257 feature type re assignment (#262)

* filter the feature collection by feature type * check in some experimental code * set VerifyInformationModel.yes when adding property * use setuptools-git-versioning * minor changes according to JC comments * add warning about inaccurate git version number * move some code out of __init__.py * add reset_feature_type sub-command * add test_reset_feature_type.sh * update links * update readme * find out why the pytest hangs on Windows * find out why the pytest hangs on Windows - 2 * test if setuptools-git-versioning caused pytest hang * test if setuptools-git-versioning caused pytest hang 1 * test if setuptools-git-versioning caused pytest hang 2 * remove the damned unicode emoji * bing back good stuff * update warning message again * update test scripts
GPlates · Aug 28, 2024 · cbcce99 · cbcce99
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diff --git a/README.md b/README.md
@@ -296,68 +296,117 @@ Other documentation versions:
 
 GPlately comes with a suite of useful command line tools. These tools are designed as GPlately subcommands. Run `gplately -h` to show the list of tools.
 
-- **list**
+### **list**
 
   Display a list of available plate models from GPlates server. These model names can then be used by the Plate Model Manager to download model files over Internet. Run `gplately list -h` for details.
 
   Examples:
 
     - `gplately list`
+      (list all available plate models from GPlates server)
+
     - `gplately list -m merdith2021`
+      (show details about model merdith2021)
 
     If you are using GPlately Docker image
 
     - `docker run gplates/gplately gplately list`
     - `docker run gplates/gplately gplately list -m merdith2021`
 
-- **combine**
+### **combine**
 
   Combine multiple feature collections into one. Run `gplately combine -h` for details.
 
-- **filter**
+### **filter**
+
+  Filter feature collection by various criteria. Run `gplately filter -h` for details.
+
+  Examples: 
+
+    - `gplately filter input_file output_file -n Africa "North America"`
+        (get features whose name contains "Africa" or "North America")
+
+    - `gplately filter input_file output_file -p 701 714 715 101`
+        (get features whose plate ID is one of 701 714 715 101)
+
+    - `gplately filter input_file output_file --min-birth-age 500`
+        (get features whose birth age is older than 500Myr)
+
+    - `gplately filter input_file output_file --max-birth-age 500`
+        (get features whose birth age is younger than 500Myr)
+
+    - `gplately filter input_file output_file -n Africa "North America" -p 701 714 715 101 --min-birth-age 500`
+        (get features whose name conains "Africa" or "North America" and plate ID is one of 701 714 715 101 and birth age is older than 500Myr)
+
+    - `gplately filter input_file output_file -t gpml:Basin`
+        (get all gpml:Basin features)
+
+    - `gplately filter input_file output_file -t "gpml:IslandArc|gpml:Basin"`
+        (get all gpml:Basin and gpml:IslandArc features)
+
+    If you are using Docker, prefix `docker run gplates/gplately ` to the command, such as `docker run gplates/gplately gplately filter input_file output_file -t gpml:Basin`.
+
+    See https://github.com/GPlates/gplately/blob/master/tests-dir/unittest/test_feature_filter.sh for more examples. 
+
+### **reset_feature_type**
+
+  Reset the feature type for the selected features. Run `gplately reset_feature_type -h` for details.
+
+  Examples: 
+
+    - `gplately reset_feature_type -s gpml:ClosedContinentalBoundary -t gpml:UnclassifiedFeature input_file output_file`
+        (change all gpml:ClosedContinentalBoundary to gpml:UnclassifiedFeature)
+        
+    - `gplately reset_feature_type -s "gpml:ContinentalFragment|gpml:Coastline" -t gpml:UnclassifiedFeature input_file output_file`
+        (change all gpml:ContinentalFragment and gpml:Coastline to gpml:UnclassifiedFeature)
+        
+    - `gplately reset_feature_type -s ".*" -t gpml:UnclassifiedFeature input_file output_file` 
+        (change all feature types to gpml:UnclassifiedFeature)     
+
+    If you are using Docker, prefix `docker run gplates/gplately ` to the command, such as `docker run gplates/gplately gplately reset_feature_type -s ".*" -t gpml:UnclassifiedFeature input_file output_file`.
 
-  Filter feature collection by various criteria. See scripts/test_feature_filter.sh for usage examples. Run `gplately filter -h` for details.
+  See https://github.com/GPlates/gplately/blob/master/tests-dir/unittest/test_reset_feature_type.sh for more examples. 
 
-- **agegrid (ag)**
+### **agegrid (ag)**
 
   Create age grids for a plate model. Run `gplately agegrid -h` for details.
 
-- **fix_crossovers**
+### **fix_crossovers**
 
   Loads one or more input rotation files, fixes any crossovers and saves the rotations to output rotation files. Run `gplately fix_crossovers -h` for details.
 
-- **remove_rotations**
+### **remove_rotations**
 
   Remove one or more plate IDs from a rotation model (consisting of one or more rotation files). Run `gplately remove_rotations -h` for details.
 
-- **cleanup_topologies**
+### **cleanup_topologies**
 
   Remove any regular features not referenced by topological features. Run `gplately cleanup_topologies -h` for details.
 
-- **convert_xy_to_gplates**
+### **convert_xy_to_gplates**
 
   Converts geometry in one or more input ascii files (such as '.xy' files) to output files suitable for loading into GPlates. Run `gplately convert_xy_to_gplates -h` for details.
 
-- **diagnose_rotations**
+### **diagnose_rotations**
 
   Diagnose one or more rotation files to check for inconsistencies. Run `gplately diagnose_rotations -h` for details.
 
-- **resolve_topologies**
+### **resolve_topologies**
 
   Resolve topological plate polygons (and deforming networks) and saves (to separate files) the resolved topologies, and their boundary sections as subduction zones, mid-ocean ridges (ridge/transform) and others (not subduction zones or mid-ocean ridges). Run `gplately resolve_topologies -h` for details.
 
-- **rotation_tools**
+### **rotation_tools**
 
   Calculate stage rotations between consecutive finite rotations in plate pairs. Run `gplately rotation_tools -h` for details.
 
-- **separate_ridge_transform_segments**
+### **separate_ridge_transform_segments**
 
   Split the geometries of isochrons and mid-ocean ridges into ridge and transform segments. Run `gplately separate_ridge_transform_segments -h` for details.
 
-- **subduction_convergence**
+### **subduction_convergence**
 
   Find the convergence rates along trenches (subduction zones) over time. Run `gplately subduction_convergence -h` for details.
 
-- **gpmdb**
+### **gpmdb**
 
   Retrieve paleomagnetic data from https://www.gpmdb.net, create GPlates-compatible VGP features and save the VGP features in a .gpmlz file. Run `gplately gpmdb -h` for details.
diff --git a/gplately/__init__.py b/gplately/__init__.py
@@ -199,90 +199,26 @@
 - [__11 - AndesFluxes__](11-AndesFluxes.html): Demonstrates how the reconstructed subduction history along the Andean margin can be potentially used in the plate kinematics anylysis and data mining.
 
 """
+from .utils import dev_warning
+from .utils.check_pmm import ensure_plate_model_manager_compatible
+from .utils.log_utils import get_debug_level, setup_logging, turn_on_debug_logging
+from .utils.version import get_distribution_version
 
-__version__ = "1.3.0"
-REQUIRED_PMM_VERSION = "1.2.0"
+REQUIRED_PMM_VERSION = "1.2.0"  # TODO: get this from package meta
 USING_DEV_VERSION = True  ## change this to False before official release
 
-import os
-
-disable_dev_warning = (
-    "DISABLE_GPLATELY_DEV_WARNING" in os.environ
-    and os.environ["DISABLE_GPLATELY_DEV_WARNING"].lower() == "true"
-)
-if USING_DEV_VERSION and not disable_dev_warning:
-    print()
-    print("##########################################################################")
-    print(
-        """
-        WARNING: 
-        You are using a DEV version GPlately. Some functionalities have not been tested thoroughly.
-        The DEV version may break your code or produce wrong results due to its unstable nature(DEV in progress).
-        You might also need to install the DEV version plate_model_manager 
-        from https://github.com/michaelchin/plate-model-manager to use this DEV version GPlately.
-
-        To disable this warning, set USING_DEV_VERSION to False in __init__.py or
-        set DISABLE_GPLATELY_DEV_WARNING environment variable to true.
-        `export DISABLE_GPLATELY_DEV_WARNING=true`
-        """
-    )
-    print("##########################################################################")
-    print()
-
-import logging
-
-from .utils.log_utils import get_debug_level, setup_logging, turn_on_debug_logging
+__version__ = get_distribution_version()
 
 setup_logging()
-
-if get_debug_level() > 0:
-    turn_on_debug_logging()
-
 del setup_logging
-del os
-
-logger = logging.getLogger("gplately")
-
-
-def install_and_update_pmm():
-    import subprocess
-    import sys
-
-    subprocess.call(
-        [sys.executable, "-m", "pip", "install", "plate-model-manager", "--upgrade"]
-    )
-
-
-def check_version(installed_version, required_version):
-    """return True if the installed_version is good enough, otherwise False"""
-    installed_version_numbers = installed_version.split(".")
-    required_version_numbers = required_version.split(".")
-    if int(installed_version_numbers[0]) > int(required_version_numbers[0]):
-        return True
-    elif int(installed_version_numbers[0]) == int(required_version_numbers[0]):
-        if int(installed_version_numbers[1]) > int(required_version_numbers[1]):
-            return True
-        elif int(installed_version_numbers[1]) == int(required_version_numbers[1]):
-            if int(installed_version_numbers[2]) >= int(required_version_numbers[2]):
-                return True
-    return False
-
-
-try:
-    import plate_model_manager
-except (ImportError, ModuleNotFoundError):
-    logger.info("The plate_model_manager is not installed, installing it now!")
-    install_and_update_pmm()
-    import plate_model_manager
-
-
-if not check_version(plate_model_manager.__version__, REQUIRED_PMM_VERSION):
-    logger.info("The plate_model_manager is outdated, updating it now!")
-    install_and_update_pmm()
-    import importlib
 
-    importlib.reload(plate_model_manager)
+if USING_DEV_VERSION:
+    dev_warning.print_dev_warning(__version__)
+    dev_warning.print_using_source_code_warning(__version__)
+del dev_warning
 
+ensure_plate_model_manager_compatible(REQUIRED_PMM_VERSION)
+del ensure_plate_model_manager_compatible
 
 from . import (
     data,

diff --git a/gplately/__main__.py b/gplately/__main__.py
@@ -23,7 +23,7 @@
 
 from gplately import __version__
 
-from .commands import create_age_grids, feature_filter, list_models
+from .commands import create_age_grids, feature_filter, list_models, reset_feature_type
 from .ptt import (
     cleanup_topologies,
     convert_xy_to_gplates,
@@ -93,6 +93,9 @@ def main():
     # add "feature filter" sub-command
     feature_filter.add_parser(subparser)
 
+    # add "reset feature type" sub-command
+    reset_feature_type.add_parser(subparser)
+
     # add "create age grids" sub-command
     create_age_grids.add_parser(subparser)