easydiffraction 0.20.0__tar.gz → 0.21.1__tar.gz

easydiffraction-0.21.1/.github/workflows/pypi-publish.yml

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+# Builds a Python package and publish it to PyPI when a new tag is
+# created.
+
+name: PyPI publishing
+
+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
+
+    permissions:
+      contents: read
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+
+    steps:
+      - name: Check-out repository
+        uses: actions/checkout@v6
+        with:
+          fetch-depth: 0 # full history with tags to get the version number by versioningit
+
+      - name: Set up pixi
+        uses: ./.github/actions/setup-pixi
+
+      # Build the Python package (to dist/ folder)
+      - name: Create Python package
+        run: pixi run --frozen default-build
+
+      # Publish the package to PyPI (from dist/ folder)
+      # Instead of publishing with personal access token, we use
+      # GitHub Actions OIDC to get a short-lived token from PyPI.
+      # New publisher must be previously configured in PyPI at
+      # https://pypi.org/manage/project/easydiffraction/settings/publishing/
+      # Use the following data:
+      # Owner: easyscience
+      # Repository name: diffraction-lib
+      # Workflow name: pypi-publish.yml
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: 'dist'

easydiffraction-0.21.1/PKG-INFO

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+Metadata-Version: 2.5
+Name: easydiffraction
+Version: 0.21.1
+Summary: Diffraction data analysis
+Project-URL: Homepage, https://easydiffraction.org
+Project-URL: Documentation, https://easyscience.github.io/diffraction-lib
+Project-URL: Release Notes, https://github.com/easyscience/diffraction-lib/releases
+Project-URL: Source Code, https://github.com/easyscience/diffraction-lib
+Project-URL: Issue Tracker, https://github.com/easyscience/diffraction-lib/issues
+Author: EasyScience contributors
+License-Expression: BSD-3-Clause
+License-File: LICENSE
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.12
+Requires-Dist: asciichartpy
+Requires-Dist: asteval
+Requires-Dist: bumps
+Requires-Dist: crysfml>=0.8.0
+Requires-Dist: cryspy>=0.13.0
+Requires-Dist: darkdetect
+Requires-Dist: dfo-ls
+Requires-Dist: diffpy-pdffit2
+Requires-Dist: diffpy-utils
+Requires-Dist: emcee
+Requires-Dist: filelock
+Requires-Dist: gemmi
+Requires-Dist: h5py
+Requires-Dist: lmfit
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: pillow
+Requires-Dist: plotly
+Requires-Dist: pooch
+Requires-Dist: pybaselines>=1.1
+Requires-Dist: rich
+Requires-Dist: scipy
+Requires-Dist: sympy
+Requires-Dist: typeguard
+Requires-Dist: typer
+Requires-Dist: uncertainties
+Requires-Dist: varname
+Provides-Extra: dev
+Requires-Dist: build; extra == 'dev'
+Requires-Dist: codespell; extra == 'dev'
+Requires-Dist: copier; extra == 'dev'
+Requires-Dist: docstring-parser-fork!=0.0.15; extra == 'dev'
+Requires-Dist: docstripy; extra == 'dev'
+Requires-Dist: format-docstring; extra == 'dev'
+Requires-Dist: gitpython; extra == 'dev'
+Requires-Dist: hypothesis; extra == 'dev'
+Requires-Dist: interrogate; extra == 'dev'
+Requires-Dist: jinja2; extra == 'dev'
+Requires-Dist: jupyterquiz; extra == 'dev'
+Requires-Dist: jupytext; extra == 'dev'
+Requires-Dist: mike; extra == 'dev'
+Requires-Dist: mkdocs; extra == 'dev'
+Requires-Dist: mkdocs-autorefs; extra == 'dev'
+Requires-Dist: mkdocs-jupyter; extra == 'dev'
+Requires-Dist: mkdocs-markdownextradata-plugin; extra == 'dev'
+Requires-Dist: mkdocs-material; extra == 'dev'
+Requires-Dist: mkdocs-plugin-inline-svg; extra == 'dev'
+Requires-Dist: mkdocstrings-python; extra == 'dev'
+Requires-Dist: nbmake; extra == 'dev'
+Requires-Dist: nbqa; extra == 'dev'
+Requires-Dist: nbstripout; extra == 'dev'
+Requires-Dist: pre-commit; extra == 'dev'
+Requires-Dist: pydoclint; extra == 'dev'
+Requires-Dist: pytest; extra == 'dev'
+Requires-Dist: pytest-benchmark; extra == 'dev'
+Requires-Dist: pytest-cov; extra == 'dev'
+Requires-Dist: pytest-randomly; extra == 'dev'
+Requires-Dist: pytest-xdist; extra == 'dev'
+Requires-Dist: pyyaml; extra == 'dev'
+Requires-Dist: radon; extra == 'dev'
+Requires-Dist: ruff; extra == 'dev'
+Requires-Dist: spdx-headers; extra == 'dev'
+Requires-Dist: validate-pyproject[all]; extra == 'dev'
+Requires-Dist: versioningit; extra == 'dev'
+Description-Content-Type: text/markdown
+
+<p>
+  <picture>
+    <!-- light mode logo -->
+    <source media='(prefers-color-scheme: light)' srcset='https://raw.githubusercontent.com/easyscience/assets-branding/refs/heads/master/easydiffraction/logos/light.svg'>
+    <!-- dark mode logo -->
+    <source media='(prefers-color-scheme: dark)' srcset='https://raw.githubusercontent.com/easyscience/assets-branding/refs/heads/master/easydiffraction/logos/dark.svg'>
+    <!-- default logo == light mode logo -->
+    <img src='https://raw.githubusercontent.com/easyscience/assets-branding/refs/heads/master/easydiffraction/logos/light.svg' alt='EasyDiffraction'>
+  </picture>
+</p>
+
+**EasyDiffraction** is a software for calculating diffraction patterns
+based on a structural model and refining its parameters against
+experimental data.
+
+<!-- HOME REPOSITORY SECTION -->
+
+**EasyDiffraction** is developed both as a Python library and as a
+cross-platform desktop application.
+
+Here, we focus on the Python library. For the graphical user interface
+(GUI), please see the corresponding
+[GUI resources](https://github.com/easyscience/diffraction-app).
+
+License:
+[BSD 3-Clause](https://github.com/easyscience/diffraction-lib/blob/master/LICENSE)
+
+## Useful Links
+
+### For Users
+
+- 📖
+  [Documentation](https://easyscience.github.io/diffraction-lib/latest)
+- 🚀
+  [Getting Started](https://easyscience.github.io/diffraction-lib/latest/introduction)
+- 🧪
+  [Tutorials](https://easyscience.github.io/diffraction-lib/latest/tutorials)
+- 💬
+  [Get in Touch](https://easyscience.github.io/diffraction-lib/latest/introduction/#get-in-touch)
+- 🧾
+  [Citation](https://easyscience.github.io/diffraction-lib/latest/introduction/#citation)
+
+### For Contributors
+
+- 🧑‍💻 [Source Code](https://github.com/easyscience/diffraction-lib)
+- 🐞
+  [Issue Tracker](https://github.com/easyscience/diffraction-lib/issues)
+- 💡
+  [Discussions](https://github.com/easyscience/diffraction-lib/discussions)
+- 🤝
+  [Contributing Guide](https://github.com/easyscience/diffraction-lib/blob/master/CONTRIBUTING.md)
+- 🛡
+  [Code of Conduct](https://github.com/easyscience/.github/blob/master/CODE_OF_CONDUCT.md)

easydiffraction-0.21.1/docs/dev/issues/closed/cli-fit-command-never-saves-results-to-disk.md

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+# 137. CLI `fit` Command Never Saves Results to Disk
+
+Closed after fixing the CLI persistence boundary. `Analysis.fit()`
+updates fit state without saving the project. The CLI `fit` command now
+calls `project.save()` explicitly after a successful non-`--dry` fit, so
+updated results still persist. With `--dry`, the project path is cleared
+for the fit and the explicit save is skipped, preventing project files
+and fit sidecars from being overwritten.

easydiffraction-0.21.1/docs/dev/issues/open/lowest_live-notebook-plotly-delivery-loader-vs-native-mimetype.md

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+# 117. Live-Notebook Plotly Delivery: Loader vs Native Mimetype
+
+**Priority:** `[priority] lowest`
+
+**Type:** Display / Architecture
+
+Records the two viable strategies for rendering interactive Plotly
+figures in live notebooks, so the trade-off is not re-litigated. See
+[`plotting-docs-performance.md`](../../adrs/accepted/plotting-docs-performance.md).
+
+**Background.** Live notebooks historically rendered via
+`display(HTML(pio.to_html(..., include_plotlyjs='cdn')))`, which caused
+an empty first plot after kernel restart (the CDN `<script src>` loaded
+asynchronously while `Plotly.newPlot` ran immediately) and a loading
+gap. Two ways to fix it:
+
+- **Option 1 — Native mimetype renderer (`fig.show()`).** Emit the
+  `application/vnd.plotly.v1+json` mime bundle and let the JupyterLab
+  Plotly extension render it. Pros: simplest, lowest maintenance,
+  officially supported, no CDN, no script-in-output artifacts. Cons:
+  live notebooks lose the three custom post-script behaviours (dynamic
+  theme-sync on JupyterLab light/dark toggle, hidden-tab resize, the
+  modebar legend-toggle button); a saved `.ipynb`'s plot output is the
+  spec JSON, not self-contained HTML.
+
+- **Option 2 — Self-hosted loader (current).** Ship the vendored Plotly
+  bundle + the shared `ed-figures.js` loader in the wheel; the first
+  figure injects them once per kernel session and each figure renders
+  via `window.edFigures.renderSpec(id, spec)` delivered as a
+  `display(Javascript(...))` output, so the HTML output is just the plot
+  div (no `<script>` tags some hosts render as empty rows). Pros: keeps
+  all three custom behaviours; CDN-free/archival; unified with the docs
+  delivery. Cons: more moving parts; depends on the notebook being
+  **trusted** for a reopened (not re-run) notebook to re-render.
+
+- **Colab transport — versioned frame-local assets.** Colab isolates
+  every cell output in its own iframe, so the once-per-kernel browser
+  state assumed by Option 2 cannot cross cells. In Colab only, every
+  figure output loads the version-matched Plotly bundle and
+  `ed-figures.js` from the published documentation assets in parallel
+  (the loader only needs Plotly once it renders), then calls the same
+  `renderSpec` entry point. `google.colab.output.pauseOutputUntil` holds
+  the output frame until the figure — or a visible error message — is on
+  screen. Colab pauses outputframe auto-resizing (and the cell's later
+  outputs) while that promise is pending, so the bootstrap asks for a
+  remeasure just after it resolves; otherwise the height taken before
+  the plot replaced its placeholder stays as blank space below the
+  chart. That request is scheduled on the next paint with a timer
+  backstop, because a hidden browser tab never paints. Where that API is
+  absent, the fallback measures Colab's output area — every output of
+  the cell, so siblings are not clipped — rather than the root scroll
+  height, which is clamped to the frame viewport and so can only grow
+  it. Concurrent outputs in one cell share frame-global loading
+  promises, so each asset is fetched and parsed only once. An immutable,
+  exact-release-tag jsDelivr URL is the fallback while a new
+  documentation version is deploying or if that deployment fails. Dev
+  builds intentionally use only `/dev/` to avoid mixing arbitrary local
+  code with the loader from another revision. The browser cache avoids
+  embedding or repeatedly transferring the runtime, while all
+  loader-owned theme, resize, and legend behaviour remains intact.
+  Documentation `SHARED` mode is selected first and is unaffected.
+
+  Saved Colab outputs still depend on the host restoring their dynamic
+  scripts. Until that behaviour is confirmed manually, reopen-and-view
+  without re-running is not guaranteed; re-run a cell if its restored
+  output remains at the loading placeholder. An end-to-end test of a dev
+  build likewise requires its matching loader to have reached `/dev/`.
+
+**Current choice:** Option 2 for JupyterLab, with the frame-local asset
+transport for Colab. Revisit Option 1 if the loader proves fragile
+across notebook frontends or the maintenance cost outweighs the three
+behaviours.
+
+**Depends on:** nothing.
+
+**Recommended-priority note:** Marked **lowest**: records a settled
+delivery decision (Option 2); no action required unless the loader
+proves fragile.