Cleaning (?) headers (plumed#941)

* removed the actionRegister shortcut from bias * removed the CLTollRegister shortcut from cltools (why that is in core and not in cltools?) * Again removed some shortcuts to actionRegister.h * removed the ActionRegister.h shorcuts * rectified the style changes due to clang-format * now compiles * updated the changelog for developers in the 2.10 --------- Co-authored-by: Daniele Rapetti <[email protected]>
Iximiel · Jun 3, 2023 · 57458b6 · 57458b6
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diff --git a/CHANGES/v2.10.md b/CHANGES/v2.10.md
@@ -4,3 +4,5 @@
 
 This page contains changes that will end up in 2.10
 
+- Changes relevant for developers:
+  - Removed some shortcuts for `ActionRegister.h` (from the modules bias colvar function sasa and vatom) and `CLToolRegister.h` (from the module cltools), now the two headers can only be included with `#include "core/ActionRegister.h"` or `#include "core/CLToolRegister.h"`.
diff --git a/src/annfunc/ANN.cpp b/src/annfunc/ANN.cpp
@@ -22,7 +22,7 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "function/Function.h"
-#include "function/ActionRegister.h"
+#include "core/ActionRegister.h"
 #include "cassert"
 
 #include <string>

diff --git a/src/bias/ABMD.cpp b/src/bias/ABMD.cpp
@@ -21,7 +21,7 @@
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "Bias.h"
 #include "tools/Random.h"
-#include "ActionRegister.h"
+#include "core/ActionRegister.h"
 #include <ctime>
 
 namespace PLMD {

diff --git a/src/bias/ActionRegister.h b/src/bias/ActionRegister.h
diff --git a/src/bias/BiasValue.cpp b/src/bias/BiasValue.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "Bias.h"
-#include "ActionRegister.h"
+#include "core/ActionRegister.h"
 
 namespace PLMD {
 namespace bias {

diff --git a/src/bias/ExtendedLagrangian.cpp b/src/bias/ExtendedLagrangian.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "Bias.h"
-#include "ActionRegister.h"
+#include "core/ActionRegister.h"
 #include "tools/Random.h"
 #include "core/PlumedMain.h"
 #include "core/Atoms.h"

diff --git a/src/bias/External.cpp b/src/bias/External.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "Bias.h"
-#include "ActionRegister.h"
+#include "core/ActionRegister.h"
 #include "tools/Grid.h"
 #include "tools/Exception.h"
 #include "tools/File.h"

diff --git a/src/bias/LWalls.cpp b/src/bias/LWalls.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "Bias.h"
-#include "ActionRegister.h"
+#include "core/ActionRegister.h"
 
 namespace PLMD {
 namespace bias {

diff --git a/src/bias/MetaD.cpp b/src/bias/MetaD.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "Bias.h"
-#include "ActionRegister.h"
+#include "core/ActionRegister.h"
 #include "core/ActionSet.h"
 #include "core/PlumedMain.h"
 #include "core/Atoms.h"

diff --git a/src/bias/MovingRestraint.cpp b/src/bias/MovingRestraint.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "Bias.h"
-#include "ActionRegister.h"
+#include "core/ActionRegister.h"
 
 namespace PLMD {
 namespace bias {

diff --git a/src/bias/PBMetaD.cpp b/src/bias/PBMetaD.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "Bias.h"
-#include "ActionRegister.h"
+#include "core/ActionRegister.h"
 #include "core/ActionSet.h"
 #include "core/PlumedMain.h"
 #include "core/Atoms.h"

diff --git a/src/bias/Restraint.cpp b/src/bias/Restraint.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "Bias.h"
-#include "ActionRegister.h"
+#include "core/ActionRegister.h"
 
 namespace PLMD {
 namespace bias {

diff --git a/src/bias/UWalls.cpp b/src/bias/UWalls.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "Bias.h"
-#include "ActionRegister.h"
+#include "core/ActionRegister.h"
 
 namespace PLMD {
 namespace bias {

diff --git a/src/cltools/CLToolRegister.h b/src/cltools/CLToolRegister.h
diff --git a/src/cltools/Completion.cpp b/src/cltools/Completion.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "CLTool.h"
-#include "CLToolRegister.h"
+#include "core/CLToolRegister.h"
 #include "tools/Tools.h"
 #include "config/Config.h"
 #include "core/ActionRegister.h"

diff --git a/src/cltools/Driver.cpp b/src/cltools/Driver.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "CLTool.h"
-#include "CLToolRegister.h"
+#include "core/CLToolRegister.h"
 #include "tools/Tools.h"
 #include "core/PlumedMain.h"
 #include "core/ActionSet.h"

diff --git a/src/cltools/GenExample.cpp b/src/cltools/GenExample.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "CLTool.h"
-#include "CLToolRegister.h"
+#include "core/CLToolRegister.h"
 #include "tools/Tools.h"
 #include "config/Config.h"
 #include "core/ActionRegister.h"

diff --git a/src/cltools/GenJson.cpp b/src/cltools/GenJson.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "CLTool.h"
-#include "CLToolRegister.h"
+#include "core/CLToolRegister.h"
 #include "tools/Tools.h"
 #include "config/Config.h"
 #include "core/ActionRegister.h"

diff --git a/src/cltools/GenTemplate.cpp b/src/cltools/GenTemplate.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "CLTool.h"
-#include "CLToolRegister.h"
+#include "core/CLToolRegister.h"
 #include "tools/Tools.h"
 #include "core/ActionRegister.h"
 #include <cstdio>

diff --git a/src/cltools/Info.cpp b/src/cltools/Info.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "CLTool.h"
-#include "CLToolRegister.h"
+#include "core/CLToolRegister.h"
 #include "tools/Tools.h"
 #include "config/Config.h"
 #include <cstdio>

diff --git a/src/cltools/Manual.cpp b/src/cltools/Manual.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "CLTool.h"
-#include "CLToolRegister.h"
+#include "core/CLToolRegister.h"
 #include "tools/Tools.h"
 #include "config/Config.h"
 #include "core/ActionRegister.h"

diff --git a/src/cltools/PdbRenumber.cpp b/src/cltools/PdbRenumber.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "CLTool.h"
-#include "CLToolRegister.h"
+#include "core/CLToolRegister.h"
 #include "tools/Tools.h"
 #include "core/ActionRegister.h"
 #include "tools/IFile.h"

diff --git a/src/cltools/SimpleMD.cpp b/src/cltools/SimpleMD.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "CLTool.h"
-#include "CLToolRegister.h"
+#include "core/CLToolRegister.h"
 #include "core/PlumedMain.h"
 #include "tools/Vector.h"
 #include "tools/Random.h"

diff --git a/src/cltools/SumHills.cpp b/src/cltools/SumHills.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "CLTool.h"
-#include "CLToolRegister.h"
+#include "core/CLToolRegister.h"
 #include "tools/Tools.h"
 #include "core/Action.h"
 #include "core/ActionRegister.h"

diff --git a/src/cltools/kT.cpp b/src/cltools/kT.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "CLTool.h"
-#include "CLToolRegister.h"
+#include "core/CLToolRegister.h"
 #include "tools/Tools.h"
 #include "config/Config.h"
 #include "tools/Units.h"

diff --git a/src/cltools/pesmd.cpp b/src/cltools/pesmd.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "CLTool.h"
-#include "CLToolRegister.h"
+#include "core/CLToolRegister.h"
 #include "core/PlumedMain.h"
 #include "tools/Vector.h"
 #include "tools/Random.h"

diff --git a/src/colvar/ActionRegister.h b/src/colvar/ActionRegister.h
diff --git a/src/colvar/Angle.cpp b/src/colvar/Angle.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "Colvar.h"
-#include "ActionRegister.h"
+#include "core/ActionRegister.h"
 #include "tools/Angle.h"
 
 namespace PLMD {

diff --git a/src/colvar/Cell.cpp b/src/colvar/Cell.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "Colvar.h"
-#include "ActionRegister.h"
+#include "core/ActionRegister.h"
 
 namespace PLMD {
 namespace colvar {

diff --git a/src/colvar/Constant.cpp b/src/colvar/Constant.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "Colvar.h"
-#include "ActionRegister.h"
+#include "core/ActionRegister.h"
 #include "core/PlumedMain.h"
 #include "core/Atoms.h"
 

diff --git a/src/colvar/ContactMap.cpp b/src/colvar/ContactMap.cpp
@@ -21,7 +21,7 @@
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "Colvar.h"
 #include "tools/NeighborList.h"
-#include "ActionRegister.h"
+#include "core/ActionRegister.h"
 #include "tools/SwitchingFunction.h"
 
 namespace PLMD {

diff --git a/src/colvar/Coordination.cpp b/src/colvar/Coordination.cpp
@@ -21,7 +21,7 @@
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "CoordinationBase.h"
 #include "tools/SwitchingFunction.h"
-#include "ActionRegister.h"
+#include "core/ActionRegister.h"
 
 namespace PLMD {
 namespace colvar {

diff --git a/src/colvar/DHEnergy.cpp b/src/colvar/DHEnergy.cpp
@@ -21,7 +21,7 @@
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "CoordinationBase.h"
 #include "tools/SwitchingFunction.h"
-#include "ActionRegister.h"
+#include "core/ActionRegister.h"
 #include "core/PlumedMain.h"
 #include "core/Atoms.h"
 

diff --git a/src/colvar/DRMSD.cpp b/src/colvar/DRMSD.cpp
@@ -21,7 +21,7 @@
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "Colvar.h"
 #include "core/PlumedMain.h"
-#include "ActionRegister.h"
+#include "core/ActionRegister.h"
 #include "tools/PDB.h"
 #include "reference/DRMSD.h"
 #include "reference/MetricRegister.h"

diff --git a/src/colvar/Dimer.cpp b/src/colvar/Dimer.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "Colvar.h"
-#include "ActionRegister.h"
+#include "core/ActionRegister.h"
 #include "core/PlumedMain.h"
 
 namespace PLMD {

diff --git a/src/colvar/Dipole.cpp b/src/colvar/Dipole.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "Colvar.h"
-#include "ActionRegister.h"
+#include "core/ActionRegister.h"
 
 namespace PLMD {
 namespace colvar {

diff --git a/src/colvar/Distance.cpp b/src/colvar/Distance.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "Colvar.h"
-#include "ActionRegister.h"
+#include "core/ActionRegister.h"
 #include "tools/Pbc.h"
 
 namespace PLMD {

diff --git a/src/colvar/EEFSolv.cpp b/src/colvar/EEFSolv.cpp
@@ -23,7 +23,7 @@
 /* This class was originally written by Thomas Loehr */
 
 #include "Colvar.h"
-#include "ActionRegister.h"
+#include "core/ActionRegister.h"
 #include "core/ActionSet.h"
 #include "core/PlumedMain.h"
 #include "core/GenericMolInfo.h"

diff --git a/src/colvar/ERMSD.cpp b/src/colvar/ERMSD.cpp
@@ -27,7 +27,7 @@
 
 #include "Colvar.h"
 #include "core/PlumedMain.h"
-#include "ActionRegister.h"
+#include "core/ActionRegister.h"
 #include "tools/PDB.h"
 #include "tools/ERMSD.h"
 #include "core/Atoms.h"