Merge pull request #475 from bioimage-io/dev

Improve CI

Author: FynnBe

.github/workflows/build.yaml

@@ -5,6 +5,16 @@ on:
     branches: [main]
   pull_request:
     branches: ['**']
+  workflow_dispatch:
+    inputs:
+      force-publish:
+        description: 'Force publish even if no version change detected'
+        required: false
+        type: choice
+        options:
+          - 'true'
+          - 'false'
+        default: 'false'
 
 defaults:
   run:
@@ -143,11 +153,10 @@ jobs:
       - uses: actions/upload-artifact@v4
         with:
           name: coverage-summary
-          retention-days: 1
           path: dist
 
   conda-build:
-    needs: test # only so we run tests even if the pinned bioimageio.spec version is not yet published on conda-forge yet
+    needs: [populate-cache, test] # only so we run tests even if the pinned bioimageio.spec version is not yet published on conda-forge
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -169,14 +178,20 @@ jobs:
             pkgs/noarch
             pkgs/channeldata.json
           key: ${{ github.sha }}-packages
+      - uses: actions/cache@v4
+        with:
+          path: bioimageio_cache
+          key: ${{needs.populate-cache.outputs.cache-key}}
       - name: linux conda build test
         shell: bash -l {0}
         run: |
           mkdir -p ./pkgs/noarch
           conda-build -c conda-forge conda-recipe --output-folder ./pkgs
+        env:
+          BIOIMAGEIO_CACHE_PATH: bioimageio_cache
 
   docs:
-    needs: test
+    needs: [coverage, test]
     if: github.ref == 'refs/heads/main'
     runs-on: ubuntu-latest
     steps:
@@ -234,26 +249,51 @@ jobs:
         uses: actions/checkout@v4
         with:
           fetch-depth: 2
-      - name: Check if there is a parent commit
-        id: check-parent-commit
+          fetch-tags: true
+      - name: Get parent commit
+        if: inputs.force-publish != 'true'
+        id: get-parent-commit
         run: |
           echo "sha=$(git rev-parse --verify --quiet HEAD^)" >> $GITHUB_OUTPUT
+      - id: get-existing-tag
+        if: inputs.force-publish == 'true'
+        run: echo "existing-tag=$(git tag --points-at HEAD 'v[0-9]*.[0-9]*.[0-9]*')" >> $GITHUB_OUTPUT
 
-      - name: Detect new version
+      - name: Detect new version from last commit and create tag
         id: tag-version
-        if: github.ref == 'refs/heads/main' && steps.check-parent-commit.outputs.sha
+        if: github.ref == 'refs/heads/main' && steps.get-parent-commit.outputs.sha && inputs.force-publish != 'true'
         uses: salsify/[email protected]
         with:
           create-tag: true
           version-command: |
-            python -c "from pathlib import Path;import json;print(p_src.read_text().split('__version__ = \"')[1].split('\"')[0] if (p_src:=Path('src/bioimageio/core/__init__.py')).exists() else json.loads(Path('bioimageio/core/VERSION').read_text())['version'])"
+            python -c "from pathlib import Path; p = Path('src/bioimageio/core/__init__.py'); v = p.read_text().split('__version__ = \"')[1].split('\"')[0]; print(v)"
+      - shell: python
+        id: get-new-version
+        run: |
+          import os
+          from pathlib import Path
+
+
+
+          if "${{ inputs.force-publish }}" == "true":
+              existing_tag = "${{ steps.get-existing-tag.outputs.existing-tag }}"
+              valid = existing_tag.count("v") == 1 and existing_tag.count(".") == 2 and all(part.isdigit() for part in existing_tag.lstrip("v").split("."))
+              if not valid:
+                  raise Exception(f"Current commit has invalid version tag {existing_tag}.")
+              new_version = existing_tag
+          else:
+              new_version = "${{ steps.tag-version.outputs.tag }}"
+
+          with open(os.environ['GITHUB_OUTPUT'], 'a') as f:
+              print(f"new-version={new_version}", file=f)
+
       - uses: actions/download-artifact@v4
-        if: github.ref == 'refs/heads/main' && steps.tag-version.outputs.tag
+        if: github.ref == 'refs/heads/main' && steps.get-new-version.outputs.new-version
         with:
           name: dist
           path: dist
       - name: Publish package on PyPI
-        if: github.ref == 'refs/heads/main' && steps.tag-version.outputs.tag
+        if: github.ref == 'refs/heads/main' && steps.get-new-version.outputs.new-version
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
           packages-dir: dist/
@@ -262,7 +302,7 @@ jobs:
         if: github.ref == 'refs/heads/main'
         uses: release-drafter/[email protected]
         with:
-          publish: "${{ steps.tag-version.outputs.tag != '' }}"
-          tag: '${{ steps.tag-version.outputs.tag }}'
+          publish: "${{ steps.get-new-version.outputs.new-version != '' }}"
+          tag: '${{ steps.get-new-version.outputs.new-version }}'
         env:
           GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}'

src/bioimageio/core/block_meta.py

@@ -52,7 +52,7 @@ class BlockMeta:
     The outer slice reaches from the sample member origin (0, 0) to the right halo point.
 
     ```terminal
-    ┌ ─ ─ ─ ─ ─ ─ ─ ─ ─ ─  ─ ─ ─ ─ ─ ─ ─ ┐
+    ┌ ─ ─ ─ ─ ─ ─ ─ ─ ─ ─ ─ ─ ─ ─ ─ ─ ─ ─┐
     ╷ halo(left)                         ╷
     ╷                                    ╷
     ╷  (0, 0)┏━━━━━━━━━━━━━━━━━┯━━━━━━━━━┯━━━➔

src/bioimageio/core/digest_spec.py

@@ -302,13 +302,15 @@ def get_input_halo(model: v0_5.ModelDescr, output_halo: PerMember[PerAxis[Halo]]
             axis = axes[a]
             ref_axis = {a.id: a for a in all_tensors[s.tensor_id].axes}[s.axis_id]
 
-            total_output_halo = sum(ah)
-            total_input_halo = total_output_halo * axis.scale / ref_axis.scale
-            assert (
-                total_input_halo == int(total_input_halo) and total_input_halo % 2 == 0
+            input_halo_left = ah.left * axis.scale / ref_axis.scale
+            input_halo_right = ah.right * axis.scale / ref_axis.scale
+            assert input_halo_left == int(input_halo_left), f"{input_halo_left} not int"
+            assert input_halo_right == int(input_halo_right), (
+                f"{input_halo_right} not int"
             )
+
             input_halo.setdefault(s.tensor_id, {})[a] = Halo(
-                int(total_input_halo // 2), int(total_input_halo // 2)
+                int(input_halo_left), int(input_halo_right)
             )
 
     return input_halo