Dropping support for Python 3.8 and setting Python 3.9 as minimum (#2018

)

* removing support for python 3.8

* upgrading setuptools as older ver is part of venv

* dropping python 3.8 and adding tests for 3.11

.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: ["3.8", "3.9", "3.10"]
+ python-version: ["3.9", "3.10", "3.11"]
  fail-fast: false
  runs-on: ${{ matrix.os }}
  steps:
@@ -71,7 +71,7 @@ jobs:
  strategy:
  matrix:
  os: ["windows-latest", "ubuntu-latest"]
- python-version: ["3.8", "3.9", "3.10"]
+ python-version: ["3.9", "3.10", "3.11"]
  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:

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=24.0
+PIP_VERSION=24.2
 
 define print_help
  @printf " %-28s $(2)\n" $(1)
@@ -102,7 +102,7 @@ pin-all-requirements:
 starfish/REQUIREMENTS-STRICT.txt : REQUIREMENTS.txt
  [ ! -e .$<-env ] || exit 1
  $(call create_venv, .$<-env)
- .$<-env/bin/pip install --upgrade pip==$(PIP_VERSION)
+ .$<-env/bin/pip install --upgrade --no-cache-dir pip==$(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)" >> $@
@@ -111,7 +111,7 @@ starfish/REQUIREMENTS-STRICT.txt : REQUIREMENTS.txt
 requirements/REQUIREMENTS-%.txt : requirements/REQUIREMENTS-%.txt.in REQUIREMENTS.txt
  [ ! -e .$<-env ] || exit 1
  $(call create_venv, .$<-env)
- .$<-env/bin/pip install --upgrade pip==$(PIP_VERSION)
+ .$<-env/bin/pip install --upgrade --no-cache-dir pip==$(PIP_VERSION) setuptools
  for src in $^; do \
  .$<-env/bin/pip install -r $$src; \
  done

README.rst

@@ -47,7 +47,7 @@ See `spacetx-starfish.readthedocs.io <https://spacetx-starfish.readthedocs.io/en
 Installation
 ------------
 
-starfish supports python 3.8-11 and can easily be installed from PyPI:
+starfish supports python 3.9-11 and can easily be installed from PyPI:
 
 .. code-block:: bash
 
@@ -58,8 +58,8 @@ starfish supports python 3.8-11 and can easily be installed from PyPI:
 Python Version Notice
 ---------------------
 
-starfish will be dropping support for python 3.8 in the next release due to
-minimum python=3.9 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
 ------------

docker/Dockerfile

@@ -36,7 +36,7 @@
 ##
 ## $ docker run -e TEST_ISS_KEEP_DATA=true --entrypoint=pytest spacetx/starfish -vsxk TestWithIssData
 ##
-FROM python:3.8-slim-buster
+FROM python:3.9-slim-buster
 
 RUN useradd -m starfish
 USER starfish

docs/source/installation/index.rst

@@ -3,7 +3,7 @@
 Installation
 ============
 
-Starfish supports python 3.8-11. To install the starfish package,
+Starfish supports python 3.9-11. To install the starfish package,
 first verify that your python version is compatible. You can check this by running :code:`python
 --version`.
 
@@ -12,7 +12,7 @@ The output should look similar to this:
 .. code-block:: bash
 
  $ python --version
- Python 3.8.18
+ Python 3.9.18
 
 .. warning::
  While starfish itself should work on any operating system, some napari dependencies might not be
@@ -44,7 +44,7 @@ Conda_ users can set one up like so:
 
 .. code-block:: bash
 
- $ conda create -n starfish "python=3.8"
+ $ conda create -n starfish "python=3.9"
  $ conda activate starfish
 
 Installing *starfish*
@@ -73,7 +73,7 @@ Installing *starfish* on Windows
 --------------------------------
 
 Windows (cmd.exe) users can install starfish in the same way. Again, we recommend using a conda or virtual
-environment with python 3.8+. Here is how you would install starfish in a virtual environment
+environment with python 3.9+. Here is how you would install starfish in a virtual environment
 created with python's ``venv`` module:
 
 .. code-block:: bat

examples/quick_start/plot_quick_start.py

@@ -13,13 +13,11 @@
 Prerequisites
 -------------
 
-* Python 3.6+ installed (Python 3.7 recommended)
+* Python 3.9+ installed (Python 3.10 recommended)
 * Some basic knowledge of scientific computing in Python_
 * :ref:`Starfish library installed <installation>`
-* seaborn_ is installed: :code:`pip install seaborn`
 
 .. _Python: https://docs.scipy.org/doc/numpy/user/quickstart.html
-.. _seaborn: https://seaborn.pydata.org/
 
 Starfish Pipeline
 -----------------

examples/tutorials/transforms_list.json

@@ -1 +1 @@
-{"transforms_list": [[{"r": 0}, "similarity", [[1.0, -0.0, -22.926], [0.0, 1.0, 5.673], [0.0, 0.0, 1.0]]], [{"r": 1}, "similarity", [[1.0, -0.0, -22.301], [0.0, 1.0, 1.6440000000000001], [0.0, 0.0, 1.0]]], [{"r": 2}, "similarity", [[1.0, -0.0, -22.124], [0.0, 1.0, -3.278], [0.0, 0.0, 1.0]]], [{"r": 3}, "similarity", [[1.0, -0.0, -14.998], [0.0, 1.0, -4.397], [0.0, 0.0, 1.0]]]], "version": "0.0.0"}
+{"transforms_list": [[{"r": 0}, "similarity", [[1.0, -0.0, -22.868999481201172], [0.0, 1.0, 5.85699987411499], [0.0, 0.0, 1.0]]], [{"r": 1}, "similarity", [[1.0, -0.0, -22.13599967956543], [0.0, 1.0, 1.871999979019165], [0.0, 0.0, 1.0]]], [{"r": 2}, "similarity", [[1.0, -0.0, -21.957000732421875], [0.0, 1.0, -3.5799999237060547], [0.0, 0.0, 1.0]]], [{"r": 3}, "similarity", [[1.0, -0.0, -14.98799991607666], [0.0, 1.0, -4.414999961853027], [0.0, 0.0, 1.0]]]], "version": "0.0.0"}