wrfrun 0.1.4__tar.gz → 0.1.6__tar.gz

wrfrun-0.1.6/.gitattributes

@@ -0,0 +1,5 @@
+.gitea/ export-ignore
+.github/ export-ignore
+images/ export-ignore
+.readthedocs.yaml export-ignore
+docs export-ignore

{wrfrun-0.1.4 → wrfrun-0.1.6}/.gitignore

@@ -9,6 +9,7 @@ dist/
 wrfrun.egg-info/
 .idea/
 data/
+docs/build
 
 **/*.1
 **/*.input_step1

{wrfrun-0.1.4 → wrfrun-0.1.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: wrfrun
-Version: 0.1.4
+Version: 0.1.6
 Summary: wrfrun is a comprehensive toolkit for managing and using WRF
 Keywords: WRF
 Author-Email: Syize <syizeliu@gmail.com>
@@ -18,7 +18,6 @@ Requires-Dist: PyYAML
 Requires-Dist: pandas
 Requires-Dist: f90nml
 Requires-Dist: cdsapi
-Requires-Dist: seafog
 Requires-Dist: matplotlib
 Requires-Dist: Cartopy
 Requires-Dist: wrf-python
@@ -43,10 +42,14 @@ The following are the main features that wrfrun wants to achieve. These features
 - Real-time parsing of WRF logs, feedback on simulation progress.
 - Support for adding more functionality through extensions.
 
-## Install
+## Installation
 
 Install using pip:
 
 ```bash
 pip install wrfrun
-```
+```
+
+## Documentation
+
+Please check [Wiki](https://github.com/Syize/wrfrun/wiki).

{wrfrun-0.1.4 → wrfrun-0.1.6}/README.md

@@ -16,10 +16,14 @@ The following are the main features that wrfrun wants to achieve. These features
 - Real-time parsing of WRF logs, feedback on simulation progress.
 - Support for adding more functionality through extensions.
 
-## Install
+## Installation
 
 Install using pip:
 
 ```bash
 pip install wrfrun
-```
+```
+
+## Documentation
+
+Please check [Wiki](https://github.com/Syize/wrfrun/wiki).

{wrfrun-0.1.4 → wrfrun-0.1.6}/meson.build

@@ -1,7 +1,7 @@
 project(
     'wrfrun',
     'c',
-    version: '0.1.4',
+    version: '0.1.6',
     license: 'BSD-3',
     meson_version: '>=0.64.0',
     default_options: ['warning_level=2'],

{wrfrun-0.1.4 → wrfrun-0.1.6}/pyproject.toml

@@ -1,10 +1,10 @@
 [build-system]
 build-backend = "mesonpy"
-requires = ["meson-python", "numpy<2.0.0"]
+requires = ["meson-python"]
 
 [project]
 name = "wrfrun"
-version = "0.1.4"
+version = "0.1.6"
 readme = "README.md"
 license = { text = "GPL-3.0-or-later" }
 requires-python = '>=3.10'
@@ -14,7 +14,7 @@ maintainers = [
 ]
 keywords = [ "WRF", ]
 description = "wrfrun is a comprehensive toolkit for managing and using WRF"
-dependencies = ["xarray", "netCDF4", "rich", "PyYAML", "pandas", "f90nml", "cdsapi", "seafog", "matplotlib", "Cartopy", "wrf-python", "cfgrib"]
+dependencies = ["xarray", "netCDF4", "rich", "PyYAML", "pandas", "f90nml", "cdsapi", "matplotlib", "Cartopy", "wrf-python", "cfgrib"]
 
 [project.urls]
 homepage = "https://github.com/Syize/wrfrun"

{wrfrun-0.1.4 → wrfrun-0.1.6}/wrfrun/data.py

@@ -4,7 +4,7 @@ from os.path import exists, dirname
 from typing import Union, List, Tuple
 
 from pandas import date_range
-from seafog import goos_sst_find_data
+# from seafog import goos_sst_find_data
 
 import cdsapi
 
@@ -315,9 +315,9 @@ def prepare_wps_input_data(area: Tuple[int, int, int, int]):
     download_data(start_date, end_date, hour_step, area, f"{bg_save_path}/pressure.grib",
                   data_format="grib", data_type="pressure", overwrite=True)
 
-    logger.info(f"Download NearGOOS data...")
-    download_data(start_date, end_date, hour_step, area,
-                  save_path=sst_save_path, data_type="goos", overwrite=True)
+    # logger.info(f"Download NearGOOS data...")
+    # download_data(start_date, end_date, hour_step, area,
+    #               save_path=sst_save_path, data_type="goos", overwrite=True)
 
 
 def download_data(
@@ -394,9 +394,10 @@ def download_data(
         )
         pressure_level = None
     elif data_type == "goos":
+        logger.warning(f"NEAR-GOOS SST data hasn't been supported yet")
         # download sst data
-        for _date in date_list:
-            _ = goos_sst_find_data(_date, save_path=save_path)
+        # for _date in date_list:
+        #     _ = goos_sst_find_data(_date, save_path=save_path)
 
         return ""
     else:

wrfrun-0.1.6/wrfrun/extension/goos_sst/README.md

@@ -0,0 +1,10 @@
+# GOOS SST extension
+
+This extension can replace SKT (SKin Temperature) values in ERA5 reanalysis data with the SST (Sea Surface Temperature) from GOOS (Global Ocean Observing System). A new GRIB file will be generated so you can input it to WRF through `ungrib.exe` and `metgrid.exe`.
+
+A [Vtable file](res/Vtable.ERA_GOOS_SST) is also provided for `ungrib.exe`.
+
+## Features
+
+- Replace SKT in ERA5 data with GOOS SST and write new data to a GRIB file.
+- While only ERA5 data is tested, data from other sources is supported theoretically.

wrfrun-0.1.6/wrfrun/extension/littler/README.md

@@ -0,0 +1,9 @@
+# Little R extension
+
+This extension can write data to `LITTLE_R` format for WRF data assimilation.
+
+## Features
+
+- Provide `LittleR` class to write any data to `LITTLE_R` format.
+- Write data to a zip file (end with `.zlr`, that is `Zipped Little R file`).
+- Read data from the `.zlr` file, so you can create `LITTLE_R` file with the data.

{wrfrun-0.1.4 → wrfrun-0.1.6}/wrfrun/extension/littler/utils.py

@@ -14,7 +14,7 @@ def to_fstring(var: Union[int, float, bool, str], length: Union[int, Tuple[int,
     :param var: Basic variable, can be one of the ``[int, float, bool, str]``.
     :type var: Union[int, float, bool, str]
     :param length: The length of the output string. 
-        If the type of ``var`` is ``float``, the length must contains two parameters ``(total length, decimal length)``.
+        If the type of ``var`` is ``float``, the length must contain two parameters ``(total length, decimal length)``.
     :type length: Union[int, Tuple[int, int]]
     :return: Converted string.
     :rtype: str

{wrfrun-0.1.4 → wrfrun-0.1.6}/wrfrun/extension/meson.build

@@ -6,5 +6,4 @@ py3.install_sources(
     subdir: 'wrfrun/extension'
 )
 
-subdir('goos_sst')
 subdir('littler')

{wrfrun-0.1.4 → wrfrun-0.1.6}/wrfrun/model/__init__.py

@@ -1,8 +1,5 @@
 from .geodata import *
 from .namelist import *
-from .ndown import *
 from .plot import *
 from .run import *
 from .utils import *
-from .wps import *
-from .wrf import *

{wrfrun-0.1.4 → wrfrun-0.1.6}/wrfrun/model/geodata.py

@@ -44,7 +44,7 @@ def _get_clip_area(index_area: tuple[int, int, int, int], row_num: int, col_num:
     Returns:
         tuple[int, int, int, int]: Clip area.
     """
-    # caluclate tile area
+    # calculate tile area
     tile_area = (
         col_num * tile_x + 1,
         col_num * tile_x + tile_x,

{wrfrun-0.1.4 → wrfrun-0.1.6}/wrfrun/model/meson.build

@@ -4,13 +4,11 @@ py3.install_sources(
         'core.py',
         'geodata.py',
         'namelist.py',
-        'ndown.py',
         'plot.py',
         'run.py',
         'scheme.py',
-        'wps.py',
-        'wrf.py',
-        'wrfda.py',
     ],
     subdir: 'wrfrun/model'
-)
+)
+
+subdir('utils')

{wrfrun-0.1.4 → wrfrun-0.1.6}/wrfrun/model/run.py

@@ -8,10 +8,7 @@ from wrfrun.pbs import get_core_num
 from wrfrun.utils import check_path, logger
 from .core import exec_geogrid, exec_metgrid, exec_ndown, exec_real, exec_ungrib, exec_wrf
 from .namelist import generate_namelist_file, prepare_dfi_namelist
-from .ndown import process_after_ndown
-from .utils import model_preprocess, model_postprocess
-from .wps import get_wif_dir, get_wif_prefix
-from .wrf import reconcile_namelist_metgrid
+from .utils import model_preprocess, model_postprocess, process_after_ndown, get_wif_dir, get_wif_prefix, reconcile_namelist_metgrid
 
 
 def geogrid(geogrid_tbl_file: Union[str, None] = None):
@@ -48,8 +45,8 @@ def geogrid(geogrid_tbl_file: Union[str, None] = None):
 
     exec_geogrid(get_core_num())
 
-    model_postprocess(WPS_WORK_PATH, log_save_path, startswith="geogrid.log", copy_only=False)
-    model_postprocess(WPS_WORK_PATH, output_save_path, startswith="geo_em", outputs=["namelist.wps"])
+    model_postprocess(WPS_WORK_PATH, log_save_path, startswith="geogrid.log", copy_only=False, outputs="namelist.wps")
+    model_postprocess(WPS_WORK_PATH, output_save_path, startswith="geo_em")
 
     # for _file in listdir(WPS_WORK_PATH):
     #     if _file.startswith("geogrid.log"):
@@ -205,21 +202,9 @@ def real(metgrid_path: Union[str, None] = None):
 
     exec_real(get_core_num())
 
-    model_postprocess(WRF_WORK_PATH, output_save_path, startswith=["wrfbdy", "wrfinput", "wrflow"])
+    model_postprocess(WRF_WORK_PATH, output_save_path, startswith=("wrfbdy", "wrfinput", "wrflow"))
     model_postprocess(WRF_WORK_PATH, log_save_path, startswith="rsl.", outputs="namelist.input", copy_only=False)
 
-    # for _file in listdir(WRF_WORK_PATH):
-    #     if _file.startswith("rsl."):
-    #         move(f"{WRF_WORK_PATH}/{_file}", f"{log_save_path}/{_file}")
-    #     elif _file.startswith("wrfbdy"):
-    #         copyfile(f"{WRF_WORK_PATH}/{_file}", f"{output_save_path}/{_file}")
-    #     elif _file.startswith("wrfinput"):
-    #         copyfile(f"{WRF_WORK_PATH}/{_file}", f"{output_save_path}/{_file}")
-    #     elif _file.startswith("wrflow"):
-    #         copyfile(f"{WRF_WORK_PATH}/{_file}", f"{output_save_path}/{_file}")
-    #
-    # move(f"{WRF_WORK_PATH}/namelist.input", f"{log_save_path}/namelist.input")
-
     logger.info(f"All real output files have been copied to {output_save_path}")
 
 
@@ -272,18 +257,6 @@ def dfi(real_output_path: Union[str, None] = None, update_real_output=True):
     model_postprocess(WRF_WORK_PATH, log_save_path, startswith="rsl.", outputs="namelist.input", copy_only=False)
     model_postprocess(WRF_WORK_PATH, output_save_path, outputs="wrfinput_initialized_d01")
 
-    # for _file in listdir(WRF_WORK_PATH):
-    #     if _file.startswith("rsl."):
-    #         move(f"{WRF_WORK_PATH}/{_file}", f"{log_save_path}/{_file}")
-    #     elif _file == "wrfinput_initialized_d01":
-    #         move(f"{WRF_WORK_PATH}/{_file}", f"{output_save_path}/{_file}")
-    #         if update_real_output:
-    #             move(f"{real_output_path}/wrfinput_d01", f"{real_output_path}/wrfinput_d01_before_dfi")
-    #             copyfile(f"{output_save_path}/{_file}", f"{real_output_path}/wrfinput_d01")
-    #             logger.info(f"Replace real's output \"wrfinput_d01\" with output, old file has been renamed as \"wrfinput_d01_before_dfi\"")
-    #
-    # move(f"{WRF_WORK_PATH}/namelist.input", f"{log_save_path}/namelist.input")
-
     if update_real_output:
         move(f"{real_output_path}/wrfinput_d01", f"{real_output_path}/wrfinput_d01_before_dfi")
         copyfile(f"{output_save_path}/wrfinput_initialized_d01", f"{real_output_path}/wrfinput_d01")
@@ -336,14 +309,6 @@ def wrf(wrf_input_path: Union[str, None] = None):
     model_postprocess(WRF_WORK_PATH, log_save_path, startswith="rsl.", outputs="namelist.input", copy_only=False)
     model_postprocess(WRF_WORK_PATH, output_save_path, startswith="wrfout")
 
-    # for _file in listdir(WRF_WORK_PATH):
-    #     if _file.startswith("rsl."):
-    #         move(f"{WRF_WORK_PATH}/{_file}", f"{log_save_path}/{_file}")
-    #     elif _file.startswith("wrfout"):
-    #         copyfile(f"{WRF_WORK_PATH}/{_file}", f"{output_save_path}/{_file}")
-    #
-    # move(f"{WRF_WORK_PATH}/namelist.input", f"{log_save_path}/namelist.input")
-
     logger.info(f"All wrf output files have been copied to {output_save_path}")
 
 
@@ -397,12 +362,6 @@ def ndown(wrfout_file_path: str, wrfinput_file_path: str, update_namelist=True):
 
     model_postprocess(WRF_WORK_PATH, log_save_path, startswith="rsl.", outputs="namelist.input", copy_only=False)
 
-    # for _file in listdir(WRF_WORK_PATH):
-    #     if _file.startswith("rsl."):
-    #         move(f"{WRF_WORK_PATH}/{_file}", f"{log_save_path}/{_file}")
-    #
-    # move(f"{WRF_WORK_PATH}/namelist.input", f"{log_save_path}/namelist.input")
-
     logger.info(f"Rename ndown output `wrfinput_d02` to `wrfinput_d01`")
     move(f"{WRF_WORK_PATH}/wrfinput_d02", f"{output_save_path}/wrfinput_d01")
 

wrfrun-0.1.6/wrfrun/model/utils/__init__.py

@@ -0,0 +1,5 @@
+from .core import *
+from .ndown_utils import *
+from .wps_utils import *
+from .wrf_utils import *
+from .wrfda_utils import *

wrfrun-0.1.4/wrfrun/model/utils.py → wrfrun-0.1.6/wrfrun/model/utils/core.py

@@ -1,7 +1,7 @@
 from os import listdir, makedirs
 from os.path import basename, exists
 from shutil import copyfile, move
-from typing import Tuple, Union, List
+from typing import Tuple, Union, List, Iterable
 
 from wrfrun.utils import logger
 
@@ -57,7 +57,7 @@ def model_preprocess(exec_name: str, work_path: str):
             copyfile(_file, f"{work_path}/{filename}")
 
 
-def model_postprocess(output_dir: str, save_path: str, startswith: Union[None, str, Tuple[str]] = None, endswith: Union[None, str, Tuple[str]] = None,
+def model_postprocess(output_dir: str, save_path: str, startswith: Union[None, str, Tuple[str, ...]] = None, endswith: Union[None, str, Tuple[str, ...]] = None,
                       outputs: Union[None, str, List[str]] = None, copy_only=True):
     """
     Save the results and logs from the model.
@@ -84,26 +84,35 @@ def model_postprocess(output_dir: str, save_path: str, startswith: Union[None, s
     save_file_list = []
 
     if startswith is not None:
+        _list = []
         for _file in file_list:
             if _file.startswith(startswith):
-                save_file_list.append(_file)
+                _list.append(_file)
+        save_file_list += _list
+                
+        logger.debug(f"Collect files match `startswith`: {_list}")
 
     if endswith is not None:
+        _list = []
         for _file in file_list:
             if _file.endswith(endswith):
-                save_file_list.append(_file)
+                _list.append(_file)
+        save_file_list += _list
+                
+        logger.debug(f"Collect files match `endswith`: {_list}")
 
     if outputs is not None:
-        if isinstance(outputs, str):
-            save_file_list.append(basename(outputs))
+        if isinstance(outputs, str) and outputs in file_list:
+            save_file_list.append(outputs)
         else:
-            outputs = [basename(x) for x in outputs]
+            outputs = [x for x in outputs if x in file_list]
             save_file_list += outputs
 
     if len(save_file_list) < 1:
         return
 
     save_file_list = list(set(save_file_list))
+    logger.debug(f"Files to be processed: {save_file_list}")
 
     for _file in save_file_list:
         if copy_only:

wrfrun-0.1.6/wrfrun/model/utils/meson.build

@@ -0,0 +1,11 @@
+py3.install_sources(
+    [
+        '__init__.py',
+        'core.py',
+        'ndown_utils.py',
+        'wps_utils.py',
+        'wrf_utils.py',
+        'wrfda_utils.py',
+    ],
+    subdir: 'wrfrun/model/utils'
+)

wrfrun-0.1.4/wrfrun/model/wrf.py → wrfrun-0.1.6/wrfrun/model/utils/wrf_utils.py

@@ -3,7 +3,7 @@ from shutil import move
 
 from wrfrun.core import WRFRUNConfig, WRFRUNConstants, WRFRUNNamelist
 from wrfrun.utils import check_path, logger
-from .wps import get_metgrid_levels
+from .wps_utils import get_metgrid_levels
 
 
 def reconcile_namelist_metgrid(metgrid_path: str):

{wrfrun-0.1.4 → wrfrun-0.1.6}/wrfrun/res/__init__.py

@@ -4,6 +4,7 @@ from .extension import *
 from .geogrid import *
 from .namelist import *
 from .ungrib import *
+from .job_scheduler import *
 
 
 _RES_PATH = abspath(dirname(__file__))

wrfrun-0.1.6/wrfrun/res/job_scheduler/__init__.py

@@ -0,0 +1,8 @@
+from os.path import abspath, dirname
+
+
+_RES_PATH = abspath(dirname(__file__))
+PBS_TEMPLATE = f"{_RES_PATH}/pbs.template"
+SLURM_TEMPLATE = f"{_RES_PATH}/slurm.template"
+
+__all__ = ["PBS_TEMPLATE", "SLURM_TEMPLATE"]

wrfrun-0.1.6/wrfrun/res/job_scheduler/meson.build

@@ -0,0 +1,8 @@
+py3.install_sources(
+    [
+        '__init__.py',
+        'pbs.template',
+        'slurm.template',
+    ],
+    subdir: 'wrfrun/res/job_scheduler'
+)

wrfrun-0.1.6/wrfrun/res/job_scheduler/pbs.template

@@ -0,0 +1,6 @@
+#PBS -q batch
+#PBS -N wrfrun
+#PBS -o {STDOUT_LOG_PATH}
+#PBS -e {STDERR_LOG_PATH}
+#PBS -l nodes={NODE_NUM}:ppn={CORE_NUM}
+#PBS -l walltime=9999:00:00

wrfrun-0.1.6/wrfrun/res/job_scheduler/slurm.template

@@ -0,0 +1,6 @@
+#SBATCH -J wrfrun                   %Job's name
+#SBATCH -N{NODE_NUM}                %node num
+#SBATCH -n{CORE_NUM}                %core num
+#SBATCH --time=9999:00:00           %maximum run time
+#SBATCH --output={STDOUT_LOG_PATH}  %stdout output log path
+#SBATCH --error={STDERR_LOG_PATH}   %error output log path

{wrfrun-0.1.4 → wrfrun-0.1.6}/wrfrun/res/meson.build

@@ -12,3 +12,4 @@ subdir('geogrid')
 subdir('metgrid')
 subdir('namelist')
 subdir('ungrib')
+subdir('job_scheduler')

{wrfrun-0.1.4 → wrfrun-0.1.6}/wrfrun/run.py

@@ -12,8 +12,7 @@ from .core import WRFRUNConfig, WRFRUNConstants, WRFRunServer, WRFRunServerHandl
 from .data import prepare_wps_input_data
 from .model.namelist import prepare_wps_namelist, prepare_wrf_namelist, prepare_wrfda_namelist
 from .model.plot import plot_domain_area
-from .model.wps import clear_wps_logs
-from .model.wrf import clear_wrf_logs
+from .model.utils import clear_wps_logs, clear_wrf_logs
 from .pbs import in_pbs, prepare_pbs_script
 from .utils import call_subprocess, check_path, logger, logger_add_file_handler
 from .workspace import prepare_workspace

wrfrun-0.1.4/.gitattributes

@@ -1,3 +0,0 @@
-.gitea/ export-ignore
-.github/ export-ignore
-images/ export-ignore