From eaaf8a71b5352f54e6059a45c1f36c85e0410bf3 Mon Sep 17 00:00:00 2001
From: Jan Grewe <jan.grewe@g-node.org>
Date: Wed, 22 Jul 2020 10:44:02 +0200
Subject: [PATCH] more changes and stubs for docu

---
 docs/configuration.md   |  6 ++----
 docs/getting_started.md |  3 ++-
 docs/index.md           | 28 ++++++++++++++++++++++++++--
 docs/todos.md           |  9 +++++++++
 4 files changed, 39 insertions(+), 7 deletions(-)
 create mode 100644 docs/todos.md

diff --git a/docs/configuration.md b/docs/configuration.md
index 4aa0f27..b42033a 100644
--- a/docs/configuration.md
+++ b/docs/configuration.md
@@ -5,9 +5,7 @@
 * Should work with mysql or mariaDB databases
 * if you do not have access to a database server, go back to index.md to read how to install one locally
 
-To log into the database you need the `host`, the `database name`, the `user` name, and the `password`. 
+To log into the database you need the `host`, the `database name`, the `user` name, and the `password`.
 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 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`.
diff --git a/docs/getting_started.md b/docs/getting_started.md
index f32c486..38c63f4 100644
--- a/docs/getting_started.md
+++ b/docs/getting_started.md
@@ -1,3 +1,4 @@
 # Getting started
 
-## Package contents
\ No newline at end of file
+## Package contents
+
diff --git a/docs/index.md b/docs/index.md
index 0c18917..a0345e1 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -31,8 +31,32 @@
   >> sudo pip3 install fishbook
   ```
 
-## Getting started
-
 ### 3) Connecting to the database
 
+#### Installing a local database
+
+When you want to run *fishbook* locally you need to install a local database server (either mariaDB or mysql).
+
+On Ubuntu or Linux mint use *apt* to install the server
+
+```bash
+sudo apt install mysql
+```
+
+On Fedora use *dnf*
+
+```bash
+sudo dnf install mysql
+```
+
+On MacOS the most convenient way is to use [*homebrew*](https://brew.sh)
+
+```bash
+brew install mysql
+```
+
+On Windows you probably need to download an installer...
+
+#### Database connection
+
 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
diff --git a/docs/todos.md b/docs/todos.md
new file mode 100644
index 0000000..e006823
--- /dev/null
+++ b/docs/todos.md
@@ -0,0 +1,9 @@
+# TODOs & 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