easydiffraction 0.10.2__tar.gz → 0.11.0__tar.gz

{easydiffraction-0.10.2 → easydiffraction-0.11.0}/.badgery.yaml

@@ -5,19 +5,18 @@ cards:
   - group: Tests
     type: gh_action
     title: Code/package tests (GitHub)
-    file: test.yaml
+    file: test.yml
     enabled: true
-
   - group: Tests
     type: gh_action
     title: Tutorial tests (GitHub)
-    file: tutorial-tests.yaml
+    file: tutorial-tests.yml
     enabled: true
 
   - group: Tests
     type: gh_action
     title: Package tests (PyPI)
-    file: pypi-test.yaml
+    file: pypi-test.yml
     enabled: true
 
   - group: Code Quality
@@ -60,15 +59,14 @@ cards:
     title: Docstring coverage (interrogate)
     report: reports/{branch}/coverage-docstring.txt
     enabled: true
-
   - group: Build & Release
     type: gh_action
     title: Publishing (PyPI)
-    workflow: pypi-publish.yaml
+    workflow: pypi-publish.yml
     enabled: true
 
   - group: Build & Release
     type: gh_action
     title: Docs build/deployment
-    workflow: docs.yaml
+    workflow: docs.yml
     enabled: true

easydiffraction-0.11.0/.copier-answers.yml

@@ -0,0 +1,27 @@
+# WARNING: Do not edit this file manually.
+# Any changes will be overwritten by Copier.
+_commit: v0.10.1-25-ga5301e9
+_src_path: gh:easyscience/templates
+app_docs_url: https://easyscience.github.io/diffraction-app
+app_doi: 10.5281/zenodo.18163581
+app_package_name: easydiffraction_app
+app_python: '3.13'
+app_repo_name: diffraction-app
+home_page_url: https://easyscience.github.io/diffraction
+home_repo_name: diffraction
+lib_docs_url: https://easyscience.github.io/diffraction-lib
+lib_doi: 10.5281/zenodo.18163581
+lib_package_name: easydiffraction
+lib_python_max: '3.13'
+lib_python_min: '3.11'
+lib_repo_name: diffraction-lib
+project_contact_email: support@easydiffraction.org
+project_copyright_years: 2021-2026
+project_extended_description: A software for calculating neutron powder diffraction
+    patterns based on a structural model and refining its parameters against experimental
+    data
+project_name: EasyDiffraction
+project_short_description: Diffraction data analysis
+project_shortcut: ED
+project_type: both
+template_type: lib

easydiffraction-0.11.0/.github/actions/download-artifact/action.yml

@@ -0,0 +1,50 @@
+name: 'Download artifact'
+description: 'Generic wrapper for actions/download-artifact'
+inputs:
+  name:
+    description: 'Name of the artifact to download'
+    required: true
+
+  path:
+    description: 'Destination path'
+    required: false
+    default: '.'
+
+  pattern:
+    description: 'Glob pattern to match artifact names (optional)'
+    required: false
+    default: ''
+
+  merge-multiple:
+    description: 'Merge multiple artifacts into the same directory'
+    required: false
+    default: 'false'
+
+  github-token:
+    description: 'GitHub token for cross-repo download (optional)'
+    required: false
+    default: ''
+
+  repository:
+    description: 'owner/repo for cross-repo download (optional)'
+    required: false
+    default: ''
+
+  run-id:
+    description: 'Workflow run ID for cross-run download (optional)'
+    required: false
+    default: ''
+
+runs:
+  using: 'composite'
+  steps:
+    - name: Download artifact
+      uses: actions/download-artifact@v4
+      with:
+        name: ${{ inputs.name }}
+        path: ${{ inputs.path }}
+        pattern: ${{ inputs.pattern }}
+        merge-multiple: ${{ inputs.merge-multiple }}
+        github-token: ${{ inputs.github-token }}
+        repository: ${{ inputs.repository }}
+        run-id: ${{ inputs.run-id }}

easydiffraction-0.11.0/.github/actions/github-script/action.yml

@@ -0,0 +1,19 @@
+name: 'GitHub Script'
+description: 'Wrapper for actions/github-script'
+inputs:
+  script:
+    description: 'JavaScript to run'
+    required: true
+
+  github-token:
+    description: 'GitHub token (defaults to github.token)'
+    required: false
+    default: ${{ github.token }}
+
+runs:
+  using: 'composite'
+  steps:
+    - uses: actions/github-script@v8
+      with:
+        script: ${{ inputs.script }}
+        github-token: ${{ inputs.github-token }}

easydiffraction-0.11.0/.github/actions/setup-easyscience-bot/action.yml

@@ -0,0 +1,40 @@
+name: 'Setup EasyScience bot for pushing'
+description: 'Create GitHub App token and configure git identity + origin remote'
+inputs:
+  app-id:
+    description: 'GitHub App ID'
+    required: true
+  private-key:
+    description: 'GitHub App private key (PEM)'
+    required: true
+  repositories:
+    description: 'Additional repositories to grant access to (newline-separated)'
+    required: false
+    default: ''
+
+outputs:
+  token:
+    description: 'Installation access token'
+    value: ${{ steps.app-token.outputs.token }}
+
+runs:
+  using: 'composite'
+  steps:
+    - name: Create GitHub App installation token
+      id: app-token
+      uses: actions/create-github-app-token@v2
+      with:
+        app-id: ${{ inputs.app-id }}
+        private-key: ${{ inputs.private-key }}
+        repositories: ${{ inputs.repositories }}
+
+    - name: Configure git for pushing
+      shell: bash
+      run: |
+        git config user.name "easyscience[bot]"
+        git config user.email "${{ inputs.app-id }}+easyscience[bot]@users.noreply.github.com"
+
+    - name: Configure origin remote to use the bot token
+      shell: bash
+      run: |
+        git remote set-url origin https://x-access-token:${{ steps.app-token.outputs.token }}@github.com/${{ github.repository }}.git

easydiffraction-0.11.0/.github/actions/setup-pixi/action.yml

@@ -0,0 +1,44 @@
+name: 'Setup Pixi Environment'
+description: 'Sets up pixi with common configuration'
+inputs:
+  environments:
+    description: 'Pixi environments to setup'
+    required: false
+    default: 'default'
+  activate-environment:
+    description: 'Environment to activate'
+    required: false
+    default: 'default'
+  run-install:
+    description: 'Whether to run pixi install'
+    required: false
+    default: 'true'
+  locked:
+    description: 'Whether to run pixi install --locked'
+    required: false
+    default: 'false'
+  frozen:
+    description: 'Whether to run pixi install --frozen'
+    required: false
+    default: 'true'
+  cache:
+    description: 'Whether to use cache'
+    required: false
+    default: 'false'
+  post-cleanup:
+    description: 'Whether to run post cleanup'
+    required: false
+    default: 'false'
+
+runs:
+  using: 'composite'
+  steps:
+    - uses: prefix-dev/setup-pixi@v0.9.4
+      with:
+        environments: ${{ inputs.environments }}
+        activate-environment: ${{ inputs.activate-environment }}
+        run-install: ${{ inputs.run-install }}
+        locked: ${{ inputs.locked }}
+        frozen: ${{ inputs.frozen }}
+        cache: ${{ inputs.cache }}
+        post-cleanup: ${{ inputs.post-cleanup }}

easydiffraction-0.11.0/.github/actions/upload-artifact/action.yml

@@ -0,0 +1,49 @@
+name: 'Upload artifact'
+description: 'Generic wrapper for actions/upload-artifact'
+inputs:
+  name:
+    description: 'Artifact name'
+    required: true
+
+  path:
+    description: 'File(s)/dir(s)/glob(s) to upload (newline-separated)'
+    required: true
+
+  include-hidden-files:
+    description: 'Include hidden files'
+    required: false
+    default: 'true'
+
+  if-no-files-found:
+    description: 'warn | error | ignore'
+    required: false
+    default: 'error'
+
+  compression-level:
+    description: '0-9 (0 = no compression)'
+    required: false
+    default: '0'
+
+  retention-days:
+    description: 'Retention in days (optional)'
+    required: false
+    default: ''
+
+  overwrite:
+    description: 'Overwrite an existing artifact with the same name'
+    required: false
+    default: 'false'
+
+runs:
+  using: 'composite'
+  steps:
+    - name: Upload artifact
+      uses: actions/upload-artifact@v4
+      with:
+        name: ${{ inputs.name }}
+        path: ${{ inputs.path }}
+        include-hidden-files: ${{ inputs.include-hidden-files }}
+        if-no-files-found: ${{ inputs.if-no-files-found }}
+        compression-level: ${{ inputs.compression-level }}
+        retention-days: ${{ inputs.retention-days }}
+        overwrite: ${{ inputs.overwrite }}

easydiffraction-0.11.0/.github/actions/upload-codecov/action.yml

@@ -0,0 +1,42 @@
+name: 'Upload coverage to Codecov'
+description: 'Generic wrapper for codecov/codecov-action@v5'
+
+inputs:
+  name:
+    description: 'Codecov upload name'
+    required: true
+
+  flags:
+    description: 'Codecov flags'
+    required: false
+    default: ''
+
+  files:
+    description: 'Coverage report files'
+    required: true
+
+  fail_ci_if_error:
+    description: 'Fail CI if upload fails'
+    required: false
+    default: 'true'
+
+  verbose:
+    description: 'Enable verbose output'
+    required: false
+    default: 'true'
+
+  token:
+    description: 'Codecov token'
+    required: true
+
+runs:
+  using: composite
+  steps:
+    - uses: codecov/codecov-action@v5
+      with:
+        name: ${{ inputs.name }}
+        flags: ${{ inputs.flags }}
+        files: ${{ inputs.files }}
+        fail_ci_if_error: ${{ inputs.fail_ci_if_error }}
+        verbose: ${{ inputs.verbose }}
+        token: ${{ inputs.token }}

easydiffraction-0.11.0/.github/configs/pages-deployment.json

@@ -0,0 +1,6 @@
+{
+  "source": {
+    "branch": "gh-pages",
+    "path": "/"
+  }
+}

easydiffraction-0.11.0/.github/configs/rulesets-develop.json

@@ -0,0 +1,37 @@
+{
+  "name": "develop branch",
+  "target": "branch",
+  "enforcement": "active",
+  "conditions": {
+    "ref_name": {
+      "include": ["refs/heads/develop"],
+      "exclude": []
+    }
+  },
+  "bypass_actors": [
+    {
+      "actor_id": 2476259,
+      "actor_type": "Integration",
+      "bypass_mode": "always"
+    }
+  ],
+  "rules": [
+    {
+      "type": "non_fast_forward"
+    },
+    {
+      "type": "deletion"
+    },
+    {
+      "type": "pull_request",
+      "parameters": {
+        "allowed_merge_methods": ["squash"],
+        "dismiss_stale_reviews_on_push": false,
+        "require_code_owner_review": false,
+        "require_last_push_approval": false,
+        "required_approving_review_count": 0,
+        "required_review_thread_resolution": false
+      }
+    }
+  ]
+}

easydiffraction-0.11.0/.github/configs/rulesets-gh-pages.json

@@ -0,0 +1,19 @@
+{
+  "name": "gh-pages branch",
+  "target": "branch",
+  "enforcement": "active",
+  "conditions": {
+    "ref_name": {
+      "include": ["refs/heads/gh-pages"],
+      "exclude": []
+    }
+  },
+  "rules": [
+    {
+      "type": "non_fast_forward"
+    },
+    {
+      "type": "deletion"
+    }
+  ]
+}

easydiffraction-0.11.0/.github/configs/rulesets-master.json

@@ -0,0 +1,30 @@
+{
+  "name": "master branch",
+  "target": "branch",
+  "enforcement": "active",
+  "conditions": {
+    "ref_name": {
+      "include": ["~DEFAULT_BRANCH"],
+      "exclude": []
+    }
+  },
+  "rules": [
+    {
+      "type": "non_fast_forward"
+    },
+    {
+      "type": "deletion"
+    },
+    {
+      "type": "pull_request",
+      "parameters": {
+        "allowed_merge_methods": ["merge"],
+        "dismiss_stale_reviews_on_push": false,
+        "require_code_owner_review": false,
+        "require_last_push_approval": false,
+        "required_approving_review_count": 0,
+        "required_review_thread_resolution": false
+      }
+    }
+  ]
+}

easydiffraction-0.11.0/.github/copilot-instructions.md

@@ -0,0 +1,159 @@
+# Copilot Instructions for EasyDiffraction
+
+## Project Context
+
+- Python library for crystallographic diffraction analysis, such as
+  refinement of the structural model against experimental data.
+- Support for
+  - sample_form: powder and single crystal
+  - beam_mode: time-of-flight and constant wavelength
+  - radiation_probe: neutron and x-ray
+  - scattering_type: bragg and total scattering
+- Calculations are done using external calculation libraries:
+  - `cryspy` for Bragg diffraction
+  - `crysfml` for Bragg diffraction
+  - `pdffit2` for Total scattering
+- Follow CIF naming conventions where possible. In some places, we
+  deviate for better API design, but we try to keep the spirit of the
+  CIF names.
+- Reusing the concept of datablocks and categories from CIF. We have
+  `DatablockItem` (structure or experiment) and `DatablockCollection`
+  (collection of structures or experiments), as well as `CategoryItem`
+  (single categories in CIF) and `CategoryCollection` (loop categories
+  in CIF).
+- Metadata via frozen dataclasses: `TypeInfo`, `Compatibility`,
+  `CalculatorSupport`.
+- The API is designed for scientists who use EasyDiffraction as a final
+  product in a user-friendly, intuitive way. The target users are not
+  software developers and may have little or no Python experience. The
+  design is not oriented toward developers building their own tooling on
+  top of the library, although experienced developers will find their
+  own way. Prioritize discoverability, clear error messages, and safe
+  defaults so that non-programmers are not stuck by standard API
+  conventions.
+- This project must be developed to be as error-free as possible, with
+  the same rigour applied to critical software (e.g. nuclear-plant
+  control systems). Every code path must be tested, edge cases must be
+  handled explicitly, and silent failures are not acceptable.
+
+## Code Style
+
+- Use snake_case for functions and variables, PascalCase for classes,
+  and UPPER_SNAKE_CASE for constants.
+- Use `from __future__ import annotations` in every module.
+- Type-annotate all public function signatures.
+- Docstrings on all public classes and methods (numpy style).
+- Prefer flat over nested, explicit over clever.
+- Write straightforward code; do not add defensive checks for unlikely
+  edge cases.
+- Prefer composition over deep inheritance.
+- One class per file when the class is substantial; group small related
+  classes.
+- Avoid `**kwargs`; use explicit keyword arguments for clarity,
+  autocomplete, and typo detection.
+- Do not use string-based dispatch (e.g. `getattr(self, f'_{name}')`) to
+  route to attributes or methods. Instead, write explicit named methods
+  (e.g. `_set_sample_form`, `_set_beam_mode`). This keeps the code
+  greppable, autocomplete-friendly, and type-safe.
+- Public parameters and descriptors are either **editable** (property
+  with both getter and setter) or **read-only** (property with getter
+  only). If internal code needs to mutate a read-only property, add a
+  private `_set_<name>` method instead of exposing a public setter.
+
+## Architecture
+
+- Eager imports at the top of the module by default. Use lazy imports
+  (inside a method body) only when necessary to break circular
+  dependencies or to keep `core/` free of heavy utility imports on
+  rarely-called paths (e.g. `help()`).
+- No `pkgutil` / `importlib` auto-discovery patterns.
+- No background/daemon threads.
+- No monkey-patching or runtime class mutation.
+- Do not use `__all__` in modules; instead, rely on explicit imports in
+  `__init__.py` to control the public API.
+- Do not use redundant `import X as X` aliases in `__init__.py`. Use
+  plain `from module import X`.
+- Concrete classes use `@Factory.register` decorators. To trigger
+  registration, each package's `__init__.py` must explicitly import
+  every concrete class (e.g.
+  `from .chebyshev import ChebyshevPolynomialBackground`). When adding a
+  new concrete class, always add its import to the corresponding
+  `__init__.py`.
+- Switchable categories (those whose implementation can be swapped at
+  runtime via a factory) follow a fixed naming convention on the owner
+  (experiment, structure, or analysis): `<category>` (read-only
+  property), `<category>_type` (getter + setter),
+  `show_supported_<category>_types()`, `show_current_<category>_type()`.
+  The owner class owns the type setter and the show methods; the show
+  methods delegate to `Factory.show_supported(...)` passing context.
+  Every factory-created category must have this full API, even if only
+  one implementation exists today.
+- Categories are flat siblings within their owner (datablock or
+  analysis). A category must never be a child of another category of a
+  different type. Categories can reference each other via IDs, but not
+  via parent-child nesting.
+- Every finite, closed set of values (factory tags, experiment axes,
+  category descriptors with enumerated choices) must use a `(str, Enum)`
+  class. Internal code compares against enum members, never raw strings.
+- Keep `core/` free of domain logic — only base classes and utilities.
+- Don't introduce a new abstraction until there is a concrete second use
+  case.
+- Don't add dependencies without asking.
+
+## Tutorials
+
+- Jupyter notebooks (`docs/docs/tutorials/*.ipynb`) are **generated
+  artifacts** — never edit them by hand. Edit only the corresponding
+  `*.py` script, then run `pixi run notebook-convert` followed by
+  `pixi run notebook-prepare` to regenerate the notebook.
+
+## Changes
+
+- Before implementing any structural or design change (new categories,
+  new factories, switchable-category wiring, new datablocks, CIF
+  serialisation changes), read `docs/architecture/architecture.md` to
+  understand the current design choices and conventions. Follow the
+  documented patterns (factory registration, switchable-category naming,
+  metadata classification, etc.) to stay consistent with the rest of the
+  codebase. For localised bug fixes or test updates, the rules in this
+  file are sufficient.
+- The project is in beta; do not keep legacy code or add deprecation
+  warnings. Instead, update tests and tutorials to follow the current
+  API.
+- Minimal diffs: don't rewrite working code just to reformat it.
+- Never remove or replace existing functionality as part of a new change
+  without explicit confirmation. If a refactor would drop features,
+  options, or configurations, highlight every removal and wait for
+  approval.
+- Fix only what's asked; flag adjacent issues as comments, don't fix
+  them silently.
+- Don't add new features or refactor existing code unless explicitly
+  asked.
+- Do not remove TODOs or comments unless the change fully resolves them.
+- When renaming, grep the entire project (code, tests, tutorials, docs).
+- Every change should be atomic and self-contained, small enough to be
+  described by a single commit message. Make one change, suggest the
+  commit message, then stop and wait for confirmation before starting
+  the next change.
+- When in doubt, ask for clarification before making changes.
+
+## Workflow
+
+- All open issues, design questions, and planned improvements are
+  tracked in `docs/architecture/issues_open.md`, ordered by priority.
+  When an issue is fully implemented, move it from that file to
+  `docs/architecture/issues_closed.md`. When the resolution affects the
+  architecture, update the relevant sections of
+  `docs/architecture/architecture.md`.
+- After changes, run linting and formatting fixes with `pixi run fix`.
+  Do not check what was auto-fixed, just accept the fixes and move on.
+- After changes, run unit tests with `pixi run unit-tests`.
+- After changes, run integration tests with
+  `pixi run integration-tests`.
+- After changes, run tutorial tests with `pixi run script-tests`.
+- Suggest a concise commit message (as a code block) after each change
+  (less than 72 characters, imperative mood, without prefixing with the
+  type of change). E.g.:
+  - Add ChebyshevPolynomialBackground class
+  - Implement background_type setter on Experiment
+  - Standardize switchable-category naming convention

easydiffraction-0.11.0/.github/scripts/backmerge-conflict-issue.js

@@ -0,0 +1,69 @@
+module.exports = async ({ github, context, core }) => {
+  // Repo context
+  const owner = context.repo.owner
+  const repo = context.repo.repo
+
+  // Link to the exact workflow run that detected the conflict
+  const runUrl = `${context.serverUrl}/${owner}/${repo}/actions/runs/${context.runId}`
+
+  // We use a *stable title* so we can find/reuse the same "conflict tracker" issue
+  // instead of creating a new issue on every failed run.
+  const title = 'Backmerge conflict: master → develop'
+
+  // Comment/issue body includes the run URL so maintainers can jump straight to logs.
+  const body = [
+    'Automatic backmerge failed due to merge conflicts.',
+    '',
+    `Workflow run: ${runUrl}`,
+    '',
+    'Manual resolution required.',
+  ].join('\n')
+
+  // Label applied to the tracker issue (assumed to already exist in the repo).
+  const label = '[bot] backmerge'
+
+  // Search issues by title across *open and closed* issues.
+  // Why: if the conflict was resolved previously and the issue was closed,
+  // we prefer to reopen it and append a new comment instead of creating duplicates.
+  const q = `repo:${owner}/${repo} is:issue in:title "${title}"`
+  const search = await github.rest.search.issuesAndPullRequests({
+    q,
+    per_page: 10,
+  })
+
+  // Pick the first exact-title match (search can return partial matches).
+  const existing = search.data.items.find((i) => i.title === title)
+
+  if (existing) {
+    // If a tracker issue exists, reuse it:
+    // - reopen it if needed
+    // - add a comment with the new run URL
+    if (existing.state === 'closed') {
+      await github.rest.issues.update({
+        owner,
+        repo,
+        issue_number: existing.number,
+        state: 'open',
+      })
+    }
+
+    await github.rest.issues.createComment({
+      owner,
+      repo,
+      issue_number: existing.number,
+      body,
+    })
+
+    core.notice(`Conflict issue updated: #${existing.number}`)
+    return
+  }
+
+  // No tracker issue exists yet -> create the first one.
+  await github.rest.issues.create({
+    owner,
+    repo,
+    title,
+    body,
+    labels: [label],
+  })
+}