Debug workflow 2

gplately/__init__.py

@@ -200,7 +200,17 @@
 
 """
 
-__version__ = "1.3.0"
+
+def get_distribution_version():
+    from importlib.metadata import PackageNotFoundError, version
+
+    try:
+        return version(__name__)
+    except PackageNotFoundError:
+        return "UNKNOWN VERSION"
+
+
+__version__ = get_distribution_version()
 REQUIRED_PMM_VERSION = "1.2.0"
 USING_DEV_VERSION = True  ## change this to False before official release
 
@@ -214,16 +224,9 @@
     print()
     print("##########################################################################")
     print(
-        """
+        f"""
         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`
+        git 
         """
     )
     print("##########################################################################")

gplately/commands/feature_filter.py

@@ -17,10 +17,14 @@
 
 import abc
 import argparse
+import logging
+import re
 from typing import List
 
 import pygplates
 
+logger = logging.getLogger("gplately")
+
 
 class FeatureFilter(metaclass=abc.ABCMeta):
     @classmethod
@@ -135,6 +139,34 @@ def should_keep(self, feature: pygplates.Feature) -> bool:
         return False
 
 
+class FeatureTypeFilter(FeatureFilter):
+    """filter features by the feature type(regular expression)
+
+    examples:
+        - gplately filter "$IN_FILE" output/basins.gpmlz -t gpml:Basin
+        - gplately filter "$IN_FILE" output/basin_islandarc.gpmlz -t "gpml:IslandArc|gpml:Basin"
+
+    :param feature_type_re: the regular expression to match the feature type
+
+    """
+
+    def __init__(self, feature_type_re: str):
+        self._feature_type_re = feature_type_re
+
+    def should_keep(self, feature: pygplates.Feature) -> bool:
+        feature_type = feature.get_feature_type()
+        if re.fullmatch(self._feature_type_re, feature_type.to_qualified_string()):
+            logger.debug(
+                f"feature type match: {self._feature_type_re} {feature_type.to_qualified_string()}"
+            )
+            return True
+        else:
+            logger.debug(
+                f"feature type not match: {self._feature_type_re} {feature_type.to_qualified_string()}"
+            )
+            return False
+
+
 def filter_feature_collection(
     feature_collection: pygplates.FeatureCollection, filters: List[FeatureFilter]
 ):
@@ -168,27 +200,56 @@ def add_parser(subparser):
     filter_cmd.add_argument("filter_input_file", type=str)
     filter_cmd.add_argument("filter_output_file", type=str)
 
+    # filter by feature name
     name_group = filter_cmd.add_mutually_exclusive_group()
-    name_group.add_argument("-n", "--names", type=str, dest="names", nargs="+")
     name_group.add_argument(
-        "--exclude-names", type=str, dest="exclude_names", nargs="+"
+        "-n", "--names", type=str, dest="names", nargs="+", metavar="feature_name"
+    )
+    name_group.add_argument(
+        "--exclude-names",
+        type=str,
+        dest="exclude_names",
+        nargs="+",
+        metavar="feature_name",
     )
 
+    # filter by plate ID
     pid_group = filter_cmd.add_mutually_exclusive_group()
-    pid_group.add_argument("-p", "--pids", type=int, dest="pids", nargs="+")
-    pid_group.add_argument("--exclude-pids", type=int, dest="exclude_pids", nargs="+")
+    pid_group.add_argument(
+        "-p", "--pids", type=int, dest="pids", nargs="+", metavar="pid"
+    )
+    pid_group.add_argument(
+        "--exclude-pids", type=int, dest="exclude_pids", nargs="+", metavar="pid"
+    )
 
+    # filter by birth age
     birth_age_group = filter_cmd.add_mutually_exclusive_group()
     birth_age_group.add_argument(
-        "-a", "--min-birth-age", type=float, dest="min_birth_age"
+        "-a",
+        "--min-birth-age",
+        type=float,
+        dest="min_birth_age",
+        metavar="min_birth_age",
+    )
+    birth_age_group.add_argument(
+        "--max-birth-age", type=float, dest="max_birth_age", metavar="max_birth_age"
     )
-    birth_age_group.add_argument("--max-birth-age", type=float, dest="max_birth_age")
 
     filter_cmd.add_argument(
         "--case-sensitive", dest="case_sensitive", action="store_true"
     )
     filter_cmd.add_argument("--exact-match", dest="exact_match", action="store_true")
 
+    # filter by feature type
+    filter_cmd.add_argument(
+        "-t",
+        "--feature-type",
+        type=str,
+        dest="feature_type_re",
+        metavar="feature_type",
+        help="the regular expression of feature type",
+    )
+
 
 def run_filter_feature_collection(args):
     """Filter the input feature collection according to command line arguments."""
@@ -224,12 +285,15 @@ def run_filter_feature_collection(args):
     elif args.min_birth_age is not None:
         filters.append(BirthAgeFilter(args.min_birth_age))
 
+    if args.feature_type_re is not None:
+        filters.append(FeatureTypeFilter(args.feature_type_re))
+
     new_fc = filter_feature_collection(
         input_feature_collection,
         filters,
     )
 
     new_fc.write(args.filter_output_file)
-    print(
+    logger.info(
         f"Done! The filtered feature collection has been saved to {args.filter_output_file}."
     )

gplately/commands/reset_feature_type.py

@@ -0,0 +1,15 @@
+import pygplates
+
+new_fc = pygplates.FeatureCollection()
+for f in pygplates.FeatureCollection("shapes_continents.gpml"):
+    # print(f.get_feature_type())
+    new_f = pygplates.Feature(
+        pygplates.FeatureType.gpml_unclassified_feature,
+        f.get_feature_id(),
+        pygplates.VerifyInformationModel.yes,
+    )
+    for p in f:
+        new_f.add(p.get_name(), p.get_value(), pygplates.VerifyInformationModel.yes)
+    new_fc.add(new_f)
+
+new_fc.write("new_shapes_continents.gpmlz")

pyproject.toml

@@ -1,7 +1,10 @@
 [build-system]
-requires      = ["setuptools>=61.0.0", "wheel"]
+requires      = ["setuptools>=61.0.0", "wheel", "setuptools-git-versioning"]
 build-backend = "setuptools.build_meta"
 
+[tool.setuptools-git-versioning]
+enabled = true
+
 [project]
 name = "gplately"
 dynamic = ["version"]
@@ -42,8 +45,8 @@ where = ["."]
 exclude = ['*.examples*','*.notebooks*','tests-dir*','Notebooks*', 'scripts*']
 namespaces = true
 
-[tool.setuptools.dynamic]
-version = {attr = "gplately.__version__"}
+#[tool.setuptools.dynamic]
+#version = {attr = "gplately.__version__"}
 
 [project.optional-dependencies]
 dev = ["black", "bumpver", "isort", "pip-tools", "pytest"]

scripts/test_feature_filter.sh

@@ -60,3 +60,11 @@ gplately filter "$IN_FILE" output/no_africa_north_america.gpmlz --exclude-names
 # get features whose name does not conain "Africa" or "North America" and plate ID is not in 401 702
 
 gplately filter "$IN_FILE" output/no_africa_north_america_no_401_702.gpmlz --exclude-names Africa "North America" --exclude-pids 401 702
+
+# get all gpml:Basin features
+
+gplately filter "$IN_FILE" output/basins.gpmlz -t gpml:Basin 
+
+# get all gpml:Basin + gpml:IslandArc features
+
+gplately filter "$IN_FILE" output/basin_islandarc.gpmlz -t "gpml:IslandArc|gpml:Basin"

tests-dir/unittest/test_plate_model.py

@@ -3,6 +3,11 @@
 from common import MODEL_REPO_DIR
 from plate_model_manager import PlateModelManager
 
+import gplately
+
+print(gplately.__version__)
+print(gplately.__file__)
+
 
 def main():
     pm_manger = PlateModelManager()