dbbs-lab · Helveg · May 27, 2020 · May 27, 2020 · Jul 13, 2020 · Jul 13, 2020
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,4 @@
+__pycache__
+*.egg-info
+dist/*
+build/*
diff --git a/.pipnest/settings b/.pipnest/settings
@@ -0,0 +1,3 @@
+{
+
+}
diff --git a/.travis.yml b/.travis.yml
@@ -1,9 +1,12 @@
-language: generic
+language: python
 dist: bionic
 cache:
   pip: true
   directories:
     - $HOME/nest-$NEST_VERSION
+jobs:
+  include:
+    python: 3.6.9
 install:
   - export NEST_INSTALL_DIR=/home/travis/nest-$NEST_VERSION
   - source devops/check_nest_cache.sh
@@ -13,7 +16,10 @@ install:
     else
       echo "NEST cache found, skipping installation";
     fi
-  - source devops/install_cereb_nest.sh
-  - source devops/post_install_env_vars.sh
+  - export PYTHONPATH=/home/travis/nest-$NEST_VERSION/lib/python3.6/site-packages:$PYTHONPATH
+  - export NEST_MODULE_PATH=/home/travis/nest-$NEST_VERSION/lib/nest:$NEST_MODULE_PATH
+  - export SLI_PATH=/home/travis/nest-$NEST_VERSION/share/sli:$SLI_PATH
+  - python -m pip install .
 script:
-  - python3 -c "import nest; nest.Install('cerebmodule')"
+  - python /home/travis/build/dbbs-lab/cereb-nest/tests/test_install.py
+  - python -c "import nest; nest.Install('cerebmodule')"
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -0,0 +1,4 @@
+include cereb_nest/*
+include cereb_nest/sli/*
+include setup.py
+include README.md
diff --git a/README.md b/README.md
@@ -1,15 +1,36 @@
-[![Build Status](https://travis-ci.com/dbbs-lab/cereb-nest.svg?branch=master)](https://travis-ci.com/dbbs-lab/cereb-nest)
+# cereb_nest
 
-# cereb-nest
+pip installable NEST extension module, generated by pipnest.
 
-Tested with:
+## Installation instructions
 
-*branch master*: Ubuntu 18.04 and Red Hat Enterprise Linux Server 7.7 (Maipo), Python 3.7.3 and NEST Release 2.18.0
+### Using pip
 
+When installed through pip the module is built for you with CMake outside of the python
+package folder, this means that pip cannot track the real installation status. To
+uninstall and reinstall see [Uninstallation](Uninstallation).
 
-### Installation instructions
+0. Install NEST following the instructions provided here (https://www.nest-simulator.org/)
 
-0. Install NEST following the instructions provided here (http://www.nest-simulator.org/)
+1. Install using pip
+
+```
+pip install cereb_nest --no-cache-dir
+```
+
+3. Load the module after importing nest:
+
+```
+import nest
+nest.Install("cerebmodule")
+```
+
+#### Uninstallation
+
+To uninstall this module use `pip uninstall cereb_nest` and remove the
+`(lib)cerebmodule.so` files from the `lib/nest/` directory in your nest installation.
+
+### Using CMake
 
 1. Export an Environment Variable containing the installation directory of NEST. E.g.:
 ```
@@ -20,14 +41,15 @@ export NEST_INSTALL_DIR=$HOME/nest-simulator-install
 cd $HOME
 git clone https://github.com/dbbs-lab/cereb-nest/
 ```
-3. Move to cereb-nest directory and create a new folder where you will build the extension module
+3. Move to the cereb-nest directory and create a new folder where you will build the extension module
 ```
-mkdir $HOME/cereb-nest-build
-cd $HOME/cereb-nest-build
+cd cereb-nest
+mkdir build
+cd build
 ```
 4. Run the following CMake command (Tested with CMake 3.2.2)
 ```
-cmake -Dwith-nest=${NEST_INSTALL_DIR}/bin/nest-config $HOME/cereb-nest
+cmake -Dwith-nest=${NEST_INSTALL_DIR}/bin/nest-config ../cereb_nest
 ```
 
 The resulting output should be something similar to:
@@ -56,7 +78,7 @@ Make sure to set the environment variables:
  [...]
 ```
 
-5. Execute the last two lines, generated by the CMake command. 
+5. Execute the last two lines, generated by the CMake command.
 ```
 export NEST_MODULE_PATH=/home/alberto/nest-simulator-install/lib/nest:$NEST_MODULE_PATH
 export SLI_PATH=/home/alberto/nest-simulator-install/share/nest/sli:$SLI_PATH

diff --git a/CMakeLists.txt → cereb_nest/CMakeLists.txt b/CMakeLists.txt → cereb_nest/CMakeLists.txt
diff --git a/LICENSE → cereb_nest/LICENSE b/LICENSE → cereb_nest/LICENSE
diff --git a/Sgritta2017.h → cereb_nest/Sgritta2017.h b/Sgritta2017.h → cereb_nest/Sgritta2017.h
diff --git a/cerebmodule.cpp → cereb_nest/cerebmodule.cpp b/cerebmodule.cpp → cereb_nest/cerebmodule.cpp
diff --git a/cerebmodule.h → cereb_nest/cerebmodule.h b/cerebmodule.h → cereb_nest/cerebmodule.h
diff --git a/eglif_cond_alpha_multisyn.cpp → cereb_nest/eglif_cond_alpha_multisyn.cpp b/eglif_cond_alpha_multisyn.cpp → cereb_nest/eglif_cond_alpha_multisyn.cpp
diff --git a/eglif_cond_alpha_multisyn.h → cereb_nest/eglif_cond_alpha_multisyn.h b/eglif_cond_alpha_multisyn.h → cereb_nest/eglif_cond_alpha_multisyn.h
diff --git a/iSTDP.h → cereb_nest/iSTDP.h b/iSTDP.h → cereb_nest/iSTDP.h
diff --git a/mynames.cpp → cereb_nest/mynames.cpp b/mynames.cpp → cereb_nest/mynames.cpp
diff --git a/mynames.h → cereb_nest/mynames.h b/mynames.h → cereb_nest/mynames.h
diff --git a/sli/cerebmodule-init.sli → cereb_nest/sli/cerebmodule-init.sli b/sli/cerebmodule-init.sli → cereb_nest/sli/cerebmodule-init.sli
diff --git a/stdp_connection_alpha.cpp → cereb_nest/stdp_connection_alpha.cpp b/stdp_connection_alpha.cpp → cereb_nest/stdp_connection_alpha.cpp
diff --git a/stdp_connection_alpha.h → cereb_nest/stdp_connection_alpha.h b/stdp_connection_alpha.h → cereb_nest/stdp_connection_alpha.h
diff --git a/stdp_connection_cosexp.cpp → cereb_nest/stdp_connection_cosexp.cpp b/stdp_connection_cosexp.cpp → cereb_nest/stdp_connection_cosexp.cpp
diff --git a/stdp_connection_cosexp.h → cereb_nest/stdp_connection_cosexp.h b/stdp_connection_cosexp.h → cereb_nest/stdp_connection_cosexp.h
diff --git a/stdp_connection_sinexp.cpp → cereb_nest/stdp_connection_sinexp.cpp b/stdp_connection_sinexp.cpp → cereb_nest/stdp_connection_sinexp.cpp
diff --git a/stdp_connection_sinexp.h → cereb_nest/stdp_connection_sinexp.h b/stdp_connection_sinexp.h → cereb_nest/stdp_connection_sinexp.h
diff --git a/volume_transmitter_alberto.cpp → cereb_nest/volume_transmitter_alberto.cpp b/volume_transmitter_alberto.cpp → cereb_nest/volume_transmitter_alberto.cpp
diff --git a/volume_transmitter_alberto.h → cereb_nest/volume_transmitter_alberto.h b/volume_transmitter_alberto.h → cereb_nest/volume_transmitter_alberto.h
diff --git a/devops/install_cereb_nest.sh b/devops/install_cereb_nest.sh
@@ -2,7 +2,7 @@ PREVIOUS_DIR=$PWD
 mkdir build
 cd build
 CEREBNEST_BUILD_DIR=$PWD
-cmake -Dwith-nest=${NEST_INSTALL_DIR}/bin/nest-config ..
+cmake -Dwith-nest=${NEST_INSTALL_DIR}/bin/nest-config ../cereb_nest
 export NEST_MODULE_PATH=${NEST_INSTALL_DIR}/lib/nest:$NEST_MODULE_PATH
 export SLI_PATH=${NEST_INSTALL_DIR}/share/nest/sli:$SLI_PATH
 make

diff --git a/devops/install_nest.sh b/devops/install_nest.sh
@@ -3,12 +3,18 @@ echo "Empty cache, starting NEST v$NEST_VERSION installation."
 echo ""
 export MY_BEFORE_DIR=$PWD
 cd /home/travis
-wget https://github.com/nest/nest-simulator/archive/v$NEST_VERSION.tar.gz -O nest-simulator-$NEST_VERSION.tar.gz
-tar -xzf nest-simulator-$NEST_VERSION.tar.gz
+git clone --depth 1 https://github.com/dbbs-lab/nest-simulator nest-simulator-$NEST_VERSION
 mkdir nest-simulator-$NEST_VERSION-build
 mkdir nest-install-$NEST_VERSION
 cd nest-simulator-$NEST_VERSION-build
-cmake -Dwith-python=3 -DPYTHON_LIBRARY=/usr/lib/x86_64-linux-gnu/libpython3.6m.so -DPYTHON_INCLUDE_DIR=/usr/include/python3.6m/ -DCMAKE_INSTALL_PREFIX:PATH=/home/travis/nest-$NEST_VERSION /home/travis/nest-simulator-$NEST_VERSION
+ls /home/travis/virtualenv
+ls /home/travis/virtualenv/python3.6.9
+ls /home/travis/virtualenv/python3.6.9/bin
+cmake -Dwith-python=3 \
+  -DPYTHON_LIBRARY=/usr/lib/x86_64-linux-gnu/libpython3.6m.so \
+  -DPYTHON_INCLUDE_DIR=/usr/include/python3.6m/ \
+  -DCMAKE_INSTALL_PREFIX:PATH=/home/travis/nest-$NEST_VERSION \
+  /home/travis/nest-simulator-$NEST_VERSION
 make
 make install
 cd $MY_BEFORE_DIR
diff --git a/setup.py b/setup.py
@@ -0,0 +1,104 @@
+#!/usr/bin/env python
+import os, sys
+
+import subprocess
+from setuptools import setup, Extension
+from setuptools.dist import Distribution
+from setuptools.command.build_ext import build_ext
+from setuptools.command.install import install
+
+with open("README.md", 'r') as fp:
+    readme_text = fp.read()
+
+def check_cmake():
+    try:
+        out = subprocess.check_output(['cmake', '--version'])
+        return True
+    except OSError:
+        return False
+
+class cmake_extension(Extension):
+    def __init__(self, name):
+        Extension.__init__(self, name, sources=[])
+
+class cmake_build(build_ext):
+    def run(self):
+        if not check_cmake():
+            raise RuntimeError('CMake is not available. CMake 3.12 is required.')
+
+        import nest
+
+        nest_install_dir = os.path.sep.join(nest.__path__[0].split(os.path.sep)[:-4])
+        mod = os.getenv("NEST_MODULE_PATH", "")
+        mod_dir = os.path.join(nest_install_dir, "lib", "nest")
+        if mod_dir not in mod:
+            raise Exception(
+                f"Please make sure 'NEST_MODULE_PATH' env var contains '{mod_dir}' for the installation to succeed.\n"
+                + f"Current value: '{mod}'"
+            )
+
+
+        # Installation dir of nest, required for the cmake command
+        nest_config = os.path.join(nest_install_dir, "bin", "nest-config")
+        # Name of the extension, will be used to determine folder name
+        ext_name = self.extensions[0].name
+        # The path where CMake will be configured and Arbor will be built.
+        build_directory = os.path.abspath(self.build_temp)
+        # The path where the package will be copied after building.
+        lib_directory = os.path.abspath(self.build_lib)
+        # The path where the built libraries end up
+        source_path = build_directory
+        # Where to copy the package after it is built, so that whatever the next phase is
+        # can copy it into the target 'prefix' path.
+        dest_path = os.path.join(lib_directory, ext_name)
+
+        cmake_args = [
+            '-DCMAKE_BUILD_TYPE=Release', # we compile with debug symbols in release mode.
+            "-Dwith-nest=" + nest_config
+        ]
+        build_args = ['--config', 'Release']
+
+        env = os.environ.copy()
+        if not os.path.exists(self.build_temp):
+            os.makedirs(self.build_temp)
+
+        cmake_list_dir = os.path.join(os.path.abspath(os.path.dirname(__file__)), ext_name)
+        print('-'*20, 'Configure CMake')
+        subprocess.check_call(['cmake', cmake_list_dir] + cmake_args,
+                              cwd=self.build_temp, env=env)
+
+        print('-'*20, 'Build')
+        cmake_cmd = ['cmake', '--build', '.'] + build_args
+        subprocess.check_call(cmake_cmd,
+                              cwd=self.build_temp)
+
+        cmake_cmd = ['make', 'install']
+        subprocess.check_call(cmake_cmd,
+                              cwd=self.build_temp)
+
+        # Copy from build path to some other place from whence it will later be installed.
+        # ... or something like that
+        # ... setuptools is an enigma monkey patched on a mystery
+        if not os.path.exists(dest_path):
+            os.makedirs(dest_path, exist_ok=True)
+        self.copy_tree(source_path, dest_path)
+
+setup(
+    name="cereb_nest",
+    version="1.0.0",
+    description="pip installable NEST extension module, generated by pipnest.",
+    license="MIT",
+    author="Alice Geminiani",
+    author_email="[email protected]",
+    url="https://github.com/Helveg/pipnest",
+    long_description=readme_text,
+    long_description_content_type="text/markdown",
+    zip_safe=False,
+    packages=['cereb_nest'],
+    package_data={'cereb_nest': ['*', 'sli/*', 'doc/*']},
+    ext_modules=[cmake_extension("cereb_nest")],
+    cmdclass={
+        'build_ext': cmake_build,
+    },
+    include_package_data = True,
+)
diff --git a/Tests/Check_Models.py → tests/Check_Models.py b/Tests/Check_Models.py → tests/Check_Models.py
diff --git a/Tests/Check_MultiThreading.py → tests/Check_MultiThreading.py b/Tests/Check_MultiThreading.py → tests/Check_MultiThreading.py
diff --git a/Tests/Compare_with_Ground_Truth1.py → tests/Compare_with_Ground_Truth1.py b/Tests/Compare_with_Ground_Truth1.py → tests/Compare_with_Ground_Truth1.py
diff --git a/Tests/Compare_with_Ground_Truth2.py → tests/Compare_with_Ground_Truth2.py b/Tests/Compare_with_Ground_Truth2.py → tests/Compare_with_Ground_Truth2.py
diff --git a/Tests/Compare_with_Ground_Truth3.py → tests/Compare_with_Ground_Truth3.py b/Tests/Compare_with_Ground_Truth3.py → tests/Compare_with_Ground_Truth3.py
diff --git a/Tests/GR_65600.dat → tests/GR_65600.dat b/Tests/GR_65600.dat → tests/GR_65600.dat