.. SHERLOCK PIPEline documentation master file, created by sphinx-quickstart on Thu Jul 8 08:43:51 2021. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. ============================================= Installation ============================================= Firstly, you must know that *SHERLOCK* is a package that lies on many different dependencies whose versions are fixed. Hence, we strongly encourage all the users to use a *Python* virtual environment, preferently built with a conda distribution. If anaconda is available in your distribution, please try using it. You can install it following the next instructions https://docs.anaconda.com/free/anaconda/install/linux/ Once you installed it, you'd have to create a new environment for *SHERLOCK*: `conda create -n sherlockenv python=3.10 anaconda` Some of the *SHERLOCK* dependencies need ``numpy`` and ``Cython`` before being installed and therefore you should install them before trying the SHERLOCK installation. Take also into account that the dependencies brought by SHERLOCK also need additional operating system tools that need to be installed separately (C++ compiler, Fortran compiler, etc). So, be aware of counting with the next OS packages installed in your environment (e.g. for Python3 in a Linux distribution): .. code-block:: build-essential libssl-dev python3.10 python3-pip libbz2-dev libssl-dev libreadline-dev libffi-dev libsqlite3-dev tk-dev libpng-dev libfreetype6-dev llvm-9 llvm-9-dev gfortran gcc locales python3-tk python3.10-dev In case you are running a non-Linux distribution you will need to guess your OS packages matching the ones we mention for Linux. Therefore, once you have got the OS tools, the *SHERLOCK* package can be installed in several ways. The cleanest one is by running:: conda activate sherlockenv wget https://raw.githubusercontent.com/PlanetHunters/SHERLOCK/master/requirements.txt python3 -m pip install -r requirements.txt An additional installation method is running the next commands:: conda activate sherlockenv python3 -m pip install numpy python3 -m pip install Cython python3 -m pip install sherlockpipe ------------- Docker usage ------------- If you are not running on Linux or you're just curious, you can also use our Docker image from `DockerHub `_ or build it from our `Dockerfile `_. Therefore, you can also use as a Singularity container meanwhile they support Docker. You would need to install `Docker `_. Once you've got it, the steps to get the *SHERLOCK* container up and running are:: sudo docker pull sherlockpipe/sherlockpipe:latest sudo docker run -v someAbsoluteDirectoryFromYourHost:/home/sherlock --name sherlock -it sherlockpipe/sherlockpipe:latest /bin/bash This way you will be logged into a container with the ability of running *SHERLOCK*, with your host work directory mounted into the *SHERLOCK* container. Let's say that you have prepared a `properties.yaml` file with a *SHERLOCK* execution definition into your host work directory. You could then execute the next commands in your container:: cd /home/sherlock python3 -m sherlockpipe --properties properties.yaml --explore And voilà! *SHERLOCK* should be running in explore mode for your defined targets. Any outputs created by *SHERLOCK* in the current directory are automatically mapped into your host work directory, so you can inspect them easily on your machine. ------------- Dependencies ------------- All the needed dependencies should be included by your `pip` installation of *SHERLOCK*. If you are interested you can inspect the requirements list under `setup.py `_. -------- Testing -------- **SHERLOCK** comes with a light automated tests suite that can be executed with: ``tox`` This suite tests several points from the pipeline for the supported *Python* versions: * The construction of the ``SHERLOCK`` *Python* object. * The parameters setup of the ``SHERLOCK`` *Python* object. * The provisioning of objects of interest files. * Load and filtering of objects of interest. * Different kind of short **SHERLOCK** executions. In case you want to test the entire *SHERLOCK* functionality we encourage you to run some (or all) the `manual examples `_. If so, please read the instructions provided there to execute them.