Merge pull request #638 from migueldiascosta/master

release EasyBuild v4.2.2

.github/workflows/check_with_codespell.sh

@@ -1 +1 @@
-codespell --skip='.git,version-specific,scripts' --ignore-words-list=atleast,ninjs,simpy,proovread --quiet-level=2; retVal=$?; if [ $retVal -eq 1 ]; then echo 'Got one expected warning, so success!';  else $(exit $retVal); fi;
+codespell --skip='.git,version-specific,scripts' --ignore-words-list=atleast,ninjs,simpy,proovread,namd --quiet-level=2; retVal=$?; if [ $retVal -eq 1 ]; then echo 'Got one expected warning, so success!';  else $(exit $retVal); fi;

.travis.yml

@@ -13,7 +13,7 @@ script:
   # still added to the exit code (which is a just a count of spelling
   # suggestions). Since we know we have one of these, we allow for that.
   # see https://github.com/easybuilders/easybuild/pull/485 for details
-  - codespell --skip=".git,version-specific,scripts" --ignore-words-list=atleast,ninjs,simpy,proovread --quiet-level=2; retVal=$?; if [ $retVal -eq 1 ]; then echo "Got one expected warning, so success!";  else $(exit $retVal); fi;
+  - codespell --skip=".git,version-specific,scripts" --ignore-words-list=atleast,ninjs,simpy,proovread,namd --quiet-level=2; retVal=$?; if [ $retVal -eq 1 ]; then echo "Got one expected warning, so success!";  else $(exit $retVal); fi;
   - flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
   - READTHEDOCS=1 sphinx-build docs build
   # test installation too (using options that don't require to have a modules tool installed)

docs/Changelog.rst

@@ -5,6 +5,7 @@ Changelog for EasyBuild documentation
 
 (for EasyBuild release notes, see :ref:`release_notes`)
 
+* **release 20200708.01** (`July 8th 2020`): update release notes for EasyBuild v4.2.2 (see :ref:`release_notes_eb422`)
 * **release 20200520.01** (`May 20th 2020`): update release notes for EasyBuild v4.2.1 (see :ref:`release_notes_eb421`)
 * **release 20200414.01** (`Apr 14th 2020`):
 

docs/Implementing-easyblocks.rst

@@ -254,6 +254,44 @@ redefining it entirely, since we call out to the original ``configure_step`` met
 Specific aspects of easyblocks
 ------------------------------
 
+.. _implementing_easyblocks_default_parameters:
+
+Default easyconfig parameters
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+All of the parameters which are "set" in an easyconfig file (see :ref:`vsd_avail_easyconfig_params`)
+become key-value pairs in the ``self.cfg`` dictionary.  For instance, if the easyconfig file specifies
+
+.. code:: python
+
+  name = 'example'
+  version = '2.5.3'
+  versionsuffix = '-Python-3.7.4'
+
+then these three parameters are accessible within an easyblock via
+
+.. code:: python
+
+  longform = ''.join(self.cfg['name'],'/',self.cfg['version'],self.cfg['versionsuffix'])
+
+You can use this notation successfully in your easyblock.  A few of the most commonly used parameters can be referenced
+directly,
+
+* **self.name** = ``self.cfg['name']``
+* **self.version** = ``self.cfg['version']``
+* **self.toolchain** = ``self.cfg['toolchain']``
+* **self.all_dependencies**: combines ``builddependencies``, ``dependencies``, and ``toolchain``, in one dictionary
+
+So in your easyblock code, you may replace the above expression with
+
+.. code:: python
+
+  longform = ''.join(self.name,'/',self.version,self.cfg['versionsuffix'])
+
+The other easyconfig parameters, and any additional :ref:`custom parameters
+<implementing_easyblocks_custom_parameters>` which you define for your own easyblock, will not be automatically mapped.
+You will need to use ``self.cfg`` to access them in your code.
+
 
 .. _implementing_easyblocks_custom_parameters:
 

docs/Maintainers.rst

@@ -123,9 +123,9 @@ The EasyBuild maintainers all have admin access to the different EasyBuild GitHu
 
   * GitHub: `@casparvl <https://github.com/casparvl>`_ - e-mail: ``caspar.vanleeuwen (at) surfsara.nl`` - IRC/Slack: ``Caspar Van Leeuwen``
 
-* **Davide Vanzo** (`Vanderbilt University <http://www.accre.vanderbilt.edu/>`_)
+* **Davide Vanzo** (`Microsoft <https://www.microsoft.com/>`_)
 
-  * GitHub: `@vanzod <https://github.com/vanzod>`_ - e-mail: ``davide.vanzo (at) vanderbilt.edu`` - IRC/Slack: ``vanzod``
+  * GitHub: `@vanzod <https://github.com/vanzod>`_ - e-mail: ``davide.vanzo (at) microsoft.com`` - IRC/Slack: ``vanzod``
 
 * **Lars Viklund** (`Umeå University, Sweden <http://www.umu.se/english/>`_)
 

docs/Writing_easyconfig_files.rst

@@ -197,7 +197,7 @@ Using the ``--inject-checksums`` command line option, you can let EasyBuild add
 in one or more easyconfig files (which is significantly more convenient than doing it manually).
 
 With ``--inject-checksums``, checksums are injected for all sources and patches (if any),
-as well as for all sources & patches of every extension listed in ``exts_list`` (if any).
+as well as for all sources & patches of every extension listed in ``exts_list`` (if any, see :ref:`module_extensions`).
 
 If the sources (& patches) are not available yet, EasyBuild will try to download them first; i.e.,
 the ``fetch`` step is run prior to computing & injecting the checksums.
@@ -326,7 +326,7 @@ For example, to inject checksums in *every* easyconfig file required to build HP
     ...
 
 .. note:: We are clearing ``$MODULEPATH`` and specifying a custom (empty) location to ``--installpath`` to
-          avoid that EasyBuild skips any easyconfigs because a corresponding module is already available.
+          avoid that EasyBuild skips any easyconfig because a corresponding module is already available.
 
 .. _inject_checksums_type:
 
@@ -510,12 +510,87 @@ which is equivalent to::
 
   dependencies = [('PnMPI', '1.2.0', '', True)]
 
+
 Using external modules as dependencies
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Since EasyBuild v2.1, specifying modules that are not provided via EasyBuild as dependencies is also supported.
 See :ref:`using_external_modules` for more information.
 
+
+Extensions
+~~~~~~~~~~
+
+Besides dependencies, which are found outside the software being built but are part of the site's EasyBuild installation,
+it is also possible to incorporate extensions to the software within the build.  This is done via the ``exts_list`` array.
+
+Each entry in ``exts_list`` is a three-component tuple, with the name and
+version number, and a dictionary of configuration options for the entry:
+
+.. code:: python
+
+  exts_list = [
+      ('name', 'version', { 'option':'value', 'option':'value' })
+  ]
+
+The latter may contain essentially any of the full easyconfig parameters, including ``buildopts``, ``installopts``, etc.
+Among those options, the following exceptions and special cases should be noted:
+
+* **nosource**: If set ``True``, no download will be done
+* **source_tmpl**: Template string for the file to be downloaded
+  * default is ``'%(name)s-%(version)s.tar.gz'``
+  * ``%(name)s`` and ``%(version)s`` come from the ``exts_list`` entry (above)
+* **sources**: Dictionary specifying details of where to download the extension
+  * equivalent to a single entry from the easyconfig ``sources`` list
+  * preferred to use of ``source_tmpl``
+* **start_dir**: If not set, will be derived; the easyconfig value will not be used
+
+.. code:: python
+
+  exts_list = [
+      ('llvmlite', '0.26.0', {
+          'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'],
+          'patches': ['llvmlite-0.26.0_fix-ffi-Makefile.patch'],
+          'checksums': [
+              '13e84fe6ebb0667233074b429fd44955f309dead3161ec89d9169145dbad2ebf',    # llvmlite-0.26.0.tar.gz
+              '40e6fe6de48709b45daebf8082f65ac26f73a4afdf58fc1e8099b97c575fecae',    # llvmlite-0.26.0_fix-ffi-Makefile.patch
+          ],
+      }),
+      ('singledispatch', '3.4.0.3', {
+          'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'],
+          'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'],
+      }),
+      (name, version, {
+          'source_urls': ['https://pypi.python.org/packages/source/n/numba/'],
+          'checksums': ['c62121b2d384d8b4d244ef26c1cf8bb5cb819278a80b893bf41918ad6d391258'],
+      }),
+  ]
+
+That third instance uses the ``name`` and ``version`` variables defined in the easyconfig file.  Since EasyBuild
+v4.2.2, a single-entry ``sources`` dictionary (see :ref:`_common_easyconfig_param_sources_alt`) may be included in an
+``exts_list`` entry.  For example, to download Git sources from a private repository and convert them to a tar-ball for
+installation:
+
+.. code:: python
+
+  exts_defaultclass = 'PythonPackage'
+  exts_list = [
+      ('pyCAP', '0.1', {
+          'sources': {
+              'filename': '%(name)s-%(version)s.tar.gz',
+              'git_config': {
+                  'url': 'ssh://nero.stanford.edu/data/git/Analysis',
+                  'repo_name': 'pyCAP',
+                  'tag': '%(version)s',
+              }
+          }
+      }),
+  ]
+
+Here, the template strings ``%(name)s`` and ``%(version)s`` will be substituted from the
+``exts_list`` entry elements ("pyCAP" and "0.1", respectively), not from the easyconfig values.
+
+
 .. _configure_build_install_command_options:
 
 Configure/build/install command options

docs/conf.py

@@ -41,9 +41,9 @@
 # other places throughout the built documents.
 #
 # The short X.Y version.
-version = '4.2.1'  # this is meant to reference the version of EasyBuild
+version = '4.2.2'  # this is meant to reference the version of EasyBuild
 # The full version, including alpha/beta/rc tags.
-release = '20200520.0'  # this is meant to reference the version of the documentation itself
+release = '20200708.0'  # 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: