removing support for python 3.8

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"}

requirements/REQUIREMENTS-CI.txt

@@ -1,22 +1,21 @@
 # You should not edit this file directly.  Instead, you should edit one of the following files (requirements/REQUIREMENTS-CI.txt.in) and run make requirements/REQUIREMENTS-CI.txt
-alabaster==0.7.13
+alabaster==0.7.16
 asttokens==2.4.1
 attrs==24.2.0
-Babel==2.15.0
-backcall==0.2.0
+babel==2.16.0
 backports.tarfile==1.2.0
 beautifulsoup4==4.12.3
 bleach==6.1.0
-boto3==1.34.156
-botocore==1.34.156
-certifi==2024.7.4
-cffi==1.17.0
+boto3==1.35.13
+botocore==1.35.13
+certifi==2024.8.30
+cffi==1.17.1
 charset-normalizer==3.3.2
 click==8.1.7
 commonmark==0.9.1
-contourpy==1.1.1
+contourpy==1.3.0
 coverage==7.6.1
-cryptography==43.0.0
+cryptography==43.0.1
 cycler==0.12.1
 decorator==5.1.1
 defusedxml==0.7.1
@@ -25,21 +24,21 @@ docutils==0.20.1
 entrypoints==0.4
 exceptiongroup==1.2.2
 execnet==2.1.1
-executing==2.0.1
+executing==2.1.0
 fastjsonschema==2.20.0
 flake8==7.1.1
 flake8-import-order==0.18.2
 fonttools==4.53.1
 h5py==3.11.0
-idna==3.7
-imageio==2.34.2
+idna==3.8
+imageio==2.35.1
 imagesize==1.4.1
-importlib_metadata==8.2.0
-importlib_resources==6.4.0
+importlib_metadata==8.4.0
+importlib_resources==6.4.4
 iniconfig==2.0.0
-ipython==8.12.3
+ipython==8.18.1
 jaraco.classes==3.4.0
-jaraco.context==5.3.0
+jaraco.context==6.0.1
 jaraco.functools==4.0.2
 jedi==0.19.1
 jeepney==0.8.0
@@ -51,11 +50,11 @@ jupyter_client==8.6.2
 jupyter_core==5.7.2
 jupyterlab_pygments==0.3.0
 keyring==25.3.0
-kiwisolver==1.4.5
+kiwisolver==1.4.7
 lazy_loader==0.4
 looseversion==1.3.0
-lxml==5.2.2
-lxml_html_clean==0.2.0
+lxml==5.3.0
+lxml_html_clean==0.2.2
 m2r2==0.3.3.post2
 markdown-it-py==3.0.0
 MarkupSafe==2.1.5
@@ -64,27 +63,25 @@ matplotlib-inline==0.1.7
 mccabe==0.7.0
 mdurl==0.1.2
 mistune==0.8.4
-more-itertools==10.4.0
+more-itertools==10.5.0
 mpmath==1.3.0
 mypy==1.10.1
 mypy-extensions==1.0.0
 nbclient==0.10.0
 nbconvert==6.5.4
 nbencdec==0.0.10
 nbformat==5.10.4
-networkx==3.1
+networkx==3.2.1
 nh3==0.2.18
 numpy==1.24.4
-numpydoc==1.7.0
+numpydoc==1.8.0
 packaging==24.1
-pandas==2.0.3
+pandas==2.2.2
 pandocfilters==1.5.1
 parso==0.8.4
 pexpect==4.9.0
-pickleshare==0.7.5
 pillow==10.4.0
 pkginfo==1.10.0
-pkgutil_resolve_name==1.3.10
 platformdirs==4.2.2
 pluggy==1.5.0
 prompt_toolkit==3.0.47
@@ -94,55 +91,55 @@ pycodestyle==2.12.1
 pycparser==2.22
 pyflakes==3.2.0
 Pygments==2.18.0
-pyparsing==3.1.2
+pyparsing==3.1.4
 pyrsistent==0.20.0
 pytest==8.3.2
 pytest-cov==5.0.0
 pytest-xdist==3.6.1
 python-dateutil==2.9.0.post0
 pytz==2024.1
-PyWavelets==1.4.1
+PyWavelets==1.6.0
 PyYAML==6.0.2
-pyzmq==26.1.0
+pyzmq==26.2.0
 read-roi==1.6.0
 readme_renderer==43.0
 recommonmark==0.7.1
 regional==1.1.2
 requests==2.32.3
 requests-toolbelt==1.0.0
 rfc3986==2.0.0
-rich==13.7.1
+rich==13.8.0
 s3transfer==0.10.2
 scikit-image==0.21.0
-scikit-learn==1.3.2
-scipy==1.10.1
+scikit-learn==1.5.1
+scipy==1.13.1
 seaborn==0.13.2
 SecretStorage==3.3.3
 semantic-version==2.10.0
-setuptools==56.0.0
+setuptools==74.1.2
 showit==1.1.4
 six==1.16.0
 slicedimage==4.1.1
 snowballstemmer==2.2.0
-soupsieve==2.5
-Sphinx==7.1.2
-sphinx-autodoc-typehints==2.0.1
+soupsieve==2.6
+Sphinx==7.4.7
+sphinx-autodoc-typehints==2.3.0
 sphinx-bootstrap-theme==0.8.1
 sphinx-gallery==0.17.1
 sphinx-rtd-theme==2.0.0
-sphinxcontrib-applehelp==1.0.4
-sphinxcontrib-devhelp==1.0.2
-sphinxcontrib-htmlhelp==2.0.1
+sphinxcontrib-applehelp==2.0.0
+sphinxcontrib-devhelp==2.0.0
+sphinxcontrib-htmlhelp==2.1.0
 sphinxcontrib-jquery==4.1
 sphinxcontrib-jsmath==1.0.1
 sphinxcontrib-programoutput==0.17
-sphinxcontrib-qthelp==1.0.3
-sphinxcontrib-serializinghtml==1.1.5
+sphinxcontrib-qthelp==2.0.0
+sphinxcontrib-serializinghtml==2.0.0
 stack-data==0.6.3
-sympy==1.13.1
+sympy==1.13.2
 tabulate==0.9.0
 threadpoolctl==3.5.0
-tifffile==2023.7.10
+tifffile==2024.8.30
 tinycss2==1.3.0
 tomli==2.0.1
 tornado==6.4.1
@@ -152,13 +149,13 @@ traitlets==5.14.3
 twine==5.1.1
 types-PyYAML==6.0.12.20240808
 types-requests==2.31.0.6
-types-setuptools==71.1.0.20240806
+types-setuptools==74.1.0.20240906
 types-urllib3==1.26.25.14
 typing_extensions==4.12.2
 tzdata==2024.1
-urllib3==1.26.19
-validators==0.33.0
+urllib3==1.26.20
+validators==0.34.0
 wcwidth==0.2.13
 webencodings==0.5.1
-xarray==2023.1.0
-zipp==3.19.2
+xarray==2023.8.0
+zipp==3.20.1

requirements/REQUIREMENTS-CI.txt.in

@@ -6,9 +6,10 @@ flake8-import-order
 lxml_html_clean
 # pin m2r2: https://github.com/CrossNox/m2r2/issues/52
 m2r2>=0.3.3
-mypy != 0.740
+# temporarily limiting mypy as 1.11 introduces errors
+mypy<1.11
 numpydoc
-nbencdec >= 0.0.5
+nbencdec>=0.0.5
 pycodestyle
 pytest>=4.4.0
 pytest-cov>=2.5.1