updating reopened branch pypi_description for further debugging

.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 3.9
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           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: ["3.9", "3.10", "3.11"]
+        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: ["3.9", "3.10", "3.11"]
+        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 3.9
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           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 3.9
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           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 3.9
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           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 3.9
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           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 3.9
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           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 3.9
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           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 3.9
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           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 3.9
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           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 3.9
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           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 3.9
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           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 3.9
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           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 +1,10 @@
+## [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)
@@ -273,6 +280,7 @@
 ## [0.0.33] - 2019.02.14
 - Last release without a changelog!
 
+[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

README.rst

@@ -1,9 +1,11 @@
 starfish: scalable pipelines for image-based transcriptomics
-========
+============================================================
 
-
-.. image:: docs/source/_static/design/logo.png
-    :scale: 50 %
+.. image:: https://github.com/spacetx/starfish/blob/64add94b51dbf6f8f5fd614b02c4dfbf4b0d702d/docs/source/_static/design/logo.png?raw=True
+    :alt: starfish logo
+    :width: 312
+    :height: 127
+    :align: center
 
 -----------------------------
 
@@ -23,15 +25,17 @@ starfish: scalable pipelines for image-based transcriptomics
     :target: https://spacetx-starfish.readthedocs.io/en/latest/?badge=latest
     :alt: Documentation Status
 
-.. image:: https://travis-ci.com/spacetx/starfish.svg?branch=master
-    :target: https://travis-ci.com/spacetx/starfish
+.. image:: https://github.com/spacetx/starfish/actions/workflows/starfish-prod-ci.yml/badge.svg?branch=master
+    :target: https://github.com/spacetx/starfish/actions/workflows/starfish-prod-ci.yml
+    :alt: starfish production CI
 
 .. image:: https://codecov.io/gh/spacetx/starfish/branch/master/graph/badge.svg
     :target: https://codecov.io/gh/spacetx/starfish
+    :alt: Code Coverage
 
 -------------------------------
 
-*starfish* is a Python library for processing images of image-based spatial transcriptomics.
+**starfish** is a Python library for processing images of image-based spatial transcriptomics.
 It lets you build scalable pipelines that localize and quantify RNA transcripts in image data
 generated by any FISH method, from simple RNA single-molecule FISH to combinatorial barcoded
 assays.
@@ -47,7 +51,7 @@ See `spacetx-starfish.readthedocs.io <https://spacetx-starfish.readthedocs.io/en
 Installation
 ------------
 
-starfish supports python 3.9-11 and can easily be installed from PyPI:
+starfish supports python 3.9-3.12 and can easily be installed from PyPI:
 
 .. code-block:: bash
 
@@ -70,7 +74,7 @@ We welcome contributions from our users! See our contributing.rst_ and `develope
 .. _contributing.rst: https://github.com/spacetx/starfish/blob/master/CONTRIBUTING.rst
 
 Help, support, and questions
-----------------
+----------------------------
 
 - Forum: ask on the `Image.sc forum <https://forum.image.sc/tag/starfish>`_
 - Email: `starfish@chanzuckerberg.com <mailto:starfish@chanzuckerberg.com>`_

docs/source/installation/index.rst

@@ -3,7 +3,7 @@
 Installation
 ============
 
-Starfish supports python 3.9-11. To install the starfish package,
+Starfish supports python 3.9-3.12. To install the starfish package,
 first verify that your python version is compatible. You can check this by running :code:`python
 --version`.