MRG: Merge pull request #163 from octue/release/0.1.18

Release/0.1.18

docs/source/datafile.rst

@@ -125,7 +125,7 @@ For creating new data in a new local file:
     tags = {"cleaned:True", "type:linear"}
 
 
-    with Datafile(path="path/to/local/file.dat", timestamp=None, sequence=sequence, tags=tags, mode="w") as datafile, f:
+    with Datafile(path="path/to/local/file.dat", sequence=sequence, tags=tags, mode="w") as datafile, f:
         f.write("This is some cleaned data.")
 
     datafile.to_cloud(project_name="my-project", bucket_name="my-bucket", path_in_bucket="path/to/data.dat")
@@ -141,5 +141,5 @@ For existing data in an existing local file:
     sequence = 2
     tags = {"cleaned:True", "type:linear"}
 
-    datafile = Datafile(path="path/to/local/file.dat", timestamp=None, sequence=sequence, tags=tags)
+    datafile = Datafile(path="path/to/local/file.dat", sequence=sequence, tags=tags)
     datafile.to_cloud(project_name="my-project", bucket_name="my-bucket", path_in_bucket="path/to/data.dat")

octue/resources/datafile.py

@@ -78,7 +78,7 @@ class Datafile(Taggable, Serialisable, Pathable, Loggable, Identifiable, Hashabl
     def __init__(
         self,
         path,
-        timestamp,
+        timestamp=None,
         id=ID_DEFAULT,
         logger=None,
         path_from=None,
@@ -184,7 +184,7 @@ def from_cloud(
             the datafile when the context is exited
         :return Datafile:
         """
-        datafile = cls(timestamp=None, path=storage.path.generate_gs_path(bucket_name, datafile_path))
+        datafile = cls(path=storage.path.generate_gs_path(bucket_name, datafile_path))
         datafile.get_cloud_metadata(project_name, bucket_name, datafile_path)
         custom_metadata = datafile._cloud_metadata.get("custom_metadata", {})
 
@@ -499,14 +499,14 @@ class _DatafileContextManager:
 
     Usage:
     ```
-    my_datafile = Datafile(timestamp=None, path='subfolder/subsubfolder/my_datafile.json)
+    my_datafile = Datafile(path='subfolder/subsubfolder/my_datafile.json)
     with my_datafile.open('w') as fp:
         fp.write("{}")
     ```
 
     This is equivalent to the standard python:
     ```
-    my_datafile = Datafile(timestamp=None, path='subfolder/subsubfolder/my_datafile.json)
+    my_datafile = Datafile(path='subfolder/subsubfolder/my_datafile.json)
     os.makedirs(os.path.split(my_datafile.absolute_path)[0], exist_ok=True)
     with open(my_datafile.absolute_path, 'w') as fp:
         fp.write("{}")

octue/resources/tag.py

@@ -8,7 +8,7 @@
 from octue.utils.encoders import OctueJSONEncoder
 
 
-TAG_PATTERN = re.compile(r"^$|^[A-Za-z0-9][A-Za-z0-9:\-/]*(?<![/:-])$")
+TAG_PATTERN = re.compile(r"^$|^[A-Za-z0-9][A-Za-z0-9:.\-/]*(?<![./:-])$")
 
 
 class Tag(Filterable):
@@ -82,8 +82,8 @@ def _clean(name):
 
         if not re.match(TAG_PATTERN, cleaned_name):
             raise InvalidTagException(
-                f"Invalid tag '{cleaned_name}'. Tags must contain only characters 'a-z', '0-9', ':' and '-'. They must "
-                f"not start with '-' or ':'."
+                f"Invalid tag '{cleaned_name}'. Tags must contain only characters 'a-z', 'A-Z', '0-9', ':', '.', '/' "
+                f"and '-'. They must not start with '-', ':', '/' or '.'"
             )
 
         return cleaned_name

octue/templates/template-child-services/elevation_service/requirements.txt

@@ -1 +1 @@
-octue==0.1.17
+octue==0.1.18

octue/templates/template-child-services/parent_service/requirements.txt

@@ -1 +1 @@
-octue==0.1.17
+octue==0.1.18

octue/templates/template-child-services/wind_speed_service/requirements.txt

@@ -1 +1 @@
-octue==0.1.17
+octue==0.1.18

octue/templates/template-python-fractal/requirements.txt

@@ -1,4 +1,4 @@
-octue==0.1.17
+octue==0.1.18
 
 
 # ----------- Some common libraries  -----------------------------------------------------------------------------------

octue/templates/template-using-manifests/requirements.txt

@@ -1,4 +1,4 @@
-octue==0.1.17
+octue==0.1.18
 
 
 # ----------- Some common libraries  -----------------------------------------------------------------------------------

setup.py

@@ -17,7 +17,7 @@
 
 setup(
     name="octue",
-    version="0.1.17",  # Ensure all requirements files containing octue are updated, too (e.g. docs build).
+    version="0.1.18",  # Ensure all requirements files containing octue are updated, too (e.g. docs build).
     py_modules=["cli"],
     install_requires=[
         "click>=7.1.2",

tests/base.py

@@ -47,8 +47,8 @@ def create_valid_dataset(self):
         path = os.path.join("path-within-dataset", "a_test_file.csv")
 
         files = [
-            Datafile(timestamp=None, path_from=path_from, path=path, skip_checks=False),
-            Datafile(timestamp=None, path_from=path_from, path=path, skip_checks=False),
+            Datafile(path_from=path_from, path=path, skip_checks=False),
+            Datafile(path_from=path_from, path=path, skip_checks=False),
         ]
 
         return Dataset(files=files)

tests/cloud/pub_sub/test_service.py

@@ -119,8 +119,8 @@ def test_ask_with_input_manifest(self):
         asking_service = MockService(backend=self.BACKEND, children={responding_service.id: responding_service})
 
         files = [
-            Datafile(timestamp=None, path="gs://my-dataset/hello.txt"),
-            Datafile(timestamp=None, path="gs://my-dataset/goodbye.csv"),
+            Datafile(path="gs://my-dataset/hello.txt"),
+            Datafile(path="gs://my-dataset/goodbye.csv"),
         ]
 
         input_manifest = Manifest(datasets=[Dataset(files=files)], path="gs://my-dataset", keys={"my_dataset": 0})

tests/resources/test_datafile.py

@@ -29,7 +29,7 @@ def tearDown(self):
         TEMPORARY_LOCAL_FILE_CACHE.clear()
 
     def create_valid_datafile(self):
-        return Datafile(timestamp=None, path_from=self.path_from, path=self.path, skip_checks=False)
+        return Datafile(path_from=self.path_from, path=self.path, skip_checks=False)
 
     def create_datafile_in_cloud(
         self,
@@ -57,7 +57,7 @@ def create_datafile_in_cloud(
 
     def test_instantiates(self):
         """Ensures a Datafile instantiates using only a path and generates a uuid ID"""
-        df = Datafile(timestamp=None, path="a_path")
+        df = Datafile(path="a_path")
         self.assertTrue(isinstance(df.id, str))
         self.assertEqual(type(uuid.UUID(df.id)), uuid.UUID)
         self.assertIsNone(df.sequence)
@@ -82,35 +82,35 @@ def test_setting_timestamp(self):
 
     def test_gt(self):
         """Test that datafiles can be ordered using the greater-than operator."""
-        a = Datafile(timestamp=None, path="a_path")
-        b = Datafile(timestamp=None, path="b_path")
+        a = Datafile(path="a_path")
+        b = Datafile(path="b_path")
         self.assertTrue(a < b)
 
     def test_gt_with_wrong_type(self):
         """Test that datafiles cannot be ordered compared to other types."""
         with self.assertRaises(TypeError):
-            Datafile(timestamp=None, path="a_path") < "hello"
+            Datafile(path="a_path") < "hello"
 
     def test_lt(self):
         """Test that datafiles can be ordered using the less-than operator."""
-        a = Datafile(timestamp=None, path="a_path")
-        b = Datafile(timestamp=None, path="b_path")
+        a = Datafile(path="a_path")
+        b = Datafile(path="b_path")
         self.assertTrue(b > a)
 
     def test_lt_with_wrong_type(self):
         """Test that datafiles cannot be ordered compared to other types."""
         with self.assertRaises(TypeError):
-            Datafile(timestamp=None, path="a_path") > "hello"
+            Datafile(path="a_path") > "hello"
 
     def test_checks_fail_when_file_doesnt_exist(self):
         path = "not_a_real_file.csv"
         with self.assertRaises(exceptions.FileNotFoundException) as error:
-            Datafile(timestamp=None, path=path, skip_checks=False)
+            Datafile(path=path, skip_checks=False)
         self.assertIn("No file found at", error.exception.args[0])
 
     def test_conflicting_extension_fails_check(self):
         with self.assertRaises(exceptions.InvalidInputException) as error:
-            Datafile(timestamp=None, path_from=self.path_from, path=self.path, skip_checks=False, extension="notcsv")
+            Datafile(path_from=self.path_from, path=self.path, skip_checks=False, extension="notcsv")
 
         self.assertIn("Extension provided (notcsv) does not match file extension", error.exception.args[0])
 
@@ -171,7 +171,7 @@ def test_hashes_for_the_same_datafile_are_the_same(self):
     def test_is_in_cloud(self):
         """Test whether a file is in the cloud or not can be determined."""
         self.assertFalse(self.create_valid_datafile().is_in_cloud)
-        self.assertTrue(Datafile(timestamp=None, path="gs://hello/file.txt").is_in_cloud)
+        self.assertTrue(Datafile(path="gs://hello/file.txt").is_in_cloud)
 
     def test_from_cloud_with_bare_file(self):
         """Test that a Datafile can be constructed from a file on Google Cloud storage with no custom metadata."""
@@ -311,7 +311,7 @@ def test_update_cloud_metadata(self):
         """Test that a cloud datafile's metadata can be updated."""
         _, project_name, bucket_name, path_in_bucket, _ = self.create_datafile_in_cloud()
 
-        new_datafile = Datafile(path="glib.txt", timestamp=None, cluster=32)
+        new_datafile = Datafile(path="glib.txt", cluster=32)
         new_datafile.update_cloud_metadata(project_name, bucket_name, path_in_bucket)
 
         self.assertEqual(Datafile.from_cloud(project_name, bucket_name, path_in_bucket).cluster, 32)
@@ -365,7 +365,7 @@ def test_open_with_reading_local_file(self):
         with tempfile.NamedTemporaryFile("w", delete=False) as temporary_file:
             temporary_file.write(file_contents)
 
-        datafile = Datafile(timestamp=None, path=temporary_file.name)
+        datafile = Datafile(path=temporary_file.name)
 
         with datafile.open() as f:
             self.assertEqual(f.read(), file_contents)
@@ -377,7 +377,7 @@ def test_open_with_writing_local_file(self):
         with tempfile.NamedTemporaryFile("w", delete=False) as temporary_file:
             temporary_file.write(file_contents)
 
-        datafile = Datafile(timestamp=None, path=temporary_file.name)
+        datafile = Datafile(path=temporary_file.name)
 
         with datafile.open("w") as f:
             f.write("hello")
@@ -486,7 +486,7 @@ def test_datafile_as_context_manager(self):
         temporary_file = tempfile.NamedTemporaryFile("w", delete=False)
         contents = "Here is the content."
 
-        with Datafile(path=temporary_file.name, timestamp=None, mode="w") as (datafile, f):
+        with Datafile(path=temporary_file.name, mode="w") as (datafile, f):
             f.write(contents)
 
         # Check that the cloud file has been updated.