Merge pull request #91 from scipp/update-dependencies

Update dependencies

Author: jl-wynen

.copier-answers.yml

@@ -1,5 +1,5 @@
 # Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
-_commit: 86a1e5c
+_commit: 75b9a8f
 _src_path: gh:scipp/copier_template
 description: Diffraction data reduction for the European Spallation Source
 max_python: '3.12'

.github/workflows/ci.yml

@@ -27,7 +27,7 @@ jobs:
       - uses: pre-commit/[email protected]
         with:
           extra_args: --all-files
-      - uses: pre-commit-ci/[email protected].2
+      - uses: pre-commit-ci/[email protected].3
         if: always()
         with:
           msg: Apply automatic formatting

.github/workflows/docs.yml

@@ -69,7 +69,7 @@ jobs:
           name: docs_html
           path: html/
 
-      - uses: JamesIves/[email protected].3
+      - uses: JamesIves/[email protected].4
         if: ${{ inputs.publish }}
         with:
           branch: gh-pages

.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/
@@ -39,3 +41,4 @@ docs/generated/
 *.cif
 *.rcif
 *.ort
+*.zip

.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
@@ -14,22 +14,22 @@ repos:
         args: [ --markdown-linebreak-ext=md ]
         exclude: '\.svg'
   - 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/astral-sh/ruff-pre-commit
-    rev: v0.4.3
+    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:

.python-version

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

conda/meta.yaml

@@ -9,6 +9,7 @@ source:
 
 {% 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:
@@ -28,7 +29,13 @@ 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/

docs/api-reference/index.md

@@ -27,7 +27,6 @@
    grouping
    smoothing
    types
-   uncertainty
 ```
 
 ## ESSdream

docs/conf.py

@@ -1,3 +1,6 @@
+# SPDX-License-Identifier: BSD-3-Clause
+# Copyright (c) 2024 Scipp contributors (https://github.com/scipp)
+
 import doctest
 import os
 import sys

docs/user-guide/dream/dream-data-reduction.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "f47beab6-47c9-4cfb-a70e-c00bc8daebef",
+   "id": "0",
    "metadata": {},
    "source": [
     "# DREAM data reduction\n",
@@ -15,7 +15,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "74b2df0c-6957-40c2-a48e-a4351547e87a",
+   "id": "1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -30,7 +30,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "dcaf1d53-2a81-4a31-8379-1fb3791aaeab",
+   "id": "2",
    "metadata": {},
    "source": [
     "## Create and configure the workflow\n",
@@ -41,7 +41,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b2d15f12-69d7-4c5d-9d4d-f1c13fc29103",
+   "id": "3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -50,7 +50,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "1252feab-12d2-46ac-bf74-70b32344473d",
+   "id": "4",
    "metadata": {},
    "source": [
     "We then need to set the missing parameters which are specific to each experiment\n",
@@ -60,7 +60,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "502e77cc-0253-4e71-9d97-81ff560ef99d",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -85,7 +85,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "21fb4492-e836-41d3-a2d4-9678df43b9f9",
+   "id": "6",
    "metadata": {},
    "source": [
     "## Use the workflow\n",
@@ -96,7 +96,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "93f2ba0d-f256-4b64-b8fa-42cd1081cc41",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -105,7 +105,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "478f580e-273c-4a46-8dfc-9a2ed31b0cd3",
+   "id": "8",
    "metadata": {},
    "source": [
     "We then call `compute()` to compute the result:"
@@ -114,7 +114,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6a17cf1d-0407-41dd-8a84-0975371ac70a",
+   "id": "9",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -125,7 +125,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "527623d2-0eee-456d-a4dd-764df8618ee4",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -135,7 +135,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "39dc0ea3-b30d-4a88-878c-86cf0e8e76e9",
+   "id": "11",
    "metadata": {},
    "source": [
     "We can now save the result to disk:"
@@ -144,7 +144,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f37eba41-6178-4bcb-bf3c-fa177e6112b0",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -156,7 +156,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "0898265e-7edd-4093-9dfb-6e6b2f05c766",
+   "id": "13",
    "metadata": {},
    "source": [
     "## Compute intermediate results\n",
@@ -169,7 +169,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4bd5a7d5-581f-4d04-bf11-955e55646199",
+   "id": "14",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -186,7 +186,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "185cb6ee-8e55-43d0-9505-ebe2761785ed",
+   "id": "15",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -198,7 +198,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "7f866ad4-5a0d-4c98-b5ab-a2436f97074d",
+   "id": "16",
    "metadata": {},
    "source": [
     "## Grouping by scattering angle\n",
@@ -210,7 +210,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "bc516311-1ab4-4eb7-9a0b-d83ff61e036b",
+   "id": "17",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -222,7 +222,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b19ab368-e0c4-4a03-ac20-61a442e8826e",
+   "id": "18",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -233,7 +233,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "fc25ee9c-9395-481f-bd31-3ad139859686",
+   "id": "19",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -251,7 +251,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6e414419-ccf4-420b-899d-a1fa4a6ce4ca",
+   "id": "20",
    "metadata": {},
    "outputs": [],
    "source": [