Merge branch 'devel'

# Conflicts:
#	CHANGELOG.md
#	ladim/__init__.py

CHANGELOG.md

@@ -5,7 +5,38 @@ All notable changes to the project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and the project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [1.3.5] - 2024-01-25
+## [Issues]
+### Change
+- Velocity in forcing module should return "grid speed" velocity. Rescaling
+  should happen within the forcing module, not tracking module.
+- New grid and forcing module should have a clearer separation. Grid should
+  take care of coordinate system changes, while forcing should return static
+  fields.
+### Add
+- Multiplicity to the releaser module
+
+
+## [2.0.0] - 2024-03-20
+### Changed
+- Legacy modules are removed. This may lead to nuance changes in ladim output.
+### Fixed
+- Tracker module no longer gives error if particles are deactivated
+
+
+## [1.3.5] - 2024-01-30 
+### Added
+- Text releaser module can add default values other than zero
+### Fixed
+- Allow mixture of unix and windows path slash in config file
+- Particles close to edge no longer causes errors
+### Changed
+- Output module is now called at the end of each timestep
+- New output module
+- New release module
+- New tracker module
+
+
+## [1.3.4] - 2024-01-25
 ### Fixed
 - Package now works with pandas 2.2.0
 

ladim/__init__.py

@@ -1,3 +1,3 @@
-__version__ = '1.3.5'
+__version__ = '2.0.0'
 
 from .main import main, run

ladim/config.py

@@ -0,0 +1,125 @@
+"""
+Functions for parsing configuration parameters.
+
+The module contains functions for parsing input configuration
+parameters, appending default values and converting between
+different versions of config file formats.
+"""
+import numpy as np
+
+
+def configure(module_conf):
+    import yaml
+
+    # Handle variations of input config type
+    if isinstance(module_conf, dict):
+        config_dict = module_conf
+    else:
+        config_dict = yaml.safe_load(module_conf)
+
+    if 'version' not in config_dict:
+        if 'particle_release' in config_dict:
+            config_dict['version'] = 1
+        else:
+            config_dict['version'] = 2
+
+    return _versioned_configure(config_dict)
+
+
+def _versioned_configure(config_dict):
+    if config_dict['version'] == 1:
+        config_dict = _convert_1_to_2(config_dict)
+
+    return config_dict
+
+
+def _convert_1_to_2(c):
+    # Read timedelta
+    dt_value, dt_unit = c['numerics']['dt']
+    dt_sec = np.timedelta64(dt_value, dt_unit).astype('timedelta64[s]').astype('int64')
+
+    # Read output variables
+    outvars = dict()
+    outvar_names = c['output_variables'].get('particle', []) + c['output_variables'].get('instance', [])
+    for v in outvar_names:
+        outvars[v] = c['output_variables'][v].copy()
+    for v in c['output_variables'].get('particle', []):
+        outvars[v]['kind'] = 'initial'
+    if 'release_time' in outvars and 'units' in outvars['release_time']:
+        outvars['release_time']['units'] = 'seconds since 1970-01-01'
+
+    # Read release config
+    relconf = dict(
+        file=c['files']['particle_release_file'],
+        frequency=c['particle_release'].get('release_frequency', [0, 's']),
+        colnames=c['particle_release']['variables'],
+        formats={
+            c['particle_release'][v]: v
+            for v in c['particle_release']['variables']
+            if v in c['particle_release'].keys()
+        },
+    )
+    if c['particle_release'].get('release_type', '') != 'continuous':
+        del relconf['frequency']
+    ibmvars = c.get('state', dict()).get('ibm_variables', [])
+    ibmvars += c.get('ibm', dict()).get('variables', [])
+    relconf['defaults'] = {
+        k: np.float64(0)
+        for k in ibmvars
+        if k not in relconf['colnames']
+    }
+
+    # Read ibm config
+    ibmconf_legacy = c.get('ibm', dict()).copy()
+    if 'module' in ibmconf_legacy:
+        ibmconf_legacy['ibm_module'] = ibmconf_legacy.pop('module')
+    ibmconf = dict()
+    if 'ibm_module' in ibmconf_legacy:
+        ibmconf['module'] = 'ladim.ibms.LegacyIBM'
+        ibmconf['legacy_module'] = ibmconf_legacy['ibm_module']
+        ibmconf['conf'] = dict(
+            dt=dt_sec,
+            output_instance=c.get('output_variables', {}).get('instance', []),
+            nc_attributes={k: v for k, v in outvars.items()}
+        )
+        ibmconf['conf']['ibm'] = {
+            k: v
+            for k, v in ibmconf_legacy.items()
+            if k != 'ibm_module'
+        }
+
+    config_dict = dict(
+        version=2,
+        solver=dict(
+            start=c['time_control']['start_time'],
+            stop=c['time_control']['stop_time'],
+            step=dt_sec,
+            seed=c['numerics'].get('seed', None),
+            order=['release', 'forcing', 'output', 'tracker', 'ibm', 'state'],
+        ),
+        grid=dict(
+            file=c['gridforce']['input_file'],
+            legacy_module=c['gridforce']['module'] + '.Grid',
+            start_time=np.datetime64(c['time_control']['start_time'], 's'),
+        ),
+        forcing=dict(
+            file=c['gridforce']['input_file'],
+            legacy_module=c['gridforce']['module'] + '.Forcing',
+            start_time=np.datetime64(c['time_control']['start_time'], 's'),
+            stop_time=np.datetime64(c['time_control']['stop_time'], 's'),
+            dt=dt_sec,
+            ibm_forcing=c['gridforce'].get('ibm_forcing', []),
+        ),
+        release=relconf,
+        output=dict(
+            file=c['files']['output_file'],
+            frequency=c['output_variables']['outper'],
+            variables=outvars,
+        ),
+        tracker=dict(
+            method=c['numerics']['advection'],
+            diffusion=c['numerics']['diffusion'],
+        ),
+        ibm=ibmconf,
+    )
+    return config_dict