Update of minor things (#433)

* Updating README

* Removing numbers package

* Switching off apt-spy2

* Ignore coverage reduction

Author: llaniewski

.codecov.yaml

@@ -1,2 +1,7 @@
 ignore:
   - "**/pugi*"  # ignore pugixml
+coverage:
+  status:
+    project:
+      default:
+        threshold: 100%

.github/actions/install/action.yaml

@@ -54,7 +54,7 @@ inputs:
     default: false
   bestapt:
     description: select the best APT before installing stuff
-    default: true
+    default: false
 runs:
   using: 'composite'
   steps:

.github/workflows/cpu_test.yml

@@ -1,4 +1,4 @@
-name: TESTS_GCC
+name: CPU
 
 on: [ push, pull_request ]
 

.github/workflows/gpu_comp.yml

@@ -1,4 +1,4 @@
-name: GPU
+name: CUDA
 
 on: [ push, pull_request ]
 

README.md

@@ -52,12 +52,14 @@ Nevertheless, TCLB can be compiled on Windows using the [Windows Subsystem for L
 ### Dependencies
 
 For the code to compile and work you'll need a few things:
-- [R](https://www.r-project.org/) and some R packages ([optparse](https://cran.r-project.org/package=optparse), [numbers](https://cran.r-project.org/package=numbers), [rtemplate](https://github.com/llaniewski/rtemplate), [gvector](https://github.com/llaniewski/gvector), [polyAlgebra](https://github.com/llaniewski/polyAlgebra))
+- [R](https://www.r-project.org/) and some R packages ([optparse](https://cran.r-project.org/package=optparse), [rtemplate](https://github.com/llaniewski/rtemplate), [gvector](https://github.com/llaniewski/gvector), [polyAlgebra](https://github.com/llaniewski/polyAlgebra))
 - [MPI](https://en.wikipedia.org/wiki/Message_Passing_Interface). We recommend [OpenMPI](http://www.open-mpi.org/)
-- To use your GPU, you'll need [nVidia CUDA](https://developer.nvidia.com/cuda-zone)
+- To use your GPU, you'll need [nVidia CUDA](https://developer.nvidia.com/cuda-zone) or [AMD HIP/ROCm](https://www.amd.com/en/graphics/servers-solutions-rocm)
+
+Optionally, you may need:
 - To integrate TCLB with R, you'll need R package [rinside](https://github.com/eddelbuettel/rinside)
 - To integrate TCLB with Python, you'll need [python](https://www.python.org/), [numpy](http://www.numpy.org/) with libraries and headers
-- To develop a model using Python, you'll need [python](https://www.python.org/), [sympy](http://www.sympy.org/) and R package: [rPython](https://cran.r-project.org/package=rPython)
+- To develop a model using Python, you'll need [python](https://www.python.org/), [sympy](http://www.sympy.org/) and R package [reticulate](https://cran.r-project.org/package=reticulate)
 
 You can install many of these with the provided `tools/install.sh` script (note that this requires sudo):
 ```bash
@@ -112,17 +114,19 @@ TCLB began development in 2012 with the aim at providing a framework for efficie
 
 Author: [Łukasz Łaniewski-Wołłk](https://github.com/llaniewski)
 
-Co-authors:
+Major contributors:
 * [Michał Dzikowski](https://github.com/mdzik)
+* [Travis Mitchell](https://github.com/TravisMitchell)
 
 Contributors:
-* [Wojtek Regulski](https://github.com/wojtasMEiL)
-* [Zbigniew Gawłowicz](https://github.com/zgawlowicz)
+* [Nathan Di Vaira](https://github.com/ndivaira)
+* [Grzegorz Gruszczyński](https://github.com/ggruszczynski)
+* [Bryce Hill](https://github.com/bhill23)
+* [Jon McCullough](https://github.com/JonMcCullough)
+* [Paweł Obrępalski](https://github.com/PabloOb)
+* [Wojciech Regulski](https://github.com/wojtasMEiL)
 * [Mariusz Rutkowski](https://github.com/mrutkowski-aero)
 * [Dmytro Sashko](https://github.com/shkodm)
-* [Travis Mitchell](https://github.com/TravisMitchell)
-* [Paweł Obrępalski](https://github.com/PabloOb)
-* [Grzegorz Gruszczyński](https://github.com/ggruszczynski)
 
 Developed at:
 - [Zakład Aerodynamiki](https://meil.pw.edu.pl/ZA/) at [Politechnika Warszawska (Warsaw University of Technology)](http://pw.edu.pl/)

src/configure.ac

@@ -686,8 +686,8 @@ fi
 
 AC_MSG_CHECKING([R package: optparse])
 AS_IF([$R_BIN --vanilla --slave -e 'if (!require("optparse")) stop("No");' >/dev/null 2>&1],AC_MSG_RESULT([yes]),AC_MSG_ERROR([no]))
-AC_MSG_CHECKING([R package: numbers])
-AS_IF([$R_BIN --vanilla --slave -e 'if (!require("numbers")) stop("No");' >/dev/null 2>&1],AC_MSG_RESULT([yes]),AC_MSG_ERROR([no]))
+#AC_MSG_CHECKING([R package: numbers])
+#AS_IF([$R_BIN --vanilla --slave -e 'if (!require("numbers")) stop("No");' >/dev/null 2>&1],AC_MSG_RESULT([yes]),AC_MSG_ERROR([no]))
 AC_MSG_CHECKING([R package: rtemplate])
 AS_IF([$R_BIN --vanilla --slave -e 'if (!require("rtemplate")) stop("No");' >/dev/null 2>&1],AC_MSG_RESULT([yes]),AC_MSG_ERROR([no]))
 AC_MSG_CHECKING([R package: gvector])

src/lib/feq.R

@@ -1,7 +1,10 @@
 #library(polyAlgebra)
 
-gcd <- function(a,b) ifelse (b==0, a, gcd(b, a %% b))
-library(numbers)
+gcd = function(a,b) ifelse (b==0, a, gcd(b, a %% b))
+lcm = function(a,b) (a/gcd(a,b))*b
+lcm_vec = function(x) if (length(x) == 1) x else lcm(x[1],lcm_vec(x[-1]))
+
+# library(numbers)
 
 MRT_polyMatrix = function(U) {
   if (any(U >  1)) stop("Too high velocities in calculate_feq")
@@ -25,7 +28,7 @@ MRT_integerOrtogonal = function(M) {
     g = gcd(a,b)
     a = a/g
     b = b/g
-    if (length(b) == 1) l = b else l=mLCM(b);
+    if (length(b) == 1) l = b else l = lcm_vec(b);
     M[,i] = M[,i]*l - M[,1:(i-1),drop=F] %*% (l*a/b)
   }
   M

tools/install.sh

@@ -329,11 +329,11 @@ do
 		then
 				install_rpackage_github cran/getopt
 				install_rpackage_github cran/optparse
-				install_rpackage_github cran/numbers
+#				install_rpackage_github cran/numbers
 				install_rpackage_github cran/yaml
 		else
 				install_rpackage optparse
-				install_rpackage numbers
+#				install_rpackage numbers
 				install_rpackage yaml
 		fi
 		install_rpackage_github llaniewski/rtemplate