Make parameters after password keyword-only

nsoranzo · Nov 10, 2023 · 14d9e02 · 14d9e02
1 parent 933b910
commit 14d9e02
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Showing 15 changed files with 26 additions and 16 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,4 +1,10 @@
-### Bioblend v1.2.0 - 2023-06-30
+### BioBlend v
+
+* Parameters after ``password`` in the ``__init__()`` method of the
+  ``GalaxyClient``, ``GalaxyInstance`` and ``ToolShedInstance`` classes are now
+  keyword-only.
+
+### BioBlend v1.2.0 - 2023-06-30
 
 * Dropped support for Galaxy releases 17.09-19.01. Added support for Galaxy
   release 23.1.

diff --git a/bioblend/_tests/TestGalaxyObjects.py b/bioblend/_tests/TestGalaxyObjects.py
@@ -213,7 +213,7 @@ class GalaxyObjectsTestBase(unittest.TestCase):
     def setUpClass(cls) -> None:
         galaxy_key = os.environ["BIOBLEND_GALAXY_API_KEY"]
         galaxy_url = os.environ["BIOBLEND_GALAXY_URL"]
-        cls.gi = galaxy_instance.GalaxyInstance(galaxy_url, galaxy_key)
+        cls.gi = galaxy_instance.GalaxyInstance(galaxy_url, api_key=galaxy_key)
 
 
 class TestWorkflow(GalaxyObjectsTestBase):

diff --git a/bioblend/_tests/test_util.py b/bioblend/_tests/test_util.py
@@ -49,7 +49,7 @@ def skip_unless_galaxy(min_release: Optional[str] = None) -> Callable:
     if "BIOBLEND_GALAXY_API_KEY" not in os.environ and "BIOBLEND_GALAXY_MASTER_API_KEY" in os.environ:
         galaxy_url = os.environ["BIOBLEND_GALAXY_URL"]
         galaxy_master_api_key = os.environ["BIOBLEND_GALAXY_MASTER_API_KEY"]
-        gi = bioblend.galaxy.GalaxyInstance(galaxy_url, galaxy_master_api_key)
+        gi = bioblend.galaxy.GalaxyInstance(galaxy_url, key=galaxy_master_api_key)
 
         if "BIOBLEND_GALAXY_USER_EMAIL" in os.environ:
             galaxy_user_email = os.environ["BIOBLEND_GALAXY_USER_EMAIL"]

diff --git a/bioblend/galaxy/__init__.py b/bioblend/galaxy/__init__.py
@@ -38,6 +38,7 @@ def __init__(
         key: Optional[str] = None,
         email: Optional[str] = None,
         password: Optional[str] = None,
+        *,
         verify: bool = True,
     ) -> None:
         """
@@ -81,7 +82,7 @@ def __init__(
         :param verify: Whether to verify the server's TLS certificate
         :type verify: bool
         """
-        super().__init__(url, key, email, password, verify=verify)
+        super().__init__(url, key=key, email=email, password=password, verify=verify)
         self.libraries = libraries.LibraryClient(self)
         self.histories = histories.HistoryClient(self)
         self.workflows = workflows.WorkflowClient(self)

diff --git a/bioblend/galaxy/objects/galaxy_instance.py b/bioblend/galaxy/objects/galaxy_instance.py
@@ -45,8 +45,8 @@ class GalaxyInstance:
 
     Example: get a list of all histories for a user with API key 'foo'::
 
-      from bioblend.galaxy.objects import *
-      gi = GalaxyInstance('http://127.0.0.1:8080', 'foo')
+      from bioblend.galaxy.objects import GalaxyInstance
+      gi = GalaxyInstance('http://127.0.0.1:8080', api_key='foo')
       histories = gi.histories.list()
     """
 
@@ -56,9 +56,10 @@ def __init__(
         api_key: Optional[str] = None,
         email: Optional[str] = None,
         password: Optional[str] = None,
+        *,
         verify: bool = True,
     ) -> None:
-        self.gi = bioblend.galaxy.GalaxyInstance(url, api_key, email, password, verify)
+        self.gi = bioblend.galaxy.GalaxyInstance(url, key=api_key, email=email, password=password, verify=verify)
         self.log = bioblend.log
         self.datasets = client.ObjDatasetClient(self)
         self.dataset_collections = client.ObjDatasetCollectionClient(self)

diff --git a/bioblend/galaxyclient.py b/bioblend/galaxyclient.py
@@ -36,6 +36,7 @@ def __init__(
         key: Optional[str] = None,
         email: Optional[str] = None,
         password: Optional[str] = None,
+        *,
         verify: bool = True,
         timeout: Optional[float] = None,
     ) -> None:

diff --git a/bioblend/toolshed/__init__.py b/bioblend/toolshed/__init__.py
@@ -18,6 +18,7 @@ def __init__(
         key: Optional[str] = None,
         email: Optional[str] = None,
         password: Optional[str] = None,
+        *,
         verify: bool = True,
     ) -> None:
         """
@@ -59,7 +60,7 @@ def __init__(
         :param verify: Whether to verify the server's TLS certificate
         :type verify: bool
         """
-        super().__init__(url, key, email, password, verify=verify)
+        super().__init__(url, key=key, email=email, password=password, verify=verify)
         self.categories = categories.ToolShedCategoryClient(self)
         self.repositories = repositories.ToolShedRepositoryClient(self)
         self.tools = tools.ToolShedToolClient(self)
diff --git a/docs/examples/create_user_get_api_key.py b/docs/examples/create_user_get_api_key.py
@@ -18,7 +18,7 @@
 galaxy_api_key = sys.argv[2]
 
 # Initiating Galaxy connection
-gi = bioblend.galaxy.GalaxyInstance(galaxy_url, galaxy_api_key)
+gi = bioblend.galaxy.GalaxyInstance(galaxy_url, key=galaxy_api_key)
 
 # Create a new user and get a new API key for her
 new_user = gi.users.create_local_user(sys.argv[3], sys.argv[4], sys.argv[5])

diff --git a/docs/examples/objects/list_data_libraries.py b/docs/examples/objects/list_data_libraries.py
@@ -16,7 +16,7 @@
 
 print("Initiating Galaxy connection")
 
-gi = GalaxyInstance(galaxy_url, galaxy_key)
+gi = GalaxyInstance(galaxy_url, api_key=galaxy_key)
 
 print("Retrieving Data Library list")
 

diff --git a/docs/examples/objects/list_histories.py b/docs/examples/objects/list_histories.py
@@ -16,7 +16,7 @@
 
 print("Initiating Galaxy connection")
 
-gi = GalaxyInstance(galaxy_url, galaxy_key)
+gi = GalaxyInstance(galaxy_url, api_key=galaxy_key)
 
 print("Retrieving History list")
 

diff --git a/docs/examples/objects/list_workflows.py b/docs/examples/objects/list_workflows.py
@@ -16,7 +16,7 @@
 
 print("Initiating Galaxy connection")
 
-gi = GalaxyInstance(galaxy_url, galaxy_key)
+gi = GalaxyInstance(galaxy_url, api_key=galaxy_key)
 
 print("Retrieving Workflows list")
 

diff --git a/docs/examples/objects/small.py b/docs/examples/objects/small.py
@@ -17,7 +17,7 @@
 API_KEY = os.getenv("GALAXY_API_KEY", "YOUR_API_KEY")
 if API_KEY == "YOUR_API_KEY":
     sys.exit("API_KEY not set, see the README.txt file")
-gi = GalaxyInstance(URL, API_KEY)
+gi = GalaxyInstance(URL, api_key=API_KEY)
 
 # import the workflow from the JSON dump
 

diff --git a/docs/examples/objects/w2_bacterial_reseq.py b/docs/examples/objects/w2_bacterial_reseq.py
@@ -9,7 +9,7 @@
 API_KEY = os.getenv("GALAXY_API_KEY", "YOUR_API_KEY")
 if API_KEY == "YOUR_API_KEY":
     sys.exit("API_KEY not set, see the README.txt file")
-gi = GalaxyInstance(URL, API_KEY)
+gi = GalaxyInstance(URL, api_key=API_KEY)
 
 # Select "W2 - Bacterial re-sequencing | Paired-end" from published workflows
 

diff --git a/docs/examples/objects/w3_bacterial_denovo.py b/docs/examples/objects/w3_bacterial_denovo.py
@@ -10,7 +10,7 @@
 API_KEY = os.getenv("GALAXY_API_KEY", "YOUR_API_KEY")
 if API_KEY == "YOUR_API_KEY":
     sys.exit("API_KEY not set, see the README.txt file")
-gi = GalaxyInstance(URL, API_KEY)
+gi = GalaxyInstance(URL, api_key=API_KEY)
 
 # Select "W3 - Bacterial de novo assembly | Paired-end" from published workflows
 

diff --git a/docs/examples/objects/w5_metagenomics.py b/docs/examples/objects/w5_metagenomics.py
@@ -10,7 +10,7 @@
 API_KEY = os.getenv("GALAXY_API_KEY", "YOUR_API_KEY")
 if API_KEY == "YOUR_API_KEY":
     sys.exit("API_KEY not set, see the README.txt file")
-gi = GalaxyInstance(URL, API_KEY)
+gi = GalaxyInstance(URL, api_key=API_KEY)
 
 # Select "W5 - Metagenomics" from published workflows