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This commit is contained in:
Deepak Mallubhotla 2022-01-01 15:50:49 -06:00
commit a2c1d56bc8
Signed by: deepak
GPG Key ID: 64BF53A3369104E7
15 changed files with 749 additions and 0 deletions
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.editorconfig Normal file
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root = true
# Unix-style newlines with a newline ending every file
[*]
end_of_line = lf
insert_final_newline = true
indent_style = tab

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[flake8]
ignore = W191, E501
max-line-length = 120

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* text=auto
*.py text diff=python

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# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class
# C extensions
*.so
# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
share/python-wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST
# PyInstaller
# Usually these files are written by a python script from a template
# before PyInstaller builds the exe, so as to inject date/other infos into it.
*.manifest
*.spec
# Installer logs
pip-log.txt
pip-delete-this-directory.txt
# Unit test / coverage reports
htmlcov/
.tox/
.nox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
pytest.xml
*.cover
*.py,cover
.hypothesis/
.pytest_cache/
cover/
# Translations
*.mo
*.pot
# Django stuff:
*.log
local_settings.py
db.sqlite3
db.sqlite3-journal
# Flask stuff:
instance/
.webassets-cache
# Scrapy stuff:
.scrapy
# Sphinx documentation
docs/_build/
# PyBuilder
.pybuilder/
target/
# Jupyter Notebook
.ipynb_checkpoints
# IPython
profile_default/
ipython_config.py
# pyenv
# For a library or package, you might want to ignore these files since the code is
# intended to run in multiple environments; otherwise, check them in:
# .python-version
# pipenv
# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
# However, in case of collaboration, if having platform-specific dependencies or dependencies
# having no cross-platform support, pipenv may install dependencies that don't work, or not
# install all needed dependencies.
#Pipfile.lock
# PEP 582; used by e.g. github.com/David-OConnor/pyflow
__pypackages__/
# Celery stuff
celerybeat-schedule
celerybeat.pid
# SageMath parsed files
*.sage.py
# Environments
.env
.venv
env/
venv/
ENV/
env.bak/
venv.bak/
# Spyder project settings
.spyderproject
.spyproject
# Rope project settings
.ropeproject
# mkdocs documentation
/site
# mypy
.mypy_cache/
.dmypy.json
dmypy.json
# Pyre type checker
.pyre/
# pytype static type analyzer
.pytype/
# Cython debug symbols
cython_debug/

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pipeline {
agent {
kubernetes {
label 'pdme' // all your pods will be named with this prefix, followed by a unique id
idleMinutes 5 // how long the pod will live after no jobs have run on it
yamlFile 'jenkins/ci-agent-pod.yaml' // path to the pod definition relative to the root of our project
defaultContainer 'python' // define a default container if more than a few stages use it, will default to jnlp container
}
}
options {
parallelsAlwaysFailFast()
}
environment {
POETRY_HOME="/opt/poetry"
POETRY_VERSION="1.1.12"
}
stages {
stage('Build') {
steps {
echo 'Building...'
sh 'python --version'
sh 'curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python'
sh '${POETRY_HOME}/bin/poetry --version'
sh '${POETRY_HOME}/bin/poetry install'
}
}
stage('Test') {
parallel{
stage('pytest') {
steps {
sh '${POETRY_HOME}/bin/poetry run pytest'
}
}
stage('lint') {
steps {
sh '${POETRY_HOME}/bin/poetry run flake8'
}
}
stage('mypy') {
steps {
sh '${POETRY_HOME}/bin/poetry run mypy pdme'
}
}
}
}
stage('Deploy') {
when {
buildingTag()
}
steps {
echo 'Deploying...'
sh '${POETRY_HOME}/bin/poetry publish -u ${PYPI_USR} -p ${PYPI_PSW} --build'
}
}
}
post {
always {
echo 'This will always run'
junit 'pytest.xml'
cobertura coberturaReportFile: 'coverage.xml'
mail (bcc: '',
body: "Project: ${env.JOB_NAME} <br>Build Number: ${env.BUILD_NUMBER} <br> Build URL: ${env.BUILD_URL}", cc: '', charset: 'UTF-8', from: 'jenkins@jenkins.deepak.science', mimeType: 'text/html', replyTo: 'dmallubhotla+jenkins@gmail.com', subject: "${env.JOB_NAME} #${env.BUILD_NUMBER}: Build ${currentBuild.currentResult}", to: "dmallubhotla+ci@gmail.com")
}
success {
echo 'This will run only if successful'
}
failure {
echo 'This will run only if failed'
}
unstable {
echo 'This will run only if the run was marked as unstable'
}
changed {
echo 'This will run only if the state of the Pipeline has changed'
echo 'For example, if the Pipeline was previously failing but is now successful'
}
}
}

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README.md Normal file
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# pdme - the python dipole model evaluator

29
do.sh Normal file
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#!/usr/bin/env bash
# Do - The Simplest Build Tool on Earth.
# Documentation and examples see https://github.com/8gears/do
set -Eeuo pipefail # -e "Automatic exit from bash shell script on error" -u "Treat unset variables and parameters as errors"
build() {
echo "I am ${FUNCNAME[0]}ing"
poetry build
}
test() {
echo "I am ${FUNCNAME[0]}ing"
poetry run flake8 pdme tests
poetry run mypy pdme
poetry run pytest
}
htmlcov() {
poetry run pytest --cov-report=html
}
all() {
build && test
}
"$@" # <- execute the task
[ "$#" -gt 0 ] || printf "Usage:\n\t./do.sh %s\n" "($(compgen -A function | grep '^[^_]' | paste -sd '|' -))"

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jenkins/ci-agent-pod.yaml Normal file
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apiVersion: v1
kind: Pod
spec:
containers: # list of containers that you want present for your build, you can define a default container in the Jenkinsfile
- name: python
image: python:3.8
command: ["tail", "-f", "/dev/null"] # this or any command that is bascially a noop is required, this is so that you don't overwrite the entrypoint of the base container
imagePullPolicy: Always # use cache or pull image for agent
resources: # limits the resources your build contaienr
requests:
memory: "2Gi"
cpu: "500m"
limits:
memory: "2Gi"

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pdme/__init__.py Normal file
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import logging
from pdme.meta import __version__
def get_version():
return __version__
logging.getLogger(__name__).addHandler(logging.NullHandler())

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pdme/meta.py Normal file
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from importlib.metadata import version
__version__ = version('pdme')

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poetry.lock generated Normal file
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[[package]]
name = "atomicwrites"
version = "1.4.0"
description = "Atomic file writes."
category = "dev"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
[[package]]
name = "attrs"
version = "21.4.0"
description = "Classes Without Boilerplate"
category = "dev"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
[package.extras]
dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"]
docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"]
tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "cloudpickle"]
tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "cloudpickle"]
[[package]]
name = "colorama"
version = "0.4.4"
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 = "coverage"
version = "6.2"
description = "Code coverage measurement for Python"
category = "dev"
optional = false
python-versions = ">=3.6"
[package.extras]
toml = ["tomli"]
[[package]]
name = "flake8"
version = "3.9.2"
description = "the modular source code checker: pep8 pyflakes and co"
category = "dev"
optional = false
python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
[package.dependencies]
mccabe = ">=0.6.0,<0.7.0"
pycodestyle = ">=2.7.0,<2.8.0"
pyflakes = ">=2.3.0,<2.4.0"
[[package]]
name = "iniconfig"
version = "1.1.1"
description = "iniconfig: brain-dead simple config-ini parsing"
category = "dev"
optional = false
python-versions = "*"
[[package]]
name = "mccabe"
version = "0.6.1"
description = "McCabe checker, plugin for flake8"
category = "dev"
optional = false
python-versions = "*"
[[package]]
name = "mypy"
version = "0.910"
description = "Optional static typing for Python"
category = "dev"
optional = false
python-versions = ">=3.5"
[package.dependencies]
mypy-extensions = ">=0.4.3,<0.5.0"
toml = "*"
typing-extensions = ">=3.7.4"
[package.extras]
dmypy = ["psutil (>=4.0)"]
python2 = ["typed-ast (>=1.4.0,<1.5.0)"]
[[package]]
name = "mypy-extensions"
version = "0.4.3"
description = "Experimental type system extensions for programs checked with the mypy typechecker."
category = "dev"
optional = false
python-versions = "*"
[[package]]
name = "numpy"
version = "1.22.0"
description = "NumPy is the fundamental package for array computing with Python."
category = "main"
optional = false
python-versions = ">=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 = "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 = "pycodestyle"
version = "2.7.0"
description = "Python style guide checker"
category = "dev"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
[[package]]
name = "pyflakes"
version = "2.3.1"
description = "passive checker of Python programs"
category = "dev"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
[[package]]
name = "pyparsing"
version = "3.0.6"
description = "Python parsing module"
category = "dev"
optional = false
python-versions = ">=3.6"
[package.extras]
diagrams = ["jinja2", "railroad-diagrams"]
[[package]]
name = "pytest"
version = "6.2.5"
description = "pytest: simple powerful testing with Python"
category = "dev"
optional = false
python-versions = ">=3.6"
[package.dependencies]
atomicwrites = {version = ">=1.0", markers = "sys_platform == \"win32\""}
attrs = ">=19.2.0"
colorama = {version = "*", markers = "sys_platform == \"win32\""}
iniconfig = "*"
packaging = "*"
pluggy = ">=0.12,<2.0"
py = ">=1.8.2"
toml = "*"
[package.extras]
testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xmlschema"]
[[package]]
name = "pytest-cov"
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optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
[package.dependencies]
coverage = ">=5.2.1"
pytest = ">=4.6"
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[package.extras]
testing = ["fields", "hunter", "process-tests", "six", "pytest-xdist", "virtualenv"]
[[package]]
name = "toml"
version = "0.10.2"
description = "Python Library for Tom's Obvious, Minimal Language"
category = "dev"
optional = false
python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
[[package]]
name = "typing-extensions"
version = "4.0.1"
description = "Backported and Experimental Type Hints for Python 3.6+"
category = "dev"
optional = false
python-versions = ">=3.6"
[metadata]
lock-version = "1.1"
python-versions = "^3.8,<3.10"
content-hash = "d9790d575f5c79aca211a7f2a4b3539f35ea13d0ed72d7fb796e2f36126738eb"
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36
pyproject.toml Normal file
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@ -0,0 +1,36 @@
[tool.poetry]
name = "pdme"
version = "0.0.1"
description = "Python dipole model evaluator"
authors = ["Deepak <dmallubhotla+github@gmail.com>"]
license = "GPL-3.0-only"
readme = "README.md"
[tool.poetry.dependencies]
python = "^3.8,<3.10"
numpy = "^1.21.1"
[tool.poetry.dev-dependencies]
pytest = ">=6"
flake8 = "^3.8.4"
pytest-cov = "^2.10.1"
mypy = "^0.910"
[build-system]
requires = ["poetry>=0.12"]
build-backend = "poetry.masonry.api"
[tool.pytest.ini_options]
testpaths = ["tests"]
addopts = "--junitxml pytest.xml --cov pathfinder --cov-report=xml:coverage.xml --cov-fail-under=90 --cov-report=html"
junit_family = "xunit1"
[tool.mypy]
plugins = "numpy.typing.mypy_plugin"
[[tool.mypy.overrides]]
module = [
"scipy",
"scipy.optimize"
]
ignore_missing_imports = true

29
scripts/patch.sh Normal file
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@ -0,0 +1,29 @@
#!/usr/bin/env bash
set -Eeuo pipefail
if [ -z "$(git status --porcelain)" ]; then
# Working directory clean
branch_name=$(git symbolic-ref -q HEAD)
branch_name=${branch_name##refs/heads/}
branch_name=${branch_name:-HEAD}
poetry version patch
version=`sed 's/version = "\([0-9]*.[0-9]*.[0-9]*\)"/\1/p' -n <pyproject.toml`
read -p "Create commit for version $version? " -n 1 -r
echo # (optional) move to a new line
if [[ $REPLY =~ ^[Yy]$ ]]
then
# do dangerous stuff
echo "Creating a new patch"
git add pyproject.toml
git commit -m "Created version $version"
git tag -a "$version" -m "patch.sh created version $version"
git push --tags
else
echo "Surrendering, clean up by reverting pyproject.toml..."
exit 2
fi
else
echo "Can't create patch version, working tree unclean..."
exit 1
fi

0
tests/__init__.py Normal file
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7
tests/test_pdme.py Normal file
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@ -0,0 +1,7 @@
from pdme import __version__
import pdme
def test_version():
assert __version__ == '0.0.1'
assert pdme.get_version() == __version__