From 60665fded1334cbf44120695733278a9cb9ba8f9 Mon Sep 17 00:00:00 2001 From: Tim Monko Date: Fri, 1 Aug 2025 16:35:27 -0500 Subject: [PATCH 1/9] use uv for deploy --- .github/workflows/deploy_docs.yml | 18 +++++------------- 1 file changed, 5 insertions(+), 13 deletions(-) diff --git a/.github/workflows/deploy_docs.yml b/.github/workflows/deploy_docs.yml index a33967b..f2962fd 100644 --- a/.github/workflows/deploy_docs.yml +++ b/.github/workflows/deploy_docs.yml @@ -13,27 +13,19 @@ jobs: docs: runs-on: ubuntu-latest steps: - - name: Checkout repository - uses: actions/checkout@v4 + - uses: actions/checkout@v4 with: fetch-depth: 0 - - - name: Setup python - uses: actions/setup-python@v5 + - uses: astral-sh/setup-uv@v6 with: - python-version: "3.12" - - - name: Install dependencies - run: | - python -m pip install --upgrade pip setuptools wheel - python -m pip install -e .[docs] + enable-cache: true - name: Test that docs build without error if: github.event_name == 'pull_request' - run: mkdocs build --strict + run: uv run mkdocs build --strict - name: Deploy docs to GitHub Pages if: github.event_name == 'push' - run: mkdocs gh-deploy --strict --force + run: uv run mkdocs gh-deploy --strict --force From 641c02d7c3ba5a4a229f63a1e11ccc53e5989118 Mon Sep 17 00:00:00 2001 From: Tim Monko Date: Fri, 1 Aug 2025 16:49:57 -0500 Subject: [PATCH 2/9] use hatch for build --- pyproject.toml | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 2a5d1cb..9655dbb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -50,8 +50,5 @@ dev = [ "User Support" = "https://github.com/ndev-kit/docs/issues" [build-system] -requires = ["setuptools>=42.0.0", "setuptools_scm"] -build-backend = "setuptools.build_meta" - -[tool.setuptools] -py-modules = [] +requires = ["hatchling", "hatch-vcs"] +build-backend = "hatchling.build" From 9585740ca3ee34bb81813ed2438affb6918cef35 Mon Sep 17 00:00:00 2001 From: Tim Monko Date: Fri, 1 Aug 2025 16:55:03 -0500 Subject: [PATCH 3/9] use dev dependency group --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 9655dbb..a0f9567 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -38,7 +38,7 @@ dependencies = [ "mkdocs-multirepo-plugin", # For fetching docs from multiple repos ] -[project.optional-dependencies] +[dependency-groups] dev = [ "pre-commit", ] From bed113ca07625613ad411b8c47c07b6d9f254c22 Mon Sep 17 00:00:00 2001 From: Tim Monko Date: Fri, 1 Aug 2025 16:56:48 -0500 Subject: [PATCH 4/9] add version for hatch --- pyproject.toml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index a0f9567..a952cf2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -52,3 +52,6 @@ dev = [ [build-system] requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" + +[tool.hatch.version] +source = "vcs" From 73eb416e8069b4583a70e286f0f722096d6b62fb Mon Sep 17 00:00:00 2001 From: Tim Monko Date: Fri, 1 Aug 2025 16:58:11 -0500 Subject: [PATCH 5/9] remove build system entirely --- pyproject.toml | 7 ------- 1 file changed, 7 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index a952cf2..1fe50f4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -48,10 +48,3 @@ dev = [ "Documentation" = "https://github.com/ndev-kit/docs#README.md" "Source Code" = "https://github.com/ndev-kit/docs" "User Support" = "https://github.com/ndev-kit/docs/issues" - -[build-system] -requires = ["hatchling", "hatch-vcs"] -build-backend = "hatchling.build" - -[tool.hatch.version] -source = "vcs" From 8d3ae4b3424e26d58a177e2d1761b12cd770c62e Mon Sep 17 00:00:00 2001 From: Tim Monko Date: Sat, 2 Aug 2025 14:50:18 -0500 Subject: [PATCH 6/9] use ndev-kit.github.io (#4) --- mkdocs.yml | 6 +++--- pyproject.toml | 8 ++++---- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/mkdocs.yml b/mkdocs.yml index 2923f02..3070a08 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -1,8 +1,8 @@ site_name: nDev Documentation -site_url: https://ndev-kit.github.io/docs/ +site_url: https://ndev-kit.github.io/ site_description: Documentation for nDev ecosystem tools and packages -repo_name: ndev-kit/docs -repo_url: https://github.com/ndev-kit/docs +repo_name: ndev-kit/ndev-kit.github.io +repo_url: https://github.com/ndev-kit/ndev-kit.github.io copyright: Copyright © 2023-2025 Tim Monko & nDev Kit Contributors theme: diff --git a/pyproject.toml b/pyproject.toml index 1fe50f4..a77553a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -44,7 +44,7 @@ dev = [ ] [project.urls] -"Bug Tracker" = "https://github.com/ndev-kit/docs/issues" -"Documentation" = "https://github.com/ndev-kit/docs#README.md" -"Source Code" = "https://github.com/ndev-kit/docs" -"User Support" = "https://github.com/ndev-kit/docs/issues" +"Bug Tracker" = "https://github.com/ndev-kit/ndev-kit.github.io/issues" +"Documentation" = "https://github.com/ndev-kit/ndev-kit.github.io#README.md" +"Source Code" = "https://github.com/ndev-kit/ndev-kit.github.io" +"User Support" = "https://github.com/ndev-kit/ndev-kit.github.io/issues" From fc26854a56a47b6d52364754c8506b8a53cd9c09 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 26 Nov 2025 13:57:26 -0600 Subject: [PATCH 7/9] ci(dependabot): bump the actions group across 1 directory with 2 updates (#6) Bumps the actions group with 2 updates in the / directory: [actions/checkout](https://github.com/actions/checkout) and [astral-sh/setup-uv](https://github.com/astral-sh/setup-uv). Updates `actions/checkout` from 4 to 5 - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/v4...v5) Updates `astral-sh/setup-uv` from 6 to 7 - [Release notes](https://github.com/astral-sh/setup-uv/releases) - [Commits](https://github.com/astral-sh/setup-uv/compare/v6...v7) --- updated-dependencies: - dependency-name: actions/checkout dependency-version: '5' dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: astral-sh/setup-uv dependency-version: '7' dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/deploy_docs.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/deploy_docs.yml b/.github/workflows/deploy_docs.yml index f2962fd..d9be258 100644 --- a/.github/workflows/deploy_docs.yml +++ b/.github/workflows/deploy_docs.yml @@ -13,10 +13,10 @@ jobs: docs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v5 with: fetch-depth: 0 - - uses: astral-sh/setup-uv@v6 + - uses: astral-sh/setup-uv@v7 with: enable-cache: true From 5aa794860de5f6eca9752a61d8e4bbfed6f3c799 Mon Sep 17 00:00:00 2001 From: Tim Monko Date: Wed, 26 Nov 2025 13:57:38 -0600 Subject: [PATCH 8/9] add pixi config with mkdocs tasks (#7) --- .gitattributes | 2 + .gitignore | 5 + pixi.lock | 1862 ++++++++++++++++++++++++++++++++++++++++++++++++ pyproject.toml | 15 + 4 files changed, 1884 insertions(+) create mode 100644 .gitattributes create mode 100644 .gitignore create mode 100644 pixi.lock diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..887a2c1 --- /dev/null +++ b/.gitattributes @@ -0,0 +1,2 @@ +# SCM syntax highlighting & preventing 3-way merges +pixi.lock merge=binary linguist-language=YAML linguist-generated=true diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..c49f432 --- /dev/null +++ b/.gitignore @@ -0,0 +1,5 @@ +# pixi environments +.pixi/* +!.pixi/config.toml + +*.egg-info/ diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 0000000..35104ff --- /dev/null +++ b/pixi.lock @@ -0,0 +1,1862 @@ +version: 6 +environments: + default: + channels: + - 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+[**Download Images for Example Pipeline**](https://github.com/ndev-kit/resources/raw/refs/heads/main/image_archives/cellpainting.zip) Then, extract the files in the ZIP folder. The images come from the [Broad Bioimage Benchmark Collection](https://bbbc.broadinstitute.org/BBBC022/). Investigate the link for the description of the images. Scale: 0.656um/pixel @@ -28,7 +27,7 @@ Channels: ## PrimaryNeuron Images -[**Download Images for Easy Machine Learning Tutorial**](https://github.com/TimMonko/napari-ndev/raw/main/docs/tutorial/primaryneurons.zip) +[**Download Images for Easy Machine Learning Tutorial**](https://github.com/ndev-kit/resources/raw/refs/heads/main/image_archives/primaryneurons.zip) These images come from my own work at the University of Minnesota in the Thomas Bastian lab. The primary neurons are derived from embryonic mouse brains, and grown for a few days in a dish. The goal is to study morphology and iron homeostasis as the neurons develop over time in conditions of iron deficiency. The images available in the tutorial are extracted from multi-scene CZI files (each original file has over 100 scenes) using the `Image Utilities` widget. Metadata from the CZI files was correct, so the widget automatically passes this downstream without any user input. @@ -46,7 +45,7 @@ Channels: ## NeuralProgenitor Images -[**Download Images for Building a Pipeline Tutorial**](https://github.com/TimMonko/napari-ndev/raw/main/docs/tutorial/neuralprogenitors.zip) +[**Download Images for Building a Pipeline Tutorial**](https://github.com/ndev-kit/resources/raw/refs/heads/main/image_archives/neuralprogenitors.zip) These images come from the Zhe Chen lab at the University of Minnesota. These come from a microscope that *very poorly* saves the images: the images are forced to be saved as RGB (dspite having only one channel in each image) and improper scaling metadata. The images available in this tutorial have already been concatenated and the metadata applied using the `Image Utilities`.