Merge branch 'master' into Multicompartment_Connection

# Conflicts:
#	bindsnet/datasets/collate.py
#	bindsnet/network/monitors.py
#	bindsnet/network/topology.py
#	bindsnet/pipeline/base_pipeline.py
#	requirements.txt
#	setup.py

Author: C-Earl

.github/workflows/python-app.yml

@@ -0,0 +1,43 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: BindsNET build status
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.9
+    - name: Install Poetry
+      env:
+        POETRY_VERSION: 1.5.1
+      run: |
+        curl -sSL https://install.python-poetry.org | python - -y &&\
+            poetry config virtualenvs.create false
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 pytest
+        # if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        poetry install
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest

.github/workflows/pythonpackage.yml

@@ -9,24 +9,26 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [3.6, 3.7, 3.8]
+        python-version: ["3.9", "3.10", "3.11"]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
+    - name: Install Poetry
+      env:
+        POETRY_VERSION: 1.5.1
+      run: |
+        curl -sSL https://install.python-poetry.org | python - -y &&\
+            poetry config virtualenvs.create false
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install -r requirements.txt
-        pip install . --progress-bar off
+        poetry install
     - name: Format with black
       run: |
-        pip install black
         black .
     - name: Test with pytest
       run: |
-        pip install pytest
         pytest

.gitignore

@@ -1,131 +1,24 @@
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*$py.class
-
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
-env/
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*.cover
-.hypothesis/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# pyenv
-.python-version
-
-# celery beat schedule file
-celerybeat-schedule
-
-# SageMath parsed files
-*.sage.py
-
-# dotenv
-.env
-
-# virtualenv
-.venv
-venv/
-ENV/
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
-
-# Datasets.
-data/
-!data/get_MNIST.sh
-
-# LSM data.
-lsm/
-
-# Results from network monitoring test.
-results/
-
-# Results from network monitoring test.
-examples/saved_checkpoints
-
-# pytest cache
-.pytest_cache/
-
-# Swap files.
-*.swp
-
-# PyCharm project folder.
-.idea/
-
-# macOS
-.DS_Store
-
-figures/
-
-# Analyzer log default directory.
-logs/
+bindsnet/__pycache__/*
+bindsnet/analysis/__pycache__/*
+bindsnet/conversion/__pycache__/*
+bindsnet/datasets/__pycache__/*
+bindsnet/environment/__pycache__/*
+bindsnet/evaluation/__pycache__/*
+bindsnet/learning/__pycache__/*
+bindsnet/encoding/__pycache__/*
+bindsnet/models/__pycache__/*
+bindsnet/network/__pycache__/*
+bindsnet/pipeline/__pycache__/*
+bindsnet/preprocessing/__pycache__/*
+test/analysis/__pycache__/*
+test/conversion/__pycache__/*
+test/encoding/__pycache__/*
+test/import/__pycache__/*
+test/models/__pycache__/*
+test/network/__pycache__/*
+test/analysis/__pycache__/*
+dist/*
+logs/*
+.pytest_cache/*
+.vscode/*
+data/*

.pre-commit-config.yaml

@@ -0,0 +1,39 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  builder: html
+  configuration: docs/source/conf.py
+  
+formats:
+  - epub
+  - pdf
+
+# We recommend specifying your dependencies to enable reproducible builds:
+# https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+    - requirements: docs/requirements.txt
+    - method: pip
+      path: docs/
+      # extra_requirements:
+        # - docs
+
+# python:
+  # version: 3.8
+  # install:
+    # - method: pip
+      # path: .
+    # - requirements: docs/requirements.txt
+  # system_packages: False

.readthedocs.yaml

@@ -2,27 +2,45 @@
 
 To clone this project locally, issue
 
-```
+```shell
 git clone https://github.com/Hananel-Hazan/bindsnet.git  # clones bindsnet repository
 ```
 
 in the directory of your choice. This will place the repository's code in a directory titled `bindsnet`.
 
-All development should take place on a branch separate from master. To create a branch, issue
+Install the project with [Poetry](https://python-poetry.org/) (current supported version - 1.1.8)
+
+```shell
+poetry install
+poetry run pre-commit install
+```
+
 
+Now you can access the project environment with `poetry shell` or run commands with `poetry run <command>`. For example, `poetry run python examples/mnist/conv_mnist.py`.
+
+Please make sure the `Poetry` environment is activated when you commit your files! The `git commit` command will invoke `pre-commit`, which is installed with Poetry too. IDEs like PyCharm have plugins for `Poetry` and will activate the environment automatically.
+
+Run the tests, they all should pass
+
+```shell
+poetry run pytest
 ```
+
+All development should take place on a branch separate from master. To create a branch, issue
+
+```shell
 git branch [branch-name]  # create new branch
 ```
 
 replacing `[branch-name]` with a simple and memorable name of choice; e.g., `git branch dan`. Switch to the newly created branch using
 
-```
+```shell
 git checkout [branch-name]  # switch to a different branch of the repository
 ```
 
 __Note__: Issue `git branch` with no arguments to list all branches currently being tracked, with an asterisk next to the currently used branch; e.g.,
 
-```
+```shell
 $ git branch  # list all branches and indicate current branch
 * dan
   devel
@@ -34,40 +52,46 @@ If new branches have been created on the remote repository, you may start tracki
 
 After making changes to the repository, issue a `git status` command to see which files have been modified. Then, use
 
-```
+```shell
 git add [file-name(s) | -A]  # add modified or newly created files
 ```
 
 to add one or more modified files (`file-name(s)`), or all modified files (`-A` or `--all`). These include newly created files. Issue
 
+```shell
+pre-commit run -a
 ```
+
+to run the `pre-commit` tool that will automatically format your code with `black`. Issue
+
+```shell
 git commit -m "[commit-message]"  # Useful messages help when reverting / searching through history 
 ```
 
 to "commit" your changes to your local repository, where `[commit-message]` is a _short yet descriptive_ note about what changes have been made.
 
 Before pushing your changes to the remote repository, you must make sure that you have an up-to-date version of the `master` code. That is, if master has been updated while you have been making your changes, your code will be out of date with respect to the master branch. Issue
 
-```
+```shell
 git pull  # gets all changes from remote repository
 git merge master  # merges changes made in master branch with those made in your branch
 ```
 
 and fix any merge conflicts that may have resulted, and re-commit after the fix with
 
-```
+```shell
 git commit  # no -m message needed; merge messages are auto-generated
 ```
 
 Push your changes back to the repository onto the same branch you are developing on. Issue
 
-```
+```shell
 git push [origin] [branch-name]  # verbose; depends on push.default behavior settings
 ```
 
 or,
 
-```
+```shell
 git push  # concise; again, depends on push.default behavior
 ```