From 3dfe425469e38e7cc7bdcbb488c1c41d18967742 Mon Sep 17 00:00:00 2001 From: Cameron Mattson Date: Wed, 29 Apr 2026 10:19:39 -0600 Subject: [PATCH 1/8] ci: add trusted publishing workflows for PyPI and TestPyPI --- .github/workflows/publish-testpypi.yml | 52 ++++++++++++++++++++++++++ .github/workflows/publish.yml | 49 ++++++++++++++++++++++++ 2 files changed, 101 insertions(+) create mode 100644 .github/workflows/publish-testpypi.yml create mode 100644 .github/workflows/publish.yml diff --git a/.github/workflows/publish-testpypi.yml b/.github/workflows/publish-testpypi.yml new file mode 100644 index 0000000..f29a64d --- /dev/null +++ b/.github/workflows/publish-testpypi.yml @@ -0,0 +1,52 @@ +name: Publish to TestPyPI + +on: + release: + types: [prereleased] + workflow_dispatch: + +jobs: + build: + name: Build distributions + runs-on: ubuntu-latest + permissions: + contents: read + steps: + - name: Checkout + uses: actions/checkout@v4 + + - name: Setup uv + uses: astral-sh/setup-uv@v4 + + - name: Setup Python + run: uv python install 3.12 + + - name: Build package + run: uv build + + - name: Upload artifacts + uses: actions/upload-artifact@v4 + with: + name: dist-artifacts + path: dist/ + + publish: + name: Publish to TestPyPI + runs-on: ubuntu-latest + needs: build + permissions: + id-token: write + environment: + name: testpypi + url: https://test.pypi.org/p/jump-image-datasets + steps: + - name: Download artifacts + uses: actions/download-artifact@v4 + with: + name: dist-artifacts + path: dist/ + + - name: Publish package + uses: pypa/gh-action-pypi-publish@release/v1 + with: + repository-url: https://test.pypi.org/legacy/ diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml new file mode 100644 index 0000000..d7d58b0 --- /dev/null +++ b/.github/workflows/publish.yml @@ -0,0 +1,49 @@ +name: Publish to PyPI + +on: + release: + types: [published] + +jobs: + build: + name: Build distributions + runs-on: ubuntu-latest + permissions: + contents: read + steps: + - name: Checkout + uses: actions/checkout@v4 + + - name: Setup uv + uses: astral-sh/setup-uv@v4 + + - name: Setup Python + run: uv python install 3.12 + + - name: Build package + run: uv build + + - name: Upload artifacts + uses: actions/upload-artifact@v4 + with: + name: dist-artifacts + path: dist/ + + publish: + name: Publish to PyPI + runs-on: ubuntu-latest + needs: build + permissions: + id-token: write + environment: + name: pypi + url: https://pypi.org/p/jump-image-datasets + steps: + - name: Download artifacts + uses: actions/download-artifact@v4 + with: + name: dist-artifacts + path: dist/ + + - name: Publish package + uses: pypa/gh-action-pypi-publish@release/v1 From 23d80b14e58b67d60968c74d2b8ed053abcc9a21 Mon Sep 17 00:00:00 2001 From: Cameron Mattson Date: Wed, 29 Apr 2026 10:19:39 -0600 Subject: [PATCH 2/8] docs: add PyPI release checklist and twine validation step --- README.md | 40 ++++++++++++++++++++++++++++++++++++++++ pyproject.toml | 1 + 2 files changed, 41 insertions(+) diff --git a/README.md b/README.md index 81d7a65..6234279 100644 --- a/README.md +++ b/README.md @@ -25,6 +25,46 @@ pip install "git+https://github.com/WayScience/jump_image_data_downloader.git" This installs the package directly from the latest code, rather than from a PyPI release. +## Release workflow + +This repo includes automated publishing workflows: + +- TestPyPI: `.github/workflows/publish-testpypi.yml` +- PyPI: `.github/workflows/publish.yml` + +Both workflows use trusted publishing (GitHub OIDC), so no long-lived API token is required. + +### Maintainer checklist + +1. Bump `version` in `pyproject.toml`. +2. Run tests: + + ```bash + uv run --group test pytest + ``` + +3. Build distributions: + + ```bash + uv build + ``` + +4. Validate package metadata/artifacts: + + ```bash + uv run --group test twine check dist/* + ``` + +5. Merge to `main`. +6. Create a GitHub prerelease (for example `v0.1.1rc1`) to publish to TestPyPI. +7. Verify install from TestPyPI in a fresh environment. +8. Create a GitHub release (for example `v0.1.1`) to publish to PyPI. +9. Verify install from PyPI: + + ```bash + pip install jump-image-datasets + ``` + ## Usage ```python diff --git a/pyproject.toml b/pyproject.toml index 94021be..6661a13 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -37,6 +37,7 @@ notebook = [ ] test = [ "pytest>=9.0.2", + "twine>=6.1.0", ] [tool.pytest.ini_options] From f478dfd9e5faf570011f407df57a0a3314734ac5 Mon Sep 17 00:00:00 2001 From: Cameron Mattson Date: Wed, 29 Apr 2026 12:21:41 -0600 Subject: [PATCH 3/8] build: bump package version to 0.1.1 and refresh lockfile --- pyproject.toml | 2 +- uv.lock | 323 ++++++++++++++++++++++++++++++++++++++++++++++++- 2 files changed, 323 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 6661a13..1e82aef 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta" [project] name = "jump-image-datasets" -version = "0.1.0" +version = "0.1.1" description = "Download and access JUMP image datasets and metadata." readme = 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b/README.md index 6234279..86017d7 100644 --- a/README.md +++ b/README.md @@ -4,6 +4,14 @@ ## Install +### Install from PyPI + +```bash +pip install jump-image-datasets +``` + +Install from PyPI for stable, versioned releases. + ### Local development with uv ```bash @@ -23,7 +31,7 @@ uv pip install -e . pip install "git+https://github.com/WayScience/jump_image_data_downloader.git" ``` -This installs the package directly from the latest code, rather than from a PyPI release. +Install from GitHub if you want the latest unreleased changes. ## Release workflow From bd80506ccb2d006095653fce14654da53467d619 Mon Sep 17 00:00:00 2001 From: Cameron Mattson Date: Wed, 29 Apr 2026 12:38:33 -0600 Subject: [PATCH 5/8] I removed the release workflow and maintainer checklist sections from the README to keep the documentation focused on user-facing install and usage guidance. This is a docs-only cleanup; publishing automation and CI behavior remain unchanged. --- README.md | 40 ---------------------------------------- 1 file changed, 40 deletions(-) diff --git a/README.md b/README.md index 86017d7..86e7a97 100644 --- a/README.md +++ b/README.md @@ -33,46 +33,6 @@ pip install "git+https://github.com/WayScience/jump_image_data_downloader.git" Install from GitHub if you want the latest unreleased changes. -## Release workflow - -This repo includes automated publishing workflows: - -- TestPyPI: `.github/workflows/publish-testpypi.yml` -- PyPI: `.github/workflows/publish.yml` - -Both workflows use trusted publishing (GitHub OIDC), so no long-lived API token is required. - -### Maintainer checklist - -1. Bump `version` in `pyproject.toml`. -2. Run tests: - - ```bash - uv run --group test pytest - ``` - -3. Build distributions: - - ```bash - uv build - ``` - -4. Validate package metadata/artifacts: - - ```bash - uv run --group test twine check dist/* - ``` - -5. Merge to `main`. -6. Create a GitHub prerelease (for example `v0.1.1rc1`) to publish to TestPyPI. -7. Verify install from TestPyPI in a fresh environment. -8. Create a GitHub release (for example `v0.1.1`) to publish to PyPI. -9. Verify install from PyPI: - - ```bash - pip install jump-image-datasets - ``` - ## Usage ```python From c5435dfb47fceb3722cc22e1c252f3de6278c625 Mon Sep 17 00:00:00 2001 From: Cameron Mattson Date: Thu, 30 Apr 2026 17:31:44 -0600 Subject: [PATCH 6/8] ci: remove TestPyPI publishing workflow Stop maintaining the separate TestPyPI release workflow by deleting `.github/workflows/publish-testpypi.yml`. This simplifies the CI/release setup in this repository and removes TestPyPI-specific automation --- .github/workflows/publish-testpypi.yml | 52 -------------------------- 1 file changed, 52 deletions(-) delete mode 100644 .github/workflows/publish-testpypi.yml diff --git a/.github/workflows/publish-testpypi.yml b/.github/workflows/publish-testpypi.yml deleted file mode 100644 index f29a64d..0000000 --- a/.github/workflows/publish-testpypi.yml +++ /dev/null @@ -1,52 +0,0 @@ -name: Publish to TestPyPI - -on: - release: - types: [prereleased] - workflow_dispatch: - -jobs: - build: - name: Build distributions - runs-on: ubuntu-latest - permissions: - contents: read - steps: - - name: Checkout - uses: actions/checkout@v4 - - - name: Setup uv - uses: astral-sh/setup-uv@v4 - - - name: Setup Python - run: uv python install 3.12 - - - name: Build package - run: uv build - - - name: Upload artifacts - uses: actions/upload-artifact@v4 - with: - name: dist-artifacts - path: dist/ - - publish: - name: Publish to TestPyPI - runs-on: ubuntu-latest - needs: build - permissions: - id-token: write - environment: - name: testpypi - url: https://test.pypi.org/p/jump-image-datasets - steps: - - name: Download artifacts - uses: actions/download-artifact@v4 - with: - name: dist-artifacts - path: dist/ - - - name: Publish package - uses: pypa/gh-action-pypi-publish@release/v1 - with: - repository-url: https://test.pypi.org/legacy/ From 4b76cc25d0667a154d0b5cb9437e6bfa0714af14 Mon Sep 17 00:00:00 2001 From: Cameron Mattson Date: Thu, 30 Apr 2026 17:33:04 -0600 Subject: [PATCH 7/8] ci: simplify publish workflow by removing explicit Python install The publish build job already runs on ubuntu-latest with Python available, and the package supports Python >=3.10. Remove the redundant `uv python install 3.12` step to reduce workflow complexity and runtime while keeping build and publish behavior unchanged. --- .github/workflows/publish.yml | 3 --- 1 file changed, 3 deletions(-) diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index d7d58b0..d3ebdbf 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -17,9 +17,6 @@ jobs: - name: Setup uv uses: astral-sh/setup-uv@v4 - - name: Setup Python - run: uv python install 3.12 - - name: Build package run: uv build From efc6a84fb1c451a88f0db16aac59e92768ed9480 Mon Sep 17 00:00:00 2001 From: Cameron Mattson Date: Thu, 30 Apr 2026 17:41:49 -0600 Subject: [PATCH 8/8] build: adopt setuptools-scm and drop twine test dependency --- pyproject.toml | 8 +- uv.lock | 324 +------------------------------------------------ 2 files changed, 6 insertions(+), 326 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 1e82aef..cd92df0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,10 +1,10 @@ [build-system] -requires = ["setuptools>=68", "wheel"] +requires = ["setuptools>=68", "setuptools_scm[toml]>=8", "wheel"] build-backend = "setuptools.build_meta" [project] name = "jump-image-datasets" -version = "0.1.1" +dynamic = ["version"] description = "Download and access JUMP image datasets and metadata." readme = "README.md" requires-python = ">=3.10" @@ -31,13 +31,15 @@ where = ["src"] [tool.setuptools.package-data] "jump_image_datasets.jump_pilot" = ["data/*.parquet"] +[tool.setuptools_scm] +tag_regex = "^(?:v)?(?P\\d+\\.\\d+\\.\\d+.*)$" + [dependency-groups] notebook = [ "jupyter>=1.1.1", ] test = [ "pytest>=9.0.2", - 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