Patch v1.1.0

.codecov.yml

@@ -0,0 +1,27 @@
+coverage:
+  precision: 2
+  round: down
+  range: "30...100"
+
+  status:
+    project: no
+    patch: yes
+    changes: no
+
+parsers:
+  gcov:
+    branch_detection:
+      conditional: yes
+      loop: yes
+      method: no
+      macro: no
+
+comment:
+  layout: "header, diff, changes, tree"
+  behavior: default
+
+ignore:
+  - "*.h"
+  - "src/test/**"           # ignore test harness code
+  - "src/den2obj.cpp"       # ignore main routine of den2obj
+  - "src/generator.cpp"     # not being tested, also only used for dataset generation

.github/workflows/build-openvdb.yml

@@ -14,7 +14,7 @@ jobs:
     steps:
     - uses: actions/checkout@v3
     - name: Install dependencies
-      run: sudo apt install -y build-essential cmake libglm-dev libtclap-dev libboost-all-dev libopenvdb-dev libtbb-dev libcppunit-dev libeigen3-dev wget
+      run: sudo apt install -y build-essential cmake libglm-dev libtclap-dev libboost-all-dev libopenvdb-dev libtbb-dev libcppunit-dev libeigen3-dev wget  liblzma-dev zlib1g-dev libbz2-dev
     - name: Get sources OpenVDB 8.2
       run: wget https://github.com/AcademySoftwareFoundation/openvdb/archive/refs/tags/v8.2.0.tar.gz && tar -xvzf v8.2.0.tar.gz
     - name: Compile and install OpenVDB 8.02

.github/workflows/build.yml

@@ -14,10 +14,25 @@ jobs:
     steps:
     - uses: actions/checkout@v3
     - name: Install dependencies
-      run: sudo apt install -y build-essential cmake libglm-dev libtclap-dev libboost-all-dev libopenvdb-dev libtbb-dev libcppunit-dev libeigen3-dev
+      run: sudo apt install -y build-essential cmake libglm-dev libtclap-dev libboost-all-dev libopenvdb-dev libtbb-dev libcppunit-dev libeigen3-dev liblzma-dev zlib1g-dev libbz2-dev gcovr
     - name: Configure CMake
-      run: mkdir build && cd build && cmake ../src
+      run: mkdir build && cd build && cmake ../src -DUSE_GCOV=1
     - name: Build
-      run: cd build && make -j3
+      run: cd build && make -j
     - name: Perform unit tests
       run: cd build && make test
+    - name: Perform code coverage
+      run: |
+        cd build
+        gcovr -r ../ . --xml-pretty -e ".*\.h" > coverage.xml
+        gcovr -r ../ . --html -e ".*\.h" > report.html
+    - name: Upload coverage report
+      uses: actions/upload-artifact@v3
+      with:
+        name: code-coverage-report
+        path: ./build/report.html
+    - name: Upload coverage reports to Codecov
+      uses: codecov/codecov-action@v3
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        files: ./build/coverage.xml

.github/workflows/stats.yml

@@ -0,0 +1,22 @@
+name: stats
+
+on:
+  push:
+    branches: [ "master", "develop" ]
+  pull_request:
+    branches: [ "master", "develop" ]
+
+jobs:
+  build-stats:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: Install packages
+      run: sudo apt update && sudo apt install -y cloc
+    - name: Collect package statistics
+      run:  cloc . --report-file=stats.txt
+    - name: Store package statistics
+      uses: actions/upload-artifact@v3
+      with:
+        name: stats
+        path: ./stats.txt

.gitignore

@@ -34,4 +34,7 @@ src/config.h
 
 # do not save doc build
 docs/_build/
-docs/userguide/build*
+docs/userguide/build*
+
+# VSCODE
+.vscode

CONTRIBUTING.md

@@ -0,0 +1,92 @@
+# Contributing
+
+When contributing to this repository, please first discuss the change you wish to make via issue,
+email, or any other method with the owners of this repository before making a change.
+
+Please note we have a code of conduct, please follow it in all your interactions with the project.
+
+## Pull Request Process
+
+1. Ensure any install or build dependencies are removed before the end of the layer when doing a
+   build.
+2. Update the README.md with details of changes to the interface, this includes new environment
+   variables, exposed ports, useful file locations and container parameters.
+3. Increase the version numbers in any examples files and the README.md to the new version that this
+   Pull Request would represent. The versioning scheme we use is [SemVer](http://semver.org/).
+4. You may merge the Pull Request in once you have the sign-off of two other developers, or if you
+   do not have permission to do that, you may request the second reviewer to merge it for you.
+
+## Code of Conduct
+
+### Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, gender identity and expression, level of experience,
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
+
+### Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+### Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+### Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+### Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at [INSERT EMAIL ADDRESS]. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+### Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at [http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/

README.md

@@ -3,6 +3,7 @@
 ![GitHub tag (latest SemVer)](https://img.shields.io/github/v/tag/ifilot/den2obj?label=version)
 [![C/C++ CI](https://github.com/ifilot/den2obj/actions/workflows/build.yml/badge.svg)](https://github.com/ifilot/den2obj/actions/workflows/build.yml)
 [![OpenVDB build CI](https://github.com/ifilot/den2obj/actions/workflows/build-openvdb.yml/badge.svg)](https://github.com/ifilot/den2obj/actions/workflows/build-openvdb.yml)
+[![codecov](https://codecov.io/gh/ifilot/bramble/graph/badge.svg?token=IZ7OGUR6DY)](https://codecov.io/gh/ifilot/den2obj)
 [![Documentation](https://github.com/ifilot/den2obj/actions/workflows/docs.yml/badge.svg)](https://den2obj.imc-tue.nl)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 
@@ -12,16 +13,7 @@ scalar fields. Den2Obj supports VASP charge files such as CHGCAR and PARCHG,
 Gaussian .cube files as well as its own .d2o format.
 
 ## Example images
-![3D Reaction-Diffusion system](img/reac_diff_3d_network_small.png)
-
-*The isosurface above represents the concentration profile of a
- reaction-diffusion system in 3D using Gray-Scott kinetics. The isosurface has
- been generated using den2obj and rendered using [Blender]
- (https://www.blender.org/).*
-
-![Molecular orbitals of CO](img/CO_mos.jpg)
-
-*The isosurfaces of the first 10 molecular orbitals of the CO molecule.*
+![Canonical valence orbitals of CH4](docs/_static/img/ch4_valence_orbitals.png)
 
 ## Compilation instructions
 
@@ -30,7 +22,7 @@ Gaussian .cube files as well as its own .d2o format.
 Getting the dependencies
 ```
 sudo apt install build-essential cmake libtclap-dev libboost-all-dev libopenvdb-dev libtbb-dev \
-pkg-config libcppunit-dev libeigen3-dev
+pkg-config libcppunit-dev libeigen3-dev liblzma-dev zlib1g-dev
 ```
 
 To compile, run the following commands:

docs/.gitignore

@@ -0,0 +1 @@
+_build/*