[!14] Resolve "Include Semantic Versioning"

Merge branch '10-include-semantic-versioning' into 'master'

ref:copasi/dune-copasi Closes [#10]

See merge request [!14]

  [#10]: gitlab.dune-project.org/NoneNone/issues/10
  [!14]: gitlab.dune-project.org/copasi/dune-copasi/merge_requests/14


Closes #10

CHANGELOG.md

+# Changelog
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+<!-- 
+Guiding Principles
+
+    Changelogs are for humans, not machines.
+    There should be an entry for every single version.
+    The same types of changes should be grouped.
+    Versions and sections should be linkable.
+    The latest version comes first.
+    The release date of each version is displayed.
+    Mention whether you follow Semantic Versioning.
+
+Types of changes
+
+    Added         for new features.
+    Changed       for changes in existing functionality.
+    Deprecated    for soon-to-be removed features.
+    Removed       for now removed features.
+    Fixed         for any bug fixes.
+    Security      in case of vulnerabilities.
+ -->
+
+## [Unreleased]
+
+## [0.1.0] - 2019-10-11
+### Added
+- [Semantic Versioning](https://semver.org/spec/v2.0.0.html)
+- Solver for reaction-diffusion systems in multiple compartments.
+
+[Unreleased]: https://gitlab.dune-project.org/copasi/dune-copasi/compare/v0.1.0...master
+[0.1.0]: https://gitlab.dune-project.org/copasi/dune-copasi/-/tags/v0.1.0
\ No newline at end of file

VERSION

+0.1.0
\ No newline at end of file

dune.module

@@ -4,7 +4,7 @@
 
 #Name of the module
 Module: dune-copasi
-Version: 0.0.0
+Version: 0.1.0
 Maintainer: santiago.ospina@iwr.uni-heidelberg.de
 #depending on
 Depends: dune-logging dune-uggrid (>= 2.6) dune-pdelab (>= 2.6) dune-multidomaingrid (>= 2.6)

python/setup.py

@@ -7,7 +7,7 @@ def dune_copasi_scripts():
     return ['./wrapper/profile_intel.py']
 
 setup(name='dune.copasi',
-  version='0.0.0',
+  version='0.1.0',
   namespace_packages=['dune'],
   description='DUNE Biochemical System Simulator for COPASI',
   author='Santiago Ospina De Los Ríos',

util/bump_version.py

+#!/bin/python2
+
+# This script updates version of the code in all places where it has to be hard coded
+# and it updates the changelog
+
+import sys
+import os
+import re
+import datetime
+
+# Regex to match and check version (taken from https://semver.org/spec/v2.0.0.html)
+default_regex = r'^(?P<major>0|[1-9]\d*)\.(?P<minor>0|[1-9]\d*)\.(?P<patch>0|[1-9]\d*)(?:-(?P<prerelease>(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\.(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\+(?P<buildmetadata>[0-9a-zA-Z-]+(?:\.[0-9a-zA-Z-]+)*))?$'
+
+def check_version_format(version):
+  if not re.match(default_regex,version):
+    raise ValueError("\"" + version + "\" is not a valid version")
+
+def get_version(path):
+  with open(path, "r") as version_file:
+    version = version_file.readline()
+    version_file.close()
+    check_version_format(version)
+  return version
+
+def update_version(path, old_version, new_version):
+  with open(path, "r") as version_file:
+    content = version_file.read()
+  with open(path, "w") as version_file:
+    version_file.write(re.sub(old_version, new_version, content))
+  return 0
+
+def main(argv):
+
+  base_path = os.path.dirname(os.path.realpath(__file__))
+  version_path = os.path.join(base_path,'../VERSION')
+  python_version_path = os.path.join(base_path,'../python/setup.py')
+  dune_version_path = os.path.join(base_path,'../dune.module')
+  changelog_path = os.path.join(base_path,'../CHANGELOG.md')
+
+  old_version = get_version(version_path)
+  print "Old version is:", old_version
+
+  if len(argv) is 0:
+    new_version = raw_input("New version: ")
+  elif len(argv) is 1:
+    new_version = argv[0]
+  else:
+    raise IOError("Too many arguments!")
+  
+  check_version_format(new_version)
+
+  # update basic version file
+  update_version(version_path,old_version,new_version)
+
+  # update python version file
+  prefix = 'version=\''
+  update_version(python_version_path,prefix+old_version,prefix+new_version)
+
+  # update dune version file
+  prefix = 'Version: '
+  update_version(dune_version_path,prefix+old_version,prefix+new_version)
+
+  project_url = "https://gitlab.dune-project.org/copasi/dune-copasi"
+
+  with open(changelog_path, "r") as changelog_file:
+    new_changelog = ''
+    for line in changelog_file.readlines():
+      if "## [Unreleased]" in line:
+        new_changelog += line +"\n"
+        new_changelog += "## [" + new_version+ "] - " + datetime.date.today().isoformat() + "\n"
+      elif "[Unreleased]: " + project_url in line:
+        new_changelog += "[Unreleased]: " + project_url+"/compare/v"+new_version+"...master\n"
+      elif "["+old_version+"]: " + project_url in line:
+        new_changelog += "["+new_version+"]: "+project_url+"/compare/v"+old_version+"..."+new_version+"\n"
+        new_changelog += line
+      else:
+        new_changelog += line
+
+  with open(changelog_path, "w") as changelog_file:
+    changelog_file.write(new_changelog)
+
+  print "New version is:", new_version
+
+  print "Changelog was updated, check that the update is correct"
+
+  print "If this is a definitive change, please set a new tag in the repository\n"
+  print "\tgit tag v"+new_version+"\n"
+
+if __name__ == "__main__":
+   main(sys.argv[1:])