From 5218b04fec1dc1246f743ee4be25c10f216633bc Mon Sep 17 00:00:00 2001 From: KeelyBrown <156026125+k034b363@users.noreply.github.com> Date: Wed, 2 Apr 2025 13:20:38 -0500 Subject: [PATCH 01/16] Add napari backend to environment.yml --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index a6d4838..dd4acdf 100644 --- a/environment.yml +++ b/environment.yml @@ -27,7 +27,7 @@ dependencies: - napari - pyqt - pytest-qt + - pyside2 channels: - conda-forge - - defaults From b595f38eeed3c6bfeb1b822e34ece47308392256 Mon Sep 17 00:00:00 2001 From: KeelyBrown <156026125+k034b363@users.noreply.github.com> Date: Thu, 3 Apr 2025 14:22:20 -0500 Subject: [PATCH 02/16] Added pyside2 to pyproject as a test Not sure this will work, so probably will revert --- pyproject.toml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 5abfaf1..c927448 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,7 +12,8 @@ dependencies = [ "plantcv", "matplotlib", "napari", - "PyQt5" + "PyQt5", + "pyside2" ] requires-python = ">=3.6" authors = [ From 42cf3e5b28cf21c321c0f370f00cf7492b36af45 Mon Sep 17 00:00:00 2001 From: KeelyBrown <156026125+k034b363@users.noreply.github.com> Date: Thu, 3 Apr 2025 14:34:20 -0500 Subject: [PATCH 03/16] Remove pyqt from environment.yml See if this is where the dependency is that is causing the build to fail --- environment.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/environment.yml b/environment.yml index dd4acdf..a54be5c 100644 --- a/environment.yml +++ b/environment.yml @@ -25,7 +25,6 @@ dependencies: - altair - vl-convert-python - napari - - pyqt - pytest-qt - pyside2 From 027870bc00b849960915e4d75675baecf8efd172 Mon Sep 17 00:00:00 2001 From: KeelyBrown <156026125+k034b363@users.noreply.github.com> Date: Thu, 3 Apr 2025 14:34:45 -0500 Subject: [PATCH 04/16] Update pyproject.toml --- pyproject.toml | 1 - 1 file changed, 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index c927448..b21fcae 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,7 +12,6 @@ dependencies = [ "plantcv", "matplotlib", "napari", - "PyQt5", "pyside2" ] requires-python = ">=3.6" From 39f7015db42e1f18f83bb84cf0cd3b67e01104b2 Mon Sep 17 00:00:00 2001 From: KeelyBrown <156026125+k034b363@users.noreply.github.com> Date: Thu, 3 Apr 2025 14:37:11 -0500 Subject: [PATCH 05/16] Update environment.yml --- environment.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/environment.yml b/environment.yml index a54be5c..6bd2563 100644 --- a/environment.yml +++ b/environment.yml @@ -25,7 +25,6 @@ dependencies: - altair - vl-convert-python - napari - - pytest-qt - pyside2 channels: From 0d1a67f744fdfed406855ecb6afa1bd81568aefb Mon Sep 17 00:00:00 2001 From: KeelyBrown <156026125+k034b363@users.noreply.github.com> Date: Thu, 3 Apr 2025 14:39:37 -0500 Subject: [PATCH 06/16] Reverting environment.yml --- environment.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 6bd2563..35df255 100644 --- a/environment.yml +++ b/environment.yml @@ -25,7 +25,8 @@ dependencies: - altair - vl-convert-python - napari - - pyside2 + - pyqt + - pytest-qt channels: - conda-forge From 8ad82211cd669108684ca73c8780b5509ee71d57 Mon Sep 17 00:00:00 2001 From: KeelyBrown <156026125+k034b363@users.noreply.github.com> Date: Thu, 3 Apr 2025 14:41:49 -0500 Subject: [PATCH 07/16] Update pyproject.toml --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index b21fcae..5abfaf1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,7 +12,7 @@ dependencies = [ "plantcv", "matplotlib", "napari", - "pyside2" + "PyQt5" ] requires-python = ">=3.6" authors = [ From 125bd0450769f022823be1131b7f6a9abf10365a Mon Sep 17 00:00:00 2001 From: KeelyBrown <156026125+k034b363@users.noreply.github.com> Date: Thu, 3 Apr 2025 14:47:31 -0500 Subject: [PATCH 08/16] Update numpy version in environment.yml --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 35df255..ce43c12 100644 --- a/environment.yml +++ b/environment.yml @@ -4,7 +4,7 @@ name: plantcv dependencies: - python=3.10 - matplotlib>=1.5 - - numpy>=1.11 + - numpy>=2 - pandas - python-dateutil - scipy From fdb7ed58f714a7875adfdb2a24ed481b86920608 Mon Sep 17 00:00:00 2001 From: KeelyBrown <156026125+k034b363@users.noreply.github.com> Date: Thu, 3 Apr 2025 14:52:29 -0500 Subject: [PATCH 09/16] Revert everything --- environment.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index ce43c12..a6d4838 100644 --- a/environment.yml +++ b/environment.yml @@ -4,7 +4,7 @@ name: plantcv dependencies: - python=3.10 - matplotlib>=1.5 - - numpy>=2 + - numpy>=1.11 - pandas - python-dateutil - scipy @@ -30,3 +30,4 @@ dependencies: channels: - conda-forge + - defaults From c7d99625624553028138233b442bd79c43d28cff Mon Sep 17 00:00:00 2001 From: Noah Fahlgren Date: Fri, 4 Apr 2025 10:43:44 -0500 Subject: [PATCH 10/16] Change backend to pyside2 --- environment.yml | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/environment.yml b/environment.yml index a6d4838..c0430e0 100644 --- a/environment.yml +++ b/environment.yml @@ -25,7 +25,7 @@ dependencies: - altair - vl-convert-python - napari - - pyqt + - pyside2 - pytest-qt channels: diff --git a/pyproject.toml b/pyproject.toml index 5abfaf1..b21fcae 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,7 +12,7 @@ dependencies = [ "plantcv", "matplotlib", "napari", - "PyQt5" + "pyside2" ] requires-python = ">=3.6" authors = [ From 3fb9e7bfb1128d23d711599278ecebf41436e6e5 Mon Sep 17 00:00:00 2001 From: Noah Fahlgren Date: Fri, 4 Apr 2025 10:45:43 -0500 Subject: [PATCH 11/16] Remove missing libegl1-mesa --- .github/workflows/continuous-integration.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/continuous-integration.yml b/.github/workflows/continuous-integration.yml index ca30610..fa70440 100644 --- a/.github/workflows/continuous-integration.yml +++ b/.github/workflows/continuous-integration.yml @@ -30,7 +30,7 @@ jobs: python-version: ${{ matrix.python-version }} - name: Install dependencies run: | - sudo apt-get install --no-install-recommends libyaml-dev libegl1-mesa libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-shape0 libxcb-cursor0 xserver-xephyr + sudo apt-get install --no-install-recommends libyaml-dev libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-shape0 libxcb-cursor0 xserver-xephyr python -m pip install --upgrade pip pip install flake8 pytest pytest-cov pytest-qt pytest-xvfb ipython anyio - name: Lint with flake8 From 2825110fd108635cd6572f01c89ebd07fc5b6ff7 Mon Sep 17 00:00:00 2001 From: Noah Fahlgren Date: Fri, 4 Apr 2025 10:50:34 -0500 Subject: [PATCH 12/16] Remove redundant dep --- pyproject.toml | 1 - 1 file changed, 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index b21fcae..d43aae3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -10,7 +10,6 @@ name = "plantcv-annotate" dynamic = ["version"] dependencies = [ "plantcv", - "matplotlib", "napari", "pyside2" ] From 8b3351cd001cbfe7ddb4e880aa1f9c99bc5d10e5 Mon Sep 17 00:00:00 2001 From: Noah Fahlgren Date: Fri, 4 Apr 2025 11:01:20 -0500 Subject: [PATCH 13/16] Change back to pyqt5 --- environment.yml | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/environment.yml b/environment.yml index c0430e0..a6d4838 100644 --- a/environment.yml +++ b/environment.yml @@ -25,7 +25,7 @@ dependencies: - altair - vl-convert-python - napari - - pyside2 + - pyqt - pytest-qt channels: diff --git a/pyproject.toml b/pyproject.toml index d43aae3..274bbe5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -11,7 +11,7 @@ dynamic = ["version"] dependencies = [ "plantcv", "napari", - "pyside2" + "PyQt5" ] requires-python = ">=3.6" authors = [ From d1dda161d8f4cf71b2d07d43b1447f70b40b5808 Mon Sep 17 00:00:00 2001 From: KeelyBrown <156026125+k034b363@users.noreply.github.com> Date: Wed, 16 Jul 2025 13:45:56 -0500 Subject: [PATCH 14/16] Update pyproject.toml --- pyproject.toml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 274bbe5..56128c3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -11,7 +11,9 @@ dynamic = ["version"] dependencies = [ "plantcv", "napari", - "PyQt5" + "PyQt5", + "PySide6" + ] requires-python = ">=3.6" authors = [ From fddde3ca53c1fbe6d524ba06f2fb661d5e0c7a3b Mon Sep 17 00:00:00 2001 From: KeelyBrown <156026125+k034b363@users.noreply.github.com> Date: Wed, 16 Jul 2025 13:46:16 -0500 Subject: [PATCH 15/16] Update environment.yml --- environment.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/environment.yml b/environment.yml index a6d4838..7d7ebcd 100644 --- a/environment.yml +++ b/environment.yml @@ -27,6 +27,7 @@ dependencies: - napari - pyqt - pytest-qt + - pyside2 channels: - conda-forge From 2c98af668260d55015eb4b1433e2b3e508230e47 Mon Sep 17 00:00:00 2001 From: KeelyBrown <156026125+k034b363@users.noreply.github.com> Date: Wed, 16 Jul 2025 14:07:10 -0500 Subject: [PATCH 16/16] Change edge_color to border_color in napari_label_classes.py --- plantcv/annotate/napari_label_classes.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/plantcv/annotate/napari_label_classes.py b/plantcv/annotate/napari_label_classes.py index 78e7f13..9e4b565 100755 --- a/plantcv/annotate/napari_label_classes.py +++ b/plantcv/annotate/napari_label_classes.py @@ -82,7 +82,7 @@ def napari_label_classes(img, classes=False, size=10, for x in classes: if x not in keys: viewer.add_points(np.array([]), name=x, symbol='square', - edge_color=random.choice(color), + border_color=random.choice(color), face_color=random.choice(color), size=size) keys = napari_classes(viewer) @@ -95,7 +95,7 @@ def napari_label_classes(img, classes=False, size=10, else: viewer.add_points(importdata[key], name=key, symbol='square', - edge_color=random.choice(color), + border_color=random.choice(color), face_color=random.choice(color), size=size)