Merge pull request #68 from RangamaniLabUCSD/development

* Update issue templates (#66)
* chore: add bug report and feature issue templates
* Support for auto copyright processing (#67)
* chore: Add automatic copyright processing scripts
Borrowed from GROMACS. Headers are updated accordingly.
* Switching to standard Helfrich (#65)
* refactor: Refactor convergence test printing
* test: Add roller boundary test example
* chore: bump geometry-central to latest
* feat: Add back pure Gaussian term. Also restoring deviatoric implementation
* refactor: Add Kg  and Kgc to python api
* style: Fix typo in boilerplate
* refactor: Move updateconfiguration into updatePrescription
* refactor: change backtracking to test with updated timestep

---------

Signed-off-by: Christopher T. Lee <ctlee@ucsd.edu>

.gitattributes

@@ -1 +1,13 @@
 .git_archival.txt  export-subst
+
+# Generic rules
+*.cpp           filter=copyright
+*.h             filter=copyright
+CMakeLists.txt  filter=copyright
+*.cmake         filter=copyright
+*.py            filter=copyright
+
+# Exceptions: files to exclude
+libraries/pcg/*     !filter
+libraries/pcg/**    !filter
+libraries/pcg/**/*  !filter

.github/ISSUE_TEMPLATE/bug.md

@@ -0,0 +1,32 @@
+---
+name: Bug Report
+about: Create a report to help us improve
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+**Summary**
+
+(Summarize the bug encountered concisely)
+
+**Mem3DG version**
+
+(Paste the output of `pymem3dg.__version__` if you are using pymem3dg or value of `mem3dg::MEM3DG_VERSION` here.)
+
+**Steps to reproduce**
+
+(Please describe how we can reproduce the bug, and share all files needed. Submitting a minimal working example isolating the issue will improve response time.)
+
+**What is the current bug behavior?**
+
+(What actually happens)
+
+**What did you expect the correct behavior to be?**
+
+(What you should see instead)
+
+**Possible fixes**
+
+(Any suggestions or thoughts are welcome. If you can, link to the line of code that might be responsible for the problem)

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,32 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: enhancement
+assignees: ''
+
+---
+
+**Summary**
+
+(Why would this be useful?)
+
+**Use cases**
+
+(Describe how the feature will make a difference - from a user point of view, not just developers.)
+
+**Impact**
+
+(What users would this matter to? Is it likely to have large impact relative to the amount of work required?)
+
+**Detailed description**
+
+(Describe the feature in detail. If this is e.g. a new algorithm you developed, are there a lot of people who have cited the paper, or other implementations available? How does it go beyond the current state of the code?)
+
+**Requirements**
+
+(Is there other stuff needed?)
+
+**Links/references/implementations**
+
+(Having a link to a paper can be a nice addition to a detailed description, but it's unlikely developers will have time to e.g. go and read a paper if you didn't have time to describe the feature in detail here. Would you be willing to write the implementation?)

.gitignore

@@ -141,7 +141,7 @@ dmypy.json
 /.vs
 /.vscode
 
-CMakeSettings.json
+/CMakeSettings.json
 docs/html/
 .polyscope.ini
 _skbuild/
@@ -157,3 +157,4 @@ python_src/pymem3dg/lib
 imgui.ini
 *.ply
 *.nc
+Testing

.pre-commit-config.yaml

@@ -41,3 +41,10 @@ repos:
     rev: 054bda51dbe278b3e86f27c890e3f3ac877d616c
     hooks:
       - id: validate-cff
+
+  - repo: local
+    hooks:
+      - id: check-copyright
+        name: Check copyright
+        entry: ./admin/copyright-precommit-check.sh
+        language: script

CMakeLists.txt

@@ -1,16 +1,17 @@
-# Membrane Dynamics in 3D using Discrete Differential Geometry (Mem3DG)
+#
+# Membrane Dynamics in 3D using Discrete Differential Geometry (Mem3DG).
+#
+# Copyright 2020- The Mem3DG Authors
+# and the project initiators Cuncheng Zhu, Christopher T. Lee, and
+# Padmini Rangamani.
 #
 # This Source Code Form is subject to the terms of the Mozilla Public
 # License, v. 2.0. If a copy of the MPL was not distributed with this
 # file, You can obtain one at http://mozilla.org/MPL/2.0/.
 #
-# Copyright (c) 2020:
-#     Laboratory for Computational Cellular Mechanobiology
-#     Cuncheng Zhu (cuzhu@eng.ucsd.edu)
-#     Christopher T. Lee (ctlee@ucsd.edu)
-#     Ravi Ramamoorthi (ravir@cs.ucsd.edu)
-#     Padmini Rangamani (prangamani@eng.ucsd.edu)
-#
+# Please help us support Mem3DG development by citing the research
+# papers on the package. Check out https://github.com/RangamaniLabUCSD/Mem3DG/
+# for more information.
 
 # Use CMAKE_MSVC_RUNTIME_LIBRARY to control linked runtime
 cmake_policy(SET CMP0091 NEW)

admin/copyright-precommit-check.sh

@@ -0,0 +1,49 @@
+#!/usr/bin/env bash
+#
+# Membrane Dynamics in 3D using Discrete Differential Geometry (Mem3DG).
+#
+# Copyright 2024- The Mem3DG Authors
+# and the project initiators Cuncheng Zhu, Christopher T. Lee, and
+# Padmini Rangamani.
+#
+# This Source Code Form is subject to the terms of the Mozilla Public
+# License, v. 2.0. If a copy of the MPL was not distributed with this
+# file, You can obtain one at http://mozilla.org/MPL/2.0/.
+#
+# Please help us support Mem3DG development, by citing the research
+# papers on the package. Check out https://github.com/RangamaniLabUCSD/Mem3DG/.
+
+# This script runs copyright header checks on modified files and
+# reports/applies the necessary changes. It is shamelessly borrowed
+# from the GROMACS project.
+#
+# See `copyright.sh -h` for a brief usage description.
+
+# Parse command-line arguments
+function usage() {
+    echo "usage: copyright-precommit-check.sh {FILES}"
+x
+}
+
+srcdir=`git rev-parse --show-toplevel`
+pushd $srcdir >/dev/null
+admin_dir=$srcdir/admin
+
+FILES=$(echo "$@" | tr " " "\n")
+FILTERED_FILES=$(echo "$FILES" | git check-attr --stdin filter | sed -e 's/.*: filter: //'| paste <(echo "$FILES") - | grep -E 'copyright$' | cut -f1)
+
+if [ -z "$FILTERED_FILES"]
+then
+    popd >/dev/null
+    exit 0
+fi
+
+if ! $admin_dir/copyright.py -F <(echo "$FILTERED_FILES") --add-missing --update-header
+then
+    echo "Copyright checking failed!"
+    exit 2
+fi
+
+# Get back to the original directory
+popd >/dev/null
+exit 0