Merge pull request #1368 from KrisThielemans/clangformat

update and run clang-format

.clang-format

@@ -25,12 +25,15 @@ BraceWrapping:
   SplitEmptyFunction: false
   SplitEmptyRecord: true
   SplitEmptyNamespace: true
+BinPackParameters: false
+BinPackArguments: false
 ColumnLimit:     130
 IndentPPDirectives: AfterHash
 PointerAlignment: Left
 SortIncludes:    false
 SortUsingDeclarations: false
 SpaceBeforeParens: ControlStatements
 PackConstructorInitializers: Never
+AllowShortFunctionsOnASingleLine: InlineOnly
 Standard:        Cpp11
 ...

.pre-commit-config.yaml

@@ -1,5 +1,5 @@
 repos:
--   repo: git://github.com/doublify/pre-commit-clang-format
+-   repo: https://github.com/doublify/pre-commit-clang-format
     rev: '62302476'
     hooks:
     -   id: clang-format

CONTRIBUTING.md

@@ -29,23 +29,25 @@ This is our recommended process. If it sounds too daunting, ask for help.
 3. Create a branch in your fork with a descriptive name and put your fixes there. If your fix is
 simple you could do it on github by editing a file, otherwise clone your project (or add a remote
 to your current git clone) and work as usual.
-4. If your change is important, add it to the release notesfor the upcoming version, [see](https://github.com/UCL/STIR/blob/master/documentation/)
+4. Configure your editor and potentially even [pre-commit](https://pre-commit.com/), see
+[documentation/devel/README.md](documentation/devel/README.md).
+5. If your change is important, add it to the release notes for the upcoming version in the [documentation folder](https://github.com/UCL/STIR/tree/master/documentation/)
 and even the [User's Guide](https://github.com/UCL/STIR/blob/master/documentation/STIR-UsersGuide.tex) or other documentation files.
-5. Use [well-formed commit messages](http://tbaggery.com/2008/04/19/a-note-about-git-commit-messages.html)
+6. Use [well-formed commit messages](http://tbaggery.com/2008/04/19/a-note-about-git-commit-messages.html)
 for each change (in particular with a single "subject" line
-followed by an empty line and then more details). If the change affects comments only, it is recommended to put `[ci skip]` in your subject line. This avoids unnecessary computation, and clogging our Travis/Appveyor queues.
-6. Push the commits to your fork and submit a [pull request (PR)](https://help.github.com/articles/creating-a-pull-request)
-(enable changes by project admins.) Give your pull request a descriptive name (i.e. don't call if *Fix #issuenumber*. Be prepared to add further commits to your branch after discussion.
-In the description of the PR, add a statement about which Issue this applies to
-using [a phrase such that github auto-closes the issue when merged to master](https://help.github.com/articles/closing-issues-using-keywords/).
-7. Be prepared to add further commits to your branch after discussion.
+followed by an empty line and then more details).
 Please by mindful about the resources used by our Continuous Integration (CI) workflows:
   - Group your commits and only push once your code compiles and tests succeed on your machine (ideally you have sensible commit messages at every stage)
   - Use specific keywords in the first line of the last commit that you push to prevent CI being run:
      - `[ci skip]` skips all CI runs (e.g. when you only change documentation, or when your update isn't ready yet)
      - `[actions skip]` does not run GitHub Actions, see [here](https://github.blog/changelog/2021-02-08-github-actions-skip-pull-request-and-push-workflows-with-skip-ci/). Note: this can be in the main commit message.
      - `[skip appveyor]` does not run Appveyor, see [here](https://www.appveyor.com/docs/how-to/filtering-commits/#skip-directive-in-commit-message)
-8. After acceptance of your PR, go home with a nice warm feeling.
+7. Push the commits to your fork and submit a [pull request (PR)](https://help.github.com/articles/creating-a-pull-request)
+(enable changes by project admins.) Give your pull request a descriptive name (i.e. don't call if *Fix #issuenumber*. Be prepared to add further commits to your branch after discussion.
+In the description of the PR, add a statement about which Issue this applies to
+using [a phrase such that github auto-closes the issue when merged to master](https://help.github.com/articles/closing-issues-using-keywords/).
+8. Be prepared to add further commits to your branch after discussion.
+9. After acceptance of your PR, go home with a nice warm feeling.
 
 Suggested reading: 
 https://help.github.com/articles/fork-a-repo/, https://git-scm.com/book/en/v2/GitHub-Contributing-to-a-Project or https://guides.github.com/activities/forking/.

documentation/STIR-developers-overview.tex

@@ -1331,7 +1331,10 @@ \section{
 
 \section{Contributing to STIR}
 See
-\R2Lurl{https://github.com/UCL/STIR/blob/master/CONTRIBUTING.md}{STIR/CONTRIBUTING.md}.
+\R2Lurl{https://github.com/UCL/STIR/blob/master/CONTRIBUTING.md}{STIR/CONTRIBUTING.md}
+and
+\R2Lurl{https://github.com/UCL/STIR/blob/master/documentation/devel/README.md}{documentation/devel/README.md}
+for more information on editor settings etc.
 
 \subsection{Continuous integration testing}
 We use GitHub Actions and Appveyor for testing of every pull-request that was submitted on GitHub. PRs

documentation/release_6.0.htm

@@ -9,7 +9,7 @@ <h1>Summary of changes in STIR release 6.0</h1>
 
     <p>This version is 99% backwards compatible with STIR 5.x for the user (see below).
       Developers might need to make code changes as 
-      detailed below. Note though that the location of installed files have changed.
+      detailed below. Note though that the <strong>locations of installed files have changed</strong>.
       Developers of other software that uses STIR via CMake will need to adapt (see below).
     </p>
     <h2>Overall summary</h2>
@@ -285,6 +285,18 @@ <h2>New deprecations for future versions</h2>
     <H2>What's new for developers (aside from what should be obvious
       from the above):</H2>
 
+    <h3>White-space and style enforcement</h3>
+    <ul>
+      <li>We now use <tt>clang-format</tt> to enforce C++-style, including white-space settings, line-breaks
+        etc. This uses the <tt>.clang-format</tt> file in the root directory of STIR. Developers should
+        configure their editor encordingly, and ideally use <tt>pre-commit</tt>. It also has
+        consequences for existing branches as you might experience more conflicts than usual
+        during a merge. More detail is in
+        <a href="https://github.com/UCL/STIR/blob/master/documentation/devel/README.md">documentation/devel/README.md</a>.<br>
+        <a href="https://github.com/UCL/STIR/pull/1368">PR #1368</a>.
+      </li>
+    </ul>
+
     <h3>Backward incompatibities</h3>
     <ul>
       <li>

examples/C++/General_Reconstruction/General_Reconstruction.cxx

@@ -5,53 +5,50 @@
 #include <iostream>
 START_NAMESPACE_STIR
 
-General_Reconstruction::
-General_Reconstruction()
+General_Reconstruction::General_Reconstruction()
 {
-    this->set_defaults();
+  this->set_defaults();
 }
 
 void
 General_Reconstruction::set_defaults()
-{
-
-}
+{}
 
 void
 General_Reconstruction::initialise_keymap()
 {
-    this->parser.add_start_key("General reconstruction");
-    this->parser.add_stop_key("End General reconstruction");
+  this->parser.add_start_key("General reconstruction");
+  this->parser.add_stop_key("End General reconstruction");
 
-    this->parser.add_parsing_key("reconstruction method", &this->reconstruction_method_sptr);
+  this->parser.add_parsing_key("reconstruction method", &this->reconstruction_method_sptr);
 }
 
 bool
 General_Reconstruction::post_processing()
 {
-    return false;
+  return false;
 }
 
 Succeeded
 General_Reconstruction::process_data()
 {
-    HighResWallClockTimer t;
-    t.reset();
-    t.start();
-
-        //return reconstruction_object.reconstruct() == Succeeded::yes ?
-        //    EXIT_SUCCESS : EXIT_FAILURE;
-        if (reconstruction_method_sptr->reconstruct() == Succeeded::yes)
-          {
-            t.stop();
-            std::cout << "Total Wall clock time: " << t.value() << " seconds" << std::endl;
-            return Succeeded::yes;
-          }
-        else
-          {
-            t.stop();
-            return Succeeded::no;
-          }
+  HighResWallClockTimer t;
+  t.reset();
+  t.start();
+
+  // return reconstruction_object.reconstruct() == Succeeded::yes ?
+  //     EXIT_SUCCESS : EXIT_FAILURE;
+  if (reconstruction_method_sptr->reconstruct() == Succeeded::yes)
+    {
+      t.stop();
+      std::cout << "Total Wall clock time: " << t.value() << " seconds" << std::endl;
+      return Succeeded::yes;
+    }
+  else
+    {
+      t.stop();
+      return Succeeded::no;
+    }
 }
 
 END_NAMESPACE_STIR

examples/C++/General_Reconstruction/General_Reconstruction.h

@@ -16,31 +16,27 @@
 #include "stir/CartesianCoordinate3D.h"
 #include "Reconstruction.h"
 
-
 START_NAMESPACE_STIR
 
 class Succeeded;
 
 class General_Reconstruction : public ParsingObject
 {
 public:
-    //!
-    //! \brief General_Reconstuction
-    //! \details Default constructor
-    General_Reconstruction();
+  //!
+  //! \brief General_Reconstuction
+  //! \details Default constructor
+  General_Reconstruction();
 
-    virtual Succeeded process_data();
-protected:
+  virtual Succeeded process_data();
 
-    void set_defaults();
-    void initialise_keymap();
-    bool post_processing();
+protected:
+  void set_defaults();
+  void initialise_keymap();
+  bool post_processing();
 
 private:
-
-    shared_ptr < Reconstruction < DiscretisedDensity < 3, float > > >
-        reconstruction_method_sptr;
-
+  shared_ptr<Reconstruction<DiscretisedDensity<3, float>>> reconstruction_method_sptr;
 };
 
 END_NAMESPACE_STIR

examples/C++/using_STIR_LOCAL/demo1.cxx

@@ -6,20 +6,20 @@
   \brief A simple program that backprojects some projection data.
 
   It illustrates
-	- basic interaction with the user,
-	- reading of images and projection data
-	- construction of a specified type of back-projector,
-	- how to use back-project all projection data
-	- output of images
+        - basic interaction with the user,
+        - reading of images and projection data
+        - construction of a specified type of back-projector,
+        - how to use back-project all projection data
+        - output of images
 
   See README.txt in the directory where this file is located.
 
-  \author Kris Thielemans      
+  \author Kris Thielemans
 */
 /*
     Copyright (C) 2004- 2011, Hammersmith Imanet Ltd
 
-    This software is distributed under the terms 
+    This software is distributed under the terms
     of the GNU General  Public Licence (GPL)
     See STIR/LICENSE.txt for details
 */
@@ -35,25 +35,21 @@
 #include "stir/utilities.h"
 #include "stir/Succeeded.h"
 
-int main()
+int
+main()
 {
   using namespace stir;
- 
+
   /////////////// input sinogram
-  const std::string input_filename =
-    ask_filename_with_extension("Input file",".hs");
+  const std::string input_filename = ask_filename_with_extension("Input file", ".hs");
 
-  shared_ptr<ProjData> 
-    proj_data_sptr(ProjData::read_from_file(input_filename));
-  shared_ptr<ProjDataInfo> 
-    proj_data_info_sptr(proj_data_sptr->get_proj_data_info_sptr()->clone());
+  shared_ptr<ProjData> proj_data_sptr(ProjData::read_from_file(input_filename));
+  shared_ptr<ProjDataInfo> proj_data_info_sptr(proj_data_sptr->get_proj_data_info_sptr()->clone());
 
   /////////////// template image (for sizes etc)
-  const std::string template_filename =
-    ask_filename_with_extension("Template image file",".hv");
+  const std::string template_filename = ask_filename_with_extension("Template image file", ".hv");
 
-  shared_ptr<DiscretisedDensity<3,float> > 
-    density_sptr(read_from_file<DiscretisedDensity<3,float> >(template_filename));
+  shared_ptr<DiscretisedDensity<3, float>> density_sptr(read_from_file<DiscretisedDensity<3, float>>(template_filename));
 
   density_sptr->fill(0);
 

examples/C++/using_STIR_LOCAL/demo2.cxx

@@ -4,23 +4,23 @@
   \file
   \ingroup examples
   \brief A small modification of demo1.cxx to ask the user for the
-	back projector she wants to use.
+        back projector she wants to use.
 
   It illustrates
-	- how to ask the user for objects for which different types
-	  exist (e.g. back-projector, forward-projectors, image processors 
-	  etc), anything based on the RegisteredObject hierarchy.
-	- that STIR is able to select basic processing units at run-time
-	- how to use the (very) basic display facilities in STIR
+        - how to ask the user for objects for which different types
+          exist (e.g. back-projector, forward-projectors, image processors
+          etc), anything based on the RegisteredObject hierarchy.
+        - that STIR is able to select basic processing units at run-time
+        - how to use the (very) basic display facilities in STIR
 
   See README.txt in the directory where this file is located.
 
-  \author Kris Thielemans      
+  \author Kris Thielemans
 */
 /*
     Copyright (C) 2004- 2012, Hammersmith Imanet Ltd
 
-    This software is distributed under the terms 
+    This software is distributed under the terms
     of the GNU General  Public Licence (GPL)
     See STIR/LICENSE.txt for details
 */
@@ -34,31 +34,26 @@
 #include "stir/Succeeded.h"
 #include "stir/display.h"
 
-int main()
+int
+main()
 {
   using namespace stir;
- 
+
   /////////////// input sinogram
-  const std::string input_filename =
-    ask_filename_with_extension("Input file",".hs");
+  const std::string input_filename = ask_filename_with_extension("Input file", ".hs");
 
-  shared_ptr<ProjData> 
-    proj_data_sptr(ProjData::read_from_file(input_filename));
-  shared_ptr<ProjDataInfo> 
-    proj_data_info_sptr(proj_data_sptr->get_proj_data_info_sptr()->clone());
+  shared_ptr<ProjData> proj_data_sptr(ProjData::read_from_file(input_filename));
+  shared_ptr<ProjDataInfo> proj_data_info_sptr(proj_data_sptr->get_proj_data_info_sptr()->clone());
 
   /////////////// template image (for sizes etc)
-  const std::string template_filename =
-    ask_filename_with_extension("Template image file",".hv");
+  const std::string template_filename = ask_filename_with_extension("Template image file", ".hv");
 
-  shared_ptr<DiscretisedDensity<3,float> > 
-    density_sptr(read_from_file<DiscretisedDensity<3,float> >(template_filename));
+  shared_ptr<DiscretisedDensity<3, float>> density_sptr(read_from_file<DiscretisedDensity<3, float>>(template_filename));
 
   density_sptr->fill(0);
 
   /////////////// back project
-  shared_ptr<BackProjectorByBin> back_projector_sptr
-    (BackProjectorByBin::ask_type_and_parameters());
+  shared_ptr<BackProjectorByBin> back_projector_sptr(BackProjectorByBin::ask_type_and_parameters());
 
   back_projector_sptr->set_up(proj_data_info_sptr, density_sptr);