Merge branch 'master' into separate-remote-files

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 4.11.4
+current_version = 4.12.0
 commit = True
 tag = True
 tag_name = {new_version}

DEPLOYMENT.md

@@ -4,6 +4,15 @@ This includes instructions for deploying Houskeeper in the Clinical Genomics :ho
 ## Steps
 When all tests are done and successful and the PR is approved by codeowners, follow these steps:
 
+### Deploy feature branch for testing
+To deploy your feature branch to test it, run
+1. `housekeeper-test-deploy <branch_name>`
+2. `housekeeper-test --help` or the command you want to test.
+
+This will pull the latest image tagged with your branch from dockerhub and make it available with `housekeeper-test`. Note that it is not necessary to paxa the environment to do this, unless you need to apply database revisions.
+
+
+### Deploy to stage and production
 1. Select "Squash and merge" to merge branch into default branch (master/main).
 2. Append version increment value `( major | minor | patch )` in the commit message to specify what kind of release is to be created.
 3. Review the details and merge the branch into master.

housekeeper/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "housekeeper"
-__version__ = "4.11.4"
+__version__ = "4.12.0"

housekeeper/cli/get.py

@@ -30,15 +30,14 @@ def get():
 @click.argument("bundle-name", required=False)
 @click.option("-i", "--bundle-id", type=int, help="Search for a bundle with bundle id")
 @click.option("-j", "--json", is_flag=True, help="Output to json format")
-@click.option("-v", "--verbose", is_flag=True, help="List files from latest version")
 @click.option(
     "-c",
     "--compact",
     is_flag=True,
     help="print compact filenames IFF verobe flag present",
 )
 @click.pass_context
-def bundle_cmd(context, bundle_name, bundle_id, json, verbose, compact):
+def bundle_cmd(context, bundle_name, bundle_id, json, compact):
     """Get bundle information from database"""
     store: Store = context.obj["store"]
     bundles = store.bundles()
@@ -64,13 +63,12 @@ def bundle_cmd(context, bundle_name, bundle_id, json, verbose, compact):
         return
     console = Console()
     console.print(get_bundles_table(result))
-    if verbose:
-        for bundle in bundles:
-            if len(bundle.versions) == 0:
-                LOG.info("No versions found for bundle %s", bundle.name)
-                return
-            version_obj = bundle.versions[0]
-            context.invoke(version_cmd, version_id=version_obj.id, verbose=True, compact=compact)
+    for bundle in bundles:
+        if len(bundle.versions) == 0:
+            LOG.info("No versions found for bundle %s", bundle.name)
+            return
+        version_obj = bundle.versions[0]
+        context.invoke(version_cmd, version_id=version_obj.id, verbose=True, compact=compact)
 
 
 @get.command("version")

setup.py

@@ -48,7 +48,7 @@ def parse_reqs(req_path="./requirements.txt"):
     # Versions should comply with PEP440. For a discussion on
     # single-sourcing the version across setup.py and the project code,
     # see http://packaging.python.org/en/latest/tutorial.html#version
-    version="4.11.4",
+    version="4.12.0",
     description=DESCRIPTION,
     long_description=LONG_DESCRIPTION,
     long_description_content_type="text/markdown",

tests/cli/get/test_get_bundle.py

@@ -27,7 +27,7 @@ def test_get_existing_bundle_name(populated_context, cli_runner, helpers):
 
 
 def test_get_existing_bundle_verbose(populated_context, cli_runner, helpers):
-    """Test to fetch an existing bundle based on name with verbose information"""
+    """Test to fetch an existing bundle based on name."""
 
     # GIVEN a context with a populated store and a cli runner
     store: Store = populated_context["store"]
@@ -39,7 +39,7 @@ def test_get_existing_bundle_verbose(populated_context, cli_runner, helpers):
 
     # WHEN trying to fetch the bundle based on bundle name
     output = helpers.get_stdout(
-        cli_runner.invoke(bundle_cmd, [bundle_name, "-v"], obj=populated_context).output
+        cli_runner.invoke(bundle_cmd, [bundle_name], obj=populated_context).output
     )
     # THEN assert that the files are printed
     assert "files" in output