Merge pull request #165 from rapidsai/branch-21.12

[RELEASE] cucim v21.12

Author: raydouglass

3rdparty/LICENSE.NVTX

@@ -0,0 +1,218 @@
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+    TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+    1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
+      to that Work or Derivative Works thereof, that is intentionally
+      submitted to Licensor for inclusion in the Work by the copyright owner
+      or by an individual or Legal Entity authorized to submit on behalf of
+      the copyright owner. For the purposes of this definition, "submitted"
+      means any form of electronic, verbal, or written communication sent
+      to the Licensor or its representatives, including but not limited to
+      communication on electronic mailing lists, source code control systems,
+      and issue tracking systems that are managed by, or on behalf of, the
+      Licensor for the purpose of discussing and improving the Work, but
+      excluding communication that is conspicuously marked or otherwise
+      designated in writing by the copyright owner as "Not a Contribution."
+
+      "Contributor" shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by Licensor and
+      subsequently incorporated within the Work.
+
+    2. Grant of Copyright License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      copyright license to reproduce, prepare Derivative Works of,
+      publicly display, publicly perform, sublicense, and distribute the
+      Work and such Derivative Works in Source or Object form.
+
+    3. Grant of Patent License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
+      use, offer to sell, sell, import, and otherwise transfer the Work,
+      where such license applies only to those patent claims licensable
+      by such Contributor that are necessarily infringed by their
+      Contribution(s) alone or by combination of their Contribution(s)
+      with the Work to which such Contribution(s) was submitted. If You
+      institute patent litigation against any entity (including a
+      cross-claim or counterclaim in a lawsuit) alleging that the Work
+      or a Contribution incorporated within the Work constitutes direct
+      or contributory patent infringement, then any patent licenses
+      granted to You under this License for that Work shall terminate
+      as of the date such litigation is filed.
+
+    4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
+      modifications, and in Source or Object form, provided that You
+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
+          attribution notices from the Source form of the Work,
+          excluding those notices that do not pertain to any part of
+          the Derivative Works; and
+
+      (d) If the Work includes a "NOTICE" text file as part of its
+          distribution, then any Derivative Works that You distribute must
+          include a readable copy of the attribution notices contained
+          within such NOTICE file, excluding those notices that do not
+          pertain to any part of the Derivative Works, in at least one
+          of the following places: within a NOTICE text file distributed
+          as part of the Derivative Works; within the Source form or
+          documentation, if provided along with the Derivative Works; or,
+          within a display generated by the Derivative Works, if and
+          wherever such third-party notices normally appear. The contents
+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
+          as modifying the License.
+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+    5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+    6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+    7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+    8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+    9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+    END OF TERMS AND CONDITIONS
+
+    APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
+      the brackets!)  The text should be enclosed in the appropriate
+      comment syntax for the file format. We also recommend that a
+      file or class name and description of purpose be included on the
+      same "printed page" as the copyright notice for easier
+      identification within third-party archives.
+
+    Copyright [yyyy] [name of copyright owner]
+
+    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.
+
+
+--- LLVM Exceptions to the Apache 2.0 License ----
+
+As an exception, if, as a result of your compiling your source code, portions
+of this Software are embedded into an Object form of such source code, you
+may redistribute such embedded portions in such Object form without complying
+with the conditions of Sections 4(a), 4(b) and 4(d) of the License.
+
+In addition, if you combine or link compiled forms of this Software with
+software that is licensed under the GPLv2 ("Combined Software") and if a
+court of competent jurisdiction determines that the patent provision (Section
+3), the indemnity provision (Section 9) or other Section of the License
+conflicts with the conditions of the GPLv2, you may retroactively and
+prospectively choose to deem waived or otherwise exclude such Section(s) of
+the License, but only in their entirety and only with respect to the Combined
+Software.

CHANGELOG.md

@@ -1,6 +1,28 @@
-# cuCIM 21.10.00 (Date TBD)
+# cuCIM 21.12.00 (Date TBD)
 
-Please see https://github.com/rapidsai/cucim/releases/tag/v21.10.00a for the latest changes to this development branch.
+Please see https://github.com/rapidsai/cucim/releases/tag/v21.12.00a for the latest changes to this development branch.
+
+# cuCIM 21.10.00 (7 Oct 2021)
+
+## 🐛 Bug Fixes
+
+- fix failing regionprops test cases ([#110](https://github.com/rapidsai/cucim/pull/110)) [@grlee77](https://github.com/grlee77)
+
+## 📖 Documentation
+
+- Forward-merge branch-21.08 to branch-21.10 ([#88](https://github.com/rapidsai/cucim/pull/88)) [@jakirkham](https://github.com/jakirkham)
+- Update PyPI cuCIM v21.08.01 README.md and CHANGELOG.md ([#87](https://github.com/rapidsai/cucim/pull/87)) [@gigony](https://github.com/gigony)
+
+## 🚀 New Features
+
+- Support raw RGB tiled TIFF ([#108](https://github.com/rapidsai/cucim/pull/108)) [@gigony](https://github.com/gigony)
+- Add a mechanism for user to know the availability of cucim.CuImage ([#107](https://github.com/rapidsai/cucim/pull/107)) [@gigony](https://github.com/gigony)
+- Enable GDS and Support Runtime Context (__enter__, __exit__) for CuFileDriver and CuImage ([#106](https://github.com/rapidsai/cucim/pull/106)) [@gigony](https://github.com/gigony)
+- Add transforms for Digital Pathology ([#100](https://github.com/rapidsai/cucim/pull/100)) [@shekhardw](https://github.com/shekhardw)
+
+## 🛠️ Improvements
+
+- ENH Replace gpuci_conda_retry with gpuci_mamba_retry ([#69](https://github.com/rapidsai/cucim/pull/69)) [@dillon-cullinan](https://github.com/dillon-cullinan)
 
 # cuCIM 21.08.00 (4 Aug 2021)
 

CMakeLists.txt

@@ -28,7 +28,7 @@ set(PROJECT_VERSION_BUILD dev)
 
 # Append local cmake module path
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/cpp/cmake/modules")
-project(libcucim VERSION ${VERSION} DESCRIPTION "libcucim" LANGUAGES CXX CUDA)
+project(libcucim VERSION ${VERSION} DESCRIPTION "libcucim" LANGUAGES CXX)
 
 ################################################################################
 # Include utilities
@@ -62,19 +62,7 @@ endif ()
 
 find_package(CUDAToolkit REQUIRED)
 set(CMAKE_CXX_STANDARD 17)
-set(CMAKE_CUDA_STANDARD 17) # Clion issue: https://youtrack.jetbrains.com/issue/CPP-19165 (fixed)
-set(CMAKE_CUDA_STANDARD_REQUIRED YES)
 set(CMAKE_CXX_STANDARD_REQUIRED YES)
-cucim_define_cuda_architectures(60;70;75;80;86)
-# https://github.com/Kitware/CMake/blob/master/Modules/Compiler/NVIDIA-CUDA.cmake#L11
-# https://gitlab.kitware.com/cmake/cmake/-/issues/19017
-# For CUDA >= 10.2, we cannot use --compiler-options as '-forward-unknown-to-host-compiler' wouldbe added by default to nvcc options.
-# For the reason, we add "${CMAKE_CXX_FLAGS}" instead of "--compiler-options ${CMAKE_CXX_FLAGS}" here.
-# ==> We changed to use "${CMAKE_CUDA_FLAGS}" instead of "${CMAKE_CXX_FLAGS}" ${CMAKE_CXX_FLAGS} can have wrong options such as '-march=nocona'
-set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} -use_fast_math -Xptxas=-v")
-set(CMAKE_CUDA_FLAGS_DEBUG "${CMAKE_CUDA_FLAGS_DEBUG} -G")
-set(CMAKE_CUDA_FLAGS_RELEASE "${CMAKE_CUDA_FLAGS_RELEASE} -lineinfo")
-set(CMAKE_CUDA_FLAGS_RELWITHDEBINFO "${CMAKE_CUDA_FLAGS_RELWITHDEBINFO} -lineinfo")
 
 # Include CUDA headers explicitly for VSCode intelli-sense
 include_directories(AFTER SYSTEM ${CMAKE_CUDA_TOOLKIT_INCLUDE_DIRECTORIES})
@@ -106,27 +94,38 @@ include(ExternalProject)
 option(CUCIM_SUPPORT_GDS "Support cufile library" ON)
 option(CUCIM_STATIC_GDS "Use static cufile library" OFF)
 option(CUCIM_SUPPORT_CUDA "Support CUDA" ON)
+option(CUCIM_SUPPORT_NVTX "Support NVTX" ON)
 
 # Setup CXX11 ABI
 # : Adds CXX11 ABI definition to the compiler command line for targets in the current directory,
 #   whether added before or after this command is invoked, and for the ones in sub-directories added after.
 add_definitions(-D_GLIBCXX_USE_CXX11_ABI=0) # TODO: create two library, one with CXX11 ABI and one without it.
 
+################################################################################
+# Define basic dependencies
+################################################################################
+# Include pthread
+# (https://cmake.org/cmake/help/v3.18/module/FindThreads.html)
+set(CMAKE_THREAD_PREFER_PTHREAD TRUE)
+set(THREADS_PREFER_PTHREAD_FLAG TRUE)
+find_package(Threads REQUIRED)
+
 ################################################################################
 # Define dependencies
 ################################################################################
 superbuild_depend(fmt)
 #superbuild_depend(boost)
 superbuild_depend(abseil)
-superbuild_depend(rmm) # this imports googletest internally
-#superbuild_depend(googletest)
+# superbuild_depend(rmm) # this imports googletest internally
+superbuild_depend(googletest)
 superbuild_depend(googlebenchmark)
 superbuild_depend(openslide)
 superbuild_depend(catch2)
 superbuild_depend(cli11)
 superbuild_depend(json)
 superbuild_depend(libcuckoo)
 superbuild_depend(boost-header-only)
+superbuild_depend(nvtx3)
 
 ################################################################################
 # Define some names
@@ -154,13 +153,8 @@ configure_file(${CMAKE_CURRENT_LIST_DIR}/examples/cpp/CMakeLists.txt.examples.re
 ################################################################################
 set(INSTALL_TARGETS
         ${CUCIM_PACKAGE_NAME}
-#        ${CUCIM_PACKAGE_NAME}-header-only
-#        rmm
         fmt-header-only
-#        spdlog_header_only # required by rmm
         cucim_benchmarks
-#        cufile_stub
-#        cucim_tests
         )
 
 install(TARGETS ${INSTALL_TARGETS}
@@ -213,6 +207,8 @@ install(DIRECTORY
 # Copy 3rdparty headers
 install(DIRECTORY
             ${deps-fmt_SOURCE_DIR}/include/
+            ${deps-nvtx3_SOURCE_DIR}/c/include/
+            ${deps-nvtx3_SOURCE_DIR}/cpp/include/
         DESTINATION
             ${CMAKE_INSTALL_INCLUDEDIR}/${CUCIM_PACKAGE_NAME}/3rdparty)
 

CONTRIBUTING.md

@@ -144,11 +144,13 @@ The build command will create the following files:
 - `./install/lib/libcucim*`
 - `./python/install/lib/_cucim.cpython-*-x86_64-linux-gnu.so`
 - `./cpp/plugins/cucim.kit.cuslide/install/lib/cucim.kit.cuslide@*.so`
+- `./cpp/plugins/cucim.kit.cumed/install/lib/cucim.kit.cumed@*.so`
 
 And, it will copy the built library files to `python/cucim/src/cucim/clara/` folder:
 - `libcucim.so.*`
 - `_cucim.cpython-*-x86_64-linux-gnu.so`
 - `cucim.kit.cuslide@*.so`
+- `cucim.kit.cumed@*.so`
 
 
 **Building `cucim`(python bindings)**
@@ -173,14 +175,14 @@ Once it is built, the subsequent build doesn't take much time.
 
 However, if a build option or dependent packages are updated, the build can be failed (due to CMakeCache.txt or existing build files). In that case, you can remove use the following commands to remove CMakeCache.txt or build folder, then build it again.
 
-1) Remove CMakeCache.txt for libcucim, cuslide plugin, and the python wrapper (pybind11).
+1) Remove CMakeCache.txt for libcucim, cuslide/cumed plugin, and the python wrapper (pybind11).
 
 ```bash
 # this command wouldn't remove already downloaded dependency so faster than `clean` subcommand
 ./run build_local clean_cache
 ```
 
-2) Remove `build-*` and `install` folder for libcucim, cuslide plugin, and the python wrapper (pybind11).
+2) Remove `build-*` and `install` folder for libcucim, cuslide/cumed plugin, and the python wrapper (pybind11).
 
 ```bash
 # this command is for clean build