Docs updated with new links and modules (#119)

docs/guide_user.rst

@@ -15,15 +15,14 @@ These can be processed from Level 0 to a Level 3 data product as an ``AWS`` obje
 
 .. code:: python
 
-   from pypromice.process.aws import AWS
+   from pypromice.process import AWS
 
     # Define input paths
     config = "src/pypromice/test/test_config1.toml"
     inpath = "src/pypromice/test/"
-    vari = "src/pypromice/process/variables.csv"
 
     # Initiate and process
-    a = AWS(config, inpath, var_file=vari)
+    a = AWS(config, inpath)
     a.process()
     
     # Get Level 3
@@ -33,15 +32,14 @@ All processing steps are executed in ``AWS.process``. These can also be broken d
 
 .. code:: python
 
-    from pypromice.process.aws import AWS
+    from pypromice.process import AWS
 
     # Define input paths
     config = "src/pypromice/test/test_config2.toml"
     inpath = "src/pypromice/test/"
-    vari = "src/pypromice/process/variables.csv"
 
     # Initiate
-    a = AWS(config, inpath, var_file=vari)
+    a = AWS(config, inpath)
 
     # Process to Level 1
     a.getL1()
@@ -65,7 +63,7 @@ The Level 0 to Level 3 processing can also be executed from a CLI using the ``ge
 
 .. code:: console
 
-    $ getL3 -v src/pypromice/process/variables.csv -m src/pypromice/process/metadata.csv -c src/pypromice/test/test_config1.toml -i src/pypromice/test -o src/pypromice/test
+    $ getL3 -c src/pypromice/test/test_config1.toml -i src/pypromice/test -o src/pypromice/test
 
 
 Loading PROMICE data
@@ -98,7 +96,7 @@ AWS data can be downloaded to file with pypromice. Open up a CLI and use the ``g
 
 .. code:: console
 
-	$ getData -n KPC_U
+	$ getData -n KPC_U_hour.csv
 
 Files are downloaded to the current directory as a CSV formatted file. Use the ``-h`` help flag to explore further input variables.
 
@@ -135,5 +133,5 @@ If you would rather handle the AWS data as an ``xarray.Dataset`` object then the
 
 .. code:: python
 
-	ds = xr.Dataset.from_dataframe(df) 
+	ds = xr.Dataset.from_dataframe(df)
 

docs/technical_data.rst

@@ -17,7 +17,7 @@ Level 0 is raw, untouched data in one of three formats:
 Level 1
 =======
 - [X] Engineering units (e.g. current or volts) converted to physical units (e.g. temperature or wind speed)
-- [ ] Invalid/bad/suspicious data flagged
+- [X] Invalid/bad/suspicious data flagged
 - [X] Multiple data files merged into one time series per station
 
 

docs/technical_process.rst

@@ -22,8 +22,8 @@ Payload decoder
 
 ``PayloadFormat`` handles the message types and decoding templates. These can be imported from file, with two default CSV files provided with pypromice - payload_formatter.csv_ and payload_type.csv_.
 
-.. _payload_formatter.csv: https://github.com/GEUS-Glaciology-and-Climate/pypromice/blob/main/src/pypromice/payload_formats.csv
-.. _payload_type.csv: https://github.com/GEUS-Glaciology-and-Climate/pypromice/blob/main/src/pypromice/payload_types.csv
+.. _payload_formatter.csv: https://github.com/GEUS-Glaciology-and-Climate/pypromice/blob/main/src/pypromice/tx/payload_formats.csv
+.. _payload_type.csv: https://github.com/GEUS-Glaciology-and-Climate/pypromice/blob/main/src/pypromice/tx/payload_types.csv
 
 
 Payload processing
@@ -38,8 +38,7 @@ The following function can be executed from a CLI to fetch ``L0`` transmission m
 .. code:: console
 	
 	$ getL0tx -a accounts.ini -p credentials.ini -c tx/config 
-	-f payload_formats.csv -t payload_types.csv -u last_aws_uid.ini 
-	-o tx
+	-u last_aws_uid.ini -o tx
 
 .. note::
 
@@ -55,13 +54,13 @@ To process from L0>>L3, the following function can be executed in a CLI.
 
 .. code:: console
 	
-	$ getL3 -v variables.csv -m metadata.csv -c config/KPC_L.toml -i . -o ../../aws-l3/tx"
+	$ getL3 -c config/KPC_L.toml -i . -o ../../aws-l3/tx"
 
 And in parallel through all configuration .toml files ``$imei_list``
 
 .. code:: console
 
-	$ parallel --bar "getL3 -v variables.csv -m metadata.csv -c ./{} -i . -o ../../aws-l3/tx" ::: $(ls $imei_list)
+	$ parallel --bar "getL3 -c ./{} -i . -o ../../aws-l3/tx" ::: $(ls $imei_list)
 
 
 Station configuration
@@ -112,4 +111,4 @@ The TOML config file has the following expectations and behaviors:
 
 	Be aware the column names should follow those defined in the variables look-up table found here_. Any column names provided that are not in this look-up table will be passed through the processing untouched.
 
-.. _here: https://github.com/GEUS-Glaciology-and-Climate/pypromice/blob/main/src/pypromice/variables.csv
+.. _here: https://github.com/GEUS-Glaciology-and-Climate/pypromice/blob/main/src/pypromice/process/variables.csv