Merge pull request #73 from PySCeS/development

Bug fix release

Author: jmrohwer

.github/workflows/cibuildwheel.yml

@@ -35,6 +35,12 @@ jobs:
           sudo hdiutil attach /tmp/gfortran.dmg &&
           sudo installer -pkg /Volumes/gfortran-10.2-Catalina/gfortran.pkg -target /
 
+      - name: Build wheels for CPython 3.10
+        uses: pypa/[email protected]
+        env:
+          CIBW_BUILD: "cp310-*"
+          CIBW_BEFORE_BUILD: pip install numpy~=1.21.0
+
       - name: Build wheels for CPython 3.9
         uses: pypa/[email protected]
         env:

MANIFEST.in

@@ -1,5 +1,6 @@
 include *.md
 include LICENCE.txt
+include requirements.txt
 include setupegg.py
 include pysces/*
 include pysces/contrib/*
@@ -18,6 +19,7 @@ include pysces/pitcon/*
 include pysces/pscmodels/*
 include pysces/tests/*
 include pysces/pysces.pth
+include pysces/version.txt
 include pysces/win32/libgfortran-3.dll
 include pysces/win32/libquadmath-0.dll
 include pysces/win32/libgcc_s_seh-1.dll

packaging/conda/conda_build_config.yaml

@@ -2,10 +2,12 @@ python:
   - 3.7
   - 3.8
   - 3.9
+  - 3.10
 numpy:
   - 1.16
   - 1.17
   - 1.20
+  - 1.21
 zip_keys:
   - python
   - numpy

packaging/conda/meta.yaml

@@ -1,6 +1,6 @@
 package:
   name: pysces
-  version: "1.0.0"
+  version: "1.0.1"
 
 source:
   # git_url: https://github.com/PySCeS/pysces.git

pysces/PyscesJWSParse.py

@@ -32,7 +32,7 @@
 from .lib import yacc
 from getpass import getuser
 from time import sleep, strftime
-from scipy import MachAr
+from numpy import MachAr
 
 MyMachArr = MachAr()
 

pysces/PyscesModel.py

@@ -4383,6 +4383,7 @@ def function_sim(s, t):
         go = True
 
         status = 0
+        lsoda_mxstep_bak = self.__settings__["lsoda_mxstep"]
         while go:
             sim_res, infodict = scipy.integrate.odeint(
                 function_sim,
@@ -4431,7 +4432,7 @@ def function_sim(s, t):
                 go = False
             else:
                 go = False
-        self.__settings__["lsoda_mxstep"] = 0
+        self.__settings__["lsoda_mxstep"] = lsoda_mxstep_bak
 
         rates = numpy.zeros((sim_res.shape[0], len(self.__reactions__)))
         if status == 0:
@@ -4999,6 +5000,7 @@ def Simulate(self, userinit=0):
             if self.sim_time[0] != 0:
                 self._sim_time_bak = copy.copy(self.sim_time)
                 self.sim_time = [0.0] + list(self._sim_time_bak)
+            self.sim_end = self.sim_time[-1]
 
         # initialises self.__inspec__[x] with self.sXi
         if userinit == 1:

pysces/PyscesStoich.py

@@ -435,7 +435,7 @@ def __init__(self, input):
         self.nmatrix_row = tuple(numpy.array(list(range(row))))
 
         # Create a machine specific instance
-        from scipy import MachAr
+        from numpy import MachAr
 
         mach_spec = MachAr()
 

pysces/core2/version.py

@@ -1,15 +1 @@
-MAJOR = 1
-MINOR = 0
-MICRO = 0
-STATUS = ''
-
-
-def current_version():
-    return '%s.%s.%s%s' % (MAJOR, MINOR, MICRO, STATUS)
-
-
-def current_version_tuple():
-    return (MAJOR, MINOR, MICRO)
-
-
-__version__ = current_version()
+from pysces.version import __version__

pysces/version.py

@@ -1,15 +1,20 @@
-MAJOR = 1
-MINOR = 0
-MICRO = 0
-STATUS = ''
+import re
+import os
 
+cwd = os.path.dirname(__file__)
+
+with open(os.path.join(cwd, 'version.txt'), 'r') as f:
+    v = f.read().strip().split('.')
+
+MAJOR = int(v[0])
+MINOR = int(v[1])
+MICRO = int(re.split('(\d+)', v[2])[1])
+STATUS = re.split('(\d+)', v[2])[2]
 
 def current_version():
     return '%s.%s.%s%s' % (MAJOR, MINOR, MICRO, STATUS)
 
-
 def current_version_tuple():
     return (MAJOR, MINOR, MICRO)
 
-
 __version__ = current_version()

pysces/version.txt

@@ -0,0 +1 @@
+1.0.1