GitHub actions

.ci/format_script.sh

@@ -2,7 +2,6 @@
 
 set -ex
 
-BASE_COMMIT=$(git rev-parse $TRAVIS_BRANCH)
 echo "Running clang-format against branch $TRAVIS_BRANCH, with hash $BASE_COMMIT"
 COMMIT_FILES=$(git diff --name-only $BASE_COMMIT | grep -i -v LinkDef)
 RESULT_OUTPUT="$(git-clang-format --commit $BASE_COMMIT --diff --binary `which clang-format` $COMMIT_FILES)"

.github/CODEOWNERS

@@ -60,7 +60,7 @@
 /gui/canvaspainter/ @Axel-Naumann @linev
 /ui5/ @linev
 
-/cmake/ @oshadura
-*.cmake @oshadura
-*/CMakeLists.txt @oshadura
-CMakeLists.txt @oshadura
+/cmake/ @bellenot
+*.cmake @bellenot
+*/CMakeLists.txt @bellenot
+CMakeLists.txt @bellenot

.github/pull_request_template.md

@@ -0,0 +1,12 @@
+# This Pull request:
+
+## Changes or fixes:
+
+
+## Checklist:
+
+- [ ] tested changes locally
+- [ ] updated the docs (if necessary)
+
+This PR fixes # 
+

.github/workflows/code_analysis.yml

@@ -0,0 +1,23 @@
+name: clang-tools code analysis
+
+on: pull_request
+  # push:
+  #   branches: [ $default-branch ]
+  # pull_request:
+  #   branches: [ $default-branch ]
+
+jobs:
+  clang-format:
+    runs-on: ubuntu-latest
+    env:
+      TRAVIS_BRANCH: ${{ github.base_ref }} 
+      TRAVIS_PULL_REQUEST_BRANCH: ${{ github.head_ref }}
+      BASE_COMMIT: ${{ github.event.pull_request.base.sha }}
+    steps:
+    - uses: actions/checkout@v2
+    - name: Fetch base_ref HEAD
+      run: git fetch --depth=1 origin +refs/heads/${{github.base_ref}}:refs/remotes/origin/${{github.base_ref}}
+    - name: install clang-format
+      run: sudo apt-get install -y clang-format
+    - name: run clang-format script
+      run: .ci/format_script.sh

.travis.yml

@@ -23,7 +23,11 @@ matrix:
   include:
     - env: TOOL=clang-format
       script: &format_script
-        - if [ "$TRAVIS_PULL_REQUEST" != "false" ]; then .ci/format_script.sh; fi
+        - |
+          if [ "$TRAVIS_PULL_REQUEST" != "false" ]; then
+            export BASE_COMMIT=$(git rev-parse $TRAVIS_BRANCH)
+            .ci/format_script.sh
+          fi
 
     - env: TOOL=clang-tidy-analyzer
       before_script: &copy_headers

CMakeLists.txt

@@ -1,4 +1,4 @@
-# Copyright (C) 1995-2019, Rene Brun and Fons Rademakers.
+# Copyright (C) 1995-2021, Rene Brun and Fons Rademakers.
 # All rights reserved.
 #
 # For the licensing terms see $ROOTSYS/LICENSE.
@@ -649,11 +649,10 @@ if(testing)
   endif()
 endif()
 
-if (${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.10.0")
-  if (${CMAKE_MINIMUM_REQUIRED_VERSION} VERSION_GREATER_EQUAL "3.10.0")
-    message(FATAL_ERROR "Remove this condition")
-  endif()
+if(${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.10.0")
   cmake_host_system_information(RESULT PROCESSOR QUERY PROCESSOR_DESCRIPTION)
+else()
+  set(PROCESSOR ${CMAKE_HOST_SYSTEM_PROCESSOR})
 endif()
 
 message(STATUS "ROOT Configuration \n

README.md

@@ -51,32 +51,11 @@ These screenshots shows some of the plots (produced using ROOT) presented when t
 
 See more screenshots on our [gallery](https://root.cern/gallery).
 
-## Download and Getting Started
-See [root.cern download page](https://root.cern/downloading-root) for the latest binary releases.
+## Installation and Getting Started
+See https://root.cern/install for installation instructions.
+For instructions on how to build ROOT from these source files, see https://root.cern/install/build_from_source.
 
-[Getting started with ROOT.](https://root.cern/get_started)
-
-## Building
-Clone the repo
-
-    $ git clone https://github.com/root-project/root.git
-
-Make a directory for building
-
-    $ mkdir build
-    $ cd build
-
-Run cmake and make
-
-    $ cmake ../root
-    $ make -j n # where n is the number of cores 
-
-Setup and run ROOT
-
-    $ source bin/thisroot.sh
-    $ root
-
-[More information](https://root.cern/building-root) regarding building.
+Our ["Getting started with ROOT"](https://root.cern/get_started) page is then the perfect place to get familiar with ROOT.
 
 ## Help and Support
 - [Forum](https://root.cern/forum/)

README/ReleaseNotes/v626/index.md

@@ -63,6 +63,8 @@ The following people have contributed to this new version:
 
 ## Histogram Libraries
 
+- Implement the `SetStats` method for `TGraph` to turn ON or OFF the statistics box display
+  for an individual `TGraph`.
 
 ## Math Libraries
 

bindings/jsmva/python/JsMVA/__init__.py

@@ -3,6 +3,7 @@
 # @package JsMVA
 # @author  Attila Bagoly <[email protected]>
 
+from IPython import get_ipython
 from IPython.core.extensions import ExtensionManager
 
 ## This function will register JsMVAMagic class to ipython
@@ -11,4 +12,4 @@ def loadExtensions():
     extMgr = ExtensionManager(ip)
     extMgr.load_extension("JsMVA.JsMVAMagic")
 
-loadExtensions()
+loadExtensions()

bindings/jupyroot/CMakeLists.txt

@@ -52,16 +52,7 @@ foreach(val RANGE ${how_many_pythons})
     target_link_libraries(${libname} PUBLIC -Wl,--unresolved-symbols=ignore-all Core)
   endif()
 
-  target_include_directories(${libname} PRIVATE ${python_include_dir})
-
-  # Disables warnings originating from deprecated register keyword in Python
-  if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU" AND CMAKE_CXX_STANDARD GREATER_EQUAL 11)
-    target_compile_options(${libname} PRIVATE -Wno-register)
-  endif()
-  if("${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang" AND CMAKE_CXX_STANDARD GREATER_EQUAL 11)
-    target_compile_options(${libname} PRIVATE -Wno-register)
-    target_compile_options(${libname} PRIVATE -Wno-deprecated-register)
-  endif()
+  target_include_directories(${libname} SYSTEM PRIVATE ${python_include_dir})
 
   # Compile .py files
   foreach(py_source ${py_sources})

bindings/jupyroot/src/IOHandler.cxx

@@ -105,7 +105,6 @@ static void InitCaptureImpl(int &savedStdStream, int *pipeHandle, int FILENO)
    fcntl(pipeHandle[0], F_SETPIPE_SZ, MAX_PIPE_SIZE);
 #endif
    dup2(pipeHandle[1], FILENO);
-   close(pipeHandle[1]);
 }
 
 void JupyROOTExecutorHandler::InitCapture()
@@ -123,6 +122,12 @@ void JupyROOTExecutorHandler::EndCapture()
       Poll();
       dup2(fSaved_stdout, STDOUT_FILENO);
       dup2(fSaved_stderr, STDERR_FILENO);
+      close(fSaved_stdout);
+      close(fSaved_stderr);
+      close(fStdout_pipe[0]);
+      close(fStdout_pipe[1]);
+      close(fStderr_pipe[0]);
+      close(fStderr_pipe[1]);
       fCapturing = false;
    }
 }

bindings/pyroot/cppyy/CPyCppyy/CMakeLists.txt

@@ -82,26 +82,19 @@ foreach(val RANGE ${how_many_pythons})
     target_compile_options(${libname} PRIVATE -Wno-cast-function-type)
   endif()
 
-  # Disables warnings originating from deprecated register keyword in Python
-  if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU" AND CMAKE_CXX_STANDARD GREATER_EQUAL 11)
-    target_compile_options(${libname} PRIVATE -Wno-register)
-  endif()
-  if("${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang" AND CMAKE_CXX_STANDARD GREATER_EQUAL 11)
-    target_compile_options(${libname} PRIVATE -Wno-register)
-    target_compile_options(${libname} PRIVATE -Wno-deprecated-register)
-  endif()
-
   # Disables warnings due to new field tp_vectorcall in Python 3.8
   if(NOT MSVC AND ${python_version_string} VERSION_GREATER_EQUAL "3.8")
     target_compile_options(${libname} PRIVATE -Wno-missing-field-initializers)
   endif()
 
+  target_include_directories(${libname}
+     SYSTEM PUBLIC ${python_include_dir})
+
   target_include_directories(${libname}
      PRIVATE
         ${CMAKE_SOURCE_DIR}/core/foundation/inc   # needed for string_view backport
         ${CMAKE_BINARY_DIR}/ginclude
      PUBLIC
-        ${python_include_dir}
         $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/inc>
         $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/src>
   )

bindings/pyroot/cppyy/CPyCppyy/src/Pythonize.cxx

@@ -653,19 +653,38 @@ PyObject* MapContains(PyObject* self, PyObject* obj)
     return result;
 }
 
+
 //- STL container iterator support --------------------------------------------
+static const ptrdiff_t PS_END_ADDR  =  7;   // non-aligned address, so no clash
+static const ptrdiff_t PS_FLAG_ADDR = 11;   // id.
+static const ptrdiff_t PS_COLL_ADDR = 13;   // id.
+
 PyObject* StlSequenceIter(PyObject* self)
 {
 // Implement python's __iter__ for std::iterator<>s
     PyObject* iter = PyObject_CallMethodObjArgs(self, PyStrings::gBegin, nullptr);
     if (iter) {
         PyObject* end = PyObject_CallMethodObjArgs(self, PyStrings::gEnd, nullptr);
-        if (end)
-            PyObject_SetAttr(iter, PyStrings::gEnd, end);
-        Py_XDECREF(end);
-
-    // add iterated collection as attribute so its refcount stays >= 1 while it's being iterated over
-        PyObject_SetAttr(iter, CPyCppyy_PyText_FromString("_collection"), self);
+        if (end) {
+            if (CPPInstance_Check(iter)) {
+            // use the data member cache to store extra state on the iterator object,
+            // without it being visible on the Python side
+                auto& dmc = ((CPPInstance*)iter)->GetDatamemberCache();
+                dmc.push_back(std::make_pair(PS_END_ADDR, end));
+
+            // set a flag, indicating first iteration (reset in __next__)
+                Py_INCREF(Py_False);
+                dmc.push_back(std::make_pair(PS_FLAG_ADDR, Py_False));
+
+            // make sure the iterated over collection remains alive for the duration
+                Py_INCREF(self);
+                dmc.push_back(std::make_pair(PS_COLL_ADDR, self));
+            } else {
+            // could store "end" on the object's dictionary anyway, but if end() returns
+            // a user-customized object, then its __next__ is probably custom, too
+                Py_DECREF(end);
+            }
+        }
     }
     return iter;
 }
@@ -856,44 +875,47 @@ Py_hash_t StlStringHash(PyObject* self)
 PyObject* StlIterNext(PyObject* self)
 {
 // Python iterator protocol __next__ for STL forward iterators.
-    PyObject* next = nullptr;
-    PyObject* last = PyObject_GetAttr(self, PyStrings::gEnd);
+    bool mustIncrement = true;
+    PyObject* last = nullptr;
+    if (CPPInstance_Check(self)) {
+        auto& dmc = ((CPPInstance*)self)->GetDatamemberCache();
+        for (auto& p: dmc) {
+            if (p.first == PS_END_ADDR) {
+                last = p.second;
+                Py_INCREF(last);
+            } else if (p.first == PS_FLAG_ADDR) {
+                mustIncrement = p.second == Py_True;
+                if (!mustIncrement) {
+                    Py_DECREF(p.second);
+                    Py_INCREF(Py_True);
+                    p.second = Py_True;
+                }
+            }
+        }
+    }
 
+    PyObject* next = nullptr;
     if (last) {
     // handle special case of empty container (i.e. self is end)
-        if (PyObject_RichCompareBool(last, self, Py_EQ) == 0) {
-        // first, get next from the _current_ iterator as internal state may change
-        // when call post or pre increment
-            next = PyObject_CallMethodObjArgs(self, PyStrings::gDeref, nullptr);
-            if (!next) PyErr_Clear();
-
-        // use postinc, even as the C++11 range-based for loops prefer preinc b/c
-        // that allows the current value from the iterator to be had from __deref__,
-        // an issue that does not come up in C++
-            static PyObject* dummy = PyInt_FromLong(1l);
-            PyObject* iter = PyObject_CallMethodObjArgs(self, PyStrings::gPostInc, dummy, nullptr);
-            if (!iter) {
-            // allow preinc, as in that case likely __deref__ is not defined and it
-            // is the iterator rather that is returned in the loop
-                PyErr_Clear();
-                iter = PyObject_CallMethodObjArgs(self, PyStrings::gPreInc, nullptr);
-            }
-            if (iter) {
-            // prefer != as per C++11 range-based for
-                int isNotEnd = PyObject_RichCompareBool(last, iter, Py_NE);
-                if (isNotEnd && !next) {
-                // if no dereference, continue iterating over the iterator
-                    Py_INCREF(iter);
-                    next = iter;
+        if (!PyObject_RichCompareBool(last, self, Py_EQ)) {
+            bool iter_valid = true;
+            if (mustIncrement) {
+            // prefer preinc, but allow post-inc; in both cases, it is "self" that has
+            // the updated state to dereference
+                PyObject* iter = PyObject_CallMethodObjArgs(self, PyStrings::gPreInc, nullptr);
+                if (!iter) {
+                    PyErr_Clear();
+                    static PyObject* dummy = PyInt_FromLong(1l);
+                    iter = PyObject_CallMethodObjArgs(self, PyStrings::gPostInc, dummy, nullptr);
                 }
-                Py_DECREF(iter);
-            } else {
-            // fail current next, even if available
-                Py_XDECREF(next);
-                next = nullptr;
+                iter_valid = iter && PyObject_RichCompareBool(last, self, Py_NE);
+                Py_XDECREF(iter);
+            }
+
+            if (iter_valid) {
+                next = PyObject_CallMethodObjArgs(self, PyStrings::gDeref, nullptr);
+                if (!next) PyErr_Clear();
             }
-        } else {
-            PyErr_SetString(PyExc_StopIteration, "");
         }
         Py_DECREF(last);
     }

bindings/pyroot/cppyy/cppyy-backend/cling/python/cppyy_backend/loader.py

@@ -85,21 +85,7 @@ def set_cling_compile_options(add_defaults = False):
         CURRENT_ARGS = os.environ['EXTRA_CLING_ARGS']
 
     if add_defaults:
-        has_avx = False
-        try:
-            with open('/proc/cpuinfo', 'r') as ci:
-                for line in ci:
-                    if 'avx' in line:
-                        has_avx = True
-                        break
-        except Exception:
-            try:
-                cli_arg = subprocess.check_output(['sysctl', 'machdep.cpu.features'])
-                has_avx = 'avx' in cli_arg.decode("utf-8").strip().lower()
-            except Exception:
-                pass
         CURRENT_ARGS += ' -O2'
-        if has_avx: CURRENT_ARGS += ' -mavx'
         os.putenv('EXTRA_CLING_ARGS', CURRENT_ARGS)
         os.environ['EXTRA_CLING_ARGS'] = CURRENT_ARGS
 

bindings/pyroot/pythonizations/CMakeLists.txt

@@ -111,23 +111,16 @@ foreach(val RANGE ${how_many_pythons})
   endif()
 
   target_include_directories(${libname}
-     PRIVATE ${python_include_dir}
-     PUBLIC  $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/inc>)
+     SYSTEM PRIVATE ${python_include_dir})
+
+  target_include_directories(${libname}
+     PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/inc>)
 
   # Disables warnings caused by Py_RETURN_TRUE/Py_RETURN_FALSE
   if(NOT MSVC)
     target_compile_options(${libname} PRIVATE -Wno-strict-aliasing)
   endif()
 
-  # Disables warnings originating from deprecated register keyword in Python
-  if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU" AND CMAKE_CXX_STANDARD GREATER_EQUAL 11)
-    target_compile_options(${libname} PRIVATE -Wno-register)
-  endif()
-  if("${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang" AND CMAKE_CXX_STANDARD GREATER_EQUAL 11)
-    target_compile_options(${libname} PRIVATE -Wno-register)
-    target_compile_options(${libname} PRIVATE -Wno-deprecated-register)
-  endif()
-
   # Compile .py files
   foreach(py_source ${py_sources})
     install(CODE "execute_process(COMMAND ${python_executable} -m py_compile ${localruntimedir}/${py_source})")