unittest coverage (#95)

* remove `__init__.py` from test directory * first draft of example test * test generated `fort.15` files against reference * Fix code style issues with oitnb * update examples * fix directories * update reference files * reduce to only testing `example_3.py` * Update best_track.py (#106) optional annotation of track times. * fix infinity comparison with string * only accept path * some summary stats of `BestTrack` (#107) * A summary stats method for `BestTrack` * Set start and end dates automatically in the case of tides + wind forcing. Co-authored-by: Keith Roberts <[email protected]> Co-authored-by: Lint Action <[email protected]> Co-authored-by: Jaime R Calzada <[email protected]> * add ADCIRC v55 ICS options (#109) * add ADCIRC v55 ICS options * fixed case where CRS has no coordinate operation * replace `CPP` with `EQUIDISTANT_CYLINDRICAL` * add ICS setter * filter ICS input to valid ADCIRC values * formatting * update `BestTrackForcing` (#111) * update `BestTrackForcing` with updates from @WPringle and @zacharyburnettnoaa done in `ensembleperturbation/tropicalcyclone/atcf.py` * Fix code style issues with oitnb * remove redundant functions * prevent rechecking name validity if not storm ID is given * fix direction and speed calculations * get correct ATCF URL from archive if it is in the storm table * remove unused imports * set default file deck and mode * copy previous record data if data does not exist * use `BEST` and file deck B for best track type * add back type hint * use EPSG * update property name * update reference files * rename `requested_record_type` to `record_type` * handle Pint `Quantity` * handle no internet * update copy method to directly copy data * set configuration on `.__init__()` Co-authored-by: Lint Action <[email protected]> * hash location columns to determine when to compute velocity * test location hashing * add tests for vortex file decks and reading from file with no internet * add reference file * use `.loc` for setting slice * suppress `SettingWithCopyWarning` when instantiating `VortexForcing` * build on Windows (#52) * if installing on Windows, download precompiled binaries for GDAL and Fiona * fix scope error * use `python setup.py install` instead of `pip install .` * remove Python 3.6 (scipy deprecation) * separately versioned builds are not needed * use sudo when installing libraries * forgot the && * add libgeos to install * add libgeos to install * add OS conditions to dependency install * use conditions for linux library install * fix not error * explicitly use ubuntu * fix key hit * remove gdal version pin * install to conda if detected * comma * update windows build * update dependencies * update dependencies * Fix code style issues with oitnb * improvements to dependency installation in setup * try subdependencies first * check package in subdependencies on every interation * use `subprocess.run()` * use `shell=True` * try `pip install` before `pipwin install` Co-authored-by: Lint Action <[email protected]> * install to `--user` in build * addressing NFOVER with DEBUG_WARN_ELEV compiler directive (#115) * addressing NFOVER with DEBUG_WARN_ELEV compiler directive * Fix code style issues with oitnb * Proposed changes to NFOVER handling. * Fixed typo. * Fixed type checking. Co-authored-by: Keith Roberts <[email protected]> Co-authored-by: Lint Action <[email protected]> Co-authored-by: Jaime R Calzada <[email protected]> * improvements to creating `VortexForcing` from file (#118) * if the given file does not exist, raise `FileNotFoundError` if the string does not contain useful data * store a filename in the `VortexForcing` object so that it can be recreated without access to internet * read from filename if it exists * optimize `.import_stations()` * Fix bug where final hull multipolygon was not being aggregated correctly * Improved interp of near-shore points for TPXO * fixed fort.13 enumeration issue * Fix code style issues with oitnb * fix merge * Fix code style issues with oitnb * Renamed kwarg for import_nodal_attributes * Fix code style issues with oitnb * add type hints + reorder setters to be after properties + use native timedelta methods + fix stations parser + other minor changes (#120) * use timedelta comparisons and division * reorder setters + use type hints * reorder setters + use type hints * fix setter before getter * Fix bug where final hull multipolygon was not being aggregated correctly * Improved interp of near-shore points for TPXO * fixed fort.13 enumeration issue * Fix code style issues with oitnb * fix merge * Fix code style issues with oitnb * Renamed kwarg for import_nodal_attributes * Fix code style issues with oitnb * Revert to previous stations parser, preseve precision of input values for outputs * Fix code style issues with oitnb * Make coastline plotting optional + disable on tests due to server blocking * Fix code style issues with oitnb * update the names the stations parser looks for to be `NSTAE`, `NSTAV`, `NSTAC`, and `NSTAM` * add test for importing stations * call `super().__init__()` in constructor * enumerate station types * Fix code style issues with oitnb * minor streamlining * turn of Windows tests * possible fix for #116 Co-authored-by: jreniel <[email protected]> Co-authored-by: Lint Action <[email protected]> * Correcting WTIMINC line for vortex forcing (NWS = 8, 19, 20). (#128) * moving WTIMINC for BestTrackForcing class into fort15.py so can use the coldstart time instead of vortex start time on WTIMINC line * add type hint * simplify if statement * update reference files Co-authored-by: zachary.burnett <[email protected]> * Feature/wind swath (#126) * adding method to compute wind swath polygon (34-kt, 50-kt or 64-kt isotach) for given best_track class * adding alphashape logic to ensure output is always a single Polygon with relatively smooth edges * adding option to set alpha to None to return the swath without alphashape operation, also adding some information * formatting * construct swath from individual convex hulls of pairs of mixed isotachs at neighboring times * formatting * split isotach retrieval into separate method * remove `lru_cache` usage * remove alphashape from dependencies Co-authored-by: zachary.burnett <[email protected]> * add equality operator to compare meshes and forcings (#129) * add equality operator to compare meshes * offload nodal equality to `Nodes` object * add test * add object checks * equality of forcings * add copy method for adcirc mesh * check for equal boundaries * test copy method * check equality of nodal attributes * check absolute of values because it is copied as negative * flip values upon reading `fort.14` but not in `.to_dict()` * flip values upon writing `fort.14` * formatting * fix writing function * log warning instead of raising exception when file exists and `overwrite` is `False` * log warning instead of raising exception when file exists and `overwrite` is `False` (2/2) * log warning instead of raising exception when file exists and `overwrite` is `False` (3/2) * reduce amount of times `VortexForcing` connects to the internet (#131) * get storm ID from dataframe * remove unecessary call to internet from storm ID setter * update tests with new storm ID getter * check by name if basin / number fails * update calls to utilize new changes * add input file * update bare `except` * only add new attribute if it doesn't already exist, also improve attribute equality check (#133) * only add new attribute if it doesn't already exist * improve equality check * revamp grid handling and writing 2dm file + mesh hull calculation (#121) * revamp grid handling and writing 2dm file * log writing durations * use `.to_string()` to write `grd` * update reference files * change print to logging * fix instances of nodes usage * fix dataframe call * simplify multipolygon generation * move polygons into interiors of others * collect stray interiors of polygons * simplify loop * don't need to explicitly create multilinestring * formatting * formatting * use new `Rings` object * merge * update equality * update reference files * catch socket block * replace area estimation (with convex hull) with actual triangle area using S equation * revert * invert all values when writing * use grd function * get array * only initialize rings of 3 or more * revert * fix accessor to pandas object * use `isclose` to determine area * update reference files * use pandas index getter * adding buffer command to make mesh envelope valid * remove polgyon testing for stations for now * Fix code style issues with oitnb * implement hull checks if requested by user during station import * add formatted logger that splits output between `stdout` and `stderr` (#132) * add formatted logger that splits output between `stdout` and `stderr` * formatting * formatting * Fix code style issues with oitnb Co-authored-by: Lint Action <[email protected]> * use new parameter in test * add print to setup.py * faster conda package check * hotfix for start date retrieval * use function to filter log output * update reference files * fix logger name * import logging * fix flake8 errors * update badges * update lead developer now that @jreniel has stepped back from active development * move `VortexForcing` into `ModelForcings` (#139) * move `VortexForcing` into `ModelForcings` * order dependencies alphabetically * import from `modelforcings` * this was incorrect syntax, my bad * move `validation` module to https://github.com/zacharyburnettNOAA/CoupledModelValidation/tree/main/coupledmodelvalidation (#140) * import from `typing` instead of directly from `collections` (deprecated) * remove `colored_traceback` * generate documentation automatically with Sphinx (#141) * remove submodule as it no longer exists * first draft of Sphinx docs * copy documentation from ADCIRCpy NOAA tech report * add figures * add references to TOC and also turn citations into footnotes * name abstract * use `coupledmodelvalidation` for `plot_fort61` * `:python:` is not a valid directive * add references to abstract, and fix references page to list all citations * add docs badge and link to docs Co-authored-by: zacharyburnett <[email protected]> * reorder TOC * fix logger * formatting * add PDF to build * update acknowledgments.rst * change `modelforcings` to `stormevents` (#142) * change `modelforcings` to `stormevents` * formatting * update documentation * update documentation * test latest version of Python * formatting * support Python 3.6 build * update to use new StormEvents API * update to use new StormEvents NHC storm list sources * formatting * this TODO has been resolved by new code in `stormevents` * test on python 3.9 * modernize dependency installation * remove call to `importlib` for python 3.6 * remove dependency on `coupledmodelvalidation` (#143) * update examples * running `example_3.py` resulted in a recursion error * Revert "running `example_3.py` resulted in a recursion error" This reverts commit c136336. * update reference files * update reference files * mkdir in tests * mkdir in tests * skip example tests that don't currently work Co-authored-by: Lint Action <[email protected]> Co-authored-by: Keith Roberts <[email protected]> Co-authored-by: Keith Roberts <[email protected]> Co-authored-by: Jaime R Calzada <[email protected]> Co-authored-by: William Pringle <[email protected]> Co-authored-by: zacharyburnett <[email protected]>
oceanmodeling · Jan 20, 2022 · a3ad291 · a3ad291
1 parent 63d8b45
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diff --git a/.gitignore b/.gitignore
@@ -1,4 +1,4 @@
-examples/outputs
+examples/output
 examples/data
 tests/data/input
 tests/data/output

diff --git a/README.md b/README.md
@@ -127,18 +127,19 @@ import shutil
 from adcircpy import AdcircMesh, AdcircRun, Tides
 from adcircpy.utilities import download_mesh
 
-MESH_URL = 'https://www.dropbox.com/s/1wk91r67cacf132/NetCDF_shinnecock_inlet.tar.bz2?dl=1'
-
 DATA_DIRECTORY = Path(__file__).parent.absolute() / 'data'
-INPUT_DIRECTORY = DATA_DIRECTORY / 'input' / 'NetCDF_Shinnecock_Inlet'
+INPUT_DIRECTORY = DATA_DIRECTORY / 'input' / 'shinnecock'
 OUTPUT_DIRECTORY = DATA_DIRECTORY / 'output' / 'example_1'
 
+MESH_URL = 'https://www.dropbox.com/s/1wk91r67cacf132/NetCDF_shinnecock_inlet.tar.bz2?dl=1'
+MESH_DIRECTORY = INPUT_DIRECTORY / 'shinnecock'
+
 download_mesh(
-    url=MESH_URL, directory=INPUT_DIRECTORY,
+    url=MESH_URL, directory=MESH_DIRECTORY,
 )
 
 # open mesh file
-mesh = AdcircMesh.open(INPUT_DIRECTORY / 'fort.14', crs=4326)
+mesh = AdcircMesh.open(MESH_DIRECTORY / 'fort.14', crs=4326)
 
 # initialize tidal forcing and constituents
 tidal_forcing = Tides()
@@ -197,18 +198,19 @@ import numpy
 from adcircpy import AdcircMesh, AdcircRun, Tides
 from adcircpy.utilities import download_mesh
 
-MESH_URL = 'https://www.dropbox.com/s/1wk91r67cacf132/NetCDF_shinnecock_inlet.tar.bz2?dl=1'
-
 DATA_DIRECTORY = Path(__file__).parent.absolute() / 'data'
-INPUT_DIRECTORY = DATA_DIRECTORY / 'input' / 'NetCDF_Shinnecock_Inlet'
+INPUT_DIRECTORY = DATA_DIRECTORY / 'input'
 OUTPUT_DIRECTORY = DATA_DIRECTORY / 'output' / 'example_2'
 
+MESH_URL = 'https://www.dropbox.com/s/1wk91r67cacf132/NetCDF_shinnecock_inlet.tar.bz2?dl=1'
+MESH_DIRECTORY = INPUT_DIRECTORY / 'shinnecock'
+
 download_mesh(
-    url=MESH_URL, directory=INPUT_DIRECTORY,
+    url=MESH_URL, directory=MESH_DIRECTORY,
 )
 
 # open mesh file
-mesh = AdcircMesh.open(INPUT_DIRECTORY / 'fort.14', crs=4326)
+mesh = AdcircMesh.open(MESH_DIRECTORY / 'fort.14', crs=4326)
 
 # generate tau0 factor
 mesh.generate_tau0()
@@ -259,26 +261,27 @@ The following code is similar to `example_1.py`, above, except it adds HURDAT Be
 job script for submission to a job manager.
 
 ```python
-from datetime import timedelta
+from datetime import datetime, timedelta
 from pathlib import Path
 
 from adcircpy import AdcircMesh, AdcircRun, Tides
 from adcircpy.forcing.winds import BestTrackForcing
 from adcircpy.server import SlurmConfig
-from tests import download_mesh
-
-MESH_URL = 'https://www.dropbox.com/s/1wk91r67cacf132/NetCDF_shinnecock_inlet.tar.bz2?dl=1'
+from adcircpy.utilities import download_mesh
 
 DATA_DIRECTORY = Path(__file__).parent.absolute() / 'data'
-INPUT_DIRECTORY = DATA_DIRECTORY / 'input' / 'NetCDF_Shinnecock_Inlet'
-OUTPUT_DIRECTORY = DATA_DIRECTORY / 'output' / 'example_3'
+INPUT_DIRECTORY = DATA_DIRECTORY / 'input'
+OUTPUT_DIRECTORY = DATA_DIRECTORY / 'output' / 'test_example_3'
+
+MESH_URL = 'https://www.dropbox.com/s/1wk91r67cacf132/NetCDF_shinnecock_inlet.tar.bz2?dl=1'
+MESH_DIRECTORY = INPUT_DIRECTORY / 'shinnecock'
 
 download_mesh(
-    url=MESH_URL, directory=INPUT_DIRECTORY,
+    url=MESH_URL, directory=MESH_DIRECTORY,
 )
 
 # open mesh file
-mesh = AdcircMesh.open(INPUT_DIRECTORY / 'fort.14', crs=4326)
+mesh = AdcircMesh.open(MESH_DIRECTORY / 'fort.14', crs=4326)
 
 # initialize tidal forcing and constituents
 tidal_forcing = Tides()
@@ -293,18 +296,24 @@ mesh.add_forcing(wind_forcing)
 slurm = SlurmConfig(
     account='account',
     ntasks=1000,
-    run_name='adcircpy/examples/example_3.py',
+    run_name='adcircpy/examples/test_example_3.py',
     partition='partition',
     walltime=timedelta(hours=8),
     mail_type='all',
     mail_user='[email protected]',
-    log_filename='example_3.log',
+    log_filename='test_example_3.log',
     modules=['intel/2020', 'impi/2020', 'netcdf/4.7.2-parallel'],
     path_prefix='$HOME/adcirc/build',
 )
 
+# set simulation dates
+spinup_time = timedelta(days=15)
+duration = timedelta(days=3)
+start_date = datetime(2012, 10, 21, 18)
+end_date = start_date + duration
+
 # instantiate driver object
-driver = AdcircRun(mesh, spinup_time=timedelta(days=15), server_config=slurm)
+driver = AdcircRun(mesh, start_date, end_date, spinup_time, server_config=slurm)
 
 # write driver state to disk
 driver.write(OUTPUT_DIRECTORY, overwrite=True)
@@ -322,20 +331,21 @@ from adcircpy import AdcircMesh, AdcircRun, Tides
 from adcircpy.forcing.waves.ww3 import WaveWatch3DataForcing
 from adcircpy.forcing.winds.atmesh import AtmosphericMeshForcing
 from adcircpy.server import SlurmConfig
-from tests import download_mesh
-
-MESH_URL = 'https://www.dropbox.com/s/1wk91r67cacf132/NetCDF_shinnecock_inlet.tar.bz2?dl=1'
+from adcircpy.utilities import download_mesh
 
 DATA_DIRECTORY = Path(__file__).parent.absolute() / 'data'
-INPUT_DIRECTORY = DATA_DIRECTORY / 'input' / 'NetCDF_Shinnecock_Inlet'
+INPUT_DIRECTORY = DATA_DIRECTORY / 'input'
 OUTPUT_DIRECTORY = DATA_DIRECTORY / 'output' / 'example_4'
 
+MESH_URL = 'https://www.dropbox.com/s/1wk91r67cacf132/NetCDF_shinnecock_inlet.tar.bz2?dl=1'
+MESH_DIRECTORY = INPUT_DIRECTORY / 'shinnecock'
+
 download_mesh(
-    url=MESH_URL, directory=INPUT_DIRECTORY,
+    url=MESH_URL, directory=MESH_DIRECTORY,
 )
 
 # open mesh file
-mesh = AdcircMesh.open(INPUT_DIRECTORY / 'fort.14', crs=4326)
+mesh = AdcircMesh.open(MESH_DIRECTORY / 'fort.14', crs=4326)
 
 # initialize tidal forcing and constituents
 tidal_forcing = Tides()

diff --git a/examples/example_1.py b/examples/example_1.py
@@ -7,18 +7,19 @@
 
 LOGGER = get_logger(__name__)
 
-MESH_URL = 'https://www.dropbox.com/s/1wk91r67cacf132/NetCDF_shinnecock_inlet.tar.bz2?dl=1'
-
 DATA_DIRECTORY = Path(__file__).parent.absolute() / 'data'
-INPUT_DIRECTORY = DATA_DIRECTORY / 'input' / 'NetCDF_Shinnecock_Inlet'
+INPUT_DIRECTORY = DATA_DIRECTORY / 'input' / 'shinnecock'
 OUTPUT_DIRECTORY = DATA_DIRECTORY / 'output' / 'example_1'
 
+MESH_URL = 'https://www.dropbox.com/s/1wk91r67cacf132/NetCDF_shinnecock_inlet.tar.bz2?dl=1'
+MESH_DIRECTORY = INPUT_DIRECTORY / 'shinnecock'
+
 download_mesh(
-    url=MESH_URL, directory=INPUT_DIRECTORY,
+    url=MESH_URL, directory=MESH_DIRECTORY,
 )
 
 # open mesh file
-mesh = AdcircMesh.open(INPUT_DIRECTORY / 'fort.14', crs=4326)
+mesh = AdcircMesh.open(MESH_DIRECTORY / 'fort.14', crs=4326)
 
 # initialize tidal forcing and constituents
 tidal_forcing = Tides()

diff --git a/examples/example_2.py b/examples/example_2.py
@@ -9,18 +9,19 @@
 
 LOGGER = get_logger(__name__)
 
-MESH_URL = 'https://www.dropbox.com/s/1wk91r67cacf132/NetCDF_shinnecock_inlet.tar.bz2?dl=1'
-
 DATA_DIRECTORY = Path(__file__).parent.absolute() / 'data'
-INPUT_DIRECTORY = DATA_DIRECTORY / 'input' / 'NetCDF_Shinnecock_Inlet'
+INPUT_DIRECTORY = DATA_DIRECTORY / 'input'
 OUTPUT_DIRECTORY = DATA_DIRECTORY / 'output' / 'example_2'
 
+MESH_URL = 'https://www.dropbox.com/s/1wk91r67cacf132/NetCDF_shinnecock_inlet.tar.bz2?dl=1'
+MESH_DIRECTORY = INPUT_DIRECTORY / 'shinnecock'
+
 download_mesh(
-    url=MESH_URL, directory=INPUT_DIRECTORY,
+    url=MESH_URL, directory=MESH_DIRECTORY,
 )
 
 # open mesh file
-mesh = AdcircMesh.open(INPUT_DIRECTORY / 'fort.14', crs=4326)
+mesh = AdcircMesh.open(MESH_DIRECTORY / 'fort.14', crs=4326)
 
 # generate tau0 factor
 mesh.generate_tau0()

diff --git a/examples/example_3.py b/examples/example_3.py
@@ -1,23 +1,24 @@
-from datetime import timedelta
+from datetime import datetime, timedelta
 from pathlib import Path
 
 from adcircpy import AdcircMesh, AdcircRun, Tides
 from adcircpy.forcing.winds import BestTrackForcing
 from adcircpy.server import SlurmConfig
 from adcircpy.utilities import download_mesh
 
-MESH_URL = 'https://www.dropbox.com/s/1wk91r67cacf132/NetCDF_shinnecock_inlet.tar.bz2?dl=1'
-
 DATA_DIRECTORY = Path(__file__).parent.absolute() / 'data'
-INPUT_DIRECTORY = DATA_DIRECTORY / 'input' / 'NetCDF_Shinnecock_Inlet'
+INPUT_DIRECTORY = DATA_DIRECTORY / 'input'
 OUTPUT_DIRECTORY = DATA_DIRECTORY / 'output' / 'example_3'
 
+MESH_URL = 'https://www.dropbox.com/s/1wk91r67cacf132/NetCDF_shinnecock_inlet.tar.bz2?dl=1'
+MESH_DIRECTORY = INPUT_DIRECTORY / 'shinnecock'
+
 download_mesh(
-    url=MESH_URL, directory=INPUT_DIRECTORY,
+    url=MESH_URL, directory=MESH_DIRECTORY,
 )
 
 # open mesh file
-mesh = AdcircMesh.open(INPUT_DIRECTORY / 'fort.14', crs=4326)
+mesh = AdcircMesh.open(MESH_DIRECTORY / 'fort.14', crs=4326)
 
 # initialize tidal forcing and constituents
 tidal_forcing = Tides()
@@ -42,8 +43,14 @@
     path_prefix='$HOME/adcirc/build',
 )
 
+# set simulation dates
+spinup_time = timedelta(days=15)
+duration = timedelta(days=3)
+start_date = datetime(2012, 10, 21, 18)
+end_date = start_date + duration
+
 # instantiate driver object
-driver = AdcircRun(mesh, spinup_time=timedelta(days=15), server_config=slurm,)
+driver = AdcircRun(mesh, start_date, end_date, spinup_time, server_config=slurm)
 
 # write driver state to disk
 driver.write(OUTPUT_DIRECTORY, overwrite=True)
diff --git a/examples/example_4.py b/examples/example_4.py
@@ -7,18 +7,19 @@
 from adcircpy.server import SlurmConfig
 from adcircpy.utilities import download_mesh
 
-MESH_URL = 'https://www.dropbox.com/s/1wk91r67cacf132/NetCDF_shinnecock_inlet.tar.bz2?dl=1'
-
 DATA_DIRECTORY = Path(__file__).parent.absolute() / 'data'
-INPUT_DIRECTORY = DATA_DIRECTORY / 'input' / 'NetCDF_Shinnecock_Inlet'
+INPUT_DIRECTORY = DATA_DIRECTORY / 'input'
 OUTPUT_DIRECTORY = DATA_DIRECTORY / 'output' / 'example_4'
 
+MESH_URL = 'https://www.dropbox.com/s/1wk91r67cacf132/NetCDF_shinnecock_inlet.tar.bz2?dl=1'
+MESH_DIRECTORY = INPUT_DIRECTORY / 'shinnecock'
+
 download_mesh(
-    url=MESH_URL, directory=INPUT_DIRECTORY,
+    url=MESH_URL, directory=MESH_DIRECTORY,
 )
 
 # open mesh file
-mesh = AdcircMesh.open(INPUT_DIRECTORY / 'fort.14', crs=4326)
+mesh = AdcircMesh.open(MESH_DIRECTORY / 'fort.14', crs=4326)
 
 # initialize tidal forcing and constituents
 tidal_forcing = Tides()

diff --git a/tests/__init__.py b/tests/__init__.py
@@ -1,7 +1,8 @@
-from difflib import Differ
+import os
 from os import PathLike
 from pathlib import Path
 import re
+from typing import Dict, List
 
 from filelock import FileLock
 import pytest
@@ -28,7 +29,9 @@ def shinnecock_mesh_directory(worker_id) -> Path:
 
 
 def check_reference_directory(
-    test_directory: PathLike, reference_directory: PathLike, skip_lines: {str: [int]} = None
+    test_directory: PathLike,
+    reference_directory: PathLike,
+    skip_lines: Dict[str, List[int]] = None,
 ):
     if not isinstance(test_directory, Path):
         test_directory = Path(test_directory)
@@ -49,21 +52,24 @@ def check_reference_directory(
                 test_lines = list(test_file.readlines())
                 reference_lines = list(reference_file.readlines())
 
-                diff = '\n'.join(Differ().compare(test_lines, reference_lines))
-                message = f'"{test_filename}" != "{reference_filename}"\n{diff}'
-
-                assert len(test_lines) == len(reference_lines), message
-
                 lines_to_skip = set()
                 for file_mask, line_indices in skip_lines.items():
-                    if file_mask in str(test_filename) or re.match(
-                        file_mask, str(test_filename)
+                    if (
+                        file_mask in str(test_filename)
+                        or re.match(file_mask, str(test_filename))
+                        and len(test_lines) > 0
                     ):
-                        lines_to_skip.update(
-                            line_index % len(test_lines) for line_index in line_indices
-                        )
+                        try:
+                            lines_to_skip.update(
+                                line_index % len(test_lines) for line_index in line_indices
+                            )
+                        except ZeroDivisionError:
+                            continue
 
                 for line_index in sorted(lines_to_skip, reverse=True):
                     del test_lines[line_index], reference_lines[line_index]
 
-                assert '\n'.join(test_lines) == '\n'.join(reference_lines), message
+                cwd = Path.cwd()
+                assert '\n'.join(test_lines) == '\n'.join(
+                    reference_lines
+                ), f'"{os.path.relpath(test_filename, cwd)}" != "{os.path.relpath(reference_filename, cwd)}"'
diff --git a/tests/data/reference/test_example_1/driver.sh b/tests/data/reference/test_example_1/driver.sh
@@ -0,0 +1,35 @@
+#!/bin/bash
+
+ulimit -s unlimited
+
+set -e
+
+NPROCS=4
+
+main() {
+  rm -rf work
+  mkdir work
+  cd work
+  ln -sf ../fort.14
+  ln -sf ../fort.13
+  ln -sf ../fort.15 ./fort.15
+  adcprep --np 4 --partmesh
+  adcprep --np 4 --prepall
+  mpiexec -n 4 padcirc
+  clean_directory
+  cd ..
+}
+
+clean_directory() {
+  rm -rf PE*
+  rm -rf partmesh.txt
+  rm -rf metis_graph.txt
+  rm -rf fort.13
+  rm -rf fort.14
+  rm -rf fort.15
+  rm -rf fort.16
+  rm -rf fort.80
+  rm -rf fort.68.nc
+}
+
+main