Updating form main

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,56 @@
+## Contributing Guidelines
+
+<!-- Please make sure you have read and understood our contributing guidelines before submitting this PR -->
+- [ ] I have read and understood the [CONTRIBUTING.md](https://github.com/Autodesk/XLB/blob/main/CONTRIBUTING.md) guidelines
+
+
+## Description
+
+<!-- 
+Thank you for your contribution! Please include a summary of the changes and the related issue. Please also include relevant motivation and context. List any dependencies that are required for this change.
+-->
+
+
+## Type of change
+
+<!-- Please select the options that are relevant. -->
+- [ ] Bug fix (non-breaking change which fixes an issue)
+- [ ] New feature (non-breaking change which adds functionality)
+- [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
+- [ ] Documentation update
+
+## How Has This Been Tested?
+
+<!-- Please describe the tests that you ran to verify your changes. Provide instructions so others can reproduce. Include details of your test environment, and the test cases you ran.
+
+- [ ] Test A
+- [ ] Test B
+-->
+- [ ] All pytest tests pass
+
+<!-- To run the tests, execute the following command from the root of the repository:
+
+```bash
+pytest
+```
+ -->
+
+
+## Linting and Code Formatting
+
+Make sure the code follows the project's linting and formatting standards. This project uses **Ruff** for linting.
+
+To run Ruff, execute the following command from the root of the repository:
+
+```bash
+ruff check .
+```
+
+<!-- You can also fix some linting errors automatically using Ruff:
+
+```bash
+ruff check . --fix
+```
+-->
+
+- [ ] Ruff passes

.github/workflows/cla.yml

@@ -9,14 +9,22 @@ jobs:
   CLA-Assistant:
     runs-on: ubuntu-latest
     steps:
+      - uses: actions/create-github-app-token@v2
+        id: app-token
+        with:
+          app-id: ${{ vars.CLA_BOT_APP_ID }}
+          private-key: ${{ secrets.CLA_BOT_PRIVATE_KEY }}
+          owner: Autodesk
+          repositories: |
+            CLA-Signatures
       - name: "CLA Assistant"
         if: (github.event.comment.body == 'recheck' || github.event.comment.body == 'I have read the CLA Document and I hereby sign the CLA') || github.event_name == 'pull_request_target'
         # Beta Release
-        uses: contributor-assistant/github-action@v2.3.0
+        uses: contributor-assistant/github-action@v2.6.1
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           # the below token should have repo scope and must be manually added by you in the repository's secret
-          PERSONAL_ACCESS_TOKEN : ${{ secrets.CLA_BOT_SECRET }}
+          PERSONAL_ACCESS_TOKEN: ${{ steps.app-token.outputs.token }}
         with:
           remote-repository-name: 'CLA-Signatures'
           remote-organization-name: 'Autodesk'

.github/workflows/lint.yml

@@ -0,0 +1,27 @@
+name: Lint
+
+on:
+  pull_request:
+    branches:
+      - major-refactoring  # Remember to add main branch later
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Check out code
+      uses: actions/checkout@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.11'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install ruff
+
+    - name: Run Ruff
+      run: ruff check .

.github/workflows/mkdocs.yml

@@ -2,7 +2,6 @@ name: mkdocs-deployment
 on:
   push:
     branches:
-      - master 
       - main
     # paths:
     #   - 'docs/**'

.gitignore

@@ -39,7 +39,7 @@ Thumbs.db
 __pycache__/
 *.py[cod]
 *$py.class
-
+**pyc
 # C extensions
 *.so
 
@@ -131,6 +131,8 @@ venv/
 ENV/
 env.bak/
 venv.bak/
+.xlb-env/
+.xlb_install_test_venvs/
 
 # Spyder project settings
 .spyderproject
@@ -149,4 +151,25 @@ dmypy.json
 
 
 # Checkpoints (default dir for XLB)
-checkpoints/*
+checkpoints/*
+
+# Ignore Python packaging build directories
+dist/
+build/
+*.egg-info/
+*.dot
+
+# Ignore h5 and xmf formats
+*.h5
+*.xmf
+
+# Ignore CSV files
+*.csv
+
+# USD files
+*.usd
+*.usda
+*.usdc
+*.usd.gz
+*.usd.zip
+*.usd.bz2

.pre-commit-config.yaml

@@ -0,0 +1,6 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.5.6
+    hooks:
+      - id: ruff
+        args: [--fix]

AUTHORS

@@ -4,4 +4,6 @@
 # For a comprehensive view of all contributors, please refer to the revision history in the source control.
 
 Mehdi Ataei (Autodesk Inc)
-Hesam Saleipour (Autodesk Inc)
+Hesam Saleipour (Autodesk Inc)
+Oliver Hennigh (NVIDIA)
+Massimiliano Meneghin (Autodesk Inc)

CHANGELOG.md

@@ -0,0 +1,30 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+- _No changes yet_  <!-- Placeholder for future changes -->
+
+
+## [0.2.1] - 2024-12-05
+
+### Fixed
+- mkdocs is now configured correctly for the new project structure
+- JAX installation is now handled correctly for different configurations (CPU, CUDA, TPU)
+- Fixed a couple of bugs in 2D regularied_bc and kbc (Warp) that emerged after merging 2d and 3d kernels
+
+### Added
+
+- Added abstraction layer for boundary condition efficient encoding/decoding of auxiliary data
+- Added the capability to add profiles to boundary conditions
+- Added prepare_fields method to the Stepper class to allow for more automatic preparation of fields
+
+## [0.2.0] - 2024-10-22
+
+### Added
+- XLB is now installable via pip
+- Complete rewrite of the codebase for better modularity and extensibility based on "Operators" design pattern
+- Added NVIDIA's Warp backend for state-of-the-art performance

CONTRIBUTING.md

@@ -38,3 +38,150 @@ If you would like to contribute your code to XLB, you should:
 
 
 When you submit your code, please include relevant tests as part of the pull request, and ensure that your comments and coding style align with the rest of the project. You can refer to the existing code for examples of the testing and style practices that the project follows.
+
+Important: Ensure that your commits are atomic and self-contained. Each PR should only make a single, cohesive change. You should also squash your commits into a single commit as described below before submitting your PR.
+
+## Detailed Contribution Guidelines
+
+### 1. Setup Your Local Environment
+
+- **Clone Your Fork:**
+  If you haven't yet cloned your copy of the repository, you can do so with the following command:
+
+  ```bash
+  git clone https://github.com/Autodesk/XLB
+  cd XLB
+  ```
+
+- **Add Upstream Remote:** Set up the upstream remote to track the original repository.
+
+  ```bash
+  git remote add upstream https://github.com/Autodesk/XLB
+  ```
+
+  You can check your remotes to ensure everything is set up correctly:
+
+  ```bash
+  git remote -v
+  ```
+
+### 2. Syncing Your Main Branch with Upstream
+
+- **Fetch Updates from Upstream:**
+  To keep your local repository up to date with the upstream `main` branch:
+
+  ```bash
+  git fetch upstream
+  ```
+
+- **Sync Your Main Branch:**
+  Checkout to your local `main` and merge the upstream changes to ensure it's always up to date:
+
+  ```bash
+  git checkout main
+  git merge upstream/main
+  ```
+
+- **Push to Your Fork (Optional):**
+  It is a good practice to also keep the fork on GitHub in sync:
+
+  ```bash
+  git push origin main
+  ```
+
+### 3. Create a Feature Branch for Your Contribution
+
+- **Create and Checkout a New Branch:**
+  Always work on a new branch for each feature or issue to keep things organized:
+  ```bash
+  git checkout -b <feature_branch_name>
+  ```
+  Choose a descriptive branch name that makes it clear what your contribution is.
+
+### 4. Make Your Changes
+
+- **Make Changes and Commit:**
+  Make all the changes you need, then stage and commit them:
+
+  ```bash
+  git add .
+  git commit -m "Description of the changes made"
+  ```
+
+- **Amend or Squash Commits (Optional):**
+  If you need to update the commit message or add more changes before pushing, you can amend your commit:
+
+  ```bash
+  git add .
+  git commit --amend
+  ```
+
+  This will let you update the commit message or include additional changes in a single commit.
+
+  To consolidate your existing commits into a single PR, first, you need to reset your branch to the point where you want the single commit to start from (likely the last commit on origin/main before your work began).
+
+  ```bash
+    git reset --soft <commit-id>
+  ```
+
+  Replace `<commit-id>` with the hash of the commit that should be the base of your PR (it is likely the last commit on origin/main before your changes, use that ID).
+
+  Now, all your work will be staged as if it’s a single set of changes. You can commit this with a new message that represents the combined work.
+
+```bash
+git commit -m "Combined changes"
+```
+
+Finally, you can push your changes to your fork with the following command:
+
+```bash
+git push --force origin <feature_branch_name>
+```
+
+### 5. Pushing Your Branch and Creating a Pull Request
+
+- **Push Your Branch to Your Fork:**
+
+  ```bash
+  git push origin <feature_branch_name>
+  ```
+
+- **Create a Pull Request (PR):**
+  Go to the repository on GitHub, and you should see an option to create a Pull Request from your recently pushed branch. Follow the steps to create the PR.
+
+### 6. Handling Feedback and Updating PR
+
+- **Make Changes Based on Feedback:**
+  If changes are requested in the PR, make those changes in your local branch and amend the commit if needed:
+  ```bash
+  git add .
+  git commit --amend
+  git push --force origin <feature_branch_name>
+  ```
+  The `--force` flag is necessary because you amended an existing commit, and you need to update the remote branch accordingly.
+
+### 7. Finalizing and Merging
+
+- **Squash Commits on Maintainer Side:**
+  When the PR is ready to be merged, the maintainer *will* squash multiple commits into a single one, or you can amend and force push until only a single commit is present.
+
+- **Sync Your Fork Main Branch Again:**
+  Once your PR is merged, make sure to sync your local and forked `main` branch again:
+
+  ```bash
+  git checkout main
+  git fetch upstream
+  git merge upstream/main
+  git push origin main
+  ```
+
+### 8. Start a New Contribution
+
+- **Create a New Branch:**
+  For each new contribution, repeat the branching step:
+  ```bash
+  git checkout main
+  git checkout -b <new_feature_branch>
+  ```
+---
+This workflow ensures every contribution is separate and cleanly managed.