Merge pull request #777 from apdavison/pyproject.toml

Switch to pyproject.toml

Author: apdavison

MANIFEST.in

@@ -4,7 +4,6 @@ include pyNN/nest/extensions/*.cpp
 include pyNN/nest/extensions/CMakeLists.txt
 include pyNN/nest/extensions/sli/*
 include pyNN/descriptions/templates/*/*.txt
-include test/parameters/*
 include test/system/*.py
 include test/system/scenarios/*.py
 include test/unittests/*.py

doc/conf.py

@@ -76,9 +76,9 @@ class MockNESTModule(mock.Mock):
 # built documents.
 #
 # The short X.Y version.
-version = '0.10'
+version = '0.11'
 # The full version, including alpha/beta/rc tags.
-release = '0.10.2.dev'
+release = '0.11.0.dev'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/developers/contributing.txt

@@ -43,10 +43,6 @@ To work on the development version::
 
     $ git checkout master
 
-To work on the latest stable release (for bug-fixes)::
-
-    $ git checkout --track origin/0.8
-
 To keep your PyNN repository up-to-date with respect to the official
 repository, add it as a remote::
 
@@ -62,12 +58,7 @@ To get PyNN onto your :envvar:`PYTHONPATH` there are many options, such as:
     * pip editable mode (`pip install -e /path/to/PyNN`)
     * creating a symbolic link named :file:`pyNN` from somewhere that is already
       on your :envvar:`PYTHONPATH`, such as the :file:`site-packages` directory,
-      to the :file:`pyNN_trunk/pyNN` directory.
-
-If you are developing with NEURON, don't forget to compile the NMODL files in
-:file:`pyNN/neuron/nmodl` by running :command:`nrnivmodl`, and to recompile any time
-you modify any of them.
-
+      to the :file:`pyNN_dev/pyNN` directory.
 
 Coding style
 ============
@@ -80,7 +71,7 @@ We try to stay fairly close to PEP8_. Please note in particular:
     - some function/method names in PyNN use ``mixedCase``, but these will
       gradually be deprecated and replaced with ``lower_case_with_underscores``.
       Any new functions or methods should use the latter.
-    - we currently target versions 2.7 and 3.6+
+    - we currently target versions 3.8+
 
 
 Testing
@@ -190,16 +181,16 @@ last time:
       you should do this on at least two Linux systems and one Mac OS X system.
     * does the documentation build without errors? You should then at least skim
       the generated HTML pages to check for obvious problems.
-    * have you updated the version numbers in :file:`setup.py`, :file:`pyNN/__init__.py`,
+    * have you updated the version numbers in :file:`pyproject.toml`, :file:`pyNN/__init__.py`,
       :file:`doc/conf.py` and :file:`doc/installation.txt`?
     * have you updated the changelog?
 
-Once you've confirmed all the above, create a source package using::
+Once you've confirmed all the above, create source and wheel packages using::
 
-    $ python setup.py sdist
+    $ python -m build
 
-and check that it installs properly (you will find it in the :file:`dist`
-subdirectory.
+and check that they install properly (you will find them in the :file:`dist`
+subdirectory).
 
 Now you should commit any changes, then tag with the release number as follows::
 
@@ -213,24 +204,16 @@ to http://neuralensemble.org/docs/PyNN/ by running::
 in the :file:`doc` directory, and then unpacking the resulting archive on the
 NeuralEnsemble server.
 
-If this is a development release (i.e. an *alpha* or *beta*), the final step is
-to upload the source package to the INCF Software Center.
-Do **not** upload development releases to PyPI.
-
-To upload a package to the INCF Software Center, log-in, and then go to the
-Contents_ tab. Click on "Add new..." then "File", then fill in the form and
-upload the source package.
-
 If this is a final release, there are a few more steps:
 
     * if it is a major release (i.e. an ``x.y.0`` release), create a new bug-fix
       branch::
 
         $ git branch x.y
 
-    * upload the source package to PyPI::
+    * upload the packages to PyPI (Do **not** upload development releases to PyPI)::
 
-        $ python setup.py sdist upload
+        $ twine upload dist/PyNN-x.y.z*
 
     * make an announcement on the `mailing list`_
 

doc/installation.txt

@@ -7,7 +7,7 @@ install and run PyNN on Windows, but this has not been tested.
 
 Installing PyNN requires:
 
-    * Python (version 3.7+)
+    * Python (version 3.8+)
     * a recent version of the NumPy_ package
     * the lazyarray_ package
     * the Neo_ package (>= 0.11.0)
@@ -32,9 +32,8 @@ The easiest way to get PyNN is to use pip_::
 If you would prefer to install manually, :doc:`download the latest
 source distribution <download>`, then run the setup script, e.g.::
 
-    $ tar xzf PyNN-0.10.1.tar.gz
-    $ cd PyNN-0.10.1
-    $ python setup.py install
+    $ tar xzf PyNN-0.11.0.tar.gz
+    $ pip install ./PyNN-0.11.0
 
 This will install it to your Python :file:`site-packages` directory, and may
 require root privileges. We strongly recommend, however, that you use a
@@ -55,30 +54,25 @@ Test it using something like the following::
    If you get a warning "Unable to install NEST extensions. Certain models may not be available" then ensure the
    program :command:`nest-config` is on your system PATH.
    If you still get this message even after adding the directory containing :command:`nest-config` to the PATH,
-   try ``pip uninstall PyNN``, then re-install with ``pip install --no-binary :all: PyNN``
+   then you will still be able to use pyNN.nest, just a small number of models will not be available.
 
-With NEURON as the simulator, make sure you install NEURON *before* you install PyNN.
-The PyNN installation will then compile PyNN-specific membrane mechanisms, which are loaded when importing the :mod:`neuron` module::
+For NEURON, PyNN will compile PyNN-specific membrane mechanisms the first time you import the :mod:`neuron` module::
 
     >>> import pyNN.neuron as sim
-    NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09
-    Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015
-    See http://www.neuron.yale.edu/neuron/credits
-
-    loading membrane mechanisms from /home/docker/dev/PyNN/pyNN/neuron/nmodl/x86_64/.libs/libnrnmech.so
-    Additional mechanisms from files
-     adexp.mod alphaisyn.mod alphasyn.mod expisyn.mod gap.mod gsfa_grr.mod hh_traub.mod
-     izhikevich.mod netstim2.mod refrac.mod reset.mod stdwa_guetig.mod stdwa_softlimits.mod
-     stdwa_songabbott.mod stdwa_symm.mod stdwa_vogels2011.mod tmgsyn.mod tmisyn.mod
-     tsodyksmarkram.mod vecstim.mod
 
-If you installed PyNN before installing NEURON, or if you update your PyNN installation,
-you will need to manually run :command:`nrnivmodl` in the :file:`pyNN/neuron/nmodl` directory.
 
 Installing NEURON
 =================
 
-Download the sources for NEURON 7.4 or later, in ``.tar.gz`` format, from `<http://www.neuron.yale.edu/neuron/download/getstd>`_.
+For recent versions of NEURON,
+
+::
+
+    $ pip install neuron
+
+may be all you need. If you have more complex needs, try the following.
+
+Download the sources for NEURON 8.0 or later, in ``.tar.gz`` format, from `<http://www.neuron.yale.edu/neuron/download/getstd>`_.
 Also download Interviews from the same location.
 
 Compile Interviews and NEURON according to the instructions given at `<http://www.neuron.yale.edu/neuron/static/download/compilestd_unix.html>`_,
@@ -92,9 +86,9 @@ Make sure that you add the Interviews and NEURON :file:`bin` directories to your
 Test that the Python support has been enabled by running::
 
     $ nrniv -python
-    NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09
-    Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015
-    See http://www.neuron.yale.edu/neuron/credits
+    NEURON -- VERSION 8.2.2 release/8.2 (93d41fafd) 2022-12-15
+    Duke, Yale, and the BlueBrain Project -- Copyright 1984-2022
+    See http://neuron.yale.edu/neuron/credits
 
     >>> import hoc
     >>> import nrn
@@ -108,35 +102,31 @@ Now test everything worked::
 
     $ python
     >>> import neuron
-    NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09
-    Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015
-    See http://www.neuron.yale.edu/neuron/credits
 
 If you run into problems, check out the `NEURON Forum`_.
 
 
 Installing NEST and PyNEST
 ==========================
 
-NEST 2.18.0 can be downloaded from `<http://www.nest-simulator.org/download/>`_.
+NEST 3.4 can be downloaded from `<http://www.nest-simulator.org/download/>`_.
 Earlier versions of NEST may not work with this version of PyNN.
-The full installation instructions are available in the file INSTALL, which you can find in the NEST source package,
-or at `<http://www.nest-simulator.org/installation/>`_.
+The full installation instructions are available at `<https://nest-simulator.readthedocs.io/en/v3.4/installation/index.html/>`_.
 
 Now try it out::
 
     $ cd ~
     $ python
     >>> import nest
-                 -- N E S T --
-      Copyright (C) 2004 The NEST Initiative
 
-    Version: v2.20.0
+                -- N E S T --
+    Copyright (C) 2004 The NEST Initiative
 
+    Version: 3.4
     ...
-    >>> nest.Models()
-    (u'ac_generator', u'aeif_cond_alpha', u'aeif_cond_alpha_RK5', u'aeif_cond_alpha_multisynapse',
-    ...
+
+    >>> nest.node_models
+    ('weight_recorder', 'gauss_rate_ipn', 'lin_rate_ipn', 'sigmoid_rate_ipn', 'sigmoid_rate_gg_1998_ipn', 'tanh_rate_ipn', ...)
 
 Check that ``'aeif_cond_alpha'`` is in the list of models. If it is not, you may need to install a newer version of the `GNU Scientific Library`_ and then recompile NEST.
 

pyNN/__init__.py

@@ -69,7 +69,8 @@
 :license: CeCILL, see LICENSE for details.
 """
 
-__version__ = '0.10.2.dev'
+__version__ = '0.11.0.dev'
 __all__ = ["common", "random", "nest", "neuron", "brian2",
            "recording", "errors", "space", "descriptions",
-           "standardmodels", "parameters", "core", "serialization"]
+           "standardmodels", "parameters", "core", "serialization",
+           "utility"]

pyNN/core.py

@@ -5,6 +5,8 @@
 :license: CeCILL, see LICENSE for details.
 """
 
+import os
+import subprocess
 import warnings
 import numpy as np
 
@@ -56,6 +58,27 @@ def ezip(*args):
         yield items[0], items[1:]
 
 
+def find(command):
+    """Try to find an executable file."""
+    path = os.environ.get("PATH", "").split(os.pathsep)
+    cmd = ''
+    for dir_name in path:
+        abs_name = os.path.abspath(os.path.normpath(os.path.join(dir_name, command)))
+        if os.path.isfile(abs_name):
+            cmd = abs_name
+            break
+    return cmd
+
+
+def run_command(path, working_directory):
+    p = subprocess.Popen(path, shell=True, stdin=subprocess.PIPE,
+                         stdout=subprocess.PIPE, stderr=subprocess.STDOUT,
+                         universal_newlines=True,
+                         cwd=working_directory)
+    stdout, stderr = p.communicate()
+    return p.returncode, stdout.split("\n")
+
+
 class IndexBasedExpression(object):
     """
     Abstract base class for general expressions that use the cell indices and projection class to

pyNN/nest/simulator.py

@@ -19,13 +19,16 @@
 :license: CeCILL, see LICENSE for details.
 """
 
-import nest
+import os.path
 import logging
 import tempfile
 import warnings
 import numpy as np
+
+import nest
+
 from .. import common
-from ..core import reraise
+from ..core import reraise, find, run_command
 
 logger = logging.getLogger("PyNN")
 name = "NEST"  # for use in annotating output data
@@ -39,6 +42,57 @@
 NEST_ARRAY_VARIABLES_TIME_DIMENSION = ("spike_times", "amplitude_times", "rate_times")
 
 
+# --- Building extensions ------------------------------------------------------
+
+def build_extensions(build_dir=None):
+    nest_config = find("nest-config")
+    if not nest_config:
+        warnings.warn("Cannot find nest-config, please check your PATH. Unable to build extensions.")
+        return
+
+    logger.debug("nest-config found at", nest_config)
+
+    build_dirs = []
+    if build_dir is not None:
+        build_dirs.append(build_dir)
+    # if a specific build directory is not provided,
+    # first try to build within the pyNN source dir
+    build_dirs.append(os.path.join(os.path.dirname(__file__), "_build"))
+    # if that directory is not writable, build in the current working directory
+    build_dirs.append(os.path.join(os.getcwd(), "_build", "nest_extensions"))
+
+    for nest_build_dir in build_dirs:
+        try:
+            os.makedirs(nest_build_dir, exist_ok=True)
+        except OSError:
+            continue
+        if os.access(nest_build_dir, os.W_OK):
+            break
+
+    if not os.access(nest_build_dir, os.W_OK):
+        warnings.warn("Cannot create build directory for nest extensions")
+        return
+
+    source_dir = os.path.join(os.path.dirname(__file__), "extensions")
+    result, stdout = run_command(f"cmake -Dwith-nest={nest_config} {source_dir}",
+                                 nest_build_dir)
+    if result != 0:
+        err_msg = "\n  ".join(stdout)
+        warnings.warn(f"Problem running cmake. Output was:\n  {err_msg}")
+    else:
+        result, stdout = run_command("make", nest_build_dir)
+        if result != 0:
+            err_msg = "\n  ".join(stdout)
+            warnings.warn(f"Unable to compile NEST extensions. Output was:\n  {err_msg}")
+        else:
+            result, stdout = run_command("make install", nest_build_dir)
+            if result != 0:
+                err_msg = "\n  ".join(stdout)
+                warnings.warn(f"Unable to install NEST extensions. Output was:\n  {err_msg}")
+            else:
+                logger.info("Successfully compiled NEST extensions.")
+
+
 # --- For implementation of get_time_step() and similar functions --------------
 
 
@@ -77,7 +131,12 @@ def __init__(self):
             nest.Install('pynn_extensions')
             self.extensions_loaded = True
         except nest.NESTError:
-            self.extensions_loaded = False
+            build_extensions()
+            try:
+                nest.Install('pynn_extensions')
+                self.extensions_loaded = True
+            except nest.NESTError:
+                self.extensions_loaded = False
         self.initialized = False
         self.optimize = False
         self.spike_precision = "off_grid"