From 0fddd1bd7387ee00438c2fa70d858ee2f9c34726 Mon Sep 17 00:00:00 2001 From: YooSunyoung <17974113+YooSunYoung@users.noreply.github.com> Date: Mon, 9 Feb 2026 10:38:42 +0100 Subject: [PATCH 1/6] Update copyright year. --- LICENSE | 2 +- docs/conf.py | 4 ++-- src/scitiff/__init__.py | 2 +- tests/package_test.py | 2 +- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/LICENSE b/LICENSE index 62b99bf..fb719eb 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ BSD 3-Clause License -Copyright (c) 2025, Scipp and ESS contributors (https://github.com/scipp) +Copyright (c) 2026, Scipp contributors (https://github.com/scipp) All rights reserved. Redistribution and use in source and binary forms, with or without diff --git a/docs/conf.py b/docs/conf.py index f6ddf63..a9c2f55 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -1,5 +1,5 @@ # SPDX-License-Identifier: BSD-3-Clause -# Copyright (c) 2025 Scipp contributors (https://github.com/scipp) +# Copyright (c) 2026 Scipp contributors (https://github.com/scipp) import doctest import os @@ -15,7 +15,7 @@ # General information about the project. project = 'SciTiff' -copyright = '2025 Scipp contributors' +copyright = '2026 Scipp contributors' author = 'Scipp contributors' html_show_sourcelink = True diff --git a/src/scitiff/__init__.py b/src/scitiff/__init__.py index fe3ec32..3db56cf 100644 --- a/src/scitiff/__init__.py +++ b/src/scitiff/__init__.py @@ -1,5 +1,5 @@ # SPDX-License-Identifier: BSD-3-Clause -# Copyright (c) 2025 Scipp contributors (https://github.com/scipp) +# Copyright (c) 2026 Scipp contributors (https://github.com/scipp) # ruff: noqa: RUF100, E402, F401, I import importlib.metadata diff --git a/tests/package_test.py b/tests/package_test.py index e4537ac..8fa9c27 100644 --- a/tests/package_test.py +++ b/tests/package_test.py @@ -1,5 +1,5 @@ # SPDX-License-Identifier: BSD-3-Clause -# Copyright (c) 2025 Scipp contributors (https://github.com/scipp) +# Copyright (c) 2026 Scipp contributors (https://github.com/scipp) """Tests of package integrity. From a7619334cb88e81ec3d9ab2f2892e2559d2d9650 Mon Sep 17 00:00:00 2001 From: YooSunyoung <17974113+YooSunYoung@users.noreply.github.com> Date: Mon, 9 Feb 2026 10:39:06 +0100 Subject: [PATCH 2/6] Update github action and remove dependabot. --- .github/dependabot.yml | 13 ------------- .github/workflows/docs.yml | 2 +- 2 files changed, 1 insertion(+), 14 deletions(-) delete mode 100644 .github/dependabot.yml diff --git a/.github/dependabot.yml b/.github/dependabot.yml deleted file mode 100644 index c8076bb..0000000 --- a/.github/dependabot.yml +++ /dev/null @@ -1,13 +0,0 @@ -version: 2 -updates: - # Note: We are not listing package-ecosystem: "github-actions". This causes - # noise in all template instances. Instead dependabot.yml in scipp/copier_template - # triggers updates of github-actions in the *template*. We then use `copier update` - # in template instances. - - package-ecosystem: "pip" - directory: "/requirements" - schedule: - interval: "daily" - allow: - - dependency-name: "scipp" - dependency-type: "direct" diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 6cd8dbb..6af49b5 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -71,7 +71,7 @@ jobs: path: html/ - run: echo "::notice::https://remote-unzip.deno.dev/${{ github.repository }}/artifacts/${{ steps.artifact-upload-step.outputs.artifact-id }}" - - uses: JamesIves/github-pages-deploy-action@v4.7.6 + - uses: JamesIves/github-pages-deploy-action@v4.8.0 if: ${{ inputs.publish }} with: branch: gh-pages From d4d3455549cde709e67f3510b1fcc7823cf3e031 Mon Sep 17 00:00:00 2001 From: YooSunyoung <17974113+YooSunYoung@users.noreply.github.com> Date: Mon, 9 Feb 2026 10:39:26 +0100 Subject: [PATCH 3/6] Update documentation build command in tox. --- tox.ini | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tox.ini b/tox.ini index f5cf092..ef25c7e 100644 --- a/tox.ini +++ b/tox.ini @@ -28,8 +28,8 @@ deps = -r requirements/docs.txt allowlist_externals=find commands = scitiff-dump-metadata-example --output docs/_static/example_metadata.json scitiff-dev-dump-schemas --output docs/_static/metadata-schema.json - python -m sphinx -j2 -v -b html -d {toxworkdir}/docs_doctrees docs html - python -m sphinx -j2 -v -b doctest -d {toxworkdir}/docs_doctrees docs html + python -m sphinx -W -j2 -v -b html -d {toxworkdir}/docs_doctrees docs html + python -m sphinx -W -j2 -v -b doctest -d {toxworkdir}/docs_doctrees -D nbsphinx_execute=never docs html find html -type f -name "*.ipynb" -not -path "html/_sources/*" -delete find docs -type f -name "example_metadata.json" -delete find docs -type f -name "metadata-schema.json" -delete @@ -46,7 +46,7 @@ commands = {[testenv:docs]commands} [testenv:linkcheck] description = Run Sphinx linkcheck deps = -r requirements/docs.txt -commands = python -m sphinx -j2 -v -b linkcheck -d {toxworkdir}/docs_doctrees docs html +commands = python -m sphinx -j2 -v -b linkcheck -d {toxworkdir}/docs_doctrees -D nbsphinx_execute=never docs html [testenv:static] description = Code formatting and static analysis From 50f4febed628dabe18cb0f5bd9b027b64751730c Mon Sep 17 00:00:00 2001 From: YooSunyoung <17974113+YooSunYoung@users.noreply.github.com> Date: Mon, 9 Feb 2026 10:43:29 +0100 Subject: [PATCH 4/6] Fix directives --- docs/user-guide/io.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/user-guide/io.ipynb b/docs/user-guide/io.ipynb index 035a19d..a249754 100644 --- a/docs/user-guide/io.ipynb +++ b/docs/user-guide/io.ipynb @@ -253,7 +253,7 @@ "source": [ "## Mask and Standard Deviation\n", "\n", - ".. warn:: This is not officially declared in the scitiff-schema.\n", + ".. attention:: This is not officially declared in the scitiff-schema.\n", "\n", "In some cases, users need to save variances and masks into the file along with the counts.\n", "\n", From 2c3d1b098e744ad2fed60f0ec8fca0ee2ea98bd8 Mon Sep 17 00:00:00 2001 From: YooSunyoung <17974113+YooSunYoung@users.noreply.github.com> Date: Mon, 9 Feb 2026 10:43:46 +0100 Subject: [PATCH 5/6] Update requests lower-bound --- pyproject.toml | 2 +- requirements/base.txt | 2 +- requirements/basetest.in | 2 +- requirements/basetest.txt | 2 +- requirements/docs.in | 2 +- requirements/docs.txt | 16 +++++++++------- requirements/nightly.in | 2 +- requirements/nightly.txt | 2 +- 8 files changed, 16 insertions(+), 14 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 15c0c02..7769068 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -41,7 +41,7 @@ dynamic = ["version"] [project.optional-dependencies] test = [ "pytest >= 8.0", - "requests >= 2.23.5" + "requests >= 2.32.5" # Tight lower-bound for better security. ] gui = [ "textual", diff --git a/requirements/base.txt b/requirements/base.txt index 28057c6..1a42f54 100644 --- a/requirements/base.txt +++ b/requirements/base.txt @@ -31,7 +31,7 @@ rpds-py==0.30.0 # via # jsonschema # referencing -scipp==26.1.1 +scipp==26.2.0 # via -r base.in tifffile==2026.1.28 # via -r base.in diff --git a/requirements/basetest.in b/requirements/basetest.in index 059be5c..42ffa39 100644 --- a/requirements/basetest.in +++ b/requirements/basetest.in @@ -8,4 +8,4 @@ # --- END OF CUSTOM SECTION --- # The following was generated by 'tox -e deps', DO NOT EDIT MANUALLY! pytest >= 8.0 -requests >= 2.23.5 +requests >= 2.32.5 diff --git a/requirements/basetest.txt b/requirements/basetest.txt index c11f92e..da37f3f 100644 --- a/requirements/basetest.txt +++ b/requirements/basetest.txt @@ -1,4 +1,4 @@ -# SHA1:52c5739d80338eadbf436d4d7d251a7df7b2d563 +# SHA1:ff6a58eaf948f36dc26a68bef4290ea123ea471c # # This file was generated by pip-compile-multi. # To update, run: diff --git a/requirements/docs.in b/requirements/docs.in index 4c0b799..2e3bd28 100644 --- a/requirements/docs.in +++ b/requirements/docs.in @@ -5,7 +5,7 @@ ipython!=8.7.0 # Breaks syntax highlighting in Jupyter code cells. myst-parser nbsphinx pydata-sphinx-theme>=0.14 -sphinx +sphinx<9.0.0 sphinx-autodoc-typehints sphinx-copybutton sphinx-design diff --git a/requirements/docs.txt b/requirements/docs.txt index f107cb7..e38a3e2 100644 --- a/requirements/docs.txt +++ b/requirements/docs.txt @@ -1,4 +1,4 @@ -# SHA1:7577c7d201e49153cdf5e9501dc68e2aa00b1463 +# SHA1:4bb3b5d3f54f6db58cb6fdfd766f5ef39e585fc3 # # This file was generated by pip-compile-multi. # To update, run: @@ -42,7 +42,7 @@ decorator==5.2.1 # via ipython defusedxml==0.7.1 # via nbconvert -docutils==0.22.4 +docutils==0.21.2 # via # myst-parser # nbsphinx @@ -58,7 +58,7 @@ idna==3.11 # via requests imagesize==1.4.1 # via sphinx -ipykernel==7.1.0 +ipykernel==7.2.0 # via -r docs.in ipython==9.10.0 # via @@ -144,7 +144,7 @@ pillow==12.1.0 # via matplotlib platformdirs==4.5.1 # via jupyter-core -plopp==25.11.0 +plopp==26.2.0 # via -r docs.in prompt-toolkit==3.0.52 # via ipython @@ -186,6 +186,8 @@ requests==2.32.5 rich==14.3.2 # via -r docs.in roman-numerals==4.1.0 + # via roman-numerals-py +roman-numerals-py==4.1.0 # via sphinx six==1.17.0 # via python-dateutil @@ -193,7 +195,7 @@ snowballstemmer==3.0.1 # via sphinx soupsieve==2.8.3 # via beautifulsoup4 -sphinx==9.0.4 +sphinx==8.2.3 # via # -r docs.in # autodoc-pydantic @@ -203,7 +205,7 @@ sphinx==9.0.4 # sphinx-autodoc-typehints # sphinx-copybutton # sphinx-design -sphinx-autodoc-typehints==3.6.1 +sphinx-autodoc-typehints==3.5.2 # via -r docs.in sphinx-copybutton==0.5.2 # via -r docs.in @@ -242,7 +244,7 @@ traitlets==5.14.3 # nbsphinx urllib3==2.6.3 # via requests -wcwidth==0.5.3 +wcwidth==0.6.0 # via prompt-toolkit webencodings==0.5.1 # via diff --git a/requirements/nightly.in b/requirements/nightly.in index d396154..8580262 100644 --- a/requirements/nightly.in +++ b/requirements/nightly.in @@ -5,7 +5,7 @@ tifffile >= 2024.7.2 jsonschema >= 4.23.0 pydantic >= 2.11 pytest >= 8.0 -requests >= 2.23.5 +requests >= 2.32.5 scipp --index-url=https://pypi.anaconda.org/scipp-nightly-wheels/simple/ --extra-index-url=https://pypi.org/simple diff --git a/requirements/nightly.txt b/requirements/nightly.txt index f2516af..05dbb23 100644 --- a/requirements/nightly.txt +++ b/requirements/nightly.txt @@ -1,4 +1,4 @@ -# SHA1:bdcc053638157965df67de34cdbf15cbbf4f0bda +# SHA1:176e5996c5af936d699ca1cc5578e91661697528 # # This file was generated by pip-compile-multi. # To update, run: From 5ff525d8b25cd642fdf3c0d1706cec930ff9e01a Mon Sep 17 00:00:00 2001 From: YooSunyoung <17974113+YooSunYoung@users.noreply.github.com> Date: Mon, 9 Feb 2026 10:43:55 +0100 Subject: [PATCH 6/6] Copier update. --- .copier-answers.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.copier-answers.yml b/.copier-answers.yml index bdee8b3..84693a2 100644 --- a/.copier-answers.yml +++ b/.copier-answers.yml @@ -1,5 +1,5 @@ # Changes here will be overwritten by Copier; NEVER EDIT MANUALLY -_commit: c89cb2e +_commit: '2888942' _src_path: gh:scipp/copier_template description: Scientific tiff format for imaging experiments. max_python: '3.13' @@ -10,4 +10,4 @@ orgname: scipp prettyname: SciTiff projectname: scitiff related_projects: Scipp,Plopp,ESSImaging,EasyImaging -year: 2025 +year: 2026