Multi barcode decoder

.github/dependabot.yml

@@ -0,0 +1,10 @@
+# Set update schedule for GitHub Actions
+
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every week
+      interval: "weekly"

.github/workflows/starfish-prod-ci.yml

@@ -15,14 +15,14 @@ jobs:
     name: Lint
     runs-on: "ubuntu-latest"
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - name: Setup Python 3.8
-        uses: actions/setup-python@v2
+      - name: Setup Python 3.9
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
 
-      - uses: actions/cache@v2
+      - uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
           key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}
@@ -41,18 +41,18 @@ jobs:
     strategy:
       matrix:
         os: ["windows-latest", "ubuntu-latest"]
-        python-version: ["3.7", "3.8", "3.9"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
       fail-fast: false
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
-      - uses: actions/cache@v2
+      - uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
           key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}
@@ -71,18 +71,18 @@ jobs:
     strategy:
       matrix:
         os: ["windows-latest", "ubuntu-latest"]
-        python-version: ["3.7", "3.8", "3.9"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
       fail-fast: false
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
-      - uses: actions/cache@v2
+      - uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
           key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}
@@ -102,7 +102,7 @@ jobs:
   #   name: Napari Pinned
   #   runs-on: "ubuntu-latest"
   #   steps:
-  #     - uses: actions/checkout@v2
+  #     - uses: actions/checkout@v4
 
   #     - name: Install dependencies
   #       run: |
@@ -125,7 +125,7 @@ jobs:
   #   needs: napari-pinned
   #   runs-on: "ubuntu-latest"
   #   steps:
-  #     - uses: actions/checkout@v2
+  #     - uses: actions/checkout@v4
 
   #     - name: Install dependencies
   #       run: |
@@ -147,7 +147,7 @@ jobs:
     needs: starfish-slow
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Build Docker Image
         run: |
@@ -162,14 +162,14 @@ jobs:
     needs: starfish-slow
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - name: Setup Python 3.8
-        uses: actions/setup-python@v2
+      - name: Setup Python 3.9
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
 
-      - uses: actions/cache@v2
+      - uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
           key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}
@@ -187,14 +187,14 @@ jobs:
     needs: starfish-slow
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - name: Setup Python 3.8
-        uses: actions/setup-python@v2
+      - name: Setup Python 3.9
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
 
-      - uses: actions/cache@v2
+      - uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
           key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}
@@ -212,14 +212,14 @@ jobs:
     needs: starfish-slow
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - name: Setup Python 3.8
-        uses: actions/setup-python@v2
+      - name: Setup Python 3.9
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
 
-      - uses: actions/cache@v2
+      - uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
           key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}
@@ -237,14 +237,14 @@ jobs:
     needs: starfish-slow
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - name: Setup Python 3.8
-        uses: actions/setup-python@v2
+      - name: Setup Python 3.9
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
 
-      - uses: actions/cache@v2
+      - uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
           key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}
@@ -262,14 +262,14 @@ jobs:
     needs: starfish-slow
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - name: Setup Python 3.8
-        uses: actions/setup-python@v2
+      - name: Setup Python 3.9
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
 
-      - uses: actions/cache@v2
+      - uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
           key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}
@@ -287,14 +287,14 @@ jobs:
     needs: starfish-slow
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - name: Setup Python 3.8
-        uses: actions/setup-python@v2
+      - name: Setup Python 3.9
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
 
-      - uses: actions/cache@v2
+      - uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
           key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}
@@ -312,14 +312,14 @@ jobs:
     needs: starfish-slow
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - name: Setup Python 3.8
-        uses: actions/setup-python@v2
+      - name: Setup Python 3.9
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
 
-      - uses: actions/cache@v2
+      - uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
           key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}
@@ -337,14 +337,14 @@ jobs:
     needs: starfish-slow
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - name: Setup Python 3.8
-        uses: actions/setup-python@v2
+      - name: Setup Python 3.9
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
 
-      - uses: actions/cache@v2
+      - uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
           key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}
@@ -362,14 +362,14 @@ jobs:
     needs: starfish-slow
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - name: Setpu Python 3.8
-        uses: actions/setup-python@v2
+      - name: Setpu Python 3.9
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
 
-      - uses: actions/cache@v2
+      - uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
           key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}
@@ -387,14 +387,14 @@ jobs:
     needs: starfish-slow
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - name: Setup Python 3.8
-        uses: actions/setup-python@v2
+      - name: Setup Python 3.9
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
 
-      - uses: actions/cache@v2
+      - uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
           key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}
@@ -412,14 +412,14 @@ jobs:
     needs: starfish-slow
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - name: Setup Python 3.8
-        uses: actions/setup-python@v2
+      - name: Setup Python 3.9
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
 
-      - uses: actions/cache@v2
+      - uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
           key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}

CHANGELOG.md

@@ -1,3 +1,65 @@
+## [0.3.2] - 2025-02-16
+- Updating CHANGELOG.md for release 0.3.2
+- Bump cryptography from 44.0.0 to 44.0.1 in /requirements (#2051)
+- rolling back to Sphinx v5 as v6-8 introduce issues on ReadTheDocs with navbar logo and sub-menus (#2050)
+- Scikit image update from 0.21 to 0.23+ (#2049)
+- Bump jinja2 from 3.1.4 to 3.1.5 in /requirements (#2048)
+- Missing pypi description fix by adding pyproject.toml (#2047)
+- Bump actions/setup-python from 2 to 5 (#2042)
+- Bump actions/cache from 2 to 4 (#2041)
+- Bump actions/checkout from 2 to 4 (#2040)
+- Create dependabot.yml to auto update Github Action versions (#2039)
+- Bump tornado from 6.4.1 to 6.4.2 in /requirements (#2038)
+- replace scipy.ndimage.filters with scipy.ndimage for scipy v2 (#2035)
+- Bump lxml-html-clean from 0.3.1 to 0.4.0 in /requirements (#2036)
+
+## [0.3.1] - 2024-11-12
+- Updating CHANGELOG.md for release 0.3.1
+- Adding support to Python 3.12 (#2027)
+- Numpy 1.26 update to support Python 3.12 (#2025)
+- fixing blob radius calculation in 2d (#2023)
+- Release 0.3.0 (#2021)
+
+## [0.3.0] - 2024-10-05
+- Dropping support for Python 3.8 and setting Python 3.9 as minimum (#2018)
+- Update readthedocs.yml (#2014)
+- Scripts and dependencies updates for Python 3.8 - 3.10 (#2009)
+- Add min_distance parameter to peak_local_max call (#2008)
+- Various Small Fixes/Improvements (#1985)
+- Updated seqFISH Decoding Method: CheckAll Decoder (#1978)
+- Bump dask from 2021.9.0 to 2021.10.0 in /requirements (#1968)
+- Revert "Revert "Fix coords assignment in CombineAdjustFeatures.run (#1965)" (#1966)" (#1967)
+- Revert "Fix coords assignment in CombineAdjustFeatures.run (#1965)" (#1966)
+- Fix coords assignment in CombineAdjustFeatures.run (#1965)
+- Add to_dict and from_dict methods to TransformsList class (#1956)
+- fix notebook tests
+- Fix check-notebooks makefile command; Add python 3.9 to slow-tests
+- Fix Sphinx docs
+- Register pytest markers
+- Remove is_volume param from testing TrackpyLocalMaxPeakFinder invocation
+- Address skimage deprecation of skimage.morphology.watershed
+- Address Xarray pending deprecation for GroupBy.apply
+- Remove usage of deprecated numpy builtin types like np.bool/np.int
+- Add n_processes parameter to FindSpotsAlgorithm.run() abstract method
+- Remove deprecated `indices` param for skimage.feature.peak_local_max
+- Resolve failure when `peak_local_max()` finds no spots
+- Fix failing nearest neighbor trace builder tests
+- Fix composite codebook decoder tests
+- Change default value of BlobDetector exclude_border parameter to False
+- Fix incorrect type annotation and improper `.data()` method call
+- Fix failing morphology utility functions
+- Fix failing LearnTransform Translation class
+- Fix failing Codebook and IntensityTable shape validator
+- Fix failing Codebook.decode_per_round_max() test
+- Update .gitignore file
+- Defer when docker-smoketest github actiosn job is run
+- Bump requirements to clear github actions cache
+- Fix broken github actions Lint job; Fix broken caching
+- Address Mypy type annotation errors
+- Update github actions to use caching; Disable Napari tests for now
+- Use `python -m pip install ...` to perform pip upgrade
+- Replace Travis CI with Github Actions
+
 ## [0.2.2] - 2021-04-29
 - Updates requirements
 - Updates to documentation
@@ -233,6 +295,9 @@
 ## [0.0.33] - 2019.02.14
 - Last release without a changelog!
 
+[0.3.2]: https://github.com/spacetx/starfish/releases/tag/0.3.2
+[0.3.1]: https://github.com/spacetx/starfish/releases/tag/0.3.1
+[0.3.0]: https://github.com/spacetx/starfish/releases/tag/0.3.0
 [0.2.2]: https://github.com/spacetx/starfish/releases/tag/0.2.2
 [0.2.1]: https://github.com/spacetx/starfish/releases/tag/0.2.1
 [0.2.0]: https://github.com/spacetx/starfish/releases/tag/0.2.0