Update docs and version bump

PCMSolver · Jan 20, 2018 · 1df8547 · 1df8547
1 parent d9ee934
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diff --git a/.githooks/license_maintainer.py b/.githooks/license_maintainer.py
@@ -52,7 +52,7 @@ def add_header(filepath, header, YEAR, AUTHORS):
                     output.append(inpt[0] + '\n')
                     inpt = inpt[1:]
                 regex = re.compile(r'Copyright \(C\).*\n')
-                repl  = r'Copyright (C) ' + YEAR + ' ' + AUTHORS + '\n'
+                repl = r'Copyright (C) ' + YEAR + ' ' + AUTHORS + '\n'
                 output.extend([re.sub(regex, repl, x) for x in inpt])
         else:
             print(('Adding header in {}'.format(filepath)))
@@ -82,7 +82,7 @@ def prepare_header(stub, YEAR, AUTHORS):
     with open(stub, 'r') as l:
         header = l.read()
         # Insert correct YEAR and AUTHORS in stub
-        rep = {'YEAR' : YEAR, 'AUTHORS' : AUTHORS}
+        rep = {'YEAR': YEAR, 'AUTHORS': AUTHORS}
         rep = dict((re.escape(k), v) for k, v in rep.items())
         pattern = re.compile("|".join(list(rep.keys())))
         header = pattern.sub(lambda m: rep[re.escape(m.group(0))], header)
@@ -105,24 +105,25 @@ def file_license(attributes):
         # Remove licensefile= from strings
         lic = [re.sub(r'licensefile\=', '', x) for x in gitattributes if 'licensefile' in x]
         # Create list of blacklisted files
-        blacklist = [fname for key, value in list(dict(list(zip(fil, lic))).items())
-                       if value == '!licensefile'
-                       for fname in glob.glob(key)]
+        blacklist = [
+            fname for key, value in list(dict(list(zip(fil, lic))).items())
+            if value == '!licensefile' for fname in glob.glob(key)
+        ]
         # Now create a dictionary with the files to be considered for
         # license header manipulation
-        file_license = {key: value
-                        for k, value in list(dict(list(zip(fil, lic))).items())
-                        for key in glob.glob(k)
-                        if key not in blacklist}
+        file_license = {
+            key: value
+            for k, value in list(dict(list(zip(fil, lic))).items()) for key in glob.glob(k) if key not in blacklist
+        }
     return file_license
 
 
 def license_maintainer():
     """
     Maintain license header in source files
     """
-    YEAR    = str(date.today().year)
-    AUTHORS = 'Roberto Di Remigio, Luca Frediani and collaborators.'
+    YEAR = str(date.today().year)
+    AUTHORS = 'Roberto Di Remigio, Luca Frediani and contributors.'
 
     script_dir = os.path.dirname(os.path.abspath(__file__))
     project_root_dir = os.path.abspath(os.path.join(script_dir, os.pardir))

diff --git a/AUTHORS.md b/AUTHORS.md
@@ -0,0 +1,14 @@
+## Individual Contributors
+
+- Roberto Di Remigio
+- Luca Frediani
+- Monica Bugeanu
+- Radovan Bast
+- T. Daniel Crawford
+- Arnfinn Hykkerud Steindal
+- Krzysztof Mozgawa
+- Lori A. Burns
+- Ville Weijo
+- Ward Poelmans
+
+This list was obtained 2018-01-20 by running `git shortlog -sn`
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,6 +1,6 @@
 # Change Log
 
-## [Unreleased]
+## [Version 1.1.12] - 2018-01-20
 
 ### Added
 
@@ -425,7 +425,8 @@
 
 ## v1.0.0 - 2014-09-30 [YANKED]
 
-[Unreleased]: https://github.com/PCMSolver/pcmsolver/compare/v1.1.11..HEAD
+[Unreleased]: https://github.com/PCMSolver/pcmsolver/compare/v1.1.12..HEAD
+[Version 1.1.11]: https://github.com/PCMSolver/pcmsolver/compare/v1.1.11...v1.1.12
 [Version 1.1.11]: https://github.com/PCMSolver/pcmsolver/compare/v1.1.10...v1.1.11
 [Version 1.1.10]: https://github.com/PCMSolver/pcmsolver/compare/v1.1.9...v1.1.10
 [Version 1.1.9]: https://github.com/PCMSolver/pcmsolver/compare/v1.1.8...v1.1.9

diff --git a/README.md b/README.md
@@ -7,25 +7,19 @@
 PCMSolver
 =========
 
-An API for the Polarizable Continuum Model.
+An API for the Polarizable Continuum Model. Copyright [Roberto Di Remigio](mailto:roberto.d.remigio@uit.no),
+[Luca Frediani](mailto:luca.frediani@uit.no) and [contributors](https://github.com/PCMSolver/pcmsolver/blob/release/1.Y/AUTHORS.md)
 
 - [Project website](https://github.com/PCMSolver/pcmsolver)
 - [Changelog](CHANGELOG.md)
 - [Documentation](http://pcmsolver.readthedocs.io)
 - [Build and test history](https://travis-ci.org/PCMSolver/pcmsolver/builds)
-- [Build dashboard](https://testboard.org/cdash/index.php?project=PCMSolver)
-- Version 1.1.11 available
+- Version 1.1.12 available
 - Licensed under [LGPLv3](LICENSE)
 - CMake infrastructure managed *via* [Autocmake](http://autocmake.readthedocs.io/)
 
-Primary test environments
-=========================
-
-All builds force custom build of the needed Boost libraries, except when
-stated otherwise.
-
 Continuous integration builds
------------------------------
+=============================
 
 All CI builds are triggered by push events to any branch.
 Travis CI runs release builds using [ccache](https://ccache.samba.org/) to speed up compilation.

diff --git a/api/PCMInput.h b/api/PCMInput.h
@@ -1,6 +1,6 @@
 /**
  * PCMSolver, an API for the Polarizable Continuum Model
- * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and collaborators.
+ * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and contributors.
  *
  * This file is part of PCMSolver.
  *

diff --git a/api/pcmsolver.f90 b/api/pcmsolver.f90
@@ -1,6 +1,6 @@
 !
 ! PCMSolver, an API for the Polarizable Continuum Model
-! Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and collaborators.
+! Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and contributors.
 !
 ! This file is part of PCMSolver.
 !

diff --git a/api/pcmsolver.h b/api/pcmsolver.h
@@ -1,6 +1,6 @@
 /**
  * PCMSolver, an API for the Polarizable Continuum Model
- * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and collaborators.
+ * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and contributors.
  *
  * This file is part of PCMSolver.
  *

diff --git a/default.nix b/default.nix
@@ -4,24 +4,20 @@ let
     owner = "NixOS";
     repo = "nixpkgs-channels";
     rev = "nixos-unstable";
-    sha256 = "0q47hjl01wylp6cdb52fyjbbx45djnz7bwfyj2mfv2lh04iph3s8";
+    sha256 = "15fcl29a97f68j1pjywmrjm31rdh1a21jz9airlsbzpl4lc3zhfi";
   });
 in
   with import nixpkgs {
     overlays = [(self: super:
-      # Within the overlay we use a recursive set, though I think we can use `self` as well.
-      rec {
-        # nix-shell -p python.pkgs.my_stuff
+      {
         python3 = super.python3.override {
-          # Careful, we're using a different self and super here!
           packageOverrides = py-self: py-super: {
             matplotlib = py-super.matplotlib.override {
               enableTk = true;
               enableQt = true;
             };
           };
         };
-        python3Packages = python3.pkgs;
       }
     )];
   };
@@ -39,22 +35,21 @@ in
       exa
       ffmpeg
       gfortran
+      gfortran.cc.lib
       graphviz
-      lldb
       pipenv
       python3Full
       python3Packages.docopt
       python3Packages.jupyter
       python3Packages.matplotlib
       python3Packages.numpy
       python3Packages.pyyaml
-      python3Packages.virtualenvwrapper
       valgrind
       zlib
     ];
     src = null;
     shellHook = ''
-      NINJA_STATUS="[Built edge %f of %t in %e sec]"
-      SOURCE_DATE_EPOCH=$(date +%s)
+    export NINJA_STATUS="[Built edge %f of %t in %e sec]"
+    SOURCE_DATE_EPOCH=$(date +%s)
     '';
   }
diff --git a/doc/conf.py b/doc/conf.py
@@ -2,9 +2,10 @@
 
 
 
+
 #
 #  PCMSolver, an API for the Polarizable Continuum Model
-#  Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and collaborators.
+#  Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and contributors.
 #
 #  This file is part of PCMSolver.
 #

diff --git a/doc/gfx/cloc_tools.py.in b/doc/gfx/cloc_tools.py.in
@@ -2,9 +2,10 @@
 
 
 
+
 #
 #  PCMSolver, an API for the Polarizable Continuum Model
-#  Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and collaborators.
+#  Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and contributors.
 #
 #  This file is part of PCMSolver.
 #

diff --git a/doc/index.rst b/doc/index.rst
@@ -20,8 +20,7 @@ With PCMSolver we aim to:
 2. create a playground for easily extending the implementation of the model.
 
 PCMSolver is distributed under the terms of the GNU Lesser General Public License.
-An archive with the currently released source can be found on `GitHub <https://github.com/PCMSolver/pcmsolver/releases>`_
-or on `zenodo <http://dx.doi.org/10.5281/zenodo.11910>`_.
+An archive with the currently released source can be found on `GitHub <https://github.com/PCMSolver/pcmsolver/releases>`_.
 
 .. literalinclude:: snippets/citation.bib
    :language: tex

diff --git a/doc/programmers/maintenance.rst b/doc/programmers/maintenance.rst
@@ -46,11 +46,28 @@ Danger.Systems Errors
 - Code style for ``.hpp``, ``.cpp``, ``.h`` files follows the conventions in
   ``.clang-format``.
 
-Bump Version
-------------
+Minting a new release
+---------------------
+
+1. Version numbering follows the guidelines of `semantic versioning <http://semver.org/>`_
+   To update, change the relevant field in the ``README.md`` file.
+2. Tidy up ``CHANGELOG.md``. This includes:
+   a. Making sure that the topmost header is the new version number, with the
+   correct release date.
+   b. Making sure that the links at the bottom of the document are correct.
+3. Run ``git shortlog -sn`` and check that the all authors are listed in
+   ``AUTHORS.md``.
+4. Update the version number in the citation snippet in
+   ``doc/snippets/citation.bib``.
+5. Commit your changes and push.
+6. If CI was happy, you can tag a new release. For example for ``v1.1.12``:
 
-Version numbering follows the guidelines of `semantic versioning <http://semver.org/>`_
-To update, change the relevant field in the ``README.md`` file.
+   .. code-block:: bash
+
+    git tag -a v1.1.12 -m "Version 1.1.12 released"
+7. Head over to GitHub and add a short release description in `web UI <https://github.com/PCMSolver/pcmsolver/releases>`_.
+8. As a final step, get the release DOI from `Zenodo <https://zenodo.org/>`_. File a pull request on
+   GitHub to update the Zenodo badge in ``README.md``.
 
 Changelog
 ---------

diff --git a/doc/snippets/citation.bib b/doc/snippets/citation.bib
@@ -1,6 +1,5 @@
 @misc{PCMSolver,
-  note = {\texttt{PCMSolver}, v1.1.10 an Application Programming Interface for the
-	Polarizable Continuum Model electrostatic problem, written by R.~Di~Remigio, L.~Frediani and K.~Mozgawa
-        with contributions from R.~Bast, J.~Juselius and V.~Weijo
-        (see http://pcmsolver.readthedocs.io/)"
+  note = {\texttt{PCMSolver}, v1.1.12 an Application Programming Interface for the
+  Polarizable Continuum Model electrostatic problem, written by R.~Di~Remigio,
+  L.~Frediani and contributors (see http://pcmsolver.readthedocs.io/)"
 }
diff --git a/include/Citation.hpp b/include/Citation.hpp
@@ -1,6 +1,6 @@
 /**
  * PCMSolver, an API for the Polarizable Continuum Model
- * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and collaborators.
+ * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and contributors.
  *
  * This file is part of PCMSolver.
  *

diff --git a/include/Config.hpp.in b/include/Config.hpp.in
@@ -1,6 +1,6 @@
 /**
  * PCMSolver, an API for the Polarizable Continuum Model
- * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and collaborators.
+ * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and contributors.
  *
  * This file is part of PCMSolver.
  *

diff --git a/include/Cxx11Workarounds.hpp b/include/Cxx11Workarounds.hpp
@@ -1,6 +1,6 @@
 /**
  * PCMSolver, an API for the Polarizable Continuum Model
- * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and collaborators.
+ * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and contributors.
  *
  * This file is part of PCMSolver.
  *

diff --git a/include/ErrorHandling.hpp b/include/ErrorHandling.hpp
@@ -1,6 +1,6 @@
 /**
  * PCMSolver, an API for the Polarizable Continuum Model
- * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and collaborators.
+ * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and contributors.
  *
  * This file is part of PCMSolver.
  *

diff --git a/include/LoggerInterface.hpp b/include/LoggerInterface.hpp
@@ -1,6 +1,6 @@
 /**
  * PCMSolver, an API for the Polarizable Continuum Model
- * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and collaborators.
+ * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and contributors.
  *
  * This file is part of PCMSolver.
  *

diff --git a/include/PhysicalConstants.hpp b/include/PhysicalConstants.hpp
@@ -1,6 +1,6 @@
 /**
  * PCMSolver, an API for the Polarizable Continuum Model
- * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and collaborators.
+ * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and contributors.
  *
  * This file is part of PCMSolver.
  *

diff --git a/include/TimerInterface.hpp b/include/TimerInterface.hpp
@@ -1,6 +1,6 @@
 /**
  * PCMSolver, an API for the Polarizable Continuum Model
- * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and collaborators.
+ * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and contributors.
  *
  * This file is part of PCMSolver.
  *

diff --git a/src/bi_operators/BIOperatorData.hpp b/src/bi_operators/BIOperatorData.hpp
@@ -1,6 +1,6 @@
 /*
  * PCMSolver, an API for the Polarizable Continuum Model
- * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and collaborators.
+ * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and contributors.
  *
  * This file is part of PCMSolver.
  *

diff --git a/src/bi_operators/BoundaryIntegralOperator.hpp b/src/bi_operators/BoundaryIntegralOperator.hpp
@@ -1,6 +1,6 @@
 /*
  * PCMSolver, an API for the Polarizable Continuum Model
- * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and collaborators.
+ * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and contributors.
  *
  * This file is part of PCMSolver.
  *

diff --git a/src/bi_operators/Collocation.cpp b/src/bi_operators/Collocation.cpp
@@ -1,6 +1,6 @@
 /*
  * PCMSolver, an API for the Polarizable Continuum Model
- * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and collaborators.
+ * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and contributors.
  *
  * This file is part of PCMSolver.
  *

diff --git a/src/bi_operators/Collocation.hpp b/src/bi_operators/Collocation.hpp
@@ -1,6 +1,6 @@
 /*
  * PCMSolver, an API for the Polarizable Continuum Model
- * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and collaborators.
+ * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and contributors.
  *
  * This file is part of PCMSolver.
  *

diff --git a/src/bi_operators/IBoundaryIntegralOperator.cpp b/src/bi_operators/IBoundaryIntegralOperator.cpp
@@ -1,6 +1,6 @@
 /*
  * PCMSolver, an API for the Polarizable Continuum Model
- * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and collaborators.
+ * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and contributors.
  *
  * This file is part of PCMSolver.
  *

diff --git a/src/bi_operators/IBoundaryIntegralOperator.hpp b/src/bi_operators/IBoundaryIntegralOperator.hpp
@@ -1,6 +1,6 @@
 /*
  * PCMSolver, an API for the Polarizable Continuum Model
- * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and collaborators.
+ * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and contributors.
  *
  * This file is part of PCMSolver.
  *

diff --git a/src/bi_operators/Numerical.cpp b/src/bi_operators/Numerical.cpp
@@ -1,6 +1,6 @@
 /*
  * PCMSolver, an API for the Polarizable Continuum Model
- * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and collaborators.
+ * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and contributors.
  *
  * This file is part of PCMSolver.
  *

diff --git a/src/bi_operators/Numerical.hpp b/src/bi_operators/Numerical.hpp
@@ -1,6 +1,6 @@
 /*
  * PCMSolver, an API for the Polarizable Continuum Model
- * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and collaborators.
+ * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and contributors.
  *
  * This file is part of PCMSolver.
  *

diff --git a/src/bi_operators/Purisima.cpp b/src/bi_operators/Purisima.cpp
@@ -1,6 +1,6 @@
 /*
  * PCMSolver, an API for the Polarizable Continuum Model
- * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and collaborators.
+ * Copyright (C) 2018 Roberto Di Remigio, Luca Frediani and contributors.
  *
  * This file is part of PCMSolver.
  *