Merge pull request #1 from pyNEMO/skeleton

Create pyDOMCFG skeleton

.github/.codecov.yml

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+coverage:
+  status:
+    project: false
+    patch: false

.github/PULL_REQUEST_TEMPLATE.md

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+<!-- Remove check-list items that aren't relevant to your change -->
+
+- [ ] Closes #xxxx
+- [ ] Tests added
+- [ ] Passes `pre-commit run --all-files`
+- [ ] Changes are documented in `whats-new.rst`
+- [ ] New functions/methods are listed in `api.rst`
+- [ ] Project, label, and assignee tabs are populated

.github/dependabot.yml

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+version: 2
+updates:
+- package-ecosystem: github-actions
+  directory: "/"
+  schedule:
+    interval: weekly
+  open-pull-requests-limit: 10

.github/workflows/cancel.yaml

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+name: Cancel
+on:
+  workflow_run:
+    workflows: ["CI"]
+    types:
+      - requested
+jobs:
+  cancel:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: styfle/cancel-workflow-action@0.9.0
+      with:
+        workflow_id: ${{ github.event.workflow.id }}

.github/workflows/ci.yaml

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+name: CI
+
+on:
+  push:
+    branches: "main"
+  pull_request:
+    branches: "*"
+  schedule:
+    - cron: "0 13 * * 1"
+
+jobs:
+  build:
+    name: Build (${{ matrix.python-version }})
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.7", "3.8", "3.9"]
+    steps:
+      - uses: actions/checkout@v2
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          environment-file: ci/environment.yml
+          activate-environment: pydomcfg_test
+          auto-update-conda: false
+          python-version: ${{ matrix.python-version }}
+          miniforge-variant: Mambaforge
+          use-mamba: true
+
+      - name: Set up conda environment
+        shell: bash -l {0}
+        run: |
+          python -m pip install -e .
+          conda list
+
+      - name: Run Tests
+        shell: bash -l {0}
+        run: pytest --cov-report term --cov-report xml
+
+      - name: Upload code coverage to Codecov
+        uses: codecov/codecov-action@v1
+        with:
+          file: ./coverage.xml
+          flags: unittests
+          env_vars: OS,PYTHON
+          name: codecov-umbrella
+          fail_ci_if_error: false
+
+  upstream-dev:
+    name: upstream-dev
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          environment-file: ci/upstream-dev-env.yml
+          activate-environment: pydomcfg_test_dev
+          auto-update-conda: false
+          miniforge-variant: Mambaforge
+          use-mamba: true
+
+      - name: Set up conda environment
+        shell: bash -l {0}
+        run: |
+          python -m pip install -e .
+          conda list
+
+      - name: Run Tests
+        shell: bash -l {0}
+        run: pytest --no-cov

.gitignore

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+
+# Created by https://www.toptal.com/developers/gitignore/api/jupyternotebooks,python,fortran
+# Edit at https://www.toptal.com/developers/gitignore?templates=jupyternotebooks,python,fortran
+
+### Fortran ###
+# Prerequisites
+*.d
+
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+
+# Fortran module files
+*.mod
+*.smod
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app
+
+### JupyterNotebooks ###
+# gitignore template for Jupyter Notebooks
+# website: http://jupyter.org/
+
+.ipynb_checkpoints
+*/.ipynb_checkpoints/*
+
+# IPython
+profile_default/
+ipython_config.py
+
+# Remove previous ipynb_checkpoints
+#   git rm -r .ipynb_checkpoints/
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+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
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+pytestdebug.log
+
+# 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/**/generated/
+docs/_build/
+doc/_build/
+doc/**/generated/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+
+# IPython
+
+# pyenv
+.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
+
+# poetry
+#poetry.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
+.env/
+.venv/
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+pythonenv*
+
+# 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/
+
+# operating system-related files
+# file properties cache/storage on macOS
+*.DS_Store
+# thumbnail cache on Windows
+Thumbs.db
+
+# profiling data
+.prof
+
+
+# End of https://www.toptal.com/developers/gitignore/api/jupyternotebooks,python,fortran

.pre-commit-config.yaml

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+# https://pre-commit.com/
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.4.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-yaml
+      - id: trailing-whitespace
+
+  - repo: https://github.com/pycqa/isort
+    rev: 5.8.0
+    hooks:
+      - id: isort
+
+  - repo: https://github.com/psf/black
+    rev: 21.5b1
+    hooks:
+      - id: black
+
+  - repo: https://github.com/keewis/blackdoc
+    rev: v0.3.3
+    hooks:
+      - id: blackdoc
+
+  - repo: https://github.com/PyCQA/flake8
+    rev: 3.9.2
+    hooks:
+       - id: flake8
+
+  - repo: https://github.com/terrencepreilly/darglint
+    rev: v1.8.0
+    hooks:
+       - id: darglint
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v0.812
+    hooks:
+      - id: mypy
+        exclude: docs
+
+  - repo: https://github.com/PyCQA/doc8
+    rev: 0.9.0a1
+    hooks:
+      - id: doc8

.readthedocs.yaml

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+# .readthedocs.yaml
+# 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/conf.py
+
+# Optionally set the version of Python and requirements required to build your docs
+conda:
+  environment: ci/docs.yml

README.rst

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+pyDOMCFG
+========
+
+.. image:: https://img.shields.io/github/workflow/status/pyNEMO/pyDOMCFG/CI?logo=github
+    :target: https://github.com/pyNEMO/pyDOMCFG/actions
+    :alt: GitHub Workflow CI Status
+
+.. image:: https://codecov.io/gh/pyNEMO/pyDOMCFG/branch/main/graph/badge.svg?token=BP296I59E8
+    :target: https://codecov.io/gh/pyNEMO/pyDOMCFG
+    :alt: Code Coverage
+
+.. image:: https://readthedocs.org/projects/pydomcfg/badge/?version=latest
+    :target: https://pydomcfg.readthedocs.io/en/latest/?badge=latest
+    :alt: Documentation Status
+
+.. image:: https://results.pre-commit.ci/badge/github/pyNEMO/pyDOMCFG/main.svg
+   :target: https://results.pre-commit.ci/latest/github/pyNEMO/pyDOMCFG/main
+   :alt: pre-commit.ci status

ci/docs.yml

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+name: pydomcfg_docs
+channels:
+  - conda-forge
+dependencies:
+  - numpydoc
+  - sphinx
+  - sphinx_rtd_theme