Re-enable license maintainer pre-commit hook

Author: robertodr

.gitattributes

@@ -1,68 +1,70 @@
 # API files
-/api/*.h   licensefile=.githooks/license-maintainer/LICENSE-C
-/api/*.F90 licensefile=.githooks/license-maintainer/LICENSE-Fortran
+api/*.h   licensefile=.githooks/license-maintainer/LICENSE-C
+api/*.F90 licensefile=.githooks/license-maintainer/LICENSE-Fortran
 
 # include directory
-/include/*.hpp         licensefile=.githooks/license-maintainer/LICENSE-C++
-/include/Config.hpp.in licensefile=.githooks/license-maintainer/LICENSE-C++
+include/*.hpp         licensefile=.githooks/license-maintainer/LICENSE-C++
+include/STLUtils.hpp  !licensefile
+include/Config.hpp.in licensefile=.githooks/license-maintainer/LICENSE-C++
 
 # bin
-/src/bin/*.cpp licensefile=.githooks/license-maintainer/LICENSE-C++
+src/bin/*.cpp licensefile=.githooks/license-maintainer/LICENSE-C++
 
 # bi_operators
-/src/bi_operators/*.hpp licensefile=.githooks/license-maintainer/LICENSE-C++
+src/bi_operators/*.hpp licensefile=.githooks/license-maintainer/LICENSE-C++
+src/bi_operators/*.cpp licensefile=.githooks/license-maintainer/LICENSE-C++
 
 # cavity
-/src/cavity/*.cpp licensefile=.githooks/license-maintainer/LICENSE-C++
-/src/cavity/*.hpp licensefile=.githooks/license-maintainer/LICENSE-C++
+src/cavity/*.hpp licensefile=.githooks/license-maintainer/LICENSE-C++
+src/cavity/*.cpp licensefile=.githooks/license-maintainer/LICENSE-C++
 
 # green
-/src/green/*.hpp                    licensefile=.githooks/license-maintainer/LICENSE-C++
-/src/green/dielectric_profile/*.hpp licensefile=.githooks/license-maintainer/LICENSE-C++
+src/green/*.hpp                    licensefile=.githooks/license-maintainer/LICENSE-C++
+src/green/*.cpp                    licensefile=.githooks/license-maintainer/LICENSE-C++
+src/green/dielectric_profile/*.hpp licensefile=.githooks/license-maintainer/LICENSE-C++
 
 # interface
-/src/interface/*.cpp licensefile=.githooks/license-maintainer/LICENSE-C++
-/src/interface/*.hpp licensefile=.githooks/license-maintainer/LICENSE-C++
+src/interface/*.hpp licensefile=.githooks/license-maintainer/LICENSE-C++
+src/interface/*.cpp licensefile=.githooks/license-maintainer/LICENSE-C++
 
 # metal
-/src/metal/*.F90 licensefile=.githooks/license-maintainer/LICENSE-Fortran
+src/metal/*.F90 licensefile=.githooks/license-maintainer/LICENSE-Fortran
 
 # pedra
-/src/pedra/*.inc                   licensefile=.githooks/license-maintainer/LICENSE-Fortran
-pedra/pedra_cavity.F90             licensefile=.githooks/license-maintainer/LICENSE-Fortran
-pedra/pedra_cavity_derivatives.F90 licensefile=.githooks/license-maintainer/LICENSE-Fortran
-pedra/pedra_cavity_interface.F90   licensefile=.githooks/license-maintainer/LICENSE-Fortran
-pedra/pedra_dblas.F90              licensefile=.githooks/license-maintainer/LICENSE-Fortran
-pedra/pedra_precision.F90          licensefile=.githooks/license-maintainer/LICENSE-Fortran
-pedra/pedra_print.F90              licensefile=.githooks/license-maintainer/LICENSE-Fortran
-pedra/pedra_symmetry.F90           licensefile=.githooks/license-maintainer/LICENSE-Fortran
-pedra/pedra_utils.F90              licensefile=.githooks/license-maintainer/LICENSE-Fortran
+src/pedra/*.inc             licensefile=.githooks/license-maintainer/LICENSE-Fortran
+src/pedra/*.F90             licensefile=.githooks/license-maintainer/LICENSE-Fortran
+src/pedra/pedra_dlapack.F90 !licensefile
 
 # solver
-/src/solver/*.cpp licensefile=.githooks/license-maintainer/LICENSE-C++
-/src/solver/*.hpp licensefile=.githooks/license-maintainer/LICENSE-C++
+src/solver/*.hpp licensefile=.githooks/license-maintainer/LICENSE-C++
+src/solver/*.cpp licensefile=.githooks/license-maintainer/LICENSE-C++
 
 # utils
-/src/utils/*.cpp licensefile=.githooks/license-maintainer/LICENSE-C++
-/src/utils/*.hpp licensefile=.githooks/license-maintainer/LICENSE-C++
+src/utils/*.hpp licensefile=.githooks/license-maintainer/LICENSE-C++
+src/utils/*.cpp licensefile=.githooks/license-maintainer/LICENSE-C++
+src/utils/cnpy.hpp !licensefile
+src/utils/cnpy.cpp !licensefile
+src/utils/legendre.h !licensefile
+src/utils/Interpolation.* !licensefile
+src/utils/Vector*         !licensefile
 
 # tests
-/tests/unit_tests.cpp             licensefile=.githooks/license-maintainer/LICENSE-C++
-/tests/TestingMolecules.hpp       licensefile=.githooks/license-maintainer/LICENSE-C++
-/tests/Fortran_host/*.F90         licensefile=.githooks/license-maintainer/LICENSE-Fortran
+tests/unit_tests.cpp             licensefile=.githooks/license-maintainer/LICENSE-C++
+tests/TestingMolecules.hpp       licensefile=.githooks/license-maintainer/LICENSE-C++
+tests/Fortran_host/*.f90         licensefile=.githooks/license-maintainer/LICENSE-Fortran
 /tests/C_host/*.h                 licensefile=.githooks/license-maintainer/LICENSE-C
 /tests/C_host/*.c                 licensefile=.githooks/license-maintainer/LICENSE-C
-/tests/bi_operators/*.cpp         licensefile=.githooks/license-maintainer/LICENSE-C++
-/tests/cpcm/*.cpp                 licensefile=.githooks/license-maintainer/LICENSE-C++
-/tests/dielectric_profile/*.cpp   licensefile=.githooks/license-maintainer/LICENSE-C++
-/tests/gepol/*.cpp                licensefile=.githooks/license-maintainer/LICENSE-C++
-/tests/green/*.hpp                licensefile=.githooks/license-maintainer/LICENSE-C++
-/tests/green/*.cpp                licensefile=.githooks/license-maintainer/LICENSE-C++
-/tests/iefpcm/*.cpp               licensefile=.githooks/license-maintainer/LICENSE-C++
-/tests/input/*.cpp                licensefile=.githooks/license-maintainer/LICENSE-C++
-/tests/numerical_quadrature/*.cpp licensefile=.githooks/license-maintainer/LICENSE-C++
+tests/bi_operators/*.cpp         licensefile=.githooks/license-maintainer/LICENSE-C++
+tests/cpcm/*.cpp                 licensefile=.githooks/license-maintainer/LICENSE-C++
+tests/dielectric_profile/*.cpp   licensefile=.githooks/license-maintainer/LICENSE-C++
+tests/gepol/*.cpp                licensefile=.githooks/license-maintainer/LICENSE-C++
+tests/green/*.hpp                licensefile=.githooks/license-maintainer/LICENSE-C++
+tests/green/*.cpp                licensefile=.githooks/license-maintainer/LICENSE-C++
+tests/iefpcm/*.cpp               licensefile=.githooks/license-maintainer/LICENSE-C++
+tests/input/*.cpp                licensefile=.githooks/license-maintainer/LICENSE-C++
+tests/numerical_quadrature/*.cpp licensefile=.githooks/license-maintainer/LICENSE-C++
 
 # tools
-/src/make_cmake_files.py   licensefile=.githooks/license-maintainer/LICENSE-Python
-/tools/pcmsolver.py.in     licensefile=.githooks/license-maintainer/LICENSE-Python
-/tests/make_cmake_files.py licensefile=.githooks/license-maintainer/LICENSE-Python
+src/make_cmake_files.py   licensefile=.githooks/license-maintainer/LICENSE-Python
+tools/pcmsolver.py.in     licensefile=.githooks/license-maintainer/LICENSE-Python
+tests/make_cmake_files.py licensefile=.githooks/license-maintainer/LICENSE-Python

.githooks/pre-commit

@@ -13,8 +13,8 @@
 # pre-commit hooks to be executed. They should be in the same .git/hooks/ folder
 # as this script. Hooks should return 0 if successful and nonzero to cancel the
 # commit. They are executed in the order in which they are listed.
-HOOKS="pre-commit-clang-format"
-#HOOKS="pre-commit-clang-format pre-commit-license-maintainer"
+#HOOKS="pre-commit-clang-format"
+HOOKS="pre-commit-license-maintainer pre-commit-clang-format"
 ###########################################################
 # There should be no need to change anything below this line.
 

CHANGELOG.md

@@ -12,6 +12,16 @@
   non compliant. The hook generates a patch and shows the command needed to
   apply it.
   _NOT recommended_ The hook can be skipped by passing the `--no-verify` option to `git commit`
+- A pre-commit hook in `.githooks/pre-commit-license-maintainer` checking the license headers.
+  **BREAKING CHANGE** Perl5 is needed to work on the code.
+  The hook is based on this [project](https://github.com/NitorCreations/license-maintainer)
+  and is configured based on the `.gitattributes` file.
+  The list of authors is automatically extracted from the `license.author`
+  field in `.git/config`. This can either be modified by hand or by invoking
+  `git config license.author="list-of-authors"`.
+  The hook will check the license headers, amend them where possible and abort
+  where not possible, showing the commands needed to update the license.
+  _NOT recommended_ The hook can be skipped by passing the `--no-verify` option to `git commit`
 - An `UNUSED` preprocessor macro to mark arguments as unused.
 - An `UNUSED_FUNCTION` preprocessor macro to mark functions as unused.
 

api/PCMInput.h

@@ -1,27 +1,25 @@
-/* pcmsolver_copyright_start */
-/*
- *     PCMSolver, an API for the Polarizable Continuum Model
- *     Copyright (C) 2013-2016 Roberto Di Remigio, Luca Frediani and contributors
- *     
- *     This file is part of PCMSolver.
- *     
- *     PCMSolver is free software: you can redistribute it and/or modify
- *     it under the terms of the GNU Lesser General Public License as published by
- *     the Free Software Foundation, either version 3 of the License, or
- *     (at your option) any later version.
- *     
- *     PCMSolver is distributed in the hope that it will be useful,
- *     but WITHOUT ANY WARRANTY; without even the implied warranty of
- *     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *     GNU Lesser General Public License for more details.
- *     
- *     You should have received a copy of the GNU Lesser General Public License
- *     along with PCMSolver.  If not, see <http://www.gnu.org/licenses/>.
- *     
- *     For information on the complete list of contributors to the
- *     PCMSolver API, see: <http://pcmsolver.readthedocs.io/>
+/**
+ * PCMSolver, an API for the Polarizable Continuum Model
+ * Copyright (C) 2016 Roberto Di Remigio, Luca Frediani and collaborators.
+ *
+ * This file is part of PCMSolver.
+ *
+ * PCMSolver is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * PCMSolver is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with PCMSolver.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ * For information on the complete list of contributors to the
+ * PCMSolver API, see: <http://pcmsolver.readthedocs.io/>
  */
-/* pcmsolver_copyright_end */
 
 #ifndef PCMINPUT_H
 #define PCMINPUT_H
@@ -31,53 +29,54 @@
 #define pcmsolver_bool_t_DEFINED
 #if (defined(__STDC__) && (__STDC_VERSION__ < 199901L)) && !defined(__cplusplus)
 typedef enum { pcmsolver_false, pcmsolver_true } pcmsolver_bool_t;
-#else /* (defined(__STDC__) || (__STDC_VERSION__ < 199901L)) && !defined(__cplusplus) */
+#else /* (defined(__STDC__) || (__STDC_VERSION__ < 199901L)) &&                     \
+         !defined(__cplusplus) */
 #include <stdbool.h>
 typedef bool pcmsolver_bool_t;
-#endif /* (defined(__STDC__) || (__STDC_VERSION__ < 199901L)) && !defined(__cplusplus) */
+#endif /* (defined(__STDC__) || (__STDC_VERSION__ < 199901L)) &&                    \
+          !defined(__cplusplus) */
 #endif /* pcmsolver_bool_t_DEFINED */
 
 /*! @struct PCMInput
  *  @brief Data structure for host-API input communication.
  */
-typedef struct PCMInput
-{
-	/// Type of cavity requested.
-	char cavity_type[8];
-	/// Wavelet cavity mesh patch level.
-	int patch_level;
-	/// Wavelet cavity mesh coarsity.
-	double coarsity;
-	/// Average tesserae area.
-	double area;
-	/// The built-in radii set to be used.
-	char radii_set[8];
-	/// Minimal distance between sampling points.
-	double min_distance;
-	/// Derivative order for the switching function.
-	int der_order;
-	/// Whether to scale or not the atomic radii.
-	pcmsolver_bool_t scaling;
-	/// Name of the .npz file for GePol cavity restart.
-	char restart_name[20];
-	/// Minimal radius for the added spheres.
-	double min_radius;
-	/// Type of solver requested.
-	char solver_type[7];
-	/// Correction in the CPCM apparent surface charge scaling factor.
-	double correction;
-	/// Name of the solvent.
-	char solvent[16];
-	/// Radius of the spherical probe mimicking the solvent.
-	double probe_radius;
-	/// Type of the integral equation to be used.
-	char equation_type[11];
-	/// Type of Green's function requested inside the cavity.
-	char inside_type[7];
-	/// Value of the static permittivity outside the cavity.
-	double outside_epsilon;
-	/// Type of Green's function requested outside the cavity.
-	char outside_type[22];
+typedef struct PCMInput {
+  /// Type of cavity requested.
+  char cavity_type[8];
+  /// Wavelet cavity mesh patch level.
+  int patch_level;
+  /// Wavelet cavity mesh coarsity.
+  double coarsity;
+  /// Average tesserae area.
+  double area;
+  /// The built-in radii set to be used.
+  char radii_set[8];
+  /// Minimal distance between sampling points.
+  double min_distance;
+  /// Derivative order for the switching function.
+  int der_order;
+  /// Whether to scale or not the atomic radii.
+  pcmsolver_bool_t scaling;
+  /// Name of the .npz file for GePol cavity restart.
+  char restart_name[20];
+  /// Minimal radius for the added spheres.
+  double min_radius;
+  /// Type of solver requested.
+  char solver_type[7];
+  /// Correction in the CPCM apparent surface charge scaling factor.
+  double correction;
+  /// Name of the solvent.
+  char solvent[16];
+  /// Radius of the spherical probe mimicking the solvent.
+  double probe_radius;
+  /// Type of the integral equation to be used.
+  char equation_type[11];
+  /// Type of Green's function requested inside the cavity.
+  char inside_type[7];
+  /// Value of the static permittivity outside the cavity.
+  double outside_epsilon;
+  /// Type of Green's function requested outside the cavity.
+  char outside_type[22];
 } PCMInput;
 
 #endif // PCMINPUT_H

api/pcmsolver.F90

@@ -1,25 +1,25 @@
-!pcmsolver_copyright_start
-!       PCMSolver, an API for the Polarizable Continuum Model
-!       Copyright (C) 2013-2016 Roberto Di Remigio, Luca Frediani and contributors
-! 
-!       This file is part of PCMSolver.
-! 
-!       PCMSolver is free software: you can redistribute it and/or modify
-!       it under the terms of the GNU Lesser General Public License as published by
-!       the Free Software Foundation, either version 3 of the License, or
-!       (at your option) any later version.
-! 
-!       PCMSolver is distributed in the hope that it will be useful,
-!       but WITHOUT ANY WARRANTY; without even the implied warranty of
-!       MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-!       GNU Lesser General Public License for more details.
-! 
-!       You should have received a copy of the GNU Lesser General Public License
-!       along with PCMSolver.  If not, see <http://www.gnu.org/licenses/>.
-! 
-!       For information on the complete list of contributors to the
-!       PCMSolver API, see: <http://pcmsolver.readthedocs.io/>
-!pcmsolver_copyright_end
+!
+! PCMSolver, an API for the Polarizable Continuum Model
+! Copyright (C) 2016 Roberto Di Remigio, Luca Frediani and collaborators.
+!
+! This file is part of PCMSolver.
+!
+! PCMSolver is free software: you can redistribute it and/or modify
+! it under the terms of the GNU Lesser General Public License as published by
+! the Free Software Foundation, either version 3 of the License, or
+! (at your option) any later version.
+!
+! PCMSolver is distributed in the hope that it will be useful,
+! but WITHOUT ANY WARRANTY; without even the implied warranty of
+! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+! GNU Lesser General Public License for more details.
+!
+! You should have received a copy of the GNU Lesser General Public License
+! along with PCMSolver.  If not, see <http://www.gnu.org/licenses/>.
+!
+! For information on the complete list of contributors to the
+! PCMSolver API, see: <http://pcmsolver.readthedocs.io/>
+!
 
 module pcmsolver