Merge pull request #271 from boegel/eb493_auto_update

auto-update docs for EasyBuild v4.9.3

docs/version-specific/easyblocks.md

@@ -172,7 +172,7 @@
       - EB_Tkinter
     - EB_QScintilla
     - EB_Qt
-    - EB_QuantumESPRESSO
+    - EB_QuantumESPRESSOconfig
     - EB_R
     - EB_Ruby
     - EB_Rust
@@ -232,6 +232,7 @@
   - EB_OpenIFS
   - EB_PALM
   - EB_ParMETIS
+  - EB_QuantumESPRESSO
   - EB_Rosetta
   - EB_SAS
   - EB_SCOTCH
@@ -250,6 +251,7 @@
       - CargoPythonPackage
     - EB_Scipion
     - JuliaPackage
+      - JuliaBundle
     - OCamlPackage
     - OctavePackage
     - PerlModule
@@ -369,6 +371,7 @@
       - CargoPythonPackage
     - EB_Scipion
     - JuliaPackage
+      - JuliaBundle
     - OCamlPackage
     - OctavePackage
     - PerlModule

docs/version-specific/easyconfig-constants.md

@@ -14,6 +14,6 @@ Constant name         |Constant value
 ``OS_TYPE``           |``Darwin``                                                   |System type (e.g. 'Linux' or 'Darwin')
 ``OS_VERSION``        |``UNKNOWN``                                                  |System version
 ``SYSTEM``            |``{'name': 'system', 'version': 'system'}``                  |System toolchain
-``SYS_PYTHON_VERSION``|``3.12.3``                                                   |System Python version (platform.python_version())
+``SYS_PYTHON_VERSION``|``3.11.9``                                                   |System Python version (platform.python_version())
 
 *(see also* ``eb --avail-easyconfig-constants`` *)*

docs/version-specific/easyconfig-templates.md

@@ -62,17 +62,19 @@ Template name     |Template value
 
 ## Template values which are defined dynamically
 
-Template name                    |Template value
----------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-``%(arch)s``                     |System architecture (e.g. x86_64, aarch64, ppc64le, ...)
-``%(sysroot)s``                  |Location root directory of system, prefix for standard paths like /usr/lib and /usr/includeas specify by the --sysroot configuration option
-``%(mpi_cmd_prefix)s``           |Prefix command for running MPI programs (with default number of ranks)
-``%(cuda_compute_capabilities)s``|Comma-separated list of CUDA compute capabilities, as specified via --cuda-compute-capabilities configuration option or via cuda_compute_capabilities easyconfig parameter
-``%(cuda_cc_cmake)s``            |List of CUDA compute capabilities suitable for use with $CUDAARCHS in CMake 3.18+
-``%(cuda_cc_space_sep)s``        |Space-separated list of CUDA compute capabilities
-``%(cuda_cc_semicolon_sep)s``    |Semicolon-separated list of CUDA compute capabilities
-``%(cuda_sm_comma_sep)s``        |Comma-separated list of sm_* values that correspond with CUDA compute capabilities
-``%(cuda_sm_space_sep)s``        |Space-separated list of sm_* values that correspond with CUDA compute capabilities
+Template name                      |Template value
+-----------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+``%(arch)s``                       |System architecture (e.g. x86_64, aarch64, ppc64le, ...)
+``%(cuda_compute_capabilities)s``  |Comma-separated list of CUDA compute capabilities, as specified via --cuda-compute-capabilities configuration option or via cuda_compute_capabilities easyconfig parameter
+``%(cuda_cc_cmake)s``              |List of CUDA compute capabilities suitable for use with $CUDAARCHS in CMake 3.18+
+``%(cuda_cc_space_sep)s``          |Space-separated list of CUDA compute capabilities
+``%(cuda_cc_space_sep_no_period)s``|Space-separated list of CUDA compute capabilities, without periods (e.g. '80 90').
+``%(cuda_cc_semicolon_sep)s``      |Semicolon-separated list of CUDA compute capabilities
+``%(cuda_sm_comma_sep)s``          |Comma-separated list of sm_* values that correspond with CUDA compute capabilities
+``%(cuda_sm_space_sep)s``          |Space-separated list of sm_* values that correspond with CUDA compute capabilities
+``%(mpi_cmd_prefix)s``             |Prefix command for running MPI programs (with default number of ranks)
+``%(software_commit)s``            |Git commit id to use for the software as specified by --software-commit command line option
+``%(sysroot)s``                    |Location root directory of system, prefix for standard paths like /usr/lib and /usr/includeas specified by the --sysroot configuration option
 
 ## Template constants that can be used in easyconfigs
 
@@ -88,7 +90,8 @@ Constant                |Template value
 ``GITHUB_RELEASE``      |GitHub release URL (if github_account easyconfig parameter is not specified, namelower is used in its place)                    |``https://github.com/%(github_account)s/%(name)s/releases/download/v%(version)s``
 ``GITHUB_LOWER_RELEASE``|GitHub release URL with lowercase name (if github_account easyconfig parameter is not specified, namelower is used in its place)|``https://github.com/%(github_account)s/%(namelower)s/releases/download/v%(version)s``
 ``GNU_SAVANNAH_SOURCE`` |download.savannah.gnu.org source url                                                                                            |``https://download-mirror.savannah.gnu.org/releases/%(namelower)s``
-``GNU_SOURCE``          |gnu.org source url                                                                                                              |``https://ftpmirror.gnu.org/gnu/%(namelower)s``
+``GNU_SOURCE``          |gnu.org source url (ftp mirror)                                                                                                 |``https://ftpmirror.gnu.org/gnu/%(namelower)s``
+``GNU_FTP_SOURCE``      |gnu.org source url (main ftp)                                                                                                   |``https://ftp.gnu.org/gnu/%(namelower)s``
 ``GOOGLECODE_SOURCE``   |googlecode.com source url                                                                                                       |``http://%(namelower)s.googlecode.com/files``
 ``LAUNCHPAD_SOURCE``    |launchpad.net source url                                                                                                        |``https://launchpad.net/%(namelower)s/%(version_major_minor)s.x/%(version)s/+download/``
 ``PYPI_SOURCE``         |pypi source url                                                                                                                 |``https://pypi.python.org/packages/source/%(nameletter)s/%(name)s``

docs/version-specific/eb-help.md

@@ -183,7 +183,7 @@ Option flag                                          |Option description
 ``--avail-toolchain-opts=AVAIL-TOOLCHAIN-OPTS``      |Show options for toolchain (type str)
 ``--check-conflicts``                                |Check for version conflicts in dependency graphs (default: False)
 ``--check-eb-deps``                                  |Check presence and version of (required and optional) EasyBuild dependencies (default: False)
-``--dep-graph=depgraph.<ext>``                       |Create dependency graph
+``--dep-graph=depgraph.<ext>``                       |Create dependency graph. Output format depends on <ext>, e.g. 'dot', 'png', 'pdf', 'gv'.
 ``--dump-env-script``                                |Dump source script to set up build environment based on toolchain/dependencies (default: False)
 ``--easystack=EASYSTACK``                            |Path to easystack file in YAML format, specifying details of a software stack
 ``--last-log``                                       |Print location to EasyBuild log file of last (failed) session (default: False)
@@ -253,6 +253,7 @@ Option flag                                                              |Option
 ``--env-for-shebang=ENV-FOR-SHEBANG``                                    |Define the env command to use when fixing shebangs (default: /usr/bin/env)
 ``--experimental``                                                       |Allow experimental code (with behaviour that can be changed/removed at any given time). (default: False)
 ``--extra-modules=EXTRA-MODULES``                                        |List of extra modules to load after setting up the build environment (type comma-separated list)
+``--extra-source-urls=URL[|URL]``                                        |Specify URLs to fetch sources from in addition to those in the easyconfig (type |-separated tuple; default: https://sources.easybuild.io)
 ``--fetch``                                                              |Allow downloading sources ignoring OS and modules tool dependencies, implies --stop=fetch, --ignore-osdeps and ignore modules tool (default: False)
 ``--filter-deps=FILTER-DEPS``                                            |List of dependencies that you do *not* want to install with EasyBuild, because equivalent OS packages are installed. (e.g. --filter-deps=zlib,ncurses) (type comma-separated list)
 ``--filter-ecs=FILTER-ECS``                                              |List of easyconfigs (given as glob patterns) to *ignore* when given on command line or auto-selected when building with --from-pr. (e.g. --filter-ecs=*intel*) (type comma-separated list)
@@ -266,7 +267,7 @@ Option flag                                                              |Option
 ``--hidden``                                                             |Install 'hidden' module file(s) by prefixing their version with '.' (default: False)
 ``--hide-deps=HIDE-DEPS``                                                |Comma separated list of dependencies that you want automatically hidden, (e.g. --hide-deps=zlib,ncurses) (type comma-separated list)
 ``--hide-toolchains=HIDE-TOOLCHAINS``                                    |Comma separated list of toolchains that you want automatically hidden, (e.g. --hide-toolchains=GCCcore) (type comma-separated list)
-``--http-header-fields-urlpat=[URLPAT::][HEADER:]FILE|FIELD``            |Set extra HTTP header FIELDs when downloading files from URL PATterns. To not log sensitive values, specify a file containing newline separated FIELDs. e.g. "^https://www.example.com::/path/to/headers.txt" or "client[A-z0-9]*.example.com': ['Authorization: Basic token']".
+``--http-header-fields-urlpat=[URLPAT::][HEADER:]FIELDVALUE|FILE``       |Set extra HTTP header FIELD when downloading files from URL PATterns. Use FILE (to hide sensitive values) and newline separated FIELDs in the same format. e.g. "^https://www.example.com::path/to/headers.txt" or "client[A-z0-9]*.example.com:: Authorization: Basic token".
 ``--ignore-checksums``                                                   |Ignore failing checksum verification (default: False)
 ``--ignore-osdeps``                                                      |Ignore any listed OS dependencies (default: False)
 ``--ignore-test-failure``                                                |Ignore a failing test step (default: False)
@@ -303,8 +304,10 @@ Option flag                                                              |Option
 ``--silence-deprecation-warnings=SILENCE-DEPRECATION-WARNINGS``          |Silence specified deprecation warnings out of (python2, Lmod6, easyconfig, toolchain) (type comma-separated list)
 ``--silence-hook-trigger``                                               |Suppress printing of debug message every time a hook is triggered (default: False)
 ``--skip-extensions``                                                    |Skip installation of extensions (default: False)
+``--skip-sanity-check``                                                  |Skip running the sanity check step (e.g. testing for installed files or running basic commands) (default: False)
 ``-t, --skip-test-cases``                                                |Skip running test cases (default: False)
 ``--skip-test-step``                                                     |Skip running the test step (e.g. unit tests) (default: False)
+``--software-commit=SOFTWARE-COMMIT``                                    |Git commit to use for the target software build (robot capabilities are automatically disabled)
 ``--sticky-bit``                                                         |Set sticky bit on newly created directories (default: False)
 ``--sysroot=SYSROOT``                                                    |Location root directory of system, prefix for standard paths like /usr/lib and /usr/include
 ``-T, --trace``                                                          |Provide more information in output to stdout on progress (default: False)

docs/version-specific/generic-easyblocks.md

@@ -857,7 +857,7 @@ easyconfig parameter|description
 
 ## ``JuliaBundle``
 
-(derives from [``Bundle``](#bundle))
+(derives from [``Bundle``](#bundle), [``JuliaPackage``](#juliapackage))
 
 
 Bundle of JuliaPackages: install Julia packages as extensions in a bundle
@@ -878,12 +878,36 @@ easyconfig parameter           |description
 ``sanity_check_all_components``|Enable sanity checks for all components                                    |``False``
 ``sanity_check_components``    |List of components for which to run sanity checks                          |``[]``
 
+### Customised steps in ``JuliaBundle`` easyblock
+
+* ``install_step`` - Prepare installation environment and dd all dependencies to project environment.
+
+
 ## ``JuliaPackage``
 
 (derives from ``ExtensionEasyBlock``)
 
+
 Builds and installs Julia Packages.
 
+Julia environment setup during installation:
+- initialize new Julia environment in 'environments' subdir in installation directory
+- remove paths in user depot '~/.julia' from DEPOT_PATH and LOAD_PATH
+- put installation directory as top DEPOT_PATH, the target depot for installations with Pkg
+- put installation environment as top LOAD_PATH, needed to precompile installed packages
+- add Julia packages found in dependencies of the easyconfig to installation environment, needed
+for Pkg to be aware of those packages and not install them again
+- add newly installed Julia packages to installation environment (automatically done by Pkg)
+
+Julia environment setup on module load:
+User depot and its shared environment for this version of Julia are kept as top paths of DEPOT_PATH and
+LOAD_PATH respectively. This ensures that the user can keep using its own environment after loading
+JuliaPackage modules, installing additional software on its personal depot while still using packages
+provided by the module. Effectively, this translates to:
+- append installation directory to list of DEPOT_PATH, only really needed to load artifacts (JLL packages)
+- append installation Project.toml file to list of LOAD_PATH, needed to load packages with `using` command
+
+
 ### Extra easyconfig parameters specific to ``JuliaPackage`` easyblock
 
 easyconfig parameter |description                                                                |default value
@@ -897,7 +921,7 @@ easyconfig parameter |description
 
 * ``configure_step`` - No separate configuration for JuliaPackage.
 
-* ``install_step`` - Install Julia package with Pkg
+* ``install_step`` - Prepare installation environment and install Julia package.
 
 
 ## ``MakeCp``
@@ -1249,8 +1273,6 @@ easyconfig parameter|description                         |default value
 
 ### Customised steps in ``RubyGem`` easyblock
 
-* ``build_step`` - No separate build procedure for Ruby Gems.
-
 * ``configure_step`` - No separate configuration for Ruby Gems.
 
 * ``install_step`` - Install Ruby Gems using gem package manager

docs/version-specific/supported-software/a/AGAT.md

@@ -12,6 +12,7 @@ version | toolchain
 --------|----------
 ``0.9.2`` | ``GCC/11.2.0``
 ``1.1.0`` | ``GCC/12.2.0``
+``1.4.0`` | ``GCC/12.3.0``
 
 
 *(quick links: [(all)](../index.md) - [0](../0/index.md) - [a](../a/index.md) - [b](../b/index.md) - [c](../c/index.md) - [d](../d/index.md) - [e](../e/index.md) - [f](../f/index.md) - [g](../g/index.md) - [h](../h/index.md) - [i](../i/index.md) - [j](../j/index.md) - [k](../k/index.md) - [l](../l/index.md) - [m](../m/index.md) - [n](../n/index.md) - [o](../o/index.md) - [p](../p/index.md) - [q](../q/index.md) - [r](../r/index.md) - [s](../s/index.md) - [t](../t/index.md) - [u](../u/index.md) - [v](../v/index.md) - [w](../w/index.md) - [x](../x/index.md) - [y](../y/index.md) - [z](../z/index.md))*

docs/version-specific/supported-software/a/ANTLR.md

@@ -14,6 +14,7 @@ version | versionsuffix | toolchain
 ``2.7.7`` | ``-Java-11`` | ``GCCcore/10.3.0``
 ``2.7.7`` | ``-Java-11`` | ``GCCcore/11.2.0``
 ``2.7.7`` | ``-Java-11`` | ``GCCcore/11.3.0``
+``2.7.7`` | ``-Java-11`` | ``GCCcore/12.3.0``
 ``2.7.7`` |  | ``GCCcore/7.3.0``
 ``2.7.7`` |  | ``GCCcore/8.2.0``
 ``2.7.7`` | ``-Java-11`` | ``GCCcore/8.3.0``

docs/version-specific/supported-software/a/APOST3D.md

@@ -0,0 +1,17 @@
+---
+search:
+  boost: 0.5
+---
+# APOST3D
+
+Open-source APOST-3D software features a large number of wavefunction analysis tools developed over the past 20 years, aiming at connecting classical chemical concepts with the electronic structure of molecules. APOST-3D relies on the identification of the atom in the molecule (AIM), and several analysis tools are implemented in the most general way so that they can be used in combination with any chosen AIM. A Fortran-based code developed at the Universitat de Girona (UdG) by P. Salvador and collaborators.
+
+*homepage*: <https://github.com/mgimferrer/APOST3D>
+
+version | toolchain
+--------|----------
+``20240527`` | ``intel-compilers/2023.1.0``
+
+
+*(quick links: [(all)](../index.md) - [0](../0/index.md) - [a](../a/index.md) - [b](../b/index.md) - [c](../c/index.md) - [d](../d/index.md) - [e](../e/index.md) - [f](../f/index.md) - [g](../g/index.md) - [h](../h/index.md) - [i](../i/index.md) - [j](../j/index.md) - [k](../k/index.md) - [l](../l/index.md) - [m](../m/index.md) - [n](../n/index.md) - [o](../o/index.md) - [p](../p/index.md) - [q](../q/index.md) - [r](../r/index.md) - [s](../s/index.md) - [t](../t/index.md) - [u](../u/index.md) - [v](../v/index.md) - [w](../w/index.md) - [x](../x/index.md) - [y](../y/index.md) - [z](../z/index.md))*
+

docs/version-specific/supported-software/a/APR-util.md

@@ -20,6 +20,7 @@ version | toolchain
 ``1.6.1`` | ``GCCcore/9.3.0``
 ``1.6.1`` | ``iomkl/2018a``
 ``1.6.3`` | ``GCCcore/12.3.0``
+``1.6.3`` | ``GCCcore/13.3.0``
 
 
 *(quick links: [(all)](../index.md) - [0](../0/index.md) - [a](../a/index.md) - [b](../b/index.md) - [c](../c/index.md) - [d](../d/index.md) - [e](../e/index.md) - [f](../f/index.md) - [g](../g/index.md) - [h](../h/index.md) - [i](../i/index.md) - [j](../j/index.md) - [k](../k/index.md) - [l](../l/index.md) - [m](../m/index.md) - [n](../n/index.md) - [o](../o/index.md) - [p](../p/index.md) - [q](../q/index.md) - [r](../r/index.md) - [s](../s/index.md) - [t](../t/index.md) - [u](../u/index.md) - [v](../v/index.md) - [w](../w/index.md) - [x](../x/index.md) - [y](../y/index.md) - [z](../z/index.md))*

docs/version-specific/supported-software/a/APR.md

@@ -20,6 +20,7 @@ version | toolchain
 ``1.7.0`` | ``GCCcore/8.2.0``
 ``1.7.0`` | ``GCCcore/9.3.0``
 ``1.7.4`` | ``GCCcore/12.3.0``
+``1.7.4`` | ``GCCcore/13.3.0``
 
 
 *(quick links: [(all)](../index.md) - [0](../0/index.md) - [a](../a/index.md) - [b](../b/index.md) - [c](../c/index.md) - [d](../d/index.md) - [e](../e/index.md) - [f](../f/index.md) - [g](../g/index.md) - [h](../h/index.md) - [i](../i/index.md) - [j](../j/index.md) - [k](../k/index.md) - [l](../l/index.md) - [m](../m/index.md) - [n](../n/index.md) - [o](../o/index.md) - [p](../p/index.md) - [q](../q/index.md) - [r](../r/index.md) - [s](../s/index.md) - [t](../t/index.md) - [u](../u/index.md) - [v](../v/index.md) - [w](../w/index.md) - [x](../x/index.md) - [y](../y/index.md) - [z](../z/index.md))*

docs/version-specific/supported-software/a/ASE.md

@@ -63,6 +63,8 @@ version | versionsuffix | toolchain
 ``3.22.1`` |  | ``iimkl/2023a``
 ``3.22.1`` |  | ``intel/2021b``
 ``3.22.1`` |  | ``intel/2022a``
+``3.23.0`` |  | ``gfbf/2023a``
+``3.23.0`` |  | ``iimkl/2023a``
 ``3.9.1.4567`` | ``-Python-2.7.11`` | ``intel/2016a``