updating reopened branch pypi_description for further debugging (#2044)

* Adding support to Python 3.12 (#2027) * updating versioneer and add python 3.12 to setup files * add python 3.12 to CI * fix: python 3.12 flake8 linting error * removing backslash sequences that raise SyntaxWarning in python 3.12+ when using sphinx-gallery to convert reST to markdown * add python 3.12 support to docs * docs: fixes to README.rst loading on PyPI project description (#2029) * Updating CHANGELOG.md for release 0.3.1 (#2030) * updating CHANGELOG.md for release 0.3.1 * Bump lxml-html-clean from 0.3.1 to 0.4.0 in /requirements (#2036) Bumps [lxml-html-clean](https://github.com/fedora-python/lxml_html_clean) from 0.3.1 to 0.4.0. - [Changelog](https://github.com/fedora-python/lxml_html_clean/blob/main/CHANGES.rst) - [Commits](fedora-python/lxml_html_clean@0.3.1...0.4.0) --- updated-dependencies: - dependency-name: lxml-html-clean dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Create dependabot.yml to update Actions version (#2033) Will automatically open PR to update: actions/cache actions/checkout actions/setup-python https://docs.github.com/en/code-security/dependabot/working-with-dependabot/keeping-your-actions-up-to-date-with-dependabot * replace scipy.ndimage.filters with scipy.ndimage for scipy v2 (#2035) * Bump tornado from 6.4.1 to 6.4.2 in /requirements (#2038) Bumps [tornado](https://github.com/tornadoweb/tornado) from 6.4.1 to 6.4.2. - [Changelog](https://github.com/tornadoweb/tornado/blob/v6.4.2/docs/releases.rst) - [Commits](tornadoweb/tornado@v6.4.1...v6.4.2) --- updated-dependencies: - dependency-name: tornado dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Github Actions auto update (#2039) * Create dependabot.yml to update Actions version Will automatically open PR to update: actions/cache actions/checkout actions/setup-python https://docs.github.com/en/code-security/dependabot/working-with-dependabot/keeping-your-actions-up-to-date-with-dependabot * moving dependabot.yml to .github/ folder * Bump actions/checkout from 2 to 4 (#2040) Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v2...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/cache from 2 to 4 (#2041) Bumps [actions/cache](https://github.com/actions/cache) from 2 to 4. - [Release notes](https://github.com/actions/cache/releases) - [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md) - [Commits](actions/cache@v2...v4) --- updated-dependencies: - dependency-name: actions/cache dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/setup-python from 2 to 5 (#2042) Bumps [actions/setup-python](https://github.com/actions/setup-python) from 2 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v2...v5) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Delete .github/workflows/dependabot.yml (#2043) Tried to delete and remove dependabot.yml file from the wrong folder, but this didn't register in PR #2039 --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
spacetx · Dec 13, 2024 · ad89f7d · ad89f7d
1 parent 082d638
commit ad89f7d
Show file tree

Hide file tree

Showing 10 changed files with 72 additions and 54 deletions.
diff --git a/.github/dependabot.yml b/.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"
diff --git a/.github/workflows/starfish-prod-ci.yml b/.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') }}
@@ -45,14 +45,14 @@ jobs:
       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') }}
@@ -75,14 +75,14 @@ jobs:
       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') }}

diff --git a/CHANGELOG.md b/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

diff --git a/requirements/REQUIREMENTS-CI.txt b/requirements/REQUIREMENTS-CI.txt
@@ -54,7 +54,7 @@ kiwisolver==1.4.7
 lazy_loader==0.4
 looseversion==1.3.0
 lxml==5.3.0
-lxml_html_clean==0.3.1
+lxml_html_clean==0.4.0
 m2r2==0.3.3.post2
 markdown-it-py==3.0.0
 MarkupSafe==3.0.1
@@ -142,7 +142,7 @@ threadpoolctl==3.5.0
 tifffile==2024.8.30
 tinycss2==1.3.0
 tomli==2.0.2
-tornado==6.4.1
+tornado==6.4.2
 tqdm==4.66.5
 trackpy==0.6.4
 traitlets==5.14.3

diff --git a/requirements/REQUIREMENTS-JUPYTER.txt b/requirements/REQUIREMENTS-JUPYTER.txt
@@ -125,7 +125,7 @@ threadpoolctl==3.5.0
 tifffile==2024.8.30
 tinycss2==1.3.0
 tomli==2.0.2
-tornado==6.4.1
+tornado==6.4.2
 tqdm==4.66.5
 trackpy==0.6.4
 traitlets==5.14.3

diff --git a/requirements/REQUIREMENTS-NAPARI-CI.txt b/requirements/REQUIREMENTS-NAPARI-CI.txt
@@ -144,7 +144,7 @@ tifffile==2024.8.30
 tomli==2.0.2
 tomli_w==1.1.0
 toolz==1.0.0
-tornado==6.4.1
+tornado==6.4.2
 tqdm==4.66.5
 trackpy==0.6.4
 traitlets==5.14.3

diff --git a/starfish/core/image/Filter/bandpass.py b/starfish/core/image/Filter/bandpass.py
@@ -14,7 +14,7 @@ class Bandpass(FilterAlgorithm):
     """
     Convolve with a Gaussian to remove short-wavelength noise and subtract out long-wavelength
     variations, retaining features of intermediate scale. This implementation relies on
-    scipy.ndimage.filters.gaussian_filter.
+    scipy.ndimage.gaussian_filter.
 
     This method is a thin wrapper around :doc:`trackpy:generated/trackpy.preprocessing.bandpass`.
 

diff --git a/starfish/core/image/Filter/mean_high_pass.py b/starfish/core/image/Filter/mean_high_pass.py
@@ -3,7 +3,7 @@
 
 import numpy as np
 import xarray as xr
-from scipy.ndimage.filters import uniform_filter
+from scipy.ndimage import uniform_filter
 
 from starfish.core.imagestack.imagestack import ImageStack
 from starfish.core.types import Levels, Number
@@ -22,7 +22,7 @@ class MeanHighPass(FilterAlgorithm):
     The mean filter is also known as a uniform or box filter. It can also be considered as a fast
     approximation to a GaussianHighPass filter.
 
-    This is a pass through for :py:func:`scipy.ndimage.filters.uniform_filter`
+    This is a pass through for :py:func:`scipy.ndimage.uniform_filter`
 
     Parameters
     ----------

diff --git a/starfish/core/spots/DecodeSpots/test/test_nearest_neighbor_trace_builder.py b/starfish/core/spots/DecodeSpots/test/test_nearest_neighbor_trace_builder.py
@@ -1,5 +1,5 @@
 import numpy as np
-from scipy.ndimage.filters import gaussian_filter
+from scipy.ndimage import gaussian_filter
 
 from starfish import ImageStack
 from starfish.core.spots.DecodeSpots.trace_builders import build_traces_nearest_neighbors

diff --git a/starfish/core/test/factories.py b/starfish/core/test/factories.py
@@ -3,7 +3,7 @@
 from typing import Tuple
 
 import numpy as np
-from scipy.ndimage.filters import gaussian_filter
+from scipy.ndimage import gaussian_filter
 from skimage import img_as_float32, img_as_uint
 
 from starfish import Codebook, ImageStack, IntensityTable