Add ruff, pre-commit, and format existing files

.github/workflows/build-change-of-basis.yml

@@ -30,9 +30,7 @@ jobs:
     - name: Install Python dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install wheel setuptools
-        python -m pip install numpy scipy matplotlib periodictable scikit-learn pytest pytest-cov numba
-        pip install git+https://github.com/bumps/bumps.git
+        python -m pip install .[dev,webview]
         python setup.py build
         mkdir unstable
 
@@ -92,7 +90,7 @@ jobs:
     - name: Update release assets and text
       uses: actions/github-script@v7
       with:
-        github-token: ${{secrets.GITHUB_TOKEN}}          
+        github-token: ${{secrets.GITHUB_TOKEN}}
         script: |
           const fs = require('fs');
           const { owner, repo } = context.repo;

.github/workflows/publish.yml

@@ -0,0 +1,113 @@
+name: Publish to PyPI
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+  release:
+    types: [published]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.config.os }}
+    strategy:
+      matrix:
+        config:
+          - { os: ubuntu-latest, py: 3.7 }
+          - { os: ubuntu-latest, py: 3.8 }
+          - { os: ubuntu-latest, py: 3.9 }
+          - { os: ubuntu-latest, py: "3.10" }
+          - { os: ubuntu-latest, py: "3.11", doc: 1, whl: 1 }
+          - { os: ubuntu-latest, py: "3.12" }
+          - { os: windows-latest, py: "3.11", exe: 1 }
+          # pure python wheels
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.config.py }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.config.py }}
+
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e .[dev,webview]
+          mkdir release
+          mkdir dist
+
+      - name: Check that the docs build (linux only)
+        if: matrix.config.doc == 1
+        run: |
+          python -m pip install sphinx
+          make -j 4 -C doc SPHINXOPTS="-W --keep-going" html
+
+      - name: Build binary wheel
+        if: matrix.config.whl == 1
+        run: |
+          python -m build
+
+      - name: Build installer
+        if: matrix.config.exe == 1
+        run: |
+          pwsh -command ".\$GITHUB_WORKSPACE\extra\build_win_installer.ps1"
+          mv dist\Refl1D*.zip release\
+
+      # See the following for how to upload to a release
+      #  https://eugene-babichenko.github.io/blog/2020/05/09/github-actions-cross-platform-auto-releases/
+      - name: Archive artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: artifacts-${{ matrix.config.os }}-${{ matrix.config.py }}
+          path: |
+            dist/*.whl
+            dist/*.zip
+            dist/*.tar.gz
+            release/*.zip
+
+  publish:
+    needs: build
+    runs-on: ubuntu-latest
+    steps:
+      - name: Retrieve all artifacts
+        uses: actions/download-artifact@v4
+        with:
+          path: artifacts
+          pattern: artifacts-*
+          merge-multiple: true
+
+      - name: show files
+        run: |
+          ls -R artifacts
+          echo "WINDOWS_INSTALLER=$(ls artifacts/release/*.zip)" >> $GITHUB_ENV
+          echo "SRC_DIST=$(ls artifacts/dist/*.tar.gz)" >> $GITHUB_ENV
+          echo "PY3_WHL=$(ls artifacts/dist/*.whl)" >> $GITHUB_ENV
+
+      - name: Update current release
+        if: startsWith(github.ref, 'refs/tags')
+        uses: johnwbyrd/update-release@v1.0.0
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          files: |
+            ${{ env.WINDOWS_INSTALLER }}
+            ${{ env.PY3_WHL }}
+
+      - name: publish distribution to Test PyPI
+        env:
+          TEST_PYPI_API_TOKEN: ${{ secrets.TEST_PYPI_API_TOKEN }}
+        if: env.TEST_PYPI_API_TOKEN != null
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          skip-existing: true
+          password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+          repository-url: https://test.pypi.org/legacy/
+          packages-dir: artifacts/dist/
+
+      - name: Publish distribution to PyPI
+        if: startsWith(github.ref, 'refs/tags')
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}
+          packages-dir: artifacts/dist/

.github/workflows/test.yml

@@ -1,122 +1,44 @@
-name: Test
+name: Test Refl1D
 
 on:
   push:
-    branches: [ master_v0 ]
+    branches: [master]
   pull_request:
-    branches: [ master_v0 ]
-  release:
-    types: [ published ]
+    branches: [master]
+  workflow_dispatch:
 
 jobs:
   test_and_build:
     runs-on: ${{ matrix.config.os }}
     strategy:
       matrix:
         config:
-          - { os: ubuntu-latest, py: 3.7 }
-          - { os: ubuntu-latest, py: 3.8 }
-          - { os: ubuntu-latest, py: 3.9 }
-          - { os: ubuntu-latest, py: "3.10" }
-          - { os: ubuntu-latest, py: "3.11", doc: 1, whl: 1 }
-          - { os: ubuntu-latest, py: "3.12" }
-          - { os: windows-latest, py: "3.11", exe: 1 }
+          - { os: ubuntu-latest, py: "3.10", doc: 1, whl: 1 }
+          - { os: windows-latest, py: "3.10", whl: 1 }
           # pure python wheels
 
     steps:
-    - uses: actions/checkout@v4
-
-    - name: Set up Python ${{ matrix.config.py }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.config.py }}
-
-    - name: Install Python dependencies
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install wheel setuptools build
-        python -m pip install numpy scipy matplotlib bumps periodictable scikit-learn pytest pytest-cov numba
-        pip install -e .
-        mkdir release
-        mkdir dist
-
-    - name: Run tests
-      run: |
-        pytest -v
-        python check_examples.py --chisq
-      env:
-        MPLBACKEND: agg
-
-    - name: Check that the docs build (linux only)
-      if: matrix.config.doc == 1
-      run: |
-        python -m pip install sphinx
-        make -j 4 -C doc SPHINXOPTS="-W --keep-going" html
-
-    - name: Build binary wheel
-      if: matrix.config.whl == 1
-      run: |
-        python -m build
-
-    - name: Build installer
-      if: matrix.config.exe == 1
-      run: |
-        pwsh -command ".\$GITHUB_WORKSPACE\extra\build_win_installer.ps1"
-        mv dist\Refl1D*.zip release\
-
-    # See the following for how to upload to a release
-    #  https://eugene-babichenko.github.io/blog/2020/05/09/github-actions-cross-platform-auto-releases/
-    - name: Archive artifacts
-      uses: actions/upload-artifact@v4
-      with:
-        name: artifacts-${{ matrix.config.os }}-${{ matrix.config.py }}
-        path: |
-          dist/*.whl
-          dist/*.zip
-          dist/*.tar.gz
-          release/*.zip
-
-  publish:
-    needs: test_and_build
-    runs-on: ubuntu-latest
-    steps:
-    - name: Retrieve all artifacts
-      uses: actions/download-artifact@v4
-      with:
-        path: artifacts
-        pattern: artifacts-*
-        merge-multiple: true
-
-    - name: show files
-      run: |
-        ls -R artifacts
-        echo "WINDOWS_INSTALLER=$(ls artifacts/release/*.zip)" >> $GITHUB_ENV
-        echo "SRC_DIST=$(ls artifacts/dist/*.tar.gz)" >> $GITHUB_ENV
-        echo "PY3_WHL=$(ls artifacts/dist/*.whl)" >> $GITHUB_ENV
-
-    - name: Update current release
-      if: startsWith(github.ref, 'refs/tags')
-      uses: johnwbyrd/update-release@v1.0.0
-      with:
-        token: ${{ secrets.GITHUB_TOKEN }}
-        files: |
-          ${{ env.WINDOWS_INSTALLER }}
-          ${{ env.PY3_WHL }}
-
-    - name: publish distribution to Test PyPI
-      env:
-        TEST_PYPI_API_TOKEN: ${{ secrets.TEST_PYPI_API_TOKEN }}
-      if: env.TEST_PYPI_API_TOKEN != null
-      uses: pypa/gh-action-pypi-publish@release/v1
-      with:
-        skip-existing: true
-        password: ${{ secrets.TEST_PYPI_API_TOKEN }}
-        repository-url: https://test.pypi.org/legacy/
-        packages-dir: artifacts/dist/
-
-    - name: Publish distribution to PyPI
-      if: startsWith(github.ref, 'refs/tags')
-      uses: pypa/gh-action-pypi-publish@release/v1
-      with:
-        password: ${{ secrets.PYPI_API_TOKEN }}
-        packages-dir: artifacts/dist/
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.config.py }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.config.py }}
+
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install .[dev,webview]
+          python setup.py build
+
+      - name: Run tests
+        run: |
+          pytest -v
+          python check_examples.py --chisq
+        env:
+          MPLBACKEND: agg
+
+      - name: Check that the docs build (linux only)
+        if: matrix.config.doc == 1
+        run: |
+          pip install sphinx
+          make -j 4 -C doc SPHINXOPTS="-W --keep-going" html

.github/workflows/unstable.yml

@@ -34,10 +34,8 @@ jobs:
 
     - name: Install Python dependencies
       run: |
-        python -m pip install --upgrade pip
-        python -m pip install wheel setuptools
-        python -m pip install numpy scipy matplotlib periodictable scikit-learn pytest pytest-cov numba
-        pip install git+https://github.com/bumps/bumps.git
+        pip install --upgrade pip
+        pip install .[dev,webview]
         python setup.py build
         mkdir unstable
 

.gitignore

@@ -23,6 +23,7 @@ refl1d-webview-client*.tgz
 /refl1d-*
 /bumps-*
 /Refl1D.pdf
+/output-*
 
 # Build
 *.so

.pre-commit-config.yaml

@@ -0,0 +1,18 @@
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.6.0
+  hooks:
+    - id: check-added-large-files
+      args: [--maxkb=8192]
+    - id: check-merge-conflict
+    - id: check-yaml
+      args: [--allow-multiple-documents]
+    - id: end-of-file-fixer
+    - id: trailing-whitespace
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.6.1
+  hooks:
+    # - id: ruff
+    #   args: [--fix, --exit-non-zero-on-fix]
+    - id: ruff-format
+      # args: [--line-length=120]

Makefile

@@ -0,0 +1,15 @@
+ROOTDIR = $(shell pwd)
+
+# This nifty perl one-liner collects all comments headed by the double "#" symbols next to each target and recycles them as comments
+.PHONY: help
+help: ## Print this help message
+	@perl -nle'print $& if m{^[/a-zA-Z_-]+:.*?## .*$$}' $(MAKEFILE_LIST) | sort | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-25s\033[0m %s\n", $$1, $$2}'
+
+
+.PHONY: lint
+lint: ## Run ruff linting
+	@ruff check --fix refl1d/ tests/ setup.py
+
+.PHONY: format
+format: ## Run ruff formatting
+	@ruff format refl1d/ tests/ setup.py