Update nimble branch

README.md

@@ -113,9 +113,9 @@ Several other methods are in testing and will likely be added in the future rele
 scientific computing community.
 
 ## Usage in Nim
-Usage within Nim is fairly straightforward. You can install it using Nimble as explained earlier, or install it directly from GitHub:
+Usage within Nim is fairly straightforward. You can install it using Nimble as explained earlier, or install it directly from GitHub, making sure to use the slightly modified `@#nimble` branch:
 ```cmd
-nimble install -y https://github.com/amkrajewski/nimplex
+nimble install -y https://github.com/amkrajewski/nimplex@#nimble
 ```
 or, if you wish to modify the source code, you can simply download the core file `nimplex.nim` and place it in your own code, as long as you have the dependencies installed, since it is standalone. 
 **Then simply follow the API documentation below.**

docs/docs.nim

@@ -25,7 +25,7 @@
 ##    ```cmd
 ##    ./nimplex -c IFP 3 10
 ##    ```
-## 2. An **compiled Python library**, which you can import and use in your Python code like so:
+## 2. A **compiled Python library**, which you can import and use in your Python code like so:
 ##    ```python
 ##    import nimplex
 ##    ```
@@ -111,9 +111,9 @@
 ##     Critically, unlike the O(N^2) distance-based graph generation methods, this approach **scales linearly** with the resulting number of nodes. Because of that, it is extremely efficient even in high-dimensional spaces, where the number of
 ##     edges goes into trillions and beyond. Nimplex can **both generate and find neighbors** for around **2M points per second in 9-dimensional space** on a modern CPU. 
 ## 
-##     As explored in the manuscript, such representations, even of different dimensions, can can then be used to efficeintly encode complex problem spaces where some prior assumptions and knowledge are available. In the Example #2 from
-##     manuscript, inspired by problem of joining titanium with stainless steel in [10.1016/j.addma.2022.102649](https://doi.org/10.1016/j.addma.2022.102649) using 3-component
-##     spaces, one encode 3 separate paths where some components are shared in predetermined fashion. This to efficiently encode the problem space in form of a structure graph (left panel below) and then use it to construct a
+##     As explored in the manuscript, such representations, even of different dimensions, can then be used to efficeintly encode complex problem spaces where some prior assumptions and knowledge are available. Consider the problem of joining
+##     titanium with stainless steel using 3-component spaces as presented in Bobbio et. al, [10.1016/j.addma.2022.102649](https://doi.org/10.1016/j.addma.2022.102649). Example #2 from the manuscript handles this problem by encoding 3
+##     separate paths where some components are shared in a predetermined fashion. This is done to efficiently encode the problem space in the form of a structure graph (left panel below) and then use it to construct a
 ##     single **simplex graph complex** (right panel below) as a single consistent structure.
 ## 
 ##     .. figure:: ../assets/Fig4.png
@@ -123,9 +123,9 @@
 ## scientific computing community.
 ## 
 ## ## Usage in Nim
-## Usage within Nim is fairly straightforward. You can install it using Nimble as explained earlier, or install it directly from GitHub:
+## Usage within Nim is fairly straightforward. You can install it using Nimble as explained earlier, or install it directly from GitHub, making sure to use the slightly modified `@#nimble` branch:
 ## ```cmd
-## nimble install -y https://github.com/amkrajewski/nimplex
+## nimble install -y https://github.com/amkrajewski/nimplex@#nimble
 ## ```
 ## or, if you wish to modify the source code, you can simply download the core file `nimplex.nim` and place it in your own code, as long as you have the dependencies installed, since it is standalone. 
 ## **Then simply follow the API documentation below.**
@@ -232,4 +232,4 @@
 ## ## API
 ## 
 ## **The following sections cover the core API of the library.** Further documentation for auxiliary functions, defined in **utils** submodule, can be found by following links under [Imports](#6) below
-## or by searching the API [Index](theindex.html) in the top left corner of this page.
+## or by searching the API [Index](theindex.html) in the top left corner of this page.

nimplex.nim

@@ -11,6 +11,7 @@ import std/sugar
 import std/times
 import std/strutils
 from std/algorithm import reverse
+from std/sequtils import foldl, mapIt
 
 # Arraymancer library for tensor operations
 import arraymancer/Tensor
@@ -402,12 +403,12 @@ proc outFunction(config: string, npyName: string, outputData: Tensor) =
     ## and the destiantion filename `npyName`, which should include the extension.
     case config[2]:
         of 'P': 
-            echo "Full Output:", outputData
+            echo "Full Output: ", outputData
         of 'N': 
             outputData.write_npy(npyName)
-            echo "Shape:", outputData.shape
+            echo "Shape: ", outputData.shape
         of 'S': 
-            echo "Shape:", outputData.shape
+            echo "Shape: ", outputData.shape
         else: 
             echo "Invalid Config"
 
@@ -434,11 +435,11 @@ proc outFunction_graph(config: string, dim: int, ndiv: int, npyName: string, out
                     else:
                         neighborsTensor[i, j] = -1
             neighborsTensor.write_npy(npyName.replace(".npy", "_neighbors.npy"))
-            echo "Nodes Shape:", outputData[0].shape
-            echo "Neighbors Lenght:", outputData[1].len
+            echo "Nodes Shape: ", outputData[0].shape
+            echo "Edges Count: ", outputData[1].mapIt(it.len).foldl(a + b, 0)
         of 'S': 
-            echo "Nodes Shape:", outputData[0].shape
-            echo "Neighbors Lenght:", outputData[1].len
+            echo "Nodes Shape: ", outputData[0].shape
+            echo "Edges Count: ", outputData[1].mapIt(it.len).foldl(a + b, 0)
         else: 
             echo "Invalid Congig"
 
@@ -495,14 +496,14 @@ when appType != "lib":
                 let tempIn = readLine(stdin)
                 if tempIn.len > 0:
                     npyName = tempIn
-                echo "Persisting to NumPy array file:", npyName
+                echo "Persisting to NumPy array file: ", npyName
 
             taskRouter(config, dim, ndiv, npyName)
 
         # Configured
         elif args[0] == "-c" or args[0] == "--config":
             let config = args[1]
-            echo "Running with configuration:", args[1..<args.len]
+            echo "Running with configuration: ", args[1..<args.len]
             configValidation(config)
 
             let dim = args[2].parseInt()
@@ -520,7 +521,7 @@ when appType != "lib":
             if config[2] == 'N':
                 if args.len == 5:
                     npyName = args[4]
-                echo "Persisting to NumPy array file:", npyName
+                echo "Persisting to NumPy array file: ", npyName
 
             taskRouter(config, dim, ndiv, npyName)
 

tests/cli.nim

@@ -3,12 +3,15 @@ import system
 import std/unittest
 import std/strutils
 import std/sequtils
-import std/sugar
 import arraymancer/Tensor
 import arraymancer/io
 import std/hashes
 import ../nimplex
 import std/sets
+import std/times
+
+let t0 = cpuTime()
+echo "***** CLI Tests *****"
 
 suite "test if correct grid output is given when nimplex is run in command line with some selected configurations":
     test "check if compiled nimplex is present in the current working directory":
@@ -22,7 +25,9 @@ suite "test if correct grid output is given when nimplex is run in command line
         let 
             (output, exitCode) = execCmdEx("./nimplex -c FIS 3 3")
             outputLines = output.splitLines
-            reference = @["Running with configuration:@[\"FIS\", \"3\", \"3\"]", "Shape:[10, 3]"]
+            reference = @[
+                "Running with configuration: @[\"FIS\", \"3\", \"3\"]", 
+                "Shape: [10, 3]"]
         check exitCode == 0
         for i in 0..<reference.len:
             check outputLines[i] == reference[i]
@@ -31,7 +36,9 @@ suite "test if correct grid output is given when nimplex is run in command line
         let 
             (output, exitCode) = execCmdEx("./nimplex -c FIS 9 12")
             outputLines = output.splitLines
-            reference = @["Running with configuration:@[\"FIS\", \"9\", \"12\"]", "Shape:[125970, 9]"]
+            reference = @[
+                "Running with configuration: @[\"FIS\", \"9\", \"12\"]", 
+                "Shape: [125970, 9]"]
         check exitCode == 0
         for i in 0..<reference.len:
             check outputLines[i] == reference[i]
@@ -40,7 +47,9 @@ suite "test if correct grid output is given when nimplex is run in command line
         let 
             (output, exitCode) = execCmdEx("./nimplex -c IIS 7 12")
             outputLines = output.splitLines
-            reference = @["Running with configuration:@[\"IIS\", \"7\", \"12\"]", "Shape:[462, 7]"]
+            reference = @[
+                "Running with configuration: @[\"IIS\", \"7\", \"12\"]",
+                "Shape: [462, 7]"]
         check exitCode == 0
         for i in 0..<reference.len:
             check outputLines[i] == reference[i]
@@ -50,8 +59,8 @@ suite "test if correct grid output is given when nimplex is run in command line
             (output, exitCode) = execCmdEx("./nimplex -c FIP 3 3")
             outputLines = output.splitLines
             reference = @[
-                "Running with configuration:@[\"FIP\", \"3\", \"3\"]", 
-                "Full Output:Tensor[system.int] of shape \"[10, 3]\" on backend \"Cpu\"", 
+                "Running with configuration: @[\"FIP\", \"3\", \"3\"]", 
+                "Full Output: Tensor[system.int] of shape \"[10, 3]\" on backend \"Cpu\"", 
                 "|0      0     3|", 
                 "|0      1     2|", 
                 "|0      2     1|", 
@@ -72,8 +81,8 @@ suite "test if correct grid output is given when nimplex is run in command line
             (output, exitCode) = execCmdEx("./nimplex -c IIP 3 5")
             outputLines = output.splitLines
             reference = @[
-                "Running with configuration:@[\"IIP\", \"3\", \"5\"]", 
-                "Full Output:Tensor[system.int] of shape \"[6, 3]\" on backend \"Cpu\"", 
+                "Running with configuration: @[\"IIP\", \"3\", \"5\"]", 
+                "Full Output: Tensor[system.int] of shape \"[6, 3]\" on backend \"Cpu\"", 
                 "|1      1     3|", 
                 "|1      2     2|", 
                 "|1      3     1|", 
@@ -145,8 +154,23 @@ suite "test if correct graph output is given when nimplex is run in command line
             (output, exitCode) = execCmdEx("./nimplex -c GIS 3 3")
             outputLines = output.splitLines
             reference = @[
-                "Running with configuration:@[\"GIS\", \"3\", \"3\"]", 
-                "Nodes Shape:[10, 3]"]
+                "Running with configuration: @[\"GIS\", \"3\", \"3\"]", 
+                "Nodes Shape: [10, 3]",
+                "Edges Count: 36"
+                ]
+        check exitCode == 0
+        for i in 0..<reference.len:
+            check outputLines[i] == reference[i]
+
+    test "generate medium size integer simplex graph (GIS 7 12) and print shape to stdout":
+        let 
+            (output, exitCode) = execCmdEx("./nimplex -c GIS 7 12")
+            outputLines = output.splitLines
+            reference = @[
+                "Running with configuration: @[\"GIS\", \"7\", \"12\"]", 
+                "Nodes Shape: [18564, 7]",
+                "Edges Count: 519792"
+                ]
         check exitCode == 0
         for i in 0..<reference.len:
             check outputLines[i] == reference[i]
@@ -156,7 +180,7 @@ suite "test if correct graph output is given when nimplex is run in command line
             (output, exitCode) = execCmdEx("./nimplex -c GIP 3 3")
             outputLines = output.splitLines
             reference = @[
-                "Running with configuration:@[\"GIP\", \"3\", \"3\"]", 
+                "Running with configuration: @[\"GIP\", \"3\", \"3\"]", 
                 "Nodes:",
                 "Tensor[system.int] of shape \"[10, 3]\" on backend \"Cpu\"", 
                 "|0      0     3|", 
@@ -181,8 +205,10 @@ suite "test if correct graph output is given when nimplex is run in command line
             (output, exitCode) = execCmdEx("./nimplex -c GFS 3 3")
             outputLines = output.splitLines
             reference = @[
-                "Running with configuration:@[\"GFS\", \"3\", \"3\"]", 
-                "Nodes Shape:[10, 3]"]
+                "Running with configuration: @[\"GFS\", \"3\", \"3\"]", 
+                "Nodes Shape: [10, 3]",
+                "Edges Count: 36"
+                ]
         check exitCode == 0
         for i in 0..<reference.len:
             check outputLines[i] == reference[i]
@@ -250,12 +276,12 @@ suite "Test NumPy exports corectness for grids":
             require fileExists("nimplex")
 
     test "generate auto-named a medium fractional internal simplex grid (IFP 7 11) and export it to NumPy (nimplex_IF_7_11.npy)":
-        let (output, exitCode) = execCmdEx("./nimplex -c IFN 7 11")
+        let (_, exitCode) = execCmdEx("./nimplex -c IFN 7 11")
         check exitCode == 0
         check fileExists("nimplex_IF_7_11.npy")
 
     test "generate a medium fractional internal simplex grid (IFP 7 11) named testExport.npy and export it to NumPy":
-        let (output, exitCode) = execCmdEx("./nimplex -c IFN 7 11 testExport.npy")
+        let (_, exitCode) = execCmdEx("./nimplex -c IFN 7 11 testExport.npy")
         check exitCode == 0
         check fileExists("testExport.npy")
 
@@ -283,13 +309,13 @@ suite "Test NumPy exports corectness for graphs":
             require fileExists("nimplex")
 
     test "generate auto-named a medium fractional simplex graph (GFP 7 11) and export it to NumPy (nimplex_GF_7_11_nodes.npy and nimplex_GF_7_11_neighbors.npy)":
-        let (output, exitCode) = execCmdEx("./nimplex -c GFN 7 11")
+        let (_, exitCode) = execCmdEx("./nimplex -c GFN 7 11")
         check exitCode == 0
         check fileExists("nimplex_GF_7_11_nodes.npy")
         check fileExists("nimplex_GF_7_11_neighbors.npy")
 
     test "generate a medium fractional simplex graph (GFP 7 11) named testExport.npy and testExport.npy and export it to NumPy":
-        let (output, exitCode) = execCmdEx("./nimplex -c GFN 7 11 testExport.npy")
+        let (_, exitCode) = execCmdEx("./nimplex -c GFN 7 11 testExport.npy")
         check exitCode == 0
         check fileExists("testExport_nodes.npy")
         check fileExists("testExport_neighbors.npy")
@@ -326,4 +352,8 @@ suite "Test NumPy exports corectness for graphs":
         check resultNeighbors.len == loadedNumpyNeighborsParsed.len
         for i in 0..<resultNeighbors.len:
             check resultNeighbors[i].toHashSet() == loadedNumpyNeighborsParsed[i].toHashSet()
-
+
+let t1 = cpuTime()
+echo "\n***** CLI BENCHMARK RESULTS *****\n"
+echo "Large Graphs:\n" & $initDuration(milliseconds = ((t1 - t0)*1e3).int) & "\n"
+echo "-----------------------------------\n"

tests/graph.nim

@@ -8,7 +8,7 @@ import std/times
 
 # SMALL GRAPHS
 let t0 = cpuTime()
-echo "*** SMALL GRAPHS ***"
+echo "***** SMALL GRAPHS *****"
 
 suite "small simplex integer 2-component (binary) graph":
     let 
@@ -174,7 +174,7 @@ suite "small simplex fractional 4-component (quaternary) graph":
 
 # LARGE GRAPHS 
 let t1 = cpuTime()
-echo "*** LARGE GRAPHS ***"
+echo "***** LARGE GRAPHS *****"
 
 suite "large simplex integer 3-component (ternary) graph":
     let 
@@ -273,6 +273,7 @@ suite "very large simplex fractional 12-component graph (1M+ nodes  / 93M+ edges
 
 # BENCHMARK RESULTS
 let t2 = cpuTime()
-echo "\n*** BENCHMARK RESULTS ***\n"
+echo "\n***** GRAPH BENCHMARK RESULTS *****\n"
 echo "Small Graphs:\n" & $initDuration(microseconds = ((t1 - t0)*1e6).int) & "\n"
-echo "Large Graphs:\n" & $initDuration(milliseconds = ((t2 - t1)*1e3).int) & "\n"
+echo "Large Graphs:\n" & $initDuration(milliseconds = ((t2 - t1)*1e3).int) & "\n"
+echo "-------------------------------------\n"

tests/grid.nim

@@ -3,8 +3,9 @@ import ../nimplex
 import arraymancer/Tensor
 import std/times
 
-let t0 = cpuTime()
 # SMALL GRIDS
+let t0 = cpuTime()
+echo "***** SMALL GRIDS *****"
 
 suite "small simplex full integer grids":
     let result = nimplex.simplex_grid(2, 5)
@@ -97,6 +98,7 @@ suite "small simplex attainable grids (binary with ndiv=6 in ternary from [1,1,1
 
 let t1 = cpuTime()
 # LARGE GRIDS
+echo "***** LARGE GRIDS *****"
 
 suite "large simplex full integer grids":
     let result = nimplex.simplex_grid(7, 24)
@@ -152,6 +154,8 @@ suite "large simplex internal fractional grids":
         for i in 0..6:
             check abs(resultCherryPick[i] - reference[i]) < 0.0001
 
+echo "***** GRIDS BENCHMARK RESULTS *****"
 let t2 = cpuTime()
 echo "Small Grids:\n" & $initDuration(microseconds = ((t1 - t0)*1e6).int) & "\n" 
 echo "Large Grids:\n" & $initDuration(milliseconds = ((t2 - t1)*1e3).int) & "\n"
+echo "---------------------------------\n"