jgrewe/fishbook
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some docu changes

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Jan Grewe 2020-07-22 10:30:18 +02:00
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README.md
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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
* 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

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docs/index.md
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# 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`
## 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`