ladim 2.0.0__py3-none-any.whl → 2.0.2__py3-none-any.whl

ladim/__init__.py

@@ -1,3 +1,3 @@
-__version__ = '2.0.0'
+__version__ = '2.0.2'
 
 from .main import main, run

ladim/__main__.py

@@ -0,0 +1,2 @@
+from . import run
+run()

ladim/gridforce/ROMS.py

@@ -15,10 +15,12 @@ import glob
 import logging
 import numpy as np
 from netCDF4 import Dataset, num2date
-
 from ladim.sample import sample2D, bilin_inv
 
 
+logger = logging.getLogger(__name__)
+
+
 class Grid:
     """Simple ROMS grid object
 
@@ -34,7 +36,7 @@ class Grid:
 
     def __init__(self, config):
 
-        logging.info("Initializing ROMS-type grid object")
+        logger.info("Initializing ROMS-type grid object")
 
         # Grid file
         if "grid_file" in config["gridforce"]:
@@ -44,14 +46,14 @@ class Grid:
             files.sort()
             grid_file = files[0]
         else:
-            logging.error("No grid file specified")
+            logger.error("No grid file specified")
             raise SystemExit(1)
 
         try:
             ncid = Dataset(grid_file)
             ncid.set_auto_mask(False)
         except OSError:
-            logging.error("Could not open grid file " + grid_file)
+            logger.error("Could not open grid file " + grid_file)
             raise SystemExit(1)
 
         # Subgrid, only considers internal grid cells
@@ -242,7 +244,7 @@ class Forcing:
 
     def __init__(self, config, grid):
 
-        logging.info("Initiating forcing")
+        logger.info("Initiating forcing")
 
         self._grid = grid  # Get the grid object, make private?
         # self.config = config["gridforce"]
@@ -255,9 +257,9 @@ class Forcing:
         files = self.find_files(config["gridforce"])
         numfiles = len(files)
         if numfiles == 0:
-            logging.error("No input file: {}".format(config["gridforce"]["input_file"]))
+            logger.error("No input file: {}".format(config["gridforce"]["input_file"]))
             raise SystemExit(3)
-        logging.info("Number of forcing files = {}".format(numfiles))
+        logger.info("Number of forcing files = {}".format(numfiles))
 
         # ---------------------------
         # Overview of all the files
@@ -357,6 +359,7 @@ class Forcing:
         all_frames = []  # All time frames
         num_frames = {}  # Number of time frames in each file
         for fname in files:
+            logger.info(f'Open forcing file {fname}')
             with Dataset(fname) as nc:
                 new_times = nc.variables["ocean_time"][:]
                 num_frames[fname] = len(new_times)
@@ -370,11 +373,11 @@ class Forcing:
         if np.any(I):
             i = I.nonzero()[0][0] + 1   # Index of first out-of-order frame
             oooframe = str(all_frames[i]).split('.')[0]  # Remove microseconds
-            logging.info(f"Time frame {i} = {oooframe} out of order")
-            logging.critical("Forcing time frames not strictly sorted")
+            logger.info(f"Time frame {i} = {oooframe} out of order")
+            logger.critical("Forcing time frames not strictly sorted")
             raise SystemExit(4)
 
-        logging.info(f"Number of available forcing times = {len(all_frames)}")
+        logger.info(f"Number of available forcing times = {len(all_frames)}")
         return all_frames, num_frames
 
     @staticmethod
@@ -382,8 +385,8 @@ class Forcing:
 
         time0 = all_frames[0]
         time1 = all_frames[-1]
-        logging.info(f"First forcing time = {time0}")
-        logging.info(f"Last forcing time = {time1}")
+        logger.info(f"First forcing time = {time0}")
+        logger.info(f"Last forcing time = {time1}")
         start_time = np.datetime64(config["start_time"])
         dt = np.timedelta64(int(config["dt"]), "s")
 
@@ -391,10 +394,10 @@ class Forcing:
         # ------------------------------------------------------
 
         if time0 > start_time:
-            logging.error("No forcing at start time")
+            logger.error("No forcing at start time")
             raise SystemExit(3)
         if time1 < config["stop_time"]:
-            logging.error("No forcing at stop time")
+            logger.error("No forcing at stop time")
             raise SystemExit(3)
 
         # Make a list steps of the forcing time steps
@@ -427,7 +430,7 @@ class Forcing:
         interpolate_velocity_in_time = True
         interpolate_ibm_forcing_in_time = False
 
-        logging.debug("Updating forcing, time step = {}".format(t))
+        logger.debug("Updating forcing, time step = {}".format(t))
         if t in self.steps:  # No time interpolation
             self.U = self.Unew
             self.V = self.Vnew
@@ -486,7 +489,7 @@ class Forcing:
 
         # Handle file opening/closing
         # Always read velocity before other fields
-        logging.info("Reading velocity for time step = {}".format(n))
+        logger.info("Reading velocity for time step = {}".format(n))
 
         # If finished a file or first read (self._nc == "")
         if not self._nc:  # First read

ladim/gridforce/zROMS.py

@@ -18,6 +18,9 @@ from netCDF4 import Dataset, num2date
 from ladim.sample import sample2D
 
 
+logger = logging.getLogger(__name__)
+
+
 class Grid:
     """Simple ROMS grid object
 
@@ -33,11 +36,11 @@ class Grid:
 
     def __init__(self, config):
 
-        logging.info("Initializing zROMS grid object")
+        logger.info("Initializing zROMS grid object")
         try:
             ncid = Dataset(config["gridforce"]["grid_file"])
         except OSError:
-            logging.error(
+            logger.error(
                 "Grid file {} not found".format(config["gridforce"]["grid_file"])
             )
             raise SystemExit(1)
@@ -188,7 +191,7 @@ class Forcing:
 
     def __init__(self, config, grid):
 
-        logging.info("Initiating forcing")
+        logger.info("Initiating forcing")
 
         self._grid = grid  # Get the grid object, make private?
 
@@ -199,9 +202,9 @@ class Forcing:
         files.sort()
         numfiles = len(files)
         if numfiles == 0:
-            logging.error("No input file: {}".format(config["gridforce"]["input_file"]))
+            logger.error("No input file: {}".format(config["gridforce"]["input_file"]))
             raise SystemExit(3)
-        logging.info("Number of forcing files = {}".format(numfiles))
+        logger.info("Number of forcing files = {}".format(numfiles))
 
         # ----------------------------------------
         # Open first file for some general info
@@ -250,14 +253,14 @@ class Forcing:
                 new_times = nc.variables["time"][:]
                 times.extend(new_times)
                 num_frames.append(len(new_times))
-        logging.info("Number of available forcing times = {:d}".format(len(times)))
+        logger.info("Number of available forcing times = {:d}".format(len(times)))
 
         # Find first/last forcing times
         # -----------------------------
         time0 = num2date(times[0], time_units)
         time1 = num2date(times[-1], time_units)
-        logging.info("time0 = {}".format(str(time0)))
-        logging.info("time1 = {}".format(str(time1)))
+        logger.info("time0 = {}".format(str(time0)))
+        logger.info("time1 = {}".format(str(time1)))
         # print(time0)
         # print(time1)
         start_time = np.datetime64(config["start_time"])
@@ -269,10 +272,10 @@ class Forcing:
         # Use logging module for this
 
         if time0 > start_time:
-            logging.error("No forcing at start time")
+            logger.error("No forcing at start time")
             raise SystemExit(3)
         if time1 < config["stop_time"]:
-            logging.error("No forcing at stop time")
+            logger.error("No forcing at stop time")
             raise SystemExit(3)
 
         # Make a list steps of the forcing time steps
@@ -362,7 +365,7 @@ class Forcing:
         interpolate_velocity_in_time = True
         interpolate_ibm_forcing_in_time = False
 
-        logging.debug("Updating forcing, time step = {}".format(t))
+        logger.debug("Updating forcing, time step = {}".format(t))
         if t in self.steps:  # No time interpolation
             self.U = self.Unew
             self.V = self.Vnew
@@ -399,7 +402,7 @@ class Forcing:
 
         # Handle file opening/closing
         # Always read velocity before other fields
-        logging.debug("Reading velocity for time step = {}".format(n))
+        logger.debug("Reading velocity for time step = {}".format(n))
         first = True
         if first:  # Open file initiallt
             self._nc = Dataset(self._files[self.file_idx[n]])

ladim/main.py

@@ -12,13 +12,14 @@ Lagrangian Advection and Diffusion Model
 # ---------------------------------
 
 import logging
-
 import ladim
-
 from .config import configure
 from .model import Model
 
 
+logger = logging.getLogger(__name__)
+
+
 def main(config_stream, loglevel=logging.INFO):
     """Main function for LADiM"""
 
@@ -67,23 +68,23 @@ def run():
 
     args = parser.parse_args()
 
-    logging.info(" ================================================")
-    logging.info(" === Lagrangian Advection and Diffusion Model ===")
-    logging.info(" ================================================\n")
+    logger.info(" ================================================")
+    logger.info(" === Lagrangian Advection and Diffusion Model ===")
+    logger.info(" ================================================\n")
 
-    logging.info(f"ladim path: {ladim.__file__.strip('__init.py__')}")
-    logging.info(f"ladim version:  {ladim.__version__}\n")
-    logging.info(f"python version:  {sys.version.split()[0]}\n")
+    logger.info(f"ladim path: {ladim.__file__.strip('__init.py__')}")
+    logger.info(f"ladim version:  {ladim.__version__}\n")
+    logger.info(f"python version:  {sys.version.split()[0]}\n")
 
-    logging.info(f"  Configuration file: {args.config_file}")
-    logging.info(f"  loglevel = {logging.getLevelName(args.loglevel)}")
+    logger.info(f"  Configuration file: {args.config_file}")
+    logger.info(f"  loglevel = {logging.getLevelName(args.loglevel)}")
 
     # =============
     # Sanity check
     # =============
 
     if not Path(args.config_file).exists():
-        logging.critical(f'Configuration file {args.config_file} not found')
+        logger.critical(f'Configuration file {args.config_file} not found')
         raise SystemExit(1)
 
     # ===================
@@ -92,7 +93,7 @@ def run():
 
     # Start message
     now = datetime.datetime.now().replace(microsecond=0)
-    logging.info(f'LADiM simulation starting, wall time={now}')
+    logger.info(f'LADiM simulation starting, wall time={now}')
 
     fp = open(args.config_file, encoding='utf8')
     ladim.main(config_stream=fp, loglevel=args.loglevel)
@@ -100,4 +101,4 @@ def run():
     # Reset logging and print final message
     logging.getLogger().setLevel(logging.INFO)
     now = datetime.datetime.now().replace(microsecond=0)
-    logging.info(f'LADiM simulation finished, wall time={now}')
+    logger.info(f'LADiM simulation finished, wall time={now}')

ladim/release.py

@@ -53,7 +53,7 @@ class TextFileReleaser(Releaser):
         self._dataframe = None
 
         # Continuous release variables
-        self._frequency = read_timedelta(frequency)
+        self._frequency = read_timedelta(frequency) / np.timedelta64(1, 's')
         self._last_release_dataframe = pd.DataFrame()
         self._last_release_time = np.int64(-4611686018427387904)
 
@@ -80,6 +80,12 @@ class TextFileReleaser(Releaser):
             stop_time=self.model.solver.time + self.model.solver.step,
         ).copy(deep=True)
 
+        # If there are no new particles, but the state is empty, we should
+        # still initialize the state by adding the appropriate columns
+        if (len(df) == 0) and ('X' not in self.model.state):
+            self.model.state.append(df.to_dict(orient='list'))
+            self._last_release_dataframe = df
+
         # If there are no new particles and we don't use continuous release,
         # we are done.
         continuous_release = bool(self._frequency)
@@ -99,7 +105,7 @@ class TextFileReleaser(Releaser):
             return
 
         # If we have continuous release, but there are no new particles and
-        # the last release is NOT recent, we should replace the empty
+        # the last release is NOT recent, we should replace empty
         # dataframe with the previously released dataframe
         if continuous_release:
             if (len(df) == 0) and not last_release_is_recent:
@@ -148,6 +154,7 @@ class TextFileReleaser(Releaser):
                 self._dataframe = self._csv_fname
 
             else:
+                # noinspection PyArgumentList
                 with open_or_relay(self._csv_fname, 'r', encoding='utf-8') as fp:
                     self._dataframe = load_release_file(
                         stream=fp,

ladim/state.py

@@ -122,6 +122,14 @@ class DynamicState(State):
             raise AttributeError(f'Attribute not defined: {item}')
         return self[item]
 
+    def __setattr__(self, item, value):
+        if item in list(self.__dict__.keys()) + ['_data', '_model', '_num_released', '_varnames']:
+            super().__setattr__(item, value)
+        elif item in self._data:
+            self._data[item] = value
+        else:
+            raise AttributeError(f"Attribute not defined: '{item}'")
+
     def __contains__(self, item):
         return item in self._data
 

{ladim-2.0.0.dist-info → ladim-2.0.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ladim
-Version: 2.0.0
+Version: 2.0.2
 Summary: Lagrangian Advection and Diffusion Model
 Home-page: https://github.com/pnsaevik/ladim
 Author: Bjørn Ådlandsvik

{ladim-2.0.0.dist-info → ladim-2.0.2.dist-info}/RECORD

@@ -1,20 +1,21 @@
-ladim/__init__.py,sha256=Ns1alQ3-vgq1Hh0sgRGMsYsmH5LnEReoG-M-ajzLg04,51
+ladim/__init__.py,sha256=0i7KXjW3S0HuMuJqk69XKrsqQE9QUVTrXRDo6jNiFEM,51
+ladim/__main__.py,sha256=8f07EMfxQllDZSgpak5ECyYHnfQFy8LaHl2xdC-aO9c,23
 ladim/config.py,sha256=6b0ikBrBnq_sSElgO2YcVtJHjQU0nyZsVyPV3q9fy5I,4233
 ladim/forcing.py,sha256=f4PpSwyilSScXeNyorTWLMgVTiat9htSLkCwAkRlJVM,3048
 ladim/grid.py,sha256=m6bQrGJ3cux7rqC8pbRXD86cOI-VQKF-XjP9m1jCIcY,2221
-ladim/main.py,sha256=wO91-nLd1gvF3V20XK5qRvvOIV4xoTOKiWFcbwV2oag,2812
+ladim/main.py,sha256=EwBkmWwQG7I0_i-xjthSTeGsoALHH-MdQ1Vvf64lv_A,2838
 ladim/model.py,sha256=jpjq_ZSh7ULpwi3_RqDb-p5SG8WcdgCPaBkSpnNWblU,3137
 ladim/output.py,sha256=Rz7iujvS7Z3LoABiJduQqyb3zPswNqhhFsywr3MLsBY,8373
-ladim/release.py,sha256=5QD0hxQNmkxGmtrQX72T5QumHeWLQMFHysJD6Sc0BUE,8067
+ladim/release.py,sha256=1j__9Gj0BD0CqVCM2KLZhio1Ia-hz1gbUIhTsa0J3Rg,8451
 ladim/sample.py,sha256=n8wRGd_VsW_qyQe1ZoTpmfZcdcwB929vsM8PoKG6JTs,8292
 ladim/solver.py,sha256=sZvYgOxzJ-EItI-IB2y8_z8Tf-SJAQSrmydlhDRa7ZQ,755
-ladim/state.py,sha256=5ICIiujsV3KOAUYagGLK7YdmhcItgJmtntZeR11nIpw,3781
+ladim/state.py,sha256=4XNIIx5sGjlqkZ6bg-dGbqzp8ujFNkHHFL2D9qCQA2w,4119
 ladim/tracker.py,sha256=VVX6T5CqiU6nGSCgLlSCC8w0UYhW273OGFE7ApPjdyI,5091
 ladim/utilities.py,sha256=r7-zShqJhh0cBctDUmtfw-GBOk1eTTYR4S72b0ouiSQ,994
-ladim/gridforce/ROMS.py,sha256=yrMr1GiDgr7VG9V630nHFdeajPY4WHLu653ZRwAk1aw,26888
+ladim/gridforce/ROMS.py,sha256=6y8ZIkAQgVPgK-zG53SKxFms4lJdkTCaP1doz7zuSyo,26965
 ladim/gridforce/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 ladim/gridforce/analytical.py,sha256=qI-1LJdjmnwwanzOdrsDZqwGgo73bT75CB7pMaxbHKM,1094
-ladim/gridforce/zROMS.py,sha256=MVA6PQuY1ukvs2E20sWY4kr5-QieeQHTrA5ruxCqbUM,22826
+ladim/gridforce/zROMS.py,sha256=t88mow91orUP-kMQiqmQ0_SnJKKG9xfycM5MMmdVljI,22853
 ladim/ibms/__init__.py,sha256=GOG75jZDmNEiLr8brxrKqIlqVj-pNR7pnPP8FUKE6hU,565
 ladim/ibms/light.py,sha256=POltHmKkX8-q3t9wXyfcseCKEq9Bq-kX1WEJYsr1lNQ,2737
 ladim/plugins/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -23,9 +24,9 @@ postladim/cellcount.py,sha256=nCFu9iJmprubn4YmPB4W0VO02GfEb90Iif7D49w1Kss,2054
 postladim/kde_plot.py,sha256=GvMWzT6VxIeXKh1cnqaGzR-4jGG_WIHGMLPpRMXIpo4,1628
 postladim/particlefile.py,sha256=0aif9wYUJ-VrpQKeCef8wB5VCiBB-gWY6sxNCUYviTA,4889
 postladim/variable.py,sha256=-2aihoppYMMmpSpCqaF31XvpinTMaH3Y01-USDIkbBc,6587
-ladim-2.0.0.dist-info/LICENSE,sha256=BgtXyjNr6Ly9nQ7ZLXKpV3r5kWRLnh5MiN0dxp0Bvfc,1085
-ladim-2.0.0.dist-info/METADATA,sha256=ap0yaeqHIhnmQiMwuH8gaCT__YNxESVoudzgFuko9Zs,1841
-ladim-2.0.0.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-ladim-2.0.0.dist-info/entry_points.txt,sha256=JDlNJo87GJaOkH0-BpAzTPLCrZcuPSdSlHNQ4XmnoRg,41
-ladim-2.0.0.dist-info/top_level.txt,sha256=TK8Gl7d6MsrAQvqKG4b6YJCbB4UL46Se3SzsI-sJAuc,16
-ladim-2.0.0.dist-info/RECORD,,
+ladim-2.0.2.dist-info/LICENSE,sha256=BgtXyjNr6Ly9nQ7ZLXKpV3r5kWRLnh5MiN0dxp0Bvfc,1085
+ladim-2.0.2.dist-info/METADATA,sha256=sjw274vLpD7oaf1g96Ik4VEI0c2grbLVml7nVXTVfoU,1841
+ladim-2.0.2.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
+ladim-2.0.2.dist-info/entry_points.txt,sha256=JDlNJo87GJaOkH0-BpAzTPLCrZcuPSdSlHNQ4XmnoRg,41
+ladim-2.0.2.dist-info/top_level.txt,sha256=TK8Gl7d6MsrAQvqKG4b6YJCbB4UL46Se3SzsI-sJAuc,16
+ladim-2.0.2.dist-info/RECORD,,

{ladim-2.0.0.dist-info → ladim-2.0.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.43.0)
+Generator: setuptools (75.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any