more docs, move fixmes

README.md

@@ -10,12 +10,4 @@ Database of data recorded in the group.
 * Question: should we store the sampling rate and hardware info in the database?
 * ID card for each cell
 
-## FIXMEs
+**FIXMEs & stuff that needs to be done, check out the to docs folder**
-
-* 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

docs/configuration.md

@@ -9,3 +9,42 @@ To log into the database you need the `host`, the `database name`, the `user` na
 Note, the selected user needs at least read access on the selected database (True? maybe also write?).
 
 The root of the fishbook package contains a file called *template_dj_local_conf.json*. copy this file to your project folder, i.e. the location from which you call your scripts, remove the `template_` prefix and fill in `database.host`, `database.user`, `database.password`.
+
+The json template looks like this:
+
+```json
+{
+    "database.host": "yourhost",
+    "database.user": "yourdatabaseusername",
+    "database.password": "yourdatabaseuserpassword",
+    "database.port": 3306,
+    "loglevel": "DEBUG",
+    "display.width": 14,
+    "display.limit": 7,
+    "safemode": false,
+    "connection.init_function": null
+}
+```
+
+### Example
+
+Let's assume you are working remotely, i.e. connecting to a remote database on a server that has the name ```foo.uni-xyz.de```. The database is up and running and allows connections via port 3306 (the default). The database is called ```fish_db``` and the user credentials are name ```baz``` and password ```bar```. The configuration file will look like this:
+
+```json
+{
+    "database.host": "foo.uni-xyz.de",
+    "database.user": "bar",
+    "database.password": "baz",
+    "database.port": 3306,
+    "loglevel": "DEBUG",
+    "display.width": 14,
+    "display.limit": 7,
+    "safemode": false,
+    "connection.init_function": null
+}
+```
+
+In case you are working with a local database the ```database.host``` entry is ```"localhost"```.
+If you ommit ```database.user``` or ```database.password``` fishbook, respectively datajoint, will ask you for the user credentials every time you run your python scripts.
+
+**Note:** This configuration file is pure text and can be easily read by anyone. It **must not** be part of public repository. **Do not add it to your version control system!**

docs/getting_started.md

@@ -1,4 +1,9 @@
-# Getting started
+# Getting started working with fishbook
+
+create a project folder and place the configuration file in it (see [configuration](./configuration.md) for more info on it)
 
 ## Package contents
 
+```python
+import fishbook as fb
+```