Feature/move docs (#43)

* Move DIACOV documentation

* DFS

* Remove DFS again

* Documentation updates

README.md

@@ -2,7 +2,6 @@
 Collection of ACCORD DA tools. So far we have jbdiagnose and associated plotting. 
 
 Desirables:
-- diacov
 - festat
 - TuneBR
 - obstat
@@ -13,14 +12,14 @@ Desirables:
 cd AccordDaTools
 mkdir build
 cd build
-cmake .. -DCMAKE_INSTALL_PREFIX=/path/to/da_tools 
+cmake .. -DCMAKE_INSTALL_PREFIX=/path/to/da_tools
 make 
 ctest
 make install
 ```
 Add DA Tools to your PATH:
 ```
-export PATH=/path/to/da_tools:$PATH
+export PATH=/path/to/da_tools/bin:$PATH
 ```
 
 ## Tools
@@ -59,85 +58,4 @@ Example:
 ```
 plotjbdiag -l 50 -t vercor -p QQ -r ./ -e IRELAND75L65 
 ```
-### VarBC
-#### VARBC.cycle data extraction
-Help/usage:
-```
-varbcdiagnose -h
-```
-
-Example:
-```
-varbcdiagnose -i /path/to/directory/with/varbc_files/ -o varbc_diag_out
-```
-
-#### VarBC coefficient time-series plotting
-Help/usage:
-```
-plotvarbccoeff -h
-```
-
-Example:
-```
-plotvarbccoeff -i varbc_diag_out/VARBC_3_16_3309_210000 -b
-```
-
-### DFS
-#### DFS computation
-The dfscomp tool reads the (ASCII) data from an unperturbed CCMA and a perturbed CCMA.
-
-Help/usage:
-```
-dfscomp -h
-```
-
-Example:
-```
-dfscomp -p CCMA_2022050112.dat -u CCMA_2022050112_unpert.dat -o dfs2022050112.dat
-```
 
-### DIACOV
-First, you should have Festat output and the DIACOV binary compiled by Harmonie stored somewhere.
-Then, create the new directory, Jb files there. Example:
-```
-mkdir DiacovTest
-cd DiacovTest
-mkdir dataTest
-cp /path/to/Jb/data dataTest/.
-```
-#### Run Diacov
-Use rundiacov script to initiate the processing of the Jb files.
-Help/usage:
-```
-rundiacov -h
-```
-
-Example:
-```
-rundiacov -i dataTest -c METCOOP25D_65_2021100300-2021111006_412 -g 2.5 -d /path/to/DIACOV
-```
-
-#### Produce diagonal stats
-When you get DIACOV output, use diag_diacov script to produce stats in ASCII format, which are suitable for further plotting.
-Help/usage:
-```
-diag_diacov -h
-```
-
-Example:
-```
-diag_diacov -i dataTest -o stats
-```
-
-#### Produce plots
-Use plotdiacov script to produce the plots from ACSII files.
-Help/usage:
-```
-plotdiacov -h
-```
-
-You can either produce the plots for all of the available stat files, or to choose specific ones. Examples:
-```
-plotdiacov -d ./stats (the plots will be saved to the same directory as stat files)
-plotdiacov -i ./stats/corqu65.dat -o ./stats/corqu65.png (if the output file name is not specified, the plot is saved to the pwd with the default name "output.png")
-```

doc/make.jl

@@ -4,7 +4,8 @@ using Documenter
 pages = [
    "Jb diagnose" => "jbdiagnose.md",
    "cv header list" => "cvheaderlist.md",
-   "VarBc Coeff" => "varbccoeff.md"
+   "VarBc Coeff" => "varbccoeff.md",
+   "DIACOV" => "diacov.md"
 ]
 
 prettyurls = get(ENV, "CI", nothing) == "true" 

doc/src/dfs.md

@@ -0,0 +1,15 @@
+#DFS
+
+## DFS computation
+The dfscomp tool reads the (ASCII) data from an unperturbed CCMA and a perturbed CCMA.
+
+Help/usage:
+```
+dfscomp -h
+```
+
+Example:
+```
+dfscomp -p CCMA_2022050112.dat -u CCMA_2022050112_unpert.dat -o dfs2022050112.dat
+```
+

doc/src/diacov.md

@@ -0,0 +1,53 @@
+# DIACOV
+
+[TOC]
+
+## Background
+ 1. First, you should have Festat output and the DIACOV binary compiled by Harmonie stored somewhere.
+ 2. Then, create the new directory, copy the DIACOV binary and Jb files there. Example:
+
+## Tools
+```
+mkdir DiacovTest
+cd DiacovTest
+cp /path/to/DIACOV .
+mkdir dataTest
+cp /path/to/Jb/data dataTest/.
+```
+#### Run Diacov
+Use rundiacov script to initiate the processing of the Jb files.
+Help/usage:
+```
+rundiacov -h
+```
+
+Example:
+```
+rundiacov -i dataTest -c METCOOP25D_65_2021100300-2021111006_412 -g 2.5 -d /path/to/DIACOV
+```
+
+#### Produce diagonal stats
+When you get DIACOV output, use diag_diacov script to produce stats in ASCII format, which are suitable for further plotting.
+Help/usage:
+```
+diag_diacov -h
+```
+
+Example:
+```
+diag_diacov -i dataTest -o stats
+```
+
+#### Produce plots
+Use plotdiacov script to produce the plots from ACSII files.
+Help/usage:
+```
+plotdiacov -h
+```
+
+You can either produce the plots for all of the available stat files, or to choose specific ones. Examples:
+```
+plotdiacov -d ./stats                                     # the plots will be saved to the same directory as stat files
+plotdiacov -i ./stats/corqu65.dat -o ./stats/corqu65.png  # if the output file name is not specified, the plot is saved to the pwd with the default name "output.png"
+```
+

doc/src/varbccoeff.md

@@ -5,21 +5,19 @@
 
 This diagnostic tool is intended for use in the evaluation of the performance of the variational bias correction (VarBC) used for satellite observations in the context of HARMONIE-AROME data assimilation systems. In particular for evaluating the performance in time of the VarBC coefficients.
 
-
-## 2. Content
-
-The tool comprises two scripts:
-
+There are tool two tools required:
 - **varbcdiagnosis** for data extraction
-
 - **plotvarbccoeff** for VarBC coefficient time-series plotting 
 
-## 3. Usage
+## 2. Tools
 
-**varbcdiagnosis** extracts VarBC coefficients for a certain satellite/instrument and all the channels with data and for 
-a certain period of time. VarBC coefficients are extracted from VARBC.cycle files.
+### VARBC.cycle data extraction
 
-Script **varbcdiagnosis** arguments:
+**varbcdiagnose** extracts VarBC coefficients for a certain satellite/instrument and all the channels with data and for a certain period of time. VarBC coefficients are extracted from VARBC.cycle files.
+
+Help/usage:
+```shell
+$~> varbcdiagnose -h
 
         -i input-directory 
            where VARBC.cycle files are stored, usually in the form ./EXP/YYYY/MM/DD/HH (EXPERIMENT, Year, Month, Day and                Hour)
@@ -35,21 +33,31 @@ Script **varbcdiagnosis** arguments:
            See https://apps.ecmwf.int/odbgov/sensor/ for more details.
 
         -h Help! Print usage information.
+```
 
+Example:
+```shell
+$~> varbcdiagnose -i /path/to/directory/with/varbc_files/ -o varbc_diag_out
+```
 
-**plotvarbccoeff** produces a plot for a selected satellite, sensor, channel and hour (optional, if not present all the assimilation cycles with observations are included). 
+### VarBC coefficient time-series plotting
 
-Script **plotvarbccoef** arguments:
+**plotvarbccoeff** produces a plot for a selected satellite, sensor, channel and hour (optional, if not present all the assimilation cycles with observations are included). 
 
+Help/usage:
+```
+$~> plotvarbccoeff -h
        -h, --help  show this help message and exit
        -i IPATH    Input file name
        -l LLOC     Legend location using matplotlib syntax
        -d LABELS   Optional experiment description
        -b          Batch mode, produce png only
+```
 
-For example for METOP-B (3), MHS (15), Channel 9 at 21 UTC (or at all assimilation cycles with data), IPATH is
-output-directory/VARBC_3_15_9_210000 (or output-directory/VARBC_3_15_9).
-
+Example: For METOP-B (3), MHS (15), Channel 9 at 21 UTC (or at all assimilation cycles with data), IPATH is output-directory/VARBC_3_15_9_210000 (or output-directory/VARBC_3_15_9).
+```
+plotvarbccoeff -i varbc_diag_out/VARBC_3_16_3309_210000 -b
+```
 
 ## 4. Interpretation