes for style

* appropriate partitioners are enabled if 'all' is specified - so no need to check in spec

* define url so spack knows how to fetch the tar.gz files for different versions
* Package Index: Build in Dockerhub

Prepare to build the package index service, packages.spack.io,
on Dockerhub.

Local build (in spack root dir):
```
docker build -t spack/packages.spack.io:latest -f share/spack/docker/package-index/Dockerfile .
```

Local test:
```
docker run -p 8080:80 spack/packages.spack.io:latest
```

* Travis-CI: Remove Docker

Remove leftover docker stages from Travis-CI.

* Simplify Split Call
Extensions have been available for a while and the overall design
seems solid enough to be feasible for extensions without losing
backward compatibility.
* lsof: fix url and checksum

* lsof: change the download url, add list url and version 4.91, 4.90
* add new package : blktrace

* modify install_tree('', prefix) to install_tree('.', prefix)
* add new package : [email protected]

* 1. add some other version for busybox
2. change Busybox class to MakefilePackage
3. move make('defconfig') and make() to build() function
4. change install_tree('', prefix) to install_tree('.', prefix)
* Add licensing; replace url with url_for_version; create .spack dir during installation; symlink wolframscript; generate spec.yaml if missing

* Reverted url change, .spack directory creation, and spec.yaml generation

* Fix formatting issues
* new package: py-arrow

* actually use dependencies from 0.14.7 not from current HEAD

* drop dependencies that dont appear in the source

* readd sphinx as doc dependency

* update dependencies

* drop doc-only dependencies
* update py-nbconvert

* add setuptools dependency, like all the other jupyter packages
  it seems to be using setuptools for some commands all the time
  but requires it for the newest version
* added dependencies, not necessarily only needed for the latest one
* depends on new packages (defusedxml, pandocfilters, testpath)
* should also be moved to pypi sources?
* '@5:@5:' is a valid spec -> intended?

* make dependencies optional

* Update dependencies and add description

* relax py-mistune dependency restriction

* Update var/spack/repos/builtin/packages/py-nbconvert/package.py

Co-Authored-By: Adam J. Stewart <[email protected]>
Fix an issue with NVCC when building with C++14.
* metabat: add versions 2.14 and 2.13

* update build environment

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

Co-Authored-By: Adam J. Stewart <[email protected]>

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

Co-Authored-By: Adam J. Stewart <[email protected]>
@koning koning merged commit f2ee7ce into koning:develop Nov 27, 2019
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