diff --git a/README.md b/README.md index 8a80048..350e00f 100644 --- a/README.md +++ b/README.md @@ -2,19 +2,20 @@ Database of data recorded in the group. +## Assumptions & Caveats - -## Assumptions & Caveats: * there is only a single subject in each dataset * each recording contains a single cell * RePro links to Cell and not to Dataset * Question: should we store the sampling rate and hardware info in the database? +* ID card for each cell ## FIXMEs + * repro must have foreign keys to dataset **and** subject * Dataset finding samplerate in stimuli.dat can be improved * Reading fi data from old-style directories * maybe delegate this to Stimulus? * implement alternative dataSources, somehow * stimulus contrast is not read from nix file (e.g. filestimulus) maybe a problem with all mutables? -* Add relacs_nix_version to dataset, could be used to decide how to read stuff, in particular, we will switch to DataFrames for most features after nixio version 1.5 \ No newline at end of file +* Add relacs_nix_version to dataset, could be used to decide how to read stuff, in particular, we will switch to DataFrames for most features after nixio version 1.5 diff --git a/docs/index.md b/docs/index.md index 3194ba7..0c18917 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,35 +1,38 @@ # How to use the fish book ## Requirements + * Python 3.5+ only, **no** python 2 * [datajoint](https://datajoint.io) to connect to the database and to map python objects to table entries. * [nixio](https://github.com/g-node/nixpy) to read the relacs-flavored nix files during import or later during data retrieval. - ## Installation -1) clone the repository +### 1) Clone the repository + + ```bash + >> git clone https://whale.am28.uni-tuebingen.de/git/jgrewe/fishbook.git + ``` -``` ->> git clone https://whale.am28.uni-tuebingen.de/git/jgrewe/fishbook.git -``` +### 2) Installation -2. installation When installing for development: install for the current user, install as "editable": - ``` + ```bash >> cd fishbook - >> pip3 install fishbook -e --user + >> pip3 install -e fishbook --user ``` - + When installing for use: - - ``` + + ```bash >> pip3 install fishbook --user - # or + # or, for system-wide installation >> sudo pip3 install fishbook ``` -3. connecting to the database - - Suppose that you intend to work on a project named `foo` use the terminal to navigate to the project directory: `cd foo` \ No newline at end of file +## Getting started + +### 3) Connecting to the database + +Suppose that you intend to work on a project named `foo` use the terminal to navigate to the project directory: `cd foo` \ No newline at end of file