Also update dependencies to build latest py-deeptools versions and
add a patch to run tests:
* Replace pypi URL with github URL to download tests
* Update dependency versions of py-pysam, py-matplotlib
* Add new py-deeptoolsintervals package as a dependency
* Add py-plotly and py-nose dependencies
* Patch setup.py to collect and run tests
UnifyCR has been renamed to UnifyFS. Renaming the Spack package is
the last step in this process.
This renames the package and changes any UnifyCRs to UnifyFS within
the package.
* Overhaul PyTorch package
* Flake8
* Distributed requires MPI, NCCL not specified correctly
* Binary was being specified incorrectly
* Run tests at install time
* Disable GLOO in addition to GLOO_IBVERBS
* Add option to disable QTDesigner plugin for qwt
Qt designer shouldn't be necessary to build downstream GUI code.
Currently `qwt^qt~tools` fails to build:
(darwin clang@10.0.1)
```
compiling qwt_designer_plugin.cpp
compiling qwt_designer_plotdialog.cpp
moc qwt_designer_plugin.h
moc qwt_designer_plotdialog.h
rcc qwt_designer_plugin.qrc
qwt_designer_plugin.h:23: Error: Undefined interface
make[1]: *** [moc/moc_qwt_designer_plugin.cpp] Error 1
make[1]: *** Waiting for unfinished jobs....
qwt_designer_plugin.cpp:17:10: fatal error: 'QDesignerFormEditorInterface' file not found
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1 error generated.
make[1]: *** [obj/qwt_designer_plugin.o] Error 1
make: *** [sub-designer-make_default-ordered] Error 2
```
* Update VTK for newer VisIt and compiler versions
Several changes/enhancements to VTK package
---
Add version 8.1.0 (default version for VisIt 3.x)
---
Tweak VTK options for version 8 and VisIt:
- only add mpi4py version option when mpi4py is enabled
- Require object factory for downstream packages
- Remove OpenGL preference for VTK 8
---
Combine +python3 into +python
The spec for using python3 should just be `+python^python@3:`.
---
Remove unused VTK cmake argument on newer version
---
Patch for Python 3 fails on VTK 6.1 (needed for VisIt 2.x):
```
==> Patch /rnsdhpc/code/spack/var/spack/repos/builtin/packages/vtk/python3.7-const-char.patch failed.
==> Error: ProcessError: Command exited with status 1:
'/usr/bin/patch' '-s' '-p' '1' '-i' '/rnsdhpc/code/spack/var/spack/repos/builtin/packages/vtk/python3.7-const-char.patch' '-d' '.'
```
and as it happens, VisIt 2.13 is incompatible with Python 3 anyway.
---
Fix compiler error:
As spack's configuration warning says, double-quotes can cause trouble:
```
==> [2019-07-29-11:47:55.269653] Warning: Quotes in command arguments can confuse scripts like configure.
The following arguments may cause problems when executed:
-DVTK_REQUIRED_OBJCXX_FLAGS=""
Quotes aren't needed because spack doesn't use a shell.
Consider removing them
```
They were being added to the compile line, causing clang to think it was
asked to compile an empty file:
```
cd /private/var/folders/fy/x2xtwh1n7fn0_0q2kk29xkv9vvmbqb/T/s3j/spack-stage/spack-stage-3nk9bwe_/spack-build/Rendering/OpenGL && /rnsdhpc/code/spack/lib/spack/env/clang/clang++ -DVTK_IN_VTK -DvtkRenderingOpenGL_EXPORTS -F/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks -DGLX_GLXEXT_LEGACY -O2 -g -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -fPIC -fvisibility=hidden -fvisibility-inlines-hidden "" -o CMakeFiles/vtkRenderingOpenGL.dir/vtkCocoaGLView.mm.o -c /rnsdhpc/code/spack/var/spack/stage/vtk-6.1.0-b2mj276iz77fadisv2me365qe27t3gxt/spack-src/Rendering/OpenGL/vtkCocoaGLView.mm
clang: error: no input files
make[2]: *** [Rendering/OpenGL/CMakeFiles/vtkRenderingOpenGL.dir/vtkCocoaGLView.mm.o] Error 1
```
* Modernize/PEP-8 visit package statements
* Add new VisIt version and patches for building on Mac
- VisIt's cmake assumes a 'vtk(tiff|jpeg|png)' *library* target exported by
VTK, but VTK 8.1.x on my configuration seems to have these as header-only
targets with library dependencies.
- Explicitly add QT path to visit configure: Without this, somehow
`${VISIT_QT_DIR}` was being set to empty, so that the build failed with
`missing /bin/moc`.
- VisIt assumes that if it isn't being built statically, QWT has been built as
a mac Framework. QWT actually is built as a framework based on whether QT
itself is.
Error message:
```
-- Looking for QWT
CMake Error at CMake/SetUpThirdParty.cmake:131 (MESSAGE):
Include Directory for QWT (/rnsdhpc/code/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/qwt-6.1.3-bmfxirweplzhjoiil4rw632evkyteuwk/lib/qwt.framework/Versions/Current/Headers) does not exist.
Call Stack (most recent call first):
CMake/FindQwt.cmake:57 (SET_UP_THIRD_PARTY)
CMakeLists.txt:1251 (INCLUDE)
```
* ADIOS 2.4.0: Add new Deps
Version 2.4.0 of ADIOS2 added new dependencies that are not
yet listed as `depends_on` and/or disabled otherwise. Add them
now to avoid picking them up from system paths, e.g. `libpng`.
* ADIOS2: Variant Defaults Change
* Python: False by default
* ADIOS1: only used prior to 2.3.0
* UnifyCR: update dependencies and build options
This adds some specifics about dependencies and conflicts and adds
additional build options and variants. UnifyCR now also has limited
fortran support.
* Remove debug statements condition on Spack debug
Change debug print statements to now be turned on when the -g cflag
is found in the flags the user sets.
* add new package: py-python-magic
* tidy up
* Update var/spack/repos/builtin/packages/py-python-magic/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* add master and dependencies
* remove gcc and make
* add variants, make doc and ch-grow dependencies optional
* capitalize description sentence
* move dependencies and variants below version block
* fix typos
* gromacs: fix simd detection for pre 2018 versions
* pre 2018 the cmake file was named differently
* fixed up post 2018 patch file which was non pretty
* Trim patch
* Create package.py
* applied reviewer suggestions
* Update package.py
* remove CamelCase from variant names
* add comment on why fetching package via git
* found typo in variant to cmake-argumentlist translation
* rename variants to ~nonuma ~nompi to be in sync with cmake-args, refine mpi@3-dependency definition
* Revert "rename variants to ~nonuma ~nompi to be in sync with cmake-args, refine mpi@3-dependency definition"
This reverts commit 58e8cf7d93c5665f0b4b50228946857734716cef.
* remove version-preference
* add checksum for singularity release 3.3.0
* update singularity doc URL
URL at the lbl.gov domain has message saying:
"This website is going away soon! Update your bookmarks!"
* add note about build log file for post-install step
* provide links to both 2.x and 3.x security docs
* remove whitespace. Passing flake8 confirmed locally this time :)
* add TODO comment for fakeroot support
The previous version does not properly install the required cmake
configuration files for blaze-lib, so find_package does not work
correctly.
This patch converts the blaze-lib package to use CMakePackage,
adds the required cmake dependency, and removes the install()
member function, which is not working correctly and is no longer
needed.
In a review of a previous pull request (
https://github.com/spack/spack/pull/10713 ) it was mentioned that the
proper way to figure out the target architecture is via
spec.architecture.target. This patch fixes this for the openblas
package.
Signed-off-by: Janne Blomqvist <janne.blomqvist@aalto.fi>
Not sure what happened between #5321 and now but the CC=CXX fix now
prevents py-matplotlib from building with the Intel compiler. I verified
with versions of py-matplotlib from 2.0.2 to 3.0.2 and intel-17.0.4 and
19.0.4 that py-matplotlib successfully builds with the Intel compiler
without that code.
* Add preCICE xSDK support
* Cleanup generation of cmake arguments
* Generalize numpy include
* Fix python spec
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Fix numpy spec
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* hunspell: write autoreconf method to triage error
This commit fixes the error described in GitHub issue
`AutotoolsPackage` class attempts to call `libtoolize`, which doesn't
exist on macOS systems that externally install `libtool` in Spack via
Homebrew -- Homebrew installzes GNU libtoolize as `glibtoolize`.
The fix is to call `autoreconf` only, and GitHub pull request #12344
makes this change in
AutotoolsPackage (https://github.com/spack/spack/pull/12344). However,
while waiting for that pull request to be merged, overriding the
`autoreconf` method achieves the same result for a self-contained
fix. This self-contained fix is necessary to fix a dependency bug in
the `hunspell` package.
* hunspell: add missing gettext dependency
* hunspell: add version 1.7.0
* add new package cromwell
* fix flake8 errors, add cromwell-womtool package
* change name of cromwell to cromwell-server
* renamed cromwell-server to just cromwell
* update description to what is in the project docs
* fixing format call for python2.6 compatibility
* Add comment that 1.0.1 versions are no longer supported
* Add comment that 1.0.2 versions are only supported up to
December 2019
* Add versions 1.0.2s, 1.0.2r, and 1.0.2p
* Add versions 1.1.0k, 1.1.0j, and 1.1.0i
* Add version 1.1.1c
* Add comment that 1.1.0 versions are only supported up to
September 2019
Resolves#11932.
Move the PIC flags from CFLAGS on the configure line to the spack
compiler wrapper for ncurses. The problem with the configure line for
autotools is that specifying CFLAGS sets the entire flags, thus
deleting the flags that configure would add itself.
By default, if CFLAGS is unspecified, then configure picks a sensible
default of `-g -O2`. But adding `-fPIC` erases these and it ends up
building unoptimized.
* Add patch to detect newer versions of MacOS and to fix a typo in
configure.ac (AM_LIBTOOLSFLAGS should be AM_LIBTOOLFLAGS)
* Remove variant declarations for unsupported languages
* Add support for quartz on MacOS
* Add optional X Window support
* Specifically build against qt@4 when building QT support
* Point to appropriate C++ standard libraries when building with
Clang on MacOS
* Disable parallel build (for all platforms)
* Increase verbosity of configure script by adding
--disable-silent-rules
* Add numpy 1.17.0
* Overhaul numpy package
* Flake8 fixes
* Undefined reference fix
* HeaderList and LibraryList need an arg
* veclibfort has no headers
* Add patch for older versions of py-numpy
* Remove py-meep hack from py-numpy package
* libflame: always add max arg hack flag
* Fix build with GCC 4.8
* Compiler flags come from self.compiler
* Only apply -std=c99 to cflags
* Try to fix libflame package
* Fix ATLAS build on macOS
* --force-clang flag added in 3.10.3
When building with GCC, c-blosc requires the -std=gnu99 flag.
Before this patch, the build would only add -std=gnu99 for GCC when
building on specific architectures; this adds -std=gnu99 in all cases
when using GCC.
When loading `openpmd-api` as a lib to build outside of
spack or to build depending spack packages, the "CMake-PUBLIC"
header-only library MPark.Variant must be available. Also,
the `*Config.cmake` package must be able to find dependent
libs if used.
* new package: py-backports-tempfile
* Update var/spack/repos/builtin/packages/py-backports-tempfile/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* remove rc version
* fix single quote
* add new version, add sha256 sums
* Update var/spack/repos/builtin/packages/py-apipkg/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* add python dependencies
* new package: py-usgs
* Update var/spack/repos/builtin/packages/py-usgs/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-usgs/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* new package: py-requests-futures
* Update var/spack/repos/builtin/packages/py-requests-futures/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
