Bump version

.ci/setup.sh

@@ -40,7 +40,7 @@ do
 done
 for repo in dune-logging dune-typetree dune-pdelab dune-multidomaingrid
 do
-  git clone -b support/dune-copasi --depth 1 --recursive https://gitlab.dune-project.org/copasi/$repo.git
+  git clone -b support/dune-copasi-v0.3 --depth 1 --recursive https://gitlab.dune-project.org/copasi/$repo.git
 done
 
 # python virtual environment does not work in windows yet

CHANGELOG.md

@@ -30,30 +30,32 @@ Types of changes
     Security      in case of vulnerabilities.
  -->
 
-## [Unreleased]
+## [Unreleased] ([git-diff][Unreleased-diff])
+
+## [0.3.0] ([git-diff][0.3.0-diff]) - 2020-10-07
 ### Added
-- User documentation !28
-- Scape VTK write by omitting `[writer]` section !24
-- Added Explicit and Diagonally Runge-Kutta time solvers !25
-- 3D simulations are now possible !27
+- User documentation [!28]
+- Scape VTK write by omitting `[writer]` section [!24]
+- Added Explicit and Diagonally Runge-Kutta time solvers [!25]
+- 3D simulations are now possible [!27]
 ### Changed
-- Improved errors when a config file is incorrect !25
-- Update meaningful logging values on the test ini file !25
-- Clean up logger output !25
-- Time stepping is now done outside the model class !25
-- Writer might write on different files on request !25
-- Move read/write responsibility to model state !25
-- States are now independent from models !25
-- Output files changed its name scheme !25
-- Configuration file changed its structure (see git diff on tests) !25
+- Improved errors when a config file is incorrect [!25]
+- Update meaningful logging values on the test ini file [!25]
+- Clean up logger output [!25]
+- Time stepping is now done outside the model class [!25]
+- Writer might write on different files on request [!25]
+- Move read/write responsibility to model state [!25]
+- States are now independent from models [!25]
+- Output files changed its name scheme [!25]
+- Configuration file changed its structure (see git diff on tests) [!25]
 ### Removed
-- Coefficient mapper and its use on local operators !25
-- Remove the operator map of objects within the model class !25
+- Coefficient mapper and its use on local operators [!25]
+- Remove the operator map of objects within the model class [!25]
 ### Fixed
-- Violation of the One-Definition-Rule due to external linkage of `LocalOperatorApply` lambdas !23
-- Error on the gaussian equation used on comparisons !23
+- Violation of the One-Definition-Rule due to external linkage of `LocalOperatorApply` lambdas [!23]
+- Error on the gaussian equation used on comparisons [!23]
 
-## [0.2.0] - 2020-02-20
+## [0.2.0] ([git-diff][0.2.0-diff]) - 2020-02-20
 ### Added
 - Code documentation
 - Data Context concept for factories
@@ -81,6 +83,16 @@ Types of changes
 - [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/v0.2.0...master
-[0.2.0]: https://gitlab.dune-project.org/copasi/dune-copasi/compare/v0.1.0...v0.2.0
-[0.1.0]: https://gitlab.dune-project.org/copasi/dune-copasi/-/tags/v0.1.0
+[Unreleased-diff]: https://gitlab.dune-project.org/copasi/dune-copasi/compare/v0.3.0...master
+[0.3.0-diff]: https://gitlab.dune-project.org/copasi/dune-copasi/compare/v0.2.0...v0.3.0
+[0.2.0-diff]: https://gitlab.dune-project.org/copasi/dune-copasi/compare/v0.1.0...v0.2.0
+
+[0.3.0]: https://gitlab.dune-project.org/copasi/dune-copasi/-/releases/v0.3.0
+[0.2.0]: https://gitlab.dune-project.org/copasi/dune-copasi/-/releases/v0.2.0
+[0.1.0]: https://gitlab.dune-project.org/copasi/dune-copasi/-/releases/v0.1.0
+
+[!28]: https://gitlab.dune-project.org/copasi/dune-copasi/-/merge_requests/28
+[!27]: https://gitlab.dune-project.org/copasi/dune-copasi/-/merge_requests/27
+[!25]: https://gitlab.dune-project.org/copasi/dune-copasi/-/merge_requests/25
+[!24]: https://gitlab.dune-project.org/copasi/dune-copasi/-/merge_requests/24
+[!23]: https://gitlab.dune-project.org/copasi/dune-copasi/-/merge_requests/23

VERSION

-0.2.0
\ No newline at end of file
+0.3.0

doc/docusaurus/docs/install_use.md

@@ -67,10 +67,10 @@ on the [DUNE GitLab](https://gitlab.dune-project.org/).
 | [dune-istl](https://gitlab.dune-project.org/core/dune-istl)                                 | == 2.7 |
 | [dune-localfunctions](https://gitlab.dune-project.org/core/dune-localfunctions)             | == 2.7 |
 | [dune-functions](https://gitlab.dune-project.org/staging/dune-functions)                    | == 2.7 |
-| [COPASI/dune-logging](https://gitlab.dune-project.org/copasi/dune-logging)                  | support/dune-copasi |
-| [COPASI/dune-typetree](https://gitlab.dune-project.org/copasi/dune-typetree)                | support/dune-copasi |
-| [COPASI/dune-pdelab](https://gitlab.dune-project.org/copasi/dune-pdelab)                    | support/dune-copasi |
-| [COPASI/dune-multidomaingrid](https://gitlab.dune-project.org/copasi/dune-multidomaingrid)  | support/dune-copasi |
+| [COPASI/dune-logging](https://gitlab.dune-project.org/copasi/dune-logging)                  | support/dune-copasi-latest |
+| [COPASI/dune-typetree](https://gitlab.dune-project.org/copasi/dune-typetree)                | support/dune-copasi-latest |
+| [COPASI/dune-pdelab](https://gitlab.dune-project.org/copasi/dune-pdelab)                    | support/dune-copasi-latest |
+| [COPASI/dune-multidomaingrid](https://gitlab.dune-project.org/copasi/dune-multidomaingrid)  | support/dune-copasi-latest |
 
 ### Installation
 
@@ -120,11 +120,11 @@ git clone -b releases/2.7 https://gitlab.dune-project.org/staging/dune-uggrid
 git clone -b releases/2.7 https://gitlab.dune-project.org/core/dune-istl
 git clone -b releases/2.7 https://gitlab.dune-project.org/core/dune-localfunctions
 git clone -b releases/2.7 https://gitlab.dune-project.org/staging/dune-functions
-git clone -b support/dune-copasi --recursive https://gitlab.dune-project.org/copasi/dune-logging
-git clone -b support/dune-copasi https://gitlab.dune-project.org/copasi/dune-typetree
-git clone -b support/dune-copasi https://gitlab.dune-project.org/copasi/dune-pdelab
-git clone -b support/dune-copasi https://gitlab.dune-project.org/copasi/dune-multidomaingrid
-git clone -b v0.2.0 https://gitlab.dune-project.org/copasi/dune-copasi
+git clone -b support/dune-copasi-latest --recursive https://gitlab.dune-project.org/copasi/dune-logging
+git clone -b support/dune-copasi-latest https://gitlab.dune-project.org/copasi/dune-typetree
+git clone -b support/dune-copasi-latest https://gitlab.dune-project.org/copasi/dune-pdelab
+git clone -b support/dune-copasi-latest https://gitlab.dune-project.org/copasi/dune-multidomaingrid
+git clone -b latest https://gitlab.dune-project.org/copasi/dune-copasi
 ```
 
 Then build and install the `DUNE` modules with the `dunecontrol` script:

docker/dependencies.dockerfile

@@ -14,8 +14,8 @@ RUN duneci-install-module -b releases/2.7 https://gitlab.dune-project.org/core/d
     && duneci-install-module -b releases/2.7 https://gitlab.dune-project.org/core/dune-istl.git \
     && duneci-install-module -b releases/2.7 https://gitlab.dune-project.org/core/dune-localfunctions.git \
     && duneci-install-module -b releases/2.7 https://gitlab.dune-project.org/quality/dune-testtools.git \
-    && duneci-install-module -b support/dune-copasi https://gitlab.dune-project.org/copasi/dune-typetree.git \
+    && duneci-install-module -b support/dune-copasi-v0.3 https://gitlab.dune-project.org/copasi/dune-typetree.git \
     && duneci-install-module -b releases/2.7 https://gitlab.dune-project.org/staging/dune-functions.git \
-    && duneci-install-module -b support/dune-copasi --recursive https://gitlab.dune-project.org/copasi/dune-logging.git \
-    && duneci-install-module -b support/dune-copasi https://gitlab.dune-project.org/copasi/dune-pdelab.git \
-    && duneci-install-module -b support/dune-copasi https://gitlab.dune-project.org/copasi/dune-multidomaingrid.git
+    && duneci-install-module -b support/dune-copasi-v0.3 --recursive https://gitlab.dune-project.org/copasi/dune-logging.git \
+    && duneci-install-module -b support/dune-copasi-v0.3 https://gitlab.dune-project.org/copasi/dune-pdelab.git \
+    && duneci-install-module -b support/dune-copasi-v0.3 https://gitlab.dune-project.org/copasi/dune-multidomaingrid.git

dune.module

@@ -4,8 +4,8 @@
 
 #Name of the module
 Module: dune-copasi
-Version: 0.2.0
+Version: 0.3.0
 Maintainer: santiago.ospina@iwr.uni-heidelberg.de
 #depending on
 Depends: dune-logging dune-uggrid (>= 2.6) dune-pdelab (>= 2.6) dune-multidomaingrid (>= 2.6)
-Suggests: dune-testtools
\ No newline at end of file
+Suggests: dune-testtools

python/setup.py

@@ -7,7 +7,7 @@ def dune_copasi_scripts():
     return ['./wrapper/profile_intel.py']
 
 setup(name='dune.copasi',
-  version='0.2.0',
+  version='0.3.0',
   namespace_packages=['dune'],
   description='DUNE Biochemical System Simulator for COPASI',
   author='Santiago Ospina De Los Ríos',

util/bump_version.py

@@ -17,7 +17,7 @@ def check_version_format(version):
 
 def get_version(path):
   with open(path, "r") as version_file:
-    version = version_file.readline()
+    version = version_file.readline().rstrip("\n")
     version_file.close()
     check_version_format(version)
   return version
@@ -46,7 +46,7 @@ def main(argv):
     new_version = argv[0]
   else:
     raise IOError("Too many arguments!")
-  
+
   check_version_format(new_version)
 
   # update basic version file
@@ -67,11 +67,12 @@ def main(argv):
     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 += "## [" + new_version+ "] ([git-diff][" + new_version + "-diff]) - " + datetime.date.today().isoformat() + "\n"
+      elif "[Unreleased-diff]: " + project_url in line:
+        new_changelog += "[Unreleased-diff]: " + project_url+"/compare/v"+new_version+"...master\n"
+        new_changelog += "["+new_version+"-diff]: "+project_url+"/compare/v"+old_version+"...v"+new_version+"\n"
+      elif "["+old_version+"]: "+project_url in line:
+        new_changelog += "["+new_version+"]: "+project_url+"/-/releases/v"+new_version+"\n"
         new_changelog += line
       else:
         new_changelog += line
@@ -83,8 +84,10 @@ def main(argv):
 
   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")
+  print("If this is a definitive change, please update documentation and set a new tag in the repository\n")
+  print("\tgit tag -s v"+new_version+"\n")
+  print("\nAlso remember to forward the branch latest to the lastest tag\n")
+  print("\tgit checkout latest && git merge --ff-only v"+new_version+"\n")
 
 if __name__ == "__main__":
    main(sys.argv[1:])