Merge pull request #48 from spm/dep-runtime

[ENH] spm-runtime dependency

Author: johmedr

.github/workflows/run_unit_tests.yml

@@ -3,23 +3,23 @@ on:
   workflow_dispatch:
   workflow_call:
   push:
-    paths: 
+    paths:
       - tests/**
       - spm/**
-      - setup.py 
+      - setup.py
       - pyproject.toml
   pull_request:
-  
+
 env:
   MLM_LICENSE_TOKEN: ${{ secrets.MATLAB_BATCH_TOKEN }}
-  
+
 jobs:
   run-unit-tests:
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: False
       matrix:
-        matlab: ["latest"]
+        matlab: ["R2025a"]
         os: [ubuntu-latest, macos-13, macos-latest, windows-latest]
         python-version: ["3.9", "3.10", "3.11", "3.12"]
         include:
@@ -41,14 +41,16 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-          
+
       - name: Check out SPM Python
         uses: actions/checkout@v4
 
       - name: Install SPM Python
-        run: python -m pip install -e .
-        
-      # Setup MATLAB and Runtime 
+        run: |
+          python -m pip install mpython-core
+          python -m pip install -e .
+
+      # Setup MATLAB and Runtime
       - name: Set up MATLAB
         uses: matlab-actions/setup-matlab@v2
         with:
@@ -73,7 +75,7 @@ jobs:
         # sometimes this step hangs when closing matlab, automatically terminating after 2 minutes solves the issue
         timeout-minutes: 2
         continue-on-error: true
-        
+
       - name: Set environment variable with MATLAB path
         shell: bash # Works on Windows as well because of shell: bash
         run: |
@@ -90,7 +92,7 @@ jobs:
           ${{ env.MATLAB_PATH }}/extern/bin/maca64"
           export PYTHONHOME=${{ env.pythonLocation }}
           mwpython -m unittest discover tests -v
-      
+
       - name: Run tests (Mac Intel)
         if: matrix.os_name == 'macOS_Intel'
         run: |
@@ -101,7 +103,7 @@ jobs:
           ${{ env.MATLAB_PATH }}/extern/bin/maci64"
           export PYTHONHOME=${{ env.pythonLocation }}
           mwpython -m unittest discover tests -v
-        
+
       - name: Run tests (Windows)
         if: matrix.os_name == 'Windows'
         shell: bash

.mpython/templates/class_header.py

@@ -1,7 +1,8 @@
-from mpython import Runtime, MatlabClass
+from mpython import MatlabClass
+from spm._runtime import Runtime, RuntimeMixin
 
 
-class <classname>(MatlabClass):
+class <classname>(RuntimeMixin, MatlabClass):
     def __init__(self, *args, **kwargs):
         <docstring>
         super().__init__()

.mpython/templates/function_header.py

@@ -0,0 +1 @@
+from spm._runtime import Runtime

MANIFEST.in

@@ -1,4 +1,3 @@
 include README.md
 include LICENSE
 include AUTHORS.txt
-recursive-include spm/_spm *.ctf

pyproject.toml

@@ -9,35 +9,52 @@ description = "Python bindings for the SPM software."
 readme = "README.md"
 license = {file = "LICENSE"}
 authors = [
-  {name = "Johan Medrano", email = "johan.medrano@ucl.ac.uk"}, 
-  {name = "Yael Balbastre", email = "y.balbastre@ucl.ac.yk"}, 
+  {name = "Johan Medrano", email = "johan.medrano@ucl.ac.uk"},
+  {name = "Yael Balbastre", email = "y.balbastre@ucl.ac.uk"},
   {name = "Yulia Bezsudnova"},
-  {name = "Arthur Mitchell"}, 
-  {name = "Peter Zeidman"}, 
-  {name = "Olivia Kowalczyk"} ]
-requires-python = ">=3.9,<3.13"
+  {name = "Arthur Mitchell"},
+  {name = "Peter Zeidman"},
+  {name = "Olivia Kowalczyk"},
+]
+requires-python = ">=3.6,<3.13"
 classifiers = [
   "Development Status :: 4 - Beta",
   "License :: OSI Approved :: GNU General Public License v2 (GPLv2)",
+  "Programming Language :: Python :: 3.6",
+  "Programming Language :: Python :: 3.7",
+  "Programming Language :: Python :: 3.8",
   "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
 ]
 dependencies = [
-    "numpy", 
-    "mpython-core<=25.4a3"
+    "mpython-core>=25.4rc1",
+    "spm-runtime-r2025a == 25.1.1 ; python_version >= '3.9'",
+    "spm-runtime-r2023a == 25.1.1 ; python_version == '3.8'",
+    "spm-runtime-r2021b == 25.1.1 ; python_version == '3.7'",
+    "spm-runtime-r2020b == 25.1.1 ; python_version == '3.6'",
 ]
 
+[project.optional-dependencies]
+latest = ["spm-runtime        == 25.1.1"]
+R2025a = ["spm-runtime-R2025a == 25.1.1"]
+R2024b = ["spm-runtime-R2024b == 25.1.1"]
+R2024a = ["spm-runtime-R2024a == 25.1.1"]
+R2023b = ["spm-runtime-R2023b == 25.1.1"]
+R2023a = ["spm-runtime-R2023a == 25.1.1"]
+R2022b = ["spm-runtime-R2022b == 25.1.1"]
+R2022a = ["spm-runtime-R2022a == 25.1.1"]
+R2021b = ["spm-runtime-R2021b == 25.1.1"]
+R2021a = ["spm-runtime-R2021a == 25.1.1"]
+R2020b = ["spm-runtime-R2020b == 25.1.1"]
+
 [project.urls]
 Repository = "https://github.com/spm/spm-python"
 
 [tool.setuptools.packages]
 find = {}
 
-[tool.setuptools.package-data]
-spm = ["_spm/_spm.ctf"]
-
 [tool.setuptools.dynamic]
 version = {attr = "spm._version.__version__"}
 

spm/__compat/__init__.py

@@ -40,5 +40,5 @@
     "spm_read_hdr",
     "spm_resss",
     "spm_spm_ui",
-    "spm_tbx_config2cfg",
+    "spm_tbx_config2cfg"
 ]

spm/__compat/loadxml.py

@@ -1,31 +1,31 @@
-from mpython import Runtime
+from spm._runtime import Runtime
 
 
 def loadxml(*args, **kwargs):
     """
-     LOADXML Load workspace variables from disk (XML file).
-         LOADXML FILENAME retrieves all variables from a file given a full
-         pathname or a MATLABPATH relative partial pathname (see PARTIALPATH).
-         If FILENAME has no extension LOAD looks for FILENAME and FILENAME.xml
-         and treats it as an XML file.
-
-         LOAD, by itself, uses the XML file named 'matlab.xml'. It is an error
-         if 'matlab.xml' is not found.
-
-         LOAD FILENAME X loads only X.
-         LOAD FILENAME X Y Z ... loads just the specified variables.  The
-         wildcard '*' loads variables that match a pattern.
-         Requested variables from FILENAME are created in the workspace.
-
-         S = LOAD(...) returns the contents of FILENAME in variable S. S is
-         a struct containing fields matching the variables retrieved.
-
-         Use the functional form of LOAD, such as LOAD('filename'), when the
-         file name is stored in a string, when an output argument is requested,
-         or if FILENAME contains spaces.
-
-         See also LOAD, XML2MAT, XMLTREE.
-
+     LOADXML Load workspace variables from disk (XML file).  
+         LOADXML FILENAME retrieves all variables from a file given a full   
+         pathname or a MATLABPATH relative partial pathname (see PARTIALPATH).  
+         If FILENAME has no extension LOAD looks for FILENAME and FILENAME.xml   
+         and treats it as an XML file.   
+           
+         LOAD, by itself, uses the XML file named 'matlab.xml'. It is an error  
+         if 'matlab.xml' is not found.  
+         
+         LOAD FILENAME X loads only X.  
+         LOAD FILENAME X Y Z ... loads just the specified variables.  The  
+         wildcard '*' loads variables that match a pattern.  
+         Requested variables from FILENAME are created in the workspace.  
+         
+         S = LOAD(...) returns the contents of FILENAME in variable S. S is  
+         a struct containing fields matching the variables retrieved.  
+           
+         Use the functional form of LOAD, such as LOAD('filename'), when the  
+         file name is stored in a string, when an output argument is requested,  
+         or if FILENAME contains spaces.  
+         
+         See also LOAD, XML2MAT, XMLTREE.  
+      
 
     [Matlab code]( https://github.com/spm/spm/blob/main/compat/loadxml.m )
 

spm/__compat/savexml.py

@@ -1,27 +1,27 @@
-from mpython import Runtime
+from spm._runtime import Runtime
 
 
 def savexml(*args, **kwargs):
     """
-     SAVEXML Save workspace variables to disk in XML.
-         SAVEXML FILENAME saves all workspace variables to the XML-file
-         named FILENAME.xml. The data may be retrieved with LOADXML. if
-         FILENAME has no extension, .xml is assumed.
-
-         SAVE, by itself, creates the XML-file named 'matlab.xml'. It is
-         an error if 'matlab.xml' is not writable.
-
-         SAVE FILENAME X saves only X.
-         SAVE FILENAME X Y Z saves X, Y, and Z. The wildcard '*' can be
-         used to save only those variables that match a pattern.
-
-         SAVE ... -APPEND adds the variables to an existing file.
-
-         Use the functional form of SAVE, such as SAVE(filename','var1','var2'),
-         when the filename or variable names are stored in strings.
-
-         See also SAVE, MAT2XML, XMLTREE.
-
+     SAVEXML Save workspace variables to disk in XML.  
+         SAVEXML FILENAME saves all workspace variables to the XML-file  
+         named FILENAME.xml. The data may be retrieved with LOADXML. if  
+         FILENAME has no extension, .xml is assumed.  
+           
+         SAVE, by itself, creates the XML-file named 'matlab.xml'. It is  
+         an error if 'matlab.xml' is not writable.  
+         
+         SAVE FILENAME X saves only X.  
+         SAVE FILENAME X Y Z saves X, Y, and Z. The wildcard '*' can be   
+         used to save only those variables that match a pattern.  
+         
+         SAVE ... -APPEND adds the variables to an existing file.  
+         
+         Use the functional form of SAVE, such as SAVE(filename','var1','var2'),  
+         when the filename or variable names are stored in strings.  
+         
+         See also SAVE, MAT2XML, XMLTREE.  
+      
 
     [Matlab code]( https://github.com/spm/spm/blob/main/compat/savexml.m )
 

spm/__compat/spm_add.py

@@ -1,27 +1,27 @@
-from mpython import Runtime
+from spm._runtime import Runtime
 
 
 def spm_add(*args, **kwargs):
     """
-      Add a series of images - a compiled routine
-        FORMAT s = spm_add(VI,VO)
-        VI    - Vector of mapped volumes (from spm_map or spm_vol).
-        VO    - Description of output volume that gets passed to
-                spm_write_plane.m
-        flags - Flags can be:
-                      'm' - masks the mean to zero or NaN wherever
-                            a zero occurs in the input images.
-        s     - Scalefactor for output image.
-       __________________________________________________________________________
-
-        spm_add computes a sum of a set of image volumes to produce an
-        integral image that is written to a named file (VI.fname).
-
-        A mean can be effected by modifying the scalefactors (and offsets) of
-        VI (see spm_mean_ui for an example). A weighted sum can be effected by
-        using different weightings for image scalefactors.
-       __________________________________________________________________________
-
+      Add a series of images - a compiled routine  
+        FORMAT s = spm_add(VI,VO)  
+        VI    - Vector of mapped volumes (from spm_map or spm_vol).  
+        VO    - Description of output volume that gets passed to  
+                spm_write_plane.m  
+        flags - Flags can be:  
+                      'm' - masks the mean to zero or NaN wherever  
+                            a zero occurs in the input images.  
+        s     - Scalefactor for output image.  
+       __________________________________________________________________________  
+         
+        spm_add computes a sum of a set of image volumes to produce an  
+        integral image that is written to a named file (VI.fname).  
+         
+        A mean can be effected by modifying the scalefactors (and offsets) of  
+        VI (see spm_mean_ui for an example). A weighted sum can be effected by  
+        using different weightings for image scalefactors.  
+       __________________________________________________________________________  
+      
 
     [Matlab code]( https://github.com/spm/spm/blob/main/compat/spm_add.m )