Release: NS AI Summer School

Signed-off-by: KyleErwin <[email protected]>

.github/workflows/black.yml

@@ -7,4 +7,4 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - uses: psf/black@stable
+      - uses: psf/black@stable

.github/workflows/build.yml

@@ -24,7 +24,11 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Upgrade pip
         run: python -m pip install --upgrade pip setuptools wheel
+      - name: Install graphviz
+        run: sudo apt-get install -y libgraphviz-dev
       - name: Install dependencies
         run: pip install -e .[test]
+      - name: Install dependencies
+        run: pip install pytest
       - name: Run tests with ${{ matrix.args }}
-        run: pytest ${{ matrix.args }}
+        run: pytest ${{ matrix.args }}

.gitignore

@@ -129,6 +129,9 @@ dmypy.json
 # Pyre type checker
 .pyre/
 
+# TODO files
+TODO
+
 # tmp files
 *tmp.*
 ___*___

.pre-commit-config.yaml

@@ -0,0 +1,12 @@
+repos:
+  -   repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v2.3.0
+      hooks:
+        -   id: check-yaml
+        -   id: end-of-file-fixer
+            files: '.*\.(py|md|)'
+        -   id: trailing-whitespace
+  -   repo: https://github.com/psf/black
+      rev: 22.3.0
+      hooks:
+        -   id: black

CODE_OF_CONDUCT.md

@@ -0,0 +1,134 @@
+
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+[INSERT CONTACT METHOD].
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
+[https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations
+

CONTRIBUTING.md

@@ -0,0 +1,96 @@
+
+# Contributing to LNN
+Thank you for considering a contribution to Logical Neural Networks, with your assistance we can help grow LNNs as the industry's tool of choice for a true `Neuro = Symbolic` platform.
+
+We commit to growing LNNs functionality, but we'd also love to see your name expanding into `x`, adding to growing our list of contributors:
+```python
+Contributions = Predicate("Contribution")
+Growth = Propostion("LNNs Growth", world=World.TRUE)
+
+Implies(Contributions(x), Growth)
+```
+
+## Software Setup
+
+* Due to the complex inference pattern of LNNs upward and downward reasoning strategy, [Pycharm](https://www.jetbrains.com/pycharm/download/) is our recommended IDE of choice for development and debugging.
+1. Make sure that the python version you are using corresponds with the [setup](https://github.com/IBM/LNN/blob/master/setup.py) file, using a fresh [conda]() environment is recommended:
+    ```commandline
+    conda create -n lnn-contrib python=3.9 -y
+    conda activate lnn-contrib
+    ```
+2. Clone the `develop` branch to keep up to date with the latest supported features:
+    ```commandline
+    git clone https://github.ibm.com/Naweed-Khan/LNN.git -b develop
+    ```
+3. Install the LNN module as editable and use the `develop` branch
+    ```commandline
+    cd LNN
+    pip install -e .
+    ```
+* Install [Black](https://black.readthedocs.io/en/stable/integrations/editors.html) as an external tool/keyboard shortcut to keep to our code style - this automates our pep8 compliance so that you can code without the styling overhead
+* Install and run pytest to ensure that the build is working correctly:
+    ```commandline
+    pip install pytest
+    pytest
+    ```
+
+You are now ready to contribute changes to the codebase
+
+##  Developing in LNN
+
+### Propose a New Issue
+
+1. You want to propose a new feature and implement it.
+   1. Post about your intended feature in an [issue](https://github.com/IBM/LNN/issues/new), and we shall discuss the design and implementation.
+   2. Once we agree that the plan looks good, go ahead and implement it.
+
+* You may also want to implement a feature or bug-fix for an outstanding issue:
+  * Pick an issue
+  * Comment that you will be working on this issue.
+  * Add yourself to the assignee list
+
+  If you need more context on a particular issue, please ask for guidance.
+
+### Branching
+
+* LNN branches should follow [git flow][git flow] style branching
+
+[<img src="https://wac-cdn.atlassian.com/dam/jcr:34c86360-8dea-4be4-92f7-6597d4d5bfae/02%20Feature%20branches.svg?cdnVersion=296" alt="git flow"/>][git flow]
+
+To create a new feature branch:
+   ```commandline
+   git checkout develop
+   git checkout -b feature/my_branch
+   ```
+
+Please be mindful of existing branches when creating a new branch.
+
+### Pull Requests
+
+1. Use `Black` formatting to ensure that code contributions abide by our code style
+2. Commits should contain one of the following tags before the commit message: `ADD`, `FIX`, `MAINT`
+3. Run `pytest` locally to ensure all changes pass
+
+   NB: All code contributions corresponding to `enhancement` issues should have additional tests accompanying the code changes, located in the `tests/` folder.
+4. Propose your code changes as a `Pull Request DRAFT` that merge into the `develop` branch.
+5. A passed draft can be changed to a formal `Pull Request`.
+6. Add a reviewer to your code so that they can get notified of the proposal - the individual should correspond to the those charged with the yellow tag
+
+### Documentation
+
+LNN documentation can be generated by running `generate_docs.sh` in [docsrc][docsrc] folder.
+
+[docsrc]: https://github.com/IBM/LNN/tree/develop/docsrc
+[git flow]: https://www.atlassian.com/git/tutorials/comparing-workflows/gitflow-workflow
+
+### Handling Circular Imports
+
+A key component in the LNN code base is the `Formula` abstract class. `Formula` is a
+class that refers to itself and the classes that inherit from it. As such, this can lead
+to circular imports. To overcome circular imports we use dictionaries that are keyed
+with the names of the subclasses and the values are the subclasses themselves. These
+dictionaries are populated in the `__init__.py` of the logic module. Thus, when one
+needs to work with a subclass, the subclass can be accessed by passing in the name of
+that subclass to the dictionary. Note that not all classes that inherit from `Formula`
+are added to these dictionaries. Please refer to `__init__.py` if you need to add an
+existing class or new class to one of the dictionaries.

LICENSE

@@ -1,4 +1,4 @@
-Copyright (C) IBM Corporation 2018-2020
+Copyright (C) IBM Corporation 2018-2022
 
                                  Apache License
                            Version 2.0, January 2004

README.md

@@ -1,45 +1,59 @@
-[![Build Status](https://github.com/IBM/LNN/actions/workflows/build.yml/badge.svg?branch=master)](https://github.com/IBM/LNN/actions/workflows/build.yml?query=branch%3Amaster)
-[![License](https://img.shields.io/github/license/IBM/LNN)](https://github.com/IBM/LNN/blob/master/LICENSE)
+[![License](https://img.shields.io/badge/license-Apache%202.0-blueviolet)](https://github.com/IBM/LNN/blob/master/LICENSE)
+[![CII Best Practices](https://bestpractices.coreinfrastructure.org/projects/5926/badge)](https://bestpractices.coreinfrastructure.org/projects/5926)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
 # Logical Neural Networks
-LNNs are a novel `Neuro = symbolic` framework designed to seamlessly provide key
+LNNs are a novel `Neuro = Symbolic` framework designed to seamlessly provide key
 properties of both neural nets (learning) and symbolic logic (knowledge and reasoning).
 
-- Every neuron has a meaning as a component of a formula in a weighted 
-  real-valued logic, yielding a highly interpretable disentangled representation. 
+- Every neuron has a meaning as a component of a formula in a weighted
+  real-valued logic, yielding a highly interpretable disentangled representation.
 - Inference is omnidirectional rather than focused on predefined target
   variables, and corresponds to logical reasoning, including classical
-  first-order logic (FOL) theorem proving as a special case.
-- The model is end-to-end differentiable, and learning minimizes a novel loss 
+  first-order logic theorem proving as a special case.
+- The model is end-to-end differentiable, and learning minimizes a novel loss
   function capturing logical contradiction, yielding resilience to inconsistent
-  knowledge. 
+  knowledge.
 - It also enables the open-world assumption by maintaining bounds on truth values
-  which can have probabilistic semantics, yielding resilience to incomplete 
+  which can have probabilistic semantics, yielding resilience to incomplete
   knowledge.
 
 ## Quickstart
-
 To install the LNN:
-1. Run: 
-   ```
-   pip install git+https://github.com/IBM/LNN.git
-   ```
-
-To install the LNN with graph plot support:
-1. Install [GraphViz](https://www.graphviz.org/download/)
-2. Run: 
-   ```
-   pip install git+https://github.com/IBM/LNN.git#egg=lnn"[plot]"
-   ```
+1. Install [GraphViz](https://www.graphviz.org/download/) and gmp (libgmp3-dev)
+      <details><summary>Tips for errors "'gmp.h' file not found" and "'graphviz/cgraph.h' file not found" on Mac</summary><div>
 
-## Documentation
+      ```bash
+      brew install graphviz
+      # check the graphviz path from `brew info graphviz`
+      export GRAPHVIZ_DIR="/usr/local/Cellar/graphviz/3.0.0"
+      pip install pygraphviz --global-option=build_ext --global-option="-I$GRAPHVIZ_DIR/include" --global-option="-L$GRAPHVIZ_DIR/lib"
+
+      brew install gmp
+      env "CFLAGS=-I/usr/local/include -L/usr/local/lib" pip install pycddlib
+      ```
+      </div></details>
+
+2. Make sure that the python version you use in line with our [setup](https://github.com/IBM/LNN/blob/master/setup.py) file, using a fresh environment is always a good idea:
+    ```commandline
+    conda create -n lnn-contrib python=3.9 -y
+    conda activate lnn-contrib
+    ```
+3. Install the `develop` branch to keep up to date with the latest supported features:
+    ```commandline
+    pip install git+https://github.com/IBM/LNN.git@develop
+    ```
 
+## Contribution
+Contributions to the LNN codebase are welcome!
+
+Please have a look at the [contribution guide](https://github.com/IBM/LNN/blob/master/CONTRIBUTING.md) for more information on how to set up the LNN for contributing and how to follow our development standards.
+
+## Documentation
 | [Read the Docs][Docs] | [Academic Papers][Papers]	| [Educational Resources][Education] | [Neuro-Symbolic AI][Neuro-Symbolic AI] | [API Overview][API] | [Python Module][Module] |
 |:-----------------------:|:---------------------------:|:-----------------:|:----------:|:-------:|:-------:|
 | [<img src=https://raw.githubusercontent.com/IBM/LNN/master/docsrc/images/icons/doc.png alt="Docs" width="60"/>][Docs] | [<img src=https://raw.githubusercontent.com/IBM/LNN/master/docsrc/images/icons/academic.png alt="Academic Papers" width="60"/>][Papers] |  [<img src=https://raw.githubusercontent.com/IBM/LNN/master/docsrc/images/icons/help.png alt="Getting Started" width="60"/>][Education] | [<img src=https://raw.githubusercontent.com/IBM/LNN/master/docsrc/images/icons/nsai.png alt="Neuro-Symbolic AI" width="60"/>][Neuro-Symbolic AI] | [<img src=https://raw.githubusercontent.com/IBM/LNN/master/docsrc/images/icons/api.png alt="API" width="60"/>][API] | [<img src=https://raw.githubusercontent.com/IBM/LNN/master/docsrc/images/icons/python.png alt="Python Module" width="60"/>][Module] |
 
-
 ## Citation
 If you use Logical Neural Networks for research, please consider citing the
 reference paper:
@@ -52,10 +66,9 @@ reference paper:
 }
 ```
 
-
-[Docs]: https://ibm.github.io/LNN/
-[Papers]: https://ibm.github.io/LNN/papers.html
-[Education]: https://ibm.github.io/LNN/education/education.html
-[API]: https://ibm.github.io/LNN/usage.html
-[Module]: https://ibm.github.io/LNN/lnn/LNN.html
+[Docs]: https://pages.github.com/IBM/LNN/introduction.html
+[Papers]: https://pages.github.com/IBM/LNN/papers.html
+[Education]: https://pages.github.com/IBM/LNN/education/education.html
+[API]: https://pages.github.com/IBM/LNN/usage.html
+[Module]: https://pages.github.com/IBM/LNN/lnn/LNN.html
 [Neuro-Symbolic AI]: https://research.ibm.com/teams/neuro-symbolic-ai

docs/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 976870eaa406da43ff4c506ff5c2007d
+config: b84c77634a33cf724ade5aeb967569d8
 tags: 645f666f9bcd5a90fca523b33c5a78b7