Merge pull request #716 from bioimage-io/dev

Update build workflow
and update 'Detect new version' job

Author: FynnBe

.github/workflows/build.yml

@@ -21,7 +21,7 @@ jobs:
             run-expensive-tests: true
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
           cache: "pip"
@@ -94,7 +94,7 @@ jobs:
         with:
           name: coverage
           path: dist
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
           python-version: "3.12"
           cache: "pip"
@@ -167,20 +167,19 @@ jobs:
 #      with:
 #        recipe-path: conda-recipe/recipe.yaml
 
-  publish-pypi:
-    name: Publish to PyPI
+  pip-build:
+    name: Build and publish to PyPI
     needs: test
-    if: github.ref == 'refs/heads/main'
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repository
         uses: actions/checkout@v4
         with:
           fetch-depth: 2
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
-          python-version: '3.13'
+          python-version: '3.10'
           cache: 'pip'
       - name: Install dependencies
         run: |
@@ -195,16 +194,16 @@ jobs:
 
       - name: Detect new version
         id: check-version
-        if: steps.check-parent-commit.outputs.sha
+        if: github.ref == 'refs/heads/main' && steps.check-parent-commit.outputs.sha
         uses: salsify/[email protected]
         with:
           create-tag: false
           version-command: |
-            python -c "from pathlib import Path;print(Path('bioimageio/spec/__init__.py').read_text().split('__version__ = \"')[1].split('\"')[0])"
+            python -c "from pathlib import Path;print(Path('src/bioimageio/spec/__init__.py').read_text().split('__version__ = \"')[1].split('\"')[0])"
 
       - name: Push tag
         id: tag-version
-        if: steps.check-version.outputs.previous-version != steps.check-version.outputs.current-version
+        if: github.ref == 'refs/heads/main' && steps.check-version.outputs.previous-version != steps.check-version.outputs.current-version
         uses: mathieudutour/[email protected]
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
@@ -215,14 +214,15 @@ jobs:
           python -m build
 
       - name: Publish package on PyPI
-        if: steps.tag-version.outputs.new_tag
+        if: github.ref == 'refs/heads/main' && steps.tag-version.outputs.new_tag
         uses: pypa/gh-action-pypi-publish@release/v1.12
         with:
           user: __token__
           password: "${{ secrets.PYPI_TOKEN }}"
           packages-dir: dist/
 
       - name: Publish the release notes
+        if: github.ref == 'refs/heads/main'
         uses: release-drafter/[email protected]
         with:
           publish: "${{ steps.tag-version.outputs.new_tag != '' }}"

changelog.md

@@ -1,6 +1,6 @@
 {% set pyproject = load_file_data('pyproject.toml') %}
 {% set version_match = load_file_regex(
-  load_file="bioimageio/spec/__init__.py",
+  load_file="src/bioimageio/spec/__init__.py",
   regex_pattern='__version__ = "(.+)"') %}
 {% set version = version_match[1] %}
 
@@ -12,7 +12,7 @@ source:
   path: ..
 
 requirements:
-  build:
+  host:
     - python {{ pyproject['project']['requires-python'] }}
     {% for dep in pyproject['build-system']['requires'] %}
     - {{ dep.lower() }}
@@ -25,6 +25,7 @@ requirements:
 
 build:
   noarch: python
+  number: 0
   script:
         - python -m pip install --no-deps --ignore-installed .
 

conda-recipe/meta.yaml

@@ -15,7 +15,7 @@ dependencies:
   - numpy[version='>=1.21']
   - packaging[version='>=17.0']
   - pip
-  - pooch
+  - platformdirs
   - pre-commit
   - psutil
   - pydantic-settings

dev/env.yaml

@@ -6,23 +6,23 @@ requires-python = ">=3.8"
 dependencies = [
     "annotated-types>=0.5.0,<1",
     "email_validator",
+    "exceptiongroup",            # TODO: remove when py3.11 is lowest supported version
     "genericache==0.5.2",
+    "httpx",
     "imageio",
     "loguru",
     "markdown",
     "numpy>=1.21",
     "packaging>=17.0",
-    "pooch>=1.5,<2",
+    "platformdirs",
     "pydantic-settings>=2.5,<3",
     "pydantic>=2.10.3,<2.12",
     "python-dateutil",
-    "httpx",
     "rich",
     "ruyaml",
     "tifffile>=2020.7.4",
     "tqdm",
     "typing-extensions",
-    "exceptiongroup",            # TODO: remove when py3.11 is lowest supported version
     "zipp",
 ]
 classifiers = [
@@ -60,7 +60,7 @@ requires = ["pip", "setuptools>=61.0"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools.packages.find]
-include = ["bioimageio"]
+where = ["src/"]
 
 [tool.setuptools.dynamic]
 version = { attr = "bioimageio.spec.__version__" }
@@ -74,7 +74,7 @@ exclude = [
     "bioimageio_cache",
     "tests/old_*",
 ]
-include = ["bioimageio", "scripts", "tests"]
+include = ["src", "scripts", "tests"]
 pythonPlatform = "All"
 pythonVersion = "3.8"
 reportDuplicateImport = "error"
@@ -106,7 +106,7 @@ useLibraryCodeForTypes = true
 
 [tool.pytest.ini_options]
 addopts = " --failed-first --doctest-modules"
-testpaths = ["bioimageio/spec", "tests"]
+testpaths = ["src", "tests"]
 
 [tool.ruff]
 line-length = 88
@@ -119,7 +119,7 @@ exclude = [
 
 [tool.coverage.report]
 omit = [
-    "bioimageio/spec/pretty_validation_errors.py",
-    "bioimageio/spec/partner_utils/imjoy/*.py",
+    "src/bioimageio/spec/pretty_validation_errors.py",
+    "src/bioimageio/spec/partner_utils/imjoy/*.py",
 ]
 exclude_also = ["if TYPE_CHECKING:", "assert_never\\("]

pyproject.toml

@@ -8,7 +8,7 @@
 from tempfile import TemporaryDirectory
 from typing import List, Literal
 
-ROOT_PATH = Path(__file__).parent.parent
+SRC_PATH = Path(__file__).parent.parent / "src"
 
 AUTOGEN_START = "# autogen: start\n"
 AUTOGEN_BODY_SINGLE = """from . import {info.latest_version_module}
@@ -113,7 +113,7 @@ def __post_init__(self):
         )
         self.all_version_modules_imports = "\n".join(avmi)
 
-        self.package_path = (ROOT_PATH / "bioimageio" / "spec" / self.target).resolve()
+        self.package_path = (SRC_PATH / "bioimageio" / "spec" / self.target).resolve()
         self.submodule_list = "\n".join(
             [
                 f"- {self.target} {vm}: `bioimageio.spec.{self.target}.{vm}."
@@ -176,7 +176,7 @@ def process(info: Info, check: bool):
 def get_ordered_version_submodules(target: str):
     matches = [
         m
-        for p in (ROOT_PATH / "bioimageio" / "spec" / target).iterdir()
+        for p in (SRC_PATH / "bioimageio" / "spec" / target).iterdir()
         if p.is_file() and (m := re.fullmatch(VERSION_MODULE_PATTERN, p.name))
     ]
     if not matches:

scripts/generate_version_submodule_imports.py

@@ -3,7 +3,7 @@
 """
 # ruff: noqa: E402
 
-__version__ = "0.5.5.1"
+__version__ = "0.5.5.2"
 from loguru import logger
 
 logger.disable("bioimageio.spec")