Changes in documentation to be compatible with readthedocs.io

README.md

@@ -12,7 +12,7 @@ The package is designed to be open, adaptable and scalable allowing future contr
 
 This work is performed in the framework of the European Multidisciplinary Seafloor and Water-Column Observatory development ([EMSOdev](http://www.emsodev.eu/)).
 
-Check the documentation on [oceanobs.readthedocs.io](http://oceanobs.readthedocs.io/).
+Check the documentation on [mooda.readthedocs.io](http://mooda.readthedocs.io/).
 
 ## Why use *mooda*
 
@@ -38,10 +38,10 @@ For the moment, the compatible source data can be from the following observatori
 
 ## More information
 
-* [Git Repository Structure](/docs/github_struct.md): Describes the git repository structure and branching model used for the oceanobs project.
+* [Git Repository Structure](/docs/github_struct.md): Describes the git repository structure and branching model used for the mooda project.
 * [Package Overview](/docs/package.md): The Python package is located in the [mooda folder](/mooda). This document describes how the python modules within the package have been structured.
-* [Installation](/docs/installation.md): Step by step manual of the installation of oceanobs. The document contains an installation guide for people without python knowledge but also for people who have already used python before.
+* [Installation](/docs/installation.md): Step by step manual of the installation of mooda. The document contains an installation guide for people without python knowledge but also for people who have already used python before.
 * [API reference](/docs/api.md): Explanation of the modules and functions of the package.
-* [Examples](/docs/examples/index_examples.md): Set of examples to use oceanobs by writing python code or running MOODA.
+* [Examples](/docs/examples/index_examples.md): Set of examples to use mooda by writing python code or running MOODA.
 * [Version log](/docs/news.md)
 * [License](LICENSE)

docs/api.md

@@ -1,6 +1,6 @@
 # API Reference
 
-This page gives an overview of all public pandas objects, functions and methods. All classes and functions exposed in oceanobs.* namespace are public.
+This page gives an overview of all public pandas objects, functions and methods. All classes and functions exposed in mooda.* namespace are public.
 
 ## WaterFrame
 

docs/github_struct.md

@@ -4,6 +4,7 @@ If you are not a regular user of GitHub, it is possible that the structure of da
 
 The GitHub repository of the mooda project is structured as follows:
 
+```bash
     mooda
     ├─ docs
     |   ├─ example_data
@@ -24,29 +25,30 @@ The GitHub repository of the mooda project is structured as follows:
     ├─ other codes
     └─ tests
         └─ data
+```
 
 Most of the files that are in the root contain code or information specific to git. If you do not want to clone the project or use a git client, they are not necessary files for you. However, we describe them below:
 
-* [.gitignore](.gitignore): In the process to sync your local git directory with the GitHub repository, files are usually built artifacts, and machine-generated data should otherwise not be uploaded. In this file, you can find the code to ignore this type of files.
-* [LICENSE](LICENSE): Public repositories on GitHub are often used to share open source software. We use an MIT License.
-* [MANIFEST.in](MANIFEST.in): It is used to collect all the files that will go into the final installer.
-* [README.md](README.md): Contains the text that you see on the repository [home page](https://github.com/rbardaji/oceanobs).
-* [mkdocs.yml](mkdocs.yml): Sets the theme and theme specific configuration of the [documentation site](https://oceanobs.readthedocs.io/).
-* [requirements-access-egim.txt](requirements-access-egim.txt): List of required python libraries to execute the module oceanobs.access.egim.py.
-* [requirements-app-mooda.txt](requirements-app-mooda.txt): List of required python libraries to execute the package oceanobs.app.mooda.
-* [requirements-waterframe.txt](requirements-waterframe.txt): List of required python libraries to execute the module oceanobs.waterframe.py.
-* [setup.cfg](setup.cfg): It contains package metadata.
-* [setup.py](setup.py): It is the python code to install the package into a python environment.
+* [.gitignore](https://github.com/rbardaji/mooda/blob/master/.gitignore): In the process to sync your local git directory with the GitHub repository, files are usually built artifacts, and machine-generated data should otherwise not be uploaded. In this file, you can find the code to ignore this type of files.
+* [LICENSE](https://github.com/rbardaji/mooda/blob/master/LICENSE): Public repositories on GitHub are often used to share open source software. We use an MIT License.
+* [MANIFEST.in](https://github.com/rbardaji/mooda/blob/master/MANIFEST.in): It is used to collect all the files that will go into the final installer.
+* [README.md](https://github.com/rbardaji/mooda/blob/master/README.md): Contains the text that you see on the repository [home page](https://github.com/rbardaji/mooda).
+* [mkdocs.yml](https://github.com/rbardaji/mooda/blob/master/mkdocs.yml): Sets the theme and theme specific configuration of the [documentation site](https://mooda.readthedocs.io/).
+* [requirements-access-egim.txt](requirements-access-egim.txt): List of required python libraries to execute the module mooda.access.egim.py.
+* [requirements-app-mooda_gui.txt](https://github.com/rbardaji/mooda/blob/master/requirements-app-mooda_gui.txt): List of required python libraries to execute the package mooda.app.mooda_gui.
+* [requirements-waterframe.txt](https://github.com/rbardaji/mooda/blob/master/requirements-waterframe.txt): List of required python libraries to execute the module mooda.waterframe.py.
+* [setup.cfg](https://github.com/rbardaji/mooda/blob/master/setup.cfg): It contains package metadata.
+* [setup.py](https://github.com/rbardaji/mooda/blob/master/setup.py): It is the python code to install the package into a python environment.
 
 The directories contain the following information:
 
-* [docs](../docs): It contains the texts that are displayed on the [documentation site](https://oceanobs.readthedocs.io/).
-* [docs/example_data](../docs/example_data): It contains the data files used in the example documentation.
-* [docs/examples](../docs/examples): It contains the texts of the example documentation.
-* [docs/img](../docs/img): It contains the images of the documentation.
+* [docs](https://github.com/rbardaji/mooda/tree/master/docs): It contains the texts that are displayed on the [documentation site](https://mooda.readthedocs.io/).
+* [docs/example_data](https://github.com/rbardaji/mooda/tree/master/docs/example_data): It contains the data files used in the example documentation.
+* [docs/examples](https://github.com/rbardaji/mooda/tree/master/docs/examples): It contains the texts of the example documentation.
+* [docs/img](https://github.com/rbardaji/mooda/tree/master/docs/img): It contains the images of the documentation.
 * [docs/img/examples](../docs/img/examples): It contains the images of the example documentation.
-* [docs/img/home](../docs/img/home): It contains the images of the main page documentation.
-* [docs/img/package](../docs/img/package): It contains the images of the package overview documentation.
-* [mooda](../mooda): **It contains the oceanobs python package.**
-* [tests](../tests): It contains the python code to test the oceanobs package. We are not using any standard to check oceanobs. We write our test routines.
-* [other_codes](../other_codes): It contains a set of python scripts that uses the oceanobs package.
+* [docs/img/home](https://github.com/rbardaji/mooda/tree/master/docs/img/home): It contains the images of the main page documentation.
+* [docs/img/package](https://github.com/rbardaji/mooda/tree/master/docs/img/package): It contains the images of the package overview documentation.
+* [mooda](https://github.com/rbardaji/mooda): **It contains the mooda python package.**
+* [tests](https://github.com/rbardaji/mooda/tree/master/tests): It contains the python code to test the mooda package. We are not using any standard to check mooda. We write our test routines.
+* [other_codes](https://github.com/rbardaji/mooda/tree/master/other_codes): It contains a set of python scripts that uses the mooda package.

docs/index.md

@@ -12,8 +12,6 @@ The package is designed to be open, adaptable and scalable allowing future contr
 
 This work is performed in the framework of the European Multidisciplinary Seafloor and Water-Column Observatory development ([EMSOdev](http://www.emsodev.eu/)).
 
-Check the documentation on [oceanobs.readthedocs.io](http://oceanobs.readthedocs.io/).
-
 ## Why use *mooda*
 
 The main problem when analyzing marine data from different research infrastructures is th lack of a unique data format and nomenclature. Regardless of the type of file i.e., CSV, NetCDF, HDF, XML, names that describe measurements (vocabularies) may vary depending on the provider/source. Although there is some effort to produce and provide documentation with standard vocabulary, until now, no consensus has been reached concerning the use of a common nomenclature to describe the measurements. For example, water temperature values can be listed as ‘TEMP,’ ‘temp,’ ‘sea_temp,’ or ‘temperature.’
@@ -34,14 +32,14 @@ For the moment, the compatible source data can be from the following observatori
 
 *Mooda* can be executed through a graphical interface with which a large part of the implemented functions can be performed.
 
-![MOODA screenshot](/docs/img/home/mooda_screenshot.png)
+![MOODA screenshot](https://github.com/rbardaji/mooda/blob/master/docs/img/home/mooda_screenshot.png?raw=true)
 
 ## More information
 
-* [Git Repository Structure](github_struct.md): Describes the git repository structure and branching model used for the oceanobs project.
+* [Git Repository Structure](github_struct.md): Describes the git repository structure and branching model used for the mooda project.
 * [Package Overview](package.md): The Python package is located in the [mooda folder](https://github.com/rbardaji/mooda/tree/master/mooda). This document describes how the python modules within the package have been structured.
-* [Installation](installation.md): Step by step manual of the installation of oceanobs. The document contains an installation guide for people without python knowledge but also for people who have already used python before.
+* [Installation](installation.md): Step by step manual of the installation of mooda. The document contains an installation guide for people without python knowledge but also for people who have already used python before.
 * [API reference](api.md): Explanation of the modules and functions of the package.
-* [Examples](./examples/index_examples.md): Set of examples to use oceanobs by writing python code or running the MOODA GUI.
+* [Examples](./examples/index_examples.md): Set of examples to use mooda by writing python code or running the MOODA GUI.
 * [Version log](news.md)
 * [License](https://github.com/rbardaji/mooda/blob/master/LICENSE)

docs/installation.md

@@ -10,15 +10,15 @@ Officially [Python](https://www.python.org/downloads/) >= 3.4.
 
 ## Installing with pip
 
-You can install oceanobs via pip with the following command:
+You can install mooda via pip with the following command:
 
 ```bat
-pip install https://github.com/rbardaji/oceanobs/archive/v2.0.0-beta.zip
+pip install mooda
 ```
 
 ## Installing from source
 
-There are many ways to clone or download the source code from [GitHub](https://github.com/rbardaji/oceanobs) on your computer. If you do not have a git client, you can press the *Download ZIP* button, which is located under the *Clone or Download* drop-down of the [GitHub page](https://github.com/rbardaji/oceanobs).
+There are many ways to clone or download the source code from [GitHub](https://github.com/rbardaji/mooda) on your computer. If you do not have a git client, you can press the *Download ZIP* button, which is located under the *Clone or Download* drop-down of the [GitHub page](https://github.com/rbardaji/mooda).
 
 Now, you only need to install the package directly from the downloaded folder. Go to the downloaded folder and write the following instruction in a terminal.
 

docs/package.md

@@ -1,23 +1,23 @@
 # Package overview
 
-Oceanobs package primary goal is to help scientists to understand their oceanographic data, i.e., to facilitate the read and the analysis of data coming from marine observatories. The package contains modules with functions to read data in different formats and translates them into an internal data format called WaterFrame. The object WaterFrame includes the scientific data and metadata but also provides for functions to process the data and make plots.
+Mooda package primary goal is to help scientists to understand their oceanographic data, i.e., to facilitate the read and the analysis of data coming from marine observatories. The package contains modules with functions to read data in different formats and translates them into an internal data format called WaterFrame. The object WaterFrame includes the scientific data and metadata but also provides for functions to process the data and make plots.
 
 Data imported to a WaterFrame will include QC Flags. If the original data does not contain the flags, they will be created during the importation. The flags help decide if the data is useful for a particular study.
 
-Oceanobs, like most of the python package, contains many modules with different classes and functions. Each module will execute a part of the specific data study. We divide the modules into three types (view Fig. 1):
+Mooda, like most of the python package, contains many modules with different classes and functions. Each module will execute a part of the specific data study. We divide the modules into three types (view Fig. 1):
 
 * Data access modules: These contain classes to download, open, and translate data incoming from marine observatories to a WaterFrame;
 * Analysis modules: These provide functions and classes for processing and analyzing data already in a WaterFrame;
 * App modules: These contain a set of classes and services to offer apps to help users to use oceanobs without the need of typing code.
 
-![Module types of oceanobs](./img/package/module_types.PNG)
+![Module types of mooda](https://github.com/rbardaji/mooda/blob/master/docs/img/package/module_types.png?raw=true)
 
-Figure 1: Module types of oceanobs
+Figure 1: Module types of mooda
 
-Data access modules are located in oceanobs/access folder. At the moment we only have implemented a module called egim.py. The module is used to download data from EMSO Generic Instrument Modules ([EGIMs](http://www.emsodev.eu)). Following the general idea of the access modules, the downloaded data is saved in WaterFrames so that it can be easily analyzed.
+Data access modules are located in mooda/access folder. At the moment we only have implemented a module called egim.py. The module is used to download data from EMSO Generic Instrument Modules ([EGIMs](http://www.emsodev.eu)). Following the general idea of the access modules, the downloaded data is saved in WaterFrames so that it can be easily analyzed.
 
-Oceanobs can also read netCDF files (with SeaDataNet format) and serialized WaterFrames as Pickle files. The functions to open this type of data have been implemented directly in the WaterFrame object since these files are not specific to a specific platform.
+Mooda can also read netCDF files (with SeaDataNet format) and serialized WaterFrames as Pickle files. The functions to open this type of data have been implemented directly in the WaterFrame object since these files are not specific to a specific platform.
 
 Analysis modules are located in the root of the package. Right now, we have waterframe.py, that contains the code of the WaterFrame object, and plotmap.py, that is a module to make data visualization on a static map.
 
-App modules are located in oceanobs/app/[name of the app] folder. The idea is that each app will be placed in a different folder inside oceanobs/app folder. We have developed an app called "Module for Ocean Observatory Data Analysis" (MOODA). With MOODA, users could use most of the oceanobs package functionalities without the need of write code.
+App modules are located in mooda/app/[name of the app] folder. The idea is that each app will be placed in a different folder inside mooda/app folder. We have developed a graphical user interface (GUI). With the GUI, users could use most of the mooda package functionalities without the need of write code.

mkdocs.yml

@@ -1,4 +1,4 @@
-site_name: oceanobs
+site_name: MOODA
 pages:
     - Home: index.md
     - Installation: installation.md

setup.py

@@ -8,7 +8,7 @@
 DESCRIPTION = 'Module for Ocean Observatory Data Analysis'
 README_FILE = os.path.join(os.path.dirname(__file__), 'README.md')
 LONG_DESCRIPTION = open(README_FILE).read()
-CLASSIFIERS = ['Development Status :: 3 - Alpha',
+CLASSIFIERS = ['Development Status :: 4 - Beta',
                'Environment :: X11 Applications :: Qt',
                'Environment :: Console',
                'Natural Language :: English',