Add Linting

.flake8

@@ -0,0 +1,3 @@
+[flake8]
+ignore = E203, W503
+max-line-length=120

.github/workflows/pre-commit.yml

@@ -0,0 +1,18 @@
+name: Run pre-commit
+on:
+  - push
+  - pull_request
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.x'
+      - name: Install pre-commit
+        run: pip install pre-commit
+      - name: Run pre-commit
+        run: pre-commit run flake8 --all-files

.pre-commit-config.yaml

@@ -0,0 +1,9 @@
+repos:
+-   repo: https://github.com/psf/black
+    rev: stable
+    hooks:
+    - id: black
+-   repo: https://github.com/PyCQA/flake8.git
+    rev: 7.3.0
+    hooks:
+    - id: flake8

README.md

@@ -164,3 +164,27 @@ make: *** [Makefile:48: elmer_grid.o] Error 1
 ```
 
 *Solution:* `sudo apt-get install libproj-dev`
+
+# Developer notes
+
+## Code formatting
+
+Automated checks for PEP8 compiance are implemented following [^1] with some modifications. Please install pre-commit first:
+
+```sh
+pipx install pre-commit
+```
+
+Then, install the pre-commit hooks by running the following command from this folder:
+
+```sh
+pre-commit install
+```
+
+The pre-commit hooks will now run automatically on every commit. 
+
+Note: You can bypass this check with `--no-verify`. Please note that the CI will also check for PEP8 compliance and fail if the code is not PEP8 compliant. Therefore, it is recommended to use the pre-commit hooks locally before pushing code to this repository.
+
+----
+
+[^1]: https://ljvmiranda921.github.io/notebook/2018/06/21/precommits-using-black-and-flake8/

pyproject.toml

@@ -0,0 +1,2 @@
+[tool.black]
+line-length = 120

requirements-dev.txt

@@ -0,0 +1 @@
+pre-commit~=4.0

src/dummy.py

@@ -2,19 +2,23 @@
 from pathlib import Path
 import argparse
 
-from ebfm import INIT, LOOP_general_functions, LOOP_climate_forcing, LOOP_EBM, LOOP_SNOW, LOOP_mass_balance
+from ebfm import (
+    INIT,
+    LOOP_general_functions,
+    LOOP_climate_forcing,
+    LOOP_EBM,
+    LOOP_SNOW,
+    LOOP_mass_balance,
+)
 from ebfm import LOOP_write_to_file, FINAL_create_restart_file
 from ebfm.grid import GridInputType
 
 from mpi4py import MPI
 from utils import setup_logging
 import logging
 
-from typing import NamedTuple
-
-
 log_levels = {
-    'file':logging.DEBUG,  # log level for logging to file
+    "file": logging.DEBUG,  # log level for logging to file
     0: logging.INFO,  # log level for rank 0
     # 1: logging.DEBUG,  # to log other ranks to console define log level here
 }
@@ -29,50 +33,68 @@ def main():
 
     parser = argparse.ArgumentParser()
 
-    parser.add_argument("--couple-to-elmer-ice",
-                        action="store_true",
-                        help="Enable coupling with Elmer/Ice models via YAC")
-
-    parser.add_argument("--couple-to-icon-atmo",
-                        action="store_true",
-                        help="Enable coupling with ICON via YAC")
-
-    parser.add_argument("--coupler-config",
-                        type=Path,
-                        help="Path to the coupling configuration file (YAC coupler_config.yaml).")
-
-    parser.add_argument("--elmer-mesh",
-                        type=Path,
-                        help="Path to the Elmer mesh file. Either --elmer-mesh or --matlab-mesh is required.")
-
-    parser.add_argument("--matlab-mesh",
-                        type=Path,
-                        help="Path to the MATLAB mesh file. Either --elmer-mesh or --matlab-mesh is required.")
-
-    parser.add_argument("--netcdf-mesh",
-                        type=Path,
-                        help="Path to the NetCDF mesh file. Optional if using --elmer-mesh. If --netcdf-mesh is provided elevations will be read from the given NetCDF mesh file.")
-
-    parser.add_argument("--is-partitioned-elmer-mesh",
-                        action="store_true",
-                        help="Indicate if the provided Elmer mesh is partitioned for parallel runs.")
-
-    parser.add_argument("--use-part",
-                        type=int,
-                        default=MPI.COMM_WORLD.rank + 1,
-                        help="If using a partitioned Elmer mesh, allows to specify which partition ID to use for this run. If not provided, the MPI rank + 1 will be used as partition ID.")
+    parser.add_argument(
+        "--couple-to-elmer-ice",
+        action="store_true",
+        help="Enable coupling with Elmer/Ice models via YAC",
+    )
+
+    parser.add_argument(
+        "--couple-to-icon-atmo",
+        action="store_true",
+        help="Enable coupling with ICON via YAC",
+    )
+
+    parser.add_argument(
+        "--coupler-config",
+        type=Path,
+        help="Path to the coupling configuration file (YAC coupler_config.yaml).",
+    )
+
+    parser.add_argument(
+        "--elmer-mesh",
+        type=Path,
+        help="Path to the Elmer mesh file. Either --elmer-mesh or --matlab-mesh is required.",
+    )
+
+    parser.add_argument(
+        "--matlab-mesh",
+        type=Path,
+        help="Path to the MATLAB mesh file. Either --elmer-mesh or --matlab-mesh is required.",
+    )
+
+    parser.add_argument(
+        "--netcdf-mesh",
+        type=Path,
+        help="Path to the NetCDF mesh file. Optional if using --elmer-mesh."
+        " If --netcdf-mesh is provided elevations will be read from the given NetCDF mesh file.",
+    )
+
+    parser.add_argument(
+        "--is-partitioned-elmer-mesh",
+        action="store_true",
+        help="Indicate if the provided Elmer mesh is partitioned for parallel runs.",
+    )
+
+    parser.add_argument(
+        "--use-part",
+        type=int,
+        default=MPI.COMM_WORLD.rank + 1,
+        help="If using a partitioned Elmer mesh, allows to specify which partition ID to use for this run. "
+        "If not provided, the MPI rank + 1 will be used as partition ID.",
+    )
 
     args = parser.parse_args()
 
-    logger.info(f"Done parsing command line arguments.")
-    logger.debug(f"Parsed the following command line arguments:")
+    logger.info("Done parsing command line arguments.")
+    logger.debug("Parsed the following command line arguments:")
     for arg, val in vars(args).items():
         logger.debug(f"  {arg}: {val}")
 
     # Model setup & initialization
-    grid, time2, io, phys    = INIT.init_config(args)
-    C                        = INIT.init_constants()
-    grid                     = INIT.init_grid(grid, io, args)
+    grid, time2, io, phys = INIT.init_config(args)
+    C = INIT.init_constants()
+    grid = INIT.init_grid(grid, io, args)
 
     OUT, IN, OUTFILE = INIT.init_initial_conditions(C, grid, io, time2)
 
@@ -81,17 +103,17 @@ def main():
         # TODO consider introducing an ebfm_adapter_config.yaml
         coupler = coupling.init(
             coupler_config=args.coupler_config,
-            ebfm_coupling_config=Path('dummies') / 'EBFM' / 'ebfm-config.yaml',
+            ebfm_coupling_config=Path("dummies") / "EBFM" / "ebfm-config.yaml",
             couple_with_icon_atmo=args.couple_to_icon_atmo,
             couple_with_elmer_ice=args.couple_to_elmer_ice,
         )
         coupling.setup(coupler, grid["mesh"], time2)
     else:
-        coupler = coupling.NoCoupler('ebfm')
+        coupler = coupling.NoCoupler("ebfm")
 
     # Time-loop
-    logger.info('Entering time loop...')
-    for t in range(1, time2['tn'] + 1):
+    logger.info("Entering time loop...")
+    for t in range(1, time2["tn"] + 1):
         # Print time to screen
         time2 = LOOP_general_functions.print_time(t, time2)
 
@@ -100,81 +122,85 @@ def main():
         # Read and prepare climate input
         if coupler and coupler.couple_to_icon_atmo:
             # Exchange data with ICON
-            logger.info('Data exchange with ICON')
-            logger.debug('Started...')
+            logger.info("Data exchange with ICON")
+            logger.debug("Started...")
             data_to_icon = {
-                'albedo': OUT['albedo'],
+                "albedo": OUT["albedo"],
             }
 
             data_from_icon = coupler.exchange_icon_atmo(data_to_icon)
 
-            logger.debug('Done.')
-            logger.debug('Received the following data from ICON:', data_from_icon)
-
-            IN['P'] = data_from_icon['pr']*time2['dt']*C['dayseconds']*1e-3   # convert units from kg m-2 s-1 to m w.e.
-            IN['snow'] = data_from_icon['pr_snow']
-            IN['SWin'] = data_from_icon['rsds']
-            IN['LWin'] = data_from_icon['rlds']
-            IN['C'] = data_from_icon['clt']
-            IN['WS'] = data_from_icon['sfcwind']
-            IN['T'] = data_from_icon['tas']
-            IN['rain'] = IN['P'] - IN['snow'] # TODO: make this more flexible and configurable
-            IN['q'][:] = 0          # TODO: Read q from ICON instead and convert to RH
-            IN['Pres'][:] = 101500  # TODO: Read Pres from ICON instead
+            logger.debug("Done.")
+            logger.debug("Received the following data from ICON:", data_from_icon)
+
+            IN["P"] = (
+                data_from_icon["pr"] * time2["dt"] * C["dayseconds"] * 1e-3
+            )  # convert units from kg m-2 s-1 to m w.e.
+            IN["snow"] = data_from_icon["pr_snow"]
+            IN["SWin"] = data_from_icon["rsds"]
+            IN["LWin"] = data_from_icon["rlds"]
+            IN["C"] = data_from_icon["clt"]
+            IN["WS"] = data_from_icon["sfcwind"]
+            IN["T"] = data_from_icon["tas"]
+            IN["rain"] = IN["P"] - IN["snow"]  # TODO: make this more flexible and configurable
+            IN["q"][:] = 0  # TODO: Read q from ICON instead and convert to RH
+            IN["Pres"][:] = 101500  # TODO: Read Pres from ICON instead
 
         IN, OUT = LOOP_climate_forcing.main(C, grid, IN, t, time2, OUT, coupler)
 
         # Run surface energy balance model
         OUT = LOOP_EBM.main(C, OUT, IN, time2, grid, coupler)
 
         # Run snow & firn model
-        OUT = LOOP_SNOW.main(C, OUT, IN, time2['dt'], grid, phys)
+        OUT = LOOP_SNOW.main(C, OUT, IN, time2["dt"], grid, phys)
 
         # Calculate surface mass balance
         OUT = LOOP_mass_balance.main(OUT, IN, C)
 
         if coupler.couple_to_elmer_ice:
             # Exchange data with Elmer
-            logger.info('Data exchange with Elmer/Ice')
-            logger.debug('Started...')
+            logger.info("Data exchange with Elmer/Ice")
+            logger.debug("Started...")
 
             data_to_elmer = {
-                'smb': OUT['smb'],
-                'T_ice': OUT['T_ice'],
-                'runoff': OUT['runoff'],
+                "smb": OUT["smb"],
+                "T_ice": OUT["T_ice"],
+                "runoff": OUT["runoff"],
             }
             data_from_elmer = coupler.exchange_elmer_ice(data_to_elmer)
-            logger.debug('Done.')
-            logger.debug('Received the following data from Elmer/Ice:', data_from_elmer)
+            logger.debug("Done.")
+            logger.debug("Received the following data from Elmer/Ice:", data_from_elmer)
 
-            IN['h'] = data_from_elmer['h']
-            grid['z'] = IN['h'][0].ravel()
+            IN["h"] = data_from_elmer["h"]
+            grid["z"] = IN["h"][0].ravel()
             # TODO add gradient field later
             # IN['dhdx'] = data_from_elmer('dhdx')
             # IN['dhdy'] = data_from_elmer('dhdy')
 
         # Write output to files (only in uncoupled run and for unpartitioned grid)
-        if not grid['is_partitioned'] and not coupler.has_coupling:
-            assert (grid['input_type'] is GridInputType.MATLAB), \
-                "Output writing currently only implemented for MATLAB input grids."
+        if not grid["is_partitioned"] and not coupler.has_coupling:
+            assert (
+                grid["input_type"] is GridInputType.MATLAB
+            ), "Output writing currently only implemented for MATLAB input grids."
             io, OUTFILE = LOOP_write_to_file.main(OUTFILE, io, OUT, grid, t, time2, C)
             pass
-        elif grid['is_partitioned'] or coupler.has_coupling:
-            logger.warning('Skipping writing output to file for coupled or partitioned runs.')
+        elif grid["is_partitioned"] or coupler.has_coupling:
+            logger.warning("Skipping writing output to file for coupled or partitioned runs.")
         else:
-            logger.error('Unhandled case in output writing.')
+            logger.error("Unhandled case in output writing.")
             raise Exception("Unhandled case in output writing.")
 
     # Write restart file
-    if not grid['is_partitioned'] and not coupler.has_coupling:
+    if not grid["is_partitioned"] and not coupler.has_coupling:
         FINAL_create_restart_file.main(OUT, io)
 
-    logger.info('Time loop completed.')
+    logger.info("Time loop completed.")
 
     if coupler.has_coupling:
         coupling.finalize(coupler)
 
-    logger.info('Closing down EBFM.')
+    logger.info("Closing down EBFM.")
+
 
 # Entry point for script execution
 if __name__ == "__main__":

src/ebfm/FINAL_create_restart_file.py

@@ -2,6 +2,7 @@
 from netCDF4 import Dataset, date2num
 import numpy as np
 
+
 def main(OUT, io):
 
     def create_boot_file():
@@ -51,7 +52,11 @@ def create_boot_file():
 
             return True
 
-    OUT['timelastsnow_netCDF'] = date2num(OUT['timelastsnow'], units="days since 1970-01-01 00:00:00", calendar="gregorian")
+    OUT["timelastsnow_netCDF"] = date2num(
+        OUT["timelastsnow"],
+        units="days since 1970-01-01 00:00:00",
+        calendar="gregorian",
+    )
     OUT = {
         "subZ": OUT["subZ"],
         "subW": OUT["subW"],
@@ -66,6 +71,5 @@ def create_boot_file():
         "alb_snow": OUT["alb_snow"],
     }
 
-
     # Create the boot file
-    create_boot_file()
+    create_boot_file()