Create basic repository structure

.gitignore

+*.pyc
+*.log
+*.pkl
+*.egg-info
+Pipfile
+Pipfile.lock
+.idea
+
+__pycache__
+.cache
+
+build
+dist
+env
+
+obmml/__version__.py
+_build

.gitlab-ci.yml

+image: python:buster
+
+# Make pip cache the installed dependencies
+variables:
+  PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip"
+cache:
+  paths:
+    - .cache/pip
+    - venv/
+
+.before_script: &test-before-script
+  before_script:
+    - python3 -V
+    - pip3 install virtualenv
+    - virtualenv venv
+    - source venv/bin/activate
+    - pip3 install flake8 pylint black codespell
+
+stages:
+  - tests
+  - deploy
+
+linters:
+  <<: *test-before-script
+
+  stage: tests
+  script:
+    - make check
+
+docs:
+  <<: *test-before-script
+
+  interruptible: true
+  stage: tests
+  script:
+    - pip3 install sphinx sphinx_rtd_theme sphinx_mdinclude
+    - make -C gdedocs html
+  artifacts:
+    paths:
+      - gdedocs/_build
+      - temp/
+    expire_in: "600"
+
+deploy:
+  stage: deploy
+  before_script:
+    - 'command -v ssh-agent >/dev/null || ( apt-get update -y && apt-get install openssh-client -y )'
+    - eval $(ssh-agent -s)
+    - echo "$SSH_DEPLOY_KEY" | tr -d '\r' | ssh-add -
+    - mkdir -p ~/.ssh
+    - chmod 700 ~/.ssh
+  variables:
+    SSH_ARGS: "-o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null"
+    GIT_STRATEGY: none
+  script:
+    - ssh ${SSH_ARGS} -p 54646 $DOCS_USER@$DOCS_HOST "setopt +o nomatch;rm -rf /home/docs/gde/**"
+    - scp ${SSH_ARGS} -P 54646 -r gdedocs/_build/html/* $DOCS_USER@$DOCS_HOST:/home/docs/gde
+    - scp ${SSH_ARGS} -P 54646 temp/index.html $DOCS_USER@$DOCS_HOST:/home/docs
+  only:
+    - tags

Makefile

+SOURCES=gdedocs
+LENGTH=96
+
+check: $(SOURCES)
+	flake8 --max-line-length=$(LENGTH) --ignore=E203,W503 $^
+	black --check --line-length $(LENGTH) $^
+	pylint -E $^
+	codespell README.md $^
+
+format: $(SOURCES)
+	black --line-length $(LENGTH) $^

README.md

 # gde-docs
 
+This is the main documentation of the Global Dynamic Exposure model. It can be found on [docs.dynamicexposure.org](http://rabotnik.docs.dynamicexposure.org/)
 
+## Copyright and copyleft 
 
-## Getting started
+Copyright (C) 2024
 
-To make it easy for you to get started with GitLab, here's a list of recommended next steps.
+* Helmholtz-Zentrum Potsdam Deutsches GeoForschungsZentrum GFZ
 
-Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
+This program is free software: you can redistribute it and/or modify it
+under the terms of the GNU Affero General Public License as published by
+the Free Software Foundation, either version 3 of the License, or (at
+your option) any later version.
 
-## Add your files
+This program is distributed in the hope that it will be useful, but
+WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero
+General Public License for more details.
 
-- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files
-- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command:
+You should have received a copy of the GNU Affero General Public License
+along with this program. If not, see http://www.gnu.org/licenses/.
 
-```
-cd existing_repo
-git remote add origin https://git.gfz-potsdam.de/globaldynamicexposure/gde-docs.git
-git branch -M main
-git push -uf origin main
-```
+Also add information on how to contact you by electronic and paper mail.
 
-## Integrate with your tools
+If your software can interact with users remotely through a computer
+network, you should also make sure that it provides a way for users to
+get its source. For example, if your program is a web application, its
+interface could display a "Source" link that leads users to an archive
+of the code. There are many ways you could offer source, and different
+solutions will be better for different programs; see section 13 for the
+specific requirements.
 
-- [ ] [Set up project integrations](https://git.gfz-potsdam.de/globaldynamicexposure/gde-docs/-/settings/integrations)
-
-## Collaborate with your team
-
-- [ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/)
-- [ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)
-- [ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically)
-- [ ] [Enable merge request approvals](https://docs.gitlab.com/ee/user/project/merge_requests/approvals/)
-- [ ] [Set auto-merge](https://docs.gitlab.com/ee/user/project/merge_requests/merge_when_pipeline_succeeds.html)
-
-## Test and Deploy
-
-Use the built-in continuous integration in GitLab.
-
-- [ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html)
-- [ ] [Analyze your code for known vulnerabilities with Static Application Security Testing (SAST)](https://docs.gitlab.com/ee/user/application_security/sast/)
-- [ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html)
-- [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/)
-- [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html)
-
-***
-
-# Editing this README
-
-When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thanks to [makeareadme.com](https://www.makeareadme.com/) for this template.
-
-## Suggestions for a good README
-
-Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
-
-## Name
-Choose a self-explaining name for your project.
-
-## Description
-Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors.
-
-## Badges
-On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge.
-
-## Visuals
-Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method.
-
-## Installation
-Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection.
-
-## Usage
-Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README.
-
-## Support
-Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc.
-
-## Roadmap
-If you have ideas for releases in the future, it is a good idea to list them in the README.
-
-## Contributing
-State if you are open to contributions and what your requirements are for accepting them.
-
-For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self.
-
-You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.
-
-## Authors and acknowledgment
-Show your appreciation to those who have contributed to the project.
-
-## License
-For open source projects, say how it is licensed.
-
-## Project status
-If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers.
+See the [LICENSE](./LICENSE) for the full license text.

gdedocs/Makefile

+# Copyright (C) 2024:
+#   Helmholtz-Zentrum Potsdam Deutsches GeoForschungsZentrum GFZ
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or (at
+# your option) any later version.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero
+# General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see http://www.gnu.org/licenses/.
+
+
+# Minimal makefile for Sphinx documentation
+
+# You can set these variables from the command line.
+SPHINXOPTS  =
+SPHINXBUILD = sphinx-build
+SPHINXPROJ  = gdedocs
+SOURCEDIR   = .
+BUILDDIR    = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+livehtml:
+	sphinx-autobuild -b html $(SOURCEDIR) $(ALLSPHINXOPTS) $(BUILDDIR)/html
+
+clean:
+	rm -rf $(BUILDDIR)/*
+	rm -rf auto_examples/
+
+.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 $(SPHINXOPTS).
+# The code is autogenerated by `sphinx-quickstart`
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

gdedocs/_templates/footer.html

+<!--Copyright (C) 2024:-->
+<!--  Helmholtz-Zentrum Potsdam Deutsches GeoForschungsZentrum GFZ-->
+
+<!--This program is free software: you can redistribute it and/or modify it-->
+<!--under the terms of the GNU Affero General Public License as published by-->
+<!--the Free Software Foundation, either version 3 of the License, or (at-->
+<!--your option) any later version.-->
+
+<!--This program is distributed in the hope that it will be useful, but-->
+<!--WITHOUT ANY WARRANTY; without even the implied warranty of-->
+<!--MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero-->
+<!--General Public License for more details.-->
+
+<!--You should have received a copy of the GNU Affero General Public License-->
+<!--along with this program. If not, see http://www.gnu.org/licenses/.-->
+
+
+{% extends "!footer.html" %}
+{% block extrafooter %}
+{{ super() }}
+&#169; 2024, Helmholtz-Zentrum Potsdam Deutsches GeoForschungsZentrum GFZ.
+<a rel="license" href="https://www.gnu.org/licenses/agpl-3.0.en.html"></a><br />This work is licensed under the <a rel="license" href="https://www.gnu.org/licenses/agpl-3.0.en.html">GNU Affero General Public License</a>.
+{% endblock %}

gdedocs/conf.py

+#!/usr/bin/env python3
+
+# Copyright (C) 2024:
+#   Helmholtz-Zentrum Potsdam Deutsches GeoForschungsZentrum GFZ
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or (at
+# your option) any later version.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero
+# General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see http://www.gnu.org/licenses/.
+
+
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# Project information:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "Documentation of the Global Dynamic Exposure Model"
+copyright = "AGPLv3+"
+author = "Oostwegel, L.J.N."
+release = "1.0"
+
+
+# General configuration:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
+    "sphinx_rtd_theme",
+    "sphinx_mdinclude",
+]
+
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+autosummary_generate = True
+autodoc_member_order = "bysource"
+autodoc_default_options = {
+    "members": True,
+    "show-inheritance": True,
+}
+
+
+# Options for HTML output:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "sphinx_rtd_theme"
+html_static_path = ["_static"]
+html_show_copyright = False
+html_show_sphinx = False
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = "default"

gdedocs/index.rst

+Welcome to Global Dynamic Exposure Model documentation!
+=======================================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+Exposure Library
+----------------
+.. raw:: html
+
+    <a href="../exposurelib/">Documentation to the Exposure library</a>
+
+
+Rabotnik
+--------
+.. raw:: html
+
+    <a href="../rabotnik/">Documentation to Rabotnik</a>
+
+
+OBM-ML
+--------
+.. raw:: html
+
+    <a href="../obmml/">Documentation to OBM-ML</a>
+
+
+Fork this project
+==================
+
+* https://git.gfz-potsdam.de/globaldynamicexposure/gde-docs