Add initial Bayesian analysis implementation with BUMPS DREAM

.codecov.yml

@@ -0,0 +1,26 @@
+# Codecov configuration
+# https://docs.codecov.com/docs/codecov-yaml
+
+github_checks:
+  annotations: true
+
+comment:
+  layout: 'reach, diff, flags, files'
+  behavior: default
+  require_changes: false
+  require_base: false
+  require_head: true
+
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 1%
+        # Make project coverage informational (won't block PR)
+        informational: true
+    patch:
+      default:
+        target: auto
+        # Require patch coverage but with threshold
+        threshold: 1%

.copier-answers.yml

@@ -1,6 +1,6 @@
 # WARNING: Do not edit this file manually.
 # Any changes will be overwritten by Copier.
-_commit: v0.11.1-12-gbb9bb30
+_commit: v0.11.4
 _src_path: gh:easyscience/templates
 app_docs_url: https://easyscience.github.io/diffraction-app
 app_doi: 10.5281/zenodo.18163581

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

@@ -33,7 +33,7 @@ inputs:
 runs:
   using: 'composite'
   steps:
-    - uses: prefix-dev/setup-pixi@v0.9.4
+    - uses: prefix-dev/setup-pixi@v0.9.5
       with:
         environments: ${{ inputs.environments }}
         activate-environment: ${{ inputs.activate-environment }}

.github/copilot-instructions.md

@@ -77,7 +77,7 @@
 ## Testing
 
 - Every new module, class, or bug fix ships with tests. See
-  `docs/architecture/architecture.md` §10 for the full strategy.
+  `docs/dev/architecture.md` §10 for the full strategy.
 - Unit tests mirror the source tree:
   `src/easydiffraction/<pkg>/<mod>.py` →
   `tests/unit/easydiffraction/<pkg>/test_<mod>.py`. Verify with
@@ -102,8 +102,8 @@
 
 - Before any structural/design change (new categories, factories,
   switchable-category wiring, datablocks, CIF serialisation), read
-  `docs/architecture/architecture.md` and follow documented patterns.
-  Localised bug fixes or test updates need only this file.
+  `docs/dev/architecture.md` and follow documented patterns. Localised
+  bug fixes or test updates need only this file.
 - Project is in beta: no legacy shims, no deprecation warnings — update
   tests and tutorials to the current API.
 - Minimal diffs; don't reformat working code. Fix only what's asked;
@@ -146,13 +146,12 @@ Non-trivial changes use a two-phase workflow:
 
 Notes:
 
-- `pixi run fix` regenerates `docs/architecture/package-structure-*.md`
+- `pixi run fix` regenerates `docs/dev/package-structure-*.md`
   automatically — never edit those by hand. Don't review auto-fixes;
   accept and move on. Then `pixi run check` until clean.
 - Open issues / design questions / planned improvements live in
-  `docs/architecture/issues_open.md` (priority-ordered). On resolution,
-  move to `docs/architecture/issues_closed.md` and update
-  `architecture.md` if affected.
+  `docs/dev/issues_open.md` (priority-ordered). On resolution, move to
+  `docs/dev/issues_closed.md` and update `architecture.md` if affected.
 
 ### Planning
 

.github/workflows/coverage.yml

@@ -5,8 +5,6 @@ on:
   push:
     branches:
       - develop
-    # Do not run on version tags (those are handled by other workflows)
-    tags-ignore: ['v*']
   # Trigger the workflow on pull request
   pull_request:
   # Allows you to run this workflow manually from the Actions tab

.github/workflows/dashboard.yml

@@ -32,9 +32,13 @@ jobs:
       - name: Set up pixi
         uses: ./.github/actions/setup-pixi
 
+      # Install badgery into the active Pixi environment without modifying
+      # pixi.toml/pixi.lock. Using `pixi add` here re-solves the whole project
+      # and rebuilds the local editable package, which can cause intermittent
+      # Linux CI failures (`Text file busy`, os error 26).
       - name: Install badgery
         shell: bash
-        run: pixi add --pypi --git https://github.com/enhantica/badgery badgery
+        run: pixi run python -m pip install git+https://github.com/enhantica/badgery
 
       - name: Run docstring coverage and code complexity/maintainability checks
         run: |

.github/workflows/issues-labels.yml

@@ -1,6 +1,5 @@
-# Verifies if the current issue has at least one real `[scope]` label and one
-# real `[priority]` label. If either is missing, the workflow adds a reminder
-# label with a warning emoji.
+# Verifies if the current issue has at least one `[scope]` label and one
+# `[priority]` label. If either is missing, the workflow adds a reminder label.
 
 name: Issue labels check
 
@@ -20,130 +19,22 @@ jobs:
       cancel-in-progress: true
 
     steps:
-      - name: Checkout repository
-        uses: actions/checkout@v6
-
-      - name: Sync missing-label reminders
-        uses: ./.github/actions/github-script
+      - name: Ensure [scope] label
+        uses: Rindrics/expect-label-prefix@v1.2.1
         with:
-          script: |
-            const fs = require('fs');
-
-            const issueNumber = context.issue.number;
-            const action = context.payload.action;
-            const changedLabel = context.payload.label?.name ?? null;
-            const labels = context.payload.issue.labels.map(({ name }) => name);
-            const requirements = [
-              {
-                prefix: '[scope] ',
-                reminder: '[scope] ⚠️ label needed',
-              },
-              {
-                prefix: '[priority] ',
-                reminder: '[priority] ⚠️ label needed',
-              },
-            ];
-
-            const labelsToAdd = [];
-            const labelsToRemove = [];
-            const evaluations = [];
-
-            console.log(`::group::Issue label check for #${issueNumber}`);
-            console.log(`Event action: ${action}`);
-            if (changedLabel) {
-              console.log(`Event label: ${changedLabel}`);
-            }
-            console.log(
-              `Current labels: ${labels.length > 0 ? labels.join(', ') : '(none)'}`,
-            );
-
-            for (const { prefix, reminder } of requirements) {
-              const matchingRealLabels = labels.filter(
-                (name) => name.startsWith(prefix) && name !== reminder,
-              );
-              const hasRealLabel = matchingRealLabels.length > 0;
-              const hasReminderLabel = labels.includes(reminder);
-
-              evaluations.push({
-                prefix,
-                reminder,
-                matchingRealLabels,
-                hasReminderLabel,
-              });
-
-              if (hasRealLabel && hasReminderLabel) {
-                labelsToRemove.push(reminder);
-              } else if (!hasRealLabel && !hasReminderLabel) {
-                labelsToAdd.push(reminder);
-              }
-            }
-
-            for (const evaluation of evaluations) {
-              if (evaluation.matchingRealLabels.length > 0) {
-                console.log(
-                  `Found required ${evaluation.prefix}label(s): ${evaluation.matchingRealLabels.join(', ')}`,
-                );
-              } else {
-                console.log(`Missing required ${evaluation.prefix}label.`);
-              }
-
-              if (evaluation.hasReminderLabel) {
-                console.log(`Reminder label already present: ${evaluation.reminder}`);
-              }
-            }
-
-            if (labelsToAdd.length > 0) {
-              console.log(`Adding reminder labels: ${labelsToAdd.join(', ')}`);
-              await github.rest.issues.addLabels({
-                owner: context.repo.owner,
-                repo: context.repo.repo,
-                issue_number: context.issue.number,
-                labels: labelsToAdd,
-              });
-            }
-
-            for (const name of labelsToRemove) {
-              console.log(`Removing reminder label: ${name}`);
-              await github.rest.issues.removeLabel({
-                owner: context.repo.owner,
-                repo: context.repo.repo,
-                issue_number: context.issue.number,
-                name,
-              });
-            }
-
-            if (labelsToAdd.length === 0 && labelsToRemove.length === 0) {
-              console.log('No label changes required.');
-            }
-
-            console.log('::endgroup::');
-
-            if (process.env.GITHUB_STEP_SUMMARY) {
-              const summaryLines = [
-                '### Issue Label Check',
-                `- Issue: #${issueNumber}`,
-                `- Event: ${action}`,
-                `- Trigger label: ${changedLabel ?? '(none)'}`,
-                `- Current labels: ${labels.length > 0 ? labels.join(', ') : '(none)'}`,
-                '',
-                '#### Requirement status',
-                ...evaluations.map((evaluation) => {
-                  const status =
-                    evaluation.matchingRealLabels.length > 0
-                      ? `found ${evaluation.matchingRealLabels.join(', ')}`
-                      : 'missing';
-                  const reminder = evaluation.hasReminderLabel
-                    ? `reminder present: ${evaluation.reminder}`
-                    : `reminder absent: ${evaluation.reminder}`;
-                  return `- ${evaluation.prefix}: ${status}; ${reminder}`;
-                }),
-                '',
-                `- Labels to add: ${labelsToAdd.length > 0 ? labelsToAdd.join(', ') : '(none)'}`,
-                `- Labels to remove: ${labelsToRemove.length > 0 ? labelsToRemove.join(', ') : '(none)'}`,
-              ];
-
-              fs.appendFileSync(
-                process.env.GITHUB_STEP_SUMMARY,
-                `${summaryLines.join('\n')}\n`,
-              );
-            }
+          repository_full_name: ${{ github.repository }}
+          token: ${{ github.token }}
+          label_prefix: '[scope]'
+          label_separator: ' '
+          add_label: 'true'
+          default_label: '[scope] ⚠️ label needed'
+
+      - name: Ensure [priority] label
+        uses: Rindrics/expect-label-prefix@v1.2.1
+        with:
+          repository_full_name: ${{ github.repository }}
+          token: ${{ github.token }}
+          label_prefix: '[priority]'
+          label_separator: ' '
+          add_label: 'true'
+          default_label: '[priority] ⚠️ label needed'

.github/workflows/pr-labels.yml

@@ -1,63 +1,45 @@
 # Verifies if a pull request has at least one label from a set of valid
 # labels before it can be merged.
 #
-# NOTE:
-# This workflow may be triggered twice in quick succession when a PR is
-# created:
-#   1) `opened`  — when the pull request is initially created
-#   2) `labeled` — if labels are added immediately after creation
-# (e.g. by manual labeling, another workflow, or GitHub App).
-#
-# These are separate GitHub events, so two workflow runs can be started.
-# The `concurrency` configuration below ensures that only the latest run
-# for the same PR remains active, canceling any previous in-progress
-# run.
+# The label validation is delegated to `mheap/github-action-required-labels`,
+# which checks the current PR labels via the GitHub API and can add or update a
+# PR comment when the required label set is missing.
 
 name: PR labels check
 
 on:
   pull_request_target:
     types: [opened, labeled, unlabeled, synchronize]
 
-concurrency:
-  group: pr-labels-${{ github.event.pull_request.number }}
-  cancel-in-progress: true
-
 permissions:
-  pull-requests: read
+  issues: write
+  pull-requests: write
 
 jobs:
   check-labels:
     runs-on: ubuntu-latest
 
     steps:
-      - name: Check for valid labels
-        run: |
-          PR_LABELS=$(echo '${{ toJson(github.event.pull_request.labels.*.name) }}' | jq -r '.[]')
-
-          echo "Current PR labels: $PR_LABELS"
-          VALID_LABELS=(
-            "[bot] release"
-            "[scope] bug"
-            "[scope] documentation"
-            "[scope] enhancement"
-            "[scope] maintenance"
-            "[scope] significant"
-          )
-
-          found=false
-          for label in "${VALID_LABELS[@]}"; do
-            if echo "$PR_LABELS" | grep -Fxq "$label"; then
-              echo "✅ Found valid label: $label"
-              found=true
-              break
-            fi
-          done
-
-          if [ "$found" = false ]; then
-            echo "ERROR: PR must have at least one of the following labels:"
-            for label in "${VALID_LABELS[@]}"; do
-              echo "       - $label"
-            done
-            exit 1
-          fi
+      - name: Checkout repository
+        uses: actions/checkout@v6
+
+      - name: Setup easyscience[bot]
+        id: bot
+        uses: ./.github/actions/setup-easyscience-bot
+        with:
+          app-id: ${{ vars.EASYSCIENCE_APP_ID }}
+          private-key: ${{ secrets.EASYSCIENCE_APP_KEY }}
+
+      - uses: mheap/github-action-required-labels@v5
+        with:
+          token: ${{ steps.bot.outputs.token }}
+          add_comment: true
+          mode: minimum
+          count: 1
+          labels: |
+            [bot] release
+            [scope] bug
+            [scope] documentation
+            [scope] enhancement
+            [scope] maintenance
+            [scope] significant

.github/workflows/test.yml

@@ -248,10 +248,10 @@ jobs:
               exit 1
             fi
 
-            whl_url="file://$(python -c 'import os,sys; print(os.path.abspath(sys.argv[1]))' "${whl_path[0]}")"
+            whl_abs_path="$(python -c 'import os,sys; print(os.path.abspath(sys.argv[1]))' "${whl_path[0]}")"
 
-            echo "Adding easydiffraction from: $whl_url"
-            pixi add --pypi "easydiffraction[dev] @ ${whl_url}"
+            echo "Adding easydiffraction from: $whl_abs_path"
+            pixi add --pypi "easydiffraction[dev] @ ${whl_abs_path}"
 
             echo "Exiting pixi project directory"
             cd ..

CONTRIBUTING.md

@@ -249,6 +249,12 @@ or to run only Python linting checks:
 pixi run py-lint-check
 ```
 
+To add missing license headers:
+
+```bash
+pixi run spdx-add
+```
+
 Some formatting issues can be fixed automatically:
 
 ```bash