Use pytest template to improve tests and coverage reports

Author: adrien-berchet

.coveragerc

@@ -0,0 +1,4 @@
+[paths]
+source =
+	bluepyparallel
+	*/bluepyparallel/bluepyparallel

.gitlab-ci.yml

@@ -4,9 +4,6 @@ include:
         - /ci/lib/tox-bb5.yml
         - /ci/jobs/check-version.yml
         - /ci/jobs/lint.yml
-        - /ci/jobs/py36.yml
-        - /ci/jobs/py37.yml
-        - /ci/jobs/py38.yml
         - /ci/jobs/docs.yml
         - /ci/jobs/build-package.yml
         - /ci/jobs/publish-package.yml
@@ -15,15 +12,13 @@ include:
    - project: neuromath/ci
      file:
         - /ci/jobs/auto-release.yml
+        - /ci/lib/pytest-template.yml
+        - /ci/jobs/py36.yml
+        - /ci/jobs/py37.yml
+        - /ci/jobs/py38.yml
+        - /ci/jobs/coverage.yml
 
-py36:
-  variables:
-    bb5_cpus_per_task: 6
-
-py37:
-  variables:
-    bb5_cpus_per_task: 6
-
-py38:
+.tox-template:
   variables:
+    EXTRA_MODULES: archive/2021-05:py-mpi4py
     bb5_cpus_per_task: 6

.pylintrc

@@ -113,7 +113,7 @@ def _evaluate_basic(
 
 
 def _prepare_db(db_url, to_evaluate, df, resume, task_ids):
-    """ "Prepare db."""
+    """Prepare db."""
     db = DataBase(db_url)
 
     if resume and db.exists("df"):

bluepyparallel/evaluator.py

@@ -102,7 +102,7 @@ def _chunksize_to_kwargs(self, chunk_size, kwargs, label="chunk_size"):
 
 
 class NoDaemonProcess(multiprocessing.Process):
-    """Class that represents a non-daemon process"""
+    """Class that represents a non-daemon process."""
 
     # pylint: disable=dangerous-default-value
 
@@ -111,17 +111,17 @@ def __init__(self, group=None, target=None, name=None, args=(), kwargs={}):
         super().__init__(group=None, target=target, name=name, args=args, kwargs=kwargs)
 
     def _get_daemon(self):  # pylint: disable=no-self-use
-        """Get daemon flag"""
+        """Get daemon flag."""
         return False  # pragma: no cover
 
     def _set_daemon(self, value):
-        """Set daemon flag"""
+        """Set daemon flag."""
 
     daemon = property(_get_daemon, _set_daemon)
 
 
 class NestedPool(Pool):  # pylint: disable=abstract-method
-    """Class that represents a MultiProcessing nested pool"""
+    """Class that represents a MultiProcessing nested pool."""
 
     Process = NoDaemonProcess
 
@@ -146,7 +146,6 @@ class MultiprocessingFactory(ParallelFactory):
 
     def __init__(self, batch_size=None, chunk_size=None, processes=None, **kwargs):
         """Initialize multiprocessing factory."""
-
         super().__init__(batch_size, chunk_size)
 
         self.nb_processes = processes or os.cpu_count()
@@ -280,7 +279,7 @@ def __init__(
         scheduler_file=None,
         address=None,
         dask_config=None,
-        **kwargs
+        **kwargs,
     ):
         super().__init__(
             batch_size, chunk_size, scheduler_file=scheduler_file, address=address, **kwargs
@@ -308,7 +307,6 @@ def _with_batches(self, *args, **kwargs):
 
     def get_mapper(self, batch_size=None, chunk_size=None, **kwargs):
         """Get a Dask mapper."""
-
         self._chunksize_to_kwargs(chunk_size, kwargs, label="chunksize")
         if not kwargs.get("chunksize"):
             kwargs["npartitions"] = self.nb_processes or 1

bluepyparallel/parallel.py

@@ -1,3 +1,3 @@
-"""Package version"""
+"""Package version."""
 # pragma: no cover
 VERSION = "0.0.7.dev0"

bluepyparallel/version.py

@@ -0,0 +1,104 @@
+# BLACK
+[tool.black]
+line-length = 100
+target-version = ["py36"]
+
+# PYLINT
+[tool.pylint.messages-control]
+# C0103 -  Invalid name "%s" (should match %s) - matches too many things, like variables w/ single char names
+# C0325 - superfluous-parens
+# I0013 - Ignore the 'Ignoring entire file' warning
+# R0205 - useless-object-inheritance
+# R0401 - cyclic-import
+# R0801 - Similar lines in %d files
+# R0903 - Too Few public methods
+# R0904 - Too Many public methods
+# R0921 - Abstract class not referenced
+# R0922 - Abstract class is only referenced 1 times
+# W0141 - Used builtin function 'map'
+# W0142 - Used * or ** magic
+# W0232 - Class has no __init__ method
+# W0511 - TODO in code
+# W0622 - redefined-builti
+disable = [
+	"C0103",
+	"C0112",
+	"C0116",
+	"C0302",
+	"C0325",
+	"C0330",
+	"C0415",
+	"E1133",
+	"E231",
+	"I0013",
+	"R0201",
+	"R0205",
+	"R0401",
+	"R0801",
+	"R0903",
+	"R0904",
+	"R0921",
+	"R0922",
+	"W0141",
+	"W0142",
+	"W0221",
+	"W0232",
+	"W0511",
+	"W0622",
+]
+
+[tool.pylint.format]
+# Maximum number of characters on a single line.
+max-line-length = 100
+
+[tool.pylint.design]
+# Maximum number of arguments for function / method
+max-args = 15
+# Argument names that match this expression will be ignored. Default to name
+# with leading underscore
+ignored-argument-names = "args|kwargs|_.*"
+# Maximum number of locals for function / method body
+max-locals = 25
+# Maximum number of return / yield for function / method body
+max-returns = 6
+# Maximum number of branch for function / method body
+max-branches = 20
+# Maximum number of statements in function / method body
+max-statements = 60
+# Maximum number of parents for a class (see R0901).
+max-parents = 10
+# Maximum number of attributes for a class (see R0902).
+max-attributes = 40
+# Minimum number of public methods for a class (see R0903).
+min-public-methods = 0
+# Maximum number of public methods for a class (see R0904).
+max-public-methods = 60
+
+[tool.pylint.similarities]
+# Minimum lines number of a similarity.
+min-similarity-lines = 25
+# Ignore comments when computing similarities.
+ignore-comments = true
+# Ignore docstrings when computing similarities.
+ignore-docstrings = true
+
+[tool.pylint.typecheck]
+# List of module names for which member attributes should not be checked
+# (useful for modules/projects where namespaces are manipulated during runtime
+# and thus existing member attributes cannot be deduced by static analysis. It
+# supports qualified module names, as well as Unix pattern matching.
+ignored-modules = []
+
+# PYDOCSTYLE
+[tool.pydocstyle]
+add-ignore = [
+	"D107",
+	"D413",
+]
+convention = "google"
+
+# ISORT
+[tool.isort]
+line_length = 100
+profile = "black"
+force_single_line = true

pyproject.toml

@@ -1,9 +1,9 @@
-#!/usr/bin/env python
-
+"""Setup for the BluePyParallel package."""
 import imp
 import sys
 
-from setuptools import setup, find_packages
+from setuptools import find_packages
+from setuptools import setup
 
 if sys.version_info < (3, 6):
     sys.exit("Sorry, Python < 3.6 is not supported")
@@ -51,10 +51,10 @@
     packages=find_packages(exclude=["tests"]),
     python_requires=">=3.6",
     classifiers=[
-        'Programming Language :: Python',
-        'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.6',
-        'Programming Language :: Python :: 3.7',
-        'Programming Language :: Python :: 3.8',
+        "Programming Language :: Python",
+        "Programming Language :: Python :: 3",
+        "Programming Language :: Python :: 3.6",
+        "Programming Language :: Python :: 3.7",
+        "Programming Language :: Python :: 3.8",
     ],
 )

setup.py

@@ -0,0 +1 @@
+"""Tests for the BluePyParallel package."""

tests/__init__.py

@@ -11,16 +11,19 @@
 
 @pytest.fixture
 def db_url(tmpdir):
+    """The DB URL."""
     return tmpdir / "db.sql"
 
 
 @pytest.fixture(params=[None, "multiprocessing", "ipyparallel", "dask", "dask_dataframe"])
 def factory_type(request):
+    """The factory type."""
     return request.param
 
 
 @pytest.fixture(scope="session")
 def dask_cluster():
+    """The dask cluster."""
     cluster = dask.distributed.LocalCluster()
     yield cluster
     cluster.close()
@@ -36,6 +39,7 @@ def dask_cluster():
     ]
 )
 def parallel_factory(factory_type, dask_cluster, request):
+    """The parallel factory."""
     factory_kwargs = copy.deepcopy(request.param)
     if factory_type in ["dask", "dask_dataframe"]:
         factory_kwargs["address"] = dask_cluster