Merge pull request #98 from PySCeS/development

Bugfix Release 1.2.1

.zenodo.json

@@ -3,9 +3,9 @@
 	"license": "BSD-3-Clause",
 	"title": "The Python Simulator for Cellular Systems: PySCeS",
 	"notes": "If you use this software, please cite it using the information provided in this metadata.",
-	"version": "1.2.0",
+	"version": "1.2.1",
 	"upload_type": "software",
-	"publication_date": "2024-02-14",
+	"publication_date": "2024-05-10",
 	"creators": [{
 			"orcid": "0000-0002-5293-5321",
 			"affiliation": "Vrije Universiteit Amsterdam",

CITATION.cff

@@ -1,6 +1,6 @@
 # YAML 1.2
 ---
-cff-version: "1.2.0"
+cff-version: "1.2.1"
 message: "If you use this software, please cite it using the information provided in this metadata."
 authors:
   -
@@ -14,9 +14,9 @@ authors:
     affiliation: "Stellenbosch University"
     orcid: "https://orcid.org/0000-0001-6288-8904"
 title: "The Python Simulator for Cellular Systems: PySCeS"
-version: "1.2.0"
-repository-code: "https://github.com/PySCeS/pysces/tree/1.2.0"
-date-released: 2024-02-14
+version: "1.2.1"
+repository-code: "https://github.com/PySCeS/pysces/tree/1.2.1"
+date-released: 2024-05-10
 doi: "10.5281/zenodo.2600905"
 license: "BSD-3-Clause"
 url: https://pysces.github.io

INSTALL.md

@@ -2,20 +2,24 @@
 
 Binary install packages for all three OSs and recent Python versions are 
 provided. Anaconda packages are available for 64-bit Windows and Linux, as well as 
-macOS *x86_64* architecture. Apple Silicon (*arm64*) macOS users should install with 
-`pip` (see below). Anaconda users can conveniently install PySCeS with:
+macOS *x86_64* and Apple Silicon (*arm64*) architectures. Anaconda users can 
+conveniently install PySCeS with:
 
 ```bash
 $ conda install -c conda-forge -c pysces pysces
 ```  
 
 Any dependencies will be installed automatically, including the optional dependencies 
-*Assimulo*, *ipyparallel* and *libSBML*. 
+*Assimulo*, *ipyparallel* and *libSBML*.
+> **NOTE:** Anaconda packages are only provided for Python versions 3.9-3.11. The 
+> reason is that Assimulo has not been ported to Python 3.12 and still depends on 
+> `numpy.distutils`. As soon as this has happened, PySCeS Anaconda packages for 3.12 
+> will be built.
 
 Alternatively, you can use *pip* to
-install PySCeS from PyPI. Core dependencies will be installed automatically. Wheels 
-are available for 64-bit Windows and Linux, as well as macOS architectures *x86_64* and 
-*arm64* (starting from PySCeS version 1.2.0).
+install PySCeS from PyPI. Core dependencies will be installed automatically. Wheels
+are available for 64-bit Windows and Linux, as well as macOS architectures *x86_64* and
+*arm64* (starting from PySCeS version 1.2.0, supporting Python 3.11 and 3.12).
 
 ```bash
 $ pip install pysces

pysces/PyscesModel.py

@@ -33,6 +33,7 @@
 
             '''
 import os, copy, time
+import re
 import pickle
 import warnings
 try:
@@ -4814,14 +4815,21 @@ def _update_assignment_rule_code(self, rule):
                 or s in self.__rules__
                 or s in self.__species__
             ):
-                # catch any _init so it doesn't get replaced
-                replacements.append((s + '_init', '_zzzz_'))
+                # deal with substrings in symbols
+                partialmatches = []
+                for sym in rule['symbols']:
+                    if not re.fullmatch(s, sym) and re.search(s, sym):
+                        partialmatches.append(sym)
+                # catch any partial matches so they don't get replaced
+                for e in enumerate(partialmatches):
+                    replacements.append((e[1], f'_zzzz_{e[0]}_z'))
                 # replace symbol to get sim data
                 replacements.append(
-                    ('self.' + s, 'self.data_sim.getSimData("' + s + '")[p:q,1]')
+                    (f'self.{s}', f'self.data_sim.getSimData("{s}")[p:q,1]')
                 )
-                # revert the _init
-                replacements.append(('_zzzz_', s + '_init'))
+                # revert the partial match symbol
+                for e in enumerate(partialmatches):
+                    replacements.append((f'_zzzz_{e[0]}_z', e[1]))
 
         for old, new in replacements:
             rule['data_sim_string'] = rule['data_sim_string'].replace(old, new)

pysces/PyscesStoich.py

@@ -753,19 +753,12 @@ def PLUfactorize(self, a_in):
         ##  except Exception, e:
         ##  print "CLAPACK error", e
 
-        if a.shape[0] >= 500 or a.shape[1] >= 500:
-            print('\nMatrix {} using SciPy version: {} on {}'.format(a.shape, scipy.__version__, os.sys.platform))
-            print('Error 766 error detector: only report this if your Python crashes now ...')
-
         if Using_FLAPACK == 1:
             ##  results = getrf(numpy.transpose(a)) # brett 20041226
             results = getrf(a)  # brett 201106
 
         results = list(results)
 
-        if a.shape[0] >= 500 or a.shape[1] >= 500:
-            print('766 error did not occur please continue as normal {} ...'.format(a.shape))
-
         if results[2] < 0:
             print('Argument ', results['info'], ' had an illegal value')
             raise LinAlgError

pysces/version.txt

@@ -1 +1 @@
-1.2.0
+1.2.1