Merge pull request #5 from DavidStirling/compat-4-2

Zarr and build fixes
glencoesoftware · Apr 22, 2022 · 6563394 · 6563394
2 parents 16f5795 + 82d5c8b
commit 6563394
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Showing 4 changed files with 7 additions and 6 deletions.
diff --git a/cellprofiler_core/analysis/_runner.py b/cellprofiler_core/analysis/_runner.py
@@ -669,7 +669,8 @@ def start_workers(cls, num=None):
             # closed, the subprocess exits.
             if hasattr(sys, "frozen"):
                 if sys.platform == "darwin":
-                    executable = os.path.join(os.path.dirname(sys.executable), "cp")
+                    executable = os.path.join(os.path.dirname(sys.executable),
+                                              "cellprofilerapp")
                     args = [executable] + aw_args
                 elif sys.platform.startswith("linux"):
                     aw_path = os.path.join(os.path.dirname(__file__), "__init__.py")

diff --git a/cellprofiler_core/image/abstract_image/file/_file_image.py b/cellprofiler_core/image/abstract_image/file/_file_image.py
@@ -198,7 +198,6 @@ def cache_file(self):
         return True
 
     def get_full_name(self):
-        print("Getting full name {}:{}".format(self.__url, self.get_url()))
         if is_omero3d_path(self.__url):
             return self.get_url()
         self.cache_file()

diff --git a/cellprofiler_core/utilities/zarr.py b/cellprofiler_core/utilities/zarr.py
@@ -103,20 +103,20 @@ def __init__(self, path=None, url=None, perform_init=True):
         if url is not None:
             url = str(url)
             if url.lower().startswith(file_scheme):
-                url = url2pathname(url[len(file_scheme):])
+                url = url2pathname(url)
                 path = url
             elif path is None:
                 path = url
 
         self.path = path
         if path is None:
             if not url.lower().startswith('s3:'):
-                filenamme = self.download(url)
+                self.path = self.download(url)
         else:
             if sys.platform.startswith("win"):
                 self.path = self.path.replace("/", os.path.sep)
             filename = os.path.split(path)[1]
-        store = zarr.storage.FSStore(path)
+        store = zarr.storage.FSStore(self.path)
         if path.startswith('s3'):
             logger.info("Zarr is stored on S3, will try to read directly.")
             if '.zmetadata' in store:

diff --git a/setup.py b/setup.py
@@ -24,14 +24,15 @@
         "boto3==1.14.23",
         "centrosome==1.2.0",
         "docutils==0.15.2",
+        "fsspec==2022.2.0",
         "h5py==3.2.1",
         "matplotlib==3.1.3",
         "numpy==1.20.1",
         "prokaryote==2.4.4",
         "psutil==5.7.0",
         "python-bioformats==4.0.5",
         "python-javabridge==4.0.3",
-        "pyzmq==18.0.1",
+        "pyzmq==18.1.1",
         "Pillow==8.1.0",
         "scikit-image==0.18.1",
         "scipy==1.4.1",