update py versions in CI matrix (pysb#584)

* remove python 3.7 and add 3.11 in version matrix (fixes pysb#582)
* Fix one regex with a syntax that's invalid in 3.11 (flags must now come first)
* Switch test runner to to pynose, the maintained fork of nose
* Include simulator.templates in setup.py package list
* Enable python faulthandler for test runs to help diagnose errors in native code
* Update readthedocs config to define new build section (fixes pysb#585)
---------

Co-authored-by: Jeremy Muhlich <[email protected]>

.github/pysb-conda-env.yml

@@ -12,7 +12,6 @@ dependencies:
   - cython
   - matplotlib
   - networkx
-  - nose
   - h5py
   - pexpect
   - pandas
@@ -24,3 +23,4 @@ dependencies:
   - pip:
       - libroadrunner
       - python-libsbml
+      - pynose

.github/workflows/ci.yml

@@ -9,11 +9,7 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
-        exclude:
-          # Fails due to Atomizer linker/runtime issue
-          - os: windows-latest
-            python-version: 3.7
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
     defaults:
       run:
         shell: bash -l {0}
@@ -42,6 +38,8 @@ jobs:
       - name: Build PySB
         run: python setup.py build --build-lib=build/lib
       - name: Run nosetests
+        env:
+          PYTHONFAULTHANDLER: 1
         run: >
           nosetests
           build/lib/pysb

.readthedocs.yaml

@@ -2,6 +2,11 @@
 # Read the Docs configuration file
 # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
 
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.8"
+
 # Required
 version: 2
 
@@ -14,6 +19,5 @@ formats:
    - pdf
 
 python:
-   version: 3.8
    install:
    - requirements: doc/requirements.txt

pysb/export/__init__.py

@@ -187,6 +187,6 @@ def export(model, format, docstring=None):
 def pad(text, depth=0):
     "Dedent multi-line string and pad with spaces."
     text = textwrap.dedent(text)
-    text = re.sub(r'^(?m)', ' ' * depth, text)
+    text = re.sub(r'(?m)^', ' ' * depth, text)
     text += '\n'
     return text

setup.py

@@ -22,13 +22,13 @@ def main():
           url='http://pysb.org/',
           packages=['pysb', 'pysb.generator', 'pysb.importers', 'pysb.tools',
                     'pysb.examples', 'pysb.export', 'pysb.simulator',
-                    'pysb.testing', 'pysb.tests'],
+                    'pysb.simulator.templates', 'pysb.testing', 'pysb.tests'],
           scripts=['scripts/pysb_export'],
           # We should really specify some minimum versions here.
           python_requires='>=3.6',
           install_requires=['numpy', 'scipy>=1.1', 'sympy>=1.6,<1.12',
                             'networkx'],
-          setup_requires=['nose'],
+          setup_requires=['pynose'],
           tests_require=['coverage', 'pygraphviz', 'matplotlib', 'pexpect',
                          'pandas', 'h5py', 'mock', 'cython',
                          'python-libsbml', 'libroadrunner'],