Merge pull request #375 from SuperElastix/develop

SimpleITK v2.0rc1
SuperElastix · May 12, 2020 · 8244e00 · 8244e00
2 parents d4cf27f + a7cf5bd
commit 8244e00
Show file tree

Hide file tree

Showing 1,136 changed files with 9,249 additions and 6,009 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -1,31 +1,31 @@
 referenced:
   defaults: &defaults
     docker:
-     - image: circleci/python:2.7-stretch
+     - image: circleci/python:3.5-stretch
     working_directory: ~/
-    resource_class: large
+    resource_class: medium
   default_environment_keys:  &default_environment
     <<: &default_environment_keys
       CTEST_DASHBOARD_ROOT: /home/circleci
       CTEST_SOURCE_DIRECTORY: /home/circleci/SimpleITK
       CTEST_BINARY_DIRECTORY: /home/circleci/SimpleITK-build
       ROOT_BINARY_DIRECTORY: /home/circleci/SimpleITK-build
-      CTEST_BUILD_FLAGS: "-j 4"
-      CTEST_CONFIGURATION_TYPE: "Release"
+      CTEST_BUILD_FLAGS: "-j 1"
+      CTEST_CONFIGURATION_TYPE: "MinSizeRel"
       CTEST_OUTPUT_ON_FAILURE: 1
       ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS: 2
-      PARALLEL_LEVEL: 4
+      PARALLEL_LEVEL: 2
       DASHBOARD_BRANCH_DIRECTORY: /home/circleci/dashboard
       ExternalData_OBJECT_STORES: /home/circleci/.ExternalData
       CCACHE_NODIRECT: 1
   dependencies: &dependencies
     run:
       name: Dependencies
       command: |
-        sudo apt-get install -y rsync lua5.1 ccache kwstyle
+        sudo apt-get install -y rsync lua5.3 ccache
         sudo python -m pip install --upgrade pip
         sudo python -m pip install scikit-ci-addons # Provides "ctest_junit_formatter" add-on
-        sudo python -m pip install cmake==3.10.3
+        sudo python -m pip install cmake==3.13.3
   generate-hash-step: &generate-hash-step
     run:
       name: Generate external data hash
@@ -42,6 +42,7 @@ referenced:
       keys:
         - ccache-{{ arch }}-{{ .Branch }}
         - ccache-{{ arch }}-master
+        - ccache-{{ arch }}
   clone-dashboard-step: &clone-dashboard-step
      run:
        name: Cloning dashboard branch
@@ -58,7 +59,6 @@ referenced:
        name: Formatting CTest for JUnit
        when: always
        command: |
-         env
          mkdir -p /tmp/test-results
          ci_addons ctest_junit_formatter ${CTEST_BINARY_DIRECTORY} > /tmp/test-results/JUnit-${CIRCLE_NODE_INDEX}.xml
   junit-store-test-results: &junit-store-test-results
@@ -123,7 +123,7 @@ jobs:
           root: /home/circleci/SimpleITK-build
           paths:
             - "*"
-  python2.7-and-test:
+  python3.5-and-test:
     <<: *defaults
     environment:
       <<: *default_environment_keys
@@ -159,10 +159,10 @@ jobs:
             ctest -V -Ddashboard_source_config_dir:PATH="Wrapping/Python" -S "${CTEST_SOURCE_DIRECTORY}/.circleci/circleci.cmake"
       - *junit-fotmatting
       - *junit-store-test-results
-  python3.6-and-test:
+  python3.7-and-test:
     <<: *defaults
     docker:
-     - image: circleci/python:3.6-stretch
+     - image: circleci/python:3.7-stretch
     environment:
       <<: *default_environment_keys
       CTEST_BUILD_FLAGS: "-j 2"
@@ -255,6 +255,7 @@ jobs:
       - run:
           name: Prerequisite Dependencies
           command: |
+            sudo apt-get update -y
             sudo apt-get install -y python-pip
       - *dependencies
       - *env-step
@@ -324,27 +325,18 @@ workflows:
                  - gh-pages
                  - dashboard
                  - hooks
-      - python2.7-and-test:
+      - python3.5-and-test:
           requires:
             - build-and-test
-          filters:
-            branches:
-               ignore: next
-      - python3.6-and-test:
+      - python3.7-and-test:
           requires:
             - build-and-test
       - r-and-test:
           requires:
             - build-and-test
-          filters:
-            branches:
-               ignore: next
       - java-and-test:
           requires:
             - build-and-test
-          filters:
-            branches:
-               ignore: next
 
   nightly:
     triggers:

diff --git a/.gitattributes b/.gitattributes
@@ -28,4 +28,7 @@
 *.java           whitespace=tab-in-indent,no-lf-at-eof
 *.rb             whitespace=tab-in-indent,no-lf-at-eof
 *.R              whitespace=tab-in-indent,no-lf-at-eof
-*.tcl whitespace=tab-in-indent,no-lf-at-eof
+*.tcl            whitespace=tab-in-indent,no-lf-at-eof
+
+Wrapping/Java/JavaDoc.i              hooks-max-size=2097152
+Wrapping/Python/PythonDocstrings.i   hooks-max-size=2097152
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -1,32 +1,134 @@
-
-# Development
+# Contributing to SimpleITK
 
 We welcome contributions from the community!
 
-SimpleITK uses the [Git](http://git-scm.com/) distributed version control system. The main repository is hosted on [itk.org](https://itk.org/SimpleITK.git) and mirrored to [Github](https://github.com/SimpleITK/SimpleITK.git). We are currently using Github for pull requests, and issue tracking.
+SimpleITK uses the [Git](http://git-scm.com/) distributed version control system. The main repository is hosted on [Github](https://github.com/SimpleITK/SimpleITK.git) and the [Insight Software Consortium](https://github.com/InsightSoftwareConsortium/SimpleITK). For pull requests and issue tracking  Github is also used.
+
+There are many ways to contribute to SimpleITK:
+ - Report Bugs and Issues
+ - Improve SimpleITK Examples and Documentation
+ - Request new features
+ - Enhance the code coverage
+ - Contribute code to fix bugs or add new features.
+
+## Setup for development
+
+The following documentation is for an advanced contributor who is already familiar with git and GitHub workflow. The [ITK](https://github.com/InsightSoftwareConsortium/ITK) documentation may provide more details, or many online resource can orient you.
+
+After you have cloned and forked the SimpleITK repository run the following command from the root:
+```
+./Utilities/SetupForDevelopment.sh
+```
+
+This script will configure your local checkout with the `upstream` repository and your own fork. Additionally, local hooks and aliases are added.
+
+## Workflow
+
+Submitting code to SimpleITK follows the standard pull request GitHub workflow. More information can be found [here](https://guides.github.com/activities/forking/) and [here](https://guides.github.com/introduction/flow/) regarding the workflow and getting your computer setup.
 
-# Contribute
+SimpleITK uses a branchy workflow where each PR should be a new topic branch. Locally, you create a branch with a concise and precise name then commit your changes to that branch. The branch should be based on your target branch which will usually be `master` for new features and improvements or `release` for back patches such as bugs fixes.
 
-To submit code to SimpleITK, simply follow the standard GitHub workflow to make a pull request. More information can be found [here](https://guides.github.com/activities/forking/) and [here](https://gist.github.com/Chaser324/ce0505fbed06b947d962) regarding the workflow and getting your computer setup.
+After completing the local branch, push it to your fork, then create a GitHub pull request in the SimpleITK upstream repository. The pull request is then required to have an approving *code review*, and the *continuous integration* testing pass before the topic is merged into the upstream repository.
 
-New feature topics should be based on the `master` branch, while bugs fixes for the recent release should be based on the `release` branch. A topic should *never* be based on the `next` branch.
+### How to contribute with the right workflow using github commands
 
-## Setup
+1. Setup
+Fork the repo
+https://github.com/SimpleITK/SimpleITK.git
 
-After cloning the repository, run `./Utilities/SetupForDevelopment.sh` from within the SimpleITK repository to setup Git hooks. Say "no" to setting up access to itk.org as only core developers need access for merging pull requests.
+clone to your laptop
+``` shell
+git clone https://github.com/<username>/SimpleITK.git
+```
+Go to the folder
+``` shell
+cd SimpleITK
+```
+Check the repo
+```shell
+git remote -v
+origin  https://github.com/<username>/SimpleITK.git (fetch)
+origin  https://github.com/<username>/SimpleITK.git (push)
+```
+Add the upstream
+``` shell
+git remote add upstream https://github.com/SimpleITK/SimpleITK.git
+```
+Check the repos again
+```shell
+git remote -v
+origin  https://github.com/<username>/SimpleITK.git (fetch)
+origin  https://github.com/<username>/SimpleITK.git (push)
+upstream        https://github.com/SimpleITK/SimpleITK.git (fetch)
+upstream        https://github.com/SimpleITK/SimpleITK.git (push)
+```
+Download the upstream repo in to your local
+``` shell
+git fetch upstream
+```
+You will see something like this:
+``` shell
+ * [new branch]        dashboard  -> upstream/dashboard
+ * [new branch]        master     -> upstream/master
+ * [new branch]        release    -> upstream/release
+```
+2. Start a branch
+Create your new branch where "newdocumentation" is the name of the new branch. you can change the name
+``` shell
+git checkout -b newdocumentation upstream/master
+Branch 'newdocumentation' set up to track remote branch 'master' from 'upstream'.
+Switched to a new branch 'newdocumentation'
+```
+To check the branches to type this:
+``` shell
+git branch
+```
+The name with the * in front is the branch that you are.
+``` shell
+  master
+* newdocumentation
+```
+3. Create a Pull Request
+Work on the project and when you are done save the files and add, commit and push to origin
+``` shell
+git status
+git add .
+git commit -m"a new commit"
+git push origin
+```
+Once you push it go to your fork repo
+``` shell
+<username>/SimpleITK
+```
+Click on the green button name "compare & pull request" and submit your pull request
 
-This setup script also sets up some alias for the legacy ITK's Gerrit review system.
+4. Update a Pull Request
+ When you update your Pull Request you save the files and add, commit and push to origin.
+ ``` shell
+git status
+git add .
+git commit -m"a new commit"
+git push origin
+```
+Once you push it go to your fork repo
+``` shell
+<username>/SimpleITK
+```
+You will not see again the green button name "compare & pull request". That mean that your request have been update it. You can now go to your pull request (PR) in the https://github.com/SimpleITK/SimpleITK.git and click in the pull request tab, then click on your PR and check the comments and more.
 
 ## Branches
 
-* **next** - An unstable branch which contains future features for testing. These will be tested nightly on [CDash](https://open.cdash.org/index.php?project=SimpleITK). If the tests pass, then they will be merged into master. Pull requests should never be based on this branch, however this is the default branch you should push changes to.
-* **master** - Stable branch of the code and suitable for most users when building SimpleITK. New features should be based on this branch.
-* **release** - Branch of the code from the stable release. Patches which are bug fixes for the most recent releae should be based on the `release` branch.
+* **master** - Stable branch of the code which is expected to available to users when building SimpleITK. New features should be based on this branch.
+* **release** - Branch of the code from the stable release. Patches which are bug fixes for the most recent release should be based on the `release` branch.
+* **dashboard** - CMake scripts used for continuous integration and nightly testing
 
 ## Testing
 
 Testing is very important for SimpleITK, to ensure quality and reliable code that "just works". Please include tests in pull request that add features or fix bugs.
 
-Pull request will be reviewed and run through the continuous integration building and testing infrastructure to ensure quality code before being merged into the **next** branch for nightly testing.
+Pull requests are run through the continuous integration building and
+testing infrastructure to ensure quality code. Many options are tested
+on the PR, but more are run when merged into master. It is important
+to check the [CDash Dashboard](https://open.cdash.org/index.php?project=SimpleITK) to verify no new warnings or regression test failures are introduced after your patch has been merged.
 
-The comprehensive regression testing is reported to the [CDash Dashboard](https://open.cdash.org/index.php?project=SimpleITK). This include the extensive nightly testing on the **next** branch, nightly distributions packages on the **release** or **master** branch, and continuous integration from Github pull requests.
+The regression testing is reported to the [CDash Dashboard](https://open.cdash.org/index.php?project=SimpleITK).
diff --git a/.hooks-config.bash b/.hooks-config.bash
@@ -1,6 +1,6 @@
 #==========================================================================
 #
-#   Copyright Insight Software Consortium
+#   Copyright NumFOCUS
 #
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -0,0 +1,19 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: all
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.7
+  install:
+    - requirements: docs/requirements.txt
diff --git a/.travis.yml b/.travis.yml
@@ -33,9 +33,11 @@ matrix:
       compiler: gcc
 
 before_script:
-  - mkdir -p ${SIMPLEELASTIX_BUILD_DIR}
-  - pwd
-  - ls -lR
+  - sudo apt-get remove cmake && sudo apt-get install swig lua5.3 libinsighttoolkit4-dev doxygen graphviz
+  - cd ${ExternalData_OBJECT_STORES} && if [[ ! -e ${CMAKE_DOWNLOAD_FILE} ]]; then curl -sSO https://cmake.org/files/v3.6/${CMAKE_DOWNLOAD_FILE}; fi
+  - echo "y\n" | sudo bash "${ExternalData_OBJECT_STORES}/${CMAKE_DOWNLOAD_FILE}" --prefix=/usr/local --exclude-subdir
+  - cmake --version
+  - mkdir -p ${SIMPLEITK_BUILD_DIR}
 
 script:
   - if [[ ! -e ${ITK_BUILD_DIR}/ITKConfig.cmake ]]; then

diff --git a/CMake/CTestCustom.cmake.in b/CMake/CTestCustom.cmake.in
@@ -14,13 +14,6 @@ SET(CTEST_CUSTOM_COVERAGE_EXCLUDE
 
  # Exclude files from the Testing directories
  ".*/Testing/.*"
-
- # Exclude files from the Utilities directories
- ".*/Utilities/.*"
-
- # exclude certain wrapping files
- "/Wrapping/SimpleITKLuaMain.cxx"
- "/Wrapping/.*_wrap.cxx"
  )
 
 SET(CTEST_CUSTOM_WARNING_EXCEPTION
@@ -62,6 +55,9 @@ SET(CTEST_CUSTOM_WARNING_EXCEPTION
   # Warning when compiling ITK v4.5.1 with clang
   "clang: warning: argument unused during.*-fno-ipa-cp-clone"
 
+  # Warning when compiling SWIG
+  "clang: warning: argument unused.*-ansi"
+
   # Warning from RHEL5 GCC 4.1 about visibility change
   "warning: lowering visibility of .* to match its type"
 
@@ -70,6 +66,9 @@ SET(CTEST_CUSTOM_WARNING_EXCEPTION
 
   # Warning from RH5 gcc 4.1.2
   "tr1/mu_iterate.h.* warning: unused parameter '__tuple'"
+
+  # Warning on CircleCI
+  "Warning: Permanently added.*to the list of known hosts"
 )
 
 SET(CTEST_CUSTOM_ERROR_EXCEPTION

diff --git a/CMake/FindLuaInterp.cmake b/CMake/FindLuaInterp.cmake
@@ -10,8 +10,18 @@
 #   LUA_EXECUTABLE_FOUND          - If false, don't attempt to use lua
 #   LUA_EXECUTABLE_VERSION_STRING - version of lua found
 
+
+set(_NAMES lua)
+
+if(NOT LuaInterp_FIND_VERSION_MAJOR EQUAL 0)
+  list(INSERT _NAMES 0 lua${LuaInterp_FIND_VERSION_MAJOR})
+  if(NOT LuaInterp_FIND_VERSION_MINOR EQUAL 0)
+    list(INSERT _NAMES 0 lua${LuaInterp_FIND_VERSION_MAJOR}.${LuaInterp_FIND_VERSION_MINOR})
+  endif()
+endif()
+
 find_program(LUA_EXECUTABLE
-  NAMES lua
+  NAMES ${_NAMES}
   )
 
 if(LUA_EXECUTABLE)
@@ -38,8 +48,8 @@ endif()
 # handle the QUIETLY and REQUIRED arguments and set LUA_FOUND to TRUE if
 # all listed variables are TRUE
 include(FindPackageHandleStandardArgs)
-find_package_handle_standard_args(Lua
+find_package_handle_standard_args(LuaInterp
                                   REQUIRED_VARS LUA_EXECUTABLE
-                                  VERSION_VAR LUA_VERSION_STRING)
+                                  VERSION_VAR LUA_VERSION)
 
 mark_as_advanced(LUA_EXECUTABLE)
diff --git a/CMake/FindPythonVirtualEnv.cmake b/CMake/FindPythonVirtualEnv.cmake
@@ -48,6 +48,6 @@ endif()
 include(FindPackageHandleStandardArgs)
 find_package_handle_standard_args(PythonVirtualEnv
                                   REQUIRED_VARS PYTHON_VIRTUALENV_SCRIPT
-                                  VERSION_VAR PYTHON_VIRTUALENV_VERSION_STRING)
+                                  VERSION_VAR PYTHON_VIRTUALENV_VERSION)
 
 mark_as_advanced(PYTHON_VIRTUALENV_SCRIPT)