Merge branch 'master' of https://github.com/jgrelet/oceano2python

README.md

@@ -9,162 +9,6 @@ and extract data from header files and write result into ASCII and NetCDF OceanS
 
 The last version use an embedded Sqlite3 database to normalize, save and retreive data from memory.
 
-See the [wiki](https://github.com/jgrelet/oceano2python/wiki) for a technical description
+See the [wiki](https://github.com/jgrelet/oceano2python/wiki) for documentation and technical description
 
-## Prequisites
 
-You must install the following tools:
-
-- Visual Studio Code (<https://code.visualstudio.com/>)
-- Git (<https://git-scm.com/downloads>)
-- miniconda3 (<https://docs.conda.io/en/latest/miniconda.html>)
-
-### For Windows
-
-- chocolatey (<https://chocolatey.org/install>) and install GNU Make package (<https://community.chocolatey.org/packages/make>)
-
-## Installation from scratch with conda
-
-The program works under Windows (terminal) or Git bash as well as under Linux. It is recommended to install miniconda and to create a virtual environment oceano2python.
-
-``` bash
-conda create -n oceano2python python=3.9
-conda activate oceano2python
-conda install -c conda-forge netCDF4 toml matplotlib xarray seawater PyInstaller pysimplegui
-pip install julian notanorm
-```
-
-## Installation based on an YAML environment file
-
-``` bash
-conda env create -f environment.yml -n <new_env_name>
-```
-
-example:
-
-``` bash
-conda env create -f environment-windows.yml -n oceano2python
-```
-
-## Clone the project
-
-Change the current working directory to the location where you want the cloned directory.
-
-``` bash
-git clone https://github.com/jgrelet/oceano2python.git 
-```
-
-## Export your environment
-
-Duplicate your environment on another machine, just export it to a YAML file, replace "OS" with linux or windows:
-
-``` bash
-conda env export --no-builds > environment-<OS>.yml
-```
-
-## Configuration
-
-As the project consists of several files (modules), it is necessary to define the access path to the program in the environment variables PYTHONPATH and PATH.
-For example, under Linux:
-
-### Update your PATH in your ~/.profile
-
-``` bash
- if [ -d "/mnt/c/git/Python/oceano2python" ] ; then
-    PATH="/mnt/c/git/Python/oceano2python:$PATH"
-fi
-```
-
-### Add this line in your ~/.bashrc
-
-``` bash
-export $PYTHONPATH = /mnt/c/git/Python/oceano2python
-```
-
-## Build and run
-
-To build, run tests, build (compiled version), test examples (CTD/XBT), with GUI, you can use make:
-
-``` bash
-make test
-make build
-make ctd
-make xbt
-make ladcp
-make btl
-make tsg
-make casino
-make ctd OPT=-g   
-make ctd OPT=-d
-```
-
-or:
-
-``` bash
-make all
-```
-
-## Usage
-
-By default, the program uses the configuration file config.toml.
-
-``` bash
-cd /mnt/c/cruises/PIRATA/PIRATA-FR32/data-processing/CTD
-oceano.py data/cnv/dfr320*.cnv -c ../config.toml  -i CTD -k PRES DEPTH ETDD TEMP PSAL DENS SVEL DOX2 FLU2 FLU3 TUR3 NAVG
-oceano.py data/btl/fr320*.btl -c ../config.toml  -i BTL  -k PRES DEPTH TE01 TE02 PSA1 PSA2 DO11 DO12 DO21 DO22 FLU2
-
-cd /mnt/c/cruises/PIRATA/PIRATA-FR32/data-processing/CELERITE
-oceano.py data/XBT*.edf -c ../config.toml -i XBT -k DEPTH TEMP SVEL
-
-cd /mnt/c/cruises/PIRATA/PIRATA-FR32/data-processing/LADCP
-oceano.py profiles/*.lad -c ../config.toml -i LADCP -k DEPTH EWCT NSCT
-
-cd /mnt/c/cruises/PIRATA/PIRATA-FR32/data-processing/THERMO
-oceano.py data/*.COLCOR -c ../config.toml -i TSG -k SSJT SSTP SSPS
-
-cd /mnt/c/cruises/PIRATA/PIRATA-FR32/data-processing/CASINO
-oceano.py data/*.csv -c ../config.toml -i CASINO -k LATITUDE LONGITUDE BATH SSJT SSTP SSPS
-```
-
-This program read multiple ASCII file, extract physical parameter following ROSCOP codification at the given column, fill arrays, write header file.
-
-``` bash
-positional arguments:
-  files                 ASCII file(s) to parse
-
-optional arguments:
-  -h, --help            show this help message and exit
-  -d, --debug           display debug informations
-  --demo [{CTD,XBT,LADCP,TSG}]
-                        specify the commande line for instrument, eg CTD, XBT,
-                        TSG, LADCP
-  -c CONFIG, --config CONFIG
-                        toml configuration file, (default: tests/test.toml)
-  -i [{CTD,XBT,LADCP,TSG}], --instrument [{CTD,XBT,LADCP,TSG}]
-                        specify the instrument that produce files, eg CTD,
-                        XBT, TSG, LADCP
-  -k KEYS [KEYS ...], --keys KEYS [KEYS ...]
-                        display dictionary for key(s), (default: ['PRES',
-                        'TEMP', 'PSAL'])
-  -g, --gui             use GUI interface
-  ```
-
-The user must describe in the TOML configuration file the metadata and the structure of the files to be read, see [tests/test.toml](https://github.com/jgrelet/oceano2python/blob/master/tests/test.toml)
-
-## Developpment tools
-
-We use Visual Studio Code (VSC) with Python, better TOML, markdownlint and makefile extensions
-
-## GUI
-
-If you want use QT instead of Tk, replace in oceano.py:
-
-``` bash
-import PySimpleGUI as gs
-```
-
-with
-
-``` bash
-import PySimpleGUIQt as gs
-```