Merge pull request #206 from CosmoStat/release/v3.1.0

Release/v3.1.0

Author: ChaitanyaChawak

.github/workflows/cd.yml

@@ -17,24 +17,24 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v3
-      
+
       - name: Set up Python 3.10.11
         uses: actions/setup-python@v3
         with:
           python-version: "3.10.11"
-          
+
       - name: Check Python Version
         run: python --version
 
       - name: Install dependencies
         run: |
           python -m pip install ".[docs]"
-     
+
       - name: Build API documentation
         run: |
           make -C docs clean
           make -C docs html
-       
+
       - name: Deploy API documentation
         uses: peaceiris/actions-gh-pages@v3.5.9
         with:

.github/workflows/cd_manual.yml

@@ -13,26 +13,27 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v3
-      
+
       - name: Set up Python 3.10.11
         uses: actions/setup-python@v3
         with:
           python-version: "3.10.11"
-          
+
       - name: Check Python Version
         run: python --version
 
       - name: Install dependencies
         run: |
-          python -m pip install ".[docs]"
-     
+          python -m pip install --upgrade pip setuptools wheel
+          pip install -e ".[docs]"
+
       - name: Build API documentation
         run: |
           make -C docs clean
           make -C docs html
-       
+
       - name: Archive documentation as artifact
         uses: actions/upload-artifact@v4
         with:
           name: api-docs
-          publish_dir: docs/build/html
+          path: docs/build/html

.github/workflows/ci.yml

@@ -20,15 +20,15 @@ jobs:
     steps:
       - name: Checkout code
         uses: actions/checkout@v3
-      
+
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v3
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Install dependencies
         run: python -m pip install ".[test]"
-      
+
       - name: Test with pytest
         run: python -m pytest
 

.github/workflows/ci_manual.yml

@@ -16,14 +16,14 @@ jobs:
     steps:
       - name:
         uses: actions/checkout@v3
-      
+
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v3
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Install dependencies
         run: python -m pip install ".[test]"
-       
+
       - name: Test with pytest
         run: python -m pytest

.gitignore

@@ -89,6 +89,7 @@ instance/
 
 # Sphinx documentation
 docs/build/
+docs/_build/
 docs/source/wf_psf*.rst
 docs/source/_static/file.png
 docs/source/_static/images/logo_colab.png

.pre-commit-config.yaml

@@ -0,0 +1,46 @@
+# .pre-commit-config.yaml
+# WaveDiff pre-commit configuration
+# Globally excludes notebooks and historical papers directories
+
+default_stages: [commit]
+
+# Apply globally to all hooks
+exclude: '(^papers/|\.ipynb$)'
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-toml
+      - id: check-yaml
+      - id: trailing-whitespace
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.10.0
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+
+      - id: ruff-format
+
+  - repo: https://github.com/adamchainz/blacken-docs
+    rev: 1.19.1
+    hooks:
+      - id: blacken-docs
+        additional_dependencies: [black==24.10.0]
+        args: [-l, '120', -t, py312]
+
+  - repo: local
+    hooks:
+      - id: check-scriv-fragment
+        name: Ensure Scriv fragment exists for PR
+        entry: bash -c
+        args:
+          - |
+            CHANGED_FILES=$(git diff --cached --name-only --diff-filter=ACM | grep -E "\.py$|\.md$|\.rst$|\.yaml$" | grep -v "^docs/")
+            FRAGMENTS=$(git diff --cached --name-only --diff-filter=ACM | grep "^changelog.d/")
+            if [ -n "$CHANGED_FILES" ] && [ -z "$FRAGMENTS" ]; then
+              echo "ERROR: Please add a Scriv changelog fragment in changelog.d/ for this PR."
+              exit 1
+            fi
+        language: system

CHANGELOG.md

@@ -2,10 +2,67 @@
 
 All notable changes to WaveDiff are documented in this file.
 
+<!-- scriv-end-here -->
+
 ## [Unreleased]
 
 - Changes in progress for the next release.
+  
+<a id='changelog-v3.1.0'></a>
+# v3.1.0 — 2026-02-23
+
+## New features
+
+- Added PSF inference capabilities for generating broadband (polychromatic) PSFs from trained models given star positions and SEDs
+- Introduced `PSFInferenceEngine` class to centralize training, simulation, metrics, and inference workflows
+- Added `run_type` attribute to `DataHandler` supporting training, simulation, metrics, and inference modes
+- Implemented `ZernikeInputsFactory` class for building `ZernikeInputs` instances based on run type
+- Added `psf_model_loader.py` module for centralized model weights loading
+
+- Added configurable optimizer selection system via new `optimizer.py` module with `get_optimizer` function
+- Optimizer configuration now supports multiple input types: `RecursiveNamespace` from configs, dictionaries, or string names
+- Added support for hyperparameter overrides (learning rate, beta1/beta2, epsilon, amsgrad) via YAML or programmatic configuration
+- `RectifiedAdam` optimizer now dynamically imports TensorFlow Addons only when explicitly specified in configuration
+
+## Bug fixes
+
+- Fix logger formatting for relative RMSE metrics in `metrics.py` (values were not being displayed)
+
+## Internal changes
 
+- Added pre-commit hooks for code quality, formatting, and changelog enforcement
+- Refactored `TFPhysicalPolychromatic` and related modules to separate training vs. inference behavior
+- Enhanced `ZernikeInputs` data class with intelligent assembly based on run type and available data
+- Implemented hybrid loading pattern with eager loading in constructors and lazy-loading via property decorators
+- Centralized PSF data extraction in `data_handler` module
+- Improved code organization with new `tf_utils.py` module in `psf_models` sub-package
+- Updated configuration handling to support inference workflows via `inference_config.yaml`
+- Fixed incorrect argument name in `DataHandler` that prevented proper TensorFlow data type conversion
+- Removed deprecated `get_obs_positions` method
+- Updated documentation to include inference package
+- Refactored `build_PSF_model` to accept either Keras optimizer instances or configuration passed through `get_optimizer`
+- Added `interpolation.py` and `types.py` modules with vendored code from TensorFlow Addons repository
+- Replaced `tfa.image.interpolate_spline` with local `tfa_interpolate_spline_rbf` implementation
+- Added comprehensive unit tests in `test_optimizer.py` and `test_interpolation.py`
+- Updated README and added THIRD_PARTY_LICENSE directory with TensorFlow Addons license
+- Training now runs on TensorFlow 2.11 without requiring TensorFlow Addons installation
+- Removed TensorFlow Addons as a required dependency; RectifiedAdam optimizer now requires explicit TFA installation if needed
+- Remove deprecated/optional import tensorflow-addons statement from tf_layers.py
+- Fixed Sphinx autosummary import errors by removing core dependencies (tensorflow) from `autodoc_mock_imports` in `conf.py`.
+- Updated pyproject.toml to include all wf_psf packages under `src/` and include config/yaml files.
+- Updated example configuration files with clearer inline comments.
+- Generated API documentation for new `inference` package in `api.rst`
+- Generated API documentation for new `instrument` package in `api.rst`
+- Inference Configuration section in `configuration.md` documenting `inference_config.yaml`
+- Restructured Configuration documentation:
+  - Split workflows into "CLI Tasks" and "Additional Components" sections
+  - Added configuration file dependency table showing required vs optional files per task
+  - Clarified configuration filename flexibility (filenames customizable, internal structure fixed)
+  - Standardized section titles (Training Configuration, Metrics Configuration, etc.)
+  - Improved markdown formatting and fixed broken anchor links
+- Updated `dependencies.md` to document `tensorflow-addons` as optional dependency with manual installation instructions
+- `tensorflow-addons` from core dependencies documentation (now documented as optional)
+s
 ## [3.0.0] – 2026-01-20
 
 Major update with PSF model refactoring, masked training, and CI/doc improvements.

DEV_WORKFLOW.md

@@ -1,20 +1,20 @@
 # **WaveDiff Development Plan**
 
 ## 1.  **Define a Milestone**
-    
+
 
   * **Purpose**: Milestones mark the completion of project cycles and achievement of predefined goals. A milestone is a timeline point marking the end of a project cycle, where a set of goals defined at the start of the cycle have been completed.  Goals could be tasks associated with feature development, testing phase completion, etc. List & Open issues. 
-    
+
   * **Types of Milestones:** Differentiate between major, minor and patch release releases to track progress effectively.
-    
+
 
 Make a milestone related to a release on possibly a minor release schedule (e.g. monthly schedule). Differentiate between the different types of releases (minor, major, patch).
 
 ## 2.  **Git Workflow Branching Model (Made with** [**mermaid**](https://mermaid.js.org)**)**
 ![](assets/Git-Branching-Model.png)
 
    *   **main**: Stores official release history with tagged version numbers (see top row in the diagram above).
-    
+
    *   **develop**: This branch is the integration branch for features.
 
    *   **feature**: Branch off of `develop` for new feature development.  Features get merged to `develop` (never to main).
@@ -30,7 +30,7 @@ Make a milestone related to a release on possibly a minor release schedule (e.g.
 
 
 ## 3.  **New Branch naming conventions**
-    
+
 
 Branches created for the purpose of a Pull Request should be directly related to an open issue within the project’s issue tracker.  This ensures that all code changes are tied to specific tasks or features, facilitating better organisation and tracking of contributions. Below are the branch naming conventions:
 
@@ -51,41 +51,41 @@ Branches created for the purpose of a Pull Request should be directly related to
 Replace with the corresponding issue number and provide a brief description of the changes in \`short\_description\`.
 
 ## 4.  **Feature branch creation** 
-    
+
 
 *   Pull the latest changes from the remote repository
 
 *   Checkout `develop`
 
 *   Create a new feature branch
-    
+
 *   Ensure the feature branch’s commits align with the defined scope
-    
+
 
 **Tip**: Keep feature branch development focused on the defined scope outlined in the corresponding issue. Avoid introducing unrelated changes. Instead, open a new issue for out-of-scope features or bugs, creating a separate branch for their development.
 
 ## 5.  **Completion of development** 
-    
+
 
 *   Run training and metrics validation tests locally to confirm no breaking behaviour or errors were introduced.  Include test reports as per the PR template.
 
 *   Open a Pull Request to start the review process, ensuring to map the branch correctly to the target branch (i.e. `feature` -> `develop` or `hotfix` -> `main`).
 
 *   In the description of the Pull Request, explicitly state whether the PR resolves or closes an open issue by using one of the following formats:
-    
+
     *   "Solves #"
-        
+
     *   "Closes #"
-        
+
 
 Example: "Solves #12345" or "Closes #8679".
 
 *   Ensure that the PR meets the defined requirements and passes Continuous Integration (CI) tests.
-    
+
 *   Assign a reviewer, assign yourself as assignee, select the correct project, choose the correct label that describes the nature of the issue (e.g. bug, enhancement, etc), choose Milestone if applicable if the issue is associated with a specific milestone or target release.
-    
+
 *   Address reviewer feedback in threads and iterate as needed, implementing the requested changes or explaining why the task is implemented in the manner it is.  Respect the rule: Whoever opens the thread/conversation in the Pull Request is responsible for closing it.
-    
+
 
 ## 6.  **Merging Pull Requests** 
 
@@ -126,9 +126,9 @@ This separation keeps release notes accurate and enables clean backports
 ## 8.  **Preparing for a Release**
 
 
-*   Each milestone targets a release (feature, patch, etc).
+* Each milestone targets a release (feature, patch, etc).
 
-*   Open a PR from `develop` to `release/vX.Y.Z` upon completing a milestone
+* Create release branch with `git checkout -b release/vX.Y.Z develop` upon completing a milestone
 
 * Collect changelog fragments and generate release notes using:
 
@@ -138,28 +138,28 @@ This separation keeps release notes accurate and enables clean backports
 *   Ensure all checklist items for the release are completed.
 
 *   Merge the PR into main and tag the release.
-    
+
 
 ## 9.  **Continuous Improvement**
 
 
 *   Regularly review and refine the workflow based on team feedback and lessons learned.
-    
+
 *   Encourage collaboration and communication among team members to streamline processes and enhance productivity.
-    
+
 
 ## 10.  **Documentation and Training**
 
 
 *   Maintain up-to-date documentation outlining the development workflow and procedures.
-    
+
 *   Provide training to new team members and ensure existing members are familiar with the workflow and best practices.
 
 
 ## 11.  **Automation and Tooling**
 
 
 *   Explore automation tools to streamline repetitive tasks, such as testing, code formatting, and deployment.
-    
+
 *   Integrate with CI/CD pipelines for automated testing and deployment processes.
-    
+

README.md

@@ -1,5 +1,5 @@
-[![arXiv:2203.04908](https://img.shields.io/badge/astro--ph.IM-arXiv%3A2203.04908-B31B1B.svg)](http://arxiv.org/abs/2203.04908) 
-[![yapf](https://img.shields.io/badge/code%20style-yapf-blue.svg)](https://www.python.org/dev/peps/pep-0008/) 
+[![arXiv:2203.04908](https://img.shields.io/badge/astro--ph.IM-arXiv%3A2203.04908-B31B1B.svg)](http://arxiv.org/abs/2203.04908)
+[![yapf](https://img.shields.io/badge/code%20style-yapf-blue.svg)](https://www.python.org/dev/peps/pep-0008/)
 [![License](https://img.shields.io/badge/License-MIT-brigthgreen.svg)](https://github.com/tobias-liaudat/wf-psf/tree/master/LICENSE)
 [![Documentation](https://img.shields.io/badge/docs-online-blue)](https://cosmostat.github.io/wf-psf/)
 <h1 align='center'>WaveDiff</h1>
@@ -13,3 +13,15 @@ This repository includes:
 - A differentiable PSF model entirely built in [Tensorflow](https://github.com/tensorflow/tensorflow).
 - A [numpy-based PSF simulator](https://github.com/CosmoStat/wf-psf/tree/dummy_main/src/wf_psf/sims).
 - All the scripts, jobs and notebooks required to reproduce the results in [arXiv:2203.04908](http://arxiv.org/abs/2203.04908) and [arXiv:2111.12541](https://arxiv.org/abs/2111.12541).
+
+---------------------------------------------------------------------------
+NOTICE ABOUT THIRD-PARTY CODE
+
+This repository contains code copied from TensorFlow Addons
+(https://github.com/tensorflow/addons), specifically the 
+`interpolate_spline` and `types.py` modules.
+
+Those files are licensed under the Apache License, Version 2.0.
+The copyright and license headers are preserved in each copied file.
+
+All other code in this repository remains under the MIT License.