From ae412cb24421c9b18e9a1b92317844bdfa191290 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 22 Jan 2024 17:29:12 +0000 Subject: [PATCH 01/29] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.1.11 → v0.1.14](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.11...v0.1.14) --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8df635a..9f84305 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -24,7 +24,7 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit # Ruff version. - rev: 'v0.1.11' + rev: 'v0.1.14' hooks: - id: ruff From 266f4849136a4b11be6d4b27dffb886058e3cf2e Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 5 Feb 2024 17:32:20 +0000 Subject: [PATCH 02/29] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/psf/black: 23.12.1 → 24.1.1](https://github.com/psf/black/compare/23.12.1...24.1.1) - [github.com/astral-sh/ruff-pre-commit: v0.1.14 → v0.2.0](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.14...v0.2.0) --- .pre-commit-config.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 9f84305..5bff103 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -7,7 +7,7 @@ repos: - id: trailing-whitespace - repo: https://github.com/psf/black - rev: 23.12.1 + rev: 24.1.1 hooks: - id: black @@ -24,7 +24,7 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit # Ruff version. - rev: 'v0.1.14' + rev: 'v0.2.0' hooks: - id: ruff From 0efd2b2c03e3dcc1cd455489af5a1fc813527935 Mon Sep 17 00:00:00 2001 From: Sam Cunliffe Date: Tue, 6 Feb 2024 19:31:50 +0000 Subject: [PATCH 03/29] Expecting two warnings so nested with pytest.warns. --- src/napari_matplotlib/tests/test_util.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/napari_matplotlib/tests/test_util.py b/src/napari_matplotlib/tests/test_util.py index a8792d4..918e763 100644 --- a/src/napari_matplotlib/tests/test_util.py +++ b/src/napari_matplotlib/tests/test_util.py @@ -69,7 +69,10 @@ def test_fallback_if_missing_dimensions(mocker): test_css = " Flobble { background-color: rgb(0, 97, 163); } " mocker.patch("napari.qt.get_current_stylesheet").return_value = test_css with pytest.warns(RuntimeWarning, match="Unable to find DimensionToken"): - assert from_napari_css_get_size_of("Flobble", (1, 2)) == QSize(1, 2) + with pytest.warns(RuntimeWarning, match="Unable to find Flobble"): + assert from_napari_css_get_size_of("Flobble", (1, 2)) == QSize( + 1, 2 + ) def test_fallback_if_prelude_not_in_css(): From cd429ee947b9e8dc949851bab0ef106d157b0531 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 7 Feb 2024 09:45:06 +0000 Subject: [PATCH 04/29] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- examples/histogram.py | 1 + examples/scatter.py | 1 + examples/slice.py | 1 + 3 files changed, 3 insertions(+) diff --git a/examples/histogram.py b/examples/histogram.py index ccda491..b9ceb37 100644 --- a/examples/histogram.py +++ b/examples/histogram.py @@ -2,6 +2,7 @@ Histograms ========== """ + import napari viewer = napari.Viewer() diff --git a/examples/scatter.py b/examples/scatter.py index cd81240..00e01ec 100644 --- a/examples/scatter.py +++ b/examples/scatter.py @@ -2,6 +2,7 @@ Scatter plots ============= """ + import napari viewer = napari.Viewer() diff --git a/examples/slice.py b/examples/slice.py index 3e43443..242a16c 100644 --- a/examples/slice.py +++ b/examples/slice.py @@ -2,6 +2,7 @@ 1D slices ========= """ + import napari viewer = napari.Viewer() From 07217c621302d644a8796e878cf70bfdde2f2164 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 12 Feb 2024 17:33:44 +0000 Subject: [PATCH 05/29] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.2.0 → v0.2.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.2.0...v0.2.1) --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 5bff103..f97ded2 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -24,7 +24,7 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit # Ruff version. - rev: 'v0.2.0' + rev: 'v0.2.1' hooks: - id: ruff From 46058eea210c3b7c532d0e857f05592e15568de5 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 19 Feb 2024 17:43:22 +0000 Subject: [PATCH 06/29] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/psf/black: 24.1.1 → 24.2.0](https://github.com/psf/black/compare/24.1.1...24.2.0) - [github.com/astral-sh/ruff-pre-commit: v0.2.1 → v0.2.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.2.1...v0.2.2) --- .pre-commit-config.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index f97ded2..e57a9c8 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -7,7 +7,7 @@ repos: - id: trailing-whitespace - repo: https://github.com/psf/black - rev: 24.1.1 + rev: 24.2.0 hooks: - id: black @@ -24,7 +24,7 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit # Ruff version. - rev: 'v0.2.1' + rev: 'v0.2.2' hooks: - id: ruff From 517b2139ccfe59a4cc486467692a0e62bb9839aa Mon Sep 17 00:00:00 2001 From: David Stansby Date: Fri, 3 May 2024 15:21:40 +0100 Subject: [PATCH 07/29] Update pre-commit --- .pre-commit-config.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index e57a9c8..40048ea 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,13 +1,13 @@ repos: - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.5.0 + rev: v4.6.0 hooks: - id: check-docstring-first - id: end-of-file-fixer - id: trailing-whitespace - repo: https://github.com/psf/black - rev: 24.2.0 + rev: 24.4.2 hooks: - id: black @@ -17,14 +17,14 @@ repos: - id: napari-plugin-checks - repo: https://github.com/pre-commit/mirrors-mypy - rev: v1.8.0 + rev: v1.10.0 hooks: - id: mypy additional_dependencies: [numpy, matplotlib] - repo: https://github.com/astral-sh/ruff-pre-commit # Ruff version. - rev: 'v0.2.2' + rev: 'v0.4.2' hooks: - id: ruff From 9949427de3b7212931e2601baabf2040c7cbfe22 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Fri, 3 May 2024 15:36:11 +0100 Subject: [PATCH 08/29] Bump codecov action --- .github/workflows/test_and_deploy.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml index 8665e1d..9b24e7f 100644 --- a/.github/workflows/test_and_deploy.yml +++ b/.github/workflows/test_and_deploy.yml @@ -58,7 +58,7 @@ jobs: if: ${{ always() }} - name: Coverage - uses: codecov/codecov-action@v3 + uses: codecov/codecov-action@v4 # Don't run coverage on merge queue CI to avoid duplicating reports # to codecov. See https://github.com/matplotlib/napari-matplotlib/issues/155 if: github.event_name != 'merge_group' @@ -66,6 +66,8 @@ jobs: token: ${{ secrets.CODECOV_TOKEN }} fail_ci_if_error: true + + deploy: # this will run when you have tagged a commit, starting with "v*" # and requires that you have put your twine API key in your From ea21e54a0c30ceafb3b7c1bdbf7e9ab77f8629c7 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Fri, 3 May 2024 15:47:12 +0100 Subject: [PATCH 09/29] Suppress doc build warning --- docs/conf.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/conf.py b/docs/conf.py index 2517a59..5be3c95 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -33,6 +33,7 @@ "sphinx_automodapi.automodapi", "sphinx_automodapi.smart_resolver", "sphinx.ext.intersphinx", + "qtgallery", ] sphinx_gallery_conf = { @@ -40,6 +41,7 @@ "image_scrapers": (qtgallery.qtscraper,), "reset_modules": (qtgallery.reset_qapp,), } +suppress_warnings = ["config.cache"] qtgallery_conf = { "xvfb_size": (640, 480), From 2645f43d139202da084aba3cecaa5b19f762093b Mon Sep 17 00:00:00 2001 From: David Stansby Date: Fri, 3 May 2024 15:54:05 +0100 Subject: [PATCH 10/29] Remove napari hub preview --- .github/workflows/napari_hub_preview.yml | 21 --------------------- 1 file changed, 21 deletions(-) delete mode 100644 .github/workflows/napari_hub_preview.yml diff --git a/.github/workflows/napari_hub_preview.yml b/.github/workflows/napari_hub_preview.yml deleted file mode 100644 index c204ac4..0000000 --- a/.github/workflows/napari_hub_preview.yml +++ /dev/null @@ -1,21 +0,0 @@ -name: napari hub Preview Page # we use this name to find your preview page artifact, so don't change it! -# For more info on this action, see https://github.com/chanzuckerberg/napari-hub-preview-action/blob/main/action.yml - -on: - pull_request: - types: [ labeled ] - -jobs: - preview-page: - if: ${{ github.event.label.name == 'napari hub preview' }} - name: Preview Page Deploy - runs-on: ubuntu-latest - - steps: - - name: Checkout repo - uses: actions/checkout@v3 - - - name: napari hub Preview Page Builder - uses: chanzuckerberg/napari-hub-preview-action@v0.1 - with: - hub-ref: main From e5b9bb2b5bf5b00aaf0fcbf5598a235b08fd9c83 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Fri, 3 May 2024 15:54:42 +0100 Subject: [PATCH 11/29] Update headless gui version --- .github/workflows/docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 5b721d9..39c1ab5 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -32,7 +32,7 @@ jobs: sudo apt install graphviz --yes - name: Build Docs - uses: aganders3/headless-gui@v1 + uses: aganders3/headless-gui@v2 with: run: make html working-directory: ./docs From 8cc74cab748cc0da54e6c08ea52d8d0a119fee79 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Fri, 3 May 2024 16:01:03 +0100 Subject: [PATCH 12/29] Try stable release of napari for doc build --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 41e4e34..25aa4cf 100644 --- a/setup.cfg +++ b/setup.cfg @@ -47,7 +47,7 @@ napari.manifest = [options.extras_require] docs = - napari[all]==0.4.19rc3 + napari[all]==0.4.19 numpydoc pydantic<2 pydata-sphinx-theme From 0be3f7b70c60fd8cd44220ab4f1c6bfe24722770 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Fri, 3 May 2024 16:10:26 +0100 Subject: [PATCH 13/29] Remoe doc napari pin --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 25aa4cf..cccec1c 100644 --- a/setup.cfg +++ b/setup.cfg @@ -47,7 +47,7 @@ napari.manifest = [options.extras_require] docs = - napari[all]==0.4.19 + napari[all] numpydoc pydantic<2 pydata-sphinx-theme From 797e4605e99e2773f9ebcbe5ddd0f687e316fb6e Mon Sep 17 00:00:00 2001 From: David Stansby Date: Fri, 24 May 2024 14:00:28 +0100 Subject: [PATCH 14/29] Try custom scrapers --- docs/conf.py | 57 +++++++++++++++++++++++++++++++++++++++++++--------- setup.cfg | 1 - 2 files changed, 47 insertions(+), 11 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index 5be3c95..3c6ce6f 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -13,7 +13,7 @@ # import os # import sys # sys.path.insert(0, os.path.abspath('.')) -import qtgallery +from sphinx_gallery import scrapers # -- Project information ----------------------------------------------------- @@ -33,22 +33,59 @@ "sphinx_automodapi.automodapi", "sphinx_automodapi.smart_resolver", "sphinx.ext.intersphinx", - "qtgallery", ] + +def reset_napari(gallery_conf, fname): + from napari.settings import get_settings + from qtpy.QtWidgets import QApplication + + settings = get_settings() + settings.appearance.theme = "dark" + + # Disabling `QApplication.exec_` means example scripts can call `exec_` + # (scripts work when run normally) without blocking example execution by + # sphinx-gallery. (from qtgallery) + QApplication.exec_ = lambda _: None + + +def napari_scraper(block, block_vars, gallery_conf): + """Basic napari window scraper. + + Looks for any QtMainWindow instances and takes a screenshot of them. + + `app.processEvents()` allows Qt events to propagateo and prevents hanging. + """ + import napari + + imgpath_iter = block_vars["image_path_iterator"] + + if app := napari.qt.get_app(): + app.processEvents() + else: + return "" + + img_paths = [] + for win, img_path in zip( + reversed(napari._qt.qt_main_window._QtMainWindow._instances), + imgpath_iter, + ): + img_paths.append(img_path) + win._window.screenshot(img_path, canvas_only=False) + + napari.Viewer.close_all() + app.processEvents() + + return scrapers.figure_rst(img_paths, gallery_conf["src_dir"]) + + sphinx_gallery_conf = { "filename_pattern": ".", - "image_scrapers": (qtgallery.qtscraper,), - "reset_modules": (qtgallery.reset_qapp,), + "image_scrapers": (napari_scraper,), + "reset_modules": (reset_napari,), } suppress_warnings = ["config.cache"] -qtgallery_conf = { - "xvfb_size": (640, 480), - "xvfb_color_depth": 24, - "xfvb_use_xauth": False, - "xfvb_extra_args": [], -} numpydoc_show_class_members = False automodapi_inheritance_diagram = True diff --git a/setup.cfg b/setup.cfg index cccec1c..76fc8bf 100644 --- a/setup.cfg +++ b/setup.cfg @@ -51,7 +51,6 @@ docs = numpydoc pydantic<2 pydata-sphinx-theme - qtgallery sphinx sphinx-automodapi sphinx-gallery From 312d50c03bd9e4df775c6baa17d728affe37658b Mon Sep 17 00:00:00 2001 From: David Stansby Date: Fri, 24 May 2024 14:03:57 +0100 Subject: [PATCH 15/29] Add some type ignores --- docs/conf.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index 3c6ce6f..2818f02 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -36,7 +36,7 @@ ] -def reset_napari(gallery_conf, fname): +def reset_napari(gallery_conf, fname): # type: ignore[no-untyped-def] from napari.settings import get_settings from qtpy.QtWidgets import QApplication @@ -49,7 +49,7 @@ def reset_napari(gallery_conf, fname): QApplication.exec_ = lambda _: None -def napari_scraper(block, block_vars, gallery_conf): +def napari_scraper(block, block_vars, gallery_conf): # type: ignore[no-untyped-def] """Basic napari window scraper. Looks for any QtMainWindow instances and takes a screenshot of them. From 5c80464405f4c5205628805911c33ef9bf0e1226 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Fri, 3 May 2024 15:27:26 +0100 Subject: [PATCH 16/29] Adhere to SPEC0 --- .github/workflows/test_and_deploy.yml | 2 +- docs/changelog.rst | 9 +++++++++ pyproject.toml | 4 ++-- setup.cfg | 4 ++-- tox.ini | 4 ++-- 5 files changed, 16 insertions(+), 7 deletions(-) diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml index 9b24e7f..94cf1e9 100644 --- a/.github/workflows/test_and_deploy.yml +++ b/.github/workflows/test_and_deploy.yml @@ -20,7 +20,7 @@ jobs: fail-fast: false matrix: platform: [ubuntu-latest, macos-latest, windows-latest] - python-version: ['3.9', '3.10', '3.11'] + python-version: ['3.10', '3.11', '3.12'] steps: - uses: actions/checkout@v3 diff --git a/docs/changelog.rst b/docs/changelog.rst index 255982a..8e3e859 100644 --- a/docs/changelog.rst +++ b/docs/changelog.rst @@ -1,5 +1,14 @@ Changelog ========= +2.0.2 +----- +Dependencies +~~~~~~~~~~~~ +napari-matplotlib now adheres to `SPEC 0`_, and has: +- Dropped support for Python 3.9 +- Added support for Python 3.12 +- Added a minimum required numpy verison of 1.23 + 2.0.1 ----- Bug fixes diff --git a/pyproject.toml b/pyproject.toml index ba9f9e6..d569113 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -24,7 +24,7 @@ profile = "black" line_length = 79 [tool.ruff] -target-version = "py39" +target-version = "py310" select = ["I", "UP", "F", "E", "W", "D"] ignore = [ "D100", # Missing docstring in public module @@ -46,7 +46,7 @@ fix = true convention = "numpy" [tool.mypy] -python_version = "3.9" +python_version = "3.10" # Block below are checks that form part of mypy 'strict' mode strict = true disallow_subclassing_any = false # TODO: fix diff --git a/setup.cfg b/setup.cfg index 76fc8bf..2b74504 100644 --- a/setup.cfg +++ b/setup.cfg @@ -29,9 +29,9 @@ packages = find: install_requires = matplotlib napari - numpy + numpy>=1.23 tinycss2 -python_requires = >=3.9 +python_requires = >=3.10 include_package_data = True package_dir = =src diff --git a/tox.ini b/tox.ini index 4ec0c70..f4aed6a 100644 --- a/tox.ini +++ b/tox.ini @@ -1,12 +1,12 @@ [tox] -envlist = py{39,310,311} +envlist = py{310,311,312} isolated_build = true [gh-actions] python = - 3.9: py39 3.10: py310 3.11: py311 + 3.12: py312 [testenv] extras = testing From 891f4aa263e1d08dccd22e27f7b00941cf076268 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Fri, 24 May 2024 14:17:39 +0100 Subject: [PATCH 17/29] Ignore pydantic warning --- pyproject.toml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index d569113..bbec409 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,6 +12,8 @@ filterwarnings = [ # Coming from vispy "ignore:distutils Version classes are deprecated:DeprecationWarning", "ignore:`np.bool8` is a deprecated alias for `np.bool_`:DeprecationWarning", + # Coming from pydantic via napari + "ignore:Pickle, copy, and deepcopy support will be removed from itertools in Python 3.14.:DeprecationWarning" ] qt_api = "pyqt6" addopts = "--mpl --mpl-baseline-relative" From 52bb0a902bc4c427f159a7ab4e4f2b969d33169b Mon Sep 17 00:00:00 2001 From: David Stansby Date: Fri, 24 May 2024 14:40:06 +0100 Subject: [PATCH 18/29] pre-commit fixes --- src/napari_matplotlib/base.py | 7 +++---- src/napari_matplotlib/histogram.py | 12 ++++++------ src/napari_matplotlib/scatter.py | 8 ++++---- src/napari_matplotlib/slice.py | 4 ++-- src/napari_matplotlib/util.py | 9 +++------ 5 files changed, 18 insertions(+), 22 deletions(-) diff --git a/src/napari_matplotlib/base.py b/src/napari_matplotlib/base.py index fb9e485..c455335 100644 --- a/src/napari_matplotlib/base.py +++ b/src/napari_matplotlib/base.py @@ -1,6 +1,5 @@ import os from pathlib import Path -from typing import Optional import matplotlib.style as mplstyle import napari @@ -38,7 +37,7 @@ class BaseNapariMPLWidget(QWidget): def __init__( self, napari_viewer: napari.Viewer, - parent: Optional[QWidget] = None, + parent: QWidget | None = None, ): super().__init__(parent=parent) self.viewer = napari_viewer @@ -173,7 +172,7 @@ class NapariMPLWidget(BaseNapariMPLWidget): def __init__( self, napari_viewer: napari.viewer.Viewer, - parent: Optional[QWidget] = None, + parent: QWidget | None = None, ): super().__init__(napari_viewer=napari_viewer, parent=parent) self._setup_callbacks() @@ -282,7 +281,7 @@ class SingleAxesWidget(NapariMPLWidget): def __init__( self, napari_viewer: napari.viewer.Viewer, - parent: Optional[QWidget] = None, + parent: QWidget | None = None, ): super().__init__(napari_viewer=napari_viewer, parent=parent) self.add_single_axes() diff --git a/src/napari_matplotlib/histogram.py b/src/napari_matplotlib/histogram.py index 4076528..a0b6e09 100644 --- a/src/napari_matplotlib/histogram.py +++ b/src/napari_matplotlib/histogram.py @@ -1,4 +1,4 @@ -from typing import Any, Optional, cast +from typing import Any, cast import napari import numpy as np @@ -44,7 +44,7 @@ class HistogramWidget(SingleAxesWidget): def __init__( self, napari_viewer: napari.viewer.Viewer, - parent: Optional[QWidget] = None, + parent: QWidget | None = None, ): super().__init__(napari_viewer, parent=parent) self._update_layers(None) @@ -121,7 +121,7 @@ class FeaturesHistogramWidget(SingleAxesWidget): def __init__( self, napari_viewer: napari.viewer.Viewer, - parent: Optional[QWidget] = None, + parent: QWidget | None = None, ): super().__init__(napari_viewer, parent=parent) @@ -137,12 +137,12 @@ def __init__( self._update_layers(None) @property - def x_axis_key(self) -> Optional[str]: + def x_axis_key(self) -> str | None: """Key to access x axis data from the FeaturesTable""" return self._x_axis_key @x_axis_key.setter - def x_axis_key(self, key: Optional[str]) -> None: + def x_axis_key(self, key: str | None) -> None: self._x_axis_key = key self._draw() @@ -166,7 +166,7 @@ def _get_valid_axis_keys(self) -> list[str]: else: return self.layers[0].features.keys() - def _get_data(self) -> tuple[Optional[npt.NDArray[Any]], str]: + def _get_data(self) -> tuple[npt.NDArray[Any] | None, str]: """Get the plot data. Returns diff --git a/src/napari_matplotlib/scatter.py b/src/napari_matplotlib/scatter.py index 67d6896..98ebe92 100644 --- a/src/napari_matplotlib/scatter.py +++ b/src/napari_matplotlib/scatter.py @@ -1,4 +1,4 @@ -from typing import Any, Optional, Union +from typing import Any import napari import numpy.typing as npt @@ -100,7 +100,7 @@ class FeaturesScatterWidget(ScatterBaseWidget): def __init__( self, napari_viewer: napari.viewer.Viewer, - parent: Optional[QWidget] = None, + parent: QWidget | None = None, ): super().__init__(napari_viewer, parent=parent) @@ -118,7 +118,7 @@ def __init__( self._update_layers(None) @property - def x_axis_key(self) -> Union[str, None]: + def x_axis_key(self) -> str | None: """ Key for the x-axis data. """ @@ -133,7 +133,7 @@ def x_axis_key(self, key: str) -> None: self._draw() @property - def y_axis_key(self) -> Union[str, None]: + def y_axis_key(self) -> str | None: """ Key for the y-axis data. """ diff --git a/src/napari_matplotlib/slice.py b/src/napari_matplotlib/slice.py index 9459fa9..1924bf2 100644 --- a/src/napari_matplotlib/slice.py +++ b/src/napari_matplotlib/slice.py @@ -1,4 +1,4 @@ -from typing import Any, Optional +from typing import Any import matplotlib.ticker as mticker import napari @@ -30,7 +30,7 @@ class SliceWidget(SingleAxesWidget): def __init__( self, napari_viewer: napari.viewer.Viewer, - parent: Optional[QWidget] = None, + parent: QWidget | None = None, ): # Setup figure/axes super().__init__(napari_viewer, parent=parent) diff --git a/src/napari_matplotlib/util.py b/src/napari_matplotlib/util.py index ed99425..c54b60a 100644 --- a/src/napari_matplotlib/util.py +++ b/src/napari_matplotlib/util.py @@ -1,4 +1,3 @@ -from typing import Optional, Union from warnings import warn import napari.qt @@ -12,7 +11,7 @@ class Interval: An integer interval. """ - def __init__(self, lower_bound: Optional[int], upper_bound: Optional[int]): + def __init__(self, lower_bound: int | None, upper_bound: int | None): """ Parameters ---------- @@ -48,7 +47,7 @@ def __contains__(self, val: int) -> bool: return True @property - def _helper_text(self) -> Optional[str]: + def _helper_text(self) -> str | None: """ Helper text for widgets. """ @@ -86,9 +85,7 @@ def _has_id(nodes: list[tinycss2.ast.Node], id_name: str) -> bool: ) -def _get_dimension( - nodes: list[tinycss2.ast.Node], id_name: str -) -> Union[int, None]: +def _get_dimension(nodes: list[tinycss2.ast.Node], id_name: str) -> int | None: """ Get the value of the DimensionToken for the IdentToken `id_name`. From e7c49451e5e1b25ccef43ddba054ad4a23328e99 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Fri, 24 May 2024 14:43:04 +0100 Subject: [PATCH 19/29] Fix doc link --- docs/changelog.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/changelog.rst b/docs/changelog.rst index 8e3e859..ff2e60c 100644 --- a/docs/changelog.rst +++ b/docs/changelog.rst @@ -4,7 +4,7 @@ Changelog ----- Dependencies ~~~~~~~~~~~~ -napari-matplotlib now adheres to `SPEC 0`_, and has: +napari-matplotlib now adheres to `SPEC 0 `_, and has: - Dropped support for Python 3.9 - Added support for Python 3.12 - Added a minimum required numpy verison of 1.23 From 1818110f3a04f9948b28ca789dd34eb7e7369674 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Fri, 24 May 2024 14:46:43 +0100 Subject: [PATCH 20/29] Don't fail if codecov fails --- .github/workflows/test_and_deploy.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml index 94cf1e9..5f9ed4b 100644 --- a/.github/workflows/test_and_deploy.yml +++ b/.github/workflows/test_and_deploy.yml @@ -64,7 +64,7 @@ jobs: if: github.event_name != 'merge_group' with: token: ${{ secrets.CODECOV_TOKEN }} - fail_ci_if_error: true + fail_ci_if_error: false From 687ba2a279f0f1f5ef80b59258fe0caf6b8aa7fa Mon Sep 17 00:00:00 2001 From: David Stansby Date: Fri, 24 May 2024 14:16:47 +0100 Subject: [PATCH 21/29] Add some scientific Python repo recommendatiosn --- .github/workflows/test_and_deploy.yml | 4 ++++ pyproject.toml | 8 ++++++-- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml index 5f9ed4b..2a8b731 100644 --- a/.github/workflows/test_and_deploy.yml +++ b/.github/workflows/test_and_deploy.yml @@ -12,6 +12,10 @@ on: workflow_dispatch: merge_group: +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + jobs: test: name: ${{ matrix.platform }} py${{ matrix.python-version }} diff --git a/pyproject.toml b/pyproject.toml index bbec409..5a865b0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,5 +1,5 @@ [build-system] -requires = ["setuptools", "wheel", "setuptools_scm"] +requires = ["setuptools", "setuptools_scm"] build-backend = "setuptools.build_meta" [tool.setuptools_scm] @@ -16,7 +16,11 @@ filterwarnings = [ "ignore:Pickle, copy, and deepcopy support will be removed from itertools in Python 3.14.:DeprecationWarning" ] qt_api = "pyqt6" -addopts = "--mpl --mpl-baseline-relative" +addopts = ["--mpl", "--mpl-baseline-relative", "--strict-config", "--strict-markers", "-ra"] +minversion = "7" +testpaths = ["src/napari_matplotlib/tests"] +log_cli_level = "INFO" +xfail_strict = true [tool.black] line-length = 79 From 33a71d3231841b6452d677e2a94d0792e4ee3ffe Mon Sep 17 00:00:00 2001 From: David Stansby Date: Sat, 25 May 2024 09:29:58 +0100 Subject: [PATCH 22/29] Some more repo-review suggestions --- .pre-commit-config.yaml | 2 +- docs/conf.py | 1 + pyproject.toml | 12 ++++++++---- src/napari_matplotlib/histogram.py | 2 +- src/napari_matplotlib/tests/test_util.py | 2 +- src/napari_matplotlib/util.py | 9 +++++++-- 6 files changed, 19 insertions(+), 9 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 40048ea..79342e2 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -6,7 +6,7 @@ repos: - id: end-of-file-fixer - id: trailing-whitespace - - repo: https://github.com/psf/black + - repo: https://github.com/psf/black-pre-commit-mirror rev: 24.4.2 hooks: - id: black diff --git a/docs/conf.py b/docs/conf.py index 2818f02..f153383 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -69,6 +69,7 @@ def napari_scraper(block, block_vars, gallery_conf): # type: ignore[no-untyped- for win, img_path in zip( reversed(napari._qt.qt_main_window._QtMainWindow._instances), imgpath_iter, + strict=False, ): img_paths.append(img_path) win._window.screenshot(img_path, canvas_only=False) diff --git a/pyproject.toml b/pyproject.toml index 5a865b0..05f7df6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -31,7 +31,10 @@ line_length = 79 [tool.ruff] target-version = "py310" -select = ["I", "UP", "F", "E", "W", "D"] +fix = true + +[tool.ruff.lint] +select = ["B", "I", "UP", "F", "E", "W", "D"] ignore = [ "D100", # Missing docstring in public module "D104", # Missing docstring in public package @@ -41,14 +44,13 @@ ignore = [ "D401", # First line of docstring should be in imperative mood ] -fix = true -[tool.ruff.per-file-ignores] +[tool.ruff.lint.per-file-ignores] "docs/*" = ["D"] "examples/*" = ["D"] "src/napari_matplotlib/tests/*" = ["D"] -[tool.ruff.pydocstyle] +[tool.ruff.lint.pydocstyle] convention = "numpy" [tool.mypy] @@ -59,6 +61,8 @@ disallow_subclassing_any = false # TODO: fix warn_return_any = false # TODO: fix ignore_missing_imports = true +enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"] + [[tool.mypy.overrides]] module = [ "napari_matplotlib/tests/*", diff --git a/src/napari_matplotlib/histogram.py b/src/napari_matplotlib/histogram.py index a0b6e09..adbbae6 100644 --- a/src/napari_matplotlib/histogram.py +++ b/src/napari_matplotlib/histogram.py @@ -60,7 +60,7 @@ def on_update_layers(self) -> None: def _update_contrast_lims(self) -> None: for lim, line in zip( - self.layers[0].contrast_limits, self._contrast_lines + self.layers[0].contrast_limits, self._contrast_lines, strict=False ): line.set_xdata(lim) diff --git a/src/napari_matplotlib/tests/test_util.py b/src/napari_matplotlib/tests/test_util.py index 918e763..e966cc2 100644 --- a/src/napari_matplotlib/tests/test_util.py +++ b/src/napari_matplotlib/tests/test_util.py @@ -26,7 +26,7 @@ def test_interval(): assert 10 not in interval with pytest.raises(ValueError, match="must be an integer"): - "string" in interval # type: ignore + assert "string" in interval # type: ignore[operator] with pytest.raises(ValueError, match="must be <= upper_bound"): Interval(5, 3) diff --git a/src/napari_matplotlib/util.py b/src/napari_matplotlib/util.py index c54b60a..8d4150c 100644 --- a/src/napari_matplotlib/util.py +++ b/src/napari_matplotlib/util.py @@ -94,14 +94,18 @@ def _get_dimension(nodes: list[tinycss2.ast.Node], id_name: str) -> int | None: None if no IdentToken is found. """ cleaned_nodes = [node for node in nodes if node.type != "whitespace"] - for name, _, value, _ in zip(*(iter(cleaned_nodes),) * 4): + for name, _, value, _ in zip(*(iter(cleaned_nodes),) * 4, strict=False): if ( name.type == "ident" and value.type == "dimension" and name.value == id_name ): return value.int_value - warn(f"Unable to find DimensionToken for {id_name}", RuntimeWarning) + warn( + f"Unable to find DimensionToken for {id_name}", + RuntimeWarning, + stacklevel=1, + ) return None @@ -134,6 +138,7 @@ def from_napari_css_get_size_of( f"Unable to find {qt_element_name} or unable to find its size in " f"the current Napari stylesheet, falling back to {fallback}", RuntimeWarning, + stacklevel=1, ) return QSize(*fallback) From cf9aae9e5f2ed6acc9182a5b53110abf5f4a19ad Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 27 May 2024 17:37:35 +0000 Subject: [PATCH 23/29] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.4.2 → v0.4.5](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.2...v0.4.5) --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 79342e2..ad71481 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -24,7 +24,7 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit # Ruff version. - rev: 'v0.4.2' + rev: 'v0.4.5' hooks: - id: ruff From dea3e6d9e66187c8b3212453c076b7ec7492cbc2 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 3 Jun 2024 17:41:38 +0000 Subject: [PATCH 24/29] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.4.5 → v0.4.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.5...v0.4.7) --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index ad71481..aefedf4 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -24,7 +24,7 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit # Ruff version. - rev: 'v0.4.5' + rev: 'v0.4.7' hooks: - id: ruff From 34099bc0073e7e097773a328aaafae442a66889e Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 10 Jun 2024 17:44:38 +0000 Subject: [PATCH 25/29] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.4.7 → v0.4.8](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.7...v0.4.8) --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index aefedf4..c921bc0 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -24,7 +24,7 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit # Ruff version. - rev: 'v0.4.7' + rev: 'v0.4.8' hooks: - id: ruff From 5990ef63ad6580adadacc48ddc9548aa7c3c6d82 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 17 Jun 2024 17:41:36 +0000 Subject: [PATCH 26/29] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.4.8 → v0.4.9](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.8...v0.4.9) --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index c921bc0..2fedfd8 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -24,7 +24,7 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit # Ruff version. - rev: 'v0.4.8' + rev: 'v0.4.9' hooks: - id: ruff From 2ad5adf83523e6ae8474c7aa9b0397c8f5ff20ab Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 24 Jun 2024 17:41:57 +0000 Subject: [PATCH 27/29] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.4.9 → v0.4.10](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.9...v0.4.10) --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 2fedfd8..305eb83 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -24,7 +24,7 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit # Ruff version. - rev: 'v0.4.9' + rev: 'v0.4.10' hooks: - id: ruff From c60ff0e3e2b829f55a8906f143189a72a1868ebd Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 8 Jul 2024 17:34:35 +0000 Subject: [PATCH 28/29] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/pre-commit/mirrors-mypy: v1.10.0 → v1.10.1](https://github.com/pre-commit/mirrors-mypy/compare/v1.10.0...v1.10.1) - [github.com/astral-sh/ruff-pre-commit: v0.4.10 → v0.5.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.10...v0.5.1) --- .pre-commit-config.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 305eb83..ebae2d3 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -17,14 +17,14 @@ repos: - id: napari-plugin-checks - repo: https://github.com/pre-commit/mirrors-mypy - rev: v1.10.0 + rev: v1.10.1 hooks: - id: mypy additional_dependencies: [numpy, matplotlib] - repo: https://github.com/astral-sh/ruff-pre-commit # Ruff version. - rev: 'v0.4.10' + rev: 'v0.5.1' hooks: - id: ruff From 3cb0fe7b7ddd391039b96e6fb6ff63cff3bbcfa9 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Fri, 12 Jul 2024 15:35:23 +0200 Subject: [PATCH 29/29] Pin max napari version --- docs/changelog.rst | 4 ++++ setup.cfg | 2 +- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/docs/changelog.rst b/docs/changelog.rst index ff2e60c..697e483 100644 --- a/docs/changelog.rst +++ b/docs/changelog.rst @@ -1,13 +1,17 @@ Changelog ========= + 2.0.2 ----- Dependencies ~~~~~~~~~~~~ napari-matplotlib now adheres to `SPEC 0 `_, and has: + - Dropped support for Python 3.9 - Added support for Python 3.12 - Added a minimum required numpy verison of 1.23 +- Pinned the maximum napari version to ``< 0.5``. + Version 3.0 of ``napari-matplotlib`` will introduce support for ``napari`` version 0.5. 2.0.1 ----- diff --git a/setup.cfg b/setup.cfg index 2b74504..073478a 100644 --- a/setup.cfg +++ b/setup.cfg @@ -28,7 +28,7 @@ project_urls = packages = find: install_requires = matplotlib - napari + napari<0.5 numpy>=1.23 tinycss2 python_requires = >=3.10