cellml.recipe.api 0.8

Recipe to call CMake to build CellML API and Python bindings

Overview

This is the recipe that will build the CellML API Python bindings with all options enabled by default. Currently, there are some limitations, such as all dependencies required to build the CellML API must be installed before this recipe can be used, and I don’t think this will work under Windows at the moment.

Supported options

The recipe supports the following options:

api-version

CellML API version to build. Valid versions any versions that build via CMake and has Python bindings (>1.10), and must be present in the list of valid versions.

cmake-generator

The generator to use. Only the default option Unix Makefiles is supported, as this recipe is built on top of zc.recipe.cmmi which will make use of make and make install.

check-build

Whether to check build time dependencies. Default is off because it didn’t detect GSL libraries even though it was installed for me. Same as passing -DCHECK_BUILD:BOOL=OFF to cmake.

Other supported options:

• enable-examples

• enable-annotools

• enable-ccgs

• enable-celeds

• enable-celeds-exporter

• enable-cevas

• enable-cis

• enable-cuses

• enable-gsl-integrators

• enable-malaes

• enable-python

• enable-rdf

• enable-spros

• enable-srus

• enable-telicems

• enable-vacss

Please refer to the CellML API Documentations for what these options do.

Usage

As this egg is published on pypi, this recipe can be used right away by including a new part inside a buildout.cfg. The following is an example configuration:

[buildout]
parts =
    ...
    cellml-api
    cellmlpy

[cellml-api]
recipe = cellml.recipe.api
api-version = 1.10

[cellmlpy]
recipe = zc.recipe.egg
eggs =
interpreter = cellmlpy
scripts = cellmlpy
extra-paths = ${cellml-api:location}/lib/python

This example buildout.cfg will build the CellML API v1.10 with all the supported options enabled, and a script will be generated in bin/cellmlpy which will allow the bindings to be imported without setting PYTHONPATH and other related environmental variables. Please refer to the examples directory for more detailed instructions and other example usages of this recipe.

Copyright/License information

This software is released under the MPL/GPL/LGPL licenses.

Please refer to the file COPYING.txt for detailed copyright information, and docs directory for specific licenses that this software is released under.

Change history

0.8 (2022-04-27)

• Force a known supported CXX standard because newest gcc defaults to the incompatible c++17 standard.

0.7 (2019-01-23)

• Update distribution location.

0.6 (2018-07-31)

• Python 3 compatibility.

0.5 (2018-01-23)

• Added latest version of CellML API on github.

• Added RUNPATH into place.

0.4 (2012-11-05)

• Added CellML API 1.12.

0.3 (2012-10-03)

• Corrected typo for the TeLICeM flag.

• Added CellML API 1.11.

0.2 (2011-09-21)

• Fixed the issue where all the expected keys are assigned with an empty string even if unassigned; this caused various unwanted side effects.

• Fixed the issue where the location of this buildout recipe is undefined.

0.1 (2011-09-21)

• Initial release of the CellML API Python bindings buildout.

Detailed Documentation

Demonstration

This recipe extends on the zc.recipe.cmmi with the caveat where cmake is called instead of the ./configure scripts, yet have cmake generate Unix Makefiles such that the make/make install that cmmi calls will proceed as normal.

For the demonstration, instead of download/building the entire API, we are going to make use of the mock-ups (which is previous setup).

>>> ls(distros)
-  cellml-api-0.0fake.tgz

>>> distros_url = start_server(distros)
>>> archive_url = '%scellml-api-0.0fake.tgz' % distros_url

Let’s create our buildout, but modified so that we use our fake archive.

>>> write('buildout.cfg',
... """
... [buildout]
... parts = cellml-api
...
... [cellml-api]
... recipe = cellml.recipe.api
... api-version = 0.0fake
... """)

As our mocked up api version is not listed as an available version, buildout will die.

>>> print('start ' + system(buildout))
start...
  Installing.
  Getting ... cellml-api.
  Initializing ... cellml-api.
...
Traceback (most recent call last):
...
ValueError: api-version `0.0fake` is not a supported version of...
<BLANKLINE>

Well, since our fake version is obviously not going to be added into the listing of supported APIs, we can still provide our url and md5sum, as the original function provided by zc.recipe.cmmi is still in effect. Rewrite buildout.cfg with the desired attributes.

>>> try: from hashlib import md5
... except ImportError: from md5 import new as md5
>>> m = md5(open(join(distros, 'cellml-api-0.0fake.tgz'), 'rb'
...             ).read()).hexdigest()
>>> write('buildout.cfg',
... """
... [buildout]
... parts = cellml-api
...
... [cellml-api]
... recipe = cellml.recipe.api
... url = %s
... md5sum = %s
... """ % (archive_url, m))

>>> print('start ' + system(buildout))
start...
...
CMake Warning:
  Manually-specified variables were not used by the project:
<BLANKLINE>
    CHECK_BUILD
    ENABLE_ANNOTOOLS
    ENABLE_CCGS
    ENABLE_CELEDS
    ENABLE_CELEDS_EXPORTER
    ENABLE_CEVAS
    ENABLE_CGRS
    ENABLE_CIS
    ENABLE_CUSES
    ENABLE_EXAMPLES
    ENABLE_GSL_INTEGRATORS
    ENABLE_MALAES
    ENABLE_PYTHON
    ENABLE_RDF
    ENABLE_SPROS
    ENABLE_SRUS
    ENABLE_TELICEMS
    ENABLE_VACSS
<BLANKLINE>
<BLANKLINE>
<BLANKLINE>

Contributors

Tommy Yu, Author

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