easydiffraction 0.8.0__tar.gz → 0.9.0__tar.gz

{easydiffraction-0.8.0 → easydiffraction-0.9.0}/.github/workflows/backmerge-pr.yaml

@@ -7,6 +7,8 @@
 #   The GitHub App must be added to the develop ruleset bypass list.
 #
 # Required repo config:
+# https://github.com/organizations/easyscience/settings/secrets/actions
+# https://github.com/organizations/easyscience/settings/variables/actions
 # - Actions secret:   ES_BACKMERGE_PRIVATE_KEY  (GitHub App private key PEM)
 # - Actions variable: ES_BACKMERGE_APP_ID       (GitHub App ID)
 
@@ -14,8 +16,7 @@ name: Backmerge PR (tag -> develop)
 
 on:
   push:
-    tags:
-      - 'v*'
+    tags: ['v*']
 
 permissions:
   contents: write
@@ -30,8 +31,8 @@ jobs:
         id: app-token
         uses: actions/create-github-app-token@v2
         with:
-          app-id: ${{ vars.ES_BACKMERGE_APP_ID }}
-          private-key: ${{ secrets.ES_BACKMERGE_PRIVATE_KEY }}
+          app-id: ${{ vars.BACKMERGE_APP_ID }}
+          private-key: ${{ secrets.BACKMERGE_PRIVATE_KEY }}
 
       - name: Checkout tag commit
         uses: actions/checkout@v5
@@ -71,7 +72,7 @@ jobs:
 
           BODY="⚠️ This PR is created automatically for backmerge of a new release tag commit \`${{ steps.vars.outputs.tag }}\` into \`develop\`.
 
-          It is labeled '[maintainer] auto-pull-request' and is excluded from release notes and version bump logic."
+          It is labeled `[maintainer] auto-pull-request` and is excluded from release notes and version bump logic."
 
           if gh pr view --repo "${{ github.repository }}" --head "${{ steps.vars.outputs.branch }}" >/dev/null 2>&1; then
             echo "PR already exists for head=${{ steps.vars.outputs.branch }}"

easydiffraction-0.9.0/.github/workflows/docs.yaml

@@ -0,0 +1,192 @@
+# This workflow builds and deploys documentation for the project.
+#
+# Steps overview:
+#  Job 1: build-docs
+#   - Builds documentation (including running Jupyter notebooks to generate output cells).
+#   - Uploads the built site as a Pages artifact.
+#  Job 2: deploy-dev
+#   - Deploys the built site to GitHub Pages for development (pushes to develop/master).
+#  Job 3: deploy-prod
+#   - Deploys the built site to gh-pages branch for production (release tags starting with v*).
+#   - This triggers deployment to a custom domain via webhook.
+#
+# The action summary page will contain links to the built artifact for downloading
+# and inspecting, as well as links to both the development and production versions of
+# the deployed documentation site.
+
+name: Docs build and deployment
+
+on:
+  # Trigger the workflow on pull request
+  pull_request:
+    # Selected branches
+    branches: [master, main, develop]
+  # Trigger the workflow on push
+  push:
+    # Selected branches
+    branches: [master, main, develop]
+    # Runs on creating a new tag starting with 'v', e.g. 'v1.0.3'
+    tags: ['v*']
+  # 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
+
+# Set the environment variables to be used in all jobs defined in this workflow
+env:
+  # CI_BRANCH - the branch name (used in mkdocs.yml)
+  # For PRs: github.head_ref is the source branch
+  # For pushes: github.ref_name is the branch
+  # For tags: github.ref_name is the tag name
+  # GITHUB_REPOSITORY - the repository name (used in mkdocs.yml)
+  # NOTEBOOKS_DIR - the directory containing the Jupyter notebooks (used in mkdocs.yml)
+  DEFAULT_BRANCH: ${{ github.event.repository.default_branch }}
+  DEVELOP_BRANCH: develop
+  CI_BRANCH: ${{ github.head_ref || github.ref_name }}
+  IS_RELEASE_TAG: ${{ startsWith(github.ref, 'refs/tags/v') }}
+  GITHUB_REPOSITORY: ${{ github.repository }}
+  NOTEBOOKS_DIR: tutorials
+
+jobs:
+  # Job 1: Build the static files for the documentation site
+  build-deploy-docs:
+    strategy:
+      matrix:
+        os: [macos-14] # Use macOS to switch to dark mode for Plotly charts
+
+    runs-on: ${{ matrix.os }}
+
+    permissions:
+      contents: write # required for pushing to gh-pages branch
+
+    steps:
+      # Setting DOCS_VERSION to be used in mkdocs.yml, and then in the
+      # main.html template. It defines the versioned docs subfolder name
+      # in the gh-pages branch. If it's a release tag, use the version
+      # number without the 'v' prefix, otherwise use 'dev'.
+      # Setting RELEASE_VERSION to be used in mkdocs.yml to show
+      # the latest release version in the index.md file. If it's a
+      # release tag, use the tag name, otherwise use the branch name
+      # for development builds.
+      - name: Set extra env variables
+        shell: bash
+        run: |
+          if [[ "${IS_RELEASE_TAG}" == "true" ]]; then
+            RELEASE_VERSION="${GITHUB_REF_NAME}"
+            DOCS_VERSION="${RELEASE_VERSION#v}"
+          else
+            RELEASE_VERSION="${CI_BRANCH}"
+            DOCS_VERSION="dev"
+          fi
+          echo "RELEASE_VERSION=${RELEASE_VERSION}" >> "$GITHUB_ENV"
+          echo "DOCS_VERSION=${DOCS_VERSION}" >> "$GITHUB_ENV"
+          echo "DEPLOYMENT_URL=https://easyscience.github.io/${{ github.event.repository.name }}/${DOCS_VERSION}" >> "$GITHUB_ENV"
+
+      - name: Check-out repository
+        uses: actions/checkout@v5
+        with:
+          fetch-depth: 0 # full history with tags; needed for mike to push/deploy docs
+
+      # 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: Set up pixi
+        uses: prefix-dev/setup-pixi@v0.9.0
+        with:
+          environments: default
+          activate-environment: default
+          run-install: true
+          frozen: true
+          cache: false
+          post-cleanup: false
+
+      - name: Install and setup development dependencies
+        shell: bash
+        run: pixi run dev
+
+      - name: Clone easyscience/assets-docs and easyscience/assets-branding
+        run: |
+          cd ..
+          git clone https://github.com/easyscience/assets-docs.git
+          git clone https://github.com/easyscience/assets-branding.git
+
+      - name: Add files from cloned repositories
+        run: pixi run docs-assets
+
+      # Convert python scripts in the notebooks directory to Jupyter notebooks
+      # Strip output from the notebooks
+      # Prepare the notebooks for documentation (add colab cell, etc.)
+      # Run the notebooks to generate the output cells using multiple cores
+      # The notebooks are then used to build the documentation site
+      - name: Convert tutorial scripts to notebooks
+        run: pixi run notebook-prepare
+
+      # 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: pixi run python -c "import easydiffraction"
+
+      # Run the notebooks to generate the output cells using multiple cores
+      - name: Run notebooks
+        #  if: false # Temporarily disabled to speed up the docs build
+        run: pixi run notebook-exec
+
+      - name: Move notebooks to docs/tutorials
+        run: pixi run docs-notebooks
+
+      # 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: pixi run docs-config
+
+      # Build the static files for the documentation site for local inspection
+      # Input: docs/ directory containing the Markdown files
+      # Output: site/ directory containing the generated HTML files
+      - name: Build site for local check
+        run: pixi run docs-local
+
+      # Upload the static files from the site/ directory to be used for
+      # local check
+      - name: Upload built site as artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: site-local_edl-${{ env.RELEASE_VERSION }}
+          path: site/
+          if-no-files-found: 'error'
+          compression-level: 0
+
+      # Publish versioned docs with Mike (dev on branches, prod on tags)
+      # Configure git for pushing to gh-pages branch
+      - name: Configure git for pushing
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+
+      # Publish versioned docs with Mike. The tagged release docs go to
+      # the versioned prefix, e.g. /v1.2.3/, and also to /latest/.
+      # All other branches go to /dev/.
+      # "${RELEASE_VERSION#v}" for v0.8.3.post1 -> 0.8.3.post1
+      - name: Rebuild and deploy docs with mike
+        run: |
+          if [[ "${IS_RELEASE_TAG}" == "true" ]]; then
+            pixi run docs-deploy "${RELEASE_VERSION#v}" latest
+          else
+            pixi run docs-deploy dev
+          fi
+          pixi run docs-set-default latest
+          echo "🔗 deployment url [${{ env.DEPLOYMENT_URL }}](${{ env.DEPLOYMENT_URL }})" >> $GITHUB_STEP_SUMMARY

{easydiffraction-0.8.0 → easydiffraction-0.9.0}/.github/workflows/release-notes.yaml

@@ -38,15 +38,6 @@ jobs:
         shell: bash
         run: pixi run dev
 
-      - name: Convert tutorial scripts to notebooks
-        run: pixi run notebook-prepare
-
-      - name: Clean up unnecessary script files
-        run: rm -rf tutorials/*.py
-
-      - name: Zip the tutorials directory
-        run: zip -9 -r tutorials.zip tutorials
-
       - name: Drafts the next release notes
         id: draft
         uses: enhantica/drafterino@v2
@@ -81,7 +72,5 @@ jobs:
           tag_name: ${{ steps.draft.outputs.tag_name }}
           name: ${{ steps.draft.outputs.release_name }}
           body: ${{ steps.draft.outputs.release_notes }}
-          files: |
-            tutorials.zip
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

{easydiffraction-0.8.0 → easydiffraction-0.9.0}/.github/workflows/release-pr.yaml

@@ -6,7 +6,7 @@
 #   - Adds the label "[maintainer] auto-pull-request" so it is excluded from changelogs.
 #   - The PR body makes clear that this is automation only (no review needed).
 
-name: Release PR creation
+name: Release PR (develop -> master)
 
 on:
   # Allows you to run this workflow manually from the Actions tab

{easydiffraction-0.8.0 → easydiffraction-0.9.0}/.github/workflows/test.yaml

@@ -206,16 +206,16 @@ jobs:
             pixi run --environment $env wheel
           done
 
-      - name: Add easydiffraction package from the built wheel
+      - name: Install easydiffraction package from the built wheel
         shell: bash
         run: |
           for env in ${{ env.PIXI_ENVS }}; do
             echo "🔹🔸🔹🔸🔹   Current env: $env   🔹🔸🔹🔸🔹"
             env_prefix="${env%%-*}"
             echo "📦 Looking for wheel in dist/$env_prefix/"
-            whl_path="$(python3 -c "import pathlib; w = sorted(pathlib.Path('dist/${env_prefix}').glob('*.whl')); print(w[0].resolve().as_uri())")"
-            echo "📦 Adding easydiffraction from: $whl_path"
-            pixi add --feature $env_prefix --pypi "easydiffraction[all] @ $whl_path"
+            whl_path="$(find dist/${env_prefix} -name '*.whl' | head -1)"
+            echo "📦 Installing easydiffraction from: $whl_path"
+            pixi run --environment $env python -m uv pip install "${whl_path}[all]" --reinstall-package easydiffraction
             pixi run --environment $env easydiffraction --version
           done
 

{easydiffraction-0.8.0 → easydiffraction-0.9.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: easydiffraction
-Version: 0.8.0
+Version: 0.9.0
 Summary: Diffraction data analysis
 Project-URL: homepage, https://easydiffraction.org
 Project-URL: documentation, https://docs.easydiffraction.org/lib
@@ -56,6 +56,7 @@ Requires-Dist: diffpy-pdffit2
 Requires-Dist: diffpy-utils
 Requires-Dist: gemmi
 Requires-Dist: lmfit
+Requires-Dist: numpy<2.4
 Requires-Dist: pooch
 Requires-Dist: rich
 Requires-Dist: scipy
@@ -74,6 +75,7 @@ Requires-Dist: jinja2; extra == 'all'
 Requires-Dist: jupyter-dark-detect; extra == 'all'
 Requires-Dist: jupyterquiz; extra == 'all'
 Requires-Dist: jupytext; extra == 'all'
+Requires-Dist: mike; extra == 'all'
 Requires-Dist: mkdocs; extra == 'all'
 Requires-Dist: mkdocs-autorefs<1.3.0; extra == 'all'
 Requires-Dist: mkdocs-jupyter; extra == 'all'
@@ -115,6 +117,7 @@ Requires-Dist: ruff; extra == 'dev'
 Requires-Dist: validate-pyproject[all]; extra == 'dev'
 Requires-Dist: versioningit; extra == 'dev'
 Provides-Extra: docs
+Requires-Dist: mike; extra == 'docs'
 Requires-Dist: mkdocs; extra == 'docs'
 Requires-Dist: mkdocs-autorefs<1.3.0; extra == 'docs'
 Requires-Dist: mkdocs-jupyter; extra == 'docs'

{easydiffraction-0.8.0 → easydiffraction-0.9.0}/docs/mkdocs.yml

@@ -3,8 +3,8 @@
 ###########################
 
 # Project information
-site_name: EasyDiffraction Library
-site_url: https://docs.easydiffraction.org/lib/
+site_name: '' #EasyDiffraction Library
+site_url: https://easyscience.github.io/diffraction-lib/ #https://docs.easydiffraction.org/lib/
 
 # Repository
 repo_url: https://github.com/easyscience/diffraction-lib/
@@ -69,22 +69,22 @@ nav:
   - Tutorials:
       - Tutorials: tutorials/index.md
       - Getting Started:
-          - LBCO quick CIF: tutorials/quick_from-cif_pd-neut-cwl_LBCO-HRPT.ipynb
-          - LBCO quick code: tutorials/quick_from-code_pd-neut-cwl_LBCO-HRPT.ipynb
-          - LBCO basic: tutorials/basic_single-fit_pd-neut-cwl_LBCO-HRPT.ipynb
-          - PbSO4 advanced: tutorials/advanced_joint-fit_pd-neut-xray-cwl_PbSO4.ipynb
+          - LBCO quick CIF: tutorials/ed-1.ipynb
+          - LBCO quick code: tutorials/ed-2.ipynb
+          - LBCO basic: tutorials/ed-3.ipynb
+          - PbSO4 advanced: tutorials/ed-4.ipynb
       - Standard Diffraction:
-          - Co2SiO4 pd-neut-cwl: tutorials/cryst-struct_pd-neut-cwl_CoSiO4-D20.ipynb
-          - HS pd-neut-cwl: tutorials/cryst-struct_pd-neut-cwl_HS-HRPT.ipynb
-          - Si pd-neut-tof: tutorials/cryst-struct_pd-neut-tof_Si-SEPD.ipynb
-          - NCAF pd-neut-tof: tutorials/cryst-struct_pd-neut-tof_multidata_NCAF-WISH.ipynb
-          - LBCO+Si McStas: tutorials/cryst-struct_pd-neut-tof_multiphase-LBCO-Si_McStas.ipynb
+          - Co2SiO4 pd-neut-cwl: tutorials/ed-5.ipynb
+          - HS pd-neut-cwl: tutorials/ed-6.ipynb
+          - Si pd-neut-tof: tutorials/ed-7.ipynb
+          - NCAF pd-neut-tof: tutorials/ed-8.ipynb
+          - LBCO+Si McStas: tutorials/ed-9.ipynb
       - Pair Distribution Function:
-          - Ni pd-neut-cwl: tutorials/pdf_pd-neut-cwl_Ni.ipynb
-          - Si pd-neut-tof: tutorials/pdf_pd-neut-tof_Si-NOMAD.ipynb
-          - NaCl pd-xray: tutorials/pdf_pd-xray_NaCl.ipynb
+          - Ni pd-neut-cwl: tutorials/ed-10.ipynb
+          - Si pd-neut-tof: tutorials/ed-11.ipynb
+          - NaCl pd-xray: tutorials/ed-12.ipynb
       - Workshops & Schools:
-          - 2025 DMSC: tutorials/dmsc-summer-school-2025_analysis-powder-diffraction.ipynb
+          - 2025 DMSC: tutorials/ed-13.ipynb
   - API Reference:
       - API Reference: api-reference/index.md
       - analysis: api-reference/analysis.md

easydiffraction-0.9.0/docs/tutorials/index.md

@@ -0,0 +1,79 @@
+---
+icon: material/school
+---
+
+# :material-school: Tutorials
+
+This section presents a collection of **Jupyter Notebook** tutorials that
+demonstrate how to use EasyDiffraction for various tasks. These tutorials serve
+as self-contained, step-by-step **guides** to help users grasp the workflow of
+diffraction data analysis using EasyDiffraction.
+
+Instructions on how to run the tutorials are provided in the
+[:material-cog-box: Installation & Setup](../installation-and-setup/index.md#how-to-run-tutorials)
+section of the documentation.
+
+The tutorials are organized into the following categories.
+
+## Getting Started
+
+- [LBCO `quick` CIF](ed-1.ipynb) – A minimal example intended as a quick
+  reference for users already familiar with the EasyDiffraction API or who want
+  to see how Rietveld refinement of the La0.5Ba0.5CoO3 crystal structure can be
+  performed when both the sample model and experiment are loaded from CIF files.
+  Data collected from constant wavelength neutron powder diffraction at HRPT at
+  PSI.
+- [LBCO `quick` `code`](ed-2.ipynb) – A minimal example intended as a quick
+  reference for users already familiar with the EasyDiffraction API or who want
+  to see an example refinement when both the sample model and experiment are
+  defined directly in code. This tutorial covers a Rietveld refinement of the
+  La0.5Ba0.5CoO3 crystal structure using constant wavelength neutron powder
+  diffraction data from HRPT at PSI.
+- [LBCO `basic`](ed-3.ipynb) – Demonstrates the use of the EasyDiffraction API
+  in a simplified, user-friendly manner that closely follows the GUI workflow
+  for a Rietveld refinement of the La0.5Ba0.5CoO3 crystal structure using
+  constant wavelength neutron powder diffraction data from HRPT at PSI. This
+  tutorial provides a full explanation of the workflow with detailed comments
+  and descriptions of every step, making it suitable for users who are new to
+  EasyDiffraction or those who prefer a more guided approach.
+- [PbSO4 `advanced`](ed-4.ipynb) – Demonstrates a more flexible and advanced
+  approach to using the EasyDiffraction library, intended for users who are more
+  comfortable with Python programming. This tutorial covers a Rietveld
+  refinement of the PbSO4 crystal structure based on the joint fit of both X-ray
+  and neutron diffraction data.
+
+## Standard Diffraction
+
+- [Co2SiO4 `pd-neut-cwl`](ed-5.ipynb) – Demonstrates a Rietveld refinement of
+  the Co2SiO4 crystal structure using constant wavelength neutron powder
+  diffraction data from D20 at ILL.
+- [HS `pd-neut-cwl`](ed-6.ipynb) – Demonstrates a Rietveld refinement of the HS
+  crystal structure using constant wavelength neutron powder diffraction data
+  from HRPT at PSI.
+- [Si `pd-neut-tof`](ed-7.ipynb) – Demonstrates a Rietveld refinement of the Si
+  crystal structure using time-of-flight neutron powder diffraction data from
+  SEPD at Argonne.
+- [NCAF `pd-neut-tof`](ed-8.ipynb) – Demonstrates a Rietveld refinement of the
+  Na2Ca3Al2F14 crystal structure using two time-of-flight neutron powder
+  diffraction datasets (from two detector banks) of the WISH instrument at ISIS.
+- [LBCO+Si McStas](ed-9.ipynb) – Demonstrates a Rietveld refinement of the
+  La0.5Ba0.5CoO3 crystal structure with a small amount of Si impurity as a
+  secondary phase using time-of-flight neutron powder diffraction data simulated
+  with McStas.
+
+## Pair Distribution Function (PDF)
+
+- [Ni `pd-neut-cwl`](ed-10.ipynb) – Demonstrates a PDF analysis of Ni using data
+  collected from a constant wavelength neutron powder diffraction experiment.
+- [Si `pd-neut-tof`](ed-11.ipynb) – Demonstrates a PDF analysis of Si using data
+  collected from a time-of-flight neutron powder diffraction experiment at NOMAD
+  at SNS.
+- [NaCl `pd-xray`](ed-12.ipynb) – Demonstrates a PDF analysis of NaCl using data
+  collected from an X-ray powder diffraction experiment.
+
+## Workshops & Schools
+
+- [2025 DMSC](ed-13.ipynb) – A workshop tutorial that demonstrates a Rietveld
+  refinement of the La0.5Ba0.5CoO3 crystal structure using time-of-flight
+  neutron powder diffraction data simulated with McStas. This tutorial is
+  designed for the ESS DMSC Summer School 2025.

{easydiffraction-0.8.0 → easydiffraction-0.9.0}/docs/user-guide/first-steps.md

@@ -32,7 +32,7 @@ project = ed.Project()
 ```
 
 A complete tutorial using the `import` syntax can be found
-[here](../../tutorials/basic_single-fit_pd-neut-cwl_LBCO-HRPT/).
+[here](../../tutorials/ed-3/).
 
 ### Importing specific parts
 
@@ -59,7 +59,7 @@ project = Project()
 ```
 
 A complete tutorial using the `from` syntax can be found
-[here](../../tutorials/advanced_joint-fit_pd-neut-xray-cwl_PbSO4/).
+[here](../../tutorials/ed-4/).
 
 ## Utility functions