Merge branch 'master' into master

spacetx · Nov 20, 2024 · 4b72706 · 4b72706
2 parents bda2d40 + 233b013
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diff --git a/.github/workflows/starfish-prod-ci.yml b/.github/workflows/starfish-prod-ci.yml
@@ -17,10 +17,10 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - name: Setup Python 3.8
+      - name: Setup Python 3.9
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       - uses: actions/cache@v2
         with:
@@ -41,7 +41,7 @@ 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:
@@ -71,7 +71,7 @@ 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:
@@ -164,10 +164,10 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - name: Setup Python 3.8
+      - name: Setup Python 3.9
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       - uses: actions/cache@v2
         with:
@@ -189,10 +189,10 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - name: Setup Python 3.8
+      - name: Setup Python 3.9
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       - uses: actions/cache@v2
         with:
@@ -214,10 +214,10 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - name: Setup Python 3.8
+      - name: Setup Python 3.9
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       - uses: actions/cache@v2
         with:
@@ -239,10 +239,10 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - name: Setup Python 3.8
+      - name: Setup Python 3.9
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       - uses: actions/cache@v2
         with:
@@ -264,10 +264,10 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - name: Setup Python 3.8
+      - name: Setup Python 3.9
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       - uses: actions/cache@v2
         with:
@@ -289,10 +289,10 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - name: Setup Python 3.8
+      - name: Setup Python 3.9
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       - uses: actions/cache@v2
         with:
@@ -314,10 +314,10 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - name: Setup Python 3.8
+      - name: Setup Python 3.9
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       - uses: actions/cache@v2
         with:
@@ -339,10 +339,10 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - name: Setup Python 3.8
+      - name: Setup Python 3.9
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       - uses: actions/cache@v2
         with:
@@ -364,10 +364,10 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - name: Setpu Python 3.8
+      - name: Setpu Python 3.9
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       - uses: actions/cache@v2
         with:
@@ -389,10 +389,10 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - name: Setup Python 3.8
+      - name: Setup Python 3.9
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       - uses: actions/cache@v2
         with:
@@ -414,10 +414,10 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - name: Setup Python 3.8
+      - name: Setup Python 3.9
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       - uses: actions/cache@v2
         with:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,50 @@
+## [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 +280,8 @@
 ## [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
 [0.2.0]: https://github.com/spacetx/starfish/releases/tag/0.2.0

diff --git a/Makefile b/Makefile
@@ -12,7 +12,7 @@ DOCKER_BUILD?=1
 
 VERSION=$(shell sh -c "git describe --exact --dirty 2> /dev/null")
 # if you update this, you will need to update the version pin for the "Install Napari & Test napari (pinned)" test in .travis.yml
-PIP_VERSION=21.2.4
+PIP_VERSION=24.2
 
 define print_help
     @printf "    %-28s   $(2)\n" $(1)
@@ -80,8 +80,8 @@ help-docs:
 
 ### REQUIREMENTS #############################################
 #
-GENERATED_REQUIREMENT_FILES=starfish/REQUIREMENTS-STRICT.txt requirements/REQUIREMENTS-CI.txt requirements/REQUIREMENTS-NAPARI-CI.txt
-SOURCE_REQUIREMENT_FILES=REQUIREMENTS.txt requirements/REQUIREMENTS-CI.txt.in requirements/REQUIREMENTS-NAPARI-CI.txt.in
+GENERATED_REQUIREMENT_FILES=starfish/REQUIREMENTS-STRICT.txt requirements/REQUIREMENTS-CI.txt requirements/REQUIREMENTS-NAPARI-CI.txt requirements/REQUIREMENTS-JUPYTER.txt
+SOURCE_REQUIREMENT_FILES=REQUIREMENTS.txt requirements/REQUIREMENTS-CI.txt.in requirements/REQUIREMENTS-NAPARI-CI.txt.in requirements/REQUIREMENTS-JUPYTER.txt.in
 
 # This rule pins the requirements with the minimal set of changes required to satisfy the
 # requirements.  This is typically run when a new requirement is added, and we want to
@@ -102,8 +102,7 @@ pin-all-requirements:
 starfish/REQUIREMENTS-STRICT.txt : REQUIREMENTS.txt
 	[ ! -e .$<-env ] || exit 1
 	$(call create_venv, .$<-env)
-	.$<-env/bin/pip install --upgrade pip==$(PIP_VERSION)
-	.$<-env/bin/pip install -r $@
+	.$<-env/bin/pip install --upgrade --no-cache-dir pip==$(PIP_VERSION) setuptools
 	.$<-env/bin/pip install -r $<
 	echo "# You should not edit this file directly.  Instead, you should edit one of the following files ($^) and run make $@" >| $@
 	.$<-env/bin/pip freeze --all | grep -v "pip==$(PIP_VERSION)" >> $@
@@ -112,8 +111,7 @@ starfish/REQUIREMENTS-STRICT.txt : REQUIREMENTS.txt
 requirements/REQUIREMENTS-%.txt : requirements/REQUIREMENTS-%.txt.in REQUIREMENTS.txt
 	[ ! -e .$<-env ] || exit 1
 	$(call create_venv, .$<-env)
-	.$<-env/bin/pip install --upgrade pip==$(PIP_VERSION)
-	.$<-env/bin/pip install -r $@
+	.$<-env/bin/pip install --upgrade --no-cache-dir pip==$(PIP_VERSION) setuptools
 	for src in $^; do \
 		.$<-env/bin/pip install -r $$src; \
 	done

diff --git a/README.rst b/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.
@@ -47,19 +51,19 @@ See `spacetx-starfish.readthedocs.io <https://spacetx-starfish.readthedocs.io/en
 Installation
 ------------
 
-starfish supports python 3.7 and above and can easily be installed from PyPI:
+starfish supports python 3.9-3.12 and can easily be installed from PyPI:
 
 .. code-block:: bash
 
     $ pip install starfish[napari]
 
-`For more detailed installation instructions, see here <https://spacetx-starfish.readthedocs.io/en/latest/installation/>`_.
+`Some operating systems might need different dependencies for napari. For more detailed installation instructions, see here <https://spacetx-starfish.readthedocs.io/en/latest/installation/>`_.
 
 Python Version Notice
 ---------------------
 
-starfish will be dropping support for python 3.6 in the next release due to
-minimum python=3.7 version requirements in upstream dependencies.
+starfish will be dropping support for python 3.9 in future release when
+upstream dependencies will require a minimum python=3.10 version.
 
 Contributing
 ------------
@@ -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>`_
diff --git a/REQUIREMENTS.txt b/REQUIREMENTS.txt
@@ -1,30 +1,27 @@
-# The following requirement is here because networkx restricts the version
-# of decorator.  Since pip is not a full dependency solver, it has already
-# installed decorator before networkx is installed, and bombs after the
-# fact.
-decorator < 5.0
 click
-dataclasses==0.6
+# docutils introduces an AttributeError: module 'docutils.nodes' has no attribute 'reprunicode'
+docutils<0.21
 h5py
-jsonschema
-matplotlib
-numpy != 1.13.0, >= 1.20.0
-pandas >= 0.23.4
+# jsonschema 4.18.0 made RefResolver deprecated
+jsonschema<4.18
+# matplotlib 3.8 changes colormap module
+matplotlib<3.8
+# pinning mistune for m2r2 in CI requirements
+mistune==0.8.4
+# numpy 2.0 breaks code and migration requires additional work
+numpy<2
 read_roi
 regional
-semantic_version
-# 0.16.[012] are excluded because https://github.com/scikit-image/scikit-image/pull/3984 introduced
-# a bug into max peak finder.  0.16.3 presumably will have the fix from
-# https://github.com/scikit-image/scikit-image/pull/4263.
-scikit-image
+# scikit-image is temporarily pinned as newer versions require updating module imports
+scikit-image==0.21
 scikit-learn
-scipy
-showit >= 1.1.4
-slicedimage==4.1.1
-sympy ~= 1.5.0
-urllib3 <1.27, >=1.25.4
+seaborn
+semantic_version
+showit
+slicedimage
+sympy
 tqdm
 trackpy
 validators
-xarray >= 0.14.1
-ipywidgets
+# xarray 2023.09 causses a ValueError: new dimensions ('y', 'x') must be a superset of existing dimensions ('dim_0', 'dim_1')
+xarray<2023.09