From f63ae7fb683c07e19de0a9411ab4d9ba8410cdde Mon Sep 17 00:00:00 2001
From: "Hock, Martin" <martin.hock@fst.tu-darmstadt.de>
Date: Thu, 8 Sep 2022 20:55:36 +0200
Subject: [PATCH] Update CICD to use Poetry for tests and linting. Add coverage
to pytest.
---
.gitignore | 1 +
.gitlab-ci.yml | 73 ++++-
docs/source/conf.py | 16 +-
examples/example_parse.py | 2 +-
poetry.lock | 537 --------------------------------
pykkn/build_multi_parameters.py | 23 +-
pykkn/storage.py | 34 +-
7 files changed, 101 insertions(+), 585 deletions(-)
delete mode 100644 poetry.lock
diff --git a/.gitignore b/.gitignore
index 59c5fc7..72e7bf6 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,6 +1,7 @@
__pycache__
.pytest_cache
.vscode
+.venv
dev
htmlcov
tests/test_resources/*
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 66e5698..abc0e37 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,26 +1,73 @@
-image: python:3.10-alpine
+image:
+ name: python:latest
+ pull_policy: if-not-present
-test:
- stage: test
- tags:
+stages:
+ - linting # PEP8 and pylint
+ - testing # For unittests
+ - build-docs # install and run sphinx
+ - deploy-docs # deploy to GitLab Pages
+
+
+
+before_script:
+ #- python --version # For debugging
+ - pip install poetry # Install poetry for environment and dependency management
+ - poetry install # Install dependencies via poetry
+
+
+PEP8:
+ stage: linting
+ tags:
+ - env:docker
+ allow_failure: true # Change this after adjusting settings or improving all warnings/errors
+ script:
+ - poetry add flake8
+ - poetry run flake8 --count . --exclude .\.venv # PEP8 linting, exclude the .venv if present
+
+Pylint:
+ stage: linting
+ tags:
+ - env:docker
+ allow_failure: true # Change this after adjusting settings or improving all warnings/errors
+ script:
+ - poetry add pylint
+ - find . -type f -name '*.py' | xargs poetry run pylint -rn # Find all python files and check the code with pylint.
+ # -poetry run find . -path ./.venv -prune -false -o -name '*.py' -type f -print | xargs pylint -rn^ # --rcfile='pykkn/.pylintrc'
+
+unittests:
+ stage: testing
+ tags:
+ - docker
+ image: cimg/python:3.10
+ script:
+ #- pip install .
+ #- pip install requests pytest-cov # install dev dependencies manually
+ #- pytest --cov=pykkn Tests/
+ - poetry add pytest-cov
+ - poetry run pytest --cov=pykkn Tests/ # Run tests via pytest
+ coverage: '/TOTAL.*\s+(\d+\.\d+%)$/'
+
+build-sphinx: # build doc for testing AND for deployment
+ stage: build-docs
+ tags:
- env:docker
script:
- - pip install -U sphinx
+ - pip install -U sphinx
- pip install -U sphinx-autoapi sphinx_rtd_theme sphinx_panels
- sphinx-build -b html ./docs/source/ public
+ artifacts:
+ paths:
+ - public
rules:
- if: $CI_COMMIT_REF_NAME != $CI_DEFAULT_BRANCH
-
-pages:
- stage: deploy
- tags:
+pages: # deploy docs to GitLab Pages
+ stage: deploy-docs
+ tags:
- env:docker
- script:
- - pip install -U sphinx
- - pip install -U sphinx-autoapi sphinx_rtd_theme sphinx_panels
- - sphinx-build -b html ./docs/source/ public
+ script: [ "true" ] # GitLab requires a script section
artifacts:
paths:
- public
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 953a807..80f1e2b 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -46,16 +46,16 @@ templates_path = ['_templates']
# This pattern also affects html_static_path and html_extra_path.
exclude_patterns = []
-## Auto API setup
+# -- Auto API setup ---------------------------------------------------------
# Add path for the auto API, where is the code that should be documented
autoapi_dirs = ['../../pykkn/']
# autoapi_ignore = ["*/test_*.py"]
-#Add direction where the API documentation should be created
+# Add direction where the API documentation should be created
autoapi_root = 'reference'
-#turn off that it is automatically added to the toctree
-#autoapi_add_toctree_entry = False
+# turn off that it is automatically added to the toctree
+# autoapi_add_toctree_entry = False
autodoc_typehints = 'description'
@@ -66,13 +66,13 @@ autodoc_typehints = 'description'
# a list of builtin themes.
#
-#default theme
-#html_theme = 'alabaster'
+# default theme
+# html_theme = 'alabaster'
-#new theme according to read the docs
+# new theme according to read the docs
html_theme = "sphinx_rtd_theme"
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
\ No newline at end of file
+html_static_path = ['_static']
diff --git a/examples/example_parse.py b/examples/example_parse.py
index a9513a0..b2be83e 100644
--- a/examples/example_parse.py
+++ b/examples/example_parse.py
@@ -50,4 +50,4 @@ msmtrun.store()
result_msmtrun = pykkn_parse("example_for_docs.h5")
-result_msmtrun.show()
\ No newline at end of file
+result_msmtrun.show()
diff --git a/poetry.lock b/poetry.lock
deleted file mode 100644
index 1848888..0000000
--- a/poetry.lock
+++ /dev/null
@@ -1,537 +0,0 @@
-[[package]]
-name = "attrs"
-version = "22.1.0"
-description = "Classes Without Boilerplate"
-category = "dev"
-optional = false
-python-versions = ">=3.5"
-
-[package.extras]
-dev = ["cloudpickle", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "mypy (>=0.900,!=0.940)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "sphinx", "sphinx-notfound-page", "zope.interface"]
-docs = ["furo", "sphinx", "sphinx-notfound-page", "zope.interface"]
-tests = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "zope.interface"]
-tests_no_zope = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins"]
-
-[[package]]
-name = "certifi"
-version = "2022.6.15"
-description = "Python package for providing Mozilla's CA Bundle."
-category = "main"
-optional = false
-python-versions = ">=3.6"
-
-[[package]]
-name = "charset-normalizer"
-version = "2.1.1"
-description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
-category = "main"
-optional = false
-python-versions = ">=3.6.0"
-
-[package.extras]
-unicode_backport = ["unicodedata2"]
-
-[[package]]
-name = "colorama"
-version = "0.4.5"
-description = "Cross-platform colored terminal text."
-category = "dev"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
-
-[[package]]
-name = "h5py"
-version = "3.7.0"
-description = "Read and write HDF5 files from Python"
-category = "main"
-optional = false
-python-versions = ">=3.7"
-
-[package.dependencies]
-numpy = ">=1.14.5"
-
-[[package]]
-name = "idna"
-version = "3.3"
-description = "Internationalized Domain Names in Applications (IDNA)"
-category = "main"
-optional = false
-python-versions = ">=3.5"
-
-[[package]]
-name = "iniconfig"
-version = "1.1.1"
-description = "iniconfig: brain-dead simple config-ini parsing"
-category = "dev"
-optional = false
-python-versions = "*"
-
-[[package]]
-name = "numpy"
-version = "1.23.2"
-description = "NumPy is the fundamental package for array computing with Python."
-category = "main"
-optional = false
-python-versions = ">=3.8"
-
-[[package]]
-name = "opencv-python"
-version = "4.6.0.66"
-description = "Wrapper package for OpenCV python bindings."
-category = "main"
-optional = false
-python-versions = ">=3.6"
-
-[package.dependencies]
-numpy = [
- {version = ">=1.21.2", markers = "python_version >= \"3.10\" or python_version >= \"3.6\" and platform_system == \"Darwin\" and platform_machine == \"arm64\""},
- {version = ">=1.19.3", markers = "python_version >= \"3.6\" and platform_system == \"Linux\" and platform_machine == \"aarch64\" or python_version >= \"3.9\""},
- {version = ">=1.14.5", markers = "python_version >= \"3.7\""},
- {version = ">=1.17.3", markers = "python_version >= \"3.8\""},
-]
-
-[[package]]
-name = "packaging"
-version = "21.3"
-description = "Core utilities for Python packages"
-category = "dev"
-optional = false
-python-versions = ">=3.6"
-
-[package.dependencies]
-pyparsing = ">=2.0.2,<3.0.5 || >3.0.5"
-
-[[package]]
-name = "pandas"
-version = "1.4.4"
-description = "Powerful data structures for data analysis, time series, and statistics"
-category = "main"
-optional = false
-python-versions = ">=3.8"
-
-[package.dependencies]
-numpy = {version = ">=1.21.0", markers = "python_version >= \"3.10\""}
-python-dateutil = ">=2.8.1"
-pytz = ">=2020.1"
-
-[package.extras]
-test = ["hypothesis (>=5.5.3)", "pytest (>=6.0)", "pytest-xdist (>=1.31)"]
-
-[[package]]
-name = "pillow"
-version = "9.2.0"
-description = "Python Imaging Library (Fork)"
-category = "main"
-optional = false
-python-versions = ">=3.7"
-
-[package.extras]
-docs = ["furo", "olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-issues (>=3.0.1)", "sphinx-removed-in", "sphinxext-opengraph"]
-tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"]
-
-[[package]]
-name = "pluggy"
-version = "1.0.0"
-description = "plugin and hook calling mechanisms for python"
-category = "dev"
-optional = false
-python-versions = ">=3.6"
-
-[package.extras]
-dev = ["pre-commit", "tox"]
-testing = ["pytest", "pytest-benchmark"]
-
-[[package]]
-name = "py"
-version = "1.11.0"
-description = "library with cross-python path, ini-parsing, io, code, log facilities"
-category = "dev"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
-
-[[package]]
-name = "pyparsing"
-version = "3.0.9"
-description = "pyparsing module - Classes and methods to define and execute parsing grammars"
-category = "dev"
-optional = false
-python-versions = ">=3.6.8"
-
-[package.extras]
-diagrams = ["jinja2", "railroad-diagrams"]
-
-[[package]]
-name = "pytest"
-version = "7.1.3"
-description = "pytest: simple powerful testing with Python"
-category = "dev"
-optional = false
-python-versions = ">=3.7"
-
-[package.dependencies]
-attrs = ">=19.2.0"
-colorama = {version = "*", markers = "sys_platform == \"win32\""}
-iniconfig = "*"
-packaging = "*"
-pluggy = ">=0.12,<2.0"
-py = ">=1.8.2"
-tomli = ">=1.0.0"
-
-[package.extras]
-testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "xmlschema"]
-
-[[package]]
-name = "python-dateutil"
-version = "2.8.2"
-description = "Extensions to the standard Python datetime module"
-category = "main"
-optional = false
-python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
-
-[package.dependencies]
-six = ">=1.5"
-
-[[package]]
-name = "pytz"
-version = "2022.2.1"
-description = "World timezone definitions, modern and historical"
-category = "main"
-optional = false
-python-versions = "*"
-
-[[package]]
-name = "requests"
-version = "2.28.1"
-description = "Python HTTP for Humans."
-category = "main"
-optional = false
-python-versions = ">=3.7, <4"
-
-[package.dependencies]
-certifi = ">=2017.4.17"
-charset-normalizer = ">=2,<3"
-idna = ">=2.5,<4"
-urllib3 = ">=1.21.1,<1.27"
-
-[package.extras]
-socks = ["PySocks (>=1.5.6,!=1.5.7)"]
-use_chardet_on_py3 = ["chardet (>=3.0.2,<6)"]
-
-[[package]]
-name = "six"
-version = "1.16.0"
-description = "Python 2 and 3 compatibility utilities"
-category = "main"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
-
-[[package]]
-<<<<<<< HEAD
-name = "python-dateutil"
-version = "2.8.2"
-description = "Extensions to the standard Python datetime module"
-category = "main"
-optional = false
-python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
-
-[package.dependencies]
-six = ">=1.5"
-
-[[package]]
-name = "pytz"
-version = "2022.2.1"
-description = "World timezone definitions, modern and historical"
-category = "main"
-optional = false
-python-versions = "*"
-
-[[package]]
-name = "requests"
-version = "2.28.1"
-description = "Python HTTP for Humans."
-category = "main"
-=======
-name = "requests"
-version = "2.28.1"
-description = "Python HTTP for Humans."
-category = "dev"
->>>>>>> origin/correct-dev-dependencies
-optional = false
-python-versions = ">=3.7, <4"
-
-[package.dependencies]
-certifi = ">=2017.4.17"
-charset-normalizer = ">=2,<3"
-idna = ">=2.5,<4"
-urllib3 = ">=1.21.1,<1.27"
-
-[package.extras]
-socks = ["PySocks (>=1.5.6,!=1.5.7)"]
-use_chardet_on_py3 = ["chardet (>=3.0.2,<6)"]
-
-[[package]]
-<<<<<<< HEAD
-name = "six"
-version = "1.16.0"
-description = "Python 2 and 3 compatibility utilities"
-category = "main"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
-
-[[package]]
-=======
->>>>>>> origin/correct-dev-dependencies
-name = "tomli"
-version = "2.0.1"
-description = "A lil' TOML parser"
-category = "dev"
-optional = false
-python-versions = ">=3.7"
-
-[[package]]
-name = "urllib3"
-version = "1.26.12"
-description = "HTTP library with thread-safe connection pooling, file post, and more."
-category = "main"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, <4"
-
-[package.extras]
-brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotlipy (>=0.6.0)"]
-secure = ["certifi", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "ipaddress", "pyOpenSSL (>=0.14)", "urllib3-secure-extra"]
-socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
-
-[metadata]
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-python-versions = "^3.10"
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-
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-colorama = [
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diff --git a/pykkn/build_multi_parameters.py b/pykkn/build_multi_parameters.py
index 602b527..c5943d2 100644
--- a/pykkn/build_multi_parameters.py
+++ b/pykkn/build_multi_parameters.py
@@ -4,29 +4,34 @@ from pykkn.parameter import Parameter
def build_multi_parameters(dic: dict) -> list:
"""use this function to build multi-paremeter instances with a dictionary
- Parameter
- ---------
+ Parameters
+ ----------
dic : dict
dic is a dictionary which contains a list of parameter
their attributes as key value pairs
Format of dic
- --------------
+ -------------
{
"list_of_parameters":[
{
- "name":"name_of_parameter_1",
- "value":123
+ "name":"name_of_parameter_1",
+ "value":123
+
},
{
- "name":"name_of_parameter_2",
- "value":456
+ "name":"name_of_parameter_2",
+ "value":456
+
},
{
- "name":"name_of_parameter_3",
- "value":789
+ "name":"name_of_parameter_3",
+ "value":789
+
},
+
]
+
}
a more detailed description of this parameter will be in our document.
diff --git a/pykkn/storage.py b/pykkn/storage.py
index fd3cd80..18bf28c 100644
--- a/pykkn/storage.py
+++ b/pykkn/storage.py
@@ -44,13 +44,13 @@ class Storage:
# return self.storage_path.exists()
def store_HDF5(self, root=None):
- '''sub-method of store() for HDF5 output
+ """sub-method of store() for HDF5 output
Parameters
-----------
root : h5py.File, optional
the root of file object
- '''
+ """
# make a new HDF5 file if this is a root
if root is None:
root = h5py.File(self.storage_path, "w")
@@ -104,13 +104,13 @@ class Storage:
i.store_HDF5(root=s_grp)
def store_json(self, root=None):
- '''sub-method of store() for JSON output
+ """sub-method of store() for JSON output
Parameters
-----------
root : dict, optional
the root of dict object
- '''
+ """
if root is None:
root = {}
@@ -183,15 +183,15 @@ class Storage:
return root
def store(self, format=None, root=None):
- '''store the pykkn structure into HDF5 or JSON
+ """store the pykkn structure into HDF5 or JSON
Parameters
- -----------
+ ----------
format : str, optional
the target format, by default is HDF5, can be specified as json
root : h5py.File or dict, optional
the root of h5py.File or dict object
- '''
+ """
if format is None:
if self.storage_path is None:
# set the file saving path if it does not exist
@@ -298,8 +298,8 @@ class Storage:
def add_attrs_dict(self, dict):
"""Add a flat Dictionary of key values as a set of attributes.
- Parameters:
- ------------
+ Parameters
+ ----------
dict : str
The Dictionary consists of Key Value pairs
with the keys being the names of the attribute
@@ -311,13 +311,13 @@ class Storage:
def encode(self, object: Any) -> str:
"""encode anything as a string
- Parameters:
- -----------
+ Parameters
+ ----------
object: Any
an object which can be an instance of any class
- Returns:
- --------
+ Returns
+ -------
object_string: str
an encoded string, maybe very long if the original object is large
"""
@@ -330,13 +330,13 @@ class Storage:
def decode(self, object_string: str) -> object:
"""decode a string as its original form
- Parameters:
- -----------
+ Parameters
+ ----------
object_string: str
an encoded string
- Returns:
- --------
+ Returns
+ -------
object: object
this is a instance of its original class
"""
--
GitLab