easydiffraction 0.2.0__tar.gz → 0.3.0__tar.gz

easydiffraction-0.3.0/.github/dependabot.yml

@@ -0,0 +1,10 @@
+version: 2
+updates:
+  - package-ecosystem: pip
+    directory: /
+    schedule:
+      interval: daily
+    open-pull-requests-limit: 10
+    target-branch: develop
+    labels:
+      - dependencies

{easydiffraction-0.2.0 → easydiffraction-0.3.0}/.github/release-drafter.yml

@@ -4,17 +4,17 @@
 name-template: 'EasyDiffraction $RESOLVED_VERSION'
 tag-template: 'v$RESOLVED_VERSION'
 categories:
-- title: 'Added'
-  labels:  # Labels to use to categorize a pull request as a feature
-    - 'enhancement'
-- title: 'Fixed'
-  labels:  # Labels to use to categorize a pull request as a bug fix
-    - 'bug'
-- title: 'Changed'
-  labels:  # Labels to use to categorize a pull request as a maintenance task
-    - 'chore'
-    - 'documentation'
-    - 'refactor'
+  - title: 'Added'
+    labels: # Labels to use to categorize a pull request as a feature
+      - 'enhancement'
+  - title: 'Fixed'
+    labels: # Labels to use to categorize a pull request as a bug fix
+      - 'bug'
+  - title: 'Changed'
+    labels: # Labels to use to categorize a pull request as a maintenance task
+      - 'chore'
+      - 'documentation'
+      - 'refactor'
 change-template: '- $TITLE (#$NUMBER)'
 change-title-escapes: '\<*_&' # You can add # and @ to disable mentions, and add ` to disable code blocks.
 version-resolver:

easydiffraction-0.3.0/.github/workflows/ci-testing.yaml

@@ -0,0 +1,258 @@
+# This is the main workflow for testing the code, notebooks and package.
+# It is divided into three jobs:
+# 1. Code-quality:
+#    - Check the validity of pyproject.toml
+#    - Check code linting
+#    - Check code formatting
+#    - Check Jupyter notebooks formatting
+#    - Check formatting of Markdown, YAML, TOML, etc. files
+# 2. Test-code:
+#    - Test the code base and upload coverage to Codecov
+#    - Create the Python package
+#    - Upload the Python package for the next job
+# 3. Test-package:
+#    - Download the Python package from the previous job
+#    - Install the downloaded Python package
+#    - Test the code base
+#    - Check if Jupyter Notebooks run without errors
+
+name: Test code, notebooks and package
+
+on:
+  # Trigger the workflow on push
+  push:
+    # Every branch
+    branches:
+      - '**'
+    # But do not run this workflow on creating a new tag starting with 'v', e.g. 'v1.0.3' (see pypi-publish.yml)
+    tags-ignore:
+      - 'v*'
+  # Trigger the workflow on pull request
+  pull_request:
+    branches:
+      - '**'
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Allow only one concurrent workflow, skipping runs queued between the run in-progress and latest queued.
+# And cancel in-progress runs.
+concurrency:
+  group:
+    ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  # Job 1: Check code quality and consistency
+  code-quality:
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ['3.12']
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: '0' # full history with tags to get the version number by versioningit
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Python dependencies
+        # Install 'validate-pyproject' for checking pyproject.toml
+        # Install 'ruff' for code linting and formatting
+        # Install 'nbqa' for quality assurance of Jupyter notebooks
+        run: pip install 'validate-pyproject[all]' ruff nbqa
+
+      - name: Install npm dependencies
+        # Install 'prettier' for code formatting of Markdown, YAML, etc. files
+        # Install 'prettier-plugin-toml' plugin for code formatting of TOML files
+        run: npm install prettier prettier-plugin-toml --save-dev --save-exact
+
+      # Check the validity of pyproject.toml
+      - name: Check validity of pyproject.toml
+        id: check_pyproject
+        continue-on-error: true
+        run: validate-pyproject pyproject.toml
+
+      # Check code linting with Ruff in the project root
+      - name: Check code linting
+        id: check_code_linting
+        continue-on-error: true
+        run: ruff check .
+
+      - name: Suggestion to fix code linting issues (for *.py files)
+        if: steps.check_code_linting.outcome == 'failure'
+        run:
+          echo "In project root run 'ruff check . --fix' and commit changes to
+          fix issues."
+
+      # Check code formatting with Ruff in the project root
+      - name: Check code formatting
+        id: check_code_formatting
+        continue-on-error: true
+        run: ruff format . --check
+
+      - name: Suggestion to fix code formatting issues (for *.py files)
+        if: steps.check_code_formatting.outcome == 'failure'
+        run:
+          echo "In project root run 'ruff format .' and commit changes to fix
+          issues."
+
+      # Check Jupyter notebooks with nbQA in the sample directory
+      - name: Check Jupyter notebooks formatting
+        id: check_notebooks
+        continue-on-error: true
+        run: nbqa ruff examples/
+
+      - name: Suggestion to fix notebook formatting issues (for *.ipynb files)
+        if: steps.check_notebooks.outcome == 'failure'
+        run:
+          echo "In project root run 'nbqa ruff examples/ --fix' and commit
+          changes to fix issues."
+
+      # Check formatting of Markdown, YAML, TOML, etc. files with Prettier in the project root
+      - name: Check formatting of Markdown, YAML, TOML, etc. files
+        id: check_others_formatting
+        continue-on-error: true
+        run: npx prettier . --check --config=prettierrc.toml
+
+      - name: Suggestion to fix non-code formatting issues (for *.md, etc.)
+        if: steps.check_others_formatting.outcome == 'failure'
+        run:
+          echo "In project root run 'npx prettier . --write
+          --config=prettierrc.toml' and commit changes to fix issues."
+
+      - name: Force fail if any of the previous steps failed
+        if: |
+          steps.check_pyproject.outcome == 'failure' ||
+          steps.check_code_linting.outcome == 'failure' ||
+          steps.check_code_formatting.outcome == 'failure' || 
+          steps.check_notebooks.outcome == 'failure' || 
+          steps.check_others_formatting.outcome == 'failure'
+        run: exit 1
+
+  # Job 2: Test code and upload coverage to Codecov.
+  test-code:
+    needs: code-quality # previous job 'code-quality' need to be finished first
+
+    # current job matrix. if modified, remember to UPDATE the strategy in the next job
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-24.04, windows-2022, macos-13, macos-14]
+        python-version: ['3.10', '3.11', '3.12']
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: '0' # full history with tags to get the version number by versioningit
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Upgrade package installer for Python
+        run: python -m pip install --upgrade pip
+
+      - name: Install Python dependencies
+        run: pip install '.[dev,charts]'
+
+      - name: Run Python tests and create coverage report
+        run: >
+          pytest tests/ --cov=./ --cov-report=xml:coverage/coverage.xml
+          --junitxml=./coverage/junit.xml --color=yes -n auto
+
+      #- name: Upload test results to Codecov
+      #  if: ${{ !cancelled() }}
+      #  uses: codecov/test-results-action@v1
+      #  with:
+      #    files: ./coverage/junit.xml
+      #    fail_ci_if_error: true  # optional (default = false)
+      #    name: Pytest results
+      #    token: ${{ secrets.CODECOV_TOKEN }}
+
+      #- name: Upload coverage report to Codecov
+      #  uses: codecov/codecov-action@v4
+      #  with:
+      #    files: ./coverage/coverage.xml
+      #    env_vars: OS,PYTHON
+      #    fail_ci_if_error: true  # optional (default = false)
+      #    name: Pytest coverage
+      #    token: ${{ secrets.CODECOV_TOKEN }}
+      #  env:
+      #    OS: ${{ matrix.os }}
+      #    PYTHON: ${{ matrix.python-version }}
+
+      - name: Create Python package
+        run: python -m build --wheel --outdir dist
+
+      - name:
+          Upload zipped Python package (with tests and examples) for next job
+        uses: actions/upload-artifact@v4
+        with:
+          name:
+            EasyDiffractionLib_py${{ matrix.python-version }}_${{ matrix.os
+            }}_${{ runner.arch }}
+          path: |
+            dist/*.whl
+            tests/
+            examples/
+          if-no-files-found: 'error'
+          compression-level: 0
+
+  # Job 3: Test the package
+  test-package:
+    needs: test-code # the previous job needs to be finished first
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-24.04, windows-2022, macos-13, macos-14]
+        python-version: ['3.10', '3.11', '3.12']
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Upgrade package installer for Python
+        run: python -m pip install --upgrade pip
+
+      - name:
+          Download zipped Python package (with tests and examples) from previous
+          job
+        uses: actions/download-artifact@v4
+        with: # name or path are taken from the upload step of the previous job
+          name:
+            EasyDiffractionLib_py${{ matrix.python-version }}_${{ matrix.os
+            }}_${{ runner.arch }}
+          path: . # directory to extract downloaded zipped artifacts
+
+      # The local version must be higher than the PyPI version for pip to
+      # prefer the local version. So, after a new release and a new tag,
+      # remember to merge the master branch with the develop branch,
+      # and then create a new feature branch from the develop branch.
+      - name: Install Python package from previous job with 'dev' extras
+        run: pip install 'easydiffraction[dev]' --find-links=dist
+
+      - name: Run Python tests
+        run: >
+          pytest tests/ --color=yes -n auto
+
+      - name: Check if Jupyter Notebooks run without errors
+        shell: bash
+        run: >
+          pytest --nbmake examples/ --ignore-glob='examples/*emcee*'
+          --nbmake-timeout=300 --color=yes -n=auto

{easydiffraction-0.2.0 → easydiffraction-0.3.0}/.github/workflows/delete-old-runs.yml

@@ -11,7 +11,6 @@ on:
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
-
     inputs:
       days:
         description: 'Number of days.'
@@ -22,26 +21,32 @@ on:
         required: true
         default: 6
       delete_workflow_pattern:
-        description: 'The name or filename of the workflow. if not set then it will target all workflows.'
+        description:
+          'The name or filename of the workflow. if not set then it will target
+          all workflows.'
         required: false
       delete_workflow_by_state_pattern:
-        description: 'Remove workflow by state: active, deleted, disabled_fork, disabled_inactivity, disabled_manually'
+        description:
+          'Remove workflow by state: active, deleted, disabled_fork,
+          disabled_inactivity, disabled_manually'
         required: true
-        default: "All"
+        default: 'All'
         type: choice
         options:
-          - "All"
+          - 'All'
           - active
           - deleted
           - disabled_inactivity
           - disabled_manually
       delete_run_by_conclusion_pattern:
-        description: 'Remove workflow by conclusion: action_required, cancelled, failure, skipped, success'
+        description:
+          'Remove workflow by conclusion: action_required, cancelled, failure,
+          skipped, success'
         required: true
-        default: "All"
+        default: 'All'
         type: choice
         options:
-          - "All"
+          - 'All'
           - action_required
           - cancelled
           - failure
@@ -53,7 +58,6 @@ on:
 
 jobs:
   del-runs:
-
     runs-on: ubuntu-latest
 
     permissions:
@@ -67,7 +71,10 @@ jobs:
           repository: ${{ github.repository }}
           retain_days: ${{ github.event.inputs.days }}
           keep_minimum_runs: ${{ github.event.inputs.minimum_runs }}
-          delete_workflow_pattern: ${{ github.event.inputs.delete_workflow_pattern }}
-          delete_workflow_by_state_pattern: ${{ github.event.inputs.delete_workflow_by_state_pattern }}
-          delete_run_by_conclusion_pattern: ${{ github.event.inputs.delete_run_by_conclusion_pattern }}
+          delete_workflow_pattern:
+            ${{ github.event.inputs.delete_workflow_pattern }}
+          delete_workflow_by_state_pattern:
+            ${{ github.event.inputs.delete_workflow_by_state_pattern }}
+          delete_run_by_conclusion_pattern:
+            ${{ github.event.inputs.delete_run_by_conclusion_pattern }}
           dry_run: ${{ github.event.inputs.dry_run }}

easydiffraction-0.3.0/.github/workflows/ossar-analysis.yml

@@ -0,0 +1,40 @@
+# Integrates a collection of open source static analysis tools with
+# GitHub code scanning.
+# https://github.com/github/ossar-action
+
+name: Run security static analysis
+
+on:
+  # Runs on pull requests
+  pull_request:
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  ossar-analysis:
+    # OSSAR runs on windows-latest.
+    # ubuntu-latest and macos-latest support coming soon
+    runs-on: windows-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          # We must fetch at least the immediate parents so that if this is
+          # a pull request then we can checkout the head.
+          fetch-depth: 2
+
+      # If this run was triggered by a pull request event, then checkout
+      # the head of the pull request instead of the merge commit.
+      - run: git checkout HEAD^2
+        if: ${{ github.event_name == 'pull_request' }}
+
+      - name: Run open source static analysis tools
+        uses: github/ossar-action@main
+        id: ossar
+
+      - name: Upload results to Security tab
+        uses: github/codeql-action/upload-sarif@v3
+        with:
+          sarif_file: ${{ steps.ossar.outputs.sarifFile }}

easydiffraction-0.3.0/.github/workflows/pypi-publish.yml

@@ -0,0 +1,42 @@
+# Builds a Python package and publish it to PyPI when a new tag is
+# created.
+
+name: Upload release to PyPI
+
+on:
+  # Runs on creating a new tag starting with 'v', e.g. 'v1.0.3'
+  push:
+    tags:
+      - 'v*'
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  pypi-publish:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check-out repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: '0' # full history with tags to get the version number by versioningit
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Upgrade package installer for Python
+        run: pip install --upgrade pip
+
+      - name: Install Python dependencies
+        run: pip install '.[dev]'
+
+      - name: Create Python package
+        run: python -m build
+
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_PASSWORD }}

{easydiffraction-0.2.0 → easydiffraction-0.3.0}/.github/workflows/release-drafter.yml

@@ -10,7 +10,6 @@ on:
 
 jobs:
   update-release-draft:
-
     runs-on: ubuntu-latest
 
     steps:

easydiffraction-0.3.0/.github/workflows/verify-pr-labels.yml

@@ -0,0 +1,22 @@
+# Verifies if a pull request has at least one label from a set of valid
+# labels before it can be merged.
+
+name: Verify pull request labels
+
+on:
+  # Runs on pull requests to a repository
+  pull_request_target:
+    types: [opened, labeled, unlabeled, synchronize]
+
+jobs:
+  verify-pr-labels:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Verify pull request labels
+        uses: jesusvasquez333/verify-pr-label-action@v1.4.0
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          valid-labels: 'enhancement, bug, chore, documentation, refactor'
+          pull-request-number: ${{ github.event.pull_request.number }}
+          disable-reviews: false

{easydiffraction-0.2.0 → easydiffraction-0.3.0}/.gitignore

@@ -18,11 +18,6 @@ __pycache__
 .coverage
 .pyc
 
-# Poetry
-dist
-poetry.lock
-*.egg-info
-
 # PyInstaller
 build
 *.spec
@@ -30,6 +25,9 @@ build
 # Jupyter
 .ipynb_checkpoints
 
+# npm
+node_modules
+
 # macOS
 .DS_Store
 *.app

{easydiffraction-0.2.0 → easydiffraction-0.3.0}/CONTRIBUTING.md

@@ -1,48 +1,53 @@
 # Contributing
 
 When contributing, please first discuss the change you wish to make via issue,
-email, or any other method with the owners of this repository before making a change.
+email, or any other method with the owners of this repository before making a
+change.
 
-Please note we have a code of conduct, please follow it in all your interactions with the project.
+Please note we have a code of conduct, please follow it in all your interactions
+with the project.
 
 ## Pull Request Process
 
-1. Ensure any install or build dependencies are removed before the end of the layer when doing a 
-   build.
-2. Update the README.md with details of changes to the interface, this includes new environment 
-   variables, exposed ports, useful file locations and container parameters.
-3. Increase the version numbers in any example files and the README.md to the new version that this
-   Pull Request would represent. The versioning scheme we use is [SemVer](http://semver.org/).
-4. You may merge the Pull Request in once you have the sign-off of two other developers, or if you 
-   do not have permission to do that, you may request the second reviewer to merge it for you.
+1. Ensure any install or build dependencies are removed before the end of the
+   layer when doing a build.
+2. Update the README.md with details of changes to the interface, this includes
+   new environment variables, exposed ports, useful file locations and container
+   parameters.
+3. Increase the version numbers in any example files and the README.md to the
+   new version that this Pull Request would represent. The versioning scheme we
+   use is [SemVer](http://semver.org/).
+4. You may merge the Pull Request in once you have the sign-off of two other
+   developers, or if you do not have permission to do that, you may request the
+   second reviewer to merge it for you.
 
 ## Code of Conduct
 
 ### Our Pledge
 
 In the interest of fostering an open and welcoming environment, we as
-contributors and maintainers pledge to make participation in our project and
-our community a harassment-free experience for everyone, regardless of age, body
-size, disability, ethnicity, gender identity and expression, level of experience,
-nationality, personal appearance, race, religion, or sexual identity and
-orientation.
+contributors and maintainers pledge to make participation in our project and our
+community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, gender identity and expression, level of
+experience, nationality, personal appearance, race, religion, or sexual identity
+and orientation.
 
 ### Our Standards
 
 Examples of behavior that contributes to creating a positive environment
 include:
 
-* Being respectful of differing viewpoints and experiences
-* Gracefully accepting constructive criticism
-* Focusing on what is best for the community
+- Being respectful of differing viewpoints and experiences
+- Gracefully accepting constructive criticism
+- Focusing on what is best for the community
 
 Examples of unacceptable behavior by participants include:
 
-* Trolling, insulting/derogatory comments, and personal or political attacks
-* Public or private harassment
-* Publishing others' private information, such as a physical or electronic
+- Trolling, insulting/derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information, such as a physical or electronic
   address, without explicit permission
-* Other conduct which could reasonably be considered inappropriate in a
+- Other conduct which could reasonably be considered inappropriate in a
   professional setting
 
 ### Our Responsibilities
@@ -51,11 +56,11 @@ Project maintainers are responsible for clarifying the standards of acceptable
 behavior and are expected to take appropriate and fair corrective action in
 response to any instances of unacceptable behavior.
 
-Project maintainers 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, or to ban temporarily or
-permanently any contributor for other behaviors that they deem inappropriate,
-threatening, offensive, or harmful.
+Project maintainers 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, or to ban temporarily or permanently any
+contributor for other behaviors that they deem inappropriate, threatening,
+offensive, or harmful.
 
 ### Scope
 
@@ -72,8 +77,9 @@ Instances of abusive, harassing, or otherwise unacceptable behavior may be
 reported by contacting the project team at suport@easydiffraction.org. All
 complaints will be reviewed and investigated and will result in a response that
 is deemed necessary and appropriate to the circumstances. The project team is
-obligated to maintain confidentiality with regard to the reporter of an incident.
-Further details of specific enforcement policies may be posted separately.
+obligated to maintain confidentiality with regard to the reporter of an
+incident. Further details of specific enforcement policies may be posted
+separately.
 
 Project maintainers who do not follow or enforce the Code of Conduct in good
 faith may face temporary or permanent repercussions as determined by other
@@ -81,8 +87,8 @@ members of the project's leadership.
 
 ### Attribution
 
-This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
-available at [http://contributor-covenant.org/version/1/4][version]
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 1.4, available at [http://contributor-covenant.org/version/1/4][version]
 
 [homepage]: http://contributor-covenant.org
 [version]: http://contributor-covenant.org/version/1/4/