From 3c937345f62163c862b700a502a13c55528aecf2 Mon Sep 17 00:00:00 2001 From: bue Date: Thu, 23 Oct 2025 08:55:41 -0400 Subject: [PATCH 1/5] @ workflows : update os yml files. --- .github/workflows/apple.yml | 4 ++-- .github/workflows/linux.yml | 4 ++-- .github/workflows/windows.yml | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/apple.yml b/.github/workflows/apple.yml index 8ca2f4e..9c24b0b 100644 --- a/.github/workflows/apple.yml +++ b/.github/workflows/apple.yml @@ -18,7 +18,7 @@ jobs: fail-fast: false matrix: #python-version: ["3.14"] - python-version: ["3.10", "3.11", "3.12", "3.13"] + python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"] env: PYTHONPATH: /Users/runner/work/physicelldataloader/physicelldataloader @@ -33,7 +33,7 @@ jobs: run: | brew install ffmpeg imagemagick python -m pip install --upgrade pip - python -m pip install flake8 pytest anndata bioio matplotlib numpy pandas requests scipy vtk + python -m pip install flake8 pytest anndata bioio bioio-ome-tiff matplotlib neuroglancer numpy pandas requests scikit-image scipy vtk python -m pip install /Users/runner/work/physicelldataloader/physicelldataloader -v #if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - name: lint with flake8 diff --git a/.github/workflows/linux.yml b/.github/workflows/linux.yml index 1a01ad7..2078b30 100644 --- a/.github/workflows/linux.yml +++ b/.github/workflows/linux.yml @@ -18,7 +18,7 @@ jobs: fail-fast: false matrix: #python-version: ["3.14"] - python-version: ["3.10", "3.11", "3.12", "3.13"] + python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"] env: PYTHONPATH: /home/runner/work/physicelldataloader/physicelldataloader @@ -33,7 +33,7 @@ jobs: run: | sudo apt install ffmpeg imagemagick python -m pip install --upgrade pip - python -m pip install flake8 pytest anndata bioio matplotlib numpy pandas requests scipy vtk + python -m pip install flake8 pytest anndata bioio bioio-ome-tiff matplotlib neuroglancer numpy pandas requests scikit-image scipy vtk python -m pip install /home/runner/work/physicelldataloader/physicelldataloader -v #if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - name: lint with flake8 diff --git a/.github/workflows/windows.yml b/.github/workflows/windows.yml index 235e012..d8d55ff 100644 --- a/.github/workflows/windows.yml +++ b/.github/workflows/windows.yml @@ -18,7 +18,7 @@ jobs: fail-fast: false matrix: #python-version: ["3.14"] - python-version: ["3.10", "3.11", "3.12", "3.13"] + python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"] env: PYTHONPATH: D:\a\physicelldataloader\physicelldataloader @@ -33,7 +33,7 @@ jobs: run: | choco install ffmpeg imagemagick python -m pip install --upgrade pip - python -m pip install flake8 pytest anndata bioio matplotlib numpy pandas requests scipy vtk + python -m pip install flake8 pytest anndata bioio bioio-ome-tiff matplotlib neuroglancer numpy pandas requests scikit-image scipy vtk python -m pip install D:\a\physicelldataloader\physicelldataloader -v #echo 'set PYTHONPATH=D:\a\physicelldataloader\physicelldataloader' >> $GITHUB_ENV #if [ -f requirements.txt ]; then pip install -r requirements.txt; fi From 92f0b313104835834ba7d5e7909c9a5c98ef88be Mon Sep 17 00:00:00 2001 From: bue Date: Thu, 23 Oct 2025 08:58:10 -0400 Subject: [PATCH 2/5] @ workflows : update os yml files. --- .github/workflows/apple.yml | 4 ++-- .github/workflows/linux.yml | 4 ++-- .github/workflows/windows.yml | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/apple.yml b/.github/workflows/apple.yml index 9c24b0b..5245dbf 100644 --- a/.github/workflows/apple.yml +++ b/.github/workflows/apple.yml @@ -17,8 +17,8 @@ jobs: strategy: fail-fast: false matrix: - #python-version: ["3.14"] - python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"] + python-version: ["3.13"] + #python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"] env: PYTHONPATH: /Users/runner/work/physicelldataloader/physicelldataloader diff --git a/.github/workflows/linux.yml b/.github/workflows/linux.yml index 2078b30..99de0bf 100644 --- a/.github/workflows/linux.yml +++ b/.github/workflows/linux.yml @@ -17,8 +17,8 @@ jobs: strategy: fail-fast: false matrix: - #python-version: ["3.14"] - python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"] + python-version: ["3.13"] + #python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"] env: PYTHONPATH: /home/runner/work/physicelldataloader/physicelldataloader diff --git a/.github/workflows/windows.yml b/.github/workflows/windows.yml index d8d55ff..f908f3e 100644 --- a/.github/workflows/windows.yml +++ b/.github/workflows/windows.yml @@ -17,8 +17,8 @@ jobs: strategy: fail-fast: false matrix: - #python-version: ["3.14"] - python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"] + python-version: ["3.13"] + #python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"] env: PYTHONPATH: D:\a\physicelldataloader\physicelldataloader From 863decb558df085dd11c67eb6582c7101a651310 Mon Sep 17 00:00:00 2001 From: bue Date: Thu, 23 Oct 2025 09:22:48 -0400 Subject: [PATCH 3/5] @ workflows : setting the matplotlib backend explicitely. --- .github/workflows/apple.yml | 3 ++- .github/workflows/linux.yml | 3 ++- .github/workflows/windows.yml | 3 ++- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/.github/workflows/apple.yml b/.github/workflows/apple.yml index 5245dbf..d0242c9 100644 --- a/.github/workflows/apple.yml +++ b/.github/workflows/apple.yml @@ -17,10 +17,11 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.13"] + python-version: ["3.14"] #python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"] env: + MPLBACKEND: Agg # https://github.com/orgs/community/discussions/26434 PYTHONPATH: /Users/runner/work/physicelldataloader/physicelldataloader steps: diff --git a/.github/workflows/linux.yml b/.github/workflows/linux.yml index 99de0bf..999bed9 100644 --- a/.github/workflows/linux.yml +++ b/.github/workflows/linux.yml @@ -17,10 +17,11 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.13"] + python-version: ["3.14"] #python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"] env: + MPLBACKEND: Agg # https://github.com/orgs/community/discussions/26434 PYTHONPATH: /home/runner/work/physicelldataloader/physicelldataloader steps: diff --git a/.github/workflows/windows.yml b/.github/workflows/windows.yml index f908f3e..4ff1354 100644 --- a/.github/workflows/windows.yml +++ b/.github/workflows/windows.yml @@ -17,10 +17,11 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.13"] + python-version: ["3.14"] #python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"] env: + MPLBACKEND: Agg # https://github.com/orgs/community/discussions/26434 PYTHONPATH: D:\a\physicelldataloader\physicelldataloader steps: From f010635409b37282b9116343184ab881ce994080 Mon Sep 17 00:00:00 2001 From: bue Date: Thu, 23 Oct 2025 09:40:27 -0400 Subject: [PATCH 4/5] @ workflows : test update. --- .github/workflows/apple.yml | 2 +- .github/workflows/linux.yml | 2 +- .github/workflows/windows.yml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/apple.yml b/.github/workflows/apple.yml index d0242c9..b153eda 100644 --- a/.github/workflows/apple.yml +++ b/.github/workflows/apple.yml @@ -17,7 +17,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.14"] + python-version: ["3.13"] #python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"] env: diff --git a/.github/workflows/linux.yml b/.github/workflows/linux.yml index 999bed9..b0b9af7 100644 --- a/.github/workflows/linux.yml +++ b/.github/workflows/linux.yml @@ -17,7 +17,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.14"] + python-version: ["3.13"] #python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"] env: diff --git a/.github/workflows/windows.yml b/.github/workflows/windows.yml index 4ff1354..54361e7 100644 --- a/.github/workflows/windows.yml +++ b/.github/workflows/windows.yml @@ -17,7 +17,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.14"] + python-version: ["3.13"] #python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"] env: From ade90861acf862269fcb07d22115716c8dcae73c Mon Sep 17 00:00:00 2001 From: bue Date: Thu, 23 Oct 2025 11:15:05 -0400 Subject: [PATCH 5/5] @ worflows : enable python 3.10, 3.11, 3.12, 3.13. --- .github/workflows/apple.yml | 4 ++-- .github/workflows/linux.yml | 4 ++-- .github/workflows/windows.yml | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/apple.yml b/.github/workflows/apple.yml index b153eda..69b4683 100644 --- a/.github/workflows/apple.yml +++ b/.github/workflows/apple.yml @@ -17,8 +17,8 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.13"] - #python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"] + #python-version: ["3.14"] + python-version: ["3.10", "3.11", "3.12", "3.13"] env: MPLBACKEND: Agg # https://github.com/orgs/community/discussions/26434 diff --git a/.github/workflows/linux.yml b/.github/workflows/linux.yml index b0b9af7..4884b40 100644 --- a/.github/workflows/linux.yml +++ b/.github/workflows/linux.yml @@ -17,8 +17,8 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.13"] - #python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"] + #python-version: ["3.14"] + python-version: ["3.10", "3.11", "3.12", "3.13"] env: MPLBACKEND: Agg # https://github.com/orgs/community/discussions/26434 diff --git a/.github/workflows/windows.yml b/.github/workflows/windows.yml index 54361e7..d114976 100644 --- a/.github/workflows/windows.yml +++ b/.github/workflows/windows.yml @@ -17,8 +17,8 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.13"] - #python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"] + #python-version: ["3.14"] + python-version: ["3.10", "3.11", "3.12", "3.13"] env: MPLBACKEND: Agg # https://github.com/orgs/community/discussions/26434