👌 IMPROVE: Add full typing, type checking and test coverage (#180)

.github/workflows/ci.yml

@@ -4,37 +4,6 @@ on: [push, pull_request]
 
 jobs:
 
-    docs:
-
-        runs-on: ubuntu-latest
-
-        steps:
-        -   uses: actions/checkout@v1
-
-        -   name: Cache python dependencies
-            id: cache-pip
-            uses: actions/cache@v1
-            with:
-                path: ~/.cache/pip
-                key: pip-docs-${{ hashFiles('**/setup.json') }}
-                restore-keys:
-                    pip-docs-
-
-        -   name: Set up Python
-            uses: actions/setup-python@v2
-            with:
-                python-version: 3.8
-
-        -   name: Install python dependencies
-            run:
-                pip install -e .[docs,tests]
-
-        -   name: Build documentation
-            env:
-                READTHEDOCS: 'True'
-            run:
-                SPHINXOPTS='-nW' make -C docs html
-
     pre-commit:
 
         runs-on: ubuntu-latest
@@ -101,4 +70,14 @@ jobs:
 
         -   name: Run pytest
             run:
-                pytest -sv test
+                pytest -sv --cov=plumpy test
+
+        -   name: Create xml coverage
+            run: coverage xml
+
+        -   name: Upload coverage to Codecov
+            if: github.repository == 'aiidateam/plumpy'
+            uses: codecov/codecov-action@v1
+            with:
+                file: ./coverage.xml
+                name: plumpy

.gitignore

@@ -68,3 +68,5 @@ target/
 
 # Virtual environment directories
 /venv*/
+
+.vscode/

.pre-commit-config.yaml

@@ -34,8 +34,23 @@ repos:
             '--disable=too-many-arguments',
             '--disable=too-many-instance-attributes',
         ]
-        exclude: &exclude_files >
+        exclude: >
             (?x)^(
                 docs/source/conf.py|
                 test/.*|
             )$
+
+-   repo: local
+    hooks:
+    -   id: mypy
+        name: mypy
+        entry: mypy
+        args: [--config-file=tox.ini]
+        language: python
+        types: [python]
+        require_serial: true
+        pass_filenames: true
+        files: >
+            (?x)^(
+                plumpy/.*py|
+            )$

.readthedocs.yml

@@ -1,26 +1,13 @@
-# .readthedocs.yml
-# Read the Docs configuration file
-# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
-
-# Required
 version: 2
 
-# Build documentation in the docs/ directory with Sphinx
-sphinx:
-  configuration: docs/source/conf.py
-
-# Build documentation with MkDocs
-#mkdocs:
-#  configuration: mkdocs.yml
-
-# Optionally build your docs in additional formats such as PDF and ePub
-formats: []
-
-# Optionally set the version of Python and requirements required to build your docs
 python:
-   version: 3.6
-   install:
-      - method: pip
-        path: .
-        extra_requirements:
-           - docs
+    version: 3.8
+    install:
+        - method: pip
+          path: .
+          extra_requirements:
+            - docs
+
+sphinx:
+    builder: html
+    fail_on_warning: true

codecov.yml

@@ -0,0 +1,17 @@
+codecov:
+  notify:
+    after_n_builds: 2
+    wait_for_ci: yes
+  require_ci_to_pass: yes
+
+coverage:
+  precision: 2  # default, here for transparency
+  round: up
+  range: "70...100"  # default, here for transparency
+  status:
+    project:
+      default:
+        threshold: 0.02%
+    patch:
+      default:
+        threshold: 0.1%

docs/source/basic/concepts.rst

@@ -23,7 +23,7 @@ A process can be in one of the following states:
 * EXCEPTED
 * KILLED
 
-as defined in the :class:`ProcessState` enum.
+as defined in the :class:`~plumpy.process_states.ProcessState` enum.
 
 ::
 
@@ -45,9 +45,8 @@ as defined in the :class:`ProcessState` enum.
 Workchain
 ---------
 
-`WorkChain` is `Process`, however, not only the `Process`.
-
-A WorkChain is a series of instructions carried out with the ability to save state in between.
+A ``WorkChain`` is a sub-class of `Process`, which additionally defines a ``outline`` in its process specification.
+This is a series of instructions carried out with the ability to save state in between.
 
 The `outline` can give a succinct summary of the logical steps that the workchain will perform.
 WorkChain supporting using `If_` and `While_` to control the state flow of certain processes.

docs/source/basic/introduction.rst

@@ -1,8 +1,8 @@
 Introduction
 ============
 
-Assumuing readers are:
+Assuming readers are:
 
     1. Users from aiida-core
-    2. (?)Users who want to create tools like aiida but on other research field
+    2. Users who want to create tools like aiida but on other research field
     3. Programmers who are searching for the python workflow tools integrated with finite state machine.

docs/source/conf.py

@@ -42,11 +42,7 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 
-extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.doctest',
-    'sphinx.ext.viewcode',
-]
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.viewcode', 'sphinx.ext.intersphinx']
 # Add any paths that contain templates here, relative to this directory.
 
 # The suffix(es) of source filenames.
@@ -133,6 +129,11 @@
     (master_doc, 'plumpy.tex', 'plumpy Documentation', 'Martin Uhrin', 'manual'),
 ]
 
+intersphinx_mapping = {
+    'python': ('https://docs.python.org/3.8', None),
+    'kiwipy': ('https://kiwipy.readthedocs.io/en/latest/', None)
+}
+
 
 def run_apidoc(_):
     """Runs sphinx-apidoc when building the documentation.
@@ -219,7 +220,7 @@ def setup(app):
 
 # Warnings to ignore when using the -n (nitpicky) option
 # We should ignore any python built-in exception, for instance
-nitpick_ignore = [('py:class', 'Warning'), ('py:class', 'exceptions.Warning')]
+nitpick_ignore = []
 
 for line in open('nitpick-exceptions'):
     if line.strip() == '' or line.startswith('#'):

docs/source/gettingStarted/quickStart.rst

@@ -21,10 +21,10 @@ Process can wait, pause, play and resume
 
 The example below shows how process state transition with different action:
 
-.. literalinclude:: ../../../examples/process_waitAndResume.py
+.. literalinclude:: ../../../examples/process_wait_and_resume.py
 
-Remote controled process
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Remote controlled process
+~~~~~~~~~~~~~~~~~~~~~~~~~
 
 process start.
 

docs/source/nitpick-exceptions

@@ -1,41 +1,14 @@
-py:class  Exception
-py:class  ProcessState
-py:class  persistence.LoadSaveContext
-py:class  Bundle
-py:class  Process
-py:class  PersistedPickle
-py:class  StateMachine
+py:class builtins.dict
 
-py:class  kiwipy.Communicator
-py:class  kiwipy.Future
+py:class typing.Any
+py:class typing.Callable
+py:class typing.Optional
+py:class typing.Tuple
 
-py:class  dict
-py:class  str
-py:class  object
-py:class  bool
-py:class  type
-py:class  tuple
+py:class _asyncio.Future
+py:class asyncio.unix_events._UnixDefaultEventLoopPolicy
+py:class concurrent.futures._base.Error
 
-py:class  builtins.dict
-
-py:obj str
-
-py:class  logging.Logger
-py:class  enum.Enum
-py:class  typing.Optional
-py:class  typing.Tuple
-py:class  typing.Any
-py:class  typing.Callable
-py:class  ValidationError
-
-py:class  plumpy.InterruptException
-py:class  plumpy.CancellableAction
-py:class  plumpy.process_states.Command
-py:class  plumpy.process_states.State
-py:class  plumpy.LoopCommunicator
-py:class  plumpy.ports.PortNamespace
-
-py:func   save_instance_state
-py:func   load_instance_state
-
-py:class  concurrent.futures._base.Error
+# unavailable forward references
+py:class plumpy.process_states.Command
+py:class plumpy.process_states.State

plumpy/__init__.py

@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 # pylint: disable=undefined-variable
+# type: ignore
 import logging
 
 from .loaders import *

plumpy/base/__init__.py

@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 # pylint: disable=undefined-variable
+# type: ignore
 from .state_machine import *
 from .utils import *