Easybuild

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)

Detailed release notes available at https://easybuild.readthedocs.io/en/latest/Release_notes.html#easybuild-v4-3-0-september-13th-2020)

Detailed release notes available at https://easybuild.readthedocs.io/en/latest/Release_notes.html#easybuild-v4-2-2-july-8th-2020

Detailed release notes available at https://easybuild.readthedocs.io/en/latest/Release_notes.html#easybuild-v4-2-1-may-20th-2020

EasyBuild v4.2.0 is primarily a feature/update release, but also includes various bug fixes.

Highlights of the changes in this release include:

* (experimental) support for `--try-update-deps`, to upgrade dependencies based on available easyconfigs;

* a locking mechanism to prevent two simultaneous installations of the same easyconfig file to the same installation path (see https://easybuild.readthedocs.io/en/latest/Locks.html for more information);

* significant speedup for `-D`/`--dry-run` by avoiding useless '`module show`' calls;

* support for creating an index & using it to speed up searching for easyconfigs (see https://easybuild.readthedocs.io/en/latest/Easyconfigs_index.html for more information);

* additional GitHub integration features:
- support for targeting the easyblocks and framework repositories with `eb --new-pr` (via `--pr-target-repo`)
- support for including easyblocks from an (open) pull request via `--include-easyblocks-from-pr`
- for more information, https://easybuild.readthedocs.io/en/latest/Integration_with_GitHub.html

* probing of external modules for missing metadata that is not provided via an external module metadata file (mostly relevant for integration with the Cray Programming Environment);

* leveraging the [`archspec`](https://github.com/archspec/archspec) Python library (if it is installed) to show the "code name" of the processor in your system in the output of "`eb --show-system-info`" and in test reports uploaded to PRs via `--upload-test-report`;

* support for using templates like `%(cudaver)s` for the CUDA version (if it's included as direct dependency);

* fix for `UnicodeDecodeError` that was raised when reading a patch file that contained non-ASCII characters (if EasyBuild was being run with Python 3);

* fixed filtering of already installed extensions under `--skip` (mostly relevant for Python packages installed as bundles of extensions);

* also support `%(installdir)s` and `%(builddir)s` templates for extensions;

* take into account toolchain hierarchy when dumping easyconfig files, to avoid hardcoded subtoolchains in '`*dependencies`' easyconfig parameters (relevant when using `--try-*` options);

* take into account dependencies marked as external modules when composing template values like `%(pyver)s`;

* deprecate `rmtree2` function provided by `easybuild.tools.filetools` (the `remove_dir` function should be used instead);

* 7 new software-specific easyblocks: BerkeleyGW, CMake, ELSI, LAMMPS, libdrm, Mesa, SEPP;

* updates, enhancements & bug fixes for the `CMakeMake`, `PythonPackage` and `PythonBundle` generic easyblocks;

* updates, enhancements & bug fixes in the software-specific easyblocks for Clang, Ferret, Hypre, impi, libxml2, MATLAB, numexpr, OpenBabel, OpenBLAS, OpenCV, OpenFOAM, ParMETIS, PETSc, Python, QuantumESPRESSO, Qt, ROOT, Siesta, tbb, TensorFlow, TensorRT, Trinity, VMD, XCrySDen;

* added support for no less than 114 (!) new software packages, incl. ADIOS, ArviZ, Bonito, ELSI, FuSeq, GraphMap2, LAMMPS, MedPy, motionSegmentation, OpenAI-Gym, PyMC3, PyRe, PyTorch-Geometric, RAxML-NG, Shapely, STEAK, UQTk, Zip, ...;

* updates for already supported software, incl. Arrow 0.16.0, BUSCO 4.0.5, Clang 10.0.0, ELPA 2019.11.001, Ferret 7.5.0, GCC(core) 9.3.0, GROMACS 2020, GTK+ 3.24.13, Hypre 2.18.2, IQ-TREE 1.6.12, Java 13(.0.2), LLVM 9.0.1 + 10.0.0, likwid 5.0.1, medaka 0.12.0, numba 0.47.0, Octave 5.1.0, OpenBLAS 0.3.8, OpenBabel 3.0.0, OpenCV 4.2.0, OpenFOAM-Extend 4.1-20191120, PETSc 3.12.4, PyTorch 1.4.0, Qhull 2019.1, QuantumESPRESSO 6.5, R-bundle-Bioconductor 3.10, Racon 1.4.10, ReFrame 2.21, SLEPc 3.12.2, SimpleElastix 1.1.0, SimpleITK 1.2.4, TensorFlow 1.15.2 + 2.0.1, Trinity 2.10.0, XGBoost 0.90, xarray 0.15.1, ...;

* update Java/1.8 wrapper to Java/1.8.0_241;

* enhanced Java/11 wrapper to support both x86_64 and POWER;

* fixed source URL for ISL component in `GCCcore` easyconfigs;

* checksum fixes in easyconfigs for R 3.6.0 and 3.6.2;

* revert removal of AVX512 vmovd with 64-bit operands in binutils 2.32 easyconfigs;

* fixed packaging issue that resulted in CVS easyconfigs to be missing from EasyBuild releases;

* updated checksum/homepage in tbb easyconfigs after move to '`oneapi-src`' repository;

* various additional updates, enhancements & bug fixes;

This brings the total number of supported software packages to 1,912!
An up-to-date list of supported software is available at https://easybuild.readthedocs.io/en/latest/version-specific/Supported_software.html .

A detailed overview of all changes, which links to the respective pull requests, is available in the release notes at https://easybuild.readthedocs.io/en/latest/Release_notes.html#easybuild-v4-2-0-april-14th-2020 .

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

* 56 merged pull requests for EasyBuild framework
* 63 merged pull requests for easyblocks
* 381 merged pull requests for easyconfigs

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

This release fixes a problem where the GitHub token that EasyBuild uses for some of the GitHub integration features (like `--from-pr`, `--new-pr`, etc.) got included in plain text in the 'top-level' EasyBuild log file when the `--debug` configuration option is enabled, potentially leaving it exposed to be used by others.

**We strongly encourage that you revoke the GitHub tokens you are using currently, via https://github.com/settings/tokens, and to replace them using a new token (using "eb --install-github-token --force").**

More information is available in the [security advisory that was published](https://github.com/easybuilders/easybuild-framework/security/advisories/GHSA-2wx6-wc87-rmjm).

Detailed release notes at https://easybuild.readthedocs.io/en/latest/Release_notes.html#easybuild-v4-1-2-march-16th-2020 .