Easybuild

EasyBuild v4.4.1 is primarily a bugfix and update release, but also includes several minor enhancements.

Highlights for this release are listed below. More details are available in the [release notes](https://docs.easybuild.io/en/latest/Release_notes.html#easybuild-v4-4-1-july-6th-2021) which includes links to the respective pull requests for more detailed information.


Highlighted enhancements

(enhancements that (may) warrant updating existing installations are marked with `(***)`)

- add per-step timing information in standard output of `eb` command;

- add new hook that triggers right before writing generated module file (`module_write_hook`);

- add `ignore-test-failure` configuration option to ignore failing test step;

- enhance `ConfigureMake` generic easyblock to add support for building multiple build targets;

- 5 new custom easyblocks, for AOMP, FreeFEM, NCCL (built from source), torchvision, and UCX plugins;

- update custom easyblock for Boost to always build single and multi threaded versions;

- `(***)` enhance `sitecustomize.py` in Python easyblock to support overriding core Python packages, and allowing overriding in virtualenv;

- `(***)` updates & enhancements for various custom easyblocks, incl. Amber, Clang, FFTW, Hypre, intel-compiler, Java, OpenSSL wrapper, Perl, Python, XALT, Xmipp;

- `(***)` additional extensions for recent R easyconfigs;


Prominent bug fixes & changes

(bug fixes or changes that (may) warrant reinstalling easyconfigs are marked with `(***)`)

- add comment with test report in right location when combining `--from-pr` and `--include-easyblocks-from-pr`;

- fix crash when copying modules that were imported in easyconfig file (like `import os`);

- `(***)` fix location for modules installed with intel-compilers toolchain in `HierarchicalMNS`;

- don’t make changes to software installation directory when using `--sanity-check-only`;

- honour specified easyblock for extensions;

- change `Bundle` easyblock to also collect altroot and altversion in the module step so they are set when running `--module-only`;

- `(***)` bug fixes for various custom easyblocks, incl. GCC, intel-compilers, NVHPC, TensorFlow, VEP;

- `(***)` set minimal OpenSSL version to 1.1.1 for OpenSSL v1.1 wrapper;

- `(***)` add patch for GCC 10.2.0 to fix internal compiler error on aarch64;

- `(***)` add missing rgdal dependency to R-INLA;

- `(***)` add patch to fix uniq operation in TensorFlow 2.4.1;

- `(***)` add patch for recent GCCcore versions to fix compatibility with CUDA 11;

- `(***)` avoid using PMIx from system instead of PMIx dependency specified via `--with-pmix` for OpenMPI 4.x;

- `(***)` add patch for GCCcore 10.3.0 to prevent issues when compiling with nvcc;


Other changes

- deprecate EasyBuild bootstrap script;

- rework the dependency handling of OpenMPI to use explicit configure options to disable features if required dependency is not provided;

- side effect of this is that you need to add `--with-ucx` yourself if you want to build OpenMPI on top of a system provided UCX!

- `(***)` switch to NCCL 2.8.3 built from source for CuPy, Horovod, libgpuarray, PyTorch and TensorFlow using fosscuda/2020b;

- cleanup of easyconfigs for (bundles) of Python packages: remove default `PYPI_SOURCE` source URLs + use `PythonBundle` rather than `Bundle` easyblock;


Supported software


Support for installing 39 new software packages has been added, including (but not limited to):

- AOMP
- dSFMT
- FreeFEM
- futhark
- GenomeWorks
- hipify-clang
- microctools
- Nektar++
- OpenMM-PLUMED
- phototonic
- PyFoam
- RECON
- UCX-CUDA
- Vala

This brings the total number of supported software packages to 2,388!
An up-to-date list of supported software is available [here](https://docs.easybuild.io/en/latest/version-specific/Supported_software.html).


Various software updates have been added, including (but not limited to):
- Amber 20.11
- Bonito 0.4.0
- DOLFIN 2019.1.0.post0
- ELPA 2021.05.001
- FDS 6.7.6
- GCC 8.4.0 + 9.4.0
- GDAL 3.3.0
- Go 1.16.5
- GSL 2.7
- h5py 3.2.1
- Horovod 0.22.0
- Hypre 2.21.0
- IPython 7.25.0
- LDC 1.26.0
- libxc 5.1.5
- medaka 1.4.3
- MUMPS 5.4.0
- NCCL 2.9.9
- netCDF 4.8.0
- Nim 1.4.8
- nodejs 14.17.0
- numba 0.53.1
- NVHPC 21.5
- Octave 6.2.0
- petsc4py 3.12.0
- PySCF 1.7.6
- PyTorch 1.9.0
- R 4.0.5 + R 4.1.0
- ReFrame 3.6.2
- Ruby 3.0.1
- Score-P 7.0
- Subread 2.0.2
- SuiteSparse 5.10.1
- sympy 1.8
- TensorFlow 2.5.0
- VMD 1.9.4a51
- Z3 4.8.11


These changes result from various contributions, made by 23 different contributors:

* 27 merged pull requests for EasyBuild framework
* 41 merged pull requests for easyblocks
* 268 merged pull requests for easyconfigs


Thanks to everyone who contributed to this release in one way or another!


To upgrade to EasyBuild v4.4.1, there are [several options](https://docs.easybuild.io/en/latest/Installation.html#updating-an-existing-easybuild-installation).
Two particularly easy options include:

* `eb --install-latest-eb-release`

* `eb --from-pr 13344` use easyconfig from [PR 13344](https://github.com/easybuilders/easybuild-easyconfigs/pull/13344)

**EasyBuild v4.4.0** is primarily a feature release, but also includes several bug fixes & minor enhancements.

Highlights for this release are listed below. More details are available in the [release notes](https://docs.easybuild.io/en/latest/Release_notes.html#easybuild-v4-4-0-june-2nd-2021) which includes links to the respective pull requests for more detailed information.

Highlighted enhancements

[enhancements that (may) warrant updating existing installations are marked with `(***)`]

- performance improvements for easyconfig parsing and `eb` startup;

- support for downloading easyconfigs from multiple PRs with `--from-pr`;

- support for re-running the sanity check for existing installations (without making modifications to the installation), via "`eb --sanity-check-only`";

- toolchain definition for Fujitsu toolchain for use on Fugaku;

- allow checking whether specific libraries are (not) linked into installed binaries/libraries in sanity check (see various ways to specify banned/required libraries);

- `update_build_option` function to update specific build options after initializing the EasyBuild configuration;

- run post-install commands specified for a specific extension;

- add support for skipping the installation of extension via "`eb --skip-extensions`";

- software-specific easyblocks for FlexiBLAS and dm-reverb;

- custom easyblock to install OpenSSL wrapper for OpenSSL installed in OS, with fallback to build and install OpenSSL from source if not available in OS;

- enable `sanity_pip_check` by default for Python easyconfigs if pip >= 9.0 will be installed;

- add IceLake detection to OpenBLAS 0.3.12 and 0.3.15;



Prominent bug fixes & changes

[bug fixes or changes that (may) warrant reinstalling easyconfigs are marked with `(***)`]

- re-enable write permissions when installing with `read-only-installdir`;

- avoid metadata greedy behavior when probing for external module metadata (mostly relevant for integration with Cray Programming Environment);

- also run sanity check for extensions when using `--module-only` (you can use `--skip-extensions` to skip sanity checking of extensions when using `--module-only`);

- fix use of `--module-only` on existing installations without write permissions;

- use `unload`/`load` in `ModuleGeneratorLua.swap_module`, since `swap` is not supported by Lmod;

- update `HierarchicalMNS` to also return ‘`Toolchain/<name>/<version>`’ as `$MODULEPATH` extension for `cpe*` Cray toolchains;

- enhance `sched_getaffinity` function to avoid early crash when counting available cores on systems with more than 1024 cores;

- `(***)` enhance Python easyblock: add option to install pip with core Python, tweak defaults, create unversioned pip symlink;

- make custom easyblocks for GROMACS ad Tkinter work with --module-only;

- make sure that self.python_cmd is set before using it in `PythonPackage.sanity_check_step` to make `PythonBundle` easyblock comaptible with `--module-only`;

- `(***)` add patch to fix GCC 10.2.0 rejecting valid code on PPC;

- `(***)` update easyconfigs for binutils 2.35 to use binutils 2.35.2 source tarball instead to pick up bug fixes;

- `(***)` fix test failure in TensorFlow 2.4.1 on recent CUDA drivers;

- `(***)` add patch to fix hardcoded num_cores in DMCfun extension included with R 4.0.x;

- `(***)` fix typo in Delly easyconfig to actually do parallel build;

- `(***)` fix potential memory leak in OpenBLAS 0.3.12;

- `(***)` add patches for PyTorch 1.7.1 avoiding failures on POWER and A100;

- fix source URLs for recent Boost and Boost.Python versions;


Other changes

- tweak foss toolchain definition to switch from OpenBLAS to FlexiBLAS in `foss/2021a`;

- don’t skip sanity check for `--module-only --rebuild` (sanity check is still skipped with `--module-only --force`);

- consistently use pip to install Python packages in recent Python easyconfigs;

- deprecate adding a non-existing path to `$MODULEPATH` via `ModulesTool.use`;

- **drop support for running EasyBuild with Python 2.6**;


Supported software


Easyconfigs for 2021a version of custom toolchains:

* `foss/2021a`:
* GCC 10.3.0 + binutils 2.36.1
* OpenMPI 4.1.1
* FlexiBLAS 3.0.4 with OpenBLAS 0.3.15 as backend
* ScaLAPACK 2.1.0
* FFTW 3.3.9

* intel/2021a:
* GCC 10.3.0 + binutils 2.36.1 as base
* intel-compilers 2021.2.0
* impi 2021.2.0
* imkl 2021.2.0


Support for installing 58 new software packages has been added, including (but not limited to):
* BirdNET
* cell2location
* cryoDRGN
* FlexiBLAS
* fsom
* gemmi
* georges
* hifiasm
* intervaltree
* LDC
* librosa
* loompy
* mongolite
* NewHybrids
* pagmo
* pyfaidx
* pyfasta
* pygmo
* R-INLA
* rMATS-turbo
* SeqLib
* smithwaterman
* SSW
* TagDust
* TALON
* TranscriptClean
* xESMF

This brings the total number of supported software packages to 2,349!
An up-to-date list of supported software is available [here](https://docs.easybuild.io/en/latest/version-specific/Supported_software.html).

Various software updates have been added, including (but not limited to):
* ABINIT 9.4.1
* BLIS 0.8.1
* Bonito 0.3.8
* ccache 4.2.1
* CLHEP 2.4.4.0
* CMake 3.20.1
* CUDA(core) 11.3.0
* CuPy 8.5.0
* Eigen 3.3.9
* FFTW 3.3.9
* GATK 4.2.0.0
* GCC 10.3.0 + 11.1.0
* GDRCopy 2.2
* GLPK 5.0
* GROMACS 2021.2
* GTDB-Tk 1.5.0
* HMMER 3.3.2
* Horovod 0.21.3
* intel-compilers + impi + imkl 2021.2.0
* Julia 1.6.1
* libfabric 1.12.1
* libRmath 4.0.0
* LLVM 11.1.0
* Mesa 21.1.1
* metaWRAP 1.3
* Nim 1.4.6
* NWChem 7.0.2
* OpenBLAS 0.3.15
* openCARP 6.0
* OpenMM 7.5.0
* OpenMPI 4.1.1
* Pandoc 2.13
* Perl 5.32.1
* PMIx 3.2.3
* Primer3 2.5.0
* PyTorch 1.8.1
* Python 3.9.5
* Qt5 5.15.2
* Rmath 4.0.4
* Rust 1.52.1
* SciPy-bundle 2021.05
* snakemake 6.1.0
* UCX 1.10.0
* Valgrind 3.17.0
* X11 20210518
* YAXT 0.9.0


These changes result from various contributions, made by 19 different contributors:

* 59 merged pull requests for EasyBuild framework
* 47 merged pull requests for easyblocks
* 349 merged pull requests for easyconfigs


Thanks to everyone who contributed to this release in one way or another!


To upgrade to EasyBuild v4.4.0, there are [several options](https://docs.easybuild.io/en/latest/Installation.html#updating-an-existing-easybuild-installation).
Two particularly easy options include:

* `eb --install-latest-eb-release`
* `eb --from-pr 13012` use easyconfig from [PR 13012](https://github.com/easybuilders/easybuild-easyconfigs/pull/13012/files)

**EasyBuild v4.3.4** is primarily a bugfix/update release, but also includes several useful enhancements.

Highlights for this release are listed below, more details are available in the [release notes](https://docs.easybuild.io/en/latest/Release_notes.html#easybuild-v4-3-4-apr-9th-2021) which includes links to the respective pull requests for more detailed information.


Prominent bug fixes & changes

[bug fixes or changes that (may) warrant reinstalling easyconfigs are marked with `(***)`]

- sort output of `eb --search` in natural order (respecting numbers);

- enhance `eb` command to ensure that `easybuild.main` can be imported before settling on python* command to use;

- deprecate `--accept-eula` configuration option, renamed to `--accept-eula-for`;

- fix problem with downloading large files when running EasyBuild with a recent Python 3 version, by passing file-like object to `write_file` in `download_file` so that the data is read is chunks;

- `(***)` set $R_LIBS_SITE rather than $R_LIBS when installing R packages;

- make WRF and WPS easyblocks aware of (pre)configopts;

- remove PYPI_SOURCE source URL from easyconfigs using PythonPackage or PythonBundle;

- `(***)` enhance BWA and g2clib easyblocks to pass down compiler flags;


- `(***)` avoid 0.0.0 install version for various Python apps, including carputils, deepdiff, EMU, maze, Open-Cube-Core, pytest, Spyder, suave;

- `(***)` bump JasPer version to latest 2.0.24 for 2020b generation of easyconfigs + remove easyconfigs for ancient JasPer 2.0.1.4 with GCCcore/10.2.0;

- `(***)` update $R_LIBS_SITE rather than $R_LIBS in easyconfigs installing R packages;

- `(***)` bump pip to 20.3.4 in Python 2.7.18 easyconfig to fix unicode error;

- `(***)` fix numpy tests for recent SciPy-bundle easyconfig on POWER;

- `(***)` add patch for recent netCDF easyconfigs to fix MPI_Info_f2c issue with OpenMPI;

- `(***)` revert to Seaborn 0.10.1 as dependency for NanoPlot 1.33.0;

- `(***)` use -D_USE_METIS_5p1 in OpenSees v3.2.0 patch to correctly build on top of METIS v5.1.0;

- `(***)` rename opencv_contrib and update to OpenCV v3.4.1 with contrib versionsuffix;


Highlighted enhancements

[enhancements that (may) warrant updating existing installations are marked with `(***)`]

- avoid running expensive module use and module unuse commands when using Lmod as modules tool, update `$MODULEPATH` directly instead;

- also accept regular expression value for `--accept-eula-for`;

- update `validate_github_token` function to accept GitHub token in new format;

- enhance cuDNN and CUDA easyblocks to support aarch64;

- use `PYPI_SOURCE` as the default for `source_urls` of `PythonPackage`;

- enhance `PythonPackage` easyblock to catch faulty version (0.0.0) for installed Python packages;

- updated easyblocks for AOCC, CP2K, GROMACS, LAPACK, OpenCV, PETSc, PyTorch, VMD, VTune;

- `(***)` add libwebp and OpenEXR dependencies for OpenCV 4.2.0 easyconfig with foss/2020a;

- `(***)` add extensions to R-bundle-Bioconductor 3.12: motifmatchr (12390), OUTRIDER + FRASER;

- `(***)` add DMCfun + linkcomm + rnetcarto extensions to R v4.0.3;

Use "[`eb --rebuild --skip`](https://docs.easybuild.io/en/latest/Partial_installations.html#installing-additional-extensions-using-k-skip)" to install the missing extensions for R and R-bundle-Bioconductor.

Supported software

Additional easyconfig file for existing goblf toolchain: `goblf/2020b`

Support for installing 41 new software packages has been added, including:
* BEEF
* CDAT
* DL_POLY_4
* ESMPy
* GPyOpt
* LncLOOM
* LPJmL
* MetaEuk
* Myokit
* PyOD
* Ratatosk
* scikit-cuda
* Seeder
* YACS

This brings the total number of supported software packages to 2,288!
An up-to-date list of supported software is available [here](https://docs.easybuild.io/en/latest/version-specific/Supported_software.html).

Various software updates have been added, including (but not limited to):
* AOCC 3.0.0
* BUSCO 5.0.0
* CP2K 8.1
* CellRanger 6.0.0
* Clang 11.0.1
* dask 2021.2.0
* Extrae 3.8.0
* GROMACS 2021
* Hypre 2.20.0
* Kent_tools 411
* LAPACK 3.9.1
* libxc 5.1.3
* MUMPS 5.3.5
* NVHPC 21.2
* OpenCV 4.5.1
* PETSc 3.14.4
* PLUMED 2.7.0
* PyCUDA 2020.1
* PyOpenCL 2021.1.2
* PyTorch-Geometric 1.6.3
* pocl 1.6
* preCICE 2.2.0
* pymatgen 2022.0.4
* R 4.0.4
* RDFlib 5.0.0
* ReFrame 3.5.1
* Ruby 2.7.2
* SIMPLE 3.0.0
* SUNDIALS 5.7.0
* Seurat 4.0.1
* Spark 3.1.1
* tensorboardX 2.1
* VTK 9.0.1

These changes result from various contributions, made by 21 different contributors:

* 29 merged pull requests for EasyBuild framework
* 26 merged pull requests for easyblocks
* 220 merged pull requests for easyconfigs

Thanks to everyone who contributed to this release in one way or another!


To upgrade to EasyBuild v4.3.4, there are [several options](https://docs.easybuild.io/en/latest/Installation.html#updating-an-existing-easybuild-installation).
Two particularly easy options include:
* `eb --install-latest-eb-release`
* `eb --from-pr 12554` use easyconfig from [PR 12554](https://github.com/easybuilders/easybuild-easyconfigs/pull/12554/files)

**EasyBuild v4.3.3** is primarily a bugfix/update release, but also includes several interesting enhancements.

Highlights for this release are listed below, more details are available in the [release notes](https://docs.easybuild.io/en/latest/Release_notes.html#easybuild-v4-3-3-feb-23rd-2021), which includes links to the respective pull requests for more detailed information.

Prominent bug fixes & changes

(bug fixes that warrant reinstalling easyconfigs are marked with `(***)`)

- `(***)` filter out duplicate paths in RPATH wrapper script;
- fix UTF-8 encoding errors when running EasyBuild with Python 3.0.x-3.6.x;
- fix adding extra compiler flags via toolchainopts;
- fix OpenFOAM sanity check on POWER;
- fix Boost sanity check on POWER + aarch64;
- read MATLAB configuration file in binary mode to avoid UTF-8 encoding errors when using Python 3.6;
- fix download issues for expat, GDRCopy, Hypre in PETSc, libspatialite, MAGMA, UDUNITS;
- `(***)` use library search paths of compiler for RPATH when building binutils with system compiler;
- `(***)` fix vector mul and div with broadcasts in `-masm=intel` mode in GCCcore v9.3.0;
- `(***)` add patch to fix miscompilation bug on POWER for GCC 8.x and 9.x;
- `(***)` don’t disable optarch for Clang 11.0.0;
- `(***)` pass down compilation flags from build environment for ESMF and PDT;
- `(***)` add patch for Boost 1.74.0 to fix missing include file;
- `(***)` add missing ESMF dependency in NCO easyconfigs;
- `(***)` add patch to fix version for bam-readcount 0.8.0;
- `(***)` add missing mkl-service dependency for Theano built with `intel/2019b` + enhance sanity check;
- `(***)` fix lack of optimization for SHAPEIT4 v4.1.3;
- `(***)` add patches to fix test problems with p4est 2.2;
- `(***)` add missing gnuplot dependency for OpenFOAM from v2.4.0 to v6;
- `(***)` replace easyconfigs for bpp-core/bpp-phyl/bpp-seq v2.4.1 with a single easyconfig for BioPP v2.4.1;

Highlighted enhancements

(enhancements that (may) warrant updating existing installations are marked with `(***)`)

- support for using customized HTTP headers in when downloading files,
via `--http-header-fields-urlpat` configuration option;
- use https://sources/easybuild.io as fallback source URL;
- support for installing & using intel-compiler toolchain (versions >= 2021.x, oneAPI);
- support for running TensorFlow CPU and GPU tests;
- improved Bazel easyblock: added support for running tests, enable static linking, use build dir rather than tmpdir, verbose output;
- updated impi easyblock for impi 2021.x (oneAPI);
- updated OpenFOAM easyblock for changes in v2012;
- run motorBike tutorial case as sanity check for recent (community) OpenFOAM versions;
- `(***)` updated Clang easyblock to add support for building extra tools + leveraging hwloc and Z3 as optional dependencies;
- `(***)` enable NVPTX offload for GCCcore 9.3.0;
- `(***)` update `Java/1.8` wrapper to Java 1.8.0_281;
- `(***)` move most recent BLIS and libFLAME easyconfigs from GCC to GCCcore;
- `(***)` also build shared library in recent HDF easyconfigs + add support for HDF4 to GDAL v3.0.2 and v3.0.4;
- `(***)` enable gipaw in QuantumESPRESSO 6.6 easyconfig;
- `(***)` add tensorboard profile plugin to recent TensorFlow 2.x easyconfigs;
- `(***)` add additional extensions to Perl 5.30+, R 4.0.0, R 4.0.3, R-bundle-Bioconductor 3.11;

Use "[`eb --rebuild --skip`](https://easybuild.readthedocs.io/en/latest/Partial_installations.html#installing-additional-extensions-using-k-skip)" to install the missing extensions for R, Bioconductor, Perl, or TensorFlow.


Supported software

Easyconfig file for the new '`iibff`' toolchain: `iibff/2020b`

The `iibff` toolchain includes the following components:
- Intel compilers (on top of GCC + binutils)
- Intel MPI
- BLIS + libFLAME (BLAS/LAPACK libraries)
- ScaLAPACK
- FFTW

Additional easyconfig files for existing toolchains:
`gobff/2020b`, `goblf/2018b`, `gomkl/2020b`, `iimkl/2018a`, `iomkl/2019b`, `iomkl/2020b`


Support for installing 72 new software packages has been added, including:
- AOCC
- bgen
- CuPy
- cuTENSOR
- decona
- ftlib
- FIRESTARTER
- GPyTorch
- GraPhlAn
- intel-compilers (oneAPI)
- Kaleido
- limix
- NanopolishComp
- PHANOTATE
- PIPITS
- preCICE
- PySAT
- Raysect
- samblaster
- SeisSol
- SuperLU_DIST
- YANK


This brings the total number of supported software packages to 2,248!
An up-to-date list of supported software is available [here](https://easybuild.readthedocs.io/en/latest/version-specific/Supported_software.html).


Various software updates have been added, including (but not limited to):
- AmberTools 20
- ASE 3.21.1
- AUGUSTUS 3.4.0
- Bazel 3.7.2
- BLAST+ 2.11.0
- Bonito 0.3.5
- CGAL 5.2
- CUDAcore 11.2.1
- DendroPy 4.5.2
- FusionCatcher 1.30
- GPAW 21.1.0
- GROMACS 2020.5
- HMMER 3.3.2,
- Horovod 0.21.1
- impi 2021.1.1
- IQ-TREE 2.1.2
- JUBE 2.4.1
- medaka 1.2.0
- MPICH 3.3.2
- NVHPC 20.11
- nvtop 1.1.0
- OpenCoarrays 2.9.2
- OpenFOAM v2012
- OpenMPI 4.1.0
- PLUMED 2.6.2
- PyMC3 3.11.0
- PyTorch 1.7.1
- QuantumESPRESSO 6.7
- R 4.0.3
- R-bundle-Bioconductor 3.12
- ReFrame 3.4.1
- Salmon 1.4.0
- SEPP 4.4.0
- SuiteSparse 5.8.1
- TensorFlow 1.15.5 + 2.4.1
- Wannier90 3.1.0


These changes result from various contributions, made by 26 different contributors:

* 33 merged pull requests for EasyBuild framework
* 49 merged pull requests for easyblocks
* 327 merged pull requests for easyconfigs

Thanks to everyone who contributed to this release in one way or another!


To upgrade to EasyBuild v4.3.3, there are [several options](https://easybuild.readthedocs.io/en/latest/Installation.html#updating-an-existing-easybuild-installation).
Two particularly easy options include:
* `eb --install-latest-eb-release`
* `eb --from-pr 12255` (use easyconfig from [PR 12255](https://github.com/easybuilders/easybuild-easyconfigs/pull/12255))

but also includes several interesting enhancements.

Highlights for this release are listed below.
More details are available in the [release notes](https://easybuild.readthedocs.io/en/latest/Release_notes.html#easybuild-v4-3-2-december-10th-2020), which includes links to the respective pull requests for more detailed information.

Prominent bug fixes

(bug fixes that warrant reinstalling easyconfigs are marked with `(***)`)

- fix combination of `--copy-ec` and `--from-pr` options;
- fix regression in `apply_regex_substitutions`: also accept list of paths to patch;
- also inject -rpath options for all entries in `$LIBRARY_PATH` in RPATH wrappers;
- only configure Python with `--enable-optimizations` when compiling with (recent) GCC compiler (to fix hanging installations of Python and Tkinter);
- stop silently ignoring failing numpy tests, but include support for ignoring (failing) numpy tests;
- fix two bugs in GROMACS easyblock when using GCC & MKL for FFT and BLAS/LAPACK;
- always define `$FCCPP` in QuantumESPRESSO easyblock (not just when using Intel compilers);
- fix CPASSERT test faults on RHEL8 in CP2K easyblock;
- set `$UCX_TLS` in module for impi installation on top of UCX, and allow it to be overwritten in impi easyconfig file;
- fix `source_urls` in Geant4 easyconfigs;
- add patch for TensorFlow 2.3.1 to fix installation on Arm64;
- `(***)` add patch for GCCcore 10.2 to fix `__has_include regression` (required for building Libint);
- `(***)` set `$JUPYTER_PATH` to make Jupyter find the ipywidgets extension in recent IPython easyconfigs;
- `(***)` in-place update to magma 2.5.4 for PyTorch (to fix known bug in magma 2.5.2 which causes e.g. wrong results (NaNs) in PyTorch);
- `(***)` add missing PEAR dependency in easyconfig for GBprocesS v2.3 + enhance sanity check;
- `(***)` add missing gnuplot dependency in OpenFOAM easyconfigs (just re-generating OpenFOAM module files via `--module-only` is sufficient);
- `(***)` add patch to fix possible memory leak in OpenBLAS 0.3.3+;
- renamed software to match official name or fix name clashes: Ray-assembler + Ray-project, RStudio-Server, SUMO, XCFun;

Highlighted enhancements

(enhancements that (may) warrant updating existing installations are marked with `(***)`)

- add (experimental) support for specifying easyconfig files via an "easystack" file;
- see https://easybuild.readthedocs.io/en/latest/Easystack-files.html for more information;
- significantly speed up parsing of easyconfig files by only extracting comments from an easyconfig file when they’re actually needed;
- add support for toolchain options like '`extra_cxxflags`' to specify extra compiler options;
- add support for '`%(module_name)s`' template value;
- add support for skipping unit tests (test step) via `--skip-test-step`;
- add support for building Clang and GCC with support for OpenMP offloading to GPUs;
- update TensorFlow easyblock for upcoming TensorFlow 2.4;
- enhance PyTorch easyblock to ensure it finds MKL;
- ` (***)` enable NVPTX offload support in GCCcore 10.2.0 easyconfig;
- `(***)` add additional extensions to R 4.0.0 and Bioconductor 3.11 bundle;
- `(***)` add missing extensions for QIIME2 to Perl 5.30.2 and 5.32.0 easyconfigs;

Use ["`eb --rebuild --skip`"](https://easybuild.readthedocs.io/en/latest/Partial_installations.html#installing-additional-extensions-using-k-skip) to install the missing extensions for R, Bioconductor, or Perl.


Supported software

Easyconfig files for the updated common toolchains are included:
* `foss/2020b`
* `fosscuda/2020b`
* `intel/2020b`
* `intelcuda/2020b`


In addition, easyconfigs for the new '`gobff`' toolchain are included: `gobff/2020.11`, `gobff/2020.06-amd`.

The gobff toolchain includes the following components:
* GCC + binutils
* OpenMPI
* BLIS + libFLAME (BLAS/LAPACK libraries)
* ScaLAPACK
* FFTW

The `-amd` variant uses the AMD forks of the upstream BLIS and libFLAME libraries.

Support for installing 41 new software packages has been added, including:
* carputils
* code-server
* CRISPResso2
* fgbio
* IPM
* LLDB
* meshalyzer
* meshtool
* Metagenome-Atlas
* MLxtend
* MRChem
* nanocompore
* OpenSees
* PEST++
* pyFAI
* pymca
* scikit-bio
* SpaceRanger
* SWAT+
* WCT

This brings the total number of supported software packages to 2,175!
An up-to-date list of supported software is available [here](https://easybuild.readthedocs.io/en/latest/version-specific/Supported_software.html).

Various software updates have been added, including (but not limited to):
* Boost 1.74.0
* CUDA 11.1.1
* CellRanger 5.0.0.eb
* CheckM 1.1.3
* Clang 11.0.0
* cuDNN 8.0.4.30
* FDS 6.7.5
* FFmpeg 4.3.1
* GROMACS 2020.4
* Geant4 10.6.2
* GlobalArrays 5.8
* HDF5 1.10.7
* h5py 3.1.0
* magma 2.5.4
* matplotlib 3.3.3
* NCCL 2.8.3
* netCDF-Fortran 4.5.3
* OpenMolcas 20.10
* packmol 20.2.2
* Qt5 5.14.2
* RAxML-NG 1.0.1
* SCOTCH 6.1.0
* SciPy-bundle 2020.11 (incl. numpy 1.19.4, scipy 1.5.4, 1.1.4, ...)
* StringTie 2.1.4
* SuperLU 5.2.2
* scikit-learn 0.23.2
* snakemake 5.26.1


These changes result from various contributions, made by 27 different contributors:

* 33 merged pull requests for EasyBuild framework
* 39 merged pull requests for easyblocks
* 187 merged pull requests for easyconfigs

Thanks to everyone who contributed to this release in one way or another!


To upgrade to EasyBuild v4.3.2, there are [several options](https://easybuild.readthedocs.io/en/latest/Installation.html#updating-an-existing-easybuild-installation).
Two particularly easy options include:
* `eb --install-latest-eb-release`
* `eb --from-pr 11853` use easyconfig from [PR 11853](https://github.com/easybuilders/easybuild-easyconfigs/pull/11853)

but also includes some minor enhancements.

All details are available in the [release notes](https://easybuild.readthedocs.io/en/latest/Release_notes.html#easybuild-v4-3-1-october-29th-2020), with links to the respective pull requests.


Prominent bug fixes

(bug fixes that warrant reinstalling easyconfigs are marked with `(***)`)

- fix compatibility of EasyBuild with Python 3.9;
- fix various issues when using "sources" to specify extension sources;
- `(***)` add patches to fix miscomputation (on POWER) and performance issues for OpenBLAS 0.3.3 through 0.3.9;
- `(***)` fix source for SQLite 3.31.1;
=> incorrect source URL and filename caused SQLite 3.29.0 to be installed instead;
- `(***)` configure OpenMPI 4.x (`foss/2020a`) with `--without-verbs` when using UCX;
=> this fixes a warning message that occurs when using OpenMPI on systems with Infiniband, see also https://www.open-mpi.org/faq/?category=all#ofa-device-error;
- `(***)` add patch for OpenMPI 3.1.4 (`foss/2019b`) adding device parameters for ConnectX-6;
=> fixes warning about missing device parameters on systems with recent Infiniband cards;
- `(***)` enhance OpenFOAM easyblock to add symlinks for libraries to ensure MPI versions have preference over dummy versions;
=> fixes broken tools (like `snappyHexMesh`) in OpenFOAM installation if EasyBuild was configured to use RPATH linking (via `--rpath`);
- `(***)` patch out bug in collective primitive in TensorFlow 2.2.0;
- `(***)` remove `--no-dist-info` configuration option for SIP in recent PyQt5 easyconfigs (so pip can find SIP);
- `(***)` remove GLog and GFlags dependencies from PyTorch easyconfigs (known to cause problems on POWER);
- `(***)` fix dependency on Bowtie of v0.x in seq2HLA easyconfigs;
- `(***)` add protobuf-python as a dependency for PyTorch 1.6 (required by `caffe2.python` module);
- `(***)` add ncurses runtime dependency to Clang easyconfigs;
- `(***)` fix PyVCF easyconfig, only supports Python 2;
- `(***)` remove easyconfigs for Taiyaki that depend on PyTorch 1.3.1, since latest version still requires PyTorch 1.2.0;
- make OpenBLAS installation procedure respect the parallelism set by EasyBuild;
- fix checksum in NAMD 2.12 easyconfigs + add source URL;
- rename `jupyterhub` to `JupyterHub`;


Highlighted enhancements

(enhancements that (may) warrant updating existing installations are marked with `(***)`)

- publish test reports to easybuild-easyblocks pull request when `--include-easyblocks-from-pr` is used without `--from-pr`;
- add support for including easyblocks from multiple PRs at once via `--include-easyblocks-from-pr`;
- update TensorFlow easyblock to:
- put Bazel build files in build directory;
- avoid unnecessary runtime patching;
- add XLA build support;
- leverage installed OpenSSL/BoringSSL when cURL is used as a dependency;
- make easyblock for installing CMake aware of `--sysroot` EasyBuild configuration setting;
- update ScaLAPACK easyblock to support installation with CMake for recent versions (>= v2.1.0);
- `(***)` use more EasyBuild installed dependencies for TensorFlow 2.2.0;
- `(***)` add libevent, libfabric and PMIx dependencies to OpenMPI 4.0.3 (for `foss/2020a` & `iomkl/2020a`);
- `(***)` add additional extensions to R 4.0.0 and Bioconductor 3.11 bundle;
=> [use "`eb --rebuild --skip`" to install the missing extensions](https://easybuild.readthedocs.io/en/latest/Partial_installations.html#installing-additional-extensions-using-k-skip);
- `(***)` make libtirpc easier to use as replacement of rpc in glibc (for RHEL8);
- `(***)` build LibTIFF with `-fPIC`;


Supported software

Support for installing 75 new software packages has been added, including:
- CFDEMcoupling
- COMSOL
- DIRAC
- FRUIT (Fortran Unit Test Framework)
- GDRCopy
- mauveAligner
- MyCC
- Nek5000
- NVHPC (NVIDIA HPC SDK) + support using it as a toolchain
- OPERA-MS
- PyOpenCL
- QtPy
- SeqKit

This brings the total number of supported software packages to 2,134!
An up-to-date list of supported software is available [here](https://easybuild.readthedocs.io/en/latest/version-specific/Supported_software.html).

Easyconfigs for `fosscuda/2020a` and `intelcuda/2020a` toolchains have been added.

Various software updates have been added, including:
- ABINIT 9.2.1
- Bazel 3.6.0
- CUDA 11.0.2
- GROMACS 2020.3
- GTK+ 3.24.23
- HMMER 3.3.1
- Horovod 0.20.3
- IPython 7.18.1
- LLVM 11.0.0
- medaka 1.1.3
- Mesa 20.2.1
- PSI4 1.3.2
- PyQt5 5.15.1
- PyRETIS 2.5.0
- Python 3.8.6
- ReFrame 3.2
- Spyder 4.1.5
- Taiyaki 5.1.0
- TINKER 8.8.1
- TensorFlow 2.3.1 (with foss/2019b, fosscuda/2019b, foss/2020a)
- TRIQS 3.0.0
- UCX 1.9.0
- X11 20201008


These changes result from various contributions, made by 25 different contributors:

* 21 merged pull requests for EasyBuild framework
* 32 merged pull requests for easyblocks
* 287 merged pull requests for easyconfigs

Thanks to everyone who contributed to this release in one way or another!


To upgrade to EasyBuild v4.3.1, there are [several options](https://easybuild.readthedocs.io/en/latest/Installation.html#updating-an-existing-easybuild-installation).
Two particularly easy options include:

* `eb --install-latest-eb-release`
* `eb --from-pr 11590` use easyconfig from [PR 11590](https://github.com/easybuilders/easybuild-easyconfigs/pull/11590/files)