easydiffraction 0.3.0__tar.gz → 0.4.0__tar.gz

easydiffraction-0.4.0/.github/workflows/build-docs.yml

@@ -0,0 +1,219 @@
+name: Build and deploy docs
+
+on:
+  # Triggers the workflow on tag creation
+  push:
+    tags:
+      - 'v*'
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+env:
+  # Set the environment variables to be used in all jobs defined in this workflow
+  # Set the CI_BRANCH environment variable to be the branch name
+  # NOTE: Use the same branch name as the one of easyscience/diffraction-lib. This is
+  # required to download the Jupyter notebooks from the easyscience/diffraction-lib repository
+  # Set the NOTEBOOKS_DIR environment variable to be the directory containing the Jupyter notebooks
+  CI_BRANCH: ${{ github.head_ref || github.ref_name }}
+  NOTEBOOKS_DIR: examples
+
+jobs:
+  # Job 1: Build the static files for the documentation site
+  build-docs:
+    runs-on: macos-14 # Use macOS to switch to dark mode for Plotly charts
+
+    steps:
+      - name: Cancel previous workflow runs
+        uses: n1hility/cancel-previous-runs@v2
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+
+      # Without this step, GITHUB_REPOSITORY is not accessible from mkdocs.yml
+      - name: Get GitHub repository
+        run: echo "GITHUB_REPOSITORY=$GITHUB_REPOSITORY" >> $GITHUB_ENV
+
+      # Save the latest release version of easyscience/diffraction-lib to RELEASE_VERSION
+      # RELEASE_VERSION is used in the mkdocs.yml file to set release_version.
+      # The release_version is then needed to display the latest release version in the index.md file
+      - name: Get the latest release version of EasyDiffraction Library
+        # This method is not working in CI with the following error: "API rate limit exceeded..."
+        #run: echo "RELEASE_VERSION=$(curl https://api.github.com/repos/easyscience/diffraction-lib/releases/latest | grep -i 'tag_name' | awk -F '"' '{print $4}')" >> $GITHUB_ENV
+        # This method is not optimal and takes some more time to run, but it works and it is reliable
+        run: |
+          git clone --depth 1 https://github.com/easyscience/EasyDiffractionLib .
+          git fetch --tags
+          echo "RELEASE_VERSION=$(git describe --tags --abbrev=0)" >> $GITHUB_ENV
+
+      # Activate dark mode to create documentation with Plotly charts in dark mode
+      # Need a better solution to automatically switch the chart colour theme based on the mkdocs material switcher
+      # Something similar to mkdocs_plotly_plugin https://haoda-li.github.io/mkdocs-plotly-plugin/,
+      # but for generating documentation from notepads
+      - name: Activate dark mode
+        run: |
+          brew install dark-mode
+          dark-mode status
+          dark-mode on
+          dark-mode status
+
+      - name: Check-out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python environment
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.12'
+
+      - name: Upgrade package installer for Python
+        run: python -m pip install --upgrade pip
+
+      # Install MkDocs -- static site generator
+      # https://www.mkdocs.org
+      - name: Install MkDocs and its dependencies
+        run: >
+          pip install mkdocs mkdocs-material 'mkdocs-autorefs<1.3.0'
+          mkdocs-jupyter mkdocs-plugin-inline-svg
+          mkdocs-markdownextradata-plugin mkdocstrings-python
+
+      # Install EasyDiffraction Library to run Jupyter notebooks
+      # Install with the 'charts' and 'docs' extras
+      - name: Install EasyDiffraction Library and its dependencies
+        run: pip install 'easydiffraction[charts]'
+
+      # Download and add the extra files from the easyscience/assets-docs repository
+      - name: Get easyscience/assets-docs files
+        run: |
+          git clone https://github.com/easyscience/assets-docs.git
+          cp -R assets-docs/docs/assets/ docs/assets/
+          cp -R assets-docs/includes/ includes/
+          cp -R assets-docs/overrides/ overrides/
+
+      # Download and add the extra files from the easyscience/assets-branding repository
+      - name: Get easyscience/assets-branding files
+        run: |
+          git clone https://github.com/easyscience/assets-branding.git
+          mkdir -p docs/assets/images/
+          cp assets-branding/easydiffraction/logos/ed-logo-2_dark.svg docs/assets/images/
+          cp assets-branding/easydiffraction/logos/ed-logo-2_light.svg docs/assets/images/
+          cp assets-branding/easydiffraction/icons/ed-icon_256x256.png docs/assets/images/favicon.png
+          mkdir -p overrides/.icons/
+          cp assets-branding/easydiffraction/icons/ed-icon_bw.svg overrides/.icons/easydiffraction.svg
+          cp assets-branding/easyscience-org/icons/eso-icon_bw.svg overrides/.icons/easyscience.svg
+
+      # Copy Jupyter notebooks from the project to the docs folder
+      # The notebooks are used to generate the documentation
+      - name:
+          Copy Jupyter notebooks from ${{ env.NOTEBOOKS_DIR }}/ to docs/${{
+          env.NOTEBOOKS_DIR }}/
+        run: cp -R ${{ env.NOTEBOOKS_DIR }}/ docs/${{ env.NOTEBOOKS_DIR }}/
+
+      # The following step is needed to avoid the following message during the build:
+      # "Matplotlib is building the font cache; this may take a moment"
+      - name: Pre-build site step
+        run: python -c "import easydiffraction"
+
+      # Create the mkdocs.yml configuration file
+      # The file is created by merging two files:
+      # - assets-docs/mkdocs.yml - the common configuration (theme, plugins, etc.)
+      # - docs/mkdocs.yml - the project-specific configuration (project name, TOC, etc.)
+      - name: Create mkdocs.yml file
+        run: cat assets-docs/mkdocs.yml docs/mkdocs.yml > mkdocs.yml
+
+      # Build the static files
+      # Input: docs/ directory containing the Markdown files
+      # Output: site/ directory containing the generated HTML files
+      - name: Build site with MkDocs
+        run: |
+          export JUPYTER_PLATFORM_DIRS=1
+          mkdocs build
+
+      # Set up the Pages action to configure the static files to be deployed
+      # NOTE: The repository must have GitHub Pages enabled and configured to build using GitHub Actions
+      # This can be done via https://github.com/easyscience/diffraction-lib/settings/pages
+      # Select: Build and deploy - Source - GitHub Actions
+      - name: Setup GitHub Pages
+        uses: actions/configure-pages@v5
+
+      # Upload the static files from the site/ directory to be used in the next job
+      # This artifact is named github-pages and is a single gzip archive containing a single tar file
+      # The artifact is then used in the next job by actions/deploy-pages to deploy the static files to GitHub Pages
+      # Unfortunately, the artifact is not available for download, so extra steps below are needed to do similar things
+      - name:
+          Upload built site as artifact for
+          easyscience.github.io/diffraction-lib (all branches)
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: site/
+
+      # Upload the static files from the site/ directory to be used in the next job
+      # This extra step is needed to allow the download of the artifact in the next job
+      # for pushing its content to the branch named 'easydiffraction.org'
+      - name:
+          Upload built site as artifact for gh_pages and easydiffraction.org
+          (master branch)
+        if: ${{ env.CI_BRANCH == 'master' }}
+        uses: actions/upload-artifact@v4
+        with:
+          name: artifact # name of the artifact (without the extension zip)
+          path: site/
+          if-no-files-found: 'error'
+          compression-level: 0
+
+  # Job 2: Deploy the static files
+  deploy-docs:
+    needs: build-docs # previous job 'build-docs' need to be finished first
+
+    # Grant GITHUB_TOKEN the permissions required to make a Pages deployment
+    permissions:
+      contents: read
+      pages: write # to deploy to Pages
+      id-token: write # to verify the deployment, originates from an appropriate source
+
+    # Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+    # However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+    concurrency:
+      group: 'pages'
+      cancel-in-progress: false
+
+    # Deploy to the github-pages environment
+    environment:
+      name: github-pages # Artifact name
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    runs-on: ubuntu-latest
+
+    steps:
+      # Deploy the static files created in the previous job to GitHub Pages
+      # To allow the deployment of the static files to GitHub Pages, no
+      # restrictions on the branch name need to be set for desired branches on
+      # https://github.com/easyscience/diffraction-lib/settings/environments
+      # Currently, only develop and master branches are allowed to deploy to GitHub Pages
+      # Deployed pages are available at https://easyscience.github.io/diffraction-lib
+      - name: Deploy to easyscience.github.io/diffraction-lib (all branches)
+        uses: actions/deploy-pages@v4
+
+      # Download built site as artifact from a previous job for gh_pages and easydiffraction.org (master branch)
+      - name: Download built site from previous job (master branch)
+        if: ${{ env.CI_BRANCH == 'master' }}
+        uses: actions/download-artifact@v4
+        with: # name or path are taken from the upload step of the previous job
+          name: artifact
+          path: site/ # directory to extract downloaded zipped artifacts
+
+      # Push the site files created in the previous job to the gh_pages branch
+      # To be able to push to the gh_pages branch, the personal GitHub API access
+      # token GH_API_PERSONAL_ACCSESS_TOKEN must be set for this repository via
+      # https://github.com/easyscience/diffraction-lib/settings/secrets/actions
+      # This branch is used to deploy the site to the custom domain https://easydiffraction.org
+      # Deploying is done with a webhook: https://github.com/easyscience/diffraction-lib/settings/hooks
+      # This is done for the gh_pages branch when the site is tested with a step above
+      - name:
+          Deploy to gh_pages branch to trigger deployment to easydiffraction.org
+          (master branch)
+        if: ${{ env.CI_BRANCH == 'master' }}
+        uses: s0/git-publish-subdir-action@develop
+        env:
+          GITHUB_TOKEN: ${{ secrets.GH_API_PERSONAL_ACCSESS_TOKEN }}
+          REPO: self
+          BRANCH: gh_pages
+          FOLDER: site

easydiffraction-0.4.0/DEVELOPMENT.md

@@ -0,0 +1,123 @@
+# Development
+
+This is an example of a workflow that describes the development process.
+
+- Clone EasyDiffractionLib repository
+  ```console
+  git clone https://github.com/EasyScience/EasyDiffractionLib
+  ```
+- Go to the cloned directory
+  ```console
+  cd EasyDiffractionLib
+  ```
+- Checkout/switch to the `develop` branch
+  ```console
+  git checkout develop
+  ```
+- Create a new branch from the current one
+  ```console
+  git checkout -b new-feature
+  ```
+- Create Python environment and activate it
+  ```console
+  python3 -m venv .venv
+  source .venv/bin/activate
+  ```
+- Upgrade PIP - package installer for Python
+  ```console
+  python -m pip install --upgrade pip
+  ```
+- Install easydiffraction from root with `dev` extras for development, `charts`
+  extras for Jupyter notebooks and `docs` extras for building documentation
+  ```console
+  pip install '.[dev,charts,docs]'
+  ```
+- Make changes in the code
+  ```console
+  ...
+  ```
+- Check the validity of pyproject.toml
+  ```console
+  validate-pyproject pyproject.toml
+  ```
+- Run Ruff - Python linter and code formatter (configuration is in
+  pyproject.toml)<br/> Linting (overwriting files)
+  ```console
+  ruff check . --fix
+  ```
+  Formatting (overwriting files)
+  ```console
+  ruff format .
+  ```
+- Install and run Prettier - code formatter for Markdown, YAML, TOML, etc. files
+  (configuration in prettierrc.toml)<br/> Formatting (overwriting files)
+  ```console
+  npm install prettier prettier-plugin-toml --save-dev --save-exact
+  npx prettier . --write --config=prettierrc.toml
+  ```
+- Run python tests
+  ```console
+  pytest tests/ --color=yes -n auto
+  ```
+- Clear all Jupyter notebooks output (Only those that were changed!). Replace
+  `examples/*.ipynb` with the path to the notebook(s) you want to clear
+  ```console
+  jupyter nbconvert --clear-output --inplace examples/*.ipynb
+  ```
+- Run nbQA - Jupyter notebooks quality assurance package
+  ```console
+  nbqa ruff examples/ --fix
+  ```
+- Run Jupyter notebooks as tests
+  ```console
+  pytest --nbmake examples/ --ignore-glob='examples/*emcee*' --nbmake-timeout=300 --color=yes -n=auto
+  ```
+- Add extra files to build documentation (from `../assets-docs/` and
+  `../assets-branding/` directories)
+  ```console
+  cp -R ../assets-docs/docs/assets/ docs/assets/
+  cp -R ../assets-docs/includes/ includes/
+  cp -R ../assets-docs/overrides/ overrides/
+  mkdir -p docs/assets/images/
+  cp ../assets-branding/easydiffraction/logos/ed-logo-2_dark.svg docs/assets/images/
+  cp ../assets-branding/easydiffraction/logos/ed-logo-2_light.svg docs/assets/images/
+  <!-- cp ../assets-branding/easydiffraction/logos/edl-logo_dark.svg docs/assets/images/logo_dark.svg
+  cp ../assets-branding/easydiffraction/logos/edl-logo_light.svg docs/assets/images/logo_light.svg -->
+  cp ../assets-branding/easydiffraction/icons/ed-icon_256x256.png docs/assets/images/favicon.png
+  mkdir -p overrides/.icons/
+  cp ../assets-branding/easydiffraction/icons/ed-icon_bw.svg overrides/.icons/easydiffraction.svg
+  cp ../assets-branding/easyscience-org/icons/eso-icon_bw.svg overrides/.icons/easyscience.svg
+  cp -R examples/ docs/examples/
+  cat ../assets-docs/mkdocs.yml docs/mkdocs.yml > mkdocs.yml
+  ```
+- Build documentation with MkDocs - static site generator
+  ```console
+  export JUPYTER_PLATFORM_DIRS=1
+  mkdocs serve
+  ```
+- Test the documentation locally (built in the `site/` directory). E.g., on
+  macOS, open the site in the default browser via the terminal
+  ```console
+  open http://127.0.0.1:8000
+  ```
+- Clean up after building documentation
+  ```console
+  rm -rf site/
+  rm -rf docs/assets/
+  rm -rf includes/
+  rm -rf overrides/
+  rm -rf docs/examples/
+  rm -rf node_modules/
+  rm mkdocs.yml
+  rm package-lock.json
+  rm package.json
+  ```
+- Commit changes
+  ```console
+  git add .
+  git commit -m "Add new feature"
+  ```
+- Push the new branch to a remote repository
+  ```console
+  git push -u origin new-feature
+  ```

{easydiffraction-0.3.0 → easydiffraction-0.4.0}/LICENSE

@@ -1,6 +1,7 @@
 BSD 3-Clause License
 
-Copyright (c) 2024, EasyDiffractionLib contributors (https://github.com/EasyScience/EasyDiffractionLib)
+Copyright (c) 2025, EasyDiffraction contributors
+(https://github.com/EasyScience/EasyDiffractionLib)
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

{easydiffraction-0.3.0 → easydiffraction-0.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: easydiffraction
-Version: 0.3.0
+Version: 0.4.0
 Summary: Making diffraction data analysis and modelling easy
 Project-URL: homepage, https://easydiffraction.org
 Project-URL: documentation, https://docs.easydiffraction.org/lib
@@ -9,7 +9,8 @@ Project-URL: tracker, https://github.com/EasyScience/EasyDiffractionLib/issues
 Author-email: EasyDiffraction contributors <support@easydiffraction.org>
 License: BSD 3-Clause License
         
-        Copyright (c) 2024, EasyDiffractionLib contributors (https://github.com/EasyScience/EasyDiffractionLib)
+        Copyright (c) 2025, EasyDiffraction contributors
+        (https://github.com/EasyScience/EasyDiffractionLib)
         All rights reserved.
         
         Redistribution and use in source and binary forms, with or without
@@ -55,7 +56,7 @@ Requires-Dist: pooch
 Provides-Extra: charts
 Requires-Dist: darkdetect; extra == 'charts'
 Requires-Dist: pandas; extra == 'charts'
-Requires-Dist: plotly; extra == 'charts'
+Requires-Dist: plotly<6.0.0; extra == 'charts'
 Requires-Dist: py3dmol; extra == 'charts'
 Provides-Extra: dev
 Requires-Dist: build; extra == 'dev'
@@ -66,21 +67,30 @@ Requires-Dist: pytest; extra == 'dev'
 Requires-Dist: pytest-cov; extra == 'dev'
 Requires-Dist: pytest-xdist; extra == 'dev'
 Requires-Dist: ruff; extra == 'dev'
+Requires-Dist: validate-pyproject[all]; extra == 'dev'
 Requires-Dist: versioningit; extra == 'dev'
+Provides-Extra: docs
+Requires-Dist: mkdocs; extra == 'docs'
+Requires-Dist: mkdocs-autorefs<1.3.0; extra == 'docs'
+Requires-Dist: mkdocs-jupyter; extra == 'docs'
+Requires-Dist: mkdocs-markdownextradata-plugin; extra == 'docs'
+Requires-Dist: mkdocs-material; extra == 'docs'
+Requires-Dist: mkdocs-plugin-inline-svg; extra == 'docs'
+Requires-Dist: mkdocstrings; extra == 'docs'
 Provides-Extra: pdf
 Requires-Dist: diffpy-pdffit2; extra == 'pdf'
 Requires-Dist: diffpy-structure; extra == 'pdf'
 Requires-Dist: diffpy-utils; extra == 'pdf'
 Description-Content-Type: text/markdown
 
-<p align='left'>
+<p>
   <picture>
     <!-- light mode logo -->
-    <source media='(prefers-color-scheme: light)' srcset='https://raw.githubusercontent.com/EasyScience/BrandingResources/refs/heads/master/EasyDiffraction/logos/ed-logo_light.svg'>
+    <source media='(prefers-color-scheme: light)' srcset='https://raw.githubusercontent.com/easyscience/assets-branding/refs/heads/master/easydiffraction/logos/ed-logo-2_light.svg'>
     <!-- dark mode logo -->
-    <source media='(prefers-color-scheme: dark)' srcset='https://raw.githubusercontent.com/EasyScience/BrandingResources/refs/heads/master/EasyDiffraction/logos/ed-logo_dark.svg'>
+    <source media='(prefers-color-scheme: dark)' srcset='https://raw.githubusercontent.com/easyscience/assets-branding/refs/heads/master/easydiffraction/logos/ed-logo-2_dark.svg'>
     <!-- default logo == light mode logo -->
-    <img src='https://raw.githubusercontent.com/EasyScience/BrandingResources/refs/heads/master/EasyDiffraction/logos/ed-logo_light.svg' alt='EasyDiffraction'>
+    <img src='https://raw.githubusercontent.com/easyscience/assets-branding/refs/heads/master/easydiffraction/logos/ed-logo-2_light.svg' alt='EasyDiffraction'>
   </picture>
 </p>
 
@@ -109,8 +119,7 @@ We welcome contributions! Our vision is for **EasyDiffraction** to be a
 community-driven, open-source project supported by a diverse group of
 contributors.
 
-The project is currently maintained by the [European Spallation Source (ESS)] in
-Sweden.
+The project is currently maintained by the [European Spallation Source (ESS)].
 
 If you'd like to contribute, please refer to our [Contributing Guidelines] for
 information about our code of conduct and instructions on submitting pull

{easydiffraction-0.3.0 → easydiffraction-0.4.0}/README.md

@@ -1,11 +1,11 @@
-<p align='left'>
+<p>
   <picture>
     <!-- light mode logo -->
-    <source media='(prefers-color-scheme: light)' srcset='https://raw.githubusercontent.com/EasyScience/BrandingResources/refs/heads/master/EasyDiffraction/logos/ed-logo_light.svg'>
+    <source media='(prefers-color-scheme: light)' srcset='https://raw.githubusercontent.com/easyscience/assets-branding/refs/heads/master/easydiffraction/logos/ed-logo-2_light.svg'>
     <!-- dark mode logo -->
-    <source media='(prefers-color-scheme: dark)' srcset='https://raw.githubusercontent.com/EasyScience/BrandingResources/refs/heads/master/EasyDiffraction/logos/ed-logo_dark.svg'>
+    <source media='(prefers-color-scheme: dark)' srcset='https://raw.githubusercontent.com/easyscience/assets-branding/refs/heads/master/easydiffraction/logos/ed-logo-2_dark.svg'>
     <!-- default logo == light mode logo -->
-    <img src='https://raw.githubusercontent.com/EasyScience/BrandingResources/refs/heads/master/EasyDiffraction/logos/ed-logo_light.svg' alt='EasyDiffraction'>
+    <img src='https://raw.githubusercontent.com/easyscience/assets-branding/refs/heads/master/easydiffraction/logos/ed-logo-2_light.svg' alt='EasyDiffraction'>
   </picture>
 </p>
 
@@ -34,8 +34,7 @@ We welcome contributions! Our vision is for **EasyDiffraction** to be a
 community-driven, open-source project supported by a diverse group of
 contributors.
 
-The project is currently maintained by the [European Spallation Source (ESS)] in
-Sweden.
+The project is currently maintained by the [European Spallation Source (ESS)].
 
 If you'd like to contribute, please refer to our [Contributing Guidelines] for
 information about our code of conduct and instructions on submitting pull

easydiffraction-0.4.0/docs/analysis.md

@@ -0,0 +1,77 @@
+# Analysis
+
+This section contains information about the analysis of diffraction data in
+EasyDiffraction.
+
+### Model-dependent analysis
+
+There are two general approaches to the analysis of data: **model-dependent**
+and **model-independent**. In the following examples, we are going to focus on
+the former. However, the latter is worth briefly highlighting.
+
+A model-independent approach to analysis is where no assumptions are made about
+the system that is being studied and conclusions are drawn only from the data
+that has been observed. However, in many applications, it is desirable to
+include what we think we know about the system, and so model-dependent analysis
+is used.
+
+Model-dependent analysis involves the development of a mathematical model that
+describes the model dataset that would be found for our system. This
+mathematical model usually has parameters that are linked to the physics and
+chemistry of our system. These parameters are varied to optimise the model,
+using an optimisation algorithm, with respect to the experimental data, i.e., to
+get the best agreement between the model data and the experimental data.
+
+Below is a diagram illustrating this process:
+
+```mermaid
+flowchart LR
+    a(Propose<br/>model)
+    b(Set/change<br/>model<br/>parameter<br/>values)
+    c(Calculate<br/>model<br/>data)
+    d(Compare<br/>model data to<br/>experimental<br/>data)
+    e(Stop<br/>iteration)
+    a --> b
+    b --> c
+    c --> d
+    d-- Threshold<br/>not<br/>reached -->b
+    d-- Threshold<br/>reached -->e
+```
+
+Model-dependent analysis is popular in the analysis of neutron scattering data,
+and we will use it in the following examples.
+
+## Calculation engines
+
+EasyDiffraction is designed to be a flexible and extensible tool for calculating
+diffraction patterns. It can use different calculation engines to perform the
+calculations.
+
+We currently rely on [CrysPy](https://www.cryspy.fr) as a calculation engine.
+CrysPy is a Python library originally developed for analysing polarised neutron
+diffraction data. It is now evolving into a more general purpose library and
+covers powders and single crystals, nuclear and (commensurate) magnetic
+structures, unpolarised neutron and X-ray diffraction.
+
+Another calculation engine is
+[CrysFML](https://code.ill.fr/scientific-software/CrysFML2008). This library is
+a collection of Fortran modules for crystallographic computations. It is used in
+the software package [FullProf](https://www.ill.eu/sites/fullprof/), and we are
+currently working on its integration into EasyDiffraction.
+
+## Minimisation engines
+
+EasyDiffraction uses different third-party libraries to perform the
+model-dependent analysis.
+
+Most of the examples in this section will use the
+[lmfit](https://lmfit.github.io/lmfit-py/) package, which provides a high-level
+interface to non-linear optimisation and curve fitting problems for Python. It
+is one of the tools that can be used to fit models to the experimental data.
+
+Another package that can be used for the same purpose is
+[bumps](https://bumps.readthedocs.io/en/latest/). In addition to traditional
+optimizers which search for the best minimum they can find in the search space,
+bumps provides Bayesian uncertainty analysis which explores all viable minima
+and finds confidence intervals on the parameters based on uncertainty in the
+measured values.

easydiffraction-0.4.0/docs/dictionaries/_atom_site.md

@@ -0,0 +1,62 @@
+[coreCIF][1]{:.label-cif}
+
+# \_atom_site
+
+Data items in this category record details about the atom sites in a crystal
+structure, such as the positional coordinates and atomic displacement
+parameters. Please see the
+[IUCr page](https://www.iucr.org/__data/iucr/cifdic_html/3/CORE_DIC/CATOM_SITE.html)
+for further details.
+
+## [\_atom_site.label](https://www.iucr.org/__data/iucr/cifdic_html/3/CORE_DIC/Iatom_site.label.html)
+
+This is a unique identifier for a particular site in the asymmetric unit of the
+crystal unit cell.
+
+## [\_atom_site.type_symbol](https://www.iucr.org/__data/iucr/cifdic_html/3/CORE_DIC/Iatom_site.type_symbol.html)
+
+A code to identify the atom specie(s) occupying this site.
+
+## \_atom_site.fract
+
+Atom-site coordinates as fractions of the [\_cell_length](_cell.md) values.
+
+- [\_atom_site.fract_x](https://www.iucr.org/__data/iucr/cifdic_html/3/CORE_DIC/Iatom_site.fract_x.html)
+- [\_atom_site.fract_y](https://www.iucr.org/__data/iucr/cifdic_html/3/CORE_DIC/Iatom_site.fract_y.html)
+- [\_atom_site.fract_z](https://www.iucr.org/__data/iucr/cifdic_html/3/CORE_DIC/Iatom_site.fract_z.html)
+
+## [\_atom_site.occupancy](https://www.iucr.org/__data/iucr/cifdic_html/3/CORE_DIC/Iatom_site.occupancy.html)
+
+The fraction of the atom type present at this site.
+
+## [\_atom_site.ADP_type](https://www.iucr.org/__data/iucr/cifdic_html/3/CORE_DIC/Iatom_site.adp_type.html)
+
+Code for type of atomic displacement parameters used for the site. Currently
+only `Biso` (isotropic B) is supported.
+
+## [\_atom_site.B_iso_or_equiv](https://www.iucr.org/__data/iucr/cifdic_html/3/CORE_DIC/Iatom_site.B_iso_or_equiv.html)
+
+Isotropic atomic displacement parameter, or equivalent isotropic atomic
+displacement parameter, in angstroms squared.
+
+## [\_atom_site.site_symmetry_multiplicity](https://www.iucr.org/__data/iucr/cifdic_html/3/CORE_DIC/Iatom_site.site_symmetry_multiplicity.html)
+
+`optional parameter`
+
+The number of different sites that are generated by the application of the
+space-group symmetry to the coordinates given for this site. It is equal to the
+multiplicity given for this Wyckoff site in International Tables for
+Crystallography Vol. A (2002).
+
+## [\_atom_site.Wyckoff_symbol](https://www.iucr.org/__data/iucr/cifdic_html/3/CORE_DIC/Iatom_site.Wyckoff_symbol.html)
+
+`optional parameter`
+
+The Wyckoff symbol (letter) as listed in the space-group tables of International
+Tables for Crystallography Vol. A.
+
+<!-- prettier-ignore-start -->
+[0]: #
+[1]: https://www.iucr.org/resources/cif/dictionaries/browse/cif_core
+[2]: https://www.iucr.org/resources/cif/dictionaries/browse/cif_pd
+<!-- prettier-ignore-end -->

easydiffraction-0.4.0/docs/dictionaries/_cell.md

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+[coreCIF][1]{:.label-cif}
+
+# \_cell
+
+Data items in this category record details about the crystallographic cell
+parameters and their measurement. Please see the
+[IUCr page](https://www.iucr.org/__data/iucr/cifdic_html/3/CORE_DIC/CCELL.html)
+for further details.
+
+## \_cell.angle
+
+The angles between the bounding cell axes in degrees.
+
+- [\_cell.angle_alpha](https://www.iucr.org/__data/iucr/cifdic_html/3/CORE_DIC/Icell.angle_alpha.html)
+- [\_cell.angle_beta](https://www.iucr.org/__data/iucr/cifdic_html/3/CORE_DIC/Icell.angle_beta.html)
+- [\_cell.angle_gamma](https://www.iucr.org/__data/iucr/cifdic_html/3/CORE_DIC/Icell.angle_gamma.html)
+
+## \_cell.length
+
+The lengths of each cell axis in angstroms.
+
+- [\_cell.length_a](https://www.iucr.org/__data/iucr/cifdic_html/3/CORE_DIC/Icell.length_a.html)
+- [\_cell.length_b](https://www.iucr.org/__data/iucr/cifdic_html/3/CORE_DIC/Icell.length_b.html)
+- [\_cell.length_c](https://www.iucr.org/__data/iucr/cifdic_html/3/CORE_DIC/Icell.length_c.html)
+
+<!-- prettier-ignore-start -->
+[0]: #
+[1]: https://www.iucr.org/resources/cif/dictionaries/browse/cif_core
+[2]: https://www.iucr.org/resources/cif/dictionaries/browse/cif_pd
+<!-- prettier-ignore-end -->

easydiffraction-0.4.0/docs/dictionaries/_diffrn_radiation.md

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+[coreCIF][1]{:.label-cif}
+
+# \_diffrn_radiation
+
+Data items in this category describe the radiation used in measuring the
+diffraction intensities. Please see the
+[IUCr page](https://www.iucr.org/resources/cif/dictionaries/browse/cif_pd) for
+further details.
+
+## [\_diffrn_radiation.probe](https://www.iucr.org/resources/cif/dictionaries/browse/cif_pd)
+
+The nature of the radiation used (i.e. the name of the subatomic particle or the
+region of the electromagnetic spectrum).
+
+Supported values: `neutron` and `x-ray`
+
+<!-- prettier-ignore-start -->
+[0]: #
+[1]: https://www.iucr.org/resources/cif/dictionaries/browse/cif_core
+[2]: https://www.iucr.org/resources/cif/dictionaries/browse/cif_pd
+<!-- prettier-ignore-end -->

easydiffraction-0.4.0/docs/dictionaries/_diffrn_radiation_wavelength.md

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+[coreCIF][1]{:.label-cif}
+
+# \_diffrn_radiation_wavelength
+
+Data items in this category describe the wavelength of radiation used in
+diffraction measurements. Please see the
+[IUCr page](https://www.iucr.org/resources/cif/dictionaries/browse/cif_pd) for
+further details.
+
+## [\_diffrn_radiation_wavelength.wavelength](https://www.iucr.org/resources/cif/dictionaries/browse/cif_pd)
+
+Wavelength of the radiation used to measure the unit cell.
+
+<!-- prettier-ignore-start -->
+[0]: #
+[1]: https://www.iucr.org/resources/cif/dictionaries/browse/cif_core
+[2]: https://www.iucr.org/resources/cif/dictionaries/browse/cif_pd
+<!-- prettier-ignore-end -->