Merge pull request #793 from boegel/eb454

release EasyBuild v4.5.4
easybuilders · Mar 31, 2022 · 5b452cc · 5b452cc
2 parents 2e1572a + 7a7e9a7
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diff --git a/docs/Changelog.rst b/docs/Changelog.rst
@@ -5,6 +5,7 @@ Changelog for EasyBuild documentation
 
 (for EasyBuild release notes, see :ref:`release_notes`)
 
+* **release 20220331.01** (`Mar 31st 2022`): update release notes for EasyBuild v4.5.4 (see :ref:`release_notes_eb454`)
 * **release 20220211.01** (`Feb 11th 2022`): update release notes for EasyBuild v4.5.3 (see :ref:`release_notes_eb453`)
 * **release 20220124.01** (`Jan 24th 2022`): update release notes for EasyBuild v4.5.2 (see :ref:`release_notes_eb452`)
 * **release 20211213.01** (`Dec 13th 2021`): update release notes for EasyBuild v4.5.1 (see :ref:`release_notes_eb451`)

diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst
diff --git a/docs/Writing_easyconfig_files.rst b/docs/Writing_easyconfig_files.rst
@@ -456,10 +456,13 @@ If a recursive checkout should be made of the repository, the ``recursive`` key
 To also retain the ``.git`` directory (which holds the Git metadata for the repository),
 you can set the ``keep_git_dir`` to ``True`` (supported since EasyBuild v4.2.0).
 
+A different name for the top-level directory can be specified via ``clone_into``;
+by default the name of the repository is used.
+
 Examples:
 
   * creating a source tarball named ``example-main.tar.gz`` of the ``main`` branch of a (fictional)
-    ``test`` repository from ``https://agitserver.org/example``:
+    ``test`` repository from ``https://agitserver.org/example``, and use ``example-test`` as top-level directory name:
 
     .. code::
 
@@ -469,6 +472,7 @@ Examples:
               'url': 'https://agitserver.org/example',
               'repo_name': 'test',
               'tag': 'main',
+              'clone_into': 'example-test',
           },
       }]
 

diff --git a/docs/conf.py b/docs/conf.py
@@ -41,9 +41,9 @@
 # other places throughout the built documents.
 #
 # The short X.Y version.
-version = '4.5.3'  # this is meant to reference the version of EasyBuild
+version = '4.5.4'  # this is meant to reference the version of EasyBuild
 # The full version, including alpha/beta/rc tags.
-release = '20220211.0'  # this is meant to reference the version of the documentation itself
+release = '20220331.0'  # this is meant to reference the version of the documentation itself
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:

diff --git a/docs/version-specific/Supported_software.rst b/docs/version-specific/Supported_software.rst
diff --git a/docs/version-specific/easyblocks.rst b/docs/version-specific/easyblocks.rst
@@ -306,6 +306,19 @@
       * EB_XML
 
     * RubyGem
+    * Tarball
+
+      * BinariesTarball
+      * EB_cuDNN
+      * EB_FoldX
+      * EB_FreeSurfer
+      * EB_Gurobi
+      * EB_Hadoop
+      * EB_MTL4
+      * EB_picard
+      * EB_RepeatMasker
+      * EB_RepeatModeler
+
 
   * GoPackage
   * IntelBase
@@ -375,19 +388,6 @@
 
     * EB_Xmipp
 
-  * Tarball
-
-    * BinariesTarball
-    * EB_cuDNN
-    * EB_FoldX
-    * EB_FreeSurfer
-    * EB_Gurobi
-    * EB_Hadoop
-    * EB_MTL4
-    * EB_picard
-    * EB_RepeatMasker
-    * EB_RepeatModeler
-
   * Waf
 
 * **Extension**
@@ -448,5 +448,18 @@
       * EB_XML
 
     * RubyGem
+    * Tarball
+
+      * BinariesTarball
+      * EB_cuDNN
+      * EB_FoldX
+      * EB_FreeSurfer
+      * EB_Gurobi
+      * EB_Hadoop
+      * EB_MTL4
+      * EB_picard
+      * EB_RepeatMasker
+      * EB_RepeatModeler
+
 
 
diff --git a/docs/version-specific/easyconfig_parameters.rst b/docs/version-specific/easyconfig_parameters.rst
@@ -48,6 +48,7 @@ build parameters
 ``checksums``                      Checksums for sources and patches                                                                                                            []               
 ``configopts``                     Extra options passed to configure (default already has --prefix)                                                                             ""               
 ``cuda_compute_capabilities``      List of CUDA compute capabilities to build with (if supported)                                                                               []               
+``download_instructions``          Specify steps to aquire necessary file, if obtaining it is difficult                                                                         ""               
 ``easyblock``                      EasyBlock to use for building; if set to None, an easyblock is selected based on the software name                                           None             
 ``easybuild_version``              EasyBuild-version this spec-file was written for                                                                                             None             
 ``enhance_sanity_check``           Indicate that additional sanity check commands & paths should enhance the existin sanity check, not replace it                               False            
@@ -61,6 +62,7 @@ build parameters
 ``parallel``                       Degree of parallelism for e.g. make (default: based on the number of cores, active cpuset and restrictions in ulimit)                        None             
 ``patches``                        List of patches to apply                                                                                                                     []               
 ``postinstallcmds``                Commands to run after the install step.                                                                                                      []               
+``postinstallpatches``             Patch files to apply after running the install step.                                                                                         []               
 ``prebuildopts``                   Extra options pre-passed to build command.                                                                                                   ""               
 ``preconfigopts``                  Extra options pre-passed to configure.                                                                                                       ""               
 ``preinstallopts``                 Extra prefix options for installation.                                                                                                       ""               

diff --git a/docs/version-specific/generic_easyblocks.rst b/docs/version-specific/generic_easyblocks.rst
@@ -28,6 +28,7 @@ Extra easyconfig parameters specific to ``BinariesTarball`` easyblock
 easyconfig parameter    description                                                                                                                                                      default value
 ====================    =============================================================================================================================================================    =============
 ``install_type``        Defaults to extract tarball into clean directory. Options: 'merge' merges tarball to existing directory, 'subdir' extracts tarball into its own sub-directory    ``None``     
+``options``             Dictionary with extension options.                                                                                                                               ``{}``       
 ``preinstall_cmd``      Command to execute before installation                                                                                                                           ``None``     
 ====================    =============================================================================================================================================================    =============
 
@@ -1247,7 +1248,7 @@ easyconfig parameter                 description
 ``Tarball``
 ===========
 
-(derives from EasyBlock)
+(derives from ExtensionEasyBlock)
 
 Precompiled software supplied as a tarball:
     - will unpack binary and copy it to the install dir
@@ -1259,6 +1260,7 @@ Extra easyconfig parameters specific to ``Tarball`` easyblock
 easyconfig parameter    description                                                                                                                                                      default value
 ====================    =============================================================================================================================================================    =============
 ``install_type``        Defaults to extract tarball into clean directory. Options: 'merge' merges tarball to existing directory, 'subdir' extracts tarball into its own sub-directory    ``None``     
+``options``             Dictionary with extension options.                                                                                                                               ``{}``       
 ``preinstall_cmd``      Command to execute before installation                                                                                                                           ``None``     
 ====================    =============================================================================================================================================================    =============
 

diff --git a/docs/version-specific/toolchain_opts.rst b/docs/version-specific/toolchain_opts.rst
@@ -5,7 +5,7 @@ Available toolchain options (by toolchain)
 
 *(see also* ``eb --avail-toolchain-opts <tcname>`` *)*
 
-ClangGCC_ - CrayCCE_ - CrayGNU_ - CrayIntel_ - CrayPGI_ - FCC_ - Fujitsu_ - GCC_ - GCCcore_ - GNU_ - NVHPC_ - PGI_ - cgmpich_ - cgmpolf_ - cgmvapich2_ - cgmvolf_ - cgompi_ - cgoolf_ - ffmpi_ - foss_ - fosscuda_ - gcccuda_ - gimkl_ - gimpi_ - gimpic_ - giolf_ - giolfc_ - gmacml_ - gmkl_ - gmklc_ - gmpich2_ - gmpich_ - gmpolf_ - gmvapich2_ - gmvolf_ - goalf_ - gobff_ - goblf_ - gofbf_ - golf_ - golfc_ - gomkl_ - gomklc_ - gompi_ - gompic_ - goolf_ - goolfc_ - gpsmpi_ - gpsolf_ - gqacml_ - gsmpi_ - gsolf_ - iccifort_ - iccifortcuda_ - ictce_ - iibff_ - iimkl_ - iimklc_ - iimpi_ - iimpic_ - iiqmpi_ - impich_ - impmkl_ - intel-compilers_ - intel-para_ - intel_ - intelcuda_ - iomkl_ - iomklc_ - iompi_ - iompic_ - ipsmpi_ - iqacml_ - ismkl_ - nvompic_ - nvpsmpic_ - pmkl_ - pomkl_ - pompi_ - system_ - xlcxlf_ - xlmpich2_ - xlmpich_ - xlmvapich2_ - xlompi_
+ClangGCC_ - CrayCCE_ - CrayGNU_ - CrayIntel_ - CrayPGI_ - FCC_ - Fujitsu_ - GCC_ - GCCcore_ - GNU_ - NVHPC_ - PGI_ - cgmpich_ - cgmpolf_ - cgmvapich2_ - cgmvolf_ - cgompi_ - cgoolf_ - ffmpi_ - foss_ - fosscuda_ - gcccuda_ - gimkl_ - gimpi_ - gimpic_ - giolf_ - giolfc_ - gmacml_ - gmkl_ - gmklc_ - gmpich2_ - gmpich_ - gmpit_ - gmpolf_ - gmvapich2_ - gmvolf_ - goalf_ - gobff_ - goblf_ - gofbf_ - golf_ - golfc_ - gomkl_ - gomklc_ - gompi_ - gompic_ - goolf_ - goolfc_ - gpsmpi_ - gpsolf_ - gqacml_ - gsmpi_ - gsolf_ - iccifort_ - iccifortcuda_ - ictce_ - iibff_ - iimkl_ - iimklc_ - iimpi_ - iimpic_ - iiqmpi_ - impich_ - impmkl_ - intel-compilers_ - intel-para_ - intel_ - intelcuda_ - iomkl_ - iomklc_ - iompi_ - iompic_ - ipsmpi_ - iqacml_ - ismkl_ - nvompic_ - nvpsmpic_ - pmkl_ - pomkl_ - pompi_ - system_ - xlcxlf_ - xlmpich2_ - xlmpich_ - xlmvapich2_ - xlompi_
 
 .. _ClangGCC:
 
@@ -1443,6 +1443,52 @@ option                       description
 =========================    =======================================================================    =========
 
 
+.. _gmpit:
+
+Available options for gmpit toolchain
+-------------------------------------
+
+=========================    =======================================================================    =========
+option                       description                                                                default  
+=========================    =======================================================================    =========
+``32bit``                    Compile 32bit target                                                       ``False``
+``cciscxx``                  Use CC as CXX                                                              ``False``
+``cstd``                     Specify C standard                                                         ``None`` 
+``debug``                    Enable debug                                                               ``False``
+``defaultopt``               Default compiler optimizations                                             ``False``
+``defaultprec``              Default precision                                                          ``False``
+``extra_cflags``             Specify extra CFLAGS options.                                              ``None`` 
+``extra_cxxflags``           Specify extra CXXFLAGS options.                                            ``None`` 
+``extra_f90flags``           Specify extra F90FLAGS options.                                            ``None`` 
+``extra_fcflags``            Specify extra FCFLAGS options.                                             ``None`` 
+``extra_fflags``             Specify extra FFLAGS options.                                              ``None`` 
+``f2c``                      Generate code compatible with f2c and f77                                  ``False``
+``i8``                       Integers are 8 byte integers                                               ``False``
+``ieee``                     Adhere to IEEE-754 rules                                                   ``False``
+``loop``                     Automatic loop parallellisation                                            ``False``
+``loose``                    Loose precision                                                            ``False``
+``lowopt``                   Low compiler optimizations                                                 ``False``
+``lto``                      Enable Link Time Optimization                                              ``False``
+``noopt``                    Disable compiler optimizations                                             ``False``
+``openmp``                   Enable OpenMP                                                              ``False``
+``opt``                      High compiler optimizations                                                ``False``
+``optarch``                  Enable architecture optimizations                                          ``True`` 
+``packed-linker-options``    Pack the linker options as comma separated list                            ``False``
+``pic``                      Use PIC                                                                    ``False``
+``precise``                  High precision                                                             ``False``
+``r8``                       Real is 8 byte real                                                        ``False``
+``rpath``                    Use RPATH wrappers when --rpath is enabled in EasyBuild configuration      ``True`` 
+``shared``                   Build shared library                                                       ``False``
+``static``                   Build static library                                                       ``False``
+``strict``                   Strict (highest) precision                                                 ``False``
+``unroll``                   Unroll loops                                                               ``False``
+``usempi``                   Use MPI compiler as default compiler                                       ``False``
+``vectorize``                Enable compiler auto-vectorization, default except for noopt and lowopt    ``None`` 
+``verbose``                  Verbose output                                                             ``False``
+``veryloose``                Very loose precision                                                       ``False``
+=========================    =======================================================================    =========
+
+
 .. _gmpolf:
 
 Available options for gmpolf toolchain