1. Writing a diagnostic script or a metrics set

1.1. Basics

The development of a new diagnostic (or set of diagnostics) requires the following steps before getting started:

  • Creating a FEATURE BRANCH (see Part annex_b) in the applicable project subdirectory of the Git repository (via Git, see Section 1). Developers are encouraged to work actively through the Git repository. Regular “commits” to the repository help to document changes introduced to the ESMValTool and allow for efficient sharing of code with other developers.
  • Creating a standard namelist following the template described in Section 3.5.

General coding rules and conventions

  • Regular updates of the FEATURE BRANCH (see Part annex_b) are strongly recommended in order to keep it synchronized with the DEVELOPMENT BRANCH (see Part annex_b).
  • Modularizing all diagnostic scripts as much as possible, using the general-purpose code in lib/ and separating the diagnostic calculations from the plotting routines.
  • Before creating new functions or procedures, it should be considered to use or extend the existing routines within lib/. Each header (see Section 1.2) provides an overview of the already implemented functions and procedures.
  • Functions and procedures specific to a given diagnostic shall go in the subdirectory diag_scripts/aux/<diagnostic> (see Section Table 1.2).
  • Main namelist, diag_scripts, functions and procedures shall be documented within the respective file using the templates (see Section 3.5 and Section 1.2).
  • Each diag_script shall contain a call to the function write_reference (see also Section 1.8) in order to generate a respective acknowledgements log file (Section 1.8).

The reintegration of the feature branch into the DEVELOPMENT BRANCH (see Part annex_b) can only be done by the core development team (see Section 3.2) who shall be contacted as soon as the FEATURE BRANCH is ready for integration into the DEVELOPMENT BRANCH. Before contacting the core development team the following items should be checked:

  • The new FEATURE BRANCH runs with different configuration options.
  • If the lib/ routines have been modified, all the diagnostics using these routines have to be tested (see automated testing, Section 1.10).
  • The new code complies with the coding rules and standards (see Section 1.7) and follows the ESMValTool directory structure (see Table 1.2).
  • All authors, contributors and data are properly acknowledged and referenced in the acknowledgements log file (see Section 1.8).
  • If the new observational data are used, the scripts to “cmorize” these data shall also be made available and placed as reformat_obs_<name> into the folder reformat_scripts/obs/. Once the FEATURE BRANCH has been integrated into the DEVELOPMENT BRANCH (see Part annex_b), it shall be deleted from the repository.

1.2. Standard template

All (diagnostic) scripts and namelists in the ESMValTool are documented following the standards defined by templates (see Section 3.5 for the namelist template). The following describes the standard header for diagnostics scripts. The parts marked as [text] are the ones to be modified by the author.

  • The modification history is in reverse chronological order (i.e., most recent on top) and the last entry always contains the “written” statement (optionally with a statement such as “based on” if derived from existing code).
  • The author of each entry in the modification history is indicated with the author id as given in the author list in the master reference file (doc/MASTER_authors-refs-acknow.txt, e.g., A_surn_na = surname, name).
  • All lines should be limited to a maximum of 79 characters (see Section 1.6). Exceptions can be made to improve the readability of the code.
;;#############################################################################
;; TITLE OF THE DIAGNOSTIC
;; Author: [Name Surname (Affiliation, Country)]
;; [PROJECT-NAME]
;;#############################################################################
;; Description
;;    [A short description of the diagnostic]
;;    [Additional description of the diagnostic]
;;    [Add more bullets if required]
;;
;; Required diag_script_info attributes (diagnostics specific)
;;    [att1]: [short description]
;;        [keep the indentation if more lines are needed]
;;    [att2]: [short description]
;;
;; Optional diag_script_info attributes (diagnostic specific)
;;    [att1]: [short description]
;;    [att2]: [short description]
;;
;; Required variable_info attributes (variable specific)
;;    [att1]: [short description]
;;    [att2]: [short description]
;;
;; Optional variable_info attributes (variable specific)
;;    [att1]: [short description]
;;    [att2]: [short description]
;;
;; Caveats
;;    [List possible caveats or limitations of this diagnostic]
;;    [Features to-be-implemented shall also be mentioned here]
;;
;; Modification history
;;    [YYYYMMDD-A_X4Y4: extended...]
;;    [YYYYMMDD-A_X3Y3: bug-fixed...]
;;    [YYYYMMDD-A_X2Y2: adapted to...]
;;    [YYYYMMDD-A-X1Y1: written.]
;;
;; #############################################################################

load ...
load ...

begin
    ...
    ...
end

1.3. Library functions

The folder diag_scripts/lib/ contains general purpose routines used by several diagnostic scripts, these library routines are grouped in subfolders by language, i.e.,

diag_scripts/lib/ncl

diag_scripts/lib/python

diag_scripts/lib/R

Library routines are grouped into individual files by topic, some examples for the NCL library routines are:

  • diag_scripts/lib/ncl/latlon.ncl: routines to compute grid cell areas, weighted area averages, etc…
  • diag_scripts/lib/ncl/regridding.ncl: routines interfacing the ESMF regridding functions in NCL
  • diag_scripts/lib/ncl/statistics.ncl: statistical routines not (yet) implemented in the standard distribution of NCL
  • diag_scripts/lib/ncl/style.ncl: centralized control of NCL plot styles, e.g., defines line colors/dashes/thickness for each model name in CMIP5, based on the style files in diag_scripts/lib/ncl/styles/.

For further details on the library functions, see the documentation given in the header of the functions themselves (see Section 1.2 for a template).

1.4. Plotting functions

The folder plot_scripts/ contains general purpose routines used for plotting by the diagnostic scripts. The plotting functions should facilitate the separation of computing the diagnostic and displaying the result. To this end they should handle both the case when called directly from the diagnostic script (with data to visualize as an argument), and the case when the computed diagnostic is passed along as a netCDF file. These plotting routines are grouped in subfolders by language,

  • plot_scripts/ncl
  • plot_scripts/python
  • plot_scripts/R

Each subfolder further groups the plotting routines into files by topic, e.g., for the NCL library routines:

  • plot_scripts/ncl/contour_maps.ncl: interfaces NCL plotting routines for contour map plots, contour polar maps and adding markers to contour maps
  • plot_scripts/nc/scatterplot.ncl: interfaces NCL plotting routines for of scatter plots

For further details on the plotting functions, see the inline documentation in the functions themselves.

1.5. Adding new variables

Adding new variables requires changes to reformat_scripts/recognized_vars.dat (Section 1.5.1) and possibly also to reformat_scripts/recognized_units.dat (Section 1.5.2). In addition, a new definition file variable_defs/<varname>.ncl is needed (Section 1.5.3; see Table 3.8 for a list of currently available variable definition scripts). If the variable is a non-derived variable (explained in Section 1.5.3) it also needs to be defined in a file named reformat_scripts/cmor/CMOR_<variable>.dat (see Section 1.5.4).

1.5.1. reformat_scripts/recognized_vars.dat

New variables have to be added to reformat_scripts/recognized_vars.dat. Two lines are added per variable:

  • std_name = varname
    standard CMOR variable name
  • alt_name = alternative name 1, alternative name 2, …
    comma separated list of alternative variable names

Example (surface pressure)

  • std_name = ps
  • alt_name = aps,PS,psurf

The ESMValTool reformat scripts will look for variable “varname” in the input files. If not found, the alternative variable names “alternative name 1”, “alternative name 2”, etc. are tried before an error message is issued that the variable could not be found.

1.5.2. reformat_scripts/recognized_units.dat

The file reformat_scripts/recognized_units.dat contains a list of known units. If needed, the unit of the newly added variable can be added. There are two lines per unit:

  • std_name = unit
    standard CMOR unit
  • alt_name = alternative unit
    comma separated list of possible alternative units and corresponding conversion factor, defined as units[cmor] = units[alternative] * factor

Example (dobson units)

  • std_unit = DU
  • alt_unit = g m-2, 4.6707e-5, kg m-2, mol m-2, 2.2414e-3

1.5.3. variable_defs/varname.ncl

The file variable_defs/<varname>.ncl is a NCL script containing the declaration of the variable “varname” including its specific attributes. In case of derived variables, a function “calculate” calculating the derived variable must be defined in the script <varname>.ncl (see Table 3.8 for a list of currently available variable definition scripts).


Remarks

  1. For derived variables, a statement specifying the (standard, non-derived) variables required to calculate the derived variable is needed. In the example given below, this statement in the beginning of the NCL script looks like

    ; Requires: rsut:T2*s,rsutcs:T2*s

    In this example, the two standard variables “rsut” and “rsutcs” are needed to calculate the shortwave cloud forcing.

  2. Variable attributes are specified as attributes of the variable “variable_info” (see examples below). In order to activate the variable attributes, “variable_info” must be set to “True”. Some examples for frequently used attributes are:

    • variable_info@derived = False (True)
    • variable_info@long_name = “…”
    • variable_info@units = “…”
    • variable_info@standard_name = “…”
    • variable_info@short_name = “…”

Example (precipitation, standard variable)

; Requires: none
variable_info = True
variable_info@derived = False

Example (shortwave cloud forcing, derived variable)

; Requires: rsut:T2*s,rsutcs:T2*s

[...]

variable_info = True
variable_info@derived = True
variable_info@long_name = "CS Shortwave cloud radiation effect"
variable_info@units = "W m-2"

undef("calculate")
function calculate( index [1] : integer, \
                    variable [1] : string, \
                    field_type [1] : string )
;;                  return_val [1] : logical
;; Arguments:
;;    index - index to current infile defined in the
;;            'interface_data/ncl.interface'-file
;;    variable - Current variable as string
;;    field_type - string with field type classification
;; Return value:
;;    data_new  logical

local tmp, tmp1, tmp2, dum1, dum2, dum, i, verbosity
begin
    data_new = True
    tmp1 = read_data(index, "rsut", "T2Ms")
    tmp2 = read_data(index, "rsutcs", "T2Ms")
    dum1 = extract_data(index, tmp1, -1, 0, 0)
    dum2 = extract_data(index, tmp2, -1, 0, 0)

    dum = dum1
    dum = dum2 - dum1
    dum@long_name = variable_info@long_name
    dum@units = variable_info@units
    add_data_var(index, data_new, dum, variable)

    return(data_new)
end

1.5.4. reformat_scripts/cmor/CMOR_variable.dat

Each standard variable (non-derived) also needs a configuration file indicating the expected units of the variable. The expected units are read from the file reformat_scripts/cmor/CMOR_variable.dat which follows the definitions in the official CMOR tables for CMIP5. If this file is missing for a specific variable, it can be downloaded from http://pcmdi.github.io/cmor-site/tables.html. If a CMOR table for the new variable is not available, the user can create a new one based on the existing tables (e.g., following the example in reformat_scripts/cmor/CMOR_mmrbcfree.dat based on reformat_scripts/cmor/CMOR_mmrbc.dat).

Example, reformat_scripts/cmor/CMOR_pr.dat

SOURCE: CMIP5
!============
variable_entry:    pr
!============
modeling_realm:    atmos
!----------------------------------
! Variable attributes:
!----------------------------------
standard_name:     precipitation_flux
units:             kg m-2 s-1
cell_methods:      time: mean
cell_measures:     area: areacella
long_name:         Precipitation
comment:           at surface; includes both liquid and solid phases from  all types
                   of clouds (both large-scale and convective)
!----------------------------------
! Additional variable information:
!----------------------------------
dimensions:        longitude latitude time
out_name:          pr
type:              real
valid_min:         0
valid_max:         0.001254
ok_min_mean_abs:   2.156e-05
ok_max_mean_abs:   3.215e-05
!----------------------------------

1.6. Coding rules and standards

The purpose of the code conventions used in ESMValTool is to ensure a high degree of consistency in the code layout. Consistently structured code increases readability and understanding of the code making it easier for developers and users work with a given piece of the code base. It is important to emphasize two points:

  • Checking the code consistency should be done by software as this allows the check to be done automatically.
  • Code checkers are available at util/ncl-checker/pep8.py (NCL) and util/pep8-checker/pep8.py (Python).

The code conventions are guidelines and should be treated as such. There are circumstances when it is advisable, for various reasons such as improved readability, to ignore some of the guidelines.

Code conventions used for Python

Python code should conform to the PEP-8 style guide [PEP8 2001]. Recommended tools to check Python code is the official PEP8-checker that is provided with the ESMValTool distribution (util/pep8-checker/pep8.py) and PyFlakes.

To use it on a python file, cd into util/pep8-checker/, and run,

cd util/pep8-checker
python pep8.py <path-to-python-file>

Python: Pyflakes

Besides the PEP8-checker also the use of the ‘pyflake’-tool is recommended (see the pyflakes homepage https://pypi.python.org/pypi/pyflakes for details). For a local install of pyflakes, try virtualenv, e.g., if the virtualenv already is installed, run

source sandbox-pybot/bin/activate
pip install --upgrade pyflakes
pyflakes <python-file>

Code conventions for NCL

NCL code in ESMValTool should follow the PEP-8 style guides. An NCL adapted version of the Python PEP-8 checker is available in the ESMValTool repository (util/ncl-checker/pep8.py). Please note that the NCL checker may report some false-positive (e.g., the reading symbol -> is not recognized as such).

To use the NCL version of the PEP8-checker provided with the ESMValTool distribution, run

cd util/ncl-checker
python pep8.py <path-to-NCL-file>

The NCL-version is adaption of the Pyhton checker and works satisfactorily as long as one keeps in mind the false positives it finds due to language differences between Python and NCL. These false positives may be addressed in the future depending on priorities.

Code conventions for R

The code conventions for R should conform to the formatting produced by the R parser tree. This method is further described at “Tidying-R-code” (https://cran.r-project.org/doc/manuals/R-exts.html#Tidying-R-code). Note that this method can only be considered semi-automatic since it does preserve comments (they need to be repatched) and does not produce very nice line breaks.

1.7. Documentation of software

In order to ensure that all code can be maintained, all diagnostic packages must be well documented. It is the responsibility of the software developers to embed their documentation into the namelist and source code. For details see Sections 1.9 and 2. Documentation systems exist to organize embedded documentation into well structured, linked documents.

  • R: documentation should follow CRAN guidance.
  • Python: the Sphinx package allows embedded documentation to be assembled into indexed web pages (see Section 1.9)
  • NCL and namelists: a Sphinx extension has been developed to extract code documentation for NCL and namelists (see Section 1.9)

1.8. The acknowledgements log file

The acknowledgements log file automatically created by each diagnostic (see also Section 6.1) is written by the function write_references (interface_scripts/messaging.ncl, see below), which uses the tags defined in the master reference/acknowledgements file (doc/MASTER_authors-refs-acknow.txt) as input. This master file lists all authors and contributors (tags starting with A_), the diagnostic references (tags with D_), references for observational data (tags E_) and projects (tags P_).

The function write_references

The function write_references (defined in interface_scripts/messaging.ncl) should be called at the end of each diagnostic script in order to write the acknowledgements log file. The function has the arguments “author(s)”, “contributors”, “diagnostics”, “observations”, “projects” which are arrays of strings. All strings (“tags”) used must be defined in the master reference file doc/MASTER_authors-refs-acknow.txt. The tags are then replaced by the function write_references with their definition when writing the acknowledgements log file. All tags in the master reference file are sorted by category of which there are four in total:

A_xxx = authors, contributors (xxx = author name)
e.g., A_###

D_xxx = diagnostics
e.g., D_righi15gmd = Righi et al., Geosci. Model Dev., 8, 733-768 doi:10.5194/gmd-8-
  733-2015, 2015.

E_xxx = observational data
e.g., E_era40 = ERA40

P_xxx = project
e.g., P_embrace = EU FP7 project EMBRACE

write_references(diag_script, \
        "A_###", \
        (/"D_righi15gmd", "D_gleckler08jgr"/), \
        (/"E_kalnay96bams", "E_erainterim", "E_airs", "E_ceresebaf", "E_srb"/), \
        (/"P_embrace", "P_esmval"/))

1.9. Documentation of source code

The Sphinx documentation generator (http://sphinx-doc.org) is used to organize and format ESMValTool documentation, including text which has been extracted from source code. Sphinx can help to create documentation in a variety of formats, including HTML, LaTeX (and hence printable PDF), manual pages and plain text.

Sphinx may be obtained from http://sphinx-doc.org/install.html; an overview of its workings is available at http://sphinx-doc.org/tutorial.html. In ESMValTool, Sphinx has been used to set up the files in doc/sphinx. Running make <target> in that directory will cause the documentation to be built, and its output placed in the build/<target> subdirectory. Here, <target> is the format required for example, html, latexpdf, man or text for the four example formats mentioned above. Running make by itself will generate a complete list of output formats.

Sphinx was originally developed for documenting Python code, and one of its features is that it is able using the so-called autodoc extension to extract documentation strings from Python source files and use them in the documentation it generates. This feature apparently does not exist for NCL source files (such as those which are used in ESMValTool), but it has been mimicked (or more-or-less reverse-engineered) here via the Python script doc/sphinx/scripts/process_ncl_docs.py, which walks through a subset of the ESMValTool NCL scripts, extracts function names, argument lists and descriptions (from the comments immediately following the function definition), and assembles them in a subdirectory of doc/sphinx/source. These output files are in the so-called reStructuredText format (see, e.g., http://docutils.sourceforge.net/rst.html), which is the markup language used by Sphinx; running make in doc/sphinx builds the ESMValTool documentation from them, as noted above.

Note

See Section 2.2 for more details on how to document a new diagnostic.

1.10. Automated testing

Any changes to a programming code have the risk of introducing unwanted side effects on some other parts of a code and introduce bugs. Routine and automated testing is therefore essential to maximize the code quality and ensure integrity of all diagnostics implemented within ESMValTool.

1.10.1. Setup and general workflow

Automated testing within the ESMValTool is implemented on two complementary levels:

  • unittests are used to verify that small code units (e.g. functions/subroutines) provide the expected results
  • integration testing is used to verify that a diagnostic integrates well into the ESMValTool framework and that a diagnostic provides expected results. This is verified by comparison of the results against a set of reference data generated during the implementation of the diagnostic.

Installation of the test environment

All scripts required to run the test environment are provided together with the ESMValTool code. Two external python packages are required which can be installed using the python package manager (pip; https://pypi.python.org/pypi/pip) as follows in a linux environment:

# install nosetests (https://nose.readthedocs.org/en/latest/)``
pip install nose
# install easytest
pip install easytest

General functionality of testing framework

Each diagnostic is expected to produce a set of well-defined results. These are files in a variety of formats and types (e.g. graphics, data files, ASCII files …). While testing results of a diagnostic, a special namelist file is executed by ESMValTool which runs a diagnostic on a limited set of test data only. A small test data set is chosen to minimize executing time for testing while ensuring on the other hand that the diagnostic produces the correct results. The following general tests are implemented at the moment for diagnostics with available test data:

  • Check for file availability: a check is performed that all required output data have been successfully generated by the diagnostic. A missing file is always an indicator for a failure of the program.
  • File checksum: While the previous test only checks if a file is available, the checksum verifies if the content of a file is similar. Currently the MD5 checksum is used to verify that contents of a file are the same. The MD5 checksum is a good proxy for the similarity of two files and is used regularly to ensure integrity between files when transferring files between different computers.
  • Graphics check: For graphic files an additional test is therefore implemented which verifies that two graphical outputs are identical. This is in particular useful to verify that outputs of a diagnostic remain the same after code changes.

Testing the ESMValTool diagnostics

Unittests are implemented for each diagnostic independently. Details on running unittests using nose is as simple as going to the ESMValTool root directory and then execute the following shell command:

# run nosetests
nosetests

This will search recursively for test files and execute these tests. A statistic on success and failures is provided at the end of execution. More details on using nose can be found in the package’s documentation (https://nose.readthedocs.org/en/latest/).

To run integration tests for each diagnostic, a small script needs to be written once. An example for a file named esmvaltooltest.py is provided in Section 1.10.2. To run all tests for diagnostics implemented in this file the following command needs to be executed:

# run integration tests
python esmvaltooltest.py

A summary of success and failures is provided as output.

1.10.2. Example test implementation for a diagnostic

In the following an example is given how to implement a test environment for a new diagnostic with just a few lines of code. File: esmvaltooltest.py

"""
sample script for ESMValTool testing
"""

from esmvaltool import ESMValToolTest

"""
Define a new class for testing a particular diagnostic
"""

class PerfMetricCMIP5Test(ESMValToolTest):
    def __init__(self):
        # 1) define here the name of the test namelist
        nml_name = 'namelist_perfmetrics_CMIP5_test.xml'

        # 2) specify here the full path of the namelist
        # (relative to ESMValTool root)
        nml = 'nml/test_suites/dlr/' + nml_name

        # 3) define here the location of the reference data directory
        #    note that it is expected that the directory has the same
        #    name as the namelist
        refdir = esmval_dir + os.sep + os.path.splitext(nml_name)[0] + \
                 '/output/plots/'

        # initialize the parent class
        super(PerfMetricCMIP5Test,self).__init__(nml=nml,
              refdirectory=refdir, esmval_dir=esmval_dir)

# --------------------------------------------

# This is how you run a test
PT = PerfMetricCMIP5Test()  # create instance of test class
PT.run_nml()  # run the testing namelist
PT.run_tests(execute=False, graphics=None,
             checksum_files='all',files='all')  # perform tests

1.11. Checklist

The following table can be used as a list of items to be done/checked when writing a new diagnostic.

Table 1.1 Example checklist for implementing new diagnostics and new observational datasets.
diagnostic model data observational data
header in diagnostic code preprocessing (reformatting routines - if applicable) preprocessing (reformatting script)
header in namelist list of tools (if applicable) list of tools (if applicable)
documentation of diagnostic (.rst file + example images) References header in reformatting script (if applicable)
test data test data references
FEATURE BRANCH updated with latest DEVELOPMENT BRANCH   test data
list of tools, libraries, etc.    
references    
contact person for scientific support