Merge pull request #18 from ornlneutronimaging/qa

advance main to qa

.github/workflows/package.yml

@@ -32,7 +32,7 @@ jobs:
           echo "versioningit $(versioningit ../)"
           # build the package
           VERSION=$(versioningit ../) conda mambabuild --channel conda-forge --output-folder . .
-          conda verify noarch/mypackagename*.tar.bz2
+          conda verify noarch/bm3dornl*.tar.bz2
       - name: upload conda package to anaconda
         shell: bash -l {0}
         if: startsWith(github.ref, 'refs/tags/v')
@@ -44,4 +44,4 @@ jobs:
           CONDA_LABEL="main"
           if [ "${IS_RC}" = "true" ]; then CONDA_LABEL="rc"; fi
           echo pushing ${{ github.ref }} with label $CONDA_LABEL
-          anaconda upload --label $CONDA_LABEL conda.recipe/noarch/mypackagename*.tar.bz2
+          anaconda upload --label $CONDA_LABEL conda.recipe/noarch/bm3dornl*.tar.bz2

.github/workflows/unittest.yml

@@ -28,8 +28,8 @@ jobs:
           echo "installing additional dependencies if cannot be installed from conda"
       - name: run unit tests
         run: |
-          echo "running unit tests"
-          python -m pytest --cov=src --cov-report=xml --cov-report=term-missing tests/
+          echo "running unit tests (CPU)"
+          python -m pytest --cov=src --cov-report=xml --cov-report=term-missing -m "not cuda_required"
       - name: upload coverage to codecov
         uses: codecov/codecov-action@v4
         with:
@@ -43,4 +43,28 @@ jobs:
           # below to build the conda package in your local machine
           CHANNELS="--channel mantid/label/main --channel conda-forge"
           VERSION=$(versioningit ../) conda mambabuild $CHANNELS --output-folder . .
-          conda verify noarch/mypackagename*.tar.bz2
+          conda verify noarch/bm3dornl*.tar.bz2
+
+  linux_gpu:
+    runs-on: github-gpu-builder
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v3
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniforge-version: "latest"
+          auto-update-conda: true
+          channels: conda-forge,defaults
+          mamba-version: "*"
+          environment-file: environment.yml
+          cache-environment-key: ${{ runner.os }}-env-${{ hashFiles('**/environment.yml') }}
+          cache-downloads-key: ${{ runner.os }}-downloads-${{ hashFiles('**/environment.yml') }}
+      - name: install additional dependencies
+        run: |
+          echo "installing additional dependencies if cannot be installed from conda"
+      - name: run unit tests
+        run: |
+          echo "running unit tests (GPU)"
+          python -m pytest --cov=src --cov-report=xml --cov-report=term-missing -m "cuda_required"

.gitignore

@@ -158,3 +158,8 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+.envrc
+src/bm3dornl/_version.py
+.vscode/settings.json
+tmp/*
+dev*.ipynb

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "tests/bm3dornl-data"]
+	path = tests/bm3dornl-data
+	url = git@code.ornl.gov:sns-hfir-scse/infrastructure/test-data/bm3dornl-data.git

.pre-commit-config.yaml

@@ -13,7 +13,7 @@ repos:
     - id: trailing-whitespace
       exclude: "tests/cis_tests/.*"
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.3.7
+  rev: v0.4.10
   hooks:
     - id: ruff
       args: [--fix, --exit-non-zero-on-fix]

CONTRIBUTING.md

@@ -0,0 +1,121 @@
+# Contributing to BM3D-ORNL
+
+Thank you for considering contributing to the BM3D-ORNL project!
+We welcome contributions from the community and are grateful for your help in improving this library.
+This guide provides instructions on how to contribute to the project.
+
+## Table of Contents
+
+- [Code of Conduct](#code-of-conduct)
+- [Getting Started](#getting-started)
+- [Development Workflow](#development-workflow)
+- [Coding Standards](#coding-standards)
+- [Testing](#testing)
+- [Submitting Changes](#submitting-changes)
+- [Reporting Issues](#reporting-issues)
+- [Contact](#contact)
+
+## Code of Conduct
+
+By participating in this project, you agree to abide by the [Code of Conduct](CODE_OF_CONDUCT.md).
+
+## Getting Started
+
+1. **Fork the Repository**: Fork the [bm3dornl repository](https://github.com/ornlneutronimaging/bm3dornl) to your GitHub account.
+
+2. **Clone the Fork**: Clone your forked repository to your local machine.
+
+    ```bash
+    git clone https://github.com/your-username/bm3dornl.git
+    cd bm3dornl
+    ```
+
+3. **Set Upstream Remote**: Add the original repository as an upstream remote.
+
+    ```bash
+    git remote add upstream https://github.com/ornlneutronimaging/bm3dornl.git
+    ```
+
+4. **Create a Virtual Environment**: Set up a virtual environment to manage dependencies.
+
+    ```bash
+    micromamba create -f environment.yml
+    micromamba activate bm3dornl
+    ```
+
+## Development Workflow
+
+- **Create a Branch**: Create a new branch for your feature or bugfix.
+
+    ```bash
+    git checkout -b feature/your-feature-name
+    ```
+
+- **Make Changes**: Make your changes in the codebase. Use `pre-commit` to help you format your code and check for common issues.
+
+    ```bash
+    pre-commit install
+    ```
+
+> Note: you only need to run `pre-commit install` once. After that, the pre-commit checks will run automatically before each commit.
+
+- **Write Tests**: Write tests for your changes to ensure they are well-tested. See the [testing](#testing) section for more details.
+
+- **Commit Changes**: Commit your changes with a meaningful commit message.
+
+    ```bash
+    git add .
+    git commit -m "Description of your changes"
+    ```
+
+- **Push Changes**: Push your changes to your forked repository.
+
+    ```bash
+    git push origin feature/your-feature-name
+    ```
+
+- **Open a Pull Request**: Open a pull request (PR) from your forked repository to the `next` branch of the original repository. Provide a clear description of your changes and any relevant information.
+
+## Coding Standards
+
+- **PEP 8**: Follow the PEP 8 style guide for Python code.
+- **Docstrings**: Use `numpy` docstrings style to document all public modules, classes, and functions.
+- **Type Annotations**: Use type annotations for function signatures.
+- **Imports**: Group imports into standard library, third-party, and local module sections. Use absolute imports.
+
+## Testing
+
+We use `pytest` for testing. Ensure that your changes are covered by tests.
+
+- **Run Tests**: Run the tests using `pytest`.
+
+    ```bash
+    pytest -v
+    ```
+
+- **Check Coverage**: Check the test coverage.
+
+    ```bash
+    pytest --cov=src/bm3dornl
+    ```
+
+## Submitting Changes
+
+1. **Ensure Tests Pass**: Make sure all tests pass and the coverage is satisfactory.
+
+2. **Update Documentation**: If your changes affect the documentation, update the relevant sections.
+
+3. **Open a Pull Request**: Open a pull request with a clear description of your changes. Reference any related issues in your PR description.
+
+4. **Review Process**: Your pull request will be reviewed by the maintainers. Be prepared to make changes based on feedback.
+
+## Reporting Issues
+
+If you find a bug or have a feature request, please open an issue on the [GitHub issues page](https://github.com/ornlneutronimaging/bm3dornl/issues).
+Provide as much detail as possible, including steps to reproduce the issue if applicable.
+
+## Contact
+
+If you have any questions or need further assistance, please contact the [repo maintainer](zhangc@ornl.gov).
+
+Thank you for contributing to BM3D-ORNL!

README.md

@@ -1,114 +1,13 @@
-# python_project_template
-This repository is a template repository for Python projects under neutrons.
-After you create a new repository using this repo as template, please follow the following steps to adjust it for the new project.
+[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/ornlneutronimaging/bm3dornl/next.svg)](https://results.pre-commit.ci/latest/github/ornlneutronimaging/bm3dornl/next)
+[![Documentation Status](https://readthedocs.org/projects/bm3dornl/badge/?version=latest)](https://bm3dornl.readthedocs.io/en/latest/?badge=latest)
 
-## Codebase Adjustments
+BM3D ORNL
+=========
 
-1. Adjust the branch protection rules for the new repo. By default, we should protect the `main` (stable), `qa` (release candidate), and `next` (development) branches.
+This repository contains the BM3D ORNL code, which is a Python implementation of the BM3D denoising algorithm. The BM3D algorithm was originally proposed by K. Dabov, A. Foi, V. Katkovnik, and K. Egiazarian in the paper "Image Denoising by Sparse 3D Transform-Domain Collaborative Filtering" (2007).
+The BM3D algorithm is a state-of-the-art denoising algorithm that is widely used in the image processing community.
+The BM3D ORNL code is a Python implementation of the BM3D algorithm that has been optimized for performance using both `Numba` and `CuPy`.
+The BM3D ORNL code is designed to be easy to use and easy to integrate into existing Python workflows.
+The BM3D ORNL code is released under an open-source license, and is freely available for download and use.
 
-    1.1 Go to the `Settings` tab of the new repo.
-
-    1.2 Click on `Branches` on the left side.
-
-    1.3 Click on `Add rule` button.
-
-    1.4 Follow the instructions from Github.
-
-
-2. Change the License if MIT license is not suitable for you project. For more information about licenses, please
-refer to [Choose an open source license](https://choosealicense.com/).
-
-
-3. Update the environment dependency file `environment.yml`, which contain both runtime and development dependencies.
-For more information about conda environment file, please refer to [Conda environment file](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#creating-an-environment-file-manually).
-
-    3.1 Specify environment 'name' field to match package name
-
-    3.2 We strongly recommended using a single `environment.yml` file to manage all the dependencies,
-including the runtime and development dependencies.
-
-    3.3 Please add comments to the `environment.yml` file to explain the dependencies.
-
-    3.4 Please prune the dependencies to the minimum when possible,
-we would like the solver to figure out the dependency tree for us.
-
-
-4. Adjust pre-commit configuration file, `.pre-commit-config.yaml` to enable/disable the hooks you need.
-For more information about pre-commit, please refer to [pre-commit](https://pre-commit.com/).
-
-
-5. Having code coverage, `codecov.yaml` is **strongly recommended**,
-please refer to [Code coverage](https://coverage.readthedocs.io/en/coverage-5.5/) for more information.
-
-
-6. Adjust the demo Github action yaml files for CI/CD. For more information about Github action,
-please refer to [Github action](https://docs.github.com/en/actions).
-
-    6.1 Specify package name at: .github/workflows/package.yml#L34
-
-    6.2 Specify package name at: .github/workflows/package.yml#L46
-
-
-7. Adjust the conda recipe, `conda-recipe/meta.yaml` to provide the meta information for the conda package.
-For more information about conda recipe, please refer to [Conda build](https://docs.conda.io/projects/conda-build/en/latest/).
-
-    7.1 Specify package name at: conda.recipe/meta.yaml#L15
-
-    7.2 Update license family, if necessary: conda.recipe/meta.yaml#L42
-
-
-8. Adjust `pyproject.toml` to match your project. For more information about `pyproject.toml`,
-please refer to [pyproject.toml](https://www.python.org/dev/peps/pep-0518/).
-
-    8.1 Specify package name at: pyproject.toml#L2
-
-    8.2 Specify package description at: pyproject.toml#L3
-
-    8.3 Specify package name at: pyproject.toml#L39
-
-    8.4 Specify any terminal entry points (terminal commands) at : pyproject.toml#48.
-In the example, invoking `packagename-cli` in a terminal is equivalent to running the python script
-`from packagenamepy.packagename.import main; main()"
-
-    8.5 Projects will use a  single `pyproject.toml` file to manage all the project metadata,
-including the project name, version, author, license, etc.
-
-    8.6 Python has moved away from `setup.cfg`/`setup.py`, and we would like to follow the trend for our new projects.
-
-
-10. Specify package name at  src/packagenamepy
-
-
-11. Specify package name at: src/packagenamepy/packagename.py
-
-12. If a GUI isn't used, delete the MVP structure at src/packagenamepy:
-    11.1: mainwindow.py
-    11.2: home/
-    11.3: help/
-
-
-11. Clear the content of this file and add your own README.md as the project README file.
-We recommend putting badges of the project status at the top of the README file.
-For more information about badges, please refer to [shields.io](https://shields.io/).
-
-## Repository Adjustments
-
-### Add an access token to anaconda
-
-Here we assume your intent is to upload the conda package to the [anaconda.org/neutrons](https://anaconda.org/neutrons) organization.
-An administrator of _anaconda.org/neutrons_ must create an access token for your repository in the [access settings](https://anaconda.org/neutrons/settings/access).
-
-After created, the token must be stored in a _repository secret_:
-1. Navigate to the main page of the repository on GitHub.com.
-2. Click on the "Settings" tab.
-3. In the left sidebar, navigate to the "Security" section and select "Secrets and variables" followed by "Actions".
-4. Click on the "New repository secret" button.
-5. Enter `ANACONDA_TOKEN` for the secret name
-6. Paste the Anaconda access token
-7. Click on the "Add secret" button
-8. Test the setup by creating a release candidate tag,
-which will result in a package built and uploaded to https://anaconda.org/neutrons/mypackagename
-
-### Add an access token to codecov
-Follow the instructions in the [Confluence page](https://ornl-neutrons.atlassian.net/wiki/spaces/NDPD/pages/103546883/Coverage+reports)
-to create the access token.
+For more information, check out our [FAQ](docs/FAQ.md).

conda.recipe/meta.yaml

@@ -12,7 +12,7 @@
 {% set build_number = 0 %}
 
 package:
-  name: mypackagename
+  name: bm3dornl
   version: {{ version_number }}
 
 source: