Merge pull request #150 from Ocean-Data-Lab/116_prerelease

Add accumulated changes to main

Author: John-Ragland

.github/workflows/unit_test.yml

@@ -12,7 +12,7 @@ jobs:
     continue-on-error: ${{ matrix.experimental }}
     strategy:
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10']
+        python-version: ['3.9', '3.10']
         experimental: [false]
     steps:
     - name: Checkout Repo

.gitignore

@@ -19,6 +19,7 @@ ooipy.egg-info/
 ooi_auth.txt
 .eggs
 _ooipy_version.py
+*.nc
 
 # Environments
 .env

CITATION.cff

@@ -13,6 +13,8 @@ authors:
   given-names: "Dmitry"
 - family-names: "Abadi"
   given-names: "Shima"
+- family-names: "Dixit"
+  given-names: "Anish"
 title: "OOIPy: A Python toolbox designed to aid in the scientific analysis of Ocean Observatories Initiative (OOI) data"
 version: 1.1.3
 doi: 10.5281/zenodo.5165389

conda_envs/py3.7.yml

@@ -23,12 +23,13 @@ First Steps
     demos
 
 
-Modules Documentation
-^^^^^^^^^^^^^^^^^^^^^
+API Documentation
+^^^^^^^^^^^^^^^^^
 .. toctree::
    :maxdepth: 2
 
    hydrophone
    ctd
    request
    tools
+   scripts

conda_envs/py3.8.yml

@@ -12,10 +12,55 @@ OOIPY is available on PyPI.
 
 Install Instruction
 -------------------
-OOIPY is designed to run on Python 3.8.5. To install OOIPY, run the following command.
+OOIPY is designed to run on Python version 3.9 and above. To install OOIPY, run the following command:
 
 .. code-block :: bash
 
   pip install ooipy
 
 Please see our Getting Started Guide for a tutorial on basic OOIPY usage.
+
+
+How to setup OOIPY development environment
+==========================================
+
+1. Navigate into the folder where you wish to setup ooipy and clone the repository using this command:
+
+.. code-block :: bash
+
+  git clone https://github.com/Ocean-Data-Lab/ooipy.git
+
+2. Setup a new Conda environment using this command:
+
+.. code-block :: bash
+
+  conda create --name env_name python=3.10 pip
+
+3. Activate the environment using this command:
+
+.. code-block :: bash
+
+  source activate env_name
+
+4. Install ooipy using this command in the same directory where the repository has been cloned:
+
+.. code-block :: bash
+
+  pip install -e ooipy
+
+5. Install the development environment package requirements :
+
+.. code-block :: bash
+
+  cd ooipy
+  pip install -r dev-requirements.txt
+
+5. When this runs successfully, open a python prompt to verify if installation is proper, using this command:
+
+.. code-block :: bash
+
+  python
+  import ooipy
+  print(ooipy.__file__)
+
+If the path printed out matches the __init__.py from your local installation path for the ooipy github repository, your development environment has been properly setup.

ctd_demo.ipynb renamed to demos/ctd_demo.ipynb

@@ -0,0 +1,27 @@
+.. image:: ../../imgs/ooipy_banner2.png
+  :width: 700
+  :alt: OOIPY Logo
+  :align: left
+
+Scripts
+=======
+There are a collection of useful scripts that can be used to
+download and process data. The scripts are included in the package if downloaded with pypi,
+but can also be downloaded and run individually from the `github repo <https://github.com/Ocean-Data-Lab/ooipy/tree/master/ooipy/scripts/>`_.
+
+download_hydrophone_data
+************************
+location: ooipy/scripts/download_hydrophone_data.py
+
+This script downloads hydrophone data that is specified in a csv.
+
+Here is an example csv file:
+
+| node,start_time,end_time,file_format,downsample_factor
+| LJ03A,2019-08-03T08:00:00,2019-08-03T08:01:00,mat,64
+| AXBA1,2019-08-03T12:01:00,2019-08-03T12:02:00,mat,1
+
+The script can be run with the following command:
+
+.. code-block :: bash
+  python download_hydrophone_data.py --csv <path_to_csv> --output_path <output_directory>