diff --git a/.flake8 b/.flake8
new file mode 100644
index 0000000000000000000000000000000000000000..42d62190033f822d7cf5958b7ffb9d77681fcf5d
--- /dev/null
+++ b/.flake8
@@ -0,0 +1,14 @@
+[flake8]
+doctests = True
+exclude = .git, .eggs, __pycache__, docs, dist, venv, .tox, env, envs
+ignore =
+ # line too long, we use black
+ E501,
+ # line break before binary operator
+ W503,
+ # wrong flake defaults: see https://github.com/psf/black/issues/315, https://github.com/psf/black/issues/43
+ E203,
+ W503,
+ W504
+per-file-ignores =
+ __init__.py:F401,E402
\ No newline at end of file
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..8f4a5d31d4806e0190b48ce24da82366aa3063d4
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,184 @@
+# requirements.txt is generated dynamically in this project (e.g. make requirements)
+requirements.txt
+
+# junit reports (generated by tox)
+report/
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+envs/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# 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/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+
+# pyc files:
+*.pyc
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask instance folder
+instance/
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# IPython Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# dotenv
+.env
+
+# virtualenv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+
+# vim files
+*.sw*
+
+# VisualStudioCode
+.vscode/* # Maybe .vscode/**/* instead - see comments
+!.vscode/settings.json
+!.vscode/tasks.json
+!.vscode/launch.json
+!.vscode/extensions.json
+**/.history
+
+# folder
+tmp/
+.idea
+docs/source/
+
+### Git ###
+*.orig
+
+### Linux ###
+*~
+
+# temporary files which can be created if a process still has a handle open of a deleted file
+.fuse_hidden*
+
+# KDE directory preferences
+.directory
+
+# Linux trash folder which might appear on any partition or disk
+.Trash-*
+
+# .nfs files are created when an open file is removed but is still being accessed
+.nfs*
+
+### macOS ###
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+
+### Windows ###
+# Windows thumbnail cache files
+Thumbs.db
+ehthumbs.db
+ehthumbs_vista.db
+
+# Dump file
+*.stackdump
+
+# Folder config file
+[Dd]esktop.ini
+
+# Recycle Bin used on file shares
+$RECYCLE.BIN/
+
+# Windows Installer files
+*.cab
+*.msi
+*.msix
+*.msm
+*.msp
+
+# Windows shortcuts
+*.lnk
+
+# Latex temp files (in case you include a documentation in latex e.g.)
+*.aux
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
new file mode 100644
index 0000000000000000000000000000000000000000..2daefcf8570e3ee6714c45b3af044e67569fb161
--- /dev/null
+++ b/.gitlab-ci.yml
@@ -0,0 +1,109 @@
+image: python:latest
+
+# Change pip's cache directory to be inside the project directory since we can
+# only cache local items.
+variables:
+ PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip"
+
+# Pip's cache doesn't store the python packages
+# https://pip.pypa.io/en/stable/reference/pip_install/#caching
+#
+# If you want to also cache the installed packages, you have to install
+# them in a virtualenv and cache it as well.
+cache:
+ paths:
+ - .cache/pip
+ - venv/
+ - .cache/apt
+
+stages:
+ - build
+ - test
+ - deploy
+
+before_script:
+ - pip install virtualenv
+ - virtualenv venv
+ - source venv/bin/activate
+ - poetry install
+
+dist:
+ stage: build
+ script:
+ - mkdir -p .cache/apt
+ - apt-get update -yqq
+ - apt-get install -y gfortran libopenblas-dev liblapack-dev
+ - apt-get -o dir::cache::archives=".cache/apt" install -y -qq gfortran liblapack-dev libgmp-dev
+ - python setup.py bdist_wheel
+ # an alternative approach is to install and run:
+ - pip install dist/*
+ # run the command here
+ artifacts:
+ paths:
+ - dist/*.whl
+ expire_in: 1h
+ only:
+ - tags
+
+pages:
+ stage: build
+ script:
+ - poetry install --only docs
+ - cd docs
+ - make html
+ - cd ..
+ - mkdir -p public
+ - rm -rf public/*
+ - mv docs/_build/html/* public/ # add it to pages. Pages is exposing public/index.html
+ only:
+ - master
+ cache:
+ paths:
+ - public
+ artifacts:
+ paths:
+ - public
+ - docs
+
+lint:
+ stage: test
+ before_script:
+ - pip install -q flake8
+ script:
+ - flake8
+
+test:
+ stage: test
+ script:
+ - pip --version
+ - pip install tox # you can also use tox
+ - tox
+ coverage: '/^TOTAL.+?(\d+\%)$/'
+ artifacts:
+ # paths:
+ # pa- report/unit
+ reports:
+ junit:
+ - report/junit.xml
+pypi:
+ image: docker.km3net.de/base/python:3
+ stage: deploy
+ cache: {}
+ before_script:
+ - echo "Starting upload to pypi"
+ script:
+ # Check if current_version is already uploaded
+ - VERSION=$((python -c "import configparser; config = configparser.ConfigParser(); config.read('setup.cfg'); print(config['bumpversion']['current_version'])") 2>&1)
+ - MODULE_NAME=$((python -c "import configparser; config = configparser.ConfigParser(); config.read('setup.cfg'); print(config['metadata']['name'])") 2>&1)
+ - PACKAGE_JSON_URL="https://pypi.org/pypi/$MODULE_NAME/json"
+ - apt-get install -qq -y jq
+ - PYPI_VERSIONS=$(curl -s "$PACKAGE_JSON_URL" | jq -r '.releases | keys | .[]' | sort -V)
+ - if [[ $PYPI_VERSIONS =~ $VERSION ]]; then echo "Version $VERSION is already uploaded!"; exit 1; fi
+ # Version not already uploaded so do it now.
+ - echo "Uploading version $VERSION"
+ - pip install -U twine
+ - python setup.py sdist
+ - twine upload dist/*
+ rules:
+ # for debuggin: git commit -am "deb" && git push && bumpversion patch && git tag -l --sort=-v:refname | head -n 1 | git push origin
+ - if: $CI_COMMIT_TAG =~ /^v[0-9]+\.[0-9]+\.[0-9]+$/
\ No newline at end of file
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..b6d2326ebedc61e8324b46226aabeefae75dce69
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,29 @@
+default_language_version:
+ python: python3
+repos:
+- repo: https://github.com/ambv/black
+ rev: 22.3.0
+ hooks:
+ - id: black
+ language_version: python3.10
+- repo: https://gitlab.com/pycqa/flake8
+ rev: 3.9.2
+ hooks:
+ - id: flake8
+- repo: https://github.com/pre-commit/pre-commit-hooks
+ rev: v4.0.1
+ hooks:
+ - id: check-json
+ - id: pretty-format-json
+ args: ['--indent', '4']
+ - id: check-merge-conflict
+ - id: check-toml
+ - id: check-yaml
+ - id: debug-statements
+ - id: detect-private-key
+ - id: end-of-file-fixer
+- repo: https://github.com/asottile/blacken-docs
+ rev: v1.12.1
+ hooks:
+ - id: blacken-docs
+ additional_dependencies: [black==22.3.0]
diff --git a/.readthedocs.yml b/.readthedocs.yml
new file mode 100644
index 0000000000000000000000000000000000000000..1db793f37946026137fbe27e56e648887339190c
--- /dev/null
+++ b/.readthedocs.yml
@@ -0,0 +1,25 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+
+formats: all
+
+build:
+ image: latest
+
+# 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
+python:
+ version: 3.7
+ install:
+ - method: pip
+ path: .
+ extra_requirements:
+ - docs
diff --git a/AUTHORS.rst b/AUTHORS.rst
new file mode 100644
index 0000000000000000000000000000000000000000..db7323ffb1f36e4403ea094afa0bd6d47c398fa3
--- /dev/null
+++ b/AUTHORS.rst
@@ -0,0 +1,17 @@
+=======
+Credits
+=======
+This package was created with Cookiecutter_ and the `dboe/dough`_ project template.
+
+.. _Cookiecutter: https://github.com/audreyr/cookiecutter
+.. _`dboe/dough`: https://gitlab.com/dboe/dough
+
+Development Lead
+----------------
+
+* Daniel Böckenhoff <dboe@ipp.mpg.de>
+
+Contributors
+------------
+
+None yet. Why not be the first?
diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
new file mode 100644
index 0000000000000000000000000000000000000000..408c188f04c5bbb182aa8bcd920c2b0d60a339e1
--- /dev/null
+++ b/CONTRIBUTING.rst
@@ -0,0 +1,166 @@
+============
+Contributing
+============
+..
+ [contributing]
+
+.. highlight:: shell
+
+Contributions are welcome, and they are greatly appreciated! Every little bit
+helps, and credit will always be given.
+
+You can contribute in many ways:
+
+Types of Contributions
+----------------------
+
+Report Bugs
+~~~~~~~~~~~
+
+Report bugs at <https://gitlab.mpcdf.mpg.de/dboe/rna/-/issues/>_.
+
+If you are reporting a bug, please include:
+
+* Your operating system name and version.
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+If you want quick feedback, it is helpful to mention specific developers
+(@devloper_name) or @all. This will trigger a mail to the corresponding developer(s).
+
+Fix Bugs
+~~~~~~~~
+
+Look through the repository issues for bugs. Anything tagged with "bug" and "help
+wanted" is open to whoever wants to implement it.
+
+Implement Features
+~~~~~~~~~~~~~~~~~~
+
+Look through the remote issues for features. Anything tagged with "enhancement"
+and "help wanted" is open to whoever wants to implement it.
+
+Write Documentation
+~~~~~~~~~~~~~~~~~~~
+
+`rna` could always use more :ref name="Documentation":`documentation`, whether as part of the
+official `rna` docs, in docstrings, or even on the web in blog posts,
+articles, and such.
+
+Write pytest, unittests or doctests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+`rna` profits a lot from better :ref name="Testing":`testing`. We encourage you to add unittests
+with the `pytest` module (`unittest` module is OK, too) in the `tests` directory or doctests (as part of docstrings or in the documentation).
+
+Submit Feedback
+~~~~~~~~~~~~~~~
+
+The best way to send feedback is to file an `Issue <https://gitlab.mpcdf.mpg.de/dboe/rna/-/issues/>`_.
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+* Remember that this is a volunteer-driven project, and that contributions
+ are welcome
+
+Get Started!
+------------
+
+Ready to contribute? Here's how to set up `rna` for local development.
+
+1. Fork the `rna` repo.
+2. Clone your fork locally::
+
+ $ git clone git@gitlab.mpcdf.mpg.de:dboe/rna.git
+
+3. Set up your fork for local development::
+
+ $ cd rna/
+ $ pip install .[dev]
+
+4. Step 3. already installed `pre-commit <https://pre-commit.com/>`_. Initialize it by running::
+
+ $ pre-commit install
+
+5. Create a branch for local development::
+
+ $ git checkout -b name-of-your-bugfix-or-feature
+
+ Now you can make your changes locally.
+
+6. When you're done making changes, check that your changes pass flake8 and the
+ tests::
+
+ $ make test
+
+7. Commit your changes and push your branch to origin::
+
+ $ git add .
+ $ git commit -m "Your detailed description of your changes."
+ $ git push origin name-of-your-bugfix-or-feature
+
+8. Submit a pull request through the repository website.
+
+Pull Request Guidelines
+-----------------------
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. The pull request should include tests.
+2. If the pull request adds functionality, the docs should be updated. Put
+ your new functionality into a function with a docstring, and add the
+ feature to the list in README.rst.
+3. The pull request should work for Python 3.5, 3.6, 3.7 and 3.8, and for PyPy. Check
+ <https://gitlab.mpcdf.mpg.de/dboe/rna/-/merge_requests/>_
+ and make sure that the tests pass for all supported Python versions.
+
+Testing
+-------
+
+To run tests, use::
+
+ $ make test
+
+To run a subset of tests, you have the following options::
+
+ $ pytest tests/test_package.py
+
+ $ pytest tests/test_package.py::Test_rna::test_version_type
+
+ $ pytest --doctest-modules docs/usage.rst
+
+ $ pytest --doctest-modules rna/core.py -k "MyClass.funciton_with_doctest"
+
+Use the '--trace' option to directly jump into a pdb debugger on fails. Check out the coverage of your api with::
+
+ $ make coverage
+
+Documentation
+-------------
+To compile the documentation (including automatically generated module api docs), run::
+
+ $ make docs
+
+To run an auto-updating server, use
+
+ $ make docs-serve
+
+Use doctests as much as possible in order to have tested examples in your documentation.
+
+Style guide
+-----------
+Please follow the `google style guide <https://google.github.io/styleguide/pyguide.html>`_ illustrated
+by `this example <https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html>`_.
+
+Deploying
+---------
+
+A reminder for the maintainers on how to deploy.
+Make sure all your changes are committed.
+Then run::
+
+ $ make publish
+
+The CI will then deploy to PyPI if tests pass.
\ No newline at end of file
diff --git a/LICENSE.rst b/LICENSE.rst
new file mode 100644
index 0000000000000000000000000000000000000000..2854fc17c17e5a4e5b16e10a40957009b2e9c0c8
--- /dev/null
+++ b/LICENSE.rst
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2023, Daniel Böckenhoff
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/Makefile b/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..a3b3f26a1e81ddcf274e4bc0de81fe37590f526e
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,86 @@
+include tools/Makefile.envs
+
+test: FORCE
+ flake8 rna tests
+ pylint rna tests
+ py.test
+
+coverage: env
+ # coverage run $(MODULE) test
+ py.test --cov=$(MODULE) || true
+ # coverage report
+ coverage html
+ python -m webbrowser htmlcov/index.html
+
+clean:
+ coverage erase
+ rm -rf htmlcov
+ rm -rf docs/_build
+ rm -rf docs/source
+ rm -rf dist
+ rm -rf build
+ rm -rf report
+ rm -rf .tox
+ rm -rf .pytest_cache
+ rm -rf *.egg-info
+ # pre-commit clean
+
+publish:
+ @echo $(GITSTATUS)
+ @if [ -z $(GITSTATUS) ]; then \
+ echo "Working directory clean."; \
+ else \
+ git status; \
+ printf $(_WARN) "WAIT" "Your Git status is not clean!" ; \
+ if $(MAKE) -s confirm ; then \
+ printf $(_INFO) "OK" "Continuing" ; \
+ else \
+ printf $(_ERROR) "KO" "EXIT" ; \
+ exit 1; \
+ fi \
+ fi
+ # call optional with argument: make part=minor publish
+ poetry version $(part) # possible: major / minor / patch
+ git commit -m "release-$(poetry version --short)"
+ git tag "release-$(poetry version --short)"
+ git push
+ git push --tags
+
+untag:
+ # remove last tag. mostly, because publishing failed
+ git tag -d v$(VERSION)
+ git push origin :refs/tags/v$(VERSION)
+
+requirements: pyproject.toml
+ poetry export --without-hashes --format=requirements.txt > requirements.txt
+
+docs-clean:
+ rm -rf docs/_build
+
+docs-serve:
+ ${CONDA_RUN}poetry install --only docs
+ sphinx-autobuild docs docs/_build/ -j auto --watch my_project
+
+docs-build: docs-clean
+ ${CONDA_RUN}poetry install --only docs
+ sphinx-build -M html docs docs/_build/ -E -a -j auto -W --keep-going
+
+docs: docs-build
+ # open the html slides
+ ${CONDA_RUN}python -m webbrowser docs/_build/html/index.html
+
+update:
+ # get up to date with the cookiecutter template 'dough'
+ # first check that no changes are existing
+ @echo $(GITSTATUS)
+ @if [ -z $(GITSTATUS) ]; then \
+ echo "Working directory clean."; \
+ else \
+ git status; \
+ echo "Your status is not clean! I can not update!"; \
+ exit 1; \
+ fi
+ # Starting upgrade
+ cookiecutter_project_upgrader
+
+FORCE: ;
diff --git a/README.rst b/README.rst
new file mode 100644
index 0000000000000000000000000000000000000000..5821eb3b1fc4178795f1db6c1c618b5358d84336
--- /dev/null
+++ b/README.rst
@@ -0,0 +1,73 @@
+=====================
+library documentation
+=====================
+
+..
+ [shields-start]
+
+
+.. pypi
+.. image:: https://img.shields.io/pypi/v/rna.svg
+ :target: https://pypi.python.org/pypi/rna
+.. ci
+ .. image:: https://img.shields.io/travis/dboe/rna.svg
+ :target: https://travis-ci.com/dboe/rna
+.. image:: https://gitlab.mpcdf.mpg.de/dboe/rna/badges/master/pipeline.svg
+ :target: https://gitlab.mpcdf.mpg.de/dboe/rna/commits/master
+
+.. coverage
+.. image:: https://gitlab.mpcdf.mpg.de/dboe/rna/badges/master/coverage.svg
+ :target: https://gitlab.mpcdf.mpg.de/dboe/rna/commits/master
+
+.. readthedocs
+.. image:: https://readthedocs.org/projects/rna/badge/?version=latest
+ :target: https://rna.readthedocs.io/en/latest/?badge=latest
+ :alt: Documentation Status
+
+.. pyup crosschecks your dependencies. Github is default, gitlab more complicated: https://pyup.readthedocs.io/en/latest/readme.html#run-your-first-update
+ .. image:: https://pyup.io/repos/github/dboe/rna/shield.svg
+ :target: https://pyup.io/repos/github/dboe/rna/
+ :alt: Updates
+
+.. image:: https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white
+ :target: https://github.com/pre-commit/pre-commit
+ :alt: pre-commit
+..
+ [shields-end]
+
+Overview
+========
+..
+ [overview-start]
+
+Basic and essential code building blocks of all pythons
+
+..
+ [overview-end]
+
+
+Licensed under the ``MIT License``
+
+Resources
+---------
+..
+ [resources-start]
+
+* Source code: https://gitlab.mpcdf.mpg.de/dboe/rna
+* Documentation: https://rna.readthedocs.io
+* Pypi: https://pypi.python.org/pypi/rna
+..
+ [resources-end]
+
+
+Features
+--------
+..
+ [features-start]
+
+The following features should be highlighted:
+
+* TODO
+
+..
+ [features-end]
diff --git a/docs/Makefile b/docs/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..8607fce7795fab193404dac8f276a887a9c90a15
--- /dev/null
+++ b/docs/Makefile
@@ -0,0 +1,25 @@
+# Minimal makefile for Sphinx documentation
+#
+MODULE_PATH := $(shell cd ..; pwd)
+MODULE := $(shell basename "$(MODULE_PATH)")
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS ?=
+SPHINXBUILD ?= sphinx-build
+SOURCEDIR = .
+BUILDDIR = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+ @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+apidocs: $(MODULEPATH)/$(MODULE)/*.py apidoc-templates/*
+ sphinx-apidoc -o source/ ../$(MODULE)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+ @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/_static/index.css b/docs/_static/index.css
new file mode 100644
index 0000000000000000000000000000000000000000..40f044c1fe244332b88af989894dd41a0c5a96b8
--- /dev/null
+++ b/docs/_static/index.css
@@ -0,0 +1,73 @@
+@font-face {
+ font-family: 'inter';
+ src: url('inter.ttf') format('truetype');
+}
+
+#landing-header {
+ width: 100%;
+ display: flex;
+ flex-wrap: wrap;
+ margin-left: auto;
+ margin-top: 1rem;
+ font-family: Inter;
+}
+
+#landing-header > img {
+ width: 75%;
+ margin: auto;
+}
+
+#landing-tagline {
+ width: 100%;
+ text-align: center;
+ font-size: xx-large;
+}
+
+
+#landing-overview {
+ width: 90%;
+ display: flex;
+ flex-wrap: wrap;
+ gap: 1rem;
+ margin-top: 4rem;
+ margin-left: auto;
+ margin-right: auto;
+ justify-content: space-around;
+}
+
+
+
+@media (min-width: 992px) {
+ #landing-overview > section {
+ width: 45% !important;
+ }
+}
+
+@media (min-width: 1400px) {
+ #landing-overview > section {
+ width: 30% !important;
+ }
+}
+
+#landing-overview > section {
+ font-size: medium;
+ background-color: var(--pst-color-on-background);
+ padding: .75rem;
+ border-radius: 5px;
+ text-align: justify;
+}
+
+
+
+#landing-overview > section h2 {
+ margin-top: 0;
+ font-weight: bold;
+ font-size: medium;
+ text-transform: uppercase;
+ color: #edb641;
+}
+
+
+#landing-overview > section > p {
+ width: 100%;
+}
\ No newline at end of file
diff --git a/docs/_static/inter.ttf b/docs/_static/inter.ttf
new file mode 100644
index 0000000000000000000000000000000000000000..ec3164efa8fe938310f74b6156d3ad33ccb2fef6
Binary files /dev/null and b/docs/_static/inter.ttf differ
diff --git a/docs/_static/style.css b/docs/_static/style.css
new file mode 100644
index 0000000000000000000000000000000000000000..ca785ff3c5af458022c6a48edd3d319e3dfe51fb
--- /dev/null
+++ b/docs/_static/style.css
@@ -0,0 +1,93 @@
+.article-container p {
+ text-align: justify;
+}
+
+#version-warning {
+ top: 0;
+ position: sticky;
+ z-index: 60;
+ width: 100%;
+ height: 2.5rem;
+ display: flex;
+ column-gap: .5rem;
+ justify-content: center;
+ justify-items: center;
+ align-items: center;
+ background-color: #eee;
+ border-bottom: 2px solid #ae2828;
+}
+
+@media (prefers-color-scheme: dark) {
+ body:not([data-theme="light"]) #version-warning {
+ background-color: black;
+ }
+}
+
+
+table.docutils {
+ clear: left;
+ float: left;
+ margin: 0 1rem 1rem;
+}
+
+
+/* theme customization */
+
+html[data-theme="dark"] {
+ --color-background-primary: #1d2433;
+ --color-background-secondary: #0c101a;
+ --pst-color-on-background: #2e374a;
+ --pst-color-border: #2f2f2f;
+}
+
+html[data-theme="light"] {
+ --color-background-primary: #f8f9fb;
+ --color-background-secondary: #fff;
+}
+
+html[data-theme="light"], html[data-theme="dark"] {
+ --pst-color-background: var(--color-background-primary);
+ --pst-color-primary: #ffae57;
+}
+
+
+@media (min-width: 960px) {
+ .bd-page-width {
+ max-width: 100rem;
+ }
+}
+
+.bd-sidebar-primary {
+ display: block;
+ flex: 0 0 18%;
+}
+
+
+.bd-content, .bd-sidebar-secondary {
+ background-color: var(--color-background-secondary);
+}
+
+
+.sd-tab-content {
+ box-shadow: 0 -0.0625rem var(--sd-color-tabs-overline);
+}
+
+div.literal-block-wrapper, pre {
+ border: none;
+}
+
+.code-block-caption {
+ background-color: var(--pst-color-surface);
+}
+
+.navbar-persistent--mobile {
+ margin-left: unset;
+}
+
+.navbar-persistent--mobile:last-of-type {
+ padding-left: 1rem;
+}
+
+#navbar-icon-links a {
+ padding-top: .2rem;
+}
\ No newline at end of file
diff --git a/docs/_static/versioning.js b/docs/_static/versioning.js
new file mode 100644
index 0000000000000000000000000000000000000000..15f6c9b301978bd4e8583edc2d7696903bd0340c
--- /dev/null
+++ b/docs/_static/versioning.js
@@ -0,0 +1,114 @@
+const loadVersions = async () => {
+ const res = await fetch(DOCUMENTATION_OPTIONS.URL_ROOT + "versions.json")
+ if (res.status !== 200) {
+ return null
+ }
+ return await res.json()
+}
+
+
+const getCurrentVersion = (versions) => {
+ const baseURL = new URL(DOCUMENTATION_OPTIONS.URL_ROOT, window.location).href
+ const parts = window.location.href.replace(baseURL, "").split("/")
+ if (!parts.length) {
+ return null
+ }
+ const maybeVersion = parts[0]
+ if (maybeVersion === "lib") {
+ return versions.latest
+ }
+ if (versions.versions.includes(maybeVersion)) {
+ return maybeVersion
+ }
+ return null
+}
+
+
+const addVersionWarning = (currentVersion, latestVersion) => {
+ if (currentVersion === latestVersion) {
+ return
+ }
+
+ const navbarMain = document.getElementById("navbar-main")
+ if (!navbarMain) {
+ return
+ }
+
+ const container = document.createElement("div")
+ container.id = "version-warning"
+
+ const warningText = document.createElement("span")
+ warningText.textContent = `You are viewing the documentation for ${currentVersion === "dev" ? "a preview" : "an outdated"} version of this project.`
+ container.appendChild(warningText)
+
+ const latestLink = document.createElement("a")
+ latestLink.textContent = "Click here to go to the latest version"
+ latestLink.href = DOCUMENTATION_OPTIONS.URL_ROOT + "lib"
+ container.appendChild(latestLink)
+
+ navbarMain.before(container)
+}
+
+
+const formatVersionName = (version, isLatest) => version + (isLatest ? " (latest)" : "")
+
+
+const addVersionSelect = (currentVersion, versionSpec) => {
+ const navEnd = document.getElementById("navbar-end")
+ if (!navEnd) {
+ return
+ }
+
+ const container = document.createElement("div")
+ container.classList.add("navbar-nav")
+
+ const dropdown = document.createElement("div")
+ dropdown.classList.add("dropdown")
+ container.appendChild(dropdown)
+
+ const dropdownToggle = document.createElement("button")
+ dropdownToggle.classList.add("btn", "dropdown-toggle", "nav-item")
+ dropdownToggle.setAttribute("data-toggle", "dropdown")
+ dropdownToggle.setAttribute("type", "button")
+ dropdownToggle.textContent = `Version: ${formatVersionName(currentVersion, currentVersion === versionSpec.latest)}`
+ dropdown.appendChild(dropdownToggle)
+
+ const dropdownContent = document.createElement("div")
+ dropdownContent.classList.add("dropdown-menu")
+ dropdown.appendChild(dropdownContent)
+
+ for (const version of versionSpec.versions) {
+ const navItem = document.createElement("li")
+ navItem.classList.add("nav-item")
+
+ const navLink = document.createElement("a")
+ navLink.classList.add("nav-link", "nav-internal")
+ navLink.href = DOCUMENTATION_OPTIONS.URL_ROOT + version
+ navLink.textContent = formatVersionName(version, version === versionSpec.latest)
+ navItem.appendChild(navLink)
+
+ dropdownContent.appendChild(navItem)
+ }
+
+ navEnd.prepend(container)
+}
+
+
+const setupVersioning = (versions) => {
+ if (versions === null) {
+ return
+ }
+
+ const currentVersion = getCurrentVersion(versions)
+ if (currentVersion === null) {
+ return
+ }
+
+ addVersionWarning(currentVersion, versions.latest)
+ addVersionSelect(currentVersion, versions)
+}
+
+
+window.addEventListener("DOMContentLoaded", () => {
+ loadVersions().then(setupVersioning)
+})
diff --git a/docs/_templates/custom-class-template.rst b/docs/_templates/custom-class-template.rst
new file mode 100644
index 0000000000000000000000000000000000000000..f73eda50ec593f7393241c5d6aa4c143a66c805b
--- /dev/null
+++ b/docs/_templates/custom-class-template.rst
@@ -0,0 +1,34 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+ :members:
+ :show-inheritance:
+ :inherited-members:
+ :special-members: __call__, __add__, __mul__
+
+ {% block methods %}
+ {% if methods %}
+ .. rubric:: {{ _('Methods') }}
+
+ .. autosummary::
+ :nosignatures:
+ {% for item in methods %}
+ {%- if not item.startswith('_') %}
+ ~{{ name }}.{{ item }}
+ {%- endif -%}
+ {%- endfor %}
+ {% endif %}
+ {% endblock %}
+
+ {% block attributes %}
+ {% if attributes %}
+ .. rubric:: {{ _('Attributes') }}
+
+ .. autosummary::
+ {% for item in attributes %}
+ ~{{ name }}.{{ item }}
+ {%- endfor %}
+ {% endif %}
+ {% endblock %}
diff --git a/docs/_templates/custom-module-template.rst b/docs/_templates/custom-module-template.rst
new file mode 100644
index 0000000000000000000000000000000000000000..d066d0e4dc2e34f399f55ea38d92ed4540787317
--- /dev/null
+++ b/docs/_templates/custom-module-template.rst
@@ -0,0 +1,66 @@
+{{ fullname | escape | underline}}
+
+.. automodule:: {{ fullname }}
+
+ {% block attributes %}
+ {% if attributes %}
+ .. rubric:: Module attributes
+
+ .. autosummary::
+ :toctree:
+ {% for item in attributes %}
+ {{ item }}
+ {%- endfor %}
+ {% endif %}
+ {% endblock %}
+
+ {% block functions %}
+ {% if functions %}
+ .. rubric:: {{ _('Functions') }}
+
+ .. autosummary::
+ :toctree:
+ :nosignatures:
+ {% for item in functions %}
+ {{ item }}
+ {%- endfor %}
+ {% endif %}
+ {% endblock %}
+
+ {% block classes %}
+ {% if classes %}
+ .. rubric:: {{ _('Classes') }}
+
+ .. autosummary::
+ :toctree:
+ :template: custom-class-template.rst
+ :nosignatures:
+ {% for item in classes %}
+ {{ item }}
+ {%- endfor %}
+ {% endif %}
+ {% endblock %}
+
+ {% block exceptions %}
+ {% if exceptions %}
+ .. rubric:: {{ _('Exceptions') }}
+
+ .. autosummary::
+ :toctree:
+ {% for item in exceptions %}
+ {{ item }}
+ {%- endfor %}
+ {% endif %}
+ {% endblock %}
+
+{% block modules %}
+{% if modules %}
+.. autosummary::
+ :toctree:
+ :template: custom-module-template.rst
+ :recursive:
+{% for item in modules %}
+ {{ item }}
+{%- endfor %}
+{% endif %}
+{% endblock %}
diff --git a/docs/_templates/navbar-nav.html b/docs/_templates/navbar-nav.html
new file mode 100644
index 0000000000000000000000000000000000000000..72ed846db9401cf32d433408b92160e437407451
--- /dev/null
+++ b/docs/_templates/navbar-nav.html
@@ -0,0 +1,32 @@
+{% macro nav_link(label, target) -%}
+ <li class="nav-item">
+ <a class="nav-link nav-internal" href="{{ target if target.startswith('http') else pathto(target) }}">{{ label }}</a>
+ </li>
+{%- endmacro %}
+
+
+<nav class="navbar-nav">
+ <p class="sidebar-header-items__title"
+ role="heading"
+ aria-level="1"
+ aria-label="{{ _('Site Navigation') }}">
+ {{ _("Site Navigation") }}
+ </p>
+ <ul id="navbar-main-elements" class="navbar-nav">
+ {% for label, item in navbar_items | items %}
+ {% if item is string %}
+ {{ nav_link(label, item) }}
+ {% else %}
+ <div class="nav-item dropdown">
+ <button class="btn dropdown-toggle nav-item" type="button"
+ data-toggle="dropdown">{{ label }}</button>
+ <ul class="dropdown-menu">
+ {% for child_label, child_item in item | items %}
+ {{ nav_link(child_label, child_item) }}
+ {% endfor %}
+ </ul>
+ </div>
+ {% endif %}
+ {% endfor %}
+ </ul>
+</nav>
diff --git a/docs/about/index.rst b/docs/about/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..befeb16595a8379cde5ae67cac41e4f63c24ca18
--- /dev/null
+++ b/docs/about/index.rst
@@ -0,0 +1,5 @@
+=====
+ABOUT
+=====
+
+.. include:: ../../AUTHORS.rst
diff --git a/docs/community/index.rst b/docs/community/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..ac7b6bcf35e98139c791cb5c4b94f08849972d65
--- /dev/null
+++ b/docs/community/index.rst
@@ -0,0 +1 @@
+.. include:: ../../CONTRIBUTING.rst
diff --git a/docs/conf.py b/docs/conf.py
new file mode 100644
index 0000000000000000000000000000000000000000..dd93a5aaf6262dcdaf829fa8b6c1b7c998ea5576
--- /dev/null
+++ b/docs/conf.py
@@ -0,0 +1,106 @@
+import os
+import datetime
+try:
+ import tomllib
+except ModuleNotFoundError:
+ import tomli as tomllib
+
+__source_dir = "docs"
+with open(os.path.join(os.path.dirname(__file__), "../pyproject.toml"), "rb") as f:
+ __config = tomllib.load(f)
+
+project = __config["tool"]["poetry"]["name"]
+author = __config["tool"]["poetry"]["authors"][0]
+copyright = str(datetime.date.today().year) + ", " + author
+release = __config["tool"]["poetry"]["version"]
+
+extensions = [
+ "sphinx.ext.intersphinx",
+ "sphinx.ext.autosectionlabel",
+ "sphinx.ext.autodoc",
+ "sphinx.ext.napoleon",
+ "sphinx_design",
+ "sphinx_copybutton",
+ "sphinxcontrib.mermaid",
+ "sphinx.ext.viewcode", # Add links to highlighted source code
+ "sphinx.ext.doctest", # Test snippets in the documentation
+ "sphinx.ext.autosummary",
+ "sphinx_autodoc_typehints", # Automatically parse type hints
+]
+autosummary_generate = True # Turn on sphinx.ext.autosummary
+
+templates_path = ["_templates"]
+exclude_patterns = ["_build"]
+
+intersphinx_mapping = {
+ "python": ("https://docs.python.org/3", None),
+}
+
+napoleon_google_docstring = True
+napoleon_include_special_with_doc = True
+napoleon_use_admonition_for_examples = True
+napoleon_use_admonition_for_notes = True
+napoleon_use_admonition_for_references = False
+napoleon_attr_annotations = True
+
+autosummary_generate = True # Turn on sphinx.ext.autosummary
+html_show_sourcelink = False # Remove 'view source code' from top of page (for html, not python)
+autodoc_inherit_docstrings = True # If no docstring, inherit from base class
+set_type_checking_flag = True # Enable 'expensive' imports for sphinx_autodoc_typehints
+nbsphinx_allow_errors = True # Continue through Jupyter errors
+#autodoc_typehints = "description" # Sphinx-native method. Not as good as sphinx_autodoc_typehints
+add_module_names = False # Remove namespaces from class/method signatures
+autoclass_content = "both" # Both the class’ and the __init__ method’s docstring are concatenated
+autodoc_class_signature = "separated"
+autodoc_default_options = {
+ "special-members": "__init__",
+ "show-inheritance": True,
+}
+autodoc_member_order = "bysource"
+autodoc_typehints_format = "short"
+
+always_document_param_types = True
+typehints_defaults = "comma"
+
+auto_pytabs_min_version = (3, 7)
+auto_pytabs_max_version = (3, 11)
+
+autosectionlabel_prefix_document = True
+
+suppress_warnings = ["autosectionlabel.*"]
+
+html_theme = "pydata_sphinx_theme"
+html_static_path = ["_static"]
+html_css_files = ["style.css"]
+html_js_files = ["versioning.js"]
+html_favicon = "images/favicon.ico"
+html_logo = "images/logo.svg"
+html_show_sourcelink = False
+html_sidebars = {"about/*": []}
+html_title = f"{project} Framework"
+
+html_theme_options = {
+ "use_edit_page_button": False,
+ "show_toc_level": 4,
+ "navbar_align": "left",
+ "icon_links": [
+ {
+ "name": "Source",
+ "url": __config["tool"]["poetry"]["repository"],
+ "icon": f"fa-brands fa-{'github' if 'github' in __config['tool']['poetry']['repository'] else 'gitlab'}",
+ "type": "fontawesome",
+ },
+ ],
+ "navbar_end": ["navbar-icon-links"],
+ "navbar_persistent": ["search-button", "theme-switcher"],
+}
+
+html_context = {
+ "navbar_items": {
+ "Documentation": "lib/index",
+ "Community": {
+ "Contribution guide": "community/index",
+ },
+ "About": "about/index",
+ }
+}
diff --git a/docs/cookiecutter_input.json b/docs/cookiecutter_input.json
new file mode 100644
index 0000000000000000000000000000000000000000..6ba957deb75057490469eb920cc34cb4cca77974
--- /dev/null
+++ b/docs/cookiecutter_input.json
@@ -0,0 +1,20 @@
+{
+ "_output_dir": "/mnt/data/git/rna/.git/cookiecutter",
+ "_template": "https://gitlab.com/dboe/dough.git",
+ "author": "Daniel B\u00f6ckenhoff",
+ "continuous_integration": "y",
+ "copyright_holder": "Daniel B\u00f6ckenhoff",
+ "copyright_license": "MIT License",
+ "data_science": "n",
+ "distribution_name": "rna",
+ "email": "dboe@ipp.mpg.de",
+ "keywords": "plotting, matplotlib, pyqtgraph, backend, logging, path, argparse",
+ "package_name": "rna",
+ "package_version": "0.7.11",
+ "pypi_username": "dboe",
+ "remote_namespace": "dboe",
+ "remote_provider": "gitlab.mpcdf.mpg.de",
+ "remote_username": "dboe",
+ "summary": "Basic and essential code building blocks of all pythons"
+}
+
diff --git a/docs/images/favicon.ico b/docs/images/favicon.ico
new file mode 100644
index 0000000000000000000000000000000000000000..e0482a1bebb6c86187c50d00045e5ed9e1316b58
Binary files /dev/null and b/docs/images/favicon.ico differ
diff --git a/docs/images/logo.svg b/docs/images/logo.svg
new file mode 100644
index 0000000000000000000000000000000000000000..8e8ae8a9db12740245deaac106eadb7037d78179
--- /dev/null
+++ b/docs/images/logo.svg
@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24" width="24" height="24"><path fill="none" d="M0 0h24v24H0z"/><path d="M13 21v2.5l-3-2-3 2V21h-.5A3.5 3.5 0 0 1 3 17.5V5a3 3 0 0 1 3-3h14a1 1 0 0 1 1 1v17a1 1 0 0 1-1 1h-7zm-6-2v-2h6v2h6v-3H6.5a1.5 1.5 0 0 0 0 3H7zM7 5v2h2V5H7zm0 3v2h2V8H7zm0 3v2h2v-2H7z"/></svg>
\ No newline at end of file
diff --git a/docs/index.rst b/docs/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..26fc81f8d013d8062ebbdde2b80368c0b2d54a4c
--- /dev/null
+++ b/docs/index.rst
@@ -0,0 +1,74 @@
+.. div:: sd-text-center sd-text-primary sd-fs-1 sd-font-weight-bolder -sd-text-nowra
+
+ rna
+
+.. card::
+ :text-align: center
+ :shadow: none
+ :class-card: sd-border-0
+
+ .. include:: ../README.rst
+ :start-after: [shields-start]
+ :end-before: [shields-end]
+
+.. grid:: 1 1 2 2
+ :gutter: 1
+
+ .. grid-item::
+
+ .. grid:: 1 1 1 1
+ :gutter: 1
+
+ .. grid-item-card:: Overview
+ :link: lib/overview/index
+ :link-type: doc
+
+ .. include:: ../README.rst
+ :start-after: [overview-start]
+ :end-before: [overview-end]
+
+ .. grid-item-card:: Installation
+ :link: lib/installation/index
+ :link-type: doc
+
+ .. include:: lib/installation/index.rst
+ :start-after: [essence-start]
+ :end-before: [essence-end]
+
+ .. grid-item::
+
+ .. grid:: 1 1 1 1
+ :gutter: 1
+
+ .. grid-item-card:: Usage
+ :link: lib/usage/index
+ :link-type: doc
+
+ .. include:: lib/usage/index.rst
+ :start-after: [essence-start]
+ :end-before: [essence-end]
+
+ .. grid-item-card:: API reference
+ :link: lib/reference/index
+ :link-type: doc
+ :text-align: center
+
+ :octicon:`codescan;5em;sd-text-info`
+
+ .. grid-item-card:: API development
+ :link: community/index
+ :link-type: doc
+
+
+ .. code-block:: shell
+
+ make install
+ make test
+ make publish
+
+.. toctree::
+ :hidden:
+
+ about/index
+ community/index
+ lib/index
diff --git a/docs/lib/index.rst b/docs/lib/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..a05b601dac2bcae281461632068a79db1cd7b321
--- /dev/null
+++ b/docs/lib/index.rst
@@ -0,0 +1,17 @@
+Library documentation
+=====================
+
+.. include:: overview/index.rst
+.. include:: installation/index.rst
+.. include:: usage/index.rst
+.. include:: reference/index.rst
+
+.. toctree::
+ :caption: Documentation
+ :hidden:
+ :maxdepth: 2
+
+ overview/index
+ installation/index
+ usage/index
+ reference/index
\ No newline at end of file
diff --git a/docs/lib/installation/index.rst b/docs/lib/installation/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..d280c1004f6147fdeb854cf6ac128c1aad39a430
--- /dev/null
+++ b/docs/lib/installation/index.rst
@@ -0,0 +1,70 @@
+============
+Installation
+============
+..
+ How to get it and set it up?
+ [installation]
+
+To install rna, you have the following options:
+
+.. tab-set::
+
+ .. tab-item:: PyPi :octicon:`package`
+
+ The preferred method to install rna is to get the most recent stable release from PyPi:
+
+ ..
+ [essence-start]
+
+ .. code-block:: shell
+
+ pip install rna
+
+ ..
+ [essence-end]
+
+ If you don't have `pip`_ installed, this `Python installation guide`_ can guide you through the process.
+
+ .. _pip: https://pip.pypa.io
+ .. _Python installation guide: http://docs.python-guide.org/en/latest/starting/installation/
+
+ .. dropdown:: Extras
+ :icon: star
+
+ Install a special extra:
+ :code:`pip install rna[extra]`
+
+ All extras:
+ :code:`pip install rna[full]`
+
+ .. tab-item:: Source :octicon:`code`
+
+ First you have to retrieve the source code of rna.
+ You have the following options:
+
+ .. tab-set::
+
+ .. tab-item:: Git :octicon:`git-branch`
+
+ To clone the public repository run
+
+ .. code-block:: shell
+
+ $ git clone git://gitlab.mpcdf.mpg.de/dboe/rna
+
+ .. tab-item:: Tarball :octicon:`gift`
+
+ Either download the tarball `here <https://gitlab.mpcdf.mpg.de/dboe/rna/tarball/master>`_ or run
+
+ .. code-block:: shell
+
+ $ curl -OJL https://gitlab.mpcdf.mpg.de/dboe/rna/tarball/master
+
+
+ Once you have a copy of the source, navigate inside and install it with:
+
+ .. code-block:: shell
+
+ $ poetry install
+
+
diff --git a/docs/lib/overview/index.rst b/docs/lib/overview/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..12114824fda68dc764ad18c14ccd04e4fce44c14
--- /dev/null
+++ b/docs/lib/overview/index.rst
@@ -0,0 +1,13 @@
+========
+Overview
+========
+..
+ What is it? Why should I use it?
+ [overview-start]
+
+.. include:: ../../../README.rst
+ :start-after: [overview-start]
+ :end-before: [overview-end]
+
+..
+ [overview-end]
diff --git a/docs/lib/reference/index.rst b/docs/lib/reference/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..ce3a9726d144e83b0c08a6bf70513810c0c24f1e
--- /dev/null
+++ b/docs/lib/reference/index.rst
@@ -0,0 +1,13 @@
+=============
+API reference
+=============
+..
+ How to dive deeper? Give me the api?
+ [reference]
+
+.. autosummary::
+:toctree: _autosummary
+:template: custom-module-template.rst
+:recursive:
+
+.. automodule: rna
diff --git a/docs/lib/usage/index.rst b/docs/lib/usage/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..391c7386466d9e691f822bec13be2050827ff9d1
--- /dev/null
+++ b/docs/lib/usage/index.rst
@@ -0,0 +1,18 @@
+=====
+Usage
+=====
+..
+ How to use? Give me a primer.
+ [usage]
+
+..
+ [essence-start]
+
+To use rna in a project use
+
+.. code-block:: python
+
+ import rna
+
+..
+ [essence-end]
diff --git a/environment.yml b/environment.yml
new file mode 100644
index 0000000000000000000000000000000000000000..0234dc7c7b93212f16707b364bb26ddc316d1722
--- /dev/null
+++ b/environment.yml
@@ -0,0 +1,19 @@
+name: rna
+channels:
+ - conda-forge
+ # We want to have a reproducible setup, so we don't want default channels,
+ # which may be different for different users. All required channels should
+ # be listed explicitly here.
+ - nodefaults
+dependencies:
+ - python=3.10.* # or don't specify the version and use the latest stable Python
+ - mamba
+ - pip >=21.2 # pip must be mentioned explicitly, or conda-lock will fail
+ - pip:
+ - "poetry>=1.2.0a2"
+ - "conda-lock"
+ # - "pyyaml"
+
+plugins:
+ poetry:
+ - "poetry_bumpversion" # this is a field that is not defined by poetry but by dough
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000000000000000000000000000000000000..c5a72d7f892cc382b74eaca3b611e2dfae606ded
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,99 @@
+[tool.poetry]
+name = "rna"
+version = "0.7.11"
+description = "Basic and essential code building blocks of all pythons"
+authors = ["Daniel Böckenhoff <dboe@ipp.mpg.de>"]
+license = "MIT License"
+readme = "README.rst"
+repository = "https://gitlab.mpcdf.mpg.de/dboe/rna"
+documentation = "https://rna.readthedocs.io"
+classifiers = [
+ # find the full list of possible classifiers at https://pypi.org/classifiers/
+ "Development Status :: 3 - Alpha",
+ "License :: OSI Approved :: MIT License",
+ "Programming Language :: Python",
+ "Programming Language :: Python :: 3",
+ "Programming Language :: Python :: 3.5",
+ "Programming Language :: Python :: 3.6",
+ "Programming Language :: Python :: 3.7",
+ "Programming Language :: Python :: 3.8",
+ "Programming Language :: Python :: 3.9",
+ "Programming Language :: Python :: 3.10",
+]
+keywords = ["plotting", " matplotlib", " pyqtgraph", " backend", " logging", " path", " argparse"]
+
+[tool.poetry.dependencies]
+python = "^3.7"
+pathlib = { version = "*", python = "<3.10" }
+
+[tool.poetry.group.docs]
+optional = true
+
+[tool.poetry.group.docs.dependencies]
+black = "^22.12.0"
+httpx = "^0.23.2"
+uvicorn = "^0.20.0"
+sphinx-autobuild = "^2021.3.14"
+"sphinx-autopackagesummary" = "^1.3"
+sphinx-design = "^0.3.0"
+sphinx = "^5.3.0"
+sphinx-toolbox = "^3.2.0"
+sphinx-copybutton = "^0.5.1"
+sphinxcontrib-mermaid = "^0.7.1"
+pydata-sphinx-theme = "^0.12.0"
+sphinx-autodoc-typehints = "^1.22"
+
+[tool.poetry.group.dev.dependencies]
+ensureconda = "*" # is part of conda-lock either way
+conda-lock = "*"
+tomli = { version = ">=1.1.0", python = "<3.11" }
+pytest = "*"
+pytest-cov = "*"
+pytest-shutil = "*"
+pytest-virtualenv = "*"
+pytest-fixture-config = "*"
+pytest-xdist = "*"
+coverage = { version = "*", extras = ["toml"]}
+pylint = "*"
+flake8 = "*"
+ipdb = "*"
+mypy = "*"
+twine = "*" # for publishing
+pre-commit = "*" # https://pre-commit.com/ for hook managment
+pre-commit-hooks = "*"
+sphinx = "*" # for documentation
+cookiecutter_project_upgrader = "*"
+
+[tool.poetry.extras]
+config = ["hydra_core"]
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.coverage.report]
+show_missing = true
+exclude_lines = [
+ "pragma: no cover",
+ "if False",
+]
+
+[tool.poetry_bumpversion.file."your_package/__init__.py"]
+search = "__version__ = '{current_version}'"
+
+[tool.poetry_bumpversion.file."docs/cookiecutter_input.json"]
+search = "'package_version': '{current_version}'"
+
+[tool.pytest.ini_options]
+addopts = "--doctest-modules --ignore=env --ignore=envs --ignore=docs"
+junit_family = "xunit2"
+
+[tool.tox]
+isolated_build = true
+skip_missing_interpreters = true
+envlist = "py{35,36,37,38,39,310}"
+recreate = true
+
+[testenv]
+deps = ["pytest"]
+commands = ["pytest --import-mode importlib"]
diff --git a/rna/__init__.py b/rna/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..5b6b21b7cbfb628c6d3659f7ba346ed425daafac
--- /dev/null
+++ b/rna/__init__.py
@@ -0,0 +1,5 @@
+"""Top-level package of rna."""
+
+__author__ = """Daniel Böckenhoff"""
+__email__ = "dboe@ipp.mpg.de"
+__version__ = "0.7.11"
diff --git a/rna/__main__.py b/rna/__main__.py
new file mode 100644
index 0000000000000000000000000000000000000000..2acb97e947d01dfa561c192461beb9b2a4d8f642
--- /dev/null
+++ b/rna/__main__.py
@@ -0,0 +1,71 @@
+#!/user/bin/env python
+"""
+w7x option starter
+"""
+import sys
+import argparse
+import rna
+
+
+class SomeAction(argparse.Action):
+ """Some actions."""
+
+ def __init__(self, option_strings, dest, nargs=None, **kwargs):
+ if nargs is not None:
+ raise ValueError("nargs not allowed")
+ super().__init__(option_strings, dest, **kwargs)
+
+ def __call__(self, parser, namespace, values, option_string=None):
+ print(
+ f"Example action invoked by manage in namespace: {namespace} with values {values}"
+ " and option string {option_string}."
+ )
+ setattr(namespace, self.dest, values)
+
+ def showcase_dummy(self):
+ """
+ You can define a method to expose functionality of the class
+ """
+ print(self)
+
+
+def manage(args_):
+ """Example function."""
+ print("Managing!")
+ print(args_.x * args_.y)
+
+
+def parse_args(args_):
+ """Parse args."""
+ # create the top-level parser
+ parser = argparse.ArgumentParser(prog="rna app")
+ parser.add_argument(
+ "--version",
+ action="version",
+ version="v" + rna.__version__,
+ help="Show program's version number and exit",
+ )
+ parser = argparse.ArgumentParser(prog="rna app")
+
+ # subparsers
+ subparsers = parser.add_subparsers(help="sub-command help")
+
+ # create the parser for the "test" command
+ example_sub_parser = subparsers.add_parser("manage", help="manage something")
+ example_sub_parser.add_argument("-x", type=int, default=1)
+ example_sub_parser.add_argument("-y", type=float, default=42.0)
+ example_sub_parser.set_defaults(func=manage)
+
+ # If no arguments were used, print base-level help with possible commands.
+ if len(args_) == 0:
+ parser.print_help(file=sys.stderr)
+ sys.exit(1)
+
+ args_ = parser.parse_args(args_)
+ # let argparse do the job of calling the appropriate function after
+ # argument parsing is complete
+ return args_.func(args_)
+
+
+if __name__ == "__main__":
+ _ = parse_args(sys.argv[1:])
diff --git a/tests/.gitkeep b/tests/.gitkeep
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/tests/__init__.py b/tests/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..9fa65bb13a89d7cf3a41ffb6a7a95839bdf50164
--- /dev/null
+++ b/tests/__init__.py
@@ -0,0 +1 @@
+"""Unit test package for rna."""
diff --git a/tests/test_package.py b/tests/test_package.py
new file mode 100644
index 0000000000000000000000000000000000000000..f01fc7889744d44414388508dc463f20eabb5dc7
--- /dev/null
+++ b/tests/test_package.py
@@ -0,0 +1,21 @@
+#!/usr/bin/env python
+
+"""Tests for `rna` package."""
+
+import unittest
+import rna
+
+
+class TestPackage(unittest.TestCase):
+ """Tests for `rna` package."""
+
+ def setUp(self):
+ """Set up test fixtures, if any."""
+
+ def tearDown(self):
+ """Tear down test fixtures, if any."""
+
+ def test_version_type(self):
+ """Assure that version type is str."""
+
+ self.assertIsInstance(rna.__version__, str)
diff --git a/tools/Makefile.envs b/tools/Makefile.envs
new file mode 100644
index 0000000000000000000000000000000000000000..eff63f607b32289d155608cec8d4e079467ae897
--- /dev/null
+++ b/tools/Makefile.envs
@@ -0,0 +1,66 @@
+# Environment Management Makefile, adapted from https://github.com/hackalog/make_better_defaults
+#
+include tools/Makefile.include
+
+$(ENVLOCKFILE): environment.yml
+ifeq (conda, $(VIRTUALENV))
+ python -c "import tools; tools.env.create()"
+else
+ @printf $(_ERROR) "env" "Unsupported Environment `$(VIRTUALENV)`. Use conda." ;
+ @exit 1
+endif
+
+.PHONY: env_create
+## Set up virtual (conda) environment for this project
+env_create: $(ENVLOCKFILE)
+ifeq (conda,$(VIRTUALENV))
+ @rm -f $(ENVLOCKFILE)
+ @echo
+ @printf $(_INFO) "env" "New conda env created. Activate with:" ;
+ @echo ">>> conda activate $(ENVDIR)"
+ @echo ">>> make env_update"
+else
+ @printf $(_ERROR) "env" "Unsupported Environment `$(VIRTUALENV)`. Use conda." ;
+ @exit 1
+endif
+
+.PHONY: env_delete
+## Delete the virtual (conda) environment for this project
+env_delete:
+ifeq (conda,$(VIRTUALENV))
+ @printf $(_WARN) "env" "Deleting conda environment."
+ $(CONDA_EXE) env remove -p $(ENVDIR)
+ rm -f $(ENVLOCKFILE)
+else
+ @printf $(_ERROR) "env" "Unsupported Environment `$(VIRTUALENV)`. Use conda." ;
+ @exit 1
+endif
+
+.PHONY: env_update
+## Install or update Python Dependencies in the virtual (conda) environment
+env_update: env_enabled $(ENVLOCKFILE)
+
+.PHONY: env_enabled
+# Checktrues that the conda environment is active
+env_enabled:
+ifeq (conda,$(VIRTUALENV))
+ifneq (true,$(ENVACTIVE))
+ @printf $(_ERROR) "env" "Run `$(VIRTUALENV) activate $(ENVDIR)` before proceeding." ;
+ @exit 1
+endif
+else
+ @printf $(_ERROR) "env" "Unsupported Environment `$(VIRTUALENV)`. Use conda" ;
+ @exit 1
+endif
+
+.PHONY: check_lockfile
+# Test that an environment lockfile exists
+check_lockfile:
+ifeq (X,X$(wildcard $(ENVLOCKFILE)))
+ @printf $(_ERROR) "env" "Run `make env_update` before proceeding..." ;
+ @exit 1
+endif
+
+.PHONY: env
+## Check if environment is enabled and correctly configured
+env: env_enabled check_lockfile $(ENVLOCKFILE)
\ No newline at end of file
diff --git a/tools/Makefile.include b/tools/Makefile.include
new file mode 100644
index 0000000000000000000000000000000000000000..0dea8a8517dc0dc95a43688f1fbb84446e4c18ab
--- /dev/null
+++ b/tools/Makefile.include
@@ -0,0 +1,53 @@
+SHELL := /bin/bash# Use bash syntax
+CURRENT_PATH := $(shell pwd -P)
+MODULE := $(shell basename "$(CURRENT_PATH)")
+VERSION := $(shell python -c "import sys; import $(MODULE); sys.stdout.write($(MODULE).__version__)")
+SOURCES := $(shell find $(MODULE) -name '*.py')
+DOCUMENTATION := $(shell find . -name '*.rst')
+SPHINXSOURCEDIR = ./docs
+SPHINXBUILDDIR = docs/_build
+GITSTATUS = $(shell git status --porcelain)
+DEBUG_FILE := debug.txt
+MODULE_NAME := my_project
+PROJECT_DIR := $(shell dirname $(realpath $(lastword $(MAKEFILE_LIST))))
+PYTHON_INTERPRETER := python3
+ARCH := $(shell $(PYTHON_INTERPRETER) -c "import platform; print(platform.platform())")
+VIRTUALENV := conda
+ENVLOCKFILE := conda-linux-64.lock # conda-$(ARCH).lock ??? how to make compatible with conda-lock
+ENVDIR = $(CURRENT_PATH)/env
+ENVACTIVE = false
+ifeq (${CONDA_DEFAULT_ENV}, $(ENVDIR))
+ ENVACTIVE = true
+endif
+CONDA_EXE := $(shell which mamba)
+ifeq (,$(CONDA_EXE))
+ CONDA_EXE := $(shell which conda)
+endif
+CONDA_RUN :=
+ifneq (true,$(ENVACTIVE))
+ CONDA_RUN := conda run -p $(ENVDIR)
+endif
+
+# OPTIONS
+part ?= patch
+
+# The CI environment variable can be set to a non-empty string,
+# it'll bypass this command that will "return true", as a "yes" answer.
+# To use the "confirm" target inside another target,
+# use the " if $(MAKE) -s confirm ; " syntax.
+confirm:
+ @if [[ -z "$(CI)" ]]; then \
+ REPLY="" ; \
+ read -p "⚠ Are you sure? [y/n] > " -r ; \
+ if [[ ! $$REPLY =~ ^[Yy]$$ ]]; then \
+ printf $(_ERROR) "KO" "Stopping" ; \
+ exit 1 ; \
+ else \
+ printf $(_INFO) "OK" "Continuing" ; \
+ exit 0; \
+ fi \
+ fi
+.PHONY: confirm
+_WARN := "\033[33m[%s]\033[0m %s\n" # Yellow text for "printf"
+_INFO := "\033[32m[%s]\033[0m %s\n" # Green text for "printf"
+_ERROR := "\033[31m[%s]\033[0m %s\n" # Red text for "printf"
diff --git a/tools/__init__.py b/tools/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..1d8baba7c8a7f089bae6a6b86366d45c5ad4d0a2
--- /dev/null
+++ b/tools/__init__.py
@@ -0,0 +1,2 @@
+from . import process
+from . import env
diff --git a/tools/env.py b/tools/env.py
new file mode 100644
index 0000000000000000000000000000000000000000..7c04446543c50946a5d1b2e2d9909a2c6923a851
--- /dev/null
+++ b/tools/env.py
@@ -0,0 +1,79 @@
+import shutil
+from .process import run_shell_command
+import tempfile
+import os
+from ensureconda.resolve import platform_subdir
+
+
+TMPDIR = tempfile.gettempdir()
+BOOTSTRAPDIR = os.path.join(TMPDIR, "bootstrap")
+PROJECT_DIR = os.path.abspath(os.path.join(__file__, "../.."))
+ENVIRONMENT_YAML = "environment.yml"
+ENVIRONMENT_YAML_PATH = os.path.join(PROJECT_DIR, ENVIRONMENT_YAML)
+POETRY_LOCK = "poetry.lock"
+CONDA_LOCK = f"conda-{platform_subdir()}.lock"
+
+
+def load():
+ import yaml
+ from yaml.loader import SafeLoader
+
+ # Open the file and load the file
+ with open(ENVIRONMENT_YAML_PATH) as f:
+ data = yaml.load(f, Loader=SafeLoader)
+ return data
+
+
+def install(conda_run=""):
+ run_shell_command(f"{conda_run}poetry install")
+ run_shell_command(f"{conda_run}pre-commit install")
+
+
+def update(conda_run=""):
+ # Re-generate Conda lock file(s) based on environment.yml
+ run_shell_command(f"{conda_run}conda-lock -k explicit --conda mamba")
+ # Update Conda packages based on re-generated lock file
+ run_shell_command(f"mamba update --file {CONDA_LOCK}")
+ # Update Poetry packages and re-generate poetry.lock
+ run_shell_command(f"{conda_run}poetry update")
+
+
+def create(name="env"):
+ """
+ This create routine was initially influenced by
+ https://stackoverflow.com/questions/70851048/does-it-make-sense-to-use-conda-poetry
+ """
+ env_dir = os.path.join(PROJECT_DIR, name)
+
+ if os.path.isfile(os.path.join(env_dir, POETRY_LOCK)):
+ run_shell_command(f"conda create -p {env_dir} --file {CONDA_LOCK}")
+ install()
+
+ requirements_here = ["poetry", "mamba", "conda-lock"]
+ requirements_not_satisfied = any(
+ [shutil.which(name) is None for name in requirements_here]
+ )
+
+ run = ""
+ if requirements_not_satisfied:
+ # Use (and if necessary create) a bootstrap env
+ if not os.path.exists(BOOTSTRAPDIR):
+ run_shell_command(
+ f"conda create --yes -p {BOOTSTRAPDIR} -c conda-forge "
+ + " ".join(requirements_here)
+ )
+ run = f"conda run -p {BOOTSTRAPDIR} "
+
+ # Create conda lock file(s) from environment.yml
+ run_shell_command(f"{run}conda-lock -k explicit --conda mamba")
+ # Add conda-lock (and other packages, as needed) to pyproject.toml and poetry.lock
+
+ run_shell_command(f"{run}mamba env create -f {ENVIRONMENT_YAML} -p {env_dir}")
+ run = f"conda run -p {env_dir} "
+
+ install(conda_run=run)
+
+ # Add conda and poetry lock files
+ run_shell_command("git add *.lock")
+
+ run_shell_command("git commit -m 'lock-files'")
diff --git a/tools/process.py b/tools/process.py
new file mode 100644
index 0000000000000000000000000000000000000000..d911e4a55aeb893b7e43be550086c18acc93db76
--- /dev/null
+++ b/tools/process.py
@@ -0,0 +1,6 @@
+import subprocess
+
+def run_shell_command(command_line, *args, **kwargs):
+ command_line_args = command_line.split(" ")
+ print(f"Run command '{command_line}'")
+ subprocess.call(command_line_args, *args, **kwargs)