urgap 3.3.5__tar.gz

urgap-3.3.5/.dockerignore

@@ -0,0 +1,5 @@
+example_scripts
+.github
+.cicd
+docs
+.vscode

urgap-3.3.5/.github/workflows/docs.yaml

@@ -0,0 +1,57 @@
+name: Deploy Docs to GitHub Pages
+
+on:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: pages
+  cancel-in-progress: false
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # needed for versioningit
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install pandoc
+        run: sudo apt-get install -y pandoc
+
+      - name: Install package with docs dependencies
+        run: pip install ".[docs,cloud]"
+
+      - name: Build Sphinx docs
+        working-directory: docs
+        run: |
+          python parse_example_scripts.py
+          python parse_third_party.py
+          sphinx-build -b html source build/html
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs/build/html
+
+  deploy:
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

urgap-3.3.5/.github/workflows/gh-pages.yaml

@@ -0,0 +1,24 @@
+# t
+# test
+# For reference: https://github.com/JamesIves/github-pages-deploy-action
+name: Deploy Sphinx docu to Pages.
+on:
+  release:
+    types: [published]
+permissions:
+  contents: write
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Install and Build HTML
+        run: |
+          pip install --upgrade pip
+          pip install ./"[docs, cloud]"
+          cd docs && make sphinx-html
+      - name: Deploy HTML
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          folder: docs/build/html # The folder the action should deploy.

urgap-3.3.5/.github/workflows/main.yaml

@@ -0,0 +1,87 @@
+name: Run tests
+on:
+  push:
+    branches:
+      - dev
+      - main
+  pull_request:
+    branches:
+      - dev
+      - main
+jobs:
+  code-quality:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.13'
+      - name: Install tools
+        run: |
+          pip install ruff
+          npm install -g prettier
+          go install github.com/google/yamlfmt/cmd/yamlfmt@latest
+      - name: Run ruff
+        run: |
+          ruff check . --exclude urgap/wrappers,urgap/ext,urgap/uftypes.py,tests,docs,urgap/uctl/mcp
+      - name: Run yamlfmt
+        run: |
+          export PATH="$HOME/go/bin:$PATH"
+          yamlfmt -lint ./**/*.yaml
+      - name: Run prettier
+        run: |
+          prettier --tab-width 4 --check **/*.json
+      - name: Check for .yml files (should use .yaml)
+        run: |
+          echo "Searching for .yml files in the repository"
+          yml_files=$(find . -type f -name "*.yml")
+          if [ -n "$yml_files" ]; then
+            echo "Error: .yml files found. Please use .yaml extension instead:"
+            echo "$yml_files"
+            exit 1
+          else
+            echo "No .yml files found. All YAML files use .yaml extension."
+          fi
+  test-ubuntu:
+    runs-on: ubuntu-latest
+    needs: code-quality
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.13"
+      - name: Install dependencies
+        run: |
+          pip install uv
+          uv pip install pytest pytest-asyncio --system
+          uv pip install .["all"] --system
+      - name: Run unit tests
+        run: |
+          pytest tests/unittests
+      - name: Run integration tests
+        run: |
+          pytest tests/integrationtests
+#  test-windows:
+#    runs-on: windows-latest
+#    steps:
+#      - name: Checkout code
+#        uses: actions/checkout@v4
+#      - name: Set up Python
+#        uses: actions/setup-python@v5
+#        with:
+#          python-version: "3.13"
+#      - name: Install dependencies
+#        run: |
+#          pip install uv
+#          uv pip install pytest pytest-asyncio --system
+#          uv pip install .["all"] --system
+#      - name: Run unit tests
+#        run: |
+#          pytest tests/unittests
+#      - name: Run integration tests
+#        run: |
+#          pytest tests/integrationtests

urgap-3.3.5/.github/workflows/pypi.yaml

@@ -0,0 +1,27 @@
+name: Upload release to PyPI
+on:
+  push:
+    tags:
+      - v*
+permissions:
+  id-token: write
+  contents: read
+jobs:
+  pypi-publish:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.13
+      - name: Install build dependencies
+        run: pip install build
+      - name: Build package
+        run: python -m build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          attestations: false

urgap-3.3.5/.gitignore

@@ -0,0 +1,40 @@
+__pycache__/
+__notebooks__
+*.py[cod]
+.DS_Store
+# urgap/wrappers/GimmaSomeName/
+example_scripts/*.ujson
+example_scripts/*.txt
+docs/build/
+docs/source/code_inc
+docs/source/example_scripts.rst
+docs/source/tutorial/
+.eggs
+.idea
+.coverage
+urgap/.coverage
+urgap/version.txt
+urgap/_version.py
+.tox
+tests/integrationtests/test_t1.txt
+tests/integrationtests/test.txt.ujson
+tests/data/test_node_data/test.txt.ujson
+tests/data/**/*.ujson
+# tests/data/test_node_v*
+BSA1.canno
+BSA1.cnlcp
+BSA1.csarr
+BSA1.cseq
+BSA1.fasta.1.pepindex
+BSA1.fasta.2.pepindex
+BSA1.fasta.phr
+BSA1.fasta.pin
+BSA1.fasta.psq
+BSA1.mzML.ujson
+.vscode/
+_playground/
+_notebooks_/
+# BSA1_urgap_lookup.csv.bz2
+urgap.egg-info/
+/**/tmp
+.env

urgap-3.3.5/CONTRIBUTING.rst

@@ -0,0 +1,98 @@
+
+Contribution Guidelines
+#######################
+
+
+Summary
+*******
+
+In general, contribution to urgap is very welcome! Feel free to fork and/or clone
+urgap. If you want to improve code or contribute new features/tools/algorithms
+please read these guidelines first. If something is unclear please contact one
+of the authors for help or let us know via e.g. an issue.
+
+We are happy to include your name to the list of contributors in the `README`_.
+Drop a line to one of the developers if you want to get included (and of course
+you actually contributed something)
+
+.. _README:
+   https://github.com/urgap/urgap/blob/master/README.rst
+
+Commit messages
+***************
+
+First of all, please be concise and as descriptive (explicit is better than
+implicit :) ) as possible. It is always
+helpful to point out, which parts of urgap were changed/fixed (e.g.
+documentation or example scripts etc. ). At the same time, please avoid
+unnecessarily long messages.
+If possible, always use a headline in your commit message and list all changes as bullet points.
+
+
+Code standards and conventions
+******************************
+
+Since this a collaborative project, you will encounter different coding styles.
+Despite the fact that we know that diversity is beautiful, we need to keep some
+common line on how to code (This list may be further extended). We generally use
+black style (https://github.com/psf/black)
+Additionally this list will give you some things to think about:
+
+  | Re-think naming of variables at least twice
+  | Re-check deleting of own debug code before sending Pull requests
+  | Re-check own files created by nosetests and add it into '.gitignore' before sending Pull requests
+
+
+Test philosophy
+***************
+
+Test your code! Seriously, test you code! If you add new functionality or nodes
+at the same time provide (a) test function(s). We have already a set of tests
+and different files, which can be used for the test. Avoid adding new test files
+if possible to keep the repo small.
+
+
+Sphinx guide
+************
+
+We use Sphinx to automatically build and format the documentation. Please keep
+this style in your docstrings
+
+
+Other rules and considerations
+******************************
+
+Please focus on contributing mainly source code and refrain from adding large files (e.g. mzML files).
+For such files, please contact the urgap team so they can be committed by our labbot, which allows us
+to keep the overview of code contributions neat and clean.
+
+Merge/pull requests
+*******************
+
+Please use the pull request to push your code to the master repository. It will
+be automatically tested github actions using tox if the module is still working in
+unix environments. Pull requests will be discussed by the main dev
+team and merged into urgap.
+
+
+Issues
+******
+
+If you have an issue or problem, please first search all open issues and pull
+request to avoid duplication of efforts. If you have a fix for the problem you
+may directly open a pull request. On the other hand, if you plan to or
+are already working on implementing new stuff, you may also open an issue and
+(pre-) announce your contribution. Please tag then the issue with
+'enhancement'. In general the core team of urgap will also take care of crucial
+bugs in the main code. Since urgap is open source, we cannot maintain every detail
+and assure its compatibility and functionality (please be reminded here to test
+your code, seriously, test your code)
+
+
+Citation
+********
+
+Be reminded that in an academic world citations are the only credit that one can hope for ;)
+If you use urgap, do not forget to cite us
+
+tba

urgap-3.3.5/Dockerfile-Prefect

@@ -0,0 +1,26 @@
+FROM ghcr.io/astral-sh/uv:python3.12-bookworm
+
+RUN addgroup --system nonroot && \
+    adduser --system \
+      --ingroup nonroot \
+      --home /home/nonroot \
+      nonroot
+
+RUN mkdir -p "/home/urgap" && \
+    chown -R nonroot:nonroot /home/urgap
+
+ENV HOME=/home/nonroot
+USER nonroot
+
+# Add Urgap repo
+WORKDIR /home/urgap
+COPY dist/urgap-*.whl /tmp/
+
+# Install dependencies using uv
+RUN uv venv urgap
+ENV PATH="/home/urgap/urgap/bin:$PATH"
+RUN uv pip install $(find /tmp -name 'urgap-*.whl')"[all]" --no-cache-dir
+
+# Run checks
+RUN python -c "import urgap; print(urgap.config)"
+RUN uctl info version

urgap-3.3.5/MANIFEST.in

@@ -0,0 +1,5 @@
+include urgap/version.txt
+include urgap/config_defaults/*.json
+include urgap/citation.txt
+include urgap/uctl/server
+include LICENSE.txt README.rst pyproject.toml

urgap-3.3.5/Makefile

@@ -0,0 +1,87 @@
+ifeq ($(URGAP_HOME),)
+	URGAP_HOME := $(HOME)
+endif
+
+RED=\033[0;31m
+GREEN=\033[0;32m
+YELLOW=\033[0;33m
+OFF=\033[0m
+
+help:
+	@echo "Urgap MakeFile Options"
+	@echo " - ${GREEN}new-unode${OFF}:   create a new unode"
+	@echo " - ${GREEN}tests${OFF}:       run full testsuit"
+	@echo " - ${GREEN}black${OFF}:       run black on src code with the right parameters and exclude certain files"
+	@echo " - ${GREEN}sphinx-html${OFF}: create docu in docs folder. Requires pip install -e ./[docs]"
+
+new-unode:
+	@echo ""
+	@echo "Please fill out the Questions"
+	@echo "Will create urgap/wrapper/<your_tool_name>"
+	@echo "Urgap Home is set to be ${URGAP_HOME}"
+	@echo ""
+	@echo ".------------------- ------ -- ---         -"
+	@echo "| How to :"
+	@echo "|"
+	@echo "| wrapper_name:"
+	@echo "|   The wrapper name should include the version name following"
+	@echo "|   pep8 convention. ie should be importable as a python module"
+	@echo "|"
+	@echo "| tool:"
+	@echo "|   Defining the wrapper name ${RED}without${OFF} version, which will be used"
+	@echo "|   as a top level folder to group different versions of the same tool"
+	@echo "|   This can also be used to group a type of wrapper into a folder for convenience,"	
+	@echo "|   e.g. io for filter_csv or echo_to_file etc"	
+	@echo "|"
+	@echo "| version:"
+	@echo "|   Any string"
+	@echo "|"
+	@echo "| release data:"
+	@echo "|   Any string"
+	@echo "|"
+	@echo "| translation_style:"
+	@echo "|   Tools will mostly keep their parameters over different versions."
+	@echo "|   The translation style is in the format of {tool}_style_{X}"
+	@echo "|"
+	@echo "| exe_<platform>:"
+	@echo "|   The executables are stored in ${URGAP_HOME}/<platform>/<architecture>"
+	@echo "|   and the executable name should be defined here"
+	@echo "|"
+	@echo "| platform_independent: [True, False]"
+	@echo "|"
+	@echo "| engine_type: "
+	@echo "|   ['db-search', 'open-search', 'denovo-search', 'converter', 'test_engine']"
+	@echo "|"
+	@echo "| citation: "
+	@echo "|   Please be the appropriate citation! This is ${RED}very important${OFF} "
+	@echo "|"
+	@echo "| Note:"
+	@echo "|   - Files will be overwritten if already exist"
+	@echo "|"
+	@echo "+------------------ ---- --    -"
+	@echo ""
+	cookiecutter -f urgap/wrapper_template -o urgap/wrappers
+
+tests:
+	@echo "Running Unittests using pytest"
+	pytest tests
+
+zip-exes:
+	@echo "Creating new zip files and calculating md5s for new exes"
+	@echo "----[to be implemented ]----"
+
+black:
+	black --line-length 88 --exclude '(urgap/wrapper_template/|.tox)' .
+
+
+AUTO_GEN1 = /usr/bin/env python3 parse_example_scripts.py
+AUTO_GEN2 = /usr/bin/env python3 parse_third_party.py
+# You can set these variables from the command line.
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= cd docs;$(AUTO_GEN1);$(AUTO_GEN2);sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+sphinx-html:
+	@$(SPHINXBUILD) -M html "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

urgap-3.3.5/PKG-INFO

@@ -0,0 +1,209 @@
+Metadata-Version: 2.4
+Name: urgap
+Version: 3.3.5
+Project-URL: Source, https://mygithub.gsk.com/gsk-tech/urgap
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Education
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: MacOS :: MacOS X
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: POSIX
+Classifier: Operating System :: POSIX :: SunOS/Solaris
+Classifier: Operating System :: Unix
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Requires-Dist: click==8.3.1
+Requires-Dist: fastapi==0.123.9
+Requires-Dist: fastexcel==0.18.0
+Requires-Dist: flask-wtf==1.2.2
+Requires-Dist: flask==3.1.2
+Requires-Dist: jinja2==3.1.6
+Requires-Dist: jsonschema==4.26.0
+Requires-Dist: mcp==1.23.1
+Requires-Dist: nbformat>=4.2.0
+Requires-Dist: networkx<3.5,>=3.4.2; python_version == '3.10'
+Requires-Dist: networkx==3.6.1; python_version >= '3.11'
+Requires-Dist: openpyxl
+Requires-Dist: packaging==25.0
+Requires-Dist: pandas<2.4.0,>=1.4.2
+Requires-Dist: plotly
+Requires-Dist: polars>=1.33.0
+Requires-Dist: pygithub==2.8.1
+Requires-Dist: requests<2.33,>=2.26
+Requires-Dist: sqlalchemy==2.0.45
+Requires-Dist: tqdm==4.67.1
+Requires-Dist: uvicorn==0.40.0
+Requires-Dist: xlsxwriter==3.2.9
+Provides-Extra: all
+Requires-Dist: apache-beam==2.70.0; extra == 'all'
+Requires-Dist: azure-identity==1.25.1; extra == 'all'
+Requires-Dist: azure-keyvault-secrets==4.10.0; extra == 'all'
+Requires-Dist: azure-monitor-opentelemetry==1.8.3; extra == 'all'
+Requires-Dist: azure-servicebus==7.14.3; extra == 'all'
+Requires-Dist: azure-storage-blob==12.28.0; extra == 'all'
+Requires-Dist: azure-storage-file-datalake==12.22.0; extra == 'all'
+Requires-Dist: azure-storage-file-share==12.23.1; extra == 'all'
+Requires-Dist: cloud-sql-python-connector~=1.0; extra == 'all'
+Requires-Dist: google-apitools==0.5.35; extra == 'all'
+Requires-Dist: google-cloud-logging==3.13.0; extra == 'all'
+Requires-Dist: google-cloud-secret-manager==2.26.0; extra == 'all'
+Requires-Dist: google-cloud-storage==3.8.0; extra == 'all'
+Requires-Dist: google-crc32c==1.8.0; extra == 'all'
+Requires-Dist: mcp==1.23.1; extra == 'all'
+Requires-Dist: opentelemetry-exporter-otlp-proto-grpc==1.39.0; extra == 'all'
+Requires-Dist: opentelemetry-sdk==1.39.0; extra == 'all'
+Requires-Dist: pg8000~=1.29; extra == 'all'
+Requires-Dist: prefect-kubernetes==0.7.2; extra == 'all'
+Requires-Dist: prefect==3.6.10; extra == 'all'
+Requires-Dist: psycopg2-binary; extra == 'all'
+Requires-Dist: pymongo<5.0.0,>=3.8.0; extra == 'all'
+Requires-Dist: pysmb==1.2.13; extra == 'all'
+Requires-Dist: pyvis==0.3.2; extra == 'all'
+Provides-Extra: cloud
+Requires-Dist: apache-beam==2.70.0; extra == 'cloud'
+Requires-Dist: azure-identity==1.25.1; extra == 'cloud'
+Requires-Dist: azure-keyvault-secrets==4.10.0; extra == 'cloud'
+Requires-Dist: azure-monitor-opentelemetry==1.8.3; extra == 'cloud'
+Requires-Dist: azure-servicebus==7.14.3; extra == 'cloud'
+Requires-Dist: azure-storage-blob==12.28.0; extra == 'cloud'
+Requires-Dist: azure-storage-file-datalake==12.22.0; extra == 'cloud'
+Requires-Dist: azure-storage-file-share==12.23.1; extra == 'cloud'
+Requires-Dist: cloud-sql-python-connector~=1.0; extra == 'cloud'
+Requires-Dist: google-apitools==0.5.35; extra == 'cloud'
+Requires-Dist: google-cloud-logging==3.13.0; extra == 'cloud'
+Requires-Dist: google-cloud-secret-manager==2.26.0; extra == 'cloud'
+Requires-Dist: google-cloud-storage==3.8.0; extra == 'cloud'
+Requires-Dist: google-crc32c==1.8.0; extra == 'cloud'
+Requires-Dist: mcp==1.23.1; extra == 'cloud'
+Requires-Dist: opentelemetry-exporter-otlp-proto-grpc==1.39.0; extra == 'cloud'
+Requires-Dist: opentelemetry-sdk==1.39.0; extra == 'cloud'
+Requires-Dist: pg8000~=1.29; extra == 'cloud'
+Requires-Dist: prefect-kubernetes==0.7.2; extra == 'cloud'
+Requires-Dist: prefect==3.6.10; extra == 'cloud'
+Requires-Dist: pysmb==1.2.13; extra == 'cloud'
+Requires-Dist: pyvis==0.3.2; extra == 'cloud'
+Provides-Extra: databases
+Requires-Dist: psycopg2-binary; extra == 'databases'
+Requires-Dist: pymongo<5.0.0,>=3.8.0; extra == 'databases'
+Provides-Extra: docs
+Requires-Dist: ipython; extra == 'docs'
+Requires-Dist: nbsphinx; extra == 'docs'
+Requires-Dist: sphinx; extra == 'docs'
+Requires-Dist: sphinx-rtd-theme; extra == 'docs'
+Provides-Extra: legacy
+Requires-Dist: chemical-composition~=1.0.6; extra == 'legacy'
+Requires-Dist: flowkit; extra == 'legacy'
+Requires-Dist: unimod-mapper~=0.6.4; extra == 'legacy'
+Requires-Dist: uparma~=1.0.1; extra == 'legacy'
+Description-Content-Type: text/x-rst
+
+Urgap - node wrapping framework
+===============================
+
+Urgap is a cloud-native framework for file-based data engineering, containing abstraction layers for data and meta data, extensive re-run skipping logic and data versioning. Urgap can be incorporated with any scheduling/pipelining tool making pipeline development independent from business logic and data storage, while offering standardized logging and execution, which makes monitoring and debugging easy.
+
+Urgap gives us the governance constraints required for a decentralized data domain autonomy as Urgap will enforce shared common data IO for storage, a common meta data capturing process in form of an interface thus can be plugged into any existing processes and finally global data lineages. 
+
+|build-status-azure|
+
+.. |build-status-azure| image:: https://dev.azure.com/DevOps-RD/RD-DSO/_apis/build/status%2Fgsk-tech.urgap?repoName=gsk-tech%2Furgap&branchName=refs%2Fpull%2F388%2Fmerge
+   :target: https://dev.azure.com/DevOps-RD/RD-DSO/_build?definitionId=13513
+   :alt: ADO CI status
+
+Learn More
+----------
+
+Watch our introduction talk **urgap - unified resource governance and data provenance** by Christian Fufezan to get a comprehensive overview of urgap's design and capabilities:
+
+.. image:: https://img.youtube.com/vi/63pYK1xZPx8/0.jpg
+   :target: https://www.youtube.com/watch?v=63pYK1xZPx8
+   :alt: Watch the video
+   :width: 560
+
+How to Setup
+------------
+
+Prerequisites
+~~~~~~~~~~~~~
+
+We recommend using a virtual environment for Python projects. This guide uses `uv` for dependency management.
+
+Installation
+~~~~~~~~~~~~
+
+**Basic Installation** (local file system access only):
+
+.. code-block:: bash
+
+    uv pip install -e .
+
+**With Cloud Storage Support:**
+
+.. code-block:: bash
+
+    uv pip install -e ".[cloud]"
+
+**With All Optional Dependencies:**
+
+.. code-block:: bash
+
+    uv pip install -e ".[all]"
+
+Available extras include:
+
+* ``cloud``: Azure and Google Cloud storage backends
+* ``all``: All optional dependencies
+
+Running Tests
+~~~~~~~~~~~~~
+
+Install test dependencies:
+
+.. code-block:: bash
+
+    uv pip install pytest
+
+Run the test suite:
+
+.. code-block:: bash
+
+    pytest tests
+
+Quickstart: Writing Your First Pipeline
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The best way to learn urgap is through a complete example. Check out the end-to-end filter CSV pipeline:
+
+* **Location:** `tests/integrationtests/end2end/test_filter_csv_pipeline.py`
+* **What it demonstrates:** Complete pipeline setup, node configuration, and execution
+* **Requirements:** Everything needed to run this example is included in the repository
+
+This example can be run entirely on your local machine without any external dependencies.
+
+To run the example:
+
+.. code-block:: bash
+
+    pytest tests/integrationtests/end2end/test_filter_csv_pipeline.py
+
+Documentation
+--------------
+
+Please use sphinx in the docs folder
+
+
+.. note::
+
+    Currently CI does not include pushing the documentation to readthedocs, therefore please 
+    #. checkout the repo
+    #. pip install -e .
+    #. cd docs
+    #. make html
+    #. open docs/build/index.html