feat: update

.github/workflows/CI.yml

@@ -21,9 +21,6 @@ jobs:
       with:
         fetch-depth: 0
 
-    - name: apt update
-      run: apt update -y && apt upgrade -y
-
     - name: Build from src
       run: mkdir build && cd build && cmake -DCMAKE_BUILD_TYPE=$BUILD_TYPE .. && make -j8 && make install
 

.github/workflows/Coverage.yml

@@ -19,9 +19,6 @@ jobs:
       with:
         fetch-depth: 0
 
-    - name: apt update
-      run: apt update -y && apt upgrade -y
-
     - name: Build from src
       continue-on-error: true # The one test will most likely fail, but if we skip we lose a lot of coverage.
       run: mkdir build && cd build && cmake -DBUILD_COVERAGE=1 .. && make -j8 && make install

.gitignore

@@ -11,8 +11,7 @@ _site/
 .bundle/
 vendor/
 
-# Ignore editors
-.vscode
+# Ignore editors (but not vscode)
 /.pytest_cache/
 .cproject
 .idea

.vscode/c_cpp_properties.json

@@ -0,0 +1,23 @@
+{
+    "configurations": [
+        {
+            "name": "Linux",
+            "includePath": [
+                "${workspaceFolder}/**",
+                "${workspaceFolder}/include/**",
+                "/usr/local/cuda/include",
+                "/usr/local/include/openbabel3/",
+                "/usr/include",
+                "/usr/include/c++/11/",
+                "${workspaceFolder}/include/**"],
+            "defines": [],
+            "compilerPath": "/usr/bin/c++",
+            "cStandard": "c17",
+            "cppStandard": "gnu++17",
+            "intelliSenseMode": "linux-gcc-x64",
+            "compileCommands": "${workspaceFolder}/build/compile_commands.json",
+            "configurationProvider": "ms-vscode.cmake-tools"            
+        }
+    ],
+    "version": 4
+}

.vscode/settings.json

@@ -0,0 +1,77 @@
+{
+    "files.associations": {
+        "stdexcept": "cpp",
+        "cctype": "cpp",
+        "clocale": "cpp",
+        "cmath": "cpp",
+        "cstdarg": "cpp",
+        "cstddef": "cpp",
+        "cstdio": "cpp",
+        "cstdlib": "cpp",
+        "cstring": "cpp",
+        "ctime": "cpp",
+        "cwchar": "cpp",
+        "cwctype": "cpp",
+        "array": "cpp",
+        "atomic": "cpp",
+        "strstream": "cpp",
+        "bit": "cpp",
+        "*.tcc": "cpp",
+        "bitset": "cpp",
+        "chrono": "cpp",
+        "compare": "cpp",
+        "complex": "cpp",
+        "concepts": "cpp",
+        "condition_variable": "cpp",
+        "cstdint": "cpp",
+        "deque": "cpp",
+        "list": "cpp",
+        "map": "cpp",
+        "set": "cpp",
+        "string": "cpp",
+        "unordered_map": "cpp",
+        "unordered_set": "cpp",
+        "vector": "cpp",
+        "exception": "cpp",
+        "algorithm": "cpp",
+        "functional": "cpp",
+        "iterator": "cpp",
+        "memory": "cpp",
+        "memory_resource": "cpp",
+        "numeric": "cpp",
+        "optional": "cpp",
+        "random": "cpp",
+        "ratio": "cpp",
+        "string_view": "cpp",
+        "system_error": "cpp",
+        "tuple": "cpp",
+        "type_traits": "cpp",
+        "utility": "cpp",
+        "fstream": "cpp",
+        "initializer_list": "cpp",
+        "iomanip": "cpp",
+        "iosfwd": "cpp",
+        "iostream": "cpp",
+        "istream": "cpp",
+        "limits": "cpp",
+        "mutex": "cpp",
+        "new": "cpp",
+        "numbers": "cpp",
+        "ostream": "cpp",
+        "semaphore": "cpp",
+        "sstream": "cpp",
+        "stop_token": "cpp",
+        "streambuf": "cpp",
+        "thread": "cpp",
+        "cinttypes": "cpp",
+        "typeindex": "cpp",
+        "typeinfo": "cpp",
+        "variant": "cpp",
+        "codecvt": "cpp",
+        "cfenv": "cpp",
+        "filesystem": "cpp"
+    },
+    "C_Cpp.files.exclude": {
+        "/usr/local/include/libmolgrid/**": true
+    }
+}

.vscode/tasks.json

@@ -0,0 +1,24 @@
+{
+  "version": "2.0.0",
+  "isShelllCommand": true,
+  "tasks": [
+    {
+      "label": "build",
+      "options": {
+        "cwd": "${workspaceRoot}/build"
+      },
+      "type": "shell",
+      "command": "make -j24",
+      "group": "build"
+    },
+    {
+      "label": "build-debug",
+      "options": {
+        "cwd": "${workspaceRoot}/build-debug"
+      },
+      "type": "shell",
+      "command": "make -j24",
+      "group": "build"
+    }
+  ]
+}

CMakeLists.txt

@@ -11,6 +11,8 @@ if(NOT CMAKE_CONFIGURATION_TYPES AND NOT CMAKE_BUILD_TYPE)
   set(CMAKE_BUILD_TYPE Release)
 endif()
 
+set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
+set(CMAKE_CXX_USE_RESPONSE_FILE_FOR_INCLUDES OFF)
 include(GNUInstallDirs)
 
 option(BUILD_SHARED "Build shared library" ON)
@@ -37,8 +39,7 @@ include(GNUInstallDirs)
 # set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/${CMAKE_INSTALL_BINDIR})
 
 #dependencies
-find_package(CUDA REQUIRED)
-find_package(Boost REQUIRED COMPONENTS regex unit_test_framework program_options system filesystem iostreams)
+find_package(Boost REQUIRED COMPONENTS regex unit_test_framework program_options system filesystem iostreams serialization)
 find_package(OpenBabel3 REQUIRED)
 include_directories(SYSTEM ${OPENBABEL3_INCLUDE_DIR})
 find_package(ZLIB)
@@ -54,20 +55,25 @@ set(CMAKE_CXX_STANDARD 14)
 set(CMAKE_CUDA_STANDARD 14)
 
 if(CMAKE_CXX_COMPILER_ID MATCHES GNU)
-    set(CMAKE_CXX_FLAGS         "${CMAKE_CXX_FLAGS} -Wall -Wno-unknown-pragmas -Werror")
-    set(CMAKE_CXX_FLAGS_DEBUG   "-O0 -g3")
-    if (BUILD_COVERAGE)
-	set(CMAKE_CXX_FLAGS_RELEASE "-O3 -g -fprofile-arcs -ftest-coverage")
-    else()
-        set(CMAKE_CXX_FLAGS_RELEASE "-O3 -g")
-    endif()	
+  set(CMAKE_CXX_FLAGS         "${CMAKE_CXX_FLAGS} -Wall -Wno-unknown-pragmas -Werror")
+  include(CheckCCompilerFlag)
+  check_c_compiler_flag(-Wno-error=template-id-cdtor HAS_TEMPLATE_ID_CDTOR)
+  if (HAS_TEMPLATE_ID_CDTOR)
+    set(CMAKE_CXX_FLAGS       "${CMAKE_CXX_FLAGS} -Wno-error=template-id-cdtor")
+  endif()
+  set(CMAKE_CXX_FLAGS_DEBUG   "-O0 -g3")
+  if (BUILD_COVERAGE)
+    set(CMAKE_CXX_FLAGS_RELEASE "-O3 -g -fprofile-arcs -ftest-coverage")
+  else()
+    set(CMAKE_CXX_FLAGS_RELEASE "-O3 -g")
+  endif()
 endif()
 
 if(CUDA_VERSION_MAJOR LESS 11)
 #compile for all major architectures >= 35
- set(CMAKE_CUDA_ARCHITECTURES 35 50 60 70 75)
+  set(CMAKE_CUDA_ARCHITECTURES 35 50 60 70 75)
 else()
- set(CMAKE_CUDA_ARCHITECTURES 52 60 70 75 80)
+  set(CMAKE_CUDA_ARCHITECTURES 70 80 86)
 endif()
 
 set(CMAKE_CUDA_FLAGS_RELEASE "-O3 -g -lineinfo")

README.md

@@ -1,6 +1,6 @@
 libmolgrid
 ==========
-![Github CI](https://github.com/gnina/libmolgrid/actions/workflows/CI.yml/badge.svg)
+[![Github CI](https://github.com/gnina/libmolgrid/actions/workflows/CI.yml/badge.svg)](https://github.com/gnina/libmolgrid/actions)
 [![codecov](https://codecov.io/gh/gnina/libmolgrid/branch/master/graph/badge.svg?token=gUFisf34rf)](https://codecov.io/gh/gnina/libmolgrid)
 
 libmolgrid is under active development, but should be suitable for use by early adopters.

default.nix

@@ -1,59 +1,47 @@
-{ lib
-, stdenv
-, fetchFromGitHub
-, cmake
-, cudatoolkit
-, openbabel
-, zlib
-, boost
-, python310Packages
-, python310
-, pkg-config
+{
+  lib,
+  cmake,
+  boost,
+  python3,
+  python3Packages,
+  cudaPackages,
+  openbabel,
+  zlib,
 }:
 
-stdenv.mkDerivation rec {
+cudaPackages.backendStdenv.mkDerivation {
   pname = "libmolgrid";
-  version = "0.5.3";
-
+  version = "master";
   src = ./.;
-  # fetchFromGitHub {
-  #   owner = "gnina";
-  #   repo = "libmolgrid";
-  #   rev = "v${version}";
-  #   hash = "sha256-YdEjXfrTf9hw0nMbC2JWZ7Gf/psZ4RQ6v6GUrx5yIoA=";
-  # };
-
-  #buildFlags = [ "-stdlib=libstdc++" ];
 
   nativeBuildInputs = [
     cmake
-    pkg-config
+    cudaPackages.cuda_nvcc
   ];
 
   buildInputs = [
-    #gcc
-    cudatoolkit
+    boost.dev
+    python3
+    python3Packages.boost
+    python3Packages.numpy
+    python3Packages.openbabel-bindings
+    python3Packages.pyquaternion
+    python3Packages.pytest
+    cudaPackages.cuda_cudart
+    cudaPackages.cuda_cccl
     openbabel
-    #stdenv.cc.cc.lib
     zlib
-    boost.dev
-    python310Packages.boost
-    python310Packages.pytest
-    python310Packages.numpy
-    python310Packages.pyquaternion
-    python310Packages.openbabel-bindings
-    python310
   ];
 
-  OPENBABEL3_INCLUDE_DIR = "${openbabel}/include/openbabel3";
-
-  cmakeFlags = [ "-DOPENBABEL3_INCLUDE_DIR=${OPENBABEL3_INCLUDE_DIR}" ];
+  cmakeFlags = [
+    "-DCMAKE_CUDA_ARCHITECTURES=70;80;86"
+    "-DOPENBABEL3_INCLUDE_DIR=${openbabel}/include/openbabel3"
+  ];
 
   meta = with lib; {
-    description =
-      "Comprehensive library for fast, GPU accelerated molecular gridding for deep learning workflows";
+    description = "Comprehensive library for fast, GPU accelerated molecular gridding for deep learning workflows";
     homepage = "https://github.com/gnina/libmolgrid";
     license = licenses.asl20;
-    maintainers = with maintainers; [ ];
+    maintainers = [ ];
   };
 }