Merge branch 'rf/createwrapper-macos' into 'master'

Rf/createwrapper macos

See merge request !12

.gitlab-ci.yml

 include:
-- file: .gitlab-ci.yml
-  project: fsl/fsl-ci-rules
+ - file: .gitlab-ci.yml
+   project: fsl/fsl-ci-rules
+
 stages:
-- test
-- fsl-ci-pre
-- fsl-ci-build
-- fsl-ci-test
-- fsl-ci-deploy
-test:
+ - test
+ - fsl-ci-pre
+ - fsl-ci-build
+ - fsl-ci-test
+ - fsl-ci-deploy
+
+test:linux:
   image: python:3.7
   script:
-  - pip install pytest
-  - pytest -v .ci
+   - pip install pytest
+   - pytest -v tests
   stage: test
   tags:
-  - docker
+   - docker
+
+test:macos:
+  image: python:3.7
+  script:
+   - pip install pytest
+   - pytest -v tests
+  stage: test
+  tags:
+   - macOS
+   - shell
\ No newline at end of file

CHANGELOG.md

 # FSL base project changelog
 
+
+## 2106.2 (Tuesday 22nd June 2021)
+
+ - Fixed an issue with `createFSLWrapper` on macOS.
+
+
 ## 2106.1 (Friday 6th June 2021)
 
  - Updated the `supportedGencodes.sh` script to add JIT targets for CUDA

share/fsl/sbin/createFSLWrapper

@@ -109,5 +109,10 @@ for script in $targets; do
   fi
 
   # Preserve file permissions
-  chmod --reference="$sourceScript" "$targetScript"
+  if [[ "$OSTYPE" == "darwin"* ]]; then
+    perms=$(stat -f "%A" "$sourceScript")
+    chmod ${perms} "$targetScript"
+  else
+    chmod --reference="$sourceScript" "$targetScript"
+  fi
 done

tests/feedsRun

+#!/usr/bin/env bash
+
+fslpython ./test_create_remove_wrapper.py ${FSLDIR}
\ No newline at end of file

.ci/test_create_remove_wrapper.py → tests/test_create_remove_wrapper.py

 #!/usr/bin/env python
 #
 # test_create_remove_wrapper.py - Test the createFSLWrapper.sh and
-# removeFSLWrapper.sh scripts. Requires Python 3.7.
+# removeFSLWrapper.sh scripts. Requires Python>=3.7.
 #
 # Author: Paul McCarthy <pauldmccarthy@gmail.com>
 #
 
 
+import sys
 import os.path as op
 import subprocess as sp
 import textwrap as tw
@@ -18,6 +19,11 @@ import contextlib
 from unittest import mock
 
 
+# Paths to create/remove wrapper scripts, when
+# running from an in-source version. These may
+# be overwritten within the __main__ clause at
+# the bottom, where BASE_DIR may be provided
+# as a command-line argument.
 BASE_DIR       = op.abspath(op.join(op.dirname(__file__), '..'))
 CREATE_WRAPPER = op.join(BASE_DIR, 'share', 'fsl', 'sbin', 'createFSLWrapper')
 REMOVE_WRAPPER = op.join(BASE_DIR, 'share', 'fsl', 'sbin', 'removeFSLWrapper')
@@ -176,3 +182,19 @@ def test_create_remove_wrappers():
 
         assert not op.exists(op.join(wrapperdir, 'test_script1'))
         assert not op.exists(op.join(wrapperdir, 'test_script2'))
+
+
+if __name__ == '__main__':
+    # base dir can be speecified on command line
+    if len(sys.argv) > 1:
+        BASE_DIR       = sys.argv[1]
+        SBIN_DIR       = op.join(BASE_DIR, 'share', 'fsl', 'sbin')
+        CREATE_WRAPPER = op.join(SBIN_DIR, 'createFSLWrapper')
+        REMOVE_WRAPPER = op.join(SBIN_DIR, 'removeFSLWrapper')
+
+    thismod = sys.modules[__name__]
+    for test in dir(thismod):
+        if test.startswith('test_'):
+            test = getattr(thismod, test)
+            if callable(test):
+                test()