Merge pull request #593 from dbic/dcmstack-dev

install dcmstack straight from github until it is released

Author: yarikoptic

.github/workflows/test.yml

@@ -17,8 +17,7 @@ jobs:
           - '3.7'
           - '3.8'
           - '3.9'
-          # causes issues, disabled for now
-          # - '3.10'
+          - '3.10'
     steps:
       - name: Check out repository
         uses: actions/checkout@v3

.travis.yml

@@ -1,5 +1,6 @@
 -r requirements.txt
-# Fix version to older pytest to ease backward compatibility testing
-pytest==3.6.4
 tinydb
 inotify
+# we need master version until it gets released
+# see https://github.com/moloney/dcmstack/issues/75
+git+https://github.com/moloney/dcmstack.git

dev-requirements.txt

@@ -895,7 +895,7 @@ def  add_taskname_to_infofile(infofiles):
     for infofile in infofiles:
         meta_info = load_json(infofile)
         try:
-            meta_info['TaskName'] = (re.search('(?<=_task-)\w+',
+            meta_info['TaskName'] = (re.search(r'(?<=_task-)\w+',
                                                op.basename(infofile))
                                      .group(0).split('_')[0])
         except AttributeError:

heudiconv/convert.py

@@ -22,7 +22,7 @@
 # Ensure they are cleaned up upon exit
 atexit.register(tempdirs.cleanup)
 
-_VCS_REGEX = '%s\.(?:git|gitattributes|svn|bzr|hg)(?:%s|$)' % (op.sep, op.sep)
+_VCS_REGEX = r'%s\.(?:git|gitattributes|svn|bzr|hg)(?:%s|$)' % (op.sep, op.sep)
 
 
 @docstring_parameter(_VCS_REGEX)
@@ -161,7 +161,7 @@ def get_study_sessions(dicom_dir_template, files_opt, heuristic, outdir,
         for f in files_opt:
             if op.isdir(f):
                 files += sorted(find_files(
-                    '.*', topdir=f, exclude_vcs=True, exclude="/\.datalad/"))
+                    '.*', topdir=f, exclude_vcs=True, exclude=r"/\.datalad/"))
             else:
                 files.append(f)
 

heudiconv/parser.py

@@ -90,15 +90,18 @@ def test_reproin_largely_smoke(tmpdir, heuristic, invocation):
 
     # but there should be nothing new
     assert not ds.repo.dirty
-    assert head == ds.repo.get_hexsha()
+    # TODO: remove whenever https://github.com/datalad/datalad/issues/6843
+    # is fixed/released
+    buggy_datalad = (ds.pathobj / ".gitmodules").read_text().splitlines().count('[submodule "Halchenko"]') > 1
+    assert head == ds.repo.get_hexsha() or buggy_datalad
 
     # unless we pass 'overwrite' flag
     runner(args + ['--overwrite'])
     # but result should be exactly the same, so it still should be clean
     # and at the same commit
     assert ds.is_installed()
     assert not ds.repo.dirty
-    assert head == ds.repo.get_hexsha()
+    assert head == ds.repo.get_hexsha() or buggy_datalad
 
 
 @pytest.mark.parametrize(
@@ -121,7 +124,7 @@ def test_scans_keys_reproin(tmpdir, invocation):
             if i != 0:
                 assert(os.path.exists(pjoin(dirname(scans_keys[0]), row[0])))
                 assert(re.match(
-                    '^[\d]{4}-[\d]{2}-[\d]{2}T[\d]{2}:[\d]{2}:[\d]{2}.[\d]{6}$',
+                    r'^[\d]{4}-[\d]{2}-[\d]{2}T[\d]{2}:[\d]{2}:[\d]{2}.[\d]{6}$',
                     row[1]))
 
 

heudiconv/tests/test_heuristics.py

@@ -259,20 +259,20 @@ def json_dumps_pretty(j, indent=2, sort_keys=True):
         '[\n ]+("?[-+.0-9e]+"?,?) *\n(?= *"?[-+.0-9e]+"?)', r' \1',
         js, flags=re.MULTILINE)
     # uniform no spaces before ]
-    js_ = re.sub(" *\]", "]", js_)
+    js_ = re.sub(r" *\]", "]", js_)
     # uniform spacing before numbers
     # But that thing could screw up dates within strings which would have 2 spaces
     # in a date like Mar  3 2017, so we do negative lookahead to avoid changing
     # in those cases
     #import pdb; pdb.set_trace()
     js_ = re.sub(
-        '(?<!\w{3})'    # negative lookbehind for the month
-        '  *("?[-+.0-9e]+"?)'
-        '(?! [123]\d{3})'  # negative lookahead for a year
-        '(?P<space> ?)[ \n]*',
+        r'(?<!\w{3})'    # negative lookbehind for the month
+        r'  *("?[-+.0-9e]+"?)'
+        r'(?! [123]\d{3})'  # negative lookahead for a year
+        r'(?P<space> ?)[ \n]*',
         r' \1\g<space>', js_)
     # no spaces after [
-    js_ = re.sub('\[ ', '[', js_)
+    js_ = re.sub(r'\[ ', '[', js_)
     # the load from the original dump and reload from tuned up
     # version should result in identical values since no value
     # must be changed, just formatting.