Initial release of lava-dnf v0.1.0 (#8)

* Removed placeholder file * Removed 'lib' from gitignore Signed-off-by: Mathis Richter <[email protected]> * Added Population Process and shape validation Signed-off-by: Mathis Richter <[email protected]> * Added Population SubProcessModel Signed-off-by: Mathis Richter <[email protected]> * Make unit test for Population ProcessModel ports more explicit Signed-off-by: Mathis Richter <[email protected]> * Unit test that executes a Population Signed-off-by: Mathis Richter <[email protected]> * Modified Population ProcessModel unit test to use get_src_ports/get_dst_ports Signed-off-by: Mathis Richter <[email protected]> * Added convenience function num_neurons() Signed-off-by: Mathis Richter <[email protected]> * Added first version of connect() function Signed-off-by: Mathis Richter <[email protected]> * Added missing __init__ file Signed-off-by: Mathis Richter <[email protected]> * Added num_dims function Signed-off-by: Mathis Richter <[email protected]> * Added configuration functionality to operations Signed-off-by: Mathis Richter <[email protected]> * Added basic configuration of operations in connect() Signed-off-by: Mathis Richter <[email protected]> * Added additional top-level lava directory and moved lib inside Signed-off-by: Mathis Richter <[email protected]> * Refactored connect unit tests Signed-off-by: Mathis Richter <[email protected]> * Added check for multiple operations that change shape (not yet implemented) Signed-off-by: Mathis Richter <[email protected]> * Weights are computed for all operations Signed-off-by: Mathis Richter <[email protected]> * Fixed linter error Signed-off-by: Mathis Richter <[email protected]> * Unit testing only against the public API of connect Signed-off-by: Mathis Richter <[email protected]> * Doc strings for operations module Signed-off-by: Mathis Richter <[email protected]> * Added exception for misconfigured operations Signed-off-by: Mathis Richter <[email protected]> * Refactored validation of operations using exceptions rather than boolean returns Signed-off-by: Mathis Richter <[email protected]> * Added Weights operation Signed-off-by: Mathis Richter <[email protected]> * Unit test for computing weights now covers shapes of 0d-3d Signed-off-by: Mathis Richter <[email protected]> * Major rewrite of operations; now supporting multiple operations that change shape. Signed-off-by: Mathis Richter <[email protected]> * Added ReduceDims Operation Signed-off-by: Mathis Richter <[email protected]> * Removed redundant unit test for connect function Signed-off-by: Mathis Richter <[email protected]> * Added AbstractExpandDimsOperation Signed-off-by: Mathis Richter <[email protected]> * Added ExpandDims Operation Signed-off-by: Mathis Richter <[email protected]> * Refactored projection function to simplify interface Signed-off-by: Mathis Richter <[email protected]> * Added Reorder Operation (wip, some redesign required) Signed-off-by: Mathis Richter <[email protected]> * Rough draft of inputs module Signed-off-by: Mathis Richter <[email protected]> * Refactored operations, extracting the handling of shapes Signed-off-by: Mathis Richter <[email protected]> * Added acceptance tests in tests/acceptance; moved unit tests to tests/unit Signed-off-by: Mathis Richter <[email protected]> * Moved operation enums into separate module Signed-off-by: Mathis Richter <[email protected]> * Minor changes to docstrings Signed-off-by: Mathis Richter <[email protected]> * Added additional top-level 'src' directory and 'lava' directory under 'tests' Signed-off-by: Mathis Richter <[email protected]> * GaussInputPattern + SpikeInputGenerator + BiasInputGenerator and draft Source Processes * updating .gitignore * Cosmetics on imports Signed-off-by: Mathis Richter <[email protected]> * Added is_odd() helper function Signed-off-by: Mathis Richter <[email protected]> * Added BorderType enum Signed-off-by: Mathis Richter <[email protected]> * Fixed docstrings Signed-off-by: Mathis Richter <[email protected]> * Added rudimentary Kernel class to support development of Convolution operation Signed-off-by: Mathis Richter <[email protected]> * Added Convolution operation Signed-off-by: Mathis Richter <[email protected]> * Fixed linter warnings Signed-off-by: Mathis Richter <[email protected]> * Fixed security linter error Signed-off-by: Mathis Richter <[email protected]> * GaussInputPattern + SpikeInputGenerator done. SpikeSource not running. * Updated CI/CD based on lava-optimization Signed-off-by: Mathis Richter <[email protected]> * Added pybuilder dependency Signed-off-by: Mathis Richter <[email protected]> * First draft of a DNF 101 tutorial Signed-off-by: Mathis Richter <[email protected]> * Added gauss() function * Added SelectiveKernel * Fixed linter error * Renamed bias_mant to bias in Population * Added MultiPeakKernel * Updated example in README to new API * SpikeInput refactoring (wip) * GaussPattern + SpikeGenerator. Missing unit tests and documentation. * Updated the DNF 101 tutorial This makes assumptions about future changes to inputs and monitors. * Reordered sections of DNF tutorial and fixed minor issues * Documentation + refactor GaussPattern param validation + fixing linting errors. * Restructuring inputs directory * Unit testing. * Temporary placeholder for missing ReshapePorts * Adding parameters to SpikeGenerator + refactoring unit tests. * Skipping unit tests that have non-deterministic behavior * Skipping unit tests that have non-deterministic behavior * Changed __init__.py files to new Lava convention * Removed one more __init__.py file * Removed two more __init__.py files * Updated tutorial after feedback * Fixed non-determinism in unit tests (#3) Co-authored-by: gkarray <[email protected]> * Update requirements.txt (#2) * Fixed bugs in tutorial * Update requirements.txt * Update build.py Add project.build_depends_on("lava", url="git+https://github.com/lava-nc/lava.git) to build.py * ci-build.yml: Only run unit tests on Windows * Update ci-build.yml * Moved unit tests to be consistent with lava test directory structure * Replaced np.bool/np.int with bool/int * Replaced tau parameters with decay * Added complete type annotations * Capitalized comments * Removed Population Process and replaced it with LIF * Addressing pending error, RuntimeWarning and adding few comments. * Update ci-build.yml * Added preliminary but working raster plot * Updated tutorial to include Monitors and raster plots * Cosmetic changes to visible documents * Updated tutorial to work with new Dense implementations * Split off examples from DNF 101 tutorial * Docstring cosmetics * Minor correction in RateCodeSpikeGen + restructure and unit testing plotting.py * Operations in connect function are now optional * Fixed linter errors * Homogenizing asserts in plotting's unit tests. * Reverting plotting functions to old (num_time_steps, num_neurons) shape convention * Refactoring tutorial_dnf_regimes.ipynb * Adding colorbar to tutorial_dnf_regimes.ipynb plots. * Updated tutorials * Adding animated plot for dnf_regimes tutorial * Fixing linter errors. * Updated animated plots and added them to DNF regime tutorial * Fixed unit tests that needed changes but were blocked by PR #96 Signed-off-by: Mathis Richter <[email protected]> * Removed tags from Process Models, anticipating changes in PR#96 Signed-off-by: Mathis Richter <[email protected]> * Fixed typo in tutorial Signed-off-by: Mathis Richter <[email protected]> Co-authored-by: Ghassen Karray <[email protected]> Co-authored-by: gkarray <[email protected]> Co-authored-by: Marcus G K Williams <[email protected]>
lava-nc · Nov 29, 2021 · 5deb525 · 5deb525
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commit 5deb525
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Showing 57 changed files with 6,658 additions and 39 deletions.
diff --git a/.github/workflows/ci-build.yml b/.github/workflows/ci-build.yml
@@ -18,11 +18,9 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install pybuilder
-
     - name: Run pybuilder w/o unit tests
       run: |
         pyb analyze
-
   security-lint:
     name: Security Lint with bandit
     runs-on: ubuntu-latest
@@ -39,17 +37,15 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install pybuilder
-
     - name: Run pybuilder to lint security w/ bandit
       run: |
         pyb bandit
-
   unit-tests:
     name: Run unit tests
     runs-on: ${{ matrix.operating-system }}
     strategy:
       matrix:
-        operating-system: [ubuntu-latest, windows-latest, macos-latest]
+        operating-system: [ubuntu-latest, macos-latest]
 
     steps:
     - uses: actions/checkout@v2
@@ -63,7 +59,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install -r requirements.txt
-
+        pip install pybuilder
     - name: Run unit tests
       run: |
-        python -m unittest discover -s tests -p "test_*.py" -vvv
+        pyb -E unit
diff --git a/.gitignore b/.gitignore
@@ -113,6 +113,9 @@ venv.bak/
 .spyderproject
 .spyproject
 
+# vscode project settings
+.vscode/
+
 # Rope project settings
 .ropeproject
 

diff --git a/README.md b/README.md
@@ -41,29 +41,21 @@ Examples demonstrating basic DNF regimes and instabilities
 - Detection of input
 - Selection of input
 - Working memory of input
-- Neural oscillator
-
-Infrastructure
-- Sensor and data input/output
-- Plotting
 
 ## Example
 
 ```python
-from lava.lib.dnf.populations import Population
-from lava.lib.dnf.kernels import SelectiveKernel
-from lava.lib.dnf.connect import connect
-from lava.lib.dnf.operations import Instar, OneToOne
+from lava.proc.lif.process import LIF
+from lava.lib.dnf.kernels.kernels import SelectiveKernel
+from lava.lib.dnf.connect.connect import connect
+from lava.lib.dnf.operations.operations import Convolution
 
 # create population of 20x20 spiking neurons
-dnf = Population(shape=(20, 20))
+dnf = LIF(shape=(20, 20))
 
 # create a selective kernel
 kernel = SelectiveKernel(amp_exc=18, width_exc=[4, 4], global_inh=-15)
 
 # apply the kernel to the population to create a DNF with a selective regime
-connect(dnf, dnf, [Instar(kernel)])
+connect(dnf.s_out, dnf.a_in, [Convolution(kernel)])
 ```
-
-
-
diff --git a/build.py b/build.py
@@ -7,22 +7,22 @@
 # use_plugin("python.coverage")
 use_plugin("python.distutils")
 use_plugin("python.sphinx")
-use_plugin('python.install_dependencies')
+use_plugin("python.install_dependencies")
 use_plugin("python.pycharm")
-use_plugin('pypi:pybuilder_bandit')
+use_plugin("pypi:pybuilder_bandit")
 
 name = "lava-dnf"
 default_task = ["analyze", "publish"]
 version = "0.1.0"
-summary = "A library that provides processes and other software infrastructure to build architectures composed of Dynamic Neural Fields (DNF). This library also provides tools to direct sensory input to neural architectures and to read output, for instance for motor control. Lava-DNF is part of Lava Framework "
+summary = "A library that provides processes and other software infrastructure to build architectures composed of Dynamic Neural Fields (DNF)."
 url = "https://lava-nc.org"
 license = ["BSD-3-Clause"]
 
 
 @init
 def set_properties(project):
-    project.set_property("dir_source_main_python", "src/lava")
-    project.set_property("dir_source_unittest_python", "tests")
+    project.set_property("dir_source_main_python", "src")
+    project.set_property("dir_source_unittest_python", "tests/lava")
     project.set_property("dir_source_main_scripts", "scripts")
     project.set_property("dir_docs", "docs")
 
@@ -53,20 +53,21 @@ def set_properties(project):
         "target/*,.svn,CVS,.bzr,.hg,.git,__pycache__,.pybuilder/*",
     )
 
-    project.get_property('distutils_commands').append('build')
-    project.get_property('distutils_commands').append('sdist')
-    project.get_property('distutils_commands').append('bdist_dumb')
+    project.get_property("distutils_commands").append("build")
+    project.get_property("distutils_commands").append("sdist")
+    project.get_property("distutils_commands").append("bdist_dumb")
 
-    project.set_property('bandit_break_build', True)
-    project.set_property('bandit_include_testsources', False)
+    project.set_property("bandit_break_build", True)
+    project.set_property("bandit_include_testsources", False)
 
 
 @init(environments="unit")
 def set_properties_unit(project):
-    project.set_property("dir_source_main_python", "src/lava")
-    project.set_property("dir_source_unittest_python", "tests")
+    project.set_property("dir_source_main_python", "src")
+    project.set_property("dir_source_unittest_python", "tests/lava")
     project.set_property("dir_source_main_scripts", "scripts")
     project.set_property("dir_docs", "docs")
+    project.build_depends_on("lava", url="git+https://github.com/lava-nc/lava.git")
 
     project.set_property("sphinx_config_path", "docs")
     project.set_property("sphinx_source_dir", "docs")
@@ -82,7 +83,7 @@ def set_properties_unit(project):
     project.plugin_depends_on("sphinx_tabs")
 
     project.set_property("verbose", True)
-    
+
     project.set_property("coverage_threshold_warn", 0)
     project.set_property("coverage_break_build", False)
 
@@ -96,5 +97,5 @@ def set_properties_unit(project):
 
     project.set_property("unittest_module_glob", "test_*")
 
-    project.set_property('bandit_break_build', True)
-    project.set_property('bandit_include_testsources', False)
+    project.set_property("bandit_break_build", True)
+    project.set_property("bandit_include_testsources", False)
diff --git a/requirements.txt b/requirements.txt
@@ -0,0 +1,3 @@
+lava-nc@git+https://github.com/lava-nc/lava.git
+numpy
+scipy>=1.7.2
diff --git a/setup.py b/setup.py
@@ -33,6 +33,7 @@
 import shutil
 
 from sys import version_info
+
 py3 = version_info[0] == 3
 py2 = not py3
 if py2:
@@ -41,7 +42,9 @@
 
 def install_pyb():
     try:
-        subprocess.check_call([sys.executable, "-m", "pip", "install", "pybuilder"])
+        subprocess.check_call(
+            [sys.executable, "-m", "pip", "install", "pybuilder"]
+        )
     except subprocess.CalledProcessError as e:
         sys.exit(e.returncode)
 
@@ -64,11 +67,13 @@ def install_pyb():
 
 try:
     from pybuilder.cli import main
+
     # verbose, debug, skip all optional...
     if main("-v", "-X", "-o", "--reset-plugins", "clean", "package"):
         raise RuntimeError("PyBuilder build failed")
 
     from pybuilder.reactor import Reactor
+
     reactor = Reactor.current_instance()
     project = reactor.project
     dist_dir = project.expand_path("$dir_dist")
@@ -83,7 +88,9 @@ def install_pyb():
                 os.remove(target_file_name)
         shutil.move(src_file, script_dir)
     setup_args = sys.argv[1:]
-    subprocess.check_call([sys.executable, "setup.py"] + setup_args, cwd=script_dir)
+    subprocess.check_call(
+        [sys.executable, "setup.py"] + setup_args, cwd=script_dir
+    )
 except subprocess.CalledProcessError as e:
     exit_code = e.returncode
 sys.exit(exit_code)
diff --git a/src/lava/lib/dnf/README.md b/src/lava/lib/dnf/README.md