Merge branch 'jca-release' into release

Former-commit-id: 95018ae8b5638978ee64e565185998b5df21853a [formerly 6f1cdfb]
Former-commit-id: a91ed6facd5e1e0111be8325375def831970075c

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,29 @@
+---
+name: Bug report
+about: Create a report to help improve SCT
+
+---
+
+Hi, thanks for reporting an issue, please take some time to consider the applicable guidelines:
+https://github.com/neuropoly/spinalcordtoolbox/blob/master/CONTRIBUTING.rst#reporting-a-bug-or-requesting-a-feature
+(about how to suitably describe issues or requests) prior to deleting this blurb when about to submit the issue.
+
+### Description
+
+<Description of the issue>
+
+### Steps to Reproduce
+
+0. Install SCT <release or git revision and platform, you can use the
+   first lines of output of sct_check_dependencies>
+
+1. <First Step>
+
+2. <Second Step>
+
+3. <and so on...>
+
+**Expected behavior:** <What you expect to happen>
+
+**Actual behavior:** <What actually happens>
+

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,21 @@
+---
+name: Feature request
+about: Want improvements or new features in SCT?
+
+---
+
+Hi, thanks for opening a feature request, please take some time to consider the applicable guidelines:
+https://github.com/neuropoly/spinalcordtoolbox/blob/master/CONTRIBUTING.rst#reporting-a-bug-or-requesting-a-feature
+(about how to suitably describe issues or requests) prior to deleting this blurb when about to submit the issue.
+
+**Feature justification: Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context (references, screenshots...) about the feature request here.

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,18 +1,3 @@
-### Requirements
-
-* [ ] Is there a issue open describing the motivation for this pull request ?
-* [ ] Does the pull request need an update of the documentation ?
-* [ ] Does the pull request need additional test(s) ?
-* [ ] Clean up the warnings generated by the [style guide](https://www.jetbrains.com/help/pycharm/2017.1/code-inspection.html)
-
-### Description of the Change
-
-Explain the approach and possible drawback(s). Use labels to add context.
-
-### Steps and Constraints
-
-[The steps of reproducing the pull request]
-
-### Applicable Issues
-
-Implements or Fixes #[Issue number]
+Hi, thank you for submitting a Pull Request, please take some time to consider the guidelines:
+https://github.com/neuropoly/spinalcordtoolbox/blob/master/CONTRIBUTING.rst#contributing-code
+prior to documenting/reviewing the PR and deleting this blurb when about to submit the PR.

.travis.yml

@@ -17,9 +17,9 @@ cache:
 
 matrix:
   include:
-    - os: linux
-      python: 2.7 # Just to make travis's UI a bit prettier
-      env: SCT_MINICONDA=2 SCT_VERBOSE_INSTALL=1 MPLBACKEND=Agg
+#    - os: linux
+#      python: 2.7 # Just to make travis's UI a bit prettier
+#      env: SCT_MINICONDA=2 SCT_VERBOSE_INSTALL=1 MPLBACKEND=Agg
     - os: linux
       python: 2.7
       env: SCT_MINICONDA=2 MPLBACKEND=Agg
@@ -29,9 +29,9 @@ matrix:
     - os: osx
       language: generic
       env: SCT_MINICONDA=2 MPLBACKEND=Agg
-    - os: osx
-      language: generic
-      env: SCT_MINICONDA=2 SCT_VERBOSE_INSTALL=1 MPLBACKEND=Agg
+#    - os: osx
+#      language: generic
+#      env: SCT_MINICONDA=2 SCT_VERBOSE_INSTALL=1 MPLBACKEND=Agg
     - os: osx
       language: generic
       env: SCT_MINICONDA=3 MPLBACKEND=Agg
@@ -65,10 +65,10 @@ script:
   - pip install coverage
   - bash -c 'echo -ne "import coverage\ncov = coverage.process_startup()\n" > sitecustomize.py'
   - bash -c 'echo -ne "[run]\nconcurrency = multiprocessing\nparallel = True\n" > .coveragerc'
-  - COVERAGE_PROCESS_START="$PWD/.coveragerc" COVERAGE_FILE="$PWD/.coverage" PYTHONPATH="$PWD" sct_testing -d 1
+  - COVERAGE_PROCESS_START="$PWD/.coveragerc" COVERAGE_FILE="$PWD/.coverage" PYTHONPATH="$PWD" sct_testing -d 1 --abort-on-failure
   - coverage combine
   - ./unit_testing.sh
-  - bash -c "pip install sphinx sphinxcontrib.programoutput; cd $HOME/build/neuropoly/spinalcordtoolbox/documentation/sphinx; make html; echo"
+  - bash -c "pip install sphinx sphinxcontrib.programoutput sphinx_rtd_theme; cd $HOME/build/neuropoly/spinalcordtoolbox/documentation/sphinx; make html; echo"
   - pip install coveralls
 #  - python create_package.py -s ${TRAVIS_OS_NAME}  # test package creation
 #  - cd ../spinalcordtoolbox_v*

CHANGES.md

@@ -1,5 +1,22 @@
 # CHANGES TO RELEASE
 
+## v3.2.3 (2018-07-21)
+This release notably brings a useful feature, which now makes it possible to use single-label with -l flag for registration to the template. This feature was required by the recently-introduced [analysis pipeline for multi-parametric data when FOV is systematically centered at a particular disc or mid-vertebral level](https://github.com/sct-pipeline/multiparametric-fixed-fov). [View detailed changelog](https://github.com/neuropoly/spinalcordtoolbox/compare/v3.2.2...v3.2.3)
+
+**BUG**
+
+ - `sct_register_multimodal`: Fixed bug when using partial mask with algo=slicereg [View pull request](https://github.com/neuropoly/spinalcordtoolbox/pull/1917)
+
+**ENHANCEMENT**
+
+ - `sct_propseg`: Labels and centerline are now output with correct header if -rescale is used [View pull request](https://github.com/neuropoly/spinalcordtoolbox/pull/1926)
+ - Adding a batch size of 4 for all deep learning methods. [View pull request](https://github.com/neuropoly/spinalcordtoolbox/pull/1924)
+
+**FEATURE**
+
+ - `sct_register_to_template`: Enable single-label with -l flag [View pull request](https://github.com/neuropoly/spinalcordtoolbox/pull/1955)
+
+
 ## v3.2.2 (2018-07-08)
 Major changes to this release include a fix to SCT installation on OSX laptops with non-English encoding language. Another important fix is the inclusion of the link in `sct_download_data` for downloading the Paris'18 SCT course material. A nice enhancement is the possibility to calculate metrics slice-wise or level-wise in `sct_extract_metric`. View detailed changelog
 [View detailed changelog](https://github.com/neuropoly/spinalcordtoolbox/compare/v3.2.1...v3.2.2)