(cherry picked from commit 5514b17)

When loading a scene that contains singleton transform nodes it is possible to enter an infinite loop calling vtkMRMLTransformNode::GetTransformBetweenNodes(). This can happen if a circular loop is created between the transform nodes as their references are being updated.

Fixed by checking for duplicate transform nodes in vtkMRMLTransformNode::GetTransformBetweenNodes if the maximum transform depth is reached (100). If a loop is detected, then the transform is set to identity, and a warning is logged.

Re Slicer#6355

(cherry picked from commit 260478f)

Repeated loading of empty table node failed. The issue was that for empty tables no schema file was generated and the schema filename was set to "".
However, when the scene was loaded this empty filename was converted to an absolute path (a folder name). When this scene was saved and loaded again then loading the scene file from that path failed.

Fixed the issue by leaving empty filenames empty during scene loading (not converting them to an absolute path).

Fixes Slicer#6371

Co-authored-by: Gabriel Muller <gabriel.muller@ltrace.com.br>

(cherry picked from commit 3d66964)

This commit fixes a regression introduced in a258951 (BUG: Consolidate
vtk.util.numpy_support imports to fix UnboundLocalError) where the use
of `vtk_to_numpy` function was inadvertently removed.

(cherry picked from commit 840406b)

All 3D views were synchronized, regardless of view group ID, because due to misleading variable names, the view group ID always ended up being compared to itself.

Fixes issue reported at https://discourse.slicer.org/t/linked-control-behavior-of-threedviews-with-different-view-groups-linked-control-ignores-view-group-setup/23383/2

(cherry picked from commit c79bded)

When a control point is locked it means that its position cannot be changed by click-and-dragging in a view.
However, we still want to be able to click on a control point to jump to that position in all views.

Complete lock of all interactions with the markup can be achieved by locking the node instead of locking specific control points.

…page (Slicer#6396)

(cherry picked from commit 9c0ae2a)

Since the script injection associated with qSlicerWebWidget was done globally
and only once at the profile level, instantiating first qSlicerWebWidget
and then qSlicerExtensionsInstallWidget was preventing the customization
done in qSlicerExtensionsInstallWidget::initializeWebChannelTransport()
from being effective.

This commit addresses this by injecting the "qwebchannel_appended.js" script
on per page basis. Doing so ensures each qSlicerWebWidget (and derived
object like qSlicerExtensionsInstallWidget) will inject the expected script.

It follows up on da20135 (ENH: WIP - WebEngine support for
extension manager).

… request

(cherry picked from commit 0ac1d7c)

This commit fixes a regression introduced in 9c0ae2a (BUG: Allow multiple
qSlicerWebWidget instance injecting scripts into page) where the observation
of the profile "downloadRequested()" signal was done multiple time.

Since the download request is emitted by the default profile observed by
all web widget instances, this change ignores the request if it does not
originate from the page associated with this web widget instance.

(cherry picked from commit 9a4d0d9)

This commit is a follow up of c47d816 (ENH: Skip message boxes when testing)
and 70bb3b2 (ENH: Refactor message box utility functions)

(cherry picked from commit 423a07b)

While a markup control point is moved then the displayable managers keep checking if the active place node class is supported.
It was checked by creating a node object each time, which was an expensive operation.

Improve performance by determining if the active place node class is supported by checking if it is registered in the markups logic.

(cherry picked from commit 537eb93)

The control point table is not rebuilt anymore if any markups or display node modification is performed.
If a control point table row is updated then items are not recreated anymore

fixes Slicer#6379

(cherry picked from commit 3e7cf17)

When "Fill" method was used in Logical operators effect, sometimes masking settings had no effect.
See user error report at https://discourse.slicer.org/t/how-can-i-save-whole-heart-without-empty-spaces/23596/13

The problem was that Logical operators did not initialize the ModifierLabelmap and qMRMLSegmentEditorWidgetPrivate::updateMaskLabelmap() method
relied on having a valid ModifierLabelmap for creating the mask.

Fixed the issue by creating the mask labelmap based on the segmentation's reference image geometry (instead of the ModifierLabelmap's geometry,
which may be invalid).

(cherry picked from commit 197a96b)

When a view contained markups and interactive slice intersections, the application could crash while moving and dragging markup control points.

The problem was that when a widget was forced to release the focus the `widget->Leave(eventData)` method was called with `nullptr`, but the `Leave`
method actually required valid `eventData`.

Fixed the issue by passing valid `eventData` to `SetHasFocus` method, which then can call `Leave` with that `eventData`.

fixes Slicer#6400

…list

(cherry picked from commit 7e891f2)

vtkSlicerSegmentationsModuleLogic::ExportSegmentsToLabelmapNode crashed when no segment IDs were provided and an input colorTable node was provided.
Empty segment list means all segments are to be exported, but this segment list was updated too late.
Fixed the issue by updating the segment list earlier.

(cherry picked from commit df01d33)

This commit fixes incorrect links identified using markdown-link-check.
See https://github.com/tcort/markdown-link-check

The problematic links have been identified running the following:

  cd Slicer
  for f in $(fd -e md); do
     echo $f | xargs npx markdown-link-check;
  done

Type of updates are the following:

* Obsolete links due to transition to GitHub
  -> Previous reference was looked in "SlicerGitSVNArchive" and then
     updated with the expected on in "Slicer"

* Inconsistent reference to local document
  -> Missing ".md" suffic have been added

* Non-existent website
  -> Replaced with reference from web.archive.org

* Redirect
  -> Replaced with current URL

* Incorrectly formatted link

(cherry picked from commit 33f7f2b)

Extensions update check was not updated to work with Girder_v1 API.

(cherry picked from commit 68a506f)

This commit ensures the dataset associated with "cube-utf8.mrml" scene
is effectively downloaded.

Cherry picked from:
* 3694f90 - COMP: Fix ITK build error on macOS
* dcd132b - COMP: Update VTK backporting fix for vtkSphericalPointIterator gcc build error
* 650ed14 - BUG: Update to latest CTK version

COMP: Fix ITK build error on macOS

Includes ITK fix:

Revision: 46a71c744d4856a5166df227e13c76e8c3ef55cc
Author: Mark Asselin <mark.asselin95@gmail.com>
Date: 2022-04-09 9:51:40 PM
Message:
[Backport PR-3369] COMP: Fix Slicer vtkITK build on macOS

This commit addresses a Slicer macOS build error reported on Discourse
(see https://discourse.slicer.org/t/slicer-build-on-macos-monterey/21940)
and on GitHub (see comments on issue Slicer#5944).

The _POSIX_SOURCE preprocessor identifier is defined in several places
including by Python and several ITK ThirdParty modules. It looks like
this definition is causing unintended side effects when building vtkITK.

When itkMacro.h is #included in vtkITK, _POSIX_SOURCE causes conditional
inclusion of code using __assert_fail and __ASSERT_FUNCTION, which are
defined by GLIBC. Compiling under Clang on macOS this results in a compile error.

This commit fixes the error by checking for the __GLIBC__ preprocessor
identifier instead of __POSIX_SOURCE.
----
Modified: Modules/Core/Common/include/itkMacro.h

COMP: Update VTK backporting fix for vtkSphericalPointIterator gcc build error

List of changes:

$ git shortlog 684e8a602..efbbf9c02e --no-merges
Ben Boeckel (1):
      [Backport] vtkSphericalPointIterator: include `<memory>` for `std::unique_ptr`

Rational:

    Some C++ Standard Library headers have been changed to no longer include other headers that were being used internally by the library. As such, C++ programs that used standard library components without including the right headers will no longer compile.
    The following headers are used less widely in libstdc++ and may need to be included explicitly when compiled with GCC 11:

        (for std::numeric_limits)
        (for std::unique_ptr, std::shared_ptr etc.)
        (for std::pair, std::tuple_size, std::index_sequence etc.)
        (for members of namespace std::this_thread.)

Source: https://gcc.gnu.org/gcc-11/porting_to.html

Co-authored-by: Hu Butui <hot123tea123@gmail.com>
Co-authored-by: Rafael Palomar <rafael.palomar@ous-research.no>

BUG: Update to latest CTK version

Includes several fixes and improvements:

Revision: ec816cbb77986f6ee28c41a495e82238dee0e2d3
Author: Mikhail Polkovnikov <pmkclnl@yandex.ru>
Date: 2022-05-15 5:15:45 AM
Message:
ENH: Set a continuous CTF for the ctkVTKScalarsToColorsView as an editable function or as a read only one

Revision: c97620f43dec6b1eac894d7d9c491d2af236dc22
Author: Steve Pieper <pieper@isomics.com>
Date: 2022-05-06 3:13:39 PM
Message:
Merge pull request Slicer#1031 from lassoan/fix-clipping-during-rotation

BUG: Fix clipped view content when rotating view

Revision: 7580e14a76448da5ca83c3a7648e510563873f9a
Author: Andras Lasso <lasso@queensu.ca>
Date: 2022-05-05 7:00:54 PM
Message:
BUG: Fix clipped view content when rotating view

Camera clipping range must be reset after camera motion.

Fixes issue described here: https://discourse.slicer.org/t/extremities-of-a-long-volume-vanishing-when-rotating/23234/10?u=lassoan

Revision: a9687151baf82e16801cc565b9a2afe92d8caba3
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date: 2022-05-05 1:29:15 AM
Message:
STYLE: Explicitly associate "https" protocol with GitHub external projects

Considering that since March 2022, git protocol is not supported any more
by GitHub, this commit updates external projects to explicitly use "https"
protocol.

See https://github.blog/2021-09-01-improving-git-protocol-security-github/

Co-authored-by: Andras Lasso <lasso@queensu.ca>

Revision: a692acba8ce931b3446b0bbc0a5e1df9f0eaa9ef
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date: 2022-05-04 5:12:52 PM
Message:
ENH: Update ExternalProjectDependency system based on commontk/Artichoke@ea920eb

List of changes:

$ git shortlog 0cc99d3..ea920eb --no-merges
Andras Lasso (1):
      Add support for EXTERNAL_PROJECT_ADDITIONAL_DIRS

Jean-Christophe Fillion-Robin (13):
      ExternalProjectDependency: Remove debug statement inadvertently integrated
      Add support for "ExternalProject_Add_Dependencies"
      ExternalProject_SetIfNotDefined: Add test checking interaction with cache variable
      ExternalProject_SetIfNotDefined: If any, display corresponding cache value
      ExternalProject_SetIfNotDefined: Update docstring
      ExternalProject_Include_Dependencies: Check if superbuild variable is improperly set
      ExternalProjectDependency: Fix spellcheck
      ExternalProjectDependency: Fix variable type of automatically propagated options
      circleci: Use dockbuild/centos7-devtoolset7-gcc7 instead of dockbuild/centos6
      ExternalProjectDependency: Ensure ``User Package Registry`` look up using ``find_*`` commands is disabled
      ExternalProjectDependency: Fix CMake version check for disabling ``User Package Registry``
      doc: Update website links to https versions
      ExternalProjectDependency: Force git protocol to https

Revision: dc1bbb94703d247bb9c2af1cfe75dad4c083215c
Author: Andras Lasso <lasso@queensu.ca>
Date: 2022-05-04 2:05:12 PM
Message:
BUG: Fix CTKData git url

GitHub does not support anymore git protocol for anonymous access, but must use https instead.

Revision: 27d9dd79ecbd97c2c97d3b898f2fb6a8ec20b4c7
Author: Andras Lasso <lasso@queensu.ca>
Date: 2022-05-04 1:30:34 PM
Message:
ENH: Improve ctkLanguageComboBox

Make ctkLanguageComboBox available in Qt Designer.
Add `refreshFromDirectories()` slot to update language list (e.g., when language files are added/removed).
Remove unnecessary `onLanguageChanged()` signals emitted while the language list is being updated.

Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

Revision: b261e3f88867369dff8196c4f00c917707b4b782
Author: Mark Asselin <mark.asselin95@gmail.com>
Date: 2021-12-29 9:35:34 PM
Message:
BUG: Fix build with Slicer_USE_PYTHONQT set to OFF

Cherry picked from:
* 9f108c3 - DOC: NSIS broken link
* 71d053f - DOC: Add debugging by following the forked process (Slicer#6364)
* 73ed5d4 - DOC: Describe extension versioning requirement in extensions.md
* 0a9adf0 - DOC: Update Linux building instructions
* 887143f - DOC: Add tip for use of ccache
* ec4e6ff - DOC: Add tips subtitles
* 69c0fcf - DOC: Update windows.md

Co-authored-by: Andras Lasso <lasso@queensu.ca>
Co-authored-by: Dwij Mistry <49182142+dwijmistry11@users.noreply.github.com>
Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Co-authored-by: Fernando Bordignon <fernando@ltrace.com.br>
Co-authored-by: Rafael Palomar <rafael.palomar@ous-research.no>

Cherry picked from:
* bdc1ee0 - ENH: add WebServer module (Slicer#5999)
* d00bc5b - STYLE: Fix python lint issues in WebServer module
* fdcdbe5 - DOC: Improve Webserver module documentation
* fba5df4 - DOC: Improve Webserver module documentation (part 2)
* 9c7f205 - DOC: extra details and warnings about WebServer (Slicer#6370)
* c9a95b1 - ENH: Add DICOMweb example to webserver examples page
* 0f29c7c - BUG: Fix WebServer failing to load when Slicer built without DICOM support (Slicer#6407)

Cherry picked from:
* c4ac067 - ENH: Improve slicer.util.delayDisplay to show dialog relative to mainwindow
* a28a2c2 - BUG: Update slicer.util.delayDisplay to remove from taskbar thumbnail preview
* 7ddbe77 - ENH: Update slicer.util.messageBox to display a delayed pop in testing mode

(cherry picked from commit 80869f1)

This commit updates libarchive to fix a macOS build error specific to
debug builds.

For reference, commit libarchive/libarchive@a4c3c90bb (Remove the unused variable detected_bytes)
fixes the following build error:

```
/opt/s/LibArchive/libarchive/archive_read_support_format_mtree.c:695:10: error: variable 'detected_bytes' set but not used [-Werror,-Wunused-but-set-variable]
        ssize_t detected_bytes = 0, len, nl;
                ^
1 error generated.
```

List of changes:

$ git shortlog 1b2c437b9..6c3301111 --no-merges
AdamKorcz (1):
      Add CIFuzz

Alex Richardson (2):
      Reduce test_write_format_7zip_large_lzma1 buffer size
      Avoid millions of rand() calls() when running tests

Alex Xu (1):
      libarchive.3: update archive format list

Alexey Pelykh (1):
      Include android_lf.h only for libarchive sources

Brad King (1):
      windows: include archive_platform.h first in blake2s sources

Charly C (1):
      fix the archive_write_disk.3 man page

Christian Hesse (1):
      unescape when extracting link

Dustin Howett (3):
      windows: make sure we use the right calling convention for libc
      fix: include archive_platform in ...cpio to ensure calling convention
      Remove dependency on user32

Emil Velikov (20):
      mtree reader: return early, remove fallthrough chain
      editorconfig: add simple top-level file
      archive: constify the archive::vtable dispatch
      reader: remove unused read_filter_bidder::options
      reader: remove archive_read_filter_bidder_vtable::free stubs
      reader: remove the return type of archive_read_filter_bidder_vtable::free
      reader: introduce archive_read_filter_bidder::vtable
      reader: transform get_bidder into register_bidder
      archive: remove ::compression_{code,name}
      reader: reuse client_{open,close}_proxy more
      reader: track read_filter "can_seek" with a flag
      reader: track read_filter "can_skip" with a flag
      reader: remove unused archive_read_filter callbacks
      reader: introduce struct archive_read_filter_vtable
      cmake: fold gcc/clang sections
      cmake: drop -rdynamic aka CMP0065 NEW
      tar: demote -xa from error to a warning
      cmake: enable -fdata/function-sections and --gc-sections
      autotools: enable -fdata/function-sections and --gc-sections
      archive_digest: check return value of EVP_DigestInit()

Graham Percival (1):
      Fix Y2038 check

Grzegorz Antoniak (3):
      RAR5 reader: fixed out of bounds read in some files
      RAR5 reader: fix invalid memory access in some files
      RAR5 reader: add more checks for invalid extraction parameters

IohannRabeson (1):
      Make all the implicit cast explicit.

JFranklin13 (1):
      Add support for rar5 sfx files

Jairo (3):
      Windows support
      Update untar.c
      Update untar.c

Joerg Sonnenberger (1):
      Support ARCHIVE_EXTRACT_SECURE_NODOTDOT on Windows

Jonas Witschel (4):
      Add ARCHIVE_READDISK_NO_SPARSE to suppress reading sparse file info
      tar: expose ARCHIVE_READDISK_NO_SPARSE as --no-read-sparse
      test_sparse_basic: do not assume that holes can be read in one go
      test_sparse_basic: test ARCHIVE_READDISK_NO_SPARSE

Jung-uk Kim (2):
      Enable LZMA support for FreeBSD
      bsdtar(1): Document threads options for zstd and xz

Ken Matsui (1):
      Remove the unused variable `detected_bytes`

Martin Matuska (25):
      Libarchive 3.5.3dev
      CI: provide a more complete Ubuntu package list
      Fix following symlinks when processing the fixup list
      archive_write_set_format_cpio_binary: fix compilation on OpenBSD
      archive_write_disk_posix: fix writing fflags broken in 8a1bd5c
      CI: fix ubuntu distcheck
      dist: add missing zipx-zstd test files to Makefile.am
      zip: fix possible endless loop if reading a truncated zstd archive
      tar: fix format name typo in creation_set.c
      untar.c: style fixes
      tests: fix style in test_utils/test_main.c
      CI: add dist-artifact
      Libarchive 3.6.0dev
      Release 3.6.0
      Libarchive 3.6.1dev
      tests: reduce sample size for RAR filter test
      RAR reader: fix heap-use-after-free in RAR (v4) filter code
      ci (GitHub Actions): build on Windows 2022 and use Visual Studio 17 2022
      7zip reader: style fixes after 3962d596d
      RAR reader: fix null-dereference in RAR (v4) filter code
      build: fix detection of readdir_r() and dirfd() in configure.ac
      ISO reader: fix possible heap buffer overflow in read_children()
      RAR reader: fix heap-use-after-free in run_filters()
      Release 3.6.1
      CI: Update dependencies for Windows build

Mateusz Piotrowski (1):
      Fix use of At mdoc(7) macro

Michael Osipov (1):
      Add macro for dirfd() on HP-UX because no full POSIX.1-2008 coverage exists

Michał Górny (2):
      Fix expected error messages in test_read_format_zip_winzip_aes*
      Handle missing zlib in test_read_format_zip_7z_deflate

Peter Pentchev (1):
      Raise the lzip max dictionary size to 512MB.

Petr Malat (1):
      Support libzstd compiled with compressor disabled

Russell Greene (2):
      zstd filter writer: add threads option
      fix --threads commandline

Ryan Libby (2):
      tar: respect --ignore-zeros in c r & u modes when reading archives
      tar/test/test_option_ignore_zeros.c: test tar --ignore-zeros

Samanta Navarro (3):
      Fix size_t cast in read_mac_metadata_blob
      Ignore size of directories with regular type
      Added test case for ustar directory handling

Theo Buehler (1):
      Remove OpenSSL compat code that misuses the API

Tim Kientzle (2):
      Reorganize test code a bit
      ZIP reader: fix possible out-of-bounds read in zipx_lzma_alone_init()

Todd Richmond (1):
      zip size entry of -1 should be treated the same as 0

Walter Lozano (2):
      Add path fallback in tar
      Fix check for tape device

Wei-Cheng Pan (2):
      support rar filters
      add test

Younes El-karama (1):
      Fix typo in libarchive/archive_read_support_filter_lzop.c

Zdenek Zambersky (1):
      Fixed size filed in pax header

cielavenir (2):
      Fix 7z PPMD reading beyond boundary
      code review

jiat75 (15):
      added missing checks for canLzip, canLzma, and canXz
      Added all exported but undocumented functions to man pages
      Removed unused function.
      Added bin folder to .gitignore
      Only use deflate when size is not set if the user did not specify a compression algorithm
      Added test for writing an zip file without entry size and no compression
      Added assertions for folder
      Added new test to cmake lists
      Added copyright to new test file.
      Adding test to Makefile.am
      Reusing code from zip size known and adjusting comments
      Using the new .editorconfig to fix formatting on size unset store test
      Fixing typo in archive_read_disk man page
      Cleaned up archive_read_disk_descend functions.
      Added error message when archive extraction fails

jo620kix (2):
      ZIP reader: added support for Zstd decompression
      Add offset variable to zip_read_data_zipx_zstd

linear cannon (4):
      define printf format specifiers if not present
      import m4_ax_compile_check_sizeof.m4 from autoconf archive
      update CMake sizeof definitions to match autotools
      update BLAKE2_PACKED macro with a non-GCCism fallback

…nt size as well

(cherry picked from commit adf8985)

Models -> Display -> Slice display -> Line width now has effect when the model consists of a line.
Previously, when a line model intersected the slice the intersection point was always just 1 pixel.

Fixes issue described at https://discourse.slicer.org/t/model-linewidth/23330

…licer#6358)

(cherry picked from commit 1efef1b)

File loading performance is fixed by implementing bulk setting of color values.

Increased maximum number of accepted entries to 1 million as requested in Slicer#6354.
Loading of a file with 1 million as the maximum ID takes only a few seconds.
Colors module performance is not great with such huge tables. It takes about 20 seconds
to display a color table with 1 million entries.

fixes Slicer#6354

(cherry picked from commit 1bdfefe)

This commit ensures python launcher associated custom application
can successfully load the application environment.

It follows up on 94080fe (BUG: Ensure PythonSlicer loads extension
settings) and updates PythonLauncherSettings.ini ensuring there is no
hardcoded reference to the additional settings.

Instead of using SlicerLauncherSettings.ini, the filename is set
based on the custom application name.

(cherry picked from commit 1a0daf9)

Developers often complained that their extension build failed for some
unknown reason and frequently the issue was that they did not store the
source code in a git repository.

It is good to encourage developers to use best practices, such as version
control, but making the build fail if they build from a non-version-controlled
repository was unnecessarily strong measure.

This commit changes the behavior so that if an extension is built from a
non-git folder then the build succeeds, just a warning is displayed during
project configuration step and `NA` is used as the extension's WC revision.

Co-authored-by: Andras Lasso <lasso@queensu.ca>

(cherry picked from commit f6eb388)

Add header `<memory>` for `std::unique_ptr`.

This commit is a follow up of dcd132b (COMP: Update VTK
backporting fix for vtkSphericalPointIterator gcc build error).

Rational:

    Some C++ Standard Library headers have been changed to no longer include other headers that were being used internally by the library. As such, C++ programs that used standard library components without including the right headers will no longer compile.
    The following headers are used less widely in libstdc++ and may need to be included explicitly when compiled with GCC 11:

        (for std::numeric_limits)
        (for std::unique_ptr, std::shared_ptr etc.)
        (for std::pair, std::tuple_size, std::index_sequence etc.)
        (for members of namespace std::this_thread.)

Source: https://gcc.gnu.org/gcc-11/porting_to.html

(cherry picked from commit f8c7118)

Fix regression caused recent change in how color names are initialized in vtkMRMLColorTableNode.

Fixes Slicer#6382

(cherry picked from commit ba34656)

This commit is a follow up of e78f557 (ENH: Simplify view widgets
initialization from view nodes) that originally introduced the
vtkMRMLCameraNode::GetLayoutName/SetLayoutName.

It makes sure that the layout name associated with a given camera node
can be set to a different value after it had already been set once.

(cherry picked from commit 06a7d69)

Built-in procedural color nodes are read-only, but in the Colors module GUI the colormap was editable by clicking on the colormap and adding/moving control points.
This commit removes the control points, so the read-only nodes are not editable anymore.

see Slicer#6111

(cherry picked from commit 9867446)

When the working copy is reconfigured and a full Slicer build is not performed then qSlicerUtilsTest1 failed with:

Line 408 - Problem with isPluginBuiltIn(). Expected 0 for:
	path: /Applications/Slicer.app/Contents/Extensions-30961/plugin.txt
	applicationHomeDir: /Applications/Slicer.app

It was because Slicer revision in vtkSlicerConfigure.h and vtkSlicerVersionConfigure.h were different.

Made the test more robust by taking the version information from Slicer_REVISION, which is the same as the tested
vtkSlicerApplicationLogic::IsPluginBuiltIn method uses.

(cherry picked from commit 96ee248)

Co-authored-by: Gabriel Muller <gabriel.muller@ltrace.com.br>

Cherry picked from:
* 4d97ce7 - COMP: Fix slicerStripInstalledLibrary to effectively support list of libraries
* 3ea8ba4 - COMP: Update TBB from 2019_U9 to 2021.5.0
* 0d5fe85 - COMP: Improve TBB CMake configuration check on macOS
* 177f3b3 - COMP: Update slicerInstallLibrary to ensure tbb debug libs are not packaged
* cf83447 - COMP: Update SlicerConfig to include Slicer_USE_TBB

COMP: Fix slicerStripInstalledLibrary to effectively support list of libraries

This is a follow-up of 52f2d6c (ENH: Reduce linux package size stripping
regular symbols) where the CMake function slicerStripInstalledLibrary
was first introduced.

COMP: Update TBB from 2019_U9 to 2021.5.0

Remove TBB support for VTK 8. Since older VTK versions do not support
the updated TBB api, this commit removes support for TBB backend when
building on windows with VTK < 9.

Prior to Kitware/VTK@3e5313e71 (Replace task_scheduler_init with task_arena),
the header "tbb/task_scheduler_init.h" was required but is not available
anymore in newer TBB version.

SlicerBlockInstallTBB:
* Update rules based on new library names.
* On linux, switch to use slicerInstallLibrary to ensure
  the symlink chain is followed.
* On macOS, explicitly report an error if the CMake module
  because the libraries are copied through the fix-up process.

COMP: Improve TBB CMake configuration check on macOS

Since TBB 2021.5.0 requires at least macOS 10.15, this commit ensures
the configuration fails when the TBB backend is enabled and the
deployment target is not valid.

COMP: Update slicerInstallLibrary to ensure tbb debug libs are not packaged

This commit ensure libraries filename with suffix "_debug" are not
packaged.

COMP: Update SlicerConfig to include Slicer_USE_TBB

Co-authored-by: James Butler <jbutler@sonovol.com>

(cherry picked from commit 8c148a8)

The extensions server was queried for metadata of all previously installed extensions for all versions.
This time could add up to several seconds (or even tens of seconds on a computer with very long history of Slicer installations).

This commit changes the behavior that the extensions server is only queried for the latest version for each previously installed extension.

Also fixed ordering of revision numbers. Now numeric sorting is used instead of lexicographic.

(cherry picked from commit bb85cf9)

Custom event translation can now be specified to make click or click-and-drag set the crosshair position.

…eased

(cherry picked from commit 1e6d068)

Fixes Slicer#6406.

This change modifies the implementation of `VTKObservationMixin` to use a
'weakref.WeakKeyDictionary` rather than a flat list of registered
observations. This allows observed vtkObjects to be garbage collected if
all other references have been lost.

The registered events are stored in a nested dictionary structure to
acheive constant-time access for `removeObserver`, `hasObserver`, etc.
This also guarantees no observations are duplicated.

```
{obj: {event: {method: (group, tag, priority)}}}
```

(cherry picked from commit 7cfa0fc)

See Slicer#6243 (comment) for more information.

`unittest.TestCase` does not include a `super().__init__()` call, so we must invoke both `TestCase.__init__` along with the `__init__` for any mixins of derived classes.

`super(unittest.TestCase, self).__init__()` explicitly calls the `__init__` of the next class in the MRO, _after `unittest.TestCase`_; so adding this second `__init__` call solves the issue.

Thus, this is now supported:

```python
class MyModuleTest(ScriptedLoadableModuleTest, VTKObservationMixin):
   def runTest(self):
     self.addObserver(...)
```

…asses.

(cherry picked from commit c59fd74)

See Slicer#6243 (comment) for more information.

New tests in SlicerUtilVTKObservationMixinTests:

Ensure VTKObservationMixin functions in combination with the ScriptedLoadableModule classes:

- test_moduleWidgetMixin
- test_moduleLogicMixin
- test_moduleTestMixin

Ensure VTKObservationMixin.__init__ called exactly once in combination with ScriptedLoadableModuleTest:

- test_moduleTestInitCount

(cherry picked from commit c889092)

In July 2018, PythonSlicer replaced SlicerPython as the primary python executable in Slicer@f63a450 with SlicerPython kept for backwards compatibility.

In April 2020, SlicerPython was marked as obsolete in Slicer@d9c5ba6 and scheduled for removal.

This commits executes on the removal of SlicerPython.

(cherry picked from commit b9ac6ed)

Build support for VTK8 or VTK9 was introduced in October 2020 in Slicer@c658b7b when VTK9 support was added.

To streamline maintenance, VTK8 support is now being removed.

(cherry picked from commit a0b03e1)

VTK_COMPONENT_PREFIX and VTK_TARGET_PREFIX were previously set special based on whether
VTK8 or VTK9 was selected. Now that VTK8 support has been dropped we can apply the VTK9
prefix directly where used.

(cherry picked from commit 18a414d)

(cherry picked from commit 0caa5b1)

This commit updates "SlicerBlockInstallExternalPythonModules"
CMake module fixing the following regression introduced
in b9ac6ed (COMP: Remove support for VTK8)

  CMake Error at CMake/SlicerBlockInstallExternalPythonModules.cmake:16 (endif):
    Flow control statements are not properly nested.
  Call Stack (most recent call first):
    CMake/SlicerCPack.cmake:172 (include)
    CMake/LastConfigureStep/CMakeLists.txt:44 (include)

(cherry picked from commit d24cd5b)

Cherry picked from:
* c7cabb0 - BUG: Update onInstallDownloadFinished to ensure relevant metadata are filtered
* 05bb843 - BUG: Update testFilterExtensionMetadata to support Girder_v1
* 4fe811f - ENH: Refactor ExtensionsManagerModel introducing convertExtensionMetadata
* 49b0b89 - BUG: Ensure contributors retrieved from Girder_v1 is associated with model
* 929c114 - BUG: Ensure descriptions retrieved from Girder_v1 is associated with model
* eacbf6b - BUG: Update ExtensionsManagerModelTest::extensionMetadata to support Girder_v1
* 69f8d85 - STYLE: Simplify ExtensionsManagerModelTest removing duplicated function
* e85694f - BUG: Ensure depends retrieved from Girder_v1 is associated with model
* 8a87360 - BUG: Improve ExtensionsManagerModel::installedExtensions() determinism
* c56bf56 - ENH: Simplify extensions manager removing support for Midas_v1 server API
* 8b37395 - COMP: Update qRestAPI to fix windows link error

(cherry picked from commit 76a231d)

Plane should be considered valid even if the point is just being previewed because its position, orientation, and size are defined.

(cherry picked from commit b42cb84)

This commit fixes a regression introduced in 4fe811f (ENH: Refactor
ExtensionsManagerModel introducing convertExtensionMetadata) by making
sure the converted metadata "extension_id" is used instead of the server
key "_id". Conversion rules are encoded in function "serverToExtensionDescriptionKey"

Co-authored-by: James Butler <jbutler@sonovol.com>

(cherry picked from commit cd1b079)

Visual Studio 2019 16.11 now has the /std:c++20 switch
https://devblogs.microsoft.com/cppblog/msvc-cpp20-and-the-std-cpp20-switch/

Cherry picked from:

* fead66d - COMP: Fix -Wunused-variable in vtkMRMLScene related to latestNodeMTime
* e847604 - COMP: Fix -Wunused-* in vtkMRMLSliceIntersectionInteractionRepresentation
* e64d656 - COMP: Fix -Wdeprecated-declarations in qMRMLColorPickerWidgetTest2
* ccbb051 - COMP: Fix deprecated warning related to QWidget::getContentsMargins()
* a38d3a7 - COMP: Fix -Wdeprecated-declarations in qMRMLSceneModel
* a1e7db3 - COMP: Fix -Wunused-parameter in qMRMLMarkupsToolBar.cxx
* 874e9f2 - COMP: Fix -Wdeprecated-declarations in qMRMLSubjectHierarchyModel
* 7e6d35b - COMP: Fix -Wunused-* in vtkMRMLMarkupsROINode.cxx
* 6907b41 - COMP: Fix -Wunused-parameter and -Wunused-variable in qMRMLNodeComboBox
* 6357cd8 - COMP: Fix QStandardItem::setFlags deprecation warnings in qMRMLSubjectHierarchyModel
* 5f1db03 - COMP: Fix -Wdeprecated-declarations in qSlicerUtilsTest1.cxx related to endl
* 4233f9b - COMP: Fix -Wcatch-value in qSlicerUtilsTest1.cxx
* 0ce6227 - COMP: Fix -Wunused-parameter in vtkMRMLCameraWidgetTest1.cxx
* a0a41de - COMP: Remove use of deprecated vtkThreshold API

COMP: Fix -Wunused-variable in vtkMRMLScene related to latestNodeMTime

This commit fixes a warning introduced in 8694fc7 (BUG: Fix scene always
reported as being modified since saved)

COMP: Fix -Wunused-* in vtkMRMLSliceIntersectionInteractionRepresentation

This commit fixes -Wunused-variable and -Wunused-but-set-variable warnings
originally introduced in bc5d5b4 (ENH: Add interactive slice intersections
widget)

COMP: Fix -Wunused-parameter in vtkMRMLCameraWidgetTest1.cxx

COMP: Fix -Wunused-parameter and -Wunused-variable in qMRMLNodeComboBox

This commit fixes warnings introduced in 8324ca7 (ENH: Allow setting
node type display name for abstract node classes)

COMP: Fix -Wdeprecated-declarations in qMRMLSceneModel

This commit is a follow up of bed056e (COMP: Fix deprecation warnings
related to use of QSet::toList()) fixing the following warning. Since
Qt 5.12 is still expected to be supported (see Slicer#5804), the code is
conditionally build.

Warning:

  /path/to/Slicer/Libs/MRML/Widgets/qMRMLSceneModel.cxx: In member function ‘virtual QMimeData* qMRMLSceneModel::mimeData(const QModelIndexList&) const’:
  /path/to/Slicer/Libs/MRML/Widgets/qMRMLSceneModel.cxx:670:47: warning: ‘QSet<T> QList<T>::toSet() const [with T = QModelIndex]’ is deprecated: Use QSet<T>(list.begin(), list.end()) instead. [-Wdeprecated-declarations]
    670 |   allColumnsIndexes = allColumnsIndexes.toSet().values();
        |                                               ^
  In file included from /path/to/Qt/5.15.2/gcc_64/include/QtCore/qdebug.h:52,
                   from /path/to/Qt/5.15.2/gcc_64/include/QtCore/QDebug:1,
                   from /path/to/Slicer/Libs/MRML/Widgets/qMRMLSceneModel.cxx:22:
  /path/to/Qt/5.15.2/gcc_64/include/QtCore/qset.h:406:30: note: declared here
    406 | Q_OUTOFLINE_TEMPLATE QSet<T> QList<T>::toSet() const
        |                              ^~~~~~~~

COMP: Fix -Wunused-* in vtkMRMLMarkupsROINode.cxx

This commit fixes Wunused-variable and -Wunused-parameter warnings
introduced in 9b83257 (ENH: Allow using markups ROI node as CLI
module input)

COMP: Fix -Wdeprecated-declarations in qSlicerUtilsTest1.cxx related to endl

This commit fixes the following warning using ctk::endl introduced
in commontk/CTK@917c39f18 (ENH: Add ctk::flush and ctk::endl to fix
deprecation warnings with Qt >= 5.14)

Warning:

  /path/to/Slicer/Base/QTCore/Testing/Cxx/qSlicerUtilsTest1.cxx: In function ‘bool {anonymous}::createFile(int, const QDir&, const QString&, const QString&)’:
  /path/to/Slicer/Base/QTCore/Testing/Cxx/qSlicerUtilsTest1.cxx:55:46: warning: ‘QTextStream& QTextStreamFunctions::endl(QTextStream&)’ is deprecated: Use Qt::endl [-Wdeprecated-declarations]
     55 |   out << "Generated by qSlicerUtilsTest1" << endl;
        |                                              ^~~~
  In file included from /path/to/Qt/5.15.2/gcc_64/include/QtCore/QTextStream:1,
                   from /path/to/Slicer/Base/QTCore/Testing/Cxx/qSlicerUtilsTest1.cxx:24:
  /path/to/Qt/5.15.2/gcc_64/include/QtCore/qtextstream.h:293:75: note: declared here
    293 | Q_CORE_EXPORT QT_DEPRECATED_VERSION_X(5, 15, "Use Qt::endl") QTextStream &endl(QTextStream &s);
        |                                                                           ^~~~

COMP: Fix -Wcatch-value in qSlicerUtilsTest1.cxx

COMP: Fix -Wdeprecated-declarations in qMRMLColorPickerWidgetTest2

This commit fixes the following warning:

  /path/to/Slicer/Libs/MRML/Widgets/Testing/qMRMLColorPickerWidgetTest2.cxx: In function ‘int qMRMLColorPickerWidgetTest2(int, char**)’:
  /path/to/Slicer/Libs/MRML/Widgets/Testing/qMRMLColorPickerWidgetTest2.cxx:74:57: warning: ‘constexpr QFlags<T>::QFlags(QFlags<T>::Zero) [with Enum = QColorDialog::ColorDialogOption; QFlags<T>::Zero = int QFlags<QColorDialog::ColorDialogOption>::Private::*]’ is deprecated: Use default constructor instead [-Wdeprecated-declarations]
     74 |   ctkColorDialog::getColor(Qt::red, nullptr, "", nullptr);
        |                                                         ^
  In file included from /path/to/Qt/5.15.2/gcc_64/include/QtCore/qglobal.h:1304,
                   from /path/to/Qt/5.15.2/gcc_64/include/QtGui/qtguiglobal.h:43,
                   from /path/to/Qt/5.15.2/gcc_64/include/QtWidgets/qtwidgetsglobal.h:43,
                   from /path/to/Qt/5.15.2/gcc_64/include/QtWidgets/qapplication.h:43,
                   from /path/to/Qt/5.15.2/gcc_64/include/QtWidgets/QApplication:1,
                   from /path/to/Slicer/Libs/MRML/Widgets/Testing/qMRMLColorPickerWidgetTest2.cxx:22:
  /path/to/Qt/5.15.2/gcc_64/include/QtCore/qflags.h:123:80: note: declared here
    123 |     QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {}
        |                                                                                ^~~~~~

COMP: Fix -Wdeprecated-declarations in qMRMLSubjectHierarchyModel

This commit fixes the following warning. Since Qt 5.12 is still
expected to be supported (see Slicer#5804), the code is conditionally built.

Warning:

  /path/to/Slicer/Modules/Loadable/SubjectHierarchy/Widgets/qMRMLSubjectHierarchyModel.cxx: In member function ‘virtual QMimeData* qMRMLSubjectHierarchyModel::mimeData(const QModelIndexList&) const’:
  /path/to/Slicer/Modules/Loadable/SubjectHierarchy/Widgets/qMRMLSubjectHierarchyModel.cxx:679:47: warning: ‘QSet<T> QList<T>::toSet() const [with T = QModelIndex]’ is deprecated: Use QSet<T>(list.begin(), list.end()) instead. [-Wdeprecated-declarations]
    679 |   allColumnsIndexes = allColumnsIndexes.toSet().toList();
        |                                               ^
  In file included from /path/to/Qt/5.15.2/gcc_64/include/QtCore/qdebug.h:52,
                   from /path/to/Qt/5.15.2/gcc_64/include/QtCore/QDebug:1,
                   from /path/to/Slicer/Modules/Loadable/SubjectHierarchy/Widgets/qMRMLSubjectHierarchyModel.cxx:24:
  /path/to/Qt/5.15.2/gcc_64/include/QtCore/qset.h:406:30: note: declared here
    406 | Q_OUTOFLINE_TEMPLATE QSet<T> QList<T>::toSet() const
        |                              ^~~~~~~~
  /path/to/Slicer/Modules/Loadable/SubjectHierarchy/Widgets/qMRMLSubjectHierarchyModel.cxx:679:56: warning: ‘QList<T> QSet<T>::toList() const [with T = QModelIndex]’ is deprecated: Use values() instead. [-Wdeprecated-declarations]
    679 |   allColumnsIndexes = allColumnsIndexes.toSet().toList();
        |                                                        ^
  In file included from /path/to/Qt/5.15.2/gcc_64/include/QtCore/qdebug.h:52,
                   from /path/to/Qt/5.15.2/gcc_64/include/QtCore/QDebug:1,
                   from /path/to/Slicer/Modules/Loadable/SubjectHierarchy/Widgets/qMRMLSubjectHierarchyModel.cxx:24:
  /path/to/Qt/5.15.2/gcc_64/include/QtCore/qset.h:265:14: note: declared here
    265 |     QList<T> toList() const { return values(); }
        |              ^~~~~~

COMP: Fix QStandardItem::setFlags deprecation warnings in qMRMLSubjectHierarchyModel

This commit fixes warnings like the following:

  /path/to/Slicer/Modules/Loadable/SubjectHierarchy/Widgets/qMRMLSubjectHierarchyModel.cxx:779:34: warning: ‘constexpr QFlags<T>::QFlags(QFlags<T>::Zero) [with Enum = Qt::ItemFlag; QFlags<T>::Zero = int QFlags<Qt::ItemFlag>::Private::*]’ is deprecated: Use default constructor instead [-Wdeprecated-declarations]
    779 |         newItem->setFlags(nullptr);
        |                                  ^
  In file included from /path/to/Qt/5.15.2/gcc_64/include/QtCore/qglobal.h:1304,
                   from /path/to/Qt/5.15.2/gcc_64/include/QtCore/qalgorithms.h:43,
                   from /path/to/Qt/5.15.2/gcc_64/include/QtCore/qdebug.h:44,
                   from /path/to/Qt/5.15.2/gcc_64/include/QtCore/QDebug:1,
                   from /path/to/Slicer/Modules/Loadable/SubjectHierarchy/Widgets/qMRMLSubjectHierarchyModel.cxx:24:
  /path/to/Qt/5.15.2/gcc_64/include/QtCore/qflags.h:123:80: note: declared here
    123 |     QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {}
        |

COMP: Fix deprecated warning related to QWidget::getContentsMargins()

This commit fixes warnings like the following:

  /path/to/Slicer/Modules/Loadable/SubjectHierarchy/Widgets/qMRMLSubjectHierarchyComboBox.cxx:621:85: warning: ‘void QWidget::getContentsMargins(int*, int*, int*, int*) const’ is deprecated: use contentsMargins() [-Wdeprecated-declarations]
    621 |   container->getContentsMargins(&marginLeft, &marginTop, &marginRight, &marginBottom);
        |                                                                                     ^
  In file included from /path/to/Qt/5.15.2/gcc_64/include/QtWidgets/qframe.h:44,
                   from /path/to/Qt/5.15.2/gcc_64/include/QtWidgets/QFrame:1,
                   from /path/to/Slicer/Modules/Loadable/SubjectHierarchy/Widgets/qMRMLSubjectHierarchyComboBox.cxx:25:
  /path/to/Qt/5.15.2/gcc_64/include/QtWidgets/qwidget.h:530:10: note: declared here
    530 |     void getContentsMargins(int *left, int *top, int *right, int *bottom) const;
        |          ^~~~~~~~~~~~~~~~~~

COMP: Fix -Wunused-parameter in qMRMLMarkupsToolBar.cxx

This commit fixes a warning originally introduced
in 09d12ae (ENH: Improve control point state management and add
markups toolbar)

COMP: Remove use of deprecated vtkThreshold API

This commit fixes warnings like the following by removing use of API
deprecated in Kitware/VTK@62e5a71bf (Add setters to vtkThreshold).

Warning:

  /path/to/Slicer/Libs/MRML/Core/vtkMRMLModelDisplayNode.cxx: In constructor ‘vtkMRMLModelDisplayNode::vtkMRMLModelDisplayNode()’:
  /path/to/Slicer/Libs/MRML/Core/vtkMRMLModelDisplayNode.cxx:47:52: warning: ‘void vtkThreshold::ThresholdBetween(double, double)’ is deprecated: Use 'SetLowerThreshold', 'SetUpperThreshold' and 'SetThresholdFunction' instead. [-Wdeprecated-declarations]
     47 |   this->ThresholdFilter->ThresholdBetween(0.0, -1.0); // indicates uninitialized
        |                                                    ^
  In file included from /path/to/Slicer/Libs/MRML/Core/vtkMRMLModelDisplayNode.cxx:32:
  /path/to/Slicer-Release/VTK/Filters/Core/vtkThreshold.h:103:8: note: declared here
    103 |   void ThresholdBetween(double lower, double upper);
        |        ^~~~~~~~~~~~~~~

List of SlicerSurfaceToolbox changes:

$ git shortlog b219fee53..3515c3cca --no-merges
Jean-Christophe Fillion-Robin (1):
      COMP: Remove use of deprecated vtkThreshold API~

(cherry picked from commit 5d2004b)

The segment ID list was called early in vtkSegmentation::RemoveAllSegments, and the segments were thus not properly removed. Besides the memory leak, this caused bugs related to expecting the SegmentRemoved event, such as that the segments were not removed from Subject Hierarchy when using said function.

Fixing segmentation automated test by setting selected segment explicitly, which selection was lost due to now properly removing the segments.

Cherry picked from:
* 3a63b61 - DOC: Fix link formatting in extensions.md
* 564ccb3 - DOC: Improve FindGit & SlicerMacroExtractRepositoryInfo CMake module docs
* 43e8f5b - DOC: Added to Windows build instructions to install Windows SDK
* 7ce7736 - DOC: Add info on what additional module paths to add for compiled modules
* 0a71dea - DOC: Add information about how to use other modules from Python modules
* 3858275 - DOC: Fix typo in data_loading_and_saving.md
* 33d92d5 - DOC: Fix typos in python_faq.md
* 5d8c7a4 - DOC: Add comment to LoadableCustomMarkups/CMakeLists.txt about NO_INSTALL
* 834ec57 - DOC: Fixed segment editor effect parameter descriptions
* 4eb2ea2 - DOC: Add custom label value mapping example to script repository
* 6f5f171 - DOC: Prefer language agnostic links associated with docs.github.com
* c92c813 - DOC: Update instructions for debugging memory leaks
* 3164f12 - DOC: Clarify bug report and feature request procedures
* 192af07 - DOC: Update build instructions to include CentOS 7
* b31f165 - DOC: Update extensions manager doc strings, and remove MIDAS occurrences
* ce1b19a - DOC: Rename "Extensions Server website" to "Extensions Catalog website"
* a55104a - DOC: Improve description of loading image as segmentation
* 50d3c58 - DOC: Add information about ExtensionsIndex repository branches
* fd8a16f - DOC: Fix typo in developer_guide/extensions.md
* 6ebff00 - DOC: Improve Centos 7 build instructions
* fa651d2 - DOC: Clarify that each extension build tree can only be used for one build mode
* c48a846 - DOC: Update Slicer style guide for python to reflect Flake8 compliance
* 5794e16 - DOC: endoscopy usage (Slicer#6449)
* c5689b8 - DOC: Update segmentations.md
* f968c21 - DOC: Add description of loading segmentation with color table

Co-authored-by: Andras Lasso <lasso@queensu.ca>
Co-authored-by: kerim371 <kerim.khemraev@mail.ru>
Co-authored-by: James Butler <jbutler@sonovol.com>
Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Co-authored-by: Steve Pieper <pieper@isomics.com>

Cherry picked from:
* 3584ca0 - ENH: Refactor extensions manager
* e2cb3d2 - ENH: Do not use QSignalSpy in qSlicerExtensionsManagerModel
* fd03c69 - BUG: Fix extension update

ENH: Refactor extensions manager

Reworked the extensions manager to take advantage of new Girder_v1 APIs:
- batch download of extension metadata
- server provides extension dependency metadata

These enabled implementing the following improvements:

- Automatic update check and automatic installation can now be enabled for extensions.
  Previously, hundreds of requests were submitted to query all necessary extension
  metadata, which caused slowdowns and crashes. Now all metadata can be downloaded in
  batch (in 4 requests), very robustly, in 1-2 seconds.
  For testing purpose, batch query may also be disabled with setServerQueryWithLimitEnabled.

- If updates are available then a notification marker is displayed over the extensions
  manager toolbar icon.

- Extensions can be bookmarked and all reinstalled in a different Slicer version by a
  single click.
  Previously, all extensions that the user have ever installed was offered to be restored,
  and there was no option to remove any of them. Bookmarked extensions can be installed
  without the browser widget, which may be useful in cases where proxy servers block the
  communication between the extensions manager frontend and backend (because only the backend
  needs to be accessed).

- List of bookmarks can be edited as a simple text. This makes it easy to transfer
  favorite extensions between computers or install a set of extensions at training events.

- Extensions Manager is displayed immediately. The user does not need to wait for any downloads.
  All data is reloaded immediately from cache or downloaded asynchronously.

- The "manage" and "restore" tabs are merged into a single tab where user can install/uninstall/update/restore.

- All metadata are downloaded from Extensions Server. The metadata is cached for offline
  access and to reduce extensions server load.

- Dependent extensions are installed automatically by default, to simplify extension installation.
  Manual installation (user confirmation) can be enabled in extensions settings.

- All dependent extensions (even indirect dependencies) are determined at once before asking
  the user to install them, saving several extra clicks for some extensions.

- Extension version and update time (when the package was built) is displayed for the installed
  extension, and also if there was any update.

- Close/restart button is not enabled until batch processing (install all/update all extension)
  are completed.

- Multiple files can be selected when installing extension from file.

- Extensions server website can be opened from the extensions manager. This makes it easier to
  download extensions for offline installation from file or when firewall or proxy settings prevent
  the extensions manager from working.

- Fixed display of icons of many extensions: icons that were hosted on servers with 301-redirect were not displayed.

Fixes Slicer#5469 - Add last modified date for extensions
Fixes Slicer#5908 - Extension updates not found in stable version
Fixes Slicer#5470 - Add "Update Extension" option under Manage Extensions
Fixes Slicer#5341 - Add favorite extensions list to Extensions manager

See Slicer#4936 - Slicer 5.0 Extension Manager: Manage Extensions Tab icons

ENH: Do not use QSignalSpy in qSlicerExtensionsManagerModel

QSignalSpy is intended for testing, therefore use qRestAPI's synchronous query instead to get extensions metadata from the server.

To simplify the implementation of synchronous query, extension metadata is now always downloaded using a single query (by specifying `limit=0` query parameter).

see Slicer#6437

BUG: Fix extension update

Basic extension metadata was passed to extension download task (instead of files metadata), which did not contain archivename.

Co-authored-by: Andras Lasso <lasso@queensu.ca>
Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Co-authored-by: James Butler <jbutler@sonovol.com>

…d features

(cherry picked from commit f00f401)

Rendering changes associated with these merge requests have not
been backported:
- MR-9174: volume-light-uniforms
- MR-9231: advanced-shadows
- MR-9219: fix-specular-twosided
- MR-9207: volumetric-shadows-feature
- MR-9126: volumetric-rendering-correction

List of VTK changes:

$ git shortlog efbbf9c02..1abf75af7 --no-merges
Andrew Wilson (3):
      [Backport] Add OpenXR haptics json reading & vibration function
      [Backport] Remove doxygen grouping symbol
      [Backport] Comments and better defaults for haptic duration

David Berger (1):
      [Backport] Add SetConstrainedFontSize to vtkLeaderActor2D to enable fixed font sizes

Gaspard Thevenon (3):
      [Backport] Fix shader crash in Multi Volume Rendering without GradientTF
      [Backport] Fix 2D TF with MultiVolume
      [Backport] Add checks for number of lights and warning in vtkOpenGLGPUVolumeRayCastMapper

Ken Martin (2):
      [Backport] feat(Rendering): add coordinate systems to Prop3D
      [Backport] fix(Rendering): fix prop3d DEVICE coordinates on OpenGL

Lucas Gandel (4):
      [Backport] Fix vtkOpenXRManager singleton destructor not being called
      [Backport] Remove useless modifications to the OpenXR render window state
      [Backport] Fix OpenXR view pose
      [Backport] Fix undefined vtkOpenXRManager::GetRecommendedImageRectSize

Lucas Givord (2):
      [Backport] Fix missing check dimension in the vtkImageItem
      [Backport] Fix crash when we use renderLineAsTube without light in scene

LucasGandel (1):
      [Backport] Fix use of vtkDebugMacro in vtkOpenXRManager that is not a vtkObject

Mathieu Westphal (1):
      [Backport] Ensure XCloseDisplay is called, and at the right time

Nicolas Vuaille (1):
      [Backport] Update vtkCamera ParallelProjectionScale documentation

Sankhesh Jhaveri (4):
      [Backport] Ensure that dangling references are cleaned up
      [Backport] Remove use of deprecated cell types API for ospray
      [Backport] Avoid using variable names that shadow Windows keywords
      [Backport] Avoid using variable names that shadow Windows keywords

Scott Wittenburg (2):
      [Backport] RenderingOpenXR: Fixes to support build/run on Linux
      [Backport] OpenXR: Create graphics binding with non-null objects

Sjors Peterse (1):
      [Backport] Change vtkProp to vtkProp3D in documentation

Spiros Tsalikis (3):
      [Backport] vtkOpenXRUtilities: Remove constexpr
      [Backport] vtkOpenXRManager: Fix usage of strcmp
      [Backport] vtkOpenXRModel: Fix atomic instantiation

Stephen Hogarth (1):
      [Backport] Add Faster AddRGBPoints Routine

Thomas Galland (3):
      [Backport] Add new movement style for VR
      [Backport] Desunite ground movement and elevation in VR
      [Backport] VRInteractorStyle code refactoring

Tiffany Chhim (1):
      [Backport] Move getter for window initialization from OpenXR to VR module

Timothee Chabat (1):
      [Backport] Make wide lines have a minimal screen space size

luz paz (1):
      [Backport] Fix typos in Rendering/

(cherry picked from commit 8e049d9)

This commit backport change associated with merge request 9101
See https://gitlab.kitware.com/vtk/vtk/-/merge_requests/9101

List of changes:

$ git shortlog 1abf75af73..bccd2b8f7e --no-merges
Lucas Gandel (5):
      [Backport MR-9101] Use an alternative rendering backend in vtkOpenXRManager
      [Backport MR-9101] Add render window class to share textures between OpenGL and D3D contexts
      [Backport MR-9101] Allow OpenXR manager to use remoting
      [Backport MR-9101] Find OpenXR Remoting libraries
      [Backport MR-9101] Add test for vtkWin32OpenGLDXRenderWindow

LucasGandel (1):
      [Backport MR-9101] Fix undefined function when OpenXR remoting is disabled

…volume name is long

(cherry picked from commit 5ecfcc3)

Size of the node selector combobox was set based on first selected node by default, which resulted in very wide layout if the first segmentation or master node had long name.
Changed size adjustment mode to QComboBox::AdjustToMinimumContentsLengthWithIcon to avoid this.

Fixes the issue described here:
https://discourse.slicer.org/t/segmentations-module-dont-automatically-expand-modules-settings-pane-for-long-file-folder-paths/20260/4?u=lassoan

(cherry picked from commit 82a2259)

Related to Slicer#6437

Co-authored-by: Andras Lasso <lasso@queensu.ca>

(cherry picked from commit cc69373)

The filename that was selected in the filename dialog was not passed to the reader.

Also update qSlicerVolumesReader to revisit the logic checking
the colorNodeID property.

fixes Slicer#6429

(cherry picked from commit 457016b)

When interactive slice intersection was dragged over a markup control point the dragging got interrupted.

(cherry picked from commit 0a03716)

This commit ensures that the code path expected to be executed when testing
is enabled is done so when the AA_EnableTesting attribute is set and not
only when the command line parameter "--testing-enabled" is passed.

This allows to programmatically enable testing in test without having to
explicitly pass the argument.

(cherry picked from commit 056a9ac)

This commit updates Slicer.crt certificate bundle with [make-ca.sh][1] script using the
content of [certdata][2] associated with mozilla/gecko-dev@549b3f9,

It was auto-generated by the [update-slicer-certificate-bundle][3] GitHub action workflow.

[1]: https://github.com/Slicer/Slicer/blob/0f29c7c9a73e844cb2b1c74fad9bde9321c43d07/Base/QTCore/Resources/Certs/make-ca.sh
[2]: https://github.com/mozilla/gecko-dev/blob/549b3f9615dc6b2841a906af72d8f7e78e050034/security/nss/lib/ckfw/builtins/certdata.txt?raw=true
[3]: https://github.com/Slicer/Slicer/blob/0f29c7c9a73e844cb2b1c74fad9bde9321c43d07/.github/workflows/update-slicer-certificate-bundle.yml

(cherry picked from commit 64f6340)

"Batch processing" mode is activated automatically when a large (10+ children) branch visibility is changed.
In batch mode, item visibility change requests were mistakenly ignored.

fixes Slicer#6445

(cherry picked from commit 1026bb8)

fixes Slicer#6435

…icer#6420)

(cherry picked from commit e8d195c)

This fixes all remaining pycodestyle E2 whitespace error codes.

Bulk of updates performed using autopep8 CLI
with the following command:

  autopep8 --in-place --select E201,E202,E203,E211,E221,E222,E225,E226,E227,E228,E231,E241,E251,E261,E262,E265,E266,E271 $(git ls-files '*.py')

See https://github.com/hhatto/autopep8#readme

References:

* Whitespace after '('
  See https://www.flake8rules.com/rules/E201.html

* Whitespace before ')'
  See https://www.flake8rules.com/rules/E202.html

* Whitespace before ':'
  See https://www.flake8rules.com/rules/E203.html

* Whitespace before '('
  See https://www.flake8rules.com/rules/E211.html

* Multiple spaces before operator
  See https://www.flake8rules.com/rules/E221.html

* Multiple spaces after operator
  See https://www.flake8rules.com/rules/E222.html

* Missing whitespace around operator
  See https://www.flake8rules.com/rules/E225.html

* Missing whitespace around arithmetic operator
  See https://www.flake8rules.com/rules/E226.html

* Missing whitespace around bitwise or shift operator
  See https://www.flake8rules.com/rules/E227.html

* Missing whitespace around modulo operator
  See https://www.flake8rules.com/rules/E228.html

* Missing whitespace after ',', ';', or ':'
  See https://www.flake8rules.com/rules/E231.html

* Multiple spaces after ','
  See https://www.flake8rules.com/rules/E241.html

* Unexpected spaces around keyword / parameter equals
  See https://www.flake8rules.com/rules/E251.html

* At least two spaces before inline comment
  See https://www.flake8rules.com/rules/E261.html

* Inline comment should start with '# '
  See https://www.flake8rules.com/rules/E262.html

* Block comment should start with '# '
  See https://www.flake8rules.com/rules/E265.html

* Too many leading '#' for block comment
  See https://www.flake8rules.com/rules/E266.html

* Multiple spaces after keyword
  See https://www.flake8rules.com/rules/E271.html

This fixes all remaining pycodestyle E1 indentation error codes.

Bulk of updates performed using autopep8 CLI
with the following command:

  autopep8 --in-place --select E111,E114,E115,E116,E117,E121,E122,E123,E124,E125,E126,E127,E128,E129,E131 $(git ls-files '*.py')

See https://github.com/hhatto/autopep8#readme

References:

* Indentation is not a multiple of four
  See https://www.flake8rules.com/rules/E111.html

* Indentation is not a multiple of four (comment)
  See https://www.flake8rules.com/rules/E114.html

* Expected an indented block (comment)
  See https://www.flake8rules.com/rules/E115.html

* Unexpected indentation (comment)
  See https://www.flake8rules.com/rules/E116.html

* Over-indented
  See https://www.flake8rules.com/rules/E117.html

* Continuation line under-indented for hanging indent
  See https://www.flake8rules.com/rules/E121.html

* Continuation line missing indentation or outdented
  See https://www.flake8rules.com/rules/E122.html

* Closing bracket does not match indentation of opening bracket's line
  See https://www.flake8rules.com/rules/E123.html

* Closing bracket does not match visual indentation
  See https://www.flake8rules.com/rules/E124.html

* Continuation line with same indent as next logical line
  See https://www.flake8rules.com/rules/E125.html

* Continuation line over-indented for hanging indent
  See https://www.flake8rules.com/rules/E126.html

* Continuation line over-indented for visual indent
  See https://www.flake8rules.com/rules/E127.html

* Continuation line under-indented for visual indent
  See https://www.flake8rules.com/rules/E128.html

* Visually indented line with same indent as next logical line
  See https://www.flake8rules.com/rules/E129.html

* Continuation line unaligned for hanging indent
  See https://www.flake8rules.com/rules/E131.html

This fixes many of the pycodestyle E7 statement error codes.

Bulk of updates performed using autopep8 CLI
with the following command:

  autopep8 --in-place --select E701,E703,E712,E713,E714,E741 $(git ls-files '*.py')

See https://github.com/hhatto/autopep8#readme

References:

* Multiple statements on one line (colon)
  See https://www.flake8rules.com/rules/E701.html

* Statement ends with a semicolon
  See https://www.flake8rules.com/rules/E703.html

* Comparison to true should be 'if cond is true:' or 'if cond:'
  See https://www.flake8rules.com/rules/E712.html

* Test for membership should be 'not in'
  See https://www.flake8rules.com/rules/E713.html

* Test for object identity should be 'is not'
  See https://www.flake8rules.com/rules/E714.html

* Do not use variables named 'I', 'O', or 'l'
  See https://www.flake8rules.com/rules/E741.html

…utation

(cherry picked from commit 68373c1)

itkDCMTKFileReader was added in 2012 but it seems that current itkDCMTKFileReader in ITK works just as well.
The 2012 version has a bug (it should use (0x5200, 0x9230) instead of (0x5200, 0x9239) tag - see https://discourse.slicer.org/t/image-position-patient-attribute-0020-0032-in-dicom-file-not-handled/23950/3) therefore it makes sense to switch to the ITK implementation.

(cherry picked from commit 43a34e2)

Example:

>>> loadModel(r'c:\Users\andra\OneDrive\Projects\SlicerTesting2022\20220622-EmptyPolyData\slicer5-fail-T_Sup-O_right.vtp')
Traceback (most recent call last):
  File "<console>", line 1, in <module>
  File "C:\D\S4D\Slicer-build\bin\Python\slicer\util.py", line 820, in loadModel
    return loadNodeFromFile(filename, 'ModelFile', {}, returnNode)
  File "C:\D\S4D\Slicer-build\bin\Python\slicer\util.py", line 685, in loadNodeFromFile
    raise RuntimeError(errorMessage)
RuntimeError: Failed to load node from file: c:\Users\andra\OneDrive\Projects\SlicerTesting2022\20220622-EmptyPolyData\slicer5-fail-T_Sup-O_right.vtp
- Error: Loading c:\Users\andra\OneDrive\Projects\SlicerTesting2022\20220622-EmptyPolyData\slicer5-fail-T_Sup-O_right.vtp - ERROR: In C:\D\S4D\VTK\IO\XML\vtkXMLUnstructuredDataReader.cxx, line 393
vtkXMLPolyDataReader (00000254994D0CC0): No Points element available in first piece found in file. Reading file may fail.
- Error: Loading c:\Users\andra\OneDrive\Projects\SlicerTesting2022\20220622-EmptyPolyData\slicer5-fail-T_Sup-O_right.vtp - Failed to read node slicer5-fail-T_Sup-O_right (vtkMRMLModelNode4) from filename='c:\Users\andra\OneDrive\Projects\SlicerTesting2022\20220622-EmptyPolyData\slicer5-fail-T_Sup-O_right.vtp'

see Slicer#6447

(cherry picked from commit a5f7535)

Detailed file IO error/warning messages were displayed to the user but not logged.
Now the messages are also added to the application log.

see Slicer#6447

… functions (Slicer#6451)

(cherry picked from commit 8fe258b)

(cherry picked from commit 23744ee)

DICOMweb client library logging happened at the DEBUG level, which significantly slowed down data transfer.
The problem was that the library was reorganized and log level setting that worked on earlier versions was not effective anymore.