GEOPY-1226: OMF files failing to export and import from command line

.gitattributes

@@ -1,4 +1,8 @@
-*.pt filter=lfs diff=lfs merge=lfs -text
-*.geoh5 filter=lfs diff=lfs merge=lfs -text
-/assets/** filter=lfs diff=lfs merge=lfs -text
-*.h5 filter=lfs diff=lfs merge=lfs -text
+# can only push Git LFS objects to public forks if the repository network already has Git LFS objects
+# or you have write access to the root of the repository network.
+# (from https://docs.github.com/en/repositories/working-with-files/managing-large-files/collaboration-with-git-large-file-storage)
+#
+#*.pt filter=lfs diff=lfs merge=lfs -text
+#*.geoh5 filter=lfs diff=lfs merge=lfs -text
+#/assets/** filter=lfs diff=lfs merge=lfs -text
+#*.h5 filter=lfs diff=lfs merge=lfs -text

.pre-commit-config.yaml

@@ -10,7 +10,7 @@ ci:
 
 repos:
 -   repo: https://github.com/psf/black
-    rev: 23.1.0
+    rev: 23.3.0
     hooks:
     -   id: black
 -   repo: https://github.com/PyCQA/isort
@@ -28,12 +28,12 @@ repos:
     -   id: flake8
         files: ^omf/fileio/geoh5*
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.1
+    rev: v3.4.0
     hooks:
     -   id: pyupgrade
         args: [--py38-plus]
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.0.0
+    rev: v1.3.0
     hooks:
     -   id: mypy
         additional_dependencies: [types-six]
@@ -52,10 +52,10 @@ repos:
         exclude: (devtools|docs)/
         files: ^(omf/fileio/geoh5|tests/)
 -   repo: https://github.com/codespell-project/codespell
-    rev: v2.2.2
+    rev: v2.2.4
     hooks:
     -   id: codespell
-        exclude: (\.ipynb$)
+        exclude: (\.ipynb$|^poetry.lock$)
         entry: codespell -I .codespellignore
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.4.0
@@ -74,7 +74,7 @@ repos:
     -   id: mixed-line-ending
     -   id: name-tests-test
 -   repo: https://github.com/rstcheck/rstcheck
-    rev: v6.1.1
+    rev: v6.1.2
     hooks:
     -   id: rstcheck
         additional_dependencies: [sphinx]

README.rst

@@ -21,7 +21,7 @@ omf
 Version: 3.1.0-alpha.1
 
 API library for Open Mining Format, a new standard for mining data backed by
-the `Global Mining Standards & Guidelines Group <http://www.globalminingstandards.org/>`_.
+the `Global Mining Standards & Guidelines Group <https://gmggroup.org/>`_.
 
 .. warning::
     **Pre-Release Notice**

docs/conf.py

@@ -62,9 +62,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'0.9.3'
+version = u'3.0.0'
 # The full version, including alpha/beta/rc tags.
-release = u'0.9.3'
+release = u'3.0.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

omf/fileio/geoh5.py

@@ -647,19 +647,25 @@
         if not element.legends:
             return kwargs
 
-        ind = 0
-        alpha = 0
-        value_map = {ind: "Unknown"}
-        color_map = [np.r_[ind, [0, 0, 0], alpha]]
+        alpha = 1.0
+        value_map = {0: "Unknown"}
+        color_map = [np.r_[0, [0, 0, 0], alpha]]
 
-        for name, rgb in zip(element.legends[0].values, element.legends[1].values):
-            ind += 1
+        for legend in element.legends:
+            if isinstance(legend.values, StringArray):
+                for count, name in enumerate(legend.values):
+                    if str(name).lower() == "unknown":
+                        name = f"[{str(name).upper()}]"
 
-            if str(name).lower() == "unknown":
-                name = f"[{str(name).upper()}]"
+                    value_map[count + 1] = str(name)
 
-            value_map[ind] = str(name)
-            color_map.append(np.r_[ind, rgb, alpha])
+            else:
+                color_map.append(
+                    [
+                        np.r_[count + 1, val, alpha]
+                        for count, val in enumerate(legend.values)
+                    ]
+                )
 
         kwargs["value_map"] = value_map
         kwargs["type"] = "referenced"

omf/scripts/geoh5_to_omf.py

@@ -1,3 +1,4 @@
+import argparse
 import logging
 import sys
 from pathlib import Path
@@ -9,11 +10,19 @@
 
 
 def run():
-    geoh5_filepath = Path(sys.argv[1])
-    if len(sys.argv) < 3:
+    parser = argparse.ArgumentParser(
+        prog="geoh5_to_omf",
+        description="Converts a geoh5 file to a new OMF file.",
+    )
+    parser.add_argument("geoh5_file", type=Path)
+    parser.add_argument("-o", "--out", type=Path, required=False, default=None)
+    args = parser.parse_args()
+
+    geoh5_filepath = args.geoh5_file
+    if args.out is None:
         output_filepath = geoh5_filepath.with_suffix(".omf")
     else:
-        output_filepath = Path(sys.argv[2])
+        output_filepath = args.out
         if not output_filepath.suffix:
             output_filepath = output_filepath.with_suffix(".omf")
     if output_filepath.exists():

omf/scripts/omf_to_geoh5.py

@@ -1,3 +1,4 @@
+import argparse
 import logging
 import sys
 from pathlib import Path
@@ -9,32 +10,46 @@
 
 
 def run():
-    omf_filepath = Path(sys.argv[1])
-    output_filepath = omf_filepath.with_suffix(".geoh5")
-    compression = 5
-
-    if len(sys.argv) < 3:
+    parser = argparse.ArgumentParser(
+        prog="omf_to_geoh5",
+        description="Converts an OMF file to a new geoh5 file.",
+    )
+    parser.add_argument("omf_file", type=Path, help="Path to the OMF file to convert.")
+    parser.add_argument(
+        "-o",
+        "--out",
+        type=Path,
+        required=False,
+        default=None,
+        help=(
+            "Path to the output geoh5 file. If not specified, create the output file "
+            "at the same location as the input file, but with the geoh5 extension."
+        ),
+    )
+    parser.add_argument(
+        "--gzip",
+        type=int,
+        choices=range(0, 10),
+        default=5,
+        help="Gzip compression level (0-9) for h5 data.",
+    )
+    args = parser.parse_args()
+
+    omf_filepath = args.omf_file
+    if args.out is None:
         output_filepath = omf_filepath.with_suffix(".geoh5")
     else:
-        if sys.argv[2].isdigit():
-            compression = sys.argv[2]
-            if len(sys.argv) > 3:
-                output_filepath = Path(sys.argv[3])
-        elif isinstance(sys.argv[2], str):
-            output_filepath = Path(sys.argv[2])
-            if not output_filepath.suffix:
-                output_filepath = output_filepath.with_suffix(".geoh5")
-            if len(sys.argv) > 3:
-                compression = sys.argv[3]
-
+        output_filepath = args.out
+        if not output_filepath.suffix:
+            output_filepath = output_filepath.with_suffix(".geoh5")
     if output_filepath.exists():
         _logger.error(
             "Cowardly refuses to overwrite existing file '%s'.", output_filepath
         )
         sys.exit(1)
 
     reader = OMFReader(str(omf_filepath.absolute()))
-    GeoH5Writer(reader.get_project(), output_filepath, compression=compression)
+    GeoH5Writer(reader.get_project(), output_filepath, compression=args.gzip)
     _logger.info("geoh5 file created: %s", output_filepath)
 
 

pylintrc

@@ -374,8 +374,8 @@ min-public-methods=1
 [EXCEPTIONS]
 
 # Exceptions that will emit a warning when caught.
-overgeneral-exceptions=BaseException,
-                       Exception
+overgeneral-exceptions=builtins.BaseException,
+                       builtins.Exception
 
 
 [FORMAT]

pyproject.toml

@@ -33,7 +33,7 @@ omf_to_geoh5 = 'omf.scripts.omf_to_geoh5:run'
 
 [tool.poetry.dependencies]
 python = "^3.8,<3.11"
-geoh5py = "~0.8.0rc2"
+geoh5py = {version = "~0.8.0rc2", allow-prereleases = true}
 # geoh5py = {url = "https://github.com/MiraGeoscience/geoh5py/archive/refs/heads/release/0.8.0.zip#sha256="}
 numpy = "~1.23.5"
 properties = "~0.6.0"