Merge pull request #433 from Ensembl/jalvarez/assembly_status

Refactor assembly.status module

cicd/gitlab/parts/python.gitlab-ci.yml

@@ -96,6 +96,8 @@ python:black:
 python:pytest:
   extends: .python:test
   script:
+    - apt-get update -y
+    - apt-get install -y sqlite3
     - coverage run -m pytest --junitxml=$RUN_DIR/junit_reports.xml
   artifacts:
     when: always

pyproject.toml

@@ -52,7 +52,7 @@ dependencies = [
     "bcbio-gff == 0.7.1",
     "biopython >= 1.81",
     "ensembl-py >= 2.1.2",
-    "ensembl-utils >= 0.4.4",
+    "ensembl-utils >= 0.5.0",
     "jsonschema >= 4.6.0",
     "intervaltree >= 3.1.0",
     "mysql-connector-python >= 8.0.29",
@@ -176,6 +176,7 @@ disable = [
     "too-few-public-methods",
     "too-many-arguments",
     "too-many-locals",
+    "too-many-positional-arguments",
     "too-many-statements",
     "unspecified-encoding",
     "wildcard-import",

src/python/tests/assembly/test_download.py

@@ -12,15 +12,7 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-"""Unit testing of `ensembl.io.genomio.assembly.download` module.
-
-The unit testing is divided into one test class per submodule/class found in this module, and one test method
-per public function/class method.
-
-Typical usage example::
-    $ pytest ./assembly/test_download.py
-
-"""
+"""Unit testing of `ensembl.io.genomio.assembly.download` module."""
 
 from contextlib import nullcontext as does_not_raise
 import filecmp