ENH: Bump ITK and change http to https

InsightSoftwareConsortium · Jun 2, 2022 · da5821a · da5821a
1 parent 9afa049
commit da5821a
Show file tree

Hide file tree

Showing 13 changed files with 43 additions and 43 deletions.
diff --git a/.clang-format b/.clang-format
@@ -4,7 +4,7 @@
 ## See: https://clang.llvm.org/docs/ClangFormatStyleOptions.html for details of each option
 ##
 ## The clang-format binaries can be downloaded as part of the clang binary distributions
-## from http://releases.llvm.org/download.html
+## from https://releases.llvm.org/download.html
 ##
 ## Use the script Utilities/Maintenance/clang-format.bash to faciliate
 ## maintaining a consistent code style.

diff --git a/.github/workflows/build-test-package.yml b/.github/workflows/build-test-package.yml
@@ -13,17 +13,17 @@ jobs:
           - os: ubuntu-18.04
             c-compiler: "gcc"
             cxx-compiler: "g++"
-            itk-git-tag: "a89145bccda6a36f42cfdd45d3a6b27234ff54fe"
+            itk-git-tag: "d6acfd26bfcdec606d605beb1301bddfb17c05a6"
             cmake-build-type: "MinSizeRel"
           - os: windows-2019
             c-compiler: "cl.exe"
             cxx-compiler: "cl.exe"
-            itk-git-tag: "a89145bccda6a36f42cfdd45d3a6b27234ff54fe"
+            itk-git-tag: "d6acfd26bfcdec606d605beb1301bddfb17c05a6"
             cmake-build-type: "Release"
           - os: macos-10.15
             c-compiler: "clang"
             cxx-compiler: "clang++"
-            itk-git-tag: "a89145bccda6a36f42cfdd45d3a6b27234ff54fe"
+            itk-git-tag: "d6acfd26bfcdec606d605beb1301bddfb17c05a6"
             cmake-build-type: "MinSizeRel"
 
     steps:
@@ -134,9 +134,9 @@ jobs:
     strategy:
       max-parallel: 2
       matrix:
-        python-version: [36, 37, 38, 39]
+        python-version: [37, 38, 39, 310]
         include:
-          - itk-python-git-tag: "v5.2.0.post2"
+          - itk-python-git-tag: "v5.3rc04"
 
     steps:
     - uses: actions/checkout@v2
@@ -172,7 +172,7 @@ jobs:
       max-parallel: 2
       matrix:
         include:
-          - itk-python-git-tag: "v5.2.0.post2"
+          - itk-python-git-tag: "v5.3rc04"
 
     steps:
     - uses: actions/checkout@v2
@@ -206,9 +206,9 @@ jobs:
     strategy:
       max-parallel: 2
       matrix:
-        python-version-minor: [6, 7, 8, 9]
+        python-version-minor: [7, 8, 9, 10]
         include:
-          - itk-python-git-tag: "v5.2.0.post2"
+          - itk-python-git-tag: "v5.3rc04"
 
     steps:
     - name: Get specific version of CMake, Ninja
@@ -241,7 +241,7 @@ jobs:
       run: |
         cd ../../im
         call "C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\VC\Auxiliary\Build\vcvars64.bat"
-        set PATH="C:\P\grep;%PATH%"
+        set PATH=C:\P\grep;%PATH%
         set CC=cl.exe
         set CXX=cl.exe
         C:\Python3${{ matrix.python-version-minor }}-x64\python.exe C:\P\IPP\scripts\windows_build_module_wheels.py --py-envs "3${{ matrix.python-version-minor }}-x64" --no-cleanup

diff --git a/LICENSE b/LICENSE
@@ -1,7 +1,7 @@
 
                                  Apache License
                            Version 2.0, January 2004
-                        http://www.apache.org/licenses/
+                        https://www.apache.org/licenses/
 
    TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
 
@@ -193,7 +193,7 @@
    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
+       https://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,

diff --git a/README.rst b/README.rst
@@ -14,16 +14,16 @@ ITKSkullStripping
 Overview
 --------
 
-This is a module for the `Insight Toolkit (ITK) <http://itk.org>`_ that
+This is a module for the `Insight Toolkit (ITK) <https://itk.org>`_ that
 performs automatic skull-stripping for neuroimage analysis.
 
-For more information, see the `Insight Journal article <http://hdl.handle.net/10380/3353>`_::
+For more information, see the `Insight Journal article <https://hdl.handle.net/10380/3353>`_::
 
   Bauer S., Fejes T., Reyes M.
   Skull-Stripping Filter for ITK
   The Insight Journal. January-December. 2012.
-  http://hdl.handle.net/10380/3353
-  http://www.insight-journal.org/browse/publication/859
+  https://hdl.handle.net/10380/3353
+  https://www.insight-journal.org/browse/publication/859
 
 Installation
 -------------

diff --git a/doc/InsightArticle.cls b/doc/InsightArticle.cls
@@ -76,11 +76,11 @@
 
 % Define command to make reference to on-line Doxygen documentation
 \newcommand{\doxygen}[1]{
-\href{http://www.itk.org/Doxygen/html/classitk_1_1#1.html}{\code{itk::#1}}}  
+\href{https://www.itk.org/Doxygen/html/classitk_1_1#1.html}{\code{itk::#1}}}  
 
 % Define command to make reference to on-line Doxygen documentation
 \newcommand{\subdoxygen}[2]{
-\href{http://www.itk.org/Doxygen/html/classitk_1_1#1_1_1#2.html}{\code{itk::#1::#2}}}  
+\href{https://www.itk.org/Doxygen/html/classitk_1_1#1_1_1#2.html}{\code{itk::#1::#2}}}  
 
 % Define command for the standard comment introducing classes with similar functionalities
 \newcommand{\relatedClasses}{

diff --git a/doc/InsightJournal.sty b/doc/InsightJournal.sty
@@ -1109,11 +1109,11 @@
 %  Commands for adding the link reference to the URL in the Insight Journal
 %
 \newcommand{\urlhandle}[1]{
-\url{http://hdl.handle.net/10380/#1}}  
+\url{https://hdl.handle.net/10380/#1}}  
 
 \newcommand{\IJhandle}[1]{
-Latest version available at the \href{http://www.insight-journal.org}{Insight Journal} [\urlhandle{#1}]\\
-Distributed under \href{http://creativecommons.org/licenses/by/3.0/us/}{Creative Commons Attribution License}}
+Latest version available at the \href{https://www.insight-journal.org}{Insight Journal} [\urlhandle{#1}]\\
+Distributed under \href{https://creativecommons.org/licenses/by/3.0/us/}{Creative Commons Attribution License}}
 
 \newcommand{\IJhandlefooter}[1]{
 \fancyfoot[CO,CE]{

diff --git a/doc/article.pdf b/doc/article.pdf
diff --git a/doc/article.tex b/doc/article.tex
@@ -4,7 +4,7 @@
 % of the standard documentation for Insight.  It may be found online
 % at:
 %
-%     http://www.itk.org/
+%     https://www.itk.org/
 
 \documentclass{InsightArticle}
 

diff --git a/doc/skullStrip.bib b/doc/skullStrip.bib
@@ -85,7 +85,7 @@ @INPROCEEDINGS{Bauer2011c
   keywords = {Brain tumor,MRI,Segmentation,Skull-stripping},
   owner = {Stefan},
   timestamp = {2012.04.18},
-  url = {http://www.istb.unibe.ch/content/ssbe\_2011/ http://arxiv.org/abs/1204.0357}
+  url = {https://www.istb.unibe.ch/content/ssbe\_2011/ https://arxiv.org/abs/1204.0357}
 }
 
 @ARTICLE{Carass2011,
@@ -130,7 +130,7 @@ @ARTICLE{Carass2011
   pmid = {21458576},
   publisher = {Elsevier Inc.},
   timestamp = {2012.04.18},
-  url = {http://www.ncbi.nlm.nih.gov/pubmed/21458576}
+  url = {https://www.ncbi.nlm.nih.gov/pubmed/21458576}
 }
 
 @ARTICLE{Cocosco1997,
@@ -185,7 +185,7 @@ @ARTICLE{Eskildsen2011
   pmid = {21945694},
   publisher = {Elsevier Inc.},
   timestamp = {2012.04.18},
-  url = {http://www.ncbi.nlm.nih.gov/pubmed/21945694}
+  url = {https://www.ncbi.nlm.nih.gov/pubmed/21945694}
 }
 
 @ARTICLE{Fennema-Notestine2006,
@@ -241,7 +241,7 @@ @ARTICLE{Fennema-Notestine2006
   pmid = {15986433},
   publisher = {John Wiley \& Sons},
   timestamp = {2012.04.18},
-  url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2408865\&tool=pmcentrez\&rendertype=abstract}
+  url = {https://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2408865\&tool=pmcentrez\&rendertype=abstract}
 }
 
 @INPROCEEDINGS{Hahn2000,
@@ -277,7 +277,7 @@ @ARTICLE{Hartley2006
   owner = {Stefan},
   publisher = {Elsevier},
   timestamp = {2012.04.18},
-  url = {http://linkinghub.elsevier.com/retrieve/pii/S1053811905024407}
+  url = {https://linkinghub.elsevier.com/retrieve/pii/S1053811905024407}
 }
 
 @BOOK{Ibanez2003,
@@ -288,7 +288,7 @@ @BOOK{Ibanez2003
   file = {:C$\backslash$:/Documents and Settings/Stefan/My Documents/Files/Literature/manuals/ItkSoftwareGuide-2.4.0.pdf:pdf},
   owner = {Stefan},
   timestamp = {2012.04.18},
-  url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1.3166}
+  url = {https://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1.3166}
 }
 
 @ARTICLE{Iglesias2011,
@@ -336,7 +336,7 @@ @ARTICLE{Iglesias2011
   owner = {Stefan},
   pmid = {21880566},
   timestamp = {2012.04.18},
-  url = {http://www.ncbi.nlm.nih.gov/pubmed/21880566}
+  url = {https://www.ncbi.nlm.nih.gov/pubmed/21880566}
 }
 
 @ARTICLE{Lee2003,
@@ -356,7 +356,7 @@ @ARTICLE{Lee2003
 	index,simulated t1-weighted mri,skull-stripping},
   owner = {Stefan},
   timestamp = {2012.04.18},
-  url = {http://linkinghub.elsevier.com/retrieve/pii/S0010482503000222}
+  url = {https://linkinghub.elsevier.com/retrieve/pii/S0010482503000222}
 }
 
 @ARTICLE{Segonne2004,
@@ -378,7 +378,7 @@ @ARTICLE{Segonne2004
   owner = {Stefan},
   publisher = {Elsevier},
   timestamp = {2012.04.18},
-  url = {http://linkinghub.elsevier.com/retrieve/pii/S1053811904001880}
+  url = {https://linkinghub.elsevier.com/retrieve/pii/S1053811904001880}
 }
 
 @ARTICLE{Sadananthan2010,
@@ -396,7 +396,7 @@ @ARTICLE{Sadananthan2010
   owner = {Stefan},
   publisher = {Elsevier},
   timestamp = {2012.04.18},
-  url = {http://linkinghub.elsevier.com/retrieve/pii/S1053811909009604}
+  url = {https://linkinghub.elsevier.com/retrieve/pii/S1053811909009604}
 }
 
 @ARTICLE{Sandor1997,
@@ -441,7 +441,7 @@ @ARTICLE{Sandor1997
   owner = {Stefan},
   pmid = {9050407},
   timestamp = {2012.04.18},
-  url = {http://www.ncbi.nlm.nih.gov/pubmed/9050407}
+  url = {https://www.ncbi.nlm.nih.gov/pubmed/9050407}
 }
 
 @ARTICLE{Shattuck2009,
@@ -500,7 +500,7 @@ @ARTICLE{Shattuck2009
   pmid = {19073267},
   publisher = {Elsevier Inc.},
   timestamp = {2012.04.18},
-  url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2757629\&tool=pmcentrez\&rendertype=abstract}
+  url = {https://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2757629\&tool=pmcentrez\&rendertype=abstract}
 }
 
 @INPROCEEDINGS{Shi2011,
@@ -547,7 +547,7 @@ @ARTICLE{Smith2002a
   owner = {Stefan},
   pmid = {12391568},
   timestamp = {2012.04.18},
-  url = {http://www.ncbi.nlm.nih.gov/pubmed/12391568}
+  url = {https://www.ncbi.nlm.nih.gov/pubmed/12391568}
 }
 
 @INPROCEEDINGS{Speier2011,
@@ -578,7 +578,7 @@ @ARTICLE{Tsai2003
   file = {:C$\backslash$:/Documents and Settings/Stefan/My Documents/Files/Literature/segmentation/tsai2003.pdf:pdf},
   owner = {Stefan},
   timestamp = {2012.04.24},
-  url = {http://projecteuclid.org/euclid.cms/1119655349}
+  url = {https://projecteuclid.org/euclid.cms/1119655349}
 }
 
 @INPROCEEDINGS{Wang2011,
@@ -614,7 +614,7 @@ @ARTICLE{Zhuang2006
   owner = {Stefan},
   publisher = {Elsevier},
   timestamp = {2012.04.18},
-  url = {http://linkinghub.elsevier.com/retrieve/pii/S1053811906002126}
+  url = {https://linkinghub.elsevier.com/retrieve/pii/S1053811906002126}
 }
 
 @ARTICLE{Zitova2003,
@@ -632,6 +632,6 @@ @ARTICLE{Zitova2003
   keywords = {feature detection,feature matching,image registration,mapping function,resampling},
   owner = {Stefan},
   timestamp = {2012.04.24},
-  url = {http://linkinghub.elsevier.com/retrieve/pii/S0262885603001379}
+  url = {https://linkinghub.elsevier.com/retrieve/pii/S0262885603001379}
 }
 
diff --git a/include/itkStripTsImageFilter.h b/include/itkStripTsImageFilter.h
@@ -6,7 +6,7 @@
  *  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.txt
+ *         https://www.apache.org/licenses/LICENSE-2.0.txt
  *
  *  Unless required by applicable law or agreed to in writing, software
  *  distributed under the License is distributed on an "AS IS" BASIS,
@@ -79,7 +79,7 @@ namespace itk
  *  This code is from the Insight Journal paper:
  *    "A Skull-Stripping Filter for ITK"
  *    Bauer S., Fejes T., Reyes M.
- *    http://hdl.handle.net/10380/3353
+ *    https://hdl.handle.net/10380/3353
  *  Based on the paper:
  *    "Skull-stripping for Tumor-bearing Brain Images".
  *    Stefan Bauer, Lutz-Peter Nolte, and Mauricio Reyes.

diff --git a/include/itkStripTsImageFilter.hxx b/include/itkStripTsImageFilter.hxx
@@ -6,7 +6,7 @@
  *  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.txt
+ *         https://www.apache.org/licenses/LICENSE-2.0.txt
  *
  *  Unless required by applicable law or agreed to in writing, software
  *  distributed under the License is distributed on an "AS IS" BASIS,

diff --git a/setup.py b/setup.py
@@ -25,7 +25,7 @@
                      'Please refer to:'
                      'Bauer S., Fejes T., Reyes M.,'
                      '“Skull-Stripping Filter for ITK”, '
-                     'Insight Journal, http://hdl.handle.net/10380/3353, 2012.',
+                     'Insight Journal, https://hdl.handle.net/10380/3353, 2012.',
     classifiers=[
         "License :: OSI Approved :: Apache Software License",
         "Programming Language :: Python",

diff --git a/test/itkStripTsImageFilterTest.cxx b/test/itkStripTsImageFilterTest.cxx
@@ -6,7 +6,7 @@
  *  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.txt
+ *         https://www.apache.org/licenses/LICENSE-2.0.txt
  *
  *  Unless required by applicable law or agreed to in writing, software
  *  distributed under the License is distributed on an "AS IS" BASIS,