Merge branch 'feature/cleanup' into 'develop'

Feature/cleanup

See merge request core/sevenbridges-python!66

.coveragerc

@@ -1,3 +0,0 @@
-[run]
-omit =
-    sevenbridges/tests/*

.gitignore

@@ -21,6 +21,7 @@ pip-delete-this-directory.txt
 .tox/
 .coverage
 .coverage.*
+coverage_report/
 .cache
 .pytest_cache
 nosetests.xml
@@ -64,4 +65,3 @@ Thumbs.db
 .pydevproject
 .python-version
 .settings
-

.gitlab-ci.yml

@@ -1,4 +1,4 @@
-image: python:3.7-stretch
+image: python:3.8-buster
 
 variables:
   REQUIREMENTS: "requirements.txt"
@@ -16,13 +16,12 @@ stages:
     - pip install -U -r $REQUIREMENTS
     - export PYTHONPATH=$(pwd):$PYTHONPATH
   script:
-    - flake8 sevenbridges
-    - py.test -v --cov-config=setup.cfg
+    - flake8
+    - pytest -v --cov-config setup.cfg
   artifacts:
     paths:
       - coverage_report/*
 
-
 # Test with python 2.7
 test:2.7:
   stage: test
@@ -32,8 +31,8 @@ test:2.7:
     - pip install -U -r $REQUIREMENTS2
     - export PYTHONPATH=$(pwd):$PYTHONPATH
   script:
-    - flake8 sevenbridges
-    - py.test -v --cov=sevenbridges
+    - flake8
+    - pytest -v --cov-config setup.cfg
   image: python:2.7
 
 # Test with python 3.5
@@ -51,10 +50,15 @@ test:3.7:
   <<: *test
   image: python:3.7-stretch
 
+# Test with python 3.8
+test:3.8:
+  <<: *test
+  image: python:3.8-buster
+
 sonar:
   stage: sonar
   image: emeraldsquad/sonar-scanner:1.0.0
   script: infinity sonar scanner
   allow_failure: true
   dependencies:
-    - test:3.7
+    - test:3.8

.travis.yml

@@ -6,15 +6,16 @@ matrix:
   - python: 3.5
   - python: 3.6
   - python: 3.7
-    dist: xenial
+  - python: 3.8
+    dist: bionic
     sudo: true
 
 install:
   - if [[ $TRAVIS_PYTHON_VERSION < 3 ]]; then pip install -r requirements2.txt; else pip install -r requirements.txt; fi
 
 script:
   - flake8 sevenbridges
-  - py.test -v --cov=sevenbridges
+  - pytest -v --cov-config setup.cfg
 
 before_deploy: echo $TRAVIS_TAG > sevenbridges/VERSION
 
@@ -26,7 +27,7 @@ deploy:
   on:
     tags: true
     branch: develop
-    python: 3.7
+    python: 3.8
     distributions: sdist bdist_wheel
     repo: sbg/sevenbridges-python
   skip_cleanup: true

requirements.txt

@@ -1,11 +1,10 @@
 six>=1.10.0
 requests>=2.20.0
 
-flake8==3.7.7
-pytest==4.3.0
-pytest-cov==2.6.1
-requests-mock==1.5.2
-faker==1.0.2
-sphinx==1.5.1
+flake8==3.8.3
+pytest==6.0.1
+pytest-cov==2.10.0
+requests-mock==1.8.0
+faker==4.1.1
+sphinx==3.1.2
 sphinx_rtd_theme==0.1.9
-tox==3.7.0

requirements2.txt

@@ -1,3 +1,12 @@
--r requirements.txt
-
 futures>=3.0.4
+
+six>=1.10.0
+requests>=2.20.0
+
+flake8==3.8.3
+pytest==4.6.11
+pytest-cov==2.10.0
+requests-mock==1.8.0
+faker==3.0.1
+sphinx==1.8.5
+sphinx_rtd_theme==0.1.9

setup.cfg

@@ -1,15 +1,21 @@
 [bdist_wheel]
 universal=1
+
 [metadata]
 description-file =
     README.md
 
 [flake8]
-per-file-ignores =
-    sevenbridges/__init__.py:E402
+exclude =
+    docs/conf.py
+    sevenbridges/__init__.py
 
 [tool:pytest]
 addopts =
     --cov=sevenbridges
     --cov-report=xml:coverage_report/coverage.xml
     --cov-report=term
+
+[run]
+omit =
+    tests/*

setup.py

@@ -30,8 +30,10 @@
     license='Apache Software License 2.0',
     include_package_data=True,
     packages=find_packages(exclude=["*.tests"]),
-    keywords=['sevenbridges', 'sbg', 'api', 'cgc', 'cancer', 'genomics',
-              'cloud'],
+    keywords=[
+        'sevenbridges', 'sbg', 'api', 'cgc',
+        'cancer', 'genomics', 'cloud',
+    ],
     classifiers=[
         'License :: OSI Approved :: Apache Software License',
         'Operating System :: OS Independent',

sevenbridges/decorators.py

@@ -62,7 +62,7 @@ def deco(*args, **kwargs):
                 except excs:
                     if logger:
                         logger.warning(
-                            'HTTPError caught.Retrying ...'.format(f.__name__),
+                            'HTTPError caught.Retrying ...',
                             exc_info=True
                         )
                     time.sleep(delay)

sevenbridges/meta/collection.py

@@ -135,6 +135,6 @@ def _load(self, url):
     def __repr__(self):
         return six.text_type(
             '<VolumeCollection: items={items}>'.format(
-                total=self.total, items=len(self._items)
+                items=len(self._items)
             )
         )

sevenbridges/models/automation.py

@@ -11,7 +11,8 @@
     StringField,
     CompoundField,
     DateTimeField,
-    BooleanField
+    BooleanField,
+    IntegerField,
 )
 from sevenbridges.meta.resource import Resource
 from sevenbridges.meta.transformer import Transform
@@ -45,6 +46,7 @@ class AutomationPackage(Resource):
     created_on = DateTimeField(read_only=True)
     archived = BooleanField(read_only=True)
     custom_url = StringField()
+    memory_limit = IntegerField(read_only=False)
 
     def __eq__(self, other):
         if not hasattr(other, '__class__'):
@@ -80,13 +82,15 @@ def query(cls, automation, offset=None, limit=None, api=None):
         )
 
     @classmethod
-    def create(cls, automation, version, location, schema, api=None):
+    def create(cls, automation, version, location, schema, memory_limit=None,
+               api=None):
         """
         Create a code package.
         :param automation: Automation id.
         :param version: File ID of the uploaded code package.
         :param location: The code package version.
         :param schema: IO schema for main step of execution.
+        :param memory_limit: Memory limit in MB.
         :param api: Api instance.
         :return:
         """
@@ -106,7 +110,8 @@ def create(cls, automation, version, location, schema, api=None):
         data = {
             'version': version,
             'location': location,
-            'schema': schema
+            'schema': schema,
+            'memory_limit': memory_limit,
         }
 
         extra = {
@@ -355,6 +360,7 @@ class Automation(Resource):
     modified_on = DateTimeField(read_only=False)
     archived = BooleanField(read_only=True)
     secret_settings = DictField(read_only=False)
+    memory_limit = IntegerField(read_only=False)
     project_based = BooleanField(read_only=False)
 
     def __eq__(self, other):
@@ -402,14 +408,16 @@ def query(
 
     @classmethod
     def create(cls, name, description=None, billing_group=None,
-               secret_settings=None, project_based=None, api=None):
+               secret_settings=None, project_based=None, memory_limit=None,
+               api=None):
         """
         Create a automation template.
         :param name:  Automation name.
         :param billing_group: Automation billing group.
         :param description:  Automation description.
         :param secret_settings: Automation settings.
-        :param project_based: create project based automation template
+        :param project_based: Create project based automation template.
+        :param memory_limit: Memory limit in MB.
         :param api: Api instance.
         :return:
         """
@@ -431,6 +439,8 @@ def create(cls, name, description=None, billing_group=None,
             data['secret_settings'] = secret_settings
         if project_based:
             data['project_based'] = project_based
+        if memory_limit:
+            data['memory_limit'] = memory_limit
 
         extra = {
             'resource': cls.__name__,
@@ -679,6 +689,7 @@ class AutomationRun(Resource):
     status = StringField(read_only=True)
     message = StringField(read_only=True)
     execution_details = DictField(read_only=True)
+    memory_limit = IntegerField(read_only=False)
     project_id = StringField(read_only=True)
 
     def __eq__(self, other):
@@ -742,7 +753,7 @@ def query(cls, automation=None, package=None, status=None, name=None,
 
     @classmethod
     def create(cls, package, inputs=None, settings=None, resume_from=None,
-               name=None, secret_settings=None, api=None):
+               name=None, secret_settings=None, memory_limit=None, api=None):
         """
         Create and start a new run.
         :param package: Automation package id
@@ -752,6 +763,7 @@ def create(cls, package, inputs=None, settings=None, resume_from=None,
         :param name: Automation run name
         :param secret_settings: dict to override secret_settings from
         automation template
+        :param memory_limit: Memory limit in MB.
         :param api: sevenbridges Api instance
         :return: AutomationRun object
         """
@@ -770,6 +782,8 @@ def create(cls, package, inputs=None, settings=None, resume_from=None,
             data['name'] = name
         if secret_settings:
             data['secret_settings'] = secret_settings
+        if memory_limit:
+            data['memory_limit'] = memory_limit
 
         api = api or cls._API
         automation_run = api.post(

sevenbridges/transfer/upload.py

@@ -139,7 +139,7 @@ def __init__(self, fp, file_size, part_size, upload, retry_count,
         self.pool = api.upload_pool
         self.submitted = 0
         self.total_submitted = 0
-        self.total = total_parts(self.file_size, self.part_size)
+        self.total = total_parts(self.file_size, self.part_size) or 1
         self.parts = self.get_parts()
 
     def submit(self):
@@ -247,13 +247,11 @@ def __init__(self, file_path, project=None, parent=None, file_name=None,
         else:
             self._file_name = file_name
 
-        self._part_size = part_size  # or PartSize.UPLOAD_MINIMUM_PART_SIZE
+        self._part_size = part_size
         self._project = project
         self._parent = parent
         self._file_path = file_path
         self._file_size = os.path.getsize(self._file_path)
-        if self._file_size == 0:
-            raise SbgError('File size must not be 0.')
 
         self._verify_file_size()
 
@@ -356,6 +354,7 @@ def _finalize_upload(self):
             response = self._api.post(
                 self._URL['upload_complete'].format(upload_id=self._upload_id)
             ).json()
+            # noinspection PyArgumentList
             self._result = File(api=self._api, **response)
             self._status = TransferState.COMPLETED
 
@@ -381,7 +380,7 @@ def _abort_upload(self):
 
     @property
     def progress(self):
-        return (self._bytes_done / float(self._file_size)) * 100
+        return self._bytes_done / (float(self._file_size) * 100) or 1
 
     @property
     def status(self):
@@ -573,6 +572,9 @@ def __init__(self, file_path, automation_id, file_name=None,
             timeout=timeout,
             api=api
         )
+        if self._file_size == 0:
+            raise SbgError('File size must not be 0.')
+
         self._automation_id = automation_id
 
     def _validate_project_parent(self, parent, project):

sonar-project.properties

@@ -1,9 +1,10 @@
 sonar.projectKey=sevenbridges
-sonar.projectName=Sevenbridges-python
+sonar.projectName=sevenbridges-python
 
 sonar.sources=sevenbridges
-sonar.exclusions=sevenbridges/tests/**/*.py,coverage_report/*.xml
+sonar.exclusions=tests/**/*.py,coverage_report/*.xml
 
-sonar.test=sevenbridges/tests/**/*.py
+sonar.test=tests/**/*.py
 
 sonar.python.coverage.reportPaths=coverage_report/coverage.xml
+sonar.coverage.exclusions=tests/*

sevenbridges/tests/conftest.py → tests/conftest.py

@@ -3,7 +3,7 @@
 import requests_mock
 
 from sevenbridges import Api
-from sevenbridges.tests import providers, verifiers
+from tests import providers, verifiers
 
 generator = faker.Factory.create()