Support Python 3.12

.github/workflows/main.yml

@@ -22,24 +22,33 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-20.04, ubuntu-latest, macos-latest, windows-latest]
+        os: [ubuntu-latest, macos-13, macos-latest, windows-latest]
         python-version: ["3.6", "3.7", "3.8", "3.9", "3.10", "3.11"]
         dependencies:
           - pinned
           - fresh
         exclude:
-          - os: ubuntu-20.04
+          - os: ubuntu-latest
+            python-version: 3.6
+          - os: macos-13
+            python-version: 3.10
+          - os: macos-13
+            python-version: 3.11
+          - os: macos-latest
+            python-version: 3.6
+          - os: macos-latest
             python-version: 3.7
-          - os: ubuntu-20.04
+          - os: macos-latest
             python-version: 3.8
-          - os: ubuntu-20.04
+          - os: macos-latest
             python-version: 3.9
+        include:
           - os: ubuntu-20.04
-            python-version: "3.10"
+            python-version: 3.6
+            dependencies: pinned
           - os: ubuntu-20.04
-            python-version: "3.11"
-          - os: ubuntu-latest
             python-version: 3.6
+            dependencies: fresh
 
     env:
       # set requirements path based on Python version

README.md

@@ -110,4 +110,4 @@ To try out functions with sample images, download any of these files:
 
 Licensed under the open-source [BSD-3 license](LICENSE.txt)
 
-Author: David Young, 2017, 2023, Stephan Sanders Lab
+Author: David Young, 2017, 2024, Stephan Sanders Lab

bin/setup_venv.sh

@@ -70,7 +70,7 @@ fi
 # check for Python availability and version requirement
 py_ver_majmin="" # found Python version in x.y format
 py_ver_min=(3 6) # minimum supported Python version
-py_vers=(3.8 3.7 3.6 3.9 3.10 3.11) # range of versions currently supported
+py_vers=(3.8 3.7 3.6 3.9 3.10 3.11 3.12) # range of versions currently supported
 py_vers_prebuilt_deps=(3.6 3.7 3.8 3.9 3.10 3.11) # vers with custom prebuilt deps
 for ver in "${py_vers[@]}"; do
   # prioritize specific versions in case "python" points to lower version,

docs/install.md

@@ -14,7 +14,25 @@
 
 MagellanMapper supports several Python setups.
 
-### Install using Conda
+### Quick Install
+
+Install MagellanMapper with its graphical interface and registration tools:
+
+```shell
+pip install "magellanmapper[gui,itk]"
+```
+
+Then launch MagellanMapper:
+
+```shell
+mm
+```
+
+See [below](#dependencies) for supported Python versions and adding install groups.
+
+See our [vignette](https://github.com/sanderslab/magellanmapper/blob/master/bin/sample_cmds_bash.ipynb) for getting started on MM!
+
+### Full install using Conda
 
 If you use Conda (available [here](https://docs.conda.io/en/latest/miniconda.html)), you can install MagellanMapper into a new environment named `mag` (or replace with desired name):
 
@@ -33,7 +51,7 @@ Conda will also install Java, which we use to read proprietary image formats.
 
 The `mm` entry points was added in v1.6.0 to facilitate launching from installed packages.
 
-### Install using Pip
+### Full install using Pip
 
 Install using Pip with Python >= 3.6 (see [Python versions](#python-version-support); Python >= 3.9 and [virtual environment](https://realpython.com/python-virtual-environments-a-primer/) recommended):
 
@@ -173,7 +191,7 @@ Sometimes a virtual environment update is required for new dependencies.
 | MagellanMapper Version | Python Versions Supported | Notes |
 |-----|-----|-----|
 | 1.7 (planned) | 3.9-3.11 | 3.6-3.8 to be removed |
-| >=1.6b1 | 3.6-3.11 | Defaults to 3.9. GUI support added for 3.10-3.11 in MM 1.6b2. |
+| >=1.6b1 | 3.6-3.11 | Defaults to 3.9. GUI support added for 3.10-3.11 in MM 1.6b2, 3.12 in MM 1.6b5. |
 | 1.6a1-a3 | 3.6-3.9 | GUI support added for 3.9; MM 1.6a2 base group no longer installs GUI |
 | 1.4-1.5 | 3.6-3.9 | No GUI support in 3.9 |
 | < 1.4 | 3.6 | Initial releases |

docs/pipelines.md

@@ -1,9 +1,13 @@
 # Running Pipelines in MagellanMapper
 
-TODO: update for new pipelines
+## Vignette
+
+See our [vignette](https://github.com/sanderslab/magellanmapper/blob/master/bin/sample_cmds_bash.ipynb) for examples on using MM.
 
 ## Start a processing pipeline
 
+**Note**: This pipeline script is deprecated. See our vignette above for running similar pipelines.
+
 Automated processing will attempt to scale based on your system resources but may require some manual intervention. This pipeline has been tested on a Macbook Pro laptop and AWS EC2 Linux (RHEL and Amazon Linux based) instances.
 
 Optional dependencies:

docs/release/release_v1.6.md

@@ -7,7 +7,7 @@
 - Smoother, faster interactions with main plots, including atlas label name display, label editing, and pan and zoom navigation
 - Available as binary wheel to install without requiring the source code
 - Faster, lighter installation with fewer required dependency packages
-- Extends suppor to Python 3.11 and defaults to Python 3.9
+- Extends support to Python 3.12 and defaults to Python 3.9
 - Simpler entry point to launch MagellanMapper: `mm`
 - Supports ITK-Elastix for image registration
 - Atlases can be downloaded directly through [`BrainGlobe`](https://github.com/brainglobe/bg-atlasapi) (see the new "Atlases" panel)
@@ -199,13 +199,13 @@
 - Jupyter Notebook as a tutorial for running various tasks in the CLI (#122)
 - Documentation is now [hosted on ReadTheDocs](https://magellanmapper.readthedocs.io/en/latest/index.html), using the Furo theme (#225, #563)
 - Default arguments are documented in API auto-docs (#485)
-- Expand continuous integration testing to both pinned and fresh dependencies across Python 3.6-3.11 (#75, #101, #252, #342, #538)
+- Expand continuous integration testing to both pinned and fresh dependencies across Python 3.6-3.12 (#75, #101, #252, #342, #538, #640)
 
 ### Dependency Updates
 
 #### Python Dependency Changes
 
-- Python 3.10-3.11 are now supported (#379, #517)
+- Python 3.10-3.12 are now supported (#379, #517, #640)
 - Python 3.9 is the default version now that Python 3.6 has reached End-of-Life, and NumPy no longer supports Python 3.8 (#559, #563)
 - Python 3.6-8 have been deprecated for removal in MM v1.7 and have separate pinned dependencies (`envs/requirements_py3<n>`) (#232, #379)
 - Custom dependency binaries are now built for Python 3.8-3.11 (#379)

envs/requirements.txt

@@ -14,7 +14,7 @@ importlib_metadata==7.1.0
 importlib_resources==6.4.0
 itk==5.4rc3
 itk-core==5.4rc3
-itk-elastix==0.19.1
+itk-elastix==0.19.2
 itk-filtering==5.4rc3
 itk-io==5.4rc3
 itk-numerics==5.4rc3

magmap/atlas/ontology.py

@@ -344,20 +344,22 @@ def load(self):
         return self
 
 
-def convert_itksnap_to_df(path):
-    """Convert an ITK-SNAP labels description file to a CSV file 
-    compatible with MagellanMapper.
+def convert_itksnap_to_df(path: str):
+    """Convert an ITK-SNAP labels description file to a CSV file.
+
+    MagellanMapper can read this type of CSV file.
 
     Args:
         path: Path to description file.
 
     Returns:
         Pandas data frame of the description file.
+
     """
-    # load description file and convert contiguous spaces to separators, 
+    # load description file and convert contiguous spaces to separators,
     # remove comments, and add headers
     df = pd.read_csv(
-        path, sep="\s+", comment="#",
+        path, sep=r"\s+", comment="#",
         names=[e.value for e in config.ItkSnapLabels])
     return df
 

magmap/gui/visualizer.py

@@ -441,16 +441,16 @@ class Visualization(HasTraits):
         tooltip="Colormap for the channel. Start typing to search.")
     _imgadj_color_names = Instance(TraitsList)
     _imgadj_min = Float
-    _imgadj_min_low = Float(0)
-    _imgadj_min_high = Float
+    _imgadj_min_low = Float(0)  # must have val in Python >= 3.10
+    _imgadj_min_high = Float(1)  # must have val > min in Python >= 3.12
     _imgadj_min_auto = Bool
     _imgadj_max = Float
     _imgadj_max_low = Float(0)
-    _imgadj_max_high = Float
+    _imgadj_max_high = Float(1)
     _imgadj_max_auto = Bool
     _imgadj_brightness = Float
     _imgadj_brightness_low = Float(0)
-    _imgadj_brightness_high = Float
+    _imgadj_brightness_high = Float(1)
     _imgadj_contrast = Float
     _imgadj_alpha = Float
     _imgadj_alpha_blend = Float(0.5)

setup.py

@@ -77,7 +77,7 @@
     "url": "https://github.com/sanderslab/magellanmapper",
     "author_email": "david@textflex.com",
     "license": "BSD-3",
-    "version": "1.6b4",
+    "version": "1.6b5",
     "packages": setuptools.find_packages(),
     "scripts": [],
     "python_requires": ">=3.6",