essdiffraction 23.12.0__tar.gz → 24.9.0__tar.gz

essdiffraction-24.9.0/.copier-answers.ess.yml

@@ -0,0 +1,3 @@
+# Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
+_commit: 0951a4b
+_src_path: https://github.com/scipp/ess_template

{essdiffraction-23.12.0 → essdiffraction-24.9.0}/.copier-answers.yml

@@ -1,13 +1,13 @@
 # Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
-_commit: 8cfdb1b
+_commit: 75b9a8f
 _src_path: gh:scipp/copier_template
 description: Diffraction data reduction for the European Spallation Source
-max_python: '3.11'
-min_python: '3.9'
+max_python: '3.12'
+min_python: '3.10'
 namespace_package: ess
-nightly_deps: scipp,scippnexus,sciline,plopp,scippneutron
+nightly_deps: scipp,scippnexus,sciline,plopp,scippneutron,essreduce
 orgname: scipp
 prettyname: ESSdiffraction
 projectname: essdiffraction
-related_projects: Scipp,ScippNexus,ScippNeutron,Sciline,Plopp
-year: 2023
+related_projects: Scipp,ScippNexus,ScippNeutron,Sciline,Plopp,ESSreduce
+year: 2024

essdiffraction-24.9.0/.github/ISSUE_TEMPLATE/blank.md

@@ -0,0 +1,8 @@
+---
+name: Blank
+about: General issue that does not fit another category
+title: ''
+labels: ''
+assignees: ''
+
+---

essdiffraction-24.9.0/.github/ISSUE_TEMPLATE/high-level-requirement.yml

@@ -0,0 +1,89 @@
+name: High-level requirement
+description: Describe a high-level requirement
+title: "[Requirement] "
+labels: ["requirement"]
+projects: []
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for taking the time to provide as many details as possible for this requirement!
+  - type: input
+    id: summary
+    attributes:
+      label: Executive summary
+      description: Provide a short summary of the requirement
+      placeholder: "Example: We need to correct for X when processing Y."
+    validations:
+      required: true
+  - type: textarea
+    id: context
+    attributes:
+      label: Context and background knowledge
+      description: |
+        - What is the context of this requirement?
+        - What background knowledge is required to understand it?
+        - Does this depend on previous tasks? Provide links!
+        - Is there follow-up work?
+      placeholder: "Example: See summary on Wikipedia, or the following paper."
+    validations:
+      required: true
+  - type: textarea
+    id: inputs
+    attributes:
+      label: Inputs
+      description: |
+        Describe in detail all the input data and data properties that are known.
+        This is not about test data (see below), but about general properties of data that will be used in practice.
+      placeholder: "Example: A single 1-D spectrum with a known wavelength range."
+    validations:
+      required: true
+  - type: textarea
+    id: methodology
+    attributes:
+      label: Methodology
+      description: |
+        Describe, e.g., the computation to be performed.
+        When linking to references, please refer to the specific section, page, or equation.
+      placeholder: "Remember you can write equations such as $n\\lambda = 2d\\sin(\\theta)$ using LaTeX syntax, as well as other Markdown formatting."
+    validations:
+      required: true
+  - type: textarea
+    id: outputs
+    attributes:
+      label: Outputs
+      description: |
+        Describe in detail all the output data and data properties.
+        This is not about test data (see below), but about general properties of data that will be used in practice.
+      placeholder: "Example: The position of the peak in the spectrum."
+    validations:
+      required: true
+  - type: dropdown
+    id: interfaces
+    attributes:
+      label: Which interfaces are required?
+      multiple: true
+      options:
+        - Integrated into reduction workflow
+        - Python module / function
+        - Python script
+        - Jupyter notebook
+        - Other (please describe in comments)
+      default: 0
+    validations:
+      required: true
+  - type: textarea
+    id: testcases
+    attributes:
+      label: Test cases
+      description: How can we test this requirement? Links to tests data and reference data, or other suggestions.
+    validations:
+      required: true
+  - type: textarea
+    id: comments
+    attributes:
+      label: Comments
+      description: Do you have other comments that do not fall in the above categories?
+      placeholder: "Example: Depends on issues #1234, blocked by #666."
+    validations:
+      required: false

{essdiffraction-23.12.0 → essdiffraction-24.9.0}/.github/workflows/ci.yml

@@ -1,6 +1,3 @@
-# SPDX-License-Identifier: BSD-3-Clause
-# Copyright (c) 2023 Scipp contributors (https://github.com/scipp)
-
 name: CI
 
 on:
@@ -24,15 +21,16 @@ jobs:
         run: |
           echo "min_python=$(cat .github/workflows/python-version-ci)" >> $GITHUB_OUTPUT
           echo "min_tox_env=py$(cat .github/workflows/python-version-ci | sed 's/\.//g')" >> $GITHUB_OUTPUT
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version-file: '.github/workflows/python-version-ci'
-      - run: python -m pip install --upgrade pip
-      - run: python -m pip install -r requirements/ci.txt
-      - run: tox -e static
-      - uses: stefanzweifel/git-auto-commit-action@v5
+      - uses: pre-commit/action@v3.0.1
+        with:
+          extra_args: --all-files
+      - uses: pre-commit-ci/lite-action@v1.0.3
+        if: always()
         with:
-          commit_message: Apply automatic formatting
+          msg: Apply automatic formatting
 
   tests:
     name: Tests
@@ -48,6 +46,7 @@ jobs:
       os-variant: ${{ matrix.os }}
       python-version: ${{ matrix.python.version }}
       tox-env: ${{ matrix.python.tox-env }}
+    secrets: inherit
 
   docs:
     needs: tests
@@ -56,3 +55,4 @@ jobs:
       publish: false
       linkcheck: ${{ contains(matrix.variant.os, 'ubuntu') && github.ref == 'refs/heads/main' }}
       branch: ${{ github.head_ref == '' && github.ref_name || github.head_ref }}
+    secrets: inherit

{essdiffraction-23.12.0 → essdiffraction-24.9.0}/.github/workflows/docs.yml

@@ -1,6 +1,3 @@
-# SPDX-License-Identifier: BSD-3-Clause
-# Copyright (c) 2023 Scipp contributors (https://github.com/scipp)
-
 name: Docs
 
 on:
@@ -45,13 +42,18 @@ jobs:
   docs:
     name: Build documentation
     runs-on: 'ubuntu-22.04'
+    env:
+        ESS_PROTECTED_FILESTORE_USERNAME: ${{ secrets.ESS_PROTECTED_FILESTORE_USERNAME }}
+        ESS_PROTECTED_FILESTORE_PASSWORD: ${{ secrets.ESS_PROTECTED_FILESTORE_PASSWORD }}
+
     steps:
       - run: sudo apt install --yes graphviz pandoc
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           ref: ${{ inputs.branch == '' && github.ref_name || inputs.branch }}
+          repository: ${{ github.event.pull_request.head.repo.full_name }}
           fetch-depth: 0  # history required so cmake can determine version
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version-file: '.github/workflows/python-version-ci'
       - run: python -m pip install --upgrade pip
@@ -62,12 +64,12 @@ jobs:
         if: ${{ inputs.version == '' }}
       - run: tox -e linkcheck
         if: ${{ inputs.linkcheck }}
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: docs_html
           path: html/
 
-      - uses: JamesIves/github-pages-deploy-action@v4.4.3
+      - uses: JamesIves/github-pages-deploy-action@v4.6.4
         if: ${{ inputs.publish }}
         with:
           branch: gh-pages

{essdiffraction-23.12.0 → essdiffraction-24.9.0}/.github/workflows/nightly_at_main.yml

@@ -1,6 +1,3 @@
-# SPDX-License-Identifier: BSD-3-Clause
-# Copyright (c) 2023 Scipp contributors (https://github.com/scipp)
-
 name: Nightly test at main branch
 
 on:
@@ -34,3 +31,4 @@ jobs:
       os-variant: ${{ matrix.os }}
       python-version: ${{ matrix.python.version }}
       tox-env: ${{ matrix.python.tox-env }}
+    secrets: inherit

{essdiffraction-23.12.0 → essdiffraction-24.9.0}/.github/workflows/nightly_at_release.yml

@@ -1,6 +1,3 @@
-# SPDX-License-Identifier: BSD-3-Clause
-# Copyright (c) 2023 Scipp contributors (https://github.com/scipp)
-
 name: Nightly tests at latest release
 
 on:
@@ -41,3 +38,4 @@ jobs:
       python-version: ${{ matrix.python.version }}
       tox-env: ${{ matrix.python.tox-env }}
       checkout_ref: ${{ needs.setup.outputs.release_tag }}
+    secrets: inherit

essdiffraction-24.9.0/.github/workflows/python-version-ci

@@ -0,0 +1 @@
+3.10

{essdiffraction-23.12.0 → essdiffraction-24.9.0}/.github/workflows/release.yml

@@ -1,6 +1,3 @@
-# SPDX-License-Identifier: BSD-3-Clause
-# Copyright (c) 2023 Scipp contributors (https://github.com/scipp)
-
 name: Release
 
 on:
@@ -18,7 +15,7 @@ jobs:
     runs-on: 'ubuntu-22.04'
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: true
           fetch-depth: 0  # history required so setuptools_scm can determine version
@@ -31,7 +28,7 @@ jobs:
             boa
       - run: conda mambabuild --channel conda-forge --channel scipp --no-anaconda-upload --override-channels --output-folder conda/package conda
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: conda-package-noarch
           path: conda/package/noarch/*.tar.bz2
@@ -41,11 +38,11 @@ jobs:
     runs-on: 'ubuntu-22.04'
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0  # history required so setuptools_scm can determine version
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version-file: '.github/workflows/python-version-ci'
 
@@ -56,7 +53,7 @@ jobs:
         run: python -m build
 
       - name: Upload wheels
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: dist
           path: dist
@@ -70,8 +67,8 @@ jobs:
       id-token: write
     if: github.event_name == 'release' && github.event.action == 'published'
     steps:
-      - uses: actions/download-artifact@v3
-      - uses: pypa/gh-action-pypi-publish@v1.8.10
+      - uses: actions/download-artifact@v4
+      - uses: pypa/gh-action-pypi-publish@v1.8.14
 
   upload_conda:
     name: Deploy Conda
@@ -80,7 +77,7 @@ jobs:
     if: github.event_name == 'release' && github.event.action == 'published'
 
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
       - uses: mamba-org/setup-micromamba@v1
         with:
           environment-name: upload-env
@@ -104,7 +101,7 @@ jobs:
     permissions:
       contents: write  # This is needed so that the action can upload the asset
     steps:
-    - uses: actions/download-artifact@v3
+    - uses: actions/download-artifact@v4
     - name: Zip documentation
       run: |
         mv docs_html documentation-${{ github.ref_name }}

{essdiffraction-23.12.0 → essdiffraction-24.9.0}/.github/workflows/test.yml

@@ -1,6 +1,3 @@
-# SPDX-License-Identifier: BSD-3-Clause
-# Copyright (c) 2023 Scipp contributors (https://github.com/scipp)
-
 name: Test
 
 on:
@@ -44,20 +41,38 @@ on:
         type: string
 
 jobs:
+  package-test:
+    runs-on: ${{ inputs.os-variant }}
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          ref: ${{ inputs.checkout_ref }}
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ inputs.python-version }}
+      - run: python -m pip install --upgrade pip
+      - run: python -m pip install .
+      - run: python tests/package_test.py
+        name: Run package tests
+
   test:
     runs-on: ${{ inputs.os-variant }}
+    env:
+        ESS_PROTECTED_FILESTORE_USERNAME: ${{ secrets.ESS_PROTECTED_FILESTORE_USERNAME }}
+        ESS_PROTECTED_FILESTORE_PASSWORD: ${{ secrets.ESS_PROTECTED_FILESTORE_PASSWORD }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           ref: ${{ inputs.checkout_ref }}
-      - uses: actions/setup-python@v3
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ inputs.python-version }}
       - run: python -m pip install --upgrade pip
       - run: python -m pip install -r ${{ inputs.pip-recipe }}
       - run: tox -e ${{ inputs.tox-env }}
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         if: ${{ inputs.coverage-report }}
         with:
           name: CoverageReport

{essdiffraction-23.12.0 → essdiffraction-24.9.0}/.github/workflows/unpinned.yml

@@ -1,6 +1,3 @@
-# SPDX-License-Identifier: BSD-3-Clause
-# Copyright (c) 2023 Scipp contributors (https://github.com/scipp)
-
 name: Unpinned tests at latest release
 
 on:
@@ -41,3 +38,4 @@ jobs:
       python-version: ${{ matrix.python.version }}
       tox-env: ${{ matrix.python.tox-env }}
       checkout_ref: ${{ needs.setup.outputs.release_tag }}
+    secrets: inherit

{essdiffraction-23.12.0 → essdiffraction-24.9.0}/.gitignore

@@ -4,11 +4,13 @@ dist
 html
 .tox
 *.egg-info
+uv.lock  # we lock dependencies with pip-compile, not uv
 
 *.sw?
 
 # Environments
 venv
+.venv
 
 # Caches
 .clangd/
@@ -20,6 +22,7 @@ __pycache__/
 .pytest_cache
 .mypy_cache
 docs/generated/
+.ruff_cache
 
 # Editor settings
 .idea/
@@ -37,3 +40,5 @@ docs/generated/
 *.raw
 *.cif
 *.rcif
+*.ort
+*.zip

{essdiffraction-23.12.0 → essdiffraction-24.9.0}/.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
       - id: check-added-large-files
       - id: check-json
@@ -13,36 +13,23 @@ repos:
       - id: trailing-whitespace
         args: [ --markdown-linebreak-ext=md ]
         exclude: '\.svg'
-  - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
-        name: isort (python)
-  - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 23.11.0
-    hooks:
-      - id: black
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.6.0
+    rev: 0.7.1
     hooks:
       - id: nbstripout
         types: [ "jupyter" ]
         args: [ "--drop-empty-cells",
                 "--extra-keys 'metadata.language_info.version cell.metadata.jp-MarkdownHeadingCollapsed cell.metadata.pycharm'" ]
-  - repo: https://github.com/pycqa/flake8
-    rev: 6.1.0
-    hooks:
-      - id: flake8
-        types: ["python"]
-        additional_dependencies: ["flake8-bugbear==23.9.16"]
-  - repo: https://github.com/pycqa/bandit
-    rev: 1.7.5
-    hooks:
-      - id: bandit
-        additional_dependencies: ["bandit[toml]"]
-        args: ["-c", "pyproject.toml"]
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.2
+    hooks:
+      - id: ruff
+        args: [ --fix ]
+        types_or: [ python, pyi, jupyter ]
+      - id: ruff-format
+        types_or: [ python, pyi ]
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
+    rev: v2.3.0
     hooks:
       - id: codespell
         additional_dependencies:

essdiffraction-24.9.0/.python-version

@@ -0,0 +1 @@
+3.10

{essdiffraction-23.12.0 → essdiffraction-24.9.0}/LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2023, Scipp contributors (https://github.com/scipp)
+Copyright (c) 2024, Scipp contributors (https://github.com/scipp)
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

{essdiffraction-23.12.0/src/essdiffraction.egg-info → essdiffraction-24.9.0}/PKG-INFO

@@ -1,11 +1,11 @@
 Metadata-Version: 2.1
 Name: essdiffraction
-Version: 23.12.0
+Version: 24.9.0
 Summary: Diffraction data reduction for the European Spallation Source
 Author: Scipp contributors
 License: BSD 3-Clause License
         
-        Copyright (c) 2023, Scipp contributors (https://github.com/scipp)
+        Copyright (c) 2024, Scipp contributors (https://github.com/scipp)
         All rights reserved.
         
         Redistribution and use in source and binary forms, with or without
@@ -42,22 +42,28 @@ Classifier: Natural Language :: English
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3 :: Only
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering
 Classifier: Typing :: Typed
-Requires-Python: >=3.9
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: dask
+Requires-Dist: essreduce>=24.08.2
 Requires-Dist: graphviz
+Requires-Dist: numpy
 Requires-Dist: plopp
 Requires-Dist: pythreejs
-Requires-Dist: sciline>=23.9.1
-Requires-Dist: scipp>=23.8.0
-Requires-Dist: scippneutron>=23.9.0
+Requires-Dist: sciline>=24.06.0
+Requires-Dist: scipp>=24.09.1
+Requires-Dist: scippneutron>=24.9.0
 Requires-Dist: scippnexus>=23.12.0
+Provides-Extra: test
+Requires-Dist: pandas; extra == "test"
+Requires-Dist: pooch; extra == "test"
+Requires-Dist: pytest; extra == "test"
 
 [![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](CODE_OF_CONDUCT.md)
 [![PyPI badge](http://img.shields.io/pypi/v/essdiffraction.svg)](https://pypi.python.org/pypi/essdiffraction)

{essdiffraction-23.12.0 → essdiffraction-24.9.0}/conda/meta.yaml

@@ -6,27 +6,36 @@ package:
 source:
   path: ..
 
+
+{% set pyproject = load_file_data('pyproject.toml') %}
+{% set dependencies = pyproject.get('project', {}).get('dependencies', {}) %}
+{% set test_dependencies = pyproject.get('project', {}).get('optional-dependencies', {}).get('test', {}) %}
+
+
 requirements:
   build:
     - setuptools
     - setuptools_scm
   run:
-    - dask
-    - python>=3.8
-    - python-graphviz
-    - plopp
-    - pythreejs
-    - sciline>=23.9.1
-    - scipp>=23.8.0
-    - scippneutron>=23.11.0
-    - scippnexus>=23.12.0
-    - python>=3.9
+    - python>=3.10
+
+  {# Conda does not allow spaces between package name and version, so remove them #}
+  {% for package in dependencies %}
+    - {% if package == "graphviz" %}python-graphviz{% else %}{{ package|replace(" ", "") }}{% endif %}
+  {% endfor %}
+
 
 test:
   imports:
     - ess.diffraction
   requires:
-    - pytest
+
+  {# Conda does not allow spaces between package name and version, so remove them #}
+  {% for package in test_dependencies %}
+    - {% if package == "graphviz" %}python-graphviz{% else %}{{ package|replace(" ", "") }}{% endif %}
+  {% endfor %}
+
+
   source_files:
     - pyproject.toml
     - tests/

essdiffraction-24.9.0/docs/_templates/doc_version.html

@@ -0,0 +1,2 @@
+<!-- This will display the version of the docs -->
+Current ESSdiffraction version: {{ version }} (<a href="https://github.com/scipp/essdiffraction/releases">older versions</a>).

essdiffraction-24.9.0/docs/about/bibliography.rst

@@ -0,0 +1,4 @@
+Bibliography
+============
+
+.. bibliography::

{essdiffraction-23.12.0 → essdiffraction-24.9.0}/docs/about/index.md

@@ -12,7 +12,7 @@ ESSdiffraction is available as open source under the [BSD-3 license](https://ope
 
 Please cite the following:
 
-[![DOI](https://zenodo.org/badge/FIXME.svg)](https://zenodo.org/doi/10.5281/zenodo.FIXME)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10369509.svg)](https://zenodo.org/doi/10.5281/zenodo.10369509)
 
 To cite a specific version of ESSdiffraction, select the desired version on Zenodo to get the corresponding DOI.
 
@@ -24,3 +24,11 @@ Simply download the archive, unzip and view locally in a web browser.
 ## Source code and development
 
 ESSdiffraction is hosted and developed [on GitHub](https://github.com/scipp/essdiffraction).
+
+```{toctree}
+---
+hidden:
+---
+
+bibliography
+```

essdiffraction-24.9.0/docs/api-reference/index.md

@@ -0,0 +1,69 @@
+# API Reference
+
+## ESSpowder
+
+### Module Attributes
+```{eval-rst}
+.. currentmodule:: ess.powder
+
+.. autosummary::
+   :toctree: ../generated/attributes
+
+   providers
+   with_pixel_mask_filenames
+```
+
+### Submodules
+
+```{eval-rst}
+.. autosummary::
+   :toctree: ../generated/modules
+   :template: module-template.rst
+   :recursive:
+
+   conversion
+   correction
+   filtering
+   grouping
+   smoothing
+   types
+```
+
+## ESSdream
+
+### Top-level functions
+
+```{eval-rst}
+.. currentmodule:: ess.dream
+
+.. autosummary::
+   :toctree: ../generated/functions
+
+   instrument_view
+   DreamGeant4Workflow
+```
+
+### Submodules
+
+```{eval-rst}
+.. autosummary::
+   :toctree: ../generated/modules
+   :template: module-template.rst
+   :recursive:
+
+   data
+   io
+```
+
+## SNS powder
+
+```{eval-rst}
+.. currentmodule:: ess.snspowder
+
+.. autosummary::
+   :toctree: ../generated/modules
+   :template: module-template.rst
+   :recursive:
+
+   powgen
+```

essdiffraction-24.9.0/docs/bibliography.bib

@@ -0,0 +1,8 @@
+@book{Arblaster:2018,
+  author = {John W. Arblaster},
+  year = {2018},
+  title = {Selected Values of the Crystallographic Properties of the Elements},
+  publisher = {ASM International},
+  ISBN = {978-1-62708-154-2},
+  url = {https://www.asminternational.org/selected-values-of-the-crystallographic-properties-of-the-elements/results/-/journal_content/56/39867022/PUBLICATION/}
+}