275 agegrid cmdline continents file inclusion instructions (#294)

* fix missing continental polygons argument

* update plate-model-manager version requirements

gplately/__init__.py

@@ -204,7 +204,7 @@
 from .utils.log_utils import get_debug_level, setup_logging, turn_on_debug_logging
 from .utils.version import get_distribution_version
 
-REQUIRED_PMM_VERSION = "1.2.0"  # TODO: get this from package meta
+REQUIRED_PMM_VERSION = "1.2.1"  # TODO: get this from package meta
 USING_DEV_VERSION = True  ## change this to False before official release
 
 __version__ = get_distribution_version()
@@ -274,7 +274,6 @@
     "pygplates",
     "io_utils",
     "reconstruction",
-    "plate_model_manager",
     "ptt",
     "spatial",
     # Classes

gplately/commands/create_age_grids.py

@@ -21,20 +21,20 @@
 import multiprocessing
 import time
 import warnings
-from typing import Optional, Sequence, Union
+from typing import List
 
 from plate_model_manager import PlateModel, PlateModelManager
 
 from gplately import PlateReconstruction, PlotTopologies, SeafloorGrid
 
 from ..pygplates import FeatureCollection as gFeatureCollection
-from ..pygplates import FeaturesFunctionArgument
+from ..pygplates import FeaturesFunctionArgument  # type: ignore
 from ..pygplates import RotationModel as gRotationModel
 
 logger = logging.getLogger("gplately")
 
 
-def add_parser(parser: argparse.ArgumentParser):
+def add_parser(parser):
     """add command line argument parser"""
 
     agegrid_cmd = parser.add_parser(
@@ -74,7 +74,6 @@ def add_parser(parser: argparse.ArgumentParser):
         nargs="*",
         help="input continental polygons files",
         dest="continents_filenames",
-        default=None,
     )
     agegrid_cmd.add_argument(
         "-r",
@@ -158,14 +157,14 @@ def add_parser(parser: argparse.ArgumentParser):
 
 Example usage: 
     - gplately ag output -m merdith2021 -e 0 -s 10
-    - gplately ag plate-model-repo/muller2019/Rotations/Muller_etal_2019_CombinedRotations.rot plate-model-repo/muller2019/Topologies/Muller_etal_2019_PlateBoundaries_DeformingNetworks.gpmlz output -c plate-model-repo/muller2019/ContinentalPolygons/Global_EarthByte_GPlates_PresentDay_ContinentalPolygons_2019_v1.shp -e 0 -s 10
+    - gplately ag rotations.rot topologies.gpmlz output -c continental_polygons.gpmlz -e 0 -s 10
 """
 
 
 def create_agegrids(
     model_name: str,
-    input_filenames: Union[str, Sequence[str]],
-    continents_filenames: Union[str, Sequence[str]],
+    input_filenames: List[str],
+    continents_filenames: List[str],
     output_dir: str,
     min_time: float,
     max_time: float,
@@ -175,26 +174,47 @@ def create_agegrids(
     grid_spacing: float = 0.1,
     ridge_sampling: float = 0.5,
     initial_spreadrate: float = 75,
-    file_collection: Optional[str] = None,
+    file_collection: str = "",
     unmasked: bool = False,
+    plate_model_repo: str = "plate-model-repo",
 ) -> None:
     """Create age grids for a plate model."""
 
     if model_name:
+        if input_filenames or continents_filenames:
+            raise Exception(
+                f"The model name({model_name}) is provided with -m or --model. \n"
+                + f"But the INPUT_FILES and/or CONTINENTS_FILE are also provided. \n"
+                + f"The MODEL_NAME and (INPUT_FILES, CONTINENTS_FILE) are mutually exclusive. \n"
+                + f"You either use (-m,--model) to specify a model name or use the first positional arguments and (-c,--continents) to specify the file paths. But not both.\n"
+                + f"Fix your command line and try again."
+            )
         try:
+            # TODO: make "plate-model-repo" an optional parameter
             plate_model = PlateModelManager().get_model(
-                model_name, data_dir="plate-model-repo"
+                model_name, data_dir=plate_model_repo
             )
         except:
+            # try to use the plate model in the local folder if the network is down.
             plate_model = PlateModel(
-                model_name, data_dir="plate-model-repo", readonly=True
+                model_name, data_dir=plate_model_repo, readonly=True
+            )
+
+        if not plate_model:
+            raise Exception(
+                f"Unable to create PlateModel object for model {model_name}. "
+                + f"Check your network connection and make sure the model name is correct. Run `pmm ls` to get a list of available model names."
             )
 
         rotation_files = plate_model.get_rotation_model()
-        topology_files = plate_model.get_topologies()
-        continent_files = plate_model.get_layer("ContinentalPolygons")
+        topology_files = plate_model.get_layer(
+            "Topologies", return_none_if_not_exist=True
+        )
+        continent_files = plate_model.get_layer(
+            "ContinentalPolygons", return_none_if_not_exist=True
+        )
         if "Cratons" in plate_model.get_avail_layers():
-            continent_files += plate_model.get_layer("Cratons")
+            continent_files += plate_model.get_layer("Cratons")  # type: ignore
 
     else:
         rotation_files = []
@@ -212,8 +232,28 @@ def create_agegrids(
 
         continent_files = continents_filenames
 
+    if not rotation_files:
+        raise Exception(
+            "No rotation file(s) found. User must either provide rotation file(s) in the first positional arguments or specify a model name with (-m,--model)."
+        )
     rotations = gRotationModel(rotation_files)
+
+    if not topology_files:
+        error_msg = "No topology file(s) found. "
+        if model_name:
+            error_msg += f"Make sure the model ({model_name}) has topology. Run `pmm ls {model_name}` to check the model."
+        else:
+            error_msg += f"You need to specify the topology files in the first positional arguments."
+        raise Exception(error_msg)
     topologies = gFeatureCollection.from_file_list(topology_files)
+
+    if not continent_files:
+        error_msg = "No continental polygon file(s) found. "
+        if model_name:
+            error_msg += f"Make sure the model ({model_name}) has continental polygons. Run `pmm ls {model_name}` to check the model."
+        else:
+            error_msg += f"You need to specify the continental polygon files with (-c,--continents). Run `gplately ag -h` to see help."
+        raise Exception(error_msg)
     continents = gFeatureCollection.from_file_list(continent_files)
 
     with warnings.catch_warnings():

gplately/commands/regrid.py

@@ -30,7 +30,7 @@
 logger = logging.getLogger("gplately")
 
 
-def add_parser(parser: argparse.ArgumentParser):
+def add_parser(parser):
     """add command line argument parser"""
 
     grid_cmd = parser.add_parser(
@@ -92,19 +92,18 @@ def add_parser(parser: argparse.ArgumentParser):
     - gplately grid inputDirectory --significant-digits 2 outputDirectory
 """
 
+
 def _batch_regrid_netcdf4(
-    input_raster_filename, 
+    input_raster_filename,
     output_raster_filename,
     resample=None,
-    significant_digits=None):
+    significant_digits=None,
+):
 
-    grid = read_netcdf_grid(
-        input_raster_filename, 
-        resample=resample)
+    grid = read_netcdf_grid(input_raster_filename, resample=resample)
     write_netcdf_grid(
-        output_raster_filename, 
-        grid, 
-        significant_digits=significant_digits)
+        output_raster_filename, grid, significant_digits=significant_digits
+    )
 
     print("  {} complete!".format(output_raster_filename))
 
@@ -120,14 +119,13 @@ def _regrid_netcdf4(args):
 
     # determine if directory or filename
     p_input = pathlib.Path(args.input_grid_filename)
-    p_output= pathlib.Path(args.output_grid_filename)
+    p_output = pathlib.Path(args.output_grid_filename)
 
     if args.grid_spacing is None:
         grid_spacing = None
     else:
         grid_spacing = (args.grid_spacing, args.grid_spacing)
 
-
     if p_input.is_file():
         input_filename = p_input
         if p_output.suffix:
@@ -137,10 +135,11 @@ def _regrid_netcdf4(args):
             output_filename = p_output.joinpath(p_input.name)
 
         _batch_regrid_netcdf4(
-            input_filename, 
-            output_filename, 
-            resample=grid_spacing, 
-            significant_digits=args.significant_digits)
+            input_filename,
+            output_filename,
+            resample=grid_spacing,
+            significant_digits=args.significant_digits,
+        )
 
     elif p_input.is_dir():
         if p_output.suffix:
@@ -150,19 +149,28 @@ def _regrid_netcdf4(args):
         input_raster_filenames = []
         output_raster_filenames = []
         for pathname in p_input.iterdir():
-            if pathname.suffix == '.nc' and pathname.is_file() and not pathname.name.startswith('.'):
+            if (
+                pathname.suffix == ".nc"
+                and pathname.is_file()
+                and not pathname.name.startswith(".")
+            ):
                 input_raster_filenames.append(pathname)
                 output_raster_filenames.append(p_output.joinpath(pathname.name))
 
-        print("Found {} netCDF files. Processing...".format(len(input_raster_filenames)))
+        print(
+            "Found {} netCDF files. Processing...".format(len(input_raster_filenames))
+        )
 
         if n_jobs == 1:
-            for in_name, out_name in zip(input_raster_filenames, output_raster_filenames):
+            for in_name, out_name in zip(
+                input_raster_filenames, output_raster_filenames
+            ):
                 _batch_regrid_netcdf4(
                     in_name,
                     out_name,
                     resample=grid_spacing,
-                    significant_digits=args.significant_digits)
+                    significant_digits=args.significant_digits,
+                )
         else:
 
             with multiprocessing.Pool(n_jobs) as pool:
@@ -171,7 +179,8 @@ def _regrid_netcdf4(args):
                         _batch_regrid_netcdf4,
                         resample=grid_spacing,
                         significant_digits=args.significant_digits,
-                    ), zip(input_raster_filenames, output_raster_filenames)
+                    ),
+                    zip(input_raster_filenames, output_raster_filenames),
                 )
 
     else:

gplately/utils/dev_warning.py

@@ -61,11 +61,19 @@ def print_using_source_code_warning(version: str):
     if not disable_dev_warning:
         if os.path.isdir(
             f"{os.path.dirname(os.path.realpath(__file__))}/../.git"
-        ) or not os.path.isfile(
-            f"{os.path.dirname(os.path.realpath(__file__))}/../../../../bin/gplately"
+        ) or not (
+            os.path.isfile(
+                f"{os.path.dirname(os.path.realpath(__file__))}/../../../../bin/gplately"
+            )
+            or os.path.isfile(
+                f"{os.path.dirname(os.path.realpath(__file__))}/../../../../Scripts/gplately.exe"
+            )
         ):
             logger.warning(
-                f"The location of GPlately currently in use is {os.path.dirname(os.path.dirname(os.path.realpath(__file__)))}. "
-                + f"It seems that you are using GPlately source code directly or installed editable package with `pip install -e .`, "
+                f"It seems that you are using GPlately source code directly or installed editable package with `pip install -e .`, "
                 + f"the version number({version}) may not be accurate in these cases."
             )
+
+        logger.info(
+            f"The location of GPlately currently in use is {os.path.dirname(os.path.dirname(os.path.realpath(__file__)))}. "
+        )

pyproject.toml

@@ -36,7 +36,7 @@ dependencies = [
     "rasterio",
     "geopandas",
     "stripy",
-    "plate-model-manager>=1.2.0",
+    "plate-model-manager>=1.2.1",
     "pyyaml",
     "pygmt",
     "rioxarray",

setup.py

@@ -97,7 +97,7 @@ def _minimal_ext_cmd(cmd):
             "rasterio",
             "geopandas",
             "stripy",
-            "plate-model-manager",
+            "plate-model-manager>=1.2.1",
             "pyyaml",
             "pygmt",
             "rioxarray",