Fix/add option: do not compile fim c-extension (NeuralEnsemble#494)

* add extra no_cpp to avoid compiling of fim.cpp

* added description for no_cpp to installation documentation

* add new command "nofim" to setup.py

* add general --no-compile option, prepared for more extensions which can be individually turned off

* fix pep8

* add link for the install option to not compile also in the SPADE documentation page notes.

* add documentation for for 'no-compile' option

* add documentation for for 'no-compile-spade' option

* update reference to spade from CAD

* merge master, fix CI

.github/workflows/build_wheels.yml

@@ -11,7 +11,6 @@ on:
 # Building wheels on Ubuntu and Windows systems
 jobs:
   build_wheels:
-    if: github.event.review.state == 'approved'
     name: Build wheels on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:

doc/install.rst

@@ -42,7 +42,6 @@ Elephant requires `Python <http://python.org/>`_ 3.7, 3.8, 3.9 or 3.10.
 
            sudo apt-get install python-pip python-numpy python-scipy python-pip python-six python-tqdm
 
-
 ************
 Installation
 ************
@@ -65,7 +64,6 @@ Installation
 
               pip install elephant[extras]
 
-
         To upgrade to a newer release use the ``--upgrade`` flag:
 
            .. code-block:: sh
@@ -210,6 +208,37 @@ You can have one, both, or none installed in your system.
             using your graphics card to perform computations may make the system
             unresponsive until the compute program terminates.
 
+.. _no-compile-spade:
+***********
+Resolving compilation issues
+***********
+
+Some modules in Elephant make use of C extensions to speed up computation.
+However, those extensions need to be compiled before use. In some cases, this
+causes problems. For example, the compiler on the current machine does not
+fulfill the requirements for the extension, certain libraries are missing,
+or no compiler is available at all.
+
+In order to circumvent this problem, the following commands allow to avoid the
+compilation for specific or for all C extensions.
+
+.. tabs::
+
+    .. tab:: general
+        Use the following to install elephant without C extensions:
+
+        .. code-block:: sh
+
+            pip install elephant --install-option='--no-compile'
+
+    .. tab:: spade
+        To avoid compilation of the c++ extension ``fim.cpp`` used in :ref:`spade`, install the package with:
+
+        .. code-block:: sh
+
+            pip install elephant --install-option='--no-compile-spade'
+
+        In this case the pure python implementation of :ref:`spade` is still available.
 
 ************
 Dependencies

doc/reference/spade.rst

@@ -1,3 +1,5 @@
+.. _spade:
+
 ==============================================
 Spike Pattern Detection and Evaluation (SPADE)
 ==============================================

elephant/cell_assembly_detection.py

@@ -31,7 +31,7 @@
 
 See Also
 --------
-elephant.spade.spade : advanced synchronous patterns detection
+:ref:`spade` : advanced synchronous patterns detection
 
 Examples
 --------

elephant/spade.py

@@ -19,25 +19,36 @@
 
 Visualization
 -------------
-Visualization of SPADE analysis is covered in Viziphant:
+Visualization of SPADE analysis is covered in Viziphant e.g.:
+:func:`viziphant.patterns.plot_patterns_statistics_all`
+
+See Viziphant for more information:
+
 https://viziphant.readthedocs.io/en/latest/modules.html
 
 
 Notes
 -----
-This modules relies on the C++ implementation of the fp-growth algorithm developed by
-Forian Porrmann (available at https://github.com/fporrmann/FPG). The module replaces
-a more generic implementation of the algorithm by Christian Borgelt
-(http://www.borgelt.net/pyfim.html) that was used in previous versions of Elephant.
-If the module (fim.so) is not available in a precompiled format (currently Linux/Windows) or cannot
-be compiled on a given system during install, SPADE will make use of a pure Python implementation
-of the fast fca algorithm contained in `elephant/spade_src/fast_fca.py`, which is
+This modules relies on the C++ implementation of the fp-growth
+algorithm developed by Forian Porrmann (available at
+https://github.com/fporrmann/FPG). The module replaces a more generic
+implementation of the algorithm by Christian Borgelt (
+http://www.borgelt.net/pyfim.html) that was used in previous versions of
+Elephant.
+
+If the module ``fim.so`` is not available in a precompiled format (
+currently Linux/Windows) or cannot be compiled on a given system during
+install, SPADE will make use of a pure Python implementation of the fast fca
+algorithm contained in `elephant/spade_src/fast_fca.py`, which is
 significantly slower.
 
+See :ref:`no-compile-spade` on how to install elephant without compiling the
+``fim.so`` module.
+
 
 See Also
 --------
-elephant.cell_assembly_detection.cell_assembly_detection : another synchronous
+:doc:`cell_assembly_detection`: another synchronous
 patterns detection
 
 
@@ -984,7 +995,7 @@ def _rereference_to_last_spike(transactions, winlen):
         neurons[idx] = attribute // winlen
         bins[idx] = attribute % winlen
 
-    # rereference bins to last spike
+    # reference bins to last spike
     bins = bins.max() - bins
 
     # calculate converted transactions

setup.py

@@ -1,8 +1,11 @@
 # -*- coding: utf-8 -*-
 import os.path
 import platform
+import sys
 
 from setuptools import setup, Extension
+from setuptools.command.install import install
+from setuptools.command.develop import develop
 
 with open(os.path.join(os.path.dirname(__file__),
                        "elephant", "VERSION")) as version_file:
@@ -26,7 +29,9 @@
         libraries=[],
         extra_compile_args=[
             '-DMODULE_NAME=fim', '-DUSE_OPENMP', '-DWITH_SIG_TERM',
-            '-Dfim_EXPORTS', '-fopenmp', '/std:c++17'])
+            '-Dfim_EXPORTS', '-fopenmp', '/std:c++17'],
+        optional=True
+    )
 elif platform.system() == "Darwin":
     fim_module = Extension(
         name='elephant.spade_src.fim',
@@ -39,7 +44,9 @@
             '-Dfim_EXPORTS', '-O3', '-pedantic', '-Wextra',
             '-Weffc++', '-Wunused-result', '-Werror', '-Werror=return-type',
             '-Xpreprocessor',
-            '-fopenmp', '-std=gnu++17'])
+            '-fopenmp', '-std=gnu++17'],
+        optional=True
+    )
 elif platform.system() == "Linux":
     fim_module = Extension(
         name='elephant.spade_src.fim',
@@ -51,7 +58,9 @@
             '-DMODULE_NAME=fim', '-DUSE_OPENMP', '-DWITH_SIG_TERM',
             '-Dfim_EXPORTS', '-O3', '-pedantic', '-Wextra',
             '-Weffc++', '-Wunused-result', '-Werror',
-            '-fopenmp', '-std=gnu++17'])
+            '-fopenmp', '-std=gnu++17'],
+        optional=True
+    )
 
 setup_kwargs = {
     "name": "elephant",
@@ -87,9 +96,89 @@
         'Programming Language :: Python :: 3 :: Only',
         'Topic :: Scientific/Engineering']
 }
-# do not compile external modules on darwin
-if platform.system() in ["Windows", "Linux"]:
-    setup_kwargs["ext_modules"] = [fim_module]
 
+# no compile options and corresponding extensions
+options = {"--no-compile": None, "--no-compile-spade": fim_module}
+# check if any option was specified
+if not any([True for key in options.keys() if key in sys.argv]):
+    if platform.system() in ["Windows", "Linux"]:
+        setup_kwargs["ext_modules"] = [fim_module]
+else:  # ...any option was specified
+    # select extensions accordingly
+    extensions = [module for flag, module in options.items() if
+                  flag not in sys.argv]
+    if None in extensions:  # None indicates "--no-compile" not in sys.argv
+        extensions.remove(None)
+        setup_kwargs["ext_modules"] = extensions
+
+
+class CommandMixin(object):
+    """
+    This class acts as a superclass to integrate new commands in setuptools.
+    """
+    user_options = [
+        ('no-compile', None, 'do not compile any C++ extension'),
+        ('no-compile-spade', None, 'do not compile spade related C++ extension')  # noqa
+    ]
+
+    def initialize_options(self):
+        """
+        The method is responsible for setting default values for
+        all the options that the command supports.
+
+        Option dependencies should not be set here.
+        """
+
+        super().initialize_options()
+        # Initialize options
+        self.no_compile_spade = None
+        self.no_compile = None
+
+    def finalize_options(self):
+        """
+        Overriding a required abstract method.
+
+        This method is responsible for setting and checking the
+        final values and option dependencies for all the options
+        just before the method run is executed.
+
+        In practice, this is where the values are assigned and verified.
+        """
+
+        super().finalize_options()
+
+    def run(self):
+        """
+        Sets global which can later be used in setup.py to remove c-extensions
+        from setup call.
+        """
+        # Use options
+        global no_compile_spade
+        global no_compile
+        no_compile_spade = self.no_compile_spade
+        no_compile = self.no_compile
+
+        super().run()
+
+
+class InstallCommand(CommandMixin, install):
+    """
+    This class extends setuptools.command.install class, adding user options.
+    """
+    user_options = getattr(
+        install, 'user_options', []) + CommandMixin.user_options
+
+
+class DevelopCommand(CommandMixin, develop):
+    """
+    This class extends setuptools.command.develop class, adding user options.
+    """
+    user_options = getattr(
+        develop, 'user_options', []) + CommandMixin.user_options
+
+
+# add classes to setup-kwargs to add the user options
+setup_kwargs['cmdclass'] = {'install': InstallCommand,
+                            'develop': DevelopCommand}
 
 setup(**setup_kwargs)