Usage

To reproduce the results shown in the Lab Book, you need a running Python environment with Ana and spectrumanalyzer installed.

Install dependencies

Linux

If you are running Debian or Ubuntu you can easily download and install docker with the following command:

$ apt install docker.io

Windows / OS X

Users with different operating systmes should download and install docker directly from the docker homepage: <https://docs.docker.com/get-docker/>

Run Docker Image

Run the docker container for Jupyterlab to start developing:

$ docker run -d -p 8888:8888 -e "PASSWORD=YourSecurePassword" \
             -e GIT_URL="http://gitlab.com/ody55eus/lab-book.git" \
             --name jupyterlab \
             registry.gitlab.com/ganymede/jupyterlab:latest

If you just want the Python environment to execute the tests, use the ana tag:

$ docker run -d -p 8888:8888 -e "PASSWORD=YourSecurePassword" \
             -e GIT_URL="http://gitlab.com/ody55eus/lab-book.git" \
             --name python \
             registry.gitlab.com/ganymede/jupyterlab:ana

and execute a bash terminal inside the container:

JupyterLab: go to http://localhost:8888/ and open a terminal.
Python environment: enter the environment in a bash:

$ docker exec -it jupyterlab bash

Use this bash terminal to install the dependencies for the software packages

$ cd spectrumanalyzer && python -m pip install -e . && cd ..
$ cd ana && python -m pip install -e . && cd ..
$ cd EVE python -m pip install -e . && cd ..
$ python -m pip install coverage

Local installation

Clone the repositories (change URLs accordingly) and install spectrumanalyzer and Ana using pip:

$ python -m pip install -e git+http://gitlab.com/ody55eus/spectrumanalyzer.git
$ python -m pip install -e git+http://gitlab.com/ody55eus/ana.git
$ python -m pip install coverage

Install and start a Jupyterlab server:

$ python -m pip install jupyterlab
$ jupyterlab

Reproduce

To reproduce the plots and run the code either run the JupyterLab server or execute the test files:

$ git clone ANA_URL
$ python -m unittest discover -s ana/tests/basic
$ python -m unittest discover -s ana/tests/ana/prepair
$ python -m unittest discover -s ana/tests/ana/fit
$ python -m unittest discover -s ana/tests/ana/visualize

Create the Lab Book

To create the Lab Book use the following docker image

$ docker run -d  -e GIT_URL="http://gitlab.com/ody55eus/lab-book.git" \
             -p 8888:8888 -e "PASSWORD=YourSecurePassword" \
             --name python \
             registry.gitlab.com/ganymede/jupyterlab:ana

Run JupyterLab Server

After starting the server you can open the Jupyter notebooks at http://localhost:8888

Run Tests

optionally run tests to make sure the code is working:

$ coverage run -m pytest spectrumanalyzer
$ coverage run -m unittest discover -s tests/basic

Afterwards create the Lab Book by executing

$ make html

Run Lab Book

To run the Lab Book as static webserver download the _build directory and run the following line in the command line:

$ docker run -d -p 80:80 \
             --name nginx \
             -v /c/_build:/usr/share/nginx/html:ro \
             nginx

This will start a local webserver at http://localhost/ and mount the folder /c/_build (linux) or c:\_build (Windows) as root.