Merge remote-tracking branch 'origin/master' into ILL_loaders_cleanup

.clang-format

-BasedOnStyle: LLVM
 
+---
+BasedOnStyle: LLVM
+---
+Language: Cpp
+ColumnLimit: 120
+...

.cmake-format.json

@@ -92,14 +92,26 @@
         "MODULE_OUTPUT_DIR": 1,
         "PYQT_VERSION": 1,
         "FOLDER": 1,
-        "SIP_SRCS": "+",
+        "SIP_SRC": 1,
         "HEADER_DEPS": "+",
         "INCLUDE_DIRS": "+",
         "LINK_LIBS": "+",
-        "INSTALL_DIRS": "+",
+        "INSTALL_DIR": "+",
         "OSX_INSTALL_RPATH": "+",
         "LINUX_INSTALL_RPATH": "+"
       }
+    },
+    "add_python_package": {
+      "kwargs": {
+        "EGGLINKNAME": 1,
+        "INSTALL_LIB_DIRS": "+",
+        "INSTALL_BIN_DIR": 1,
+        "EXCLUDE_ON_INSTALL": "+"
+      },
+      "flags": [
+        "EXECUTABLE",
+        "GENERATE_SITECUSTOMIZE"
+      ]
     }
   },
   "always_wrap": [],

.flake8

@@ -13,9 +13,7 @@ exclude =
     images,
     installers,
     instrument,
-    MantidPlot,
     qt/applications/workbench/workbench/app/resources.py,
-    qt/paraview_ext,
     qt/python/mantidqt/resources.py,
     qt/python/mantidqt/dialogs/errorreports/resources_qt4.py
     qt/python/mantidqt/dialogs/errorreports/resources_qt5.py

.gitattributes

@@ -11,6 +11,6 @@
 *.dot !diff
 
 # Allowing gSoap generated files to be committed.
-/Code/Mantid/Framework/ICat/inc/MantidICat/ICat3/GSoapGenerated/ICat3H.h              hooks.MaxObjectKiB131025=2048 
+/Code/Mantid/Framework/ICat/inc/MantidICat/ICat3/GSoapGenerated/ICat3H.h              hooks.MaxObjectKiB131025=2048
 /Code/Mantid/Framework/ICat/src/ICat3/GSoapGenerated/ICat3C.cpp                       hooks.MaxObjectKiB131025=5120
 /Code/Mantid/Framework/ICat/src/ICat4/GSoapGenerated/ICat4C.cpp                       hooks.MaxObjectKiB131025=2048

.githooks/pre-commit

-#!/usr/bin/env bash
-#=============================================================================
-# Copyright 2010-2011 Kitware, Inc.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#=============================================================================
-
-die() {
-	echo 'pre-commit hook failure' 1>&2
-	echo '-----------------------' 1>&2
-	echo '' 1>&2
-	echo "$@" 1>&2
-	exit 1
-}
-
-zero='0000000000000000000000000000000000000000'
-
-#-----------------------------------------------------------------------------
-# Check for committer identity.
-advice='
-Use the commands
-
-	git config --global user.name '\''Your Name'\''
-	git config --global user.email '\''you@yourdomain.com'\''
-
-to introduce yourself to Git before committing.'
-
-# Ensure name and email are available.
-git config --get user.name > /dev/null &&
-git config --get user.email > /dev/null ||
-die 'Identity not configured!' "$advice"
-
-# Validate the name and email.
-git config --get user.name | grep ' ' > /dev/null ||
-die 'Set user.name to your Real Name (with a space), not a userid.' "$advice"
-git config --get user.email | grep '^[^@]*@[^@]*$' > /dev/null ||
-die 'Set user.email to an email address (userid@validdomain.com).' "$advice"
-
-#-----------------------------------------------------------------------------
-# Check content that will be added by this commit.
-
-if git rev-parse --verify -q HEAD > /dev/null; then
-	against=HEAD
-else
-	# Initial commit: diff against an empty tree object
-	against=4b825dc642cb6eb9a060e54bf8d69288fbee4904
-fi
-
-# Merge ("git commit" after "git merge" with conflicts or --no-commit)
-merge_head=$(git rev-parse -q --verify MERGE_HEAD) || merge_head=''
-
-# Disallow non-ascii file names.  The printable range starts at the
-# space character and ends with tilde.
-if test "$(git diff --cached --name-only --diff-filter=A -z $against |
-	   LC_ALL=C tr -d '[ -~]\0')"; then
-	die 'Non-ascii file names may not be added:
-'"$(git diff --cached --name-only --diff-filter=A $against)"
-fi
-
-#-----------------------------------------------------------------------------
-# Builtin whitespace checks.
-bad=$(git diff-index --check --cached $against -- --ignore-space-at-eol) || die "$bad"
-
-# Approximate whitespace=tab-in-indent check with Git < 1.7.2.
-git --version | grep -q " \(1\.[0-6]\|1\.7\.[01]\)" &&
-approx_tab_in_indent=true || approx_tab_in_indent=false
-check_tab() {
-	lines=$(git diff-index -p --cached $against -- "$1" |
-	        grep '^+	') &&
-	echo "$lines" |
-	while read line; do
-		echo "$1: tab in indent." &&
-		echo "$line"
-	done
-}
-
-# Reject addition of a line without a newline at end-of-file.
-check_no_lf_at_eof() {
-	lines=$(git diff-index -p --cached $against -- "$1" | tail -2)
-	if echo "$lines" | head -1 | grep -q '^+' &&
-	   echo "$lines" | tail -1 | grep -q '^\\ No newline'; then
-		echo "$1: No newline at end of file"
-	fi
-}
-
-# Custom whitespace checks.
-check_whitespace() {
-	ws=$(git check-attr whitespace -- "$file" |
-	     sed 's/^[^:]*: whitespace: //')
-	if $approx_tab_in_indent; then
-		case ",$ws," in
-			*,tab-in-indent,*) check_tab "$1" ;;
-		esac
-	fi
-	case ",$ws," in
-		*,no-lf-at-eof,*) check_no_lf_at_eof "$1" ;;
-	esac
-}
-bad=$(git diff-index --name-only --cached $against -- |
-while read file; do
-	check_whitespace "$file"
-done)
-test -z "$bad" || die "$bad"
-
-#-----------------------------------------------------------------------------
-# Check file modes and sizes.
-mode_looks_exe() {
-	case "$1" in
-		*.bat) return 0 ;;
-		*.cmd) return 0 ;;
-		*.exe) return 0 ;;
-		*.com) return 0 ;;
-	esac
-	git cat-file blob "$2" | head -1 | grep "^#\!/" > /dev/null
-}
-mode_not_exe () {
-	echo "The file '$file' has looks executable but does not have an executable mode."
-}
-mode_bad_exe () {
-	echo "The file '$file' has executable mode but does not look executable."
-}
-mode_non_file () {
-	echo "The path '$file' has a non-file mode."
-}
-check_mode() {
-	case "$dst_mode" in
-		100755) mode_looks_exe "$file" "$dst_obj" || mode_bad_exe ;;
-		100644) mode_looks_exe "$file" "$dst_obj" && mode_not_exe ;;
-		160000) ;;
-		*)	mode_non_file ;;
-	esac
-}
-
-size_max_KiB=$(git config hooks.MaxObjectKiB)
-test -n "$size_max_KiB" || size_max_KiB=1024
-size_too_large_once=""
-size_too_large_once() {
-	test -z "$size_too_large_once" || return ; size_too_large_once=done
-	echo 'At least one file is staged for commit with size larger than the limit.
-We prefer to keep large files out of the main source tree, especially
-binary files that do not compress well.  This hook disallows large files.
-
-If it is vital that this file enters the repository, speak to a dev lead.
-Remember that unit tests should typically not require loading files (see
-http://www.mantidproject.org/Unit_Test_Good_Practice#Using_files_in_Unit_tests).
-'
-# Instructions for allowing ESSENTIAL files only:
-#   A limit for specific files or patterns may be set in ".gitattributes" with
-#   the "hooks.MaxObjectKiBYYMMDD" attribute (where YYMMDD is the current date).
-#   For example, the line
-#
-#     *.c              hooks.MaxObjectKiB121207=2048
-#
-#   sets a limit of 2048 KiB for C source files, but WILL ONLY WORK on the date
-#   matching the entry. This avoids the previous behaviour that once set the
-#   hook was forever disabled if the entry was not removed afterwards.
-#   See "git help attributes" for details on the .gitattributes format.
-}
-size_too_large() {
-	size_too_large_once
-	echo "The path '$file' has size $file_KiB KiB, greater than allowed $max_KiB KiB."
-}
-size_validate_max_KiB() {
-	test "$max_KiB" -ge "0" 2>/dev/null && return 0
-	echo "The path '$file' has invalid attribute \"hooks-MaxObjectKiB=$max_KiB\"."
-	return 1
-}
-check_size() {
-	test "$dst_obj" != "$zero" || return
-	datesuffix=`date +%y%m%d`
-	hookname='hooks.MaxObjectKiB'$datesuffix
-	max_KiB=$(git check-attr $hookname -- "$file" |
-		  sed "s/^[^:]*: ${hookname}: //")
-	case "$max_KiB" in
-		'unset')       return ;; # No maximum for this object.
-		'set')         max_KiB="$size_max_KiB" ;; # Use local default.
-		'unspecified') max_KiB="$size_max_KiB" ;; # Use local default.
-		*) size_validate_max_KiB || return ;;
-	esac
-	if test "$max_KiB" -gt "0"; then
-		file_KiB=$(expr '(' $(git cat-file -s "$dst_obj") + 1023 ')' / 1024)
-		test "$file_KiB" -le "$max_KiB" || size_too_large
-	fi
-}
-
-short_commit() {
-	git rev-parse --short "$1" 2>/dev/null || echo "$1"
-}
-
-lookup_config_module_update() {
-	update=$(git config "hooks.$1.update")
-
-	# Special-case "true" to accept any update.
-	test "{$update}" = "{true}" && echo '.' && return
-
-	# Format is "aaaaaa..bbbbbb" for update aaaaaa => bbbbbb.
-	# Convert to regex "^aaaaaa[a-z0-9]* bbbbbb[a-z0-9]*$".
-	sha1ex='[a-z0-9][a-z0-9][a-z0-9][a-z0-9][a-z0-9][a-z0-9][a-z0-9]*'
-	regex='^\('"$sha1ex"'\)\.\.\('"$sha1ex"'\)$'
-	echo "$update" |
-	sed -n "/$regex/ {s/$regex/"'^\1[a-z0-9]* \2[a-z0-9]*$/;p;}' |
-	grep '.' # Return false if result is empty.
-}
-
-check_module() {
-	enabled=$(git config --get --bool hooks.submodule) || enabled=true
-	test "$enabled" = "false" && return
-
-	# Allow merged submodule updates.
-	test -n "$merge_head" &&
-	merge_obj=$(git rev-parse -q --verify "$merge_head:$file") &&
-	test "$merge_obj" = "$dst_obj" && return
-
-	# Allow module-only commits without extra work.
-	test -z "$diffs_normal" && return
-
-	# Check if module update is allowed with other changes.
-	allow=$(lookup_config_module_update "$file") || allow='none'
-	if echo "$src_obj $dst_obj" | grep "$allow" > /dev/null; then
-		return
-	fi
-	src_short=$(short_commit "$src_obj")
-	dst_short=$(short_commit "$dst_obj")
-	echo 'A submodule link is staged for commit (among other changes):
-
-  "'"$file"'"  '"$src_short => $dst_short"'
-
-This may occur by accident so we require an extra step to commit.
-If you intend to include this change in your commit, run
-
-  git config "hooks.'"$file"'.update" '"$src_short..$dst_short"'
-
-to explicitly allow the change and try the commit again.  Otherwise run
-
-  git reset HEAD -- "'"$file"'"
-
-to unstage the change.  Furthermore, if you did not intend to modify
-the submodule at all, also run
-
-  git submodule update -- "'"$file"'"
-
-to checkout the current version of the submodule in your work tree.
-Test your changes again to see if they still work with the module.
-Finally, try the commit again.
-'
-	return 1
-}
-
-check_module_rewind() {
-	parent_name="$1"
-	parent_commit="$2"
-	base=$(GIT_DIR="$file/.git" \
-	       git merge-base $src_obj $dst_obj 2>/dev/null) || base=''
-	test "$base" != "$dst_obj" && return
-	parent_short=$(short_commit "$parent_commit")
-	src_short=$(GIT_DIR="$file/.git" short_commit "$src_obj")
-	dst_short=$(GIT_DIR="$file/.git" short_commit "$dst_obj")
-	echo 'This commit would rewind a submodule link:
-
-  "'"$file"'"  '"$src_short => $dst_short"'
-
-from the newer version in '"$parent_name"' ('"$parent_short"').  Run
-
-  git reset '"$parent_name"' -- "'"$file"'"
-  git submodule update -- "'"$file"'"
-
-to checkout the newer version of the submodule in your work tree.
-Then try the commit again.
-'
-	return 1
-}
-
-diffs=$(git diff-index --cached $against -- |
-        sed -n '/^:[^:]/ {s/^://;p;}')
-diffs_normal=$(echo "$diffs" | grep -v '^...... 160000')
-diffs_module=$(echo "$diffs" | grep    '^...... 160000')
-bad=$(
-test -n "$diffs_normal" && echo "$diffs_normal" |
-while read src_mode dst_mode src_obj dst_obj status file; do
-	if test "$src_mode" != "$dst_mode" -a "$dst_mode" != "000000"; then
-		check_mode
-	fi
-	if test "$dst_mode" != "160000" -a "$dst_mode" != '000000'; then
-		check_size
-	fi
-done
-test -n "$diffs_module" && echo "$diffs_module" |
-while read src_mode dst_mode src_obj dst_obj status file; do
-	check_module_rewind HEAD "$against" &&
-	check_module ||
-	break
-done
-)
-test -z "$bad" || die "$bad"
-
-#-----------------------------------------------------------------------------
-# Merge checks.
-if test -n "$merge_head"; then
-	merge_diffs=$(git diff-index --cached $merge_head -- |
-	              sed -n '/^:[^:]/ {s/^://;p;}')
-else
-	merge_diffs=''
-fi
-merge_diffs_normal=$(echo "$merge_diffs" | grep -v '^...... 160000')
-merge_diffs_module=$(echo "$merge_diffs" | grep    '^...... 160000')
-bad=$(
-test -n "$merge_diffs_module" && echo "$merge_diffs_module" |
-while read src_mode dst_mode src_obj dst_obj status file; do
-	check_module_rewind MERGE_HEAD "$merge_head" ||
-	break
-done
-)
-test -z "$bad" || die "$bad"
-
-#-----------------------------------------------------------------------------
-# Style hooks.
-#. "$GIT_DIR/hooks/pre-commit-style"
-
-#-----------------------------------------------------------------------------
-# Chain to project-specific hook.
-#. "$GIT_DIR/hooks/hooks-chain.bash"
-#hooks_chain pre-commit "$@"
-
-# vim: set filetype=sh tabstop=8 softtabstop=8 shiftwidth=8 noexpandtab :

.github/CONTRIBUTING.md

@@ -4,7 +4,7 @@ The [developer documentation](http://developer.mantidproject.org/) has informati
  2. Clone the repository with the remotes `origin` pointing at your fork as `origin` and `mantidproject/mantid` as `upstream`. This is a [common setup](https://help.github.com/articles/configuring-a-remote-for-a-fork/).
  3. Make changes as you see fit. Please still follow the guidelines for [running the unit tests](http://developer.mantidproject.org/RunningTheUnitTests.html) and the [build servers](http://developer.mantidproject.org/AutomatedBuildProcess.html).
  4. Submit a [pull request](https://help.github.com/articles/using-pull-requests) to this branch. This is a start to the conversation.
- 
+
 If you need help, you can go to the [forum](https://forum.mantidproject.org/).
 
 Hints to make the integration of your changes easy (and happen faster):

.github/ISSUE_TEMPLATE.md

-<!-- If the issue was raised by a user they should be named here.
-**Original reporter:** [username facility]/[nobody]
--->
-
-### Expected behavior
-
-### Actual behavior
-
-### Steps to reproduce the behavior
-
-### Platforms affected

.github/ISSUE_TEMPLATE/bug_report.md

+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: 'Bug'
+assignees: ''
+
+---
+
+<!-- Issues which impact security should have a Vulnerability label added to them -->
+
+<!-- If this issue is raised on behalf of a user they should be named here.
+**Original reporter:** [username facility]/[nobody]
+-->
+
+**Describe the bug**
+<!-- A clear and concise description of what the bug is. -->
+
+**To Reproduce**
+<!--Steps to reproduce the behavior:
+
+For example
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+-->
+
+**Expected behavior**
+<!-- A clear and concise description of what you expected to happen. -->
+
+**Screenshots**
+<!--If applicable/possible, add screenshots to help explain your problem. -->
+
+**Platform/Version (please complete the following information):**
+ - OS: [e.g. Windows, RHEL 7, Ubuntu, macOS]
+ - OS Version:
+ - Mantid Version [e.g. 6.0.0]
+
+**Additional context**
+<!--Add any other context about the problem here.-->

.github/ISSUE_TEMPLATE/config.yml

+blank_issues_enabled: true
+contact_links:
+  - name: MantidProject Forum
+    url: https://forum.mantidproject.org
+    about: Please ask and answer questions here.

.github/ISSUE_TEMPLATE/investigation.md

+---
+name: Investigation
+about: Create a task to investigate options for future work
+title: 'Investigate ...'
+labels: 'Investigation'
+assignees: ''
+
+---
+
+**Describe the outcome that is desired.**
+<!--A clear and concise description of the intended outcome of the future work. Ex. Dependency A will be removed.-->
+
+**Does the outcome relate directly to a problem? Please describe.**
+<!--A clear and concise description of what the problem is. Ex. Dependency A is no longer maintained/has grown too large-->
+
+**Describe any solutions you are considering**
+<!--A clear and concise description of any solutions you've already considered.-->
+
+**Additional context**
+<!--Add any other context or screenshots about the task here.-->

.github/ISSUE_TEMPLATE/maintenance.md

+---
+name: Maintenance
+about: Create a task for maintenance of the codebase
+title: 'Investigate ...'
+labels: 'Maintenance'
+assignees: ''
+
+---
+
+**Describe the outcome that is desired.**
+<!--A clear and concise description of the intended outcome. Ex. The number of cppecheck warnings will be reduced to 0-->
+
+**Describe any solutions you are considering**
+<!--A clear and concise description of any solutions you've already considered.-->
+
+**Additional context**
+<!--Add any other context or screenshots about the task here.-->

.github/ISSUE_TEMPLATE/new_feature.md

+---
+name: New Feature
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+<!--A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]-->
+
+**Describe the solution you'd like**
+<!--A clear and concise description of what you want to happen. Consider using the language of user stories. Ex. As user/developer I need to [...]-->
+
+**Describe alternatives you've considered**
+<!--A clear and concise description of any alternative solutions or features you've considered.-->
+
+**Additional context**
+<!--Add any other context or screenshots about the feature request here.-->

.github/stale.yml

@@ -4,19 +4,28 @@ daysUntilStale: 180
 daysUntilClose: 7
 # Issues with these labels will never be considered stale
 exemptLabels:
-  - Never Stale
+  - Induction
+  - Roadmap
 # Label to use when marking an issue as stale
 staleLabel: Stale
 # Comment to post when marking an issue as stale. Set to `false` to disable
 markComment: >
   This issue has been automatically marked as stale because it has not had
-  recent activity. It will be closed in 7 days if no further activity occurs. 
-  If you feel this is incorrect please comment to keep it alive, with a reason
-  why. 
-   
-  To prevent closure, e.g. for long-term planning issues,
-  add the "Never Stale" label.
+  activity in 6 months. It will be closed in 7 days if no further activity occurs.
+
+  Allowing issues to close as stale helps us filter out issues which can wait
+  for future development time. All issues closed by stale bot act like normal issues; they can be searched for, commented on or reopened at any point.
+
+  If you'd like a closed stale issue to be considered,
+  feel free to either re-open the issue directly or contact a developer.
+
+  To extend the lifetime of an issue please comment below,
+  it helps us see that this is still affecting you and you want
+  it fixed in the near-future. Extending the lifetime of an issue
+  may cause the development team to prioritise it over other issues,
+  which may be closed as stale instead.
+
 # Comment to post when closing a stale issue. Set to `false` to disable
 closeComment: >
   This issue has been closed automatically. If this still affects you please
-  re-open this issue with a comment so we can look into resolving it.
+  re-open this issue with a comment or contact us so we can look into resolving it.

.gitignore

@@ -13,6 +13,9 @@ cmake_install.cmake
 install_manifest.txt
 compile_commands.json
 
+# Ignore CMakeUserPresets
+CMakeUserPresets.json
+
 
 # Compiled Object files
 *.slo
@@ -28,8 +31,9 @@ compile_commands.json
 *.la
 *.a
 
-# Compiled python files
-*.py[co]
+# Byte-compiled / optimized files
+__pycache__/
+*.py[cod]
 
 # Eclipse-generated files
 *.pydevproject
@@ -76,6 +80,9 @@ local.properties
 #Test results
 *.log
 
+#Coverage results
+*.gcov
+