Automatic nbatches

.github/workflows/Downgrade.yml

@@ -16,11 +16,10 @@ jobs:
     strategy:
       matrix:
         version:
-          - '1.6'
-          - '^1.6'
+          - '1.10.0'
     steps:
       - uses: actions/checkout@v4
-      - uses: julia-actions/setup-julia@v1
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
       - uses: cjdoris/julia-downgrade-compat-action@v1

.github/workflows/ci.yml

@@ -3,7 +3,7 @@ on:
   - push
   - pull_request
 env:
-  JULIA_NUM_THREADS: 2
+  JULIA_NUM_THREADS: 10 
 jobs:
   test:
     name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
@@ -12,16 +12,12 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.6'
           - 'lts'
           - 'pre'
         os:
           - ubuntu-latest
           - macOS-latest
           - windows-latest
-        exclude:
-          - version: '1.6'
-            os: macOS-latest
     steps:
       - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v2

Project.toml

@@ -25,21 +25,21 @@ Compat = "4.14.0"
 DocStringExtensions = "0.9"
 Documenter = "1.2.1"
 ForwardDiff = "0.10.13"
-LinearAlgebra = "1.6"
+LinearAlgebra = "1.10"
 Measurements = "2.11"
 NearestNeighbors = "0.4.16"
-PDBTools = "1.1"
+PDBTools = "2"
 Parameters = "0.12"
-PrecompileTools = "1"
+PrecompileTools = "1.2.1"
 ProgressMeter = "1.6"
-Random = "1.6"
+Random = "1.10"
 Setfield = "0.7, 0.8, 0.9, 1"
 StaticArrays = "1.6"
-Test = "1.6"
+Test = "1.10"
 TestItemRunner = "0.2"
 TestItems = "0.1, 1"
 Unitful = "1.19"
-julia = "1.6"
+julia = "1.10"
 
 [extras]
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"

README.md

@@ -27,7 +27,8 @@ USER GUIDE: <br>
 
 ## Installation
 
-Download and install Julia for your platform from [this http url](https://julialang.org/downloads/). Version 1.6 or greater is required.
+Download and install Julia for your platform from [this http url](https://julialang.org/downloads/). 
+Version 1.10 or greater is required.
 
 Install it as usual for registered Julia packages:
 

docs/Project.toml

@@ -1,4 +1,5 @@
 [deps]
+BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
 CellListMap = "69e1c6dd-3888-40e6-b3c8-31ac5f578864"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"

docs/src/LowLevel.md

@@ -347,9 +347,9 @@ To control these steps, set manually the `output_threaded` and `reduce` optional
 
 By default, we define:
 ```julia
-output_threaded = [ deepcopy(output) for i in 1:nbatches(cl) ]
+output_threaded = [ deepcopy(output) for i in 1:nbatches(cl, :map) ]
 ```
-where `nbatches(cl)` is the number of batches into which the computation will be divided. The number of batches is *not* necessarily equal to the number of threads available (an heuristic is used to optimize performance, as a function of the workload per batch), but can be manually set, as described in the **Number of batches** section below. 
+where `nbatches(cl, :map)` is the number of batches into which the mapped computation will be divided. The number of batches is *not* necessarily equal to the number of threads available (an heuristic is used to optimize performance, as a function of the workload per batch), but can be manually set, as described in the **Number of batches** section below. 
 
 The default reduction function just assumes the additivity of the results obtained by each batch:
 ```julia
@@ -398,7 +398,7 @@ At the same time, the homogeneity of the computation of the mapped function may
 
 Both the above considerations can be used to tunning the `nbatches` parameter of the cell list. This parameter is initialized from a tuple of integers, defining the number of batches that will be used for constructing the cell lists and for the mapping of the computations. 
 
-By default, the number of batches for the computation of the cell lists is smaller than `nthreads()` if the number of particles per cell is small. The default value by the internal function `CellListMap._nbatches_build_cell_lists(cl::CellList)`. 
+By default, the number of batches for the computation of the cell lists is smaller than `nthreads()` if the number of particles per cell is small. The default value is defined by the internal function `CellListMap._nbatches_build_cell_lists(cl::CellList)`. 
 
 The values assumed for each number of batches can bee seen by printing the `nbatches` parameter of the cell lists:
 ```julia-repl
@@ -610,7 +610,7 @@ CollapsedDocStrings = true
 
 ```@autodocs
 Modules = [CellListMap]
-Pages = ["Box.jl", "CellListMap.jl", "CellLists.jl", "CellOperations.jl", "CoreComputing.jl"]
+Pages = ["Box.jl", "CellListMap.jl", "CellLists.jl", "CellOperations.jl", "./core_computing/self.jl", "./core_computing/cross.jl"]
 Order = [:type, :function]
 ```