Merge pull request #52 from kellykochanski/kk/JOSS-fixes

JOSS review and editorial comments

CMakeLists.txt

@@ -1,20 +1,26 @@
 cmake_minimum_required (VERSION 3.9)
 
+# Use new policies on versions of CMake that have been tested
+cmake_policy(VERSION 3.9.3...3.15.4)
+
+# Let us use, e.g., PNG_ROOT=/path/to/libpng, in the environment to
+# tell find_package() where to look. Usefull on clusters.
+if(POLICY CMP0074)
+  cmake_policy(SET CMP0074 NEW)
+endif()
+
+
 project (rescal-snow
   DESCRIPTION "Simulating snow self-organization with cellular automata"
-  HOMEPAGE_URL "https://github.com/kellykochanski/rescal-snow"
   LANGUAGES C
 )
 
 set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH})
 find_package(Sanitizers)
 
-add_subdirectory(lib/libpng-1.6.37)
-add_subdirectory(lib/zlib-1.2.11)
-
-#Ugly hack needed to fix a mysterious issue on Mac
-include_directories(lib/libpng-1.6.37)
-include_directories(${CMAKE_CURRENT_BINARY_DIR}/lib/libpng-1.6.37)
+set(THREADS_PREFER_PTHREAD_FLAG TRUE)
+find_package(PNG 1.6 REQUIRED)
+find_package(Threads REQUIRED)
 
 set(COMMON_SOURCES
   src/cells.c
@@ -81,11 +87,11 @@ function(setup_target target)
   add_sanitizers(${target})
 endfunction(setup_target)
 
-target_link_libraries(rescal    PRIVATE png pthread m)
-target_link_libraries(genesis   PRIVATE png m)  
-target_link_libraries(regenesis PRIVATE m)  
-target_link_libraries(bin2png   PRIVATE png m)  
-target_link_libraries(csp2png   PRIVATE png m)  
+target_link_libraries(rescal    PRIVATE PNG::PNG Threads::Threads m)
+target_link_libraries(genesis   PRIVATE PNG::PNG m)
+target_link_libraries(regenesis PRIVATE m)
+target_link_libraries(bin2png   PRIVATE PNG::PNG m)
+target_link_libraries(csp2png   PRIVATE PNG::PNG m)
 
 setup_target(rescal)
 setup_target(genesis)

CODE_OF_CONDUCT.md

@@ -0,0 +1,50 @@
+ # Contributor Covenant Code of Conduct <a name="conduct">
+
+## Our Pledge
+In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to make
+participation in our project and our community a harassment-free experience for everyone, regardless of age, body size,
+disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status,
+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 within all project spaces, and it also applies when an individual is representing the project or its
+community in public spaces. 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
+[email protected]. 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, version 1.4, available at https://www.contributor
+covenant.org/version/1/4/code-of-conduct.html 
+For answers to common questions about this code of conduct, see https://www.contributor-covenant.org/fa
+

CONTRIBUTING.md

@@ -0,0 +1,55 @@
+# How to contribute <a name="contribute">
+
+Thank you for taking the time to contribute! We're excited to see your work.
+
+[How can I contribute?](#contribute)
+ - [Reporting bugs](#bugs)
+ - [Adding features](#features)
+    - [Git workflow and pull requests](#workflow)
+ [Code of conduct](#conduct)
+
+ ## Reporting bugs <a name="bugs">
+ Please report bugs as Github Issues. Include steps necessary to reproduce the bug, any error text, and a description of the system on which the bug occurred. 
+ For installation issues, include version numbers for the compiler, cmake, and the library dependencies.
+
+ If you think you can fix the bug, great! See the features and pull request guidelines below for how to incorporate your bugfix into the Rescal-snow github.
+
+ ## Adding features <a name="features">
+ Rescal-snow grows by adding new features. Features include:
+  - New capabilities for the Rescal-snow simulation (e.g. cohesion, or new inputs)
+  - New workflow management, analysis, or visualization scripts
+
+ The ideal feature:
+  - Satisfies a clearly-defined purpose (e.g. "Add time-varying snowfall capability")
+      - So "Fixed some typos in X.md" is a separate feature from "Added new tool for..."
+  - Is self-contained in organized files, classes, and/or functions
+  - Does not add dependencies to Rescal-snow or any existing script (optional dependencies OK)
+  - Does not remove existing capabilities or break existing tutorials
+
+We want your code to be be readable (so we can accept it), and described in the docs (so it will be found and used).
+To make this possible, features that add new capabilities to Rescal-snow should include the following documentation:
+  - Docstrings on every multi-line function
+  - Author, date, and high-level purpose information in each new script/class
+  - A tutorial or example in `docs` explaining the use of any novel capabilities
+  - A reference that makes new capabilities discoverable through either `README.md` or `docs/rescal-snow-tutorial.md`
+  - For particularly significant changes (project >1wk), appropriate additions to `NEWS.md` and `AUTHORS.md`
+
+ ### Git workflow and pull requests <a name="workflow">
+ We use the git branching workflow described [here](https://nvie.com/posts/a-successful-git-branching-model/) (if new to git, see link for useful commands).
+
+ This consists of 4 main types of branches:
+  - The `master` branch, which is changed only by new releases
+  - A `develop` branch, which collects stable inter-release changes
+  - An occasional `rescal-snow-release-X` branch which collects changes near new releases
+  - *Feature* and *bugfix* branches for active development
+
+When you add code to Rescal-snow, we encourage you to fork the code, 
+then create a bug or feature branch titled `name/purpose`, e.g. `kk/snowfall`.
+```bash
+$ git checkout -b name/purpose develop
+```
+and commit your changes.
+
+When the feature or bugfix is ready to be incorporated into Rescal-snow, open a [pull request](https://help.github.com/en/articles/creating-a-pull-request) against `develop`.
+The feature should pass the tests in [test/test.sh](test/test.sh).
+

NEWS.md

@@ -0,0 +1,154 @@
+# News and development history
+
+## rescal-snow 1.1
+
+Created in response to Journal of Open Source Software review.
+
+ - docs updated
+
+ - paper.md and paper.bib created and reviewed
+
+ - test folder added with bash testing scripts
+
+ - tutorials tested and refined
+
+ - visualization examples refined to use cellspace/heightmap tools
+
+
+## rescal-snow 1.0
+
+Split from ReSCAL. Code slimmed down to focus on DUN and SNO models, rather than RIV, CMB, etc.
+
+#### Models, templates and functionality
+
+- Added SNO model
+
+- Added snowfall ability to SNO model, with accompanying Csp_template SNOWFALL
+
+- Added sintering ability to SNOW model
+
+- Removed non-dune-related models including RIV, CMB, etc
+
+#### Tools for set-up, post-processing, and parameter space exploration
+
+- Added 'scripts/utilities' folder containing python tools for setting up large numbers of runs for parameter space explorations
+
+- Added cross-correlation analysis tool
+
+- Added fft analysis and visualization tool
+
+#### Organization
+
+- Removed many regions of commented-out code
+
+- Model output now funnelled through 'write_output' files for standardization
+
+- Model output may now be organized in output directories
+
+#### Performance and compatibility
+
+- Converted all instances of 'int' to 'int32_t' for cross-platform compatibility
+
+- Added additional AVX optimizations to the lattice gas
+
+- Removed GTK dependency; graphics now handled entirely through LIBPNG
+
+- Modified configure and make pathways to account for new dependencies
+
+## ReSCAL Version 1.6 (2016)
+
+- AVX optimization of lattice-gas propagation.
+
+- Optimization of flow interpolation.
+
+- New command-line option (-pat) for the concurrent execution of stochastic engine 
+and lattice gas, with non-deterministic algorithm.
+
+- Command-line help improved with new options -h and -hm.
+
+- More CSP templates and parameters for DUN model.
+
+- Various fixes.
+
+## ReSCAL Version 1.5
+- Relief light-shading with various colors, for colored sand and topographic 
+obstacles (DUM cells) in DUN and AVA models, and for fluid cells in RIV model.
+
+- More simple syntax for graphical options in command-line.
+
+- The graphical display readapts automatically as the window gets larger.
+
+- Better interactivity with the positioning of cross sections.
+
+- New TRACE_FLUX mode in DUN model for the calculation of the average sand flux
+over time, compatible with rotations.
+
+- New option for stability analysis in DUN model.
+
+- New parameters and transtions for the mobility of sand in DUN model.
+
+- Introduction of vegetated cells in the DUN model, with specific transitions
+and parameters.
+
+- Time metadata added in CSP format.
+
+- More CSP templates, and arguments added in previous templates.
+
+- Many tweaks and fixes.
+
+## ReSCAL Version 1.4
+
+- New FULL rotation mode for rotating the whole cellular space with support of
+periodic boundary conditions and lattice gas coupling.
+
+- More CSP templates and samples.
+
+- RIV model improved.
+
+- More graphical options and parameters.
+
+- Scripts added for video encoding.
+
+- Various fixes and optimizations.
+
+## ReSCAL Version 1.3.2
+
+- OpenMP support in lgca module.
+
+- New trace mode TRACE_PAR_COL for the tracking of colored particles.
+
+## ReSCAL Version 1.3.1
+
+- New parameter for boundary conditions.
+
+- Library gd not needed anymore.
+
+## ReSCAL Version 1.3
+
+- The time scale is calculated in DUN model, and t0 time unit can be used for all delays on the command-line.
+
+- Cellular space is automatically reoriented on images, after rotations.
+
+- New parameters with CELL_COLOR option.
+
+- Support for CSP templates in genesis.
+
+- New LIFE model implemented.
+
+## ReSCAL Version 1.2
+
+- CSP format with metadata has been implemented.
+
+- New parameters available for avalanches and lattice gaz.
+
+- Interactive display and new disposition in drawing area.
+
+## ReSCAL Version 1.1
+
+- Integration of glade interface with toolbar and statusbar.
+
+- Compatibility with gtk+ 1.x has been abandoned.
+
+## ReSCAL Version 1.0
+
+- This is the first release of ReSCAL, under the GNU General Public License.  It is far from complete. But it provides a number of predefined models with some parameters and mechanisms, included lattice gaz coupling, and real-time display with several graphical options.

Pipfile

@@ -0,0 +1,15 @@
+[[source]]
+name = "pypi"
+url = "https://pypi.org/simple"
+verify_ssl = true
+
+[dev-packages]
+
+[packages]
+numpy = "*"
+matplotlib = "*"
+scipy = "*"
+pandas = "*"
+
+[requires]
+python_version = "3.7"