Merge pull request 'jf/cla+templates' (#6) from jf/cla+templates into main

Reviewed-on: https://codeberg.org/TetGen/TetGen/pulls/6

.github/issue_template.md

@@ -0,0 +1,22 @@
+Thank you very much for your interest in TetGen! Reporting your issue helps to improve the code.
+
+### Legal
+By opening this issue, you agree to the terms of the Contributor License Agreement (CLA) stated in [CONTRIBUTING.md](https://codeberg.org/TetGen/TetGen/src/branch/main/CONTRIBUTING.md).
+
+### Kind of issue (bug, feature request...):
+
+### Issue description:
+
+### Expected behavior: 
+
+### Observed behavior: 
+
+### Environment:
+   - TeGen version:
+   - OS (e.g. MacOS 14):
+   - Architecture (e.g. x64, aarch64):
+   - Compiler vendor + version:
+
+### Minimum working example:
+
+Please attach input data which allow to reproduce the problem.

.github/pull_request_template.md

@@ -0,0 +1,12 @@
+Thank you very much for helping to improve TetGen!
+
+### Legal:
+By opening this pull request, you agree to the terms of the Contributor License Agreement (CLA) stated in [CONTRIBUTING.md](https://codeberg.org/TetGen/TetGen/src/branch/main/CONTRIBUTING.md).
+
+- [ ] I have read and agree to the Contributor License Agreement in CONTRIBUTING.md
+
+### Pull request description:
+
+
+### Test data:
+Please provide input data which help to test the feature implemented in the pull request.

CHANGELOG.md

@@ -1,5 +1,42 @@
 # TetGen: Release Notes
+## Version 1.6.0 (August 31, 2020)
 
+-   Improved the speed of the Bowyer-Watson point insertion algorithm
+    for creating Delaunay tetrahedralization.
+-   Improved the robustness of the boundary recovery algorithm (-p -Y
+    options) for creating constrained tetrahedralizations. Now the
+    default algorithm for the \`\`-p\" option (boundary recobvery) is
+    the constrained tetrahedralization algorithm. It is robust and it
+    uses less Steiner points than the constrained Delaunay
+    tetrahedralization (CDT) algorothm uses. The option to use the CDT
+    algorithm is \`\`-p -D\".
+-   A new implementation of the constrained Delaunay refinement
+    algorithm (-q option). It uses new Steiner points insertion schemes
+    to remove badly-shaped elements.
+-   Implemented a new set of mesh smoothing and mesh improvement
+    operations (-O -o) for optimizing the quality of the meshes. The
+    overall mesh quality has been improved.
+-   (Change of the -d option) To detect self-intersection in the input
+    surface mesh is now directly done in the constrained
+    tetrahedralization algorithm (the -p option).
+
+## Version 1.5.0 (November 4, 2013)
+
+-   License switched to AGPLv3
+-   Improved the efficiency of the mesh data structure
+    (tetrahedron-based).
+-   Implemented a new edge flip algorithm that does recursive
+    combination of elementary flips.
+-   Improved the Bowyer-Watson point insertion algorithm for robustness
+    and efficiency.
+-   Implemented a new algorithm for boundary recovery (the -Y option).
+-   Implemented Shewchuk\'s CDT flip algorithm (the -p option).
+-   Implemented a new Delaunay refinement algorithm (the -q option) for
+    handling small input angles (sharp features).
+-   Fully supports isolated input segments and with segment markers
+    (which do not attach to any facet).
+-   Many new options and parameters for improving mesh quality and mesh
+    optimization.
 
 ## Version 1.4.3 (September 6, 2009)
 

CMakeLists.txt

@@ -0,0 +1,14 @@
+# Set  the minimum  required version  of cmake  for a  project.
+cmake_minimum_required(VERSION 2.6)
+
+# Add an executable to the project using the specified source files.
+add_executable(tetgen tetgen.cxx predicates.cxx)
+
+#Add a library to the project using the specified source files. 
+# In Linux/Unix, it will creates the libtet.a
+add_library(tet STATIC tetgen.cxx predicates.cxx)
+
+#Set properties on a target. 
+#We use this here to set -DTETLIBRARY for when compiling the
+#library
+set_target_properties(tet PROPERTIES "COMPILE_DEFINITIONS" TETLIBRARY)

CONTRIBUTING.md

@@ -0,0 +1,56 @@
+# Contributor License Agreement (CLA)
+
+A "Contributor" is any person or entity that intentionally submits copyrighted material to the project,
+including but not limited to code, documentation, or other material, via a pull request, issue, or other means.
+
+By submitting a contribution Contributor agrees to the following terms:
+
+## Dual AGPLv3/MIT License Grant
+Contributor agrees that their contribution is provided under the GNU Affero General Public License v3 (AGPLv3) reproduced
+in the file [LICENSE](LICENSE) or any later version and, in addition, grants the contribution under the MIT License terms below:
+
+```text
+Permission is hereby granted, free of charge, to any person obtaining a copy  
+of this software and associated documentation files (the "Software"), to deal  
+in the Software without restriction, including without limitation the rights  
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell  
+copies of the Software, and to permit persons to whom the Software is  
+furnished to do so, subject to the following conditions:  
+
+The above copyright notice and this permission notice shall be included in all  
+copies or substantial portions of the Software.  
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR  
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,  
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE  
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER  
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,  
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE  
+SOFTWARE.  
+```
+
+## Annotating contributions to source code
+
+### Trivial changes
+Trivial changes (e.g., 1-2 line fixes or typo fixes) inherit the AGPLv3 license of the project and without further annotation are also licensed under MIT as specified above.
+
+### Functions and nontrivial snippets of code 
+Functions and nontrivial snippets of code by default inherit the AGPLv3 license of the project and are also licensed under MIT as specified above. They shall be marked in a PR with an SPDX header as in this example:
+  ```
+  # SPDX-License-Identifier: AGPL-3.0-or-later OR MIT
+  # Copyright (c) [Year] [Contributor Name]
+  void frobnicate(int ntet)
+  {
+  ...
+  }
+  ```
+
+## Representations and Warranties
+Contributor represents that:
+- They are legally entitled to grant the above licenses;
+- Their contributions are original works and do not violate third-party rights;
+- They are not required to grant licenses under third-party terms (e.g., employer agreements).
+
+## No Obligation
+The Project is under no obligation to accept or use any contribution.
+

LICENSE

@@ -1,66 +1,646 @@
-TetGen License
---------------
+GNU AFFERO GENERAL PUBLIC LICENSE
 
-The software (TetGen) is licensed under the terms of the  MIT  license
-with the following exceptions:
+Version 3, 19 November 2007
 
-Distribution of  modified  versions  of this code is permissible UNDER
-THE CONDITION THAT  THIS CODE AND ANY MODIFICATIONS  MADE TO IT IN THE
-SAME SOURCE FILES  tetgen.h AND tetgen.cxx  REMAIN UNDER  COPYRIGHT OF
-THE  ORIGINAL AUTHOR,  BOTH  SOURCE AND OBJECT  CODE  ARE MADE  FREELY
-AVAILABLE  WITHOUT   CHARGE,   AND  CLEAR   NOTICE  IS  GIVEN  OF  THE 
-MODIFICATIONS.
+Copyright © 2007 Free Software Foundation, Inc. <http://fsf.org/>
+Everyone is permitted to copy and distribute verbatim copies of this
+license document, but changing it is not allowed.
 
-Distribution of this code for  any  commercial purpose  is permissible
-ONLY BY DIRECT ARRANGEMENT WITH THE COPYRIGHT OWNER.
+Preamble
 
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+The GNU Affero General Public License is a free, copyleft license for
+software and other kinds of works, specifically designed to ensure
+cooperation with the community in the case of network server software.
 
-This means that TetGen is no free software, but for private, research,
-and  educational purposes it  can be  used at  absolutely no  cost and
-without further arrangements.
+The licenses for most software and other practical works are designed
+to take away your freedom to share and change the works. By contrast,
+our General Public Licenses are intended to guarantee your freedom to
+share and change all versions of a program--to make sure it remains
+free software for all its users.
 
+When we speak of free software, we are referring to freedom, not
+price. Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+them if you wish), that you receive source code or can get it if you
+want it, that you can change the software or use pieces of it in new
+free programs, and that you know you can do these things.
 
-For details, see http://tetgen.berlios.de
+Developers that use our General Public Licenses protect your rights
+with two steps: (1) assert copyright on the software, and (2) offer
+you this License which gives you legal permission to copy, distribute
+and/or modify the software.
 
-==============================================================================
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+releasing its source code to the public.
 
-TetGen
-A Quality Tetrahedral Mesh Generator and 3D Delaunay Triangulator
-Version 1.4 (Released on January 14, 2006).
+The GNU Affero General Public License is designed specifically to
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-Hang Si
-Rathausstr. 9, 10178 Berlin, Germany
-si@wias-berlin.de
+An older license, called the Affero General Public License and
+published by Affero, was designed to accomplish similar goals. This is
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+released a new version of the Affero GPL which permits relicensing
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+The precise terms and conditions for copying, distribution and
+modification follow.
 
-Distribution of  modified  versions  of this code is permissible UNDER
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-SAME SOURCE FILES  tetgen.h AND tetgen.cxx  REMAIN UNDER  COPYRIGHT OF
-THE  ORIGINAL AUTHOR,  BOTH  SOURCE AND OBJECT  CODE  ARE MADE  FREELY
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+TERMS AND CONDITIONS
 
-Distribution of this code for  any  commercial purpose  is permissible
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+    as published by the Free Software Foundation, either version 3 of
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+
+    This program 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
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+
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+You should also get your employer (if you work as a programmer) or
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+necessary. For more information on this, and how to apply and follow
+the GNU AGPL, see <http://www.gnu.org/licenses/>.

README

@@ -1,16 +0,0 @@
-This is TetGen version 1.4.3 (released on September 6, 2009, updated on December 13, 2010, updated on January 19, 2011, updated on April 15, 2011)
-
-Please see the documentation of TetGen for compiling and using TetGen.
-It is available at the following link:
-
-            http://tetgen.berlios.de/index.html
-
-TetGen may be freely copied, modified, and redistributed under the
-copyright notices stated in the file LICENSE.
-
-Please send bugs/comments to Hang Si <si@wias-berlin.de>
-
-Thank you and enjoy!
-
-Hang Si
-January 19, 2011

README.md

@@ -0,0 +1,35 @@
+TetGen
+======
+
+TetGen is a program to generate tetrahedral meshes of any 3D polyhedral domains.  TetGen generates exact constrained Delaunay tetrahedralizations, boundary conforming Delaunay meshes, and Voronoi partitions.
+
+TetGen versions up to v1.6.0 have been developed headed by [Hang Si](https://github.com/sihang0592) during his affiliation with [Weierstrass Institute for Applied Analysis and Stochastics, (WIAS) Berlin](https://www.wias-berlin.de/software/tetgen).
+
+The primary development repository is [https://codeberg.org/TetGen/TetGen](https://codeberg.org/TetGen/TetGen). Please
+open any issues in this repository. The github repository [https://github.com/TetGen/Tetgen](https://github.com/TetGen/Tetgen)
+is a mirror of the codeberg repository.
+
+This repository provides the source code of the most recent versions of TetGen.
+The following releases are provided:
+- [v1.4.3, 2011](https://codeberg.org/TetGen/TetGen/archive/v1.4.3.tar.gz): [MIT license with noncommercial clause](https://raw.githubusercontent.com/TetGen/TetGen/refs/tags/v1.4.3/LICENSE).
+- [v1.5.0, 2013](https://codeberg.org/TetGen/TetGen/archive/v1.5.0.tar.gz): [AGPLv3 license](https://www.gnu.org/licenses/agpl-3.0.html).
+- [v1.5.1, 2018](https://codeberg.org/TetGen/TetGen/archive/v1.5.1.tar.gz): [AGPLv3 license](https://www.gnu.org/licenses/agpl-3.0.html), recommended as most stable version.
+- [v1.6.0, 2020](https://codeberg.org/TetGen/TetGen/archive/v1.6.0.tar.gz): [AGPLv3 license](https://www.gnu.org/licenses/agpl-3.0.html), most recent version with some rough edges.
+
+It is planned to resume active development of TetGen in cooperation between the main developer Hang Si and  the Weierstrass Institute. Future versions of TetGen will be published via this repository.
+
+## Documentation
+- Manuals are available in https://codeberg.org/TetGen/Manuals.
+- A technical paper about TetGen is available at [Hang Si, "TetGen, a Delaunay-Based Quality Tetrahedral Mesh Generator". ACM Trans. on Mathematical Software. 41 (2), 2015](http://doi.acm.org/10.1145/2629697)
+  
+  
+## Commercial licensing
+
+TetGen versions developed at WIAS are distributed under a dual licensing scheme.  As an alternative to the use of TetGen under the AGPLv3 license, consider the option to obtain a commercial license for a fee.  These licenses are offered by the Weierstrass Institute for Applied Analysis and Stochastics (WIAS). As a rule, licenses are provided "as-is", unlimited in time for a one time fee.  Please send corresponding requests to: `tetgen at wias-berlin.de`.  Please do not forget to include some description of your company and the realm of its activities.
+
+Details about the extension of this dual licensing scheme for future versions of TetGen will be announced in due time.
+
+## Contributing
+
+By submitting a contribution (including but not limited to code, documentation, or other materials) via a pull request, issue, or other means, a contributor agrees to the terms of the contributor license agreement stated in [CONTRIBUTING.md](CONTRIBUTING.md). It is planned to revise this agreement, once the extension of the dual licensing scheme has been set up.
+

example.poly

@@ -1,132 +1,84 @@
-#
-# example.poly - Sample file of TetGen.
-#
-# A .poly file describes a piecewise linear complex (PLC)
-# This file represents a compensated magic tee junction.
-#
-# The source file is from: Vali Catina <catina@uni-bremen.de>
-#
-
-# Part 1 - node list
-54  3  0  0
-   1    -13.716000000000001  -5.0800000000000001  0
-   2    -13.716000000000001  5.0800000000000001  0
-   3    -11.43  5.0800000000000001  0
-   4    11.43  -5.0800000000000001  0
-   5    11.43  7.3659999999999997  0
-   6    -11.43  7.3659999999999997  0
-   7    0.95105651629515364  -0.37999999999999989  0
-   8    -0.95105651629515364  -0.37999999999999989  0
-   9    -0.95105651629515364  4.6200000000000001  0
-  10    0.95105651629515364  4.6200000000000001  0
-  11    -0.95105651629515353  4.6200000000000001  -0.30901699437494756
-  12    -0.58778525229247303  4.6200000000000001  -0.80901699437494756
-  13    1.2246063538223773e-16  4.6200000000000001  -1
-  14    0.58778525229247325  4.6200000000000001  -0.80901699437494734
-  15    0.95105651629515364  4.6200000000000001  -0.30901699437494734
-  16    -0.95105651629515353  -0.37999999999999989  -0.30901699437494756
-  17    -0.58778525229247303  -0.37999999999999989  -0.80901699437494756
-  18    1.2246063538223773e-16  -0.37999999999999989  -1
-  19    0.58778525229247325  -0.37999999999999989  -0.80901699437494734
-  20    0.95105651629515364  -0.37999999999999989  -0.30901699437494734
-  21    -1.5874999999999999  -0.37999999999999989  -2.9160938800395356e-16
-  22    -1.5098022196185561  -0.37999999999999989  -0.49056447857022928
-  23    -1.2843144785702287  -0.37999999999999989  -0.93310908801430126
-  24    -0.93310908801430081  -0.37999999999999989  -1.2843144785702292
-  25    -0.49056447857022878  -0.37999999999999989  -1.5098022196185563
-  26    1.9440625866930238e-16  -0.37999999999999989  -1.5874999999999999
-  27    0.49056447857022917  -0.37999999999999989  -1.5098022196185561
-  28    0.93310908801430115  -0.37999999999999989  -1.284314478570229
-  29    1.284314478570229  -0.37999999999999989  -0.93310908801430092
-  30    1.5098022196185563  -0.37999999999999989  -0.49056447857022889
-  31    1.5874999999999999  -0.37999999999999989  9.7203129334651192e-17
-  32    -1.5874999999999999  -5.0800000000000001  -2.9160938800395356e-16
-  33    -1.5098022196185561  -5.0800000000000001  -0.49056447857022928
-  34    -1.2843144785702287  -5.0800000000000001  -0.93310908801430126
-  35    -0.93310908801430081  -5.0800000000000001  -1.2843144785702292
-  36    -0.49056447857022878  -5.0800000000000001  -1.5098022196185563
-  37    1.9440625866930238e-16  -5.0800000000000001  -1.5874999999999999
-  38    0.49056447857022917  -5.0800000000000001  -1.5098022196185561
-  39    0.93310908801430115  -5.0800000000000001  -1.284314478570229
-  40    1.284314478570229  -5.0800000000000001  -0.93310908801430092
-  41    1.5098022196185563  -5.0800000000000001  -0.49056447857022889
-  42    1.5874999999999999  -5.0800000000000001  9.7203129334651192e-17
-  43    -11.43  7.3659999999999997  -5.0800000000000001
-  44    11.43  7.3659999999999997  -5.0800000000000001
-  45    -11.43  5.0800000000000001  -5.0800000000000001
-  46    11.43  5.0800000000000001  -5.0800000000000001
-  47    -13.716000000000001  5.0800000000000001  -11.43
-  48    -13.716000000000001  -5.0800000000000001  -11.43
-  49    -11.43  -5.0800000000000001  -11.43
-  50    -11.43  5.0800000000000001  -11.43
-  51    -11.43  -5.0800000000000001  -13.715999999999999
-  52    11.43  -5.0800000000000001  -13.715999999999999
-  53    11.43  5.0800000000000001  -13.715999999999999
-  54    -11.43  5.0800000000000001  -13.715999999999999
-
-# Part 2 - facet list
-29 1
-1 0  1
-14 1 2 3 6 5 4 42 31 7 10 9 8 21 32
-1 0  1
-7 9 10 15 14 13 12 11
-1 0  1
-4 8 9 11 16
-1 0  1
-4 11 12 17 16
-1 0  1
-4 12 13 18 17
-1 0  1
-4 13 14 19 18
-1 0  1
-4 14 15 20 19
-1 0  1
-4 10 7 20 15
-1 0  1
-18 7 31 30 29 28 27 26 25 24 23 22 21 8 16 17 18 19 20
-1 0  1
-4 21 22 33 32
-1 0  1
-4 22 23 34 33
-1 0  1
-4 23 24 35 34
-1 0  1
-4 24 25 36 35
-1 0  1
-4 25 26 37 36
-1 0  1
-4 26 27 38 37
-1 0  1
-4 27 28 39 38
-1 0  1
-4 28 29 40 39
-1 0  1
-4 29 30 41 40
-1 0  1
-4 30 31 42 41
-1 0  1
-4 43 45 46 44
-1 0  1
-4 5 6 43 44
-1 0  1
-6 4 5 44 46 53 52
-1 0  1
-4 6 3 45 43
-1 0  1
-4 47 48 49 50
-1 0  1
-8 3 2 47 50 54 53 46 45
-1 0  1
-17 42 4 52 51 49 48 1 32 33 34 35 36 37 38 39 40 41
-1 0  1
-4 2 1 48 47
-1 0  1
-4 50 49 51 54
-1 0  1
-4 54 51 52 53
-
-# Part 3 - hole list
-0
-
-# Part 4 - region list
-0
+28  3  0  1
+1  0  0  0  1
+2  2  0  0  1
+3  2  2  0  1
+4  0  2  0  1
+5  0  0  4  9
+6  2  0  4  9
+7  2  2  3  9
+8  0  2  3  9
+9  0  0  5  2
+10  2  0  5  2
+11  2  2  5  2
+12  0  2  5  2
+13  0.25  0.25  0.5  4
+14  1.75  0.25  0.5  4
+15  1.75  1.5  0.5  4
+16  0.25  1.5  0.5  4
+17  0.25  0.25  1  4
+18  1.75  0.25  1  4
+19  1.75  1.5  1  4
+20  0.25  1.5  1  4
+21  0.25  0  2  4
+22  1.75  0  2  4
+23  1.75  1.5  2  4
+24  0.25  1.5  2  4
+25  0.25  0  2.5  4
+26  1.75  0  2.5  4
+27  1.75  1.5  2.5  4
+28  0.25  1.5  2.5  4
+23  1
+1  0  1  # 1
+4    1  2  3  4
+1  0  9  # 2
+4    5  6  7  8
+2  1  3  # 3
+4    1  2  6  5
+4    21  22  26  25
+1  1  0  2.25
+1  0  3  # 4
+4    2  3  7  6
+1  0  3  # 5
+4    3  4  8  7
+1  0  3  # 6
+4    4  1  5  8
+1  0  2  # 7
+4    9  10  11  12
+1  0  3  # 8
+4    9  10  6  5
+1  0  3  # 9
+4    10  11  7  6
+1  0  3  # 10
+4    11  12  8  7
+1  0  3  # 11
+4    12  9  5  8
+1  0  4  # 12
+4    13  14  15  16
+1  0  4  # 13
+4    17  18  19  20
+1  0  4  # 14
+4    13  14  18  17
+1  0  4  # 15
+4    14  15  19  18
+1  0  4  # 16
+4    15  16  20  19
+1  0  4  # 17
+4    16  13  17  20
+1  0  4  # 18
+4    21  22  23  24
+1  0  4  # 19
+4    25  26  27  28
+1  0  4  # 20
+4    21  22  26  25
+1  0  4  # 21
+4    22  23  27  26
+1  0  4  # 22
+4    23  24  28  27
+1  0  4  # 23
+4    24  21  25  28
+2
+1  1  0.4  2.25
+2  1  0.4  0.75
+2
+1  1  0.25  0.1  10  0.001
+2  1  0.5  4  20  0.01

makefile

@@ -19,11 +19,9 @@ CXX = g++
 # -O2, -O3 ... to find the best optimization level.
 # ===================================================================
 
-CXXFLAGS = -g
+CXXFLAGS = -O3
 
-# PREDCXXFLAGS is for compiling J. Shewchuk's predicates. It should
-# always be equal to -O0 (no optimization). Otherwise, TetGen may not
-# work properly.
+# PREDCXXFLAGS is for compiling J. Shewchuk's predicates. 
 
 PREDCXXFLAGS = -O0
 
@@ -38,14 +36,7 @@ PREDCXXFLAGS = -O0
 #   down the speed of TetGen.  They can be skipped by define the -DNDEBUG
 #   switch.
 
-SWITCHES = -Wall -DSELF_CHECK
-
-# SWITCHES = -Wall -Wabi -Wctor-dtor-privacy \
-#            -Woverloaded-virtual -Wno-pmf-conversions -Wsign-promo \
-#            -Wsynth  -Wchar-subscripts -Wconversion -Wsign-compare \
-#            -Wcomment  -Wimplicit -Wmissing-braces -Wparentheses \
-#            -Wreturn-type -Wswitch -Wswitch-default \
-#            -Wswitch-enum -Wtrigraphs -W -DSELF_CHECK
+SWITCHES = 
 
 # RM should be set to the name of your favorite rm (file deletion program).