Merge pull request #59 from MiraGeoscience/hotfix/0.2.2

Hotfix/0.2.2

Author: sebhmg

.github/workflows/python_analysis.yml

@@ -44,6 +44,6 @@ jobs:
     uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-pytest_unix_os.yml@main
     with:
       package_manager: 'poetry'
-      python_ver: '["3.10", "3.11", "3.12"]'
+      python_ver: '["3.10"]'
       os: '["ubuntu-latest"]'
       cache_number: 1

docs/source/conf.py

@@ -27,6 +27,6 @@
 html_static_path = ["_static"]
 
 # The short X.Y version.
-version = "0.2.1"
+version = "0.2.2"
 # The full version, including alpha/beta/rc tags.
-release = "0.2.1"
+release = "0.2.2"

las_geoh5/__init__.py

@@ -6,14 +6,12 @@
 #  (see LICENSE file at the root of this source code package).
 #
 
-# flake8: noqa
-
 from __future__ import annotations
-import re
+
 from pathlib import Path
-from lasio import reader
 
-__version__ = "0.2.1"
+
+__version__ = "0.2.2"
 
 
 def assets_path() -> Path:
@@ -28,95 +26,7 @@ def assets_path() -> Path:
     return assets_folder
 
 
-# TODO: Propose change on lasio to fix possible version issue
-
-
-def configure_metadata_patterns(line, section_name):  # pylint: disable=too-many-locals
-    """Configure regular-expression patterns to parse section meta-data lines.
-
-    # OVERLOAD lasio.reader.configure_metadata_patterns
-
-    Arguments:
-        line (str): line from LAS header section
-        section_name (str): Name of the section the 'line' is from.
-
-    Returns:
-        An array of regular-expression strings (patterns).
-    """
-
-    # Default return value
-    patterns = []
-
-    # Default regular expressions for name, value and desc fields
-    name_re = r"\.?(?P<name>[^.]*)\."
-    value_re = r"(?P<value>.*):"
-    desc_re = r"(?P<descr>.*)"
-
-    # Default regular expression for unit field. Note that we
-    # attempt to match "1000 psi" as a special case which allows
-    # a single whitespace character, in contradiction to the LAS specification
-    # See GitHub issue #363 for details.
-    if "VERS" in line:
-        unit_re = r"(?P<unit>\D*)"
-    else:
-        unit_re = r"(?P<unit>([0-9]+\s)?[^\s]*)"
-
-    # Alternate regular expressions for special cases
-    name_missing_period_re = r"(?P<name>[^:]*):"
-    value_missing_period_re = r"(?P<value>.*)"
-    value_without_colon_delimiter_re = r"(?P<value>[^:]*)"
-    value_with_time_colon_re = (
-        r"(?P<value>.*?)(?:(?<!( [0-2][0-3]| hh| HH)):(?!([0-5][0-9]|mm|MM)))"
-    )
-    name_with_dots_re = r"\.?(?P<name>[^.].*[.])\."
-    no_desc_re = ""
-    no_unit_re = ""
-
-    # Configure special cases
-    # 1. missing period (assume that only name and value are present)
-    # 2. missing colon delimiter and description field
-    # 3. double_dots '..' caused by mnemonic abbreviation (with period)
-    #    next to the dot delimiter.
-    if ":" in line:
-        if not "." in line[: line.find(":")]:
-            # If there is no period, then we assume that the colon exists and
-            # everything on the left is the name, and everything on the right
-            # is the value - therefore no unit or description field.
-            name_re = name_missing_period_re
-            value_re = value_missing_period_re
-            desc_re = no_desc_re
-            unit_re = no_unit_re
-            value_with_time_colon_re = value_missing_period_re
-
-    if not ":" in line:
-        # If there isn't a colon delimiter then there isn't
-        # a description field either.
-        value_re = value_without_colon_delimiter_re
-        desc_re = no_desc_re
-
-        if ".." in line and section_name == "Curves":
-            name_re = name_with_dots_re
-    else:
-        if re.search(r"[^ ]\.\.", line) and section_name == "Curves":
-            double_dot = line.find("..")
-            desc_colon = line.rfind(":")
-
-            # Check that a double_dot is not in the
-            # description string.
-            if double_dot < desc_colon:
-                name_re = name_with_dots_re
-
-    if section_name == "Parameter":
-        # Search for a value entry with a time-value first.
-        pattern = name_re + unit_re + value_with_time_colon_re + desc_re
-        patterns.append(pattern)
-
-    # Add the regular pattern for all section_names
-    # for the Parameter section this will run after time-value pattern
-    pattern = name_re + unit_re + value_re + desc_re
-    patterns.append(pattern)
-
-    return patterns
-
-
-reader.configure_metadata_patterns = configure_metadata_patterns
+__all__ = [
+    "__version__",
+    "assets_path",
+]

las_geoh5/import_files/driver.py

@@ -17,14 +17,13 @@
 from pathlib import Path
 from shutil import move
 
-import lasio
 from geoh5py import Workspace
 from geoh5py.shared.utils import fetch_active_workspace
 from geoh5py.ui_json import InputFile
 from tqdm import tqdm
 
 from las_geoh5.import_files.params import ImportOptions, NameOptions
-from las_geoh5.import_las import las_to_drillhole
+from las_geoh5.import_las import las_to_drillhole, lasio_read
 
 
 _logger = logging.getLogger(__name__)
@@ -113,11 +112,7 @@ def run(params_json: Path, output_geoh5: Path | None = None):
                     for file in tqdm(
                         ifile.data["files"].split(";"), desc="Reading LAS files"
                     ):
-                        futures.append(
-                            pool.apply_async(
-                                lasio.read, (file,), {"mnemonic_case": "preserve"}
-                            )
-                        )
+                        futures.append(pool.apply_async(lasio_read, (file,)))
 
                     lasfiles = [future.get() for future in futures]
 

las_geoh5/import_las.py

@@ -9,6 +9,7 @@
 from __future__ import annotations
 
 import logging
+import re
 from pathlib import Path
 from typing import Any
 
@@ -24,6 +25,9 @@
 from las_geoh5.import_files.params import ImportOptions, NameOptions
 
 
+_logger = logging.getLogger(__name__)
+
+
 class LASTranslator:
     """Translator for the weakly standardized LAS file standard."""
 
@@ -182,7 +186,7 @@ def add_survey(
         survey = Path(survey)
 
     if survey.suffix == ".las":
-        file = lasio.read(survey, mnemonic_case="preserve")
+        file = lasio_read(survey)
         try:
             surveys = np.c_[get_depths(file)["depth"], file["DIP"], file["AZIM"]]
             if len(drillhole.surveys) == 1:
@@ -416,3 +420,116 @@ def las_to_drillhole(
             new_row = drillhole.surveys[0, :]
             new_row[0] = np.max(depths)
             drillhole.surveys = np.vstack([drillhole.surveys, new_row])
+
+
+def _patch_lasio_reader():
+    """Patch lasio.reader.configure_metadata_patterns to handle edge cases."""
+
+    # patch only once
+    if getattr(lasio.reader, "patched_configure_metadata_patterns", False):
+        return
+
+    _logger.debug("Patching lasio.reader.configure_metadata_patterns")
+
+    # TODO: Propose change on lasio to fix possible version issue
+
+    def configure_metadata_patterns(line, section_name):  # pylint: disable=too-many-locals
+        """Configure regular-expression patterns to parse section meta-data lines.
+
+        # OVERLOAD lasio.reader.configure_metadata_patterns
+
+        Arguments:
+            line (str): line from LAS header section
+            section_name (str): Name of the section the 'line' is from.
+
+        Returns:
+            An array of regular-expression strings (patterns).
+        """
+
+        # Default return value
+        patterns = []
+
+        # Default regular expressions for name, value and desc fields
+        name_re = r"\.?(?P<name>[^.]*)\."
+        value_re = r"(?P<value>.*):"
+        desc_re = r"(?P<descr>.*)"
+
+        # Default regular expression for unit field. Note that we
+        # attempt to match "1000 psi" as a special case which allows
+        # a single whitespace character, in contradiction to the LAS specification
+        # See GitHub issue #363 for details.
+        if "VERS" in line:
+            unit_re = r"(?P<unit>\D*)"
+        else:
+            unit_re = r"(?P<unit>([0-9]+\s)?[^\s]*)"
+
+        # Alternate regular expressions for special cases
+        name_missing_period_re = r"(?P<name>[^:]*):"
+        value_missing_period_re = r"(?P<value>.*)"
+        value_without_colon_delimiter_re = r"(?P<value>[^:]*)"
+        value_with_time_colon_re = (
+            r"(?P<value>.*?)(?:(?<!( [0-2][0-3]| hh| HH)):(?!([0-5][0-9]|mm|MM)))"
+        )
+        name_with_dots_re = r"\.?(?P<name>[^.].*[.])\."
+        no_desc_re = ""
+        no_unit_re = ""
+
+        # Configure special cases
+        # 1. missing period (assume that only name and value are present)
+        # 2. missing colon delimiter and description field
+        # 3. double_dots '..' caused by mnemonic abbreviation (with period)
+        #    next to the dot delimiter.
+        if ":" in line:
+            if "." not in line[: line.find(":")]:
+                # If there is no period, then we assume that the colon exists and
+                # everything on the left is the name, and everything on the right
+                # is the value - therefore no unit or description field.
+                name_re = name_missing_period_re
+                value_re = value_missing_period_re
+                desc_re = no_desc_re
+                unit_re = no_unit_re
+                value_with_time_colon_re = value_missing_period_re
+
+        if ":" not in line:
+            # If there isn't a colon delimiter then there isn't
+            # a description field either.
+            value_re = value_without_colon_delimiter_re
+            desc_re = no_desc_re
+
+            if ".." in line and section_name == "Curves":
+                name_re = name_with_dots_re
+        else:
+            if re.search(r"[^ ]\.\.", line) and section_name == "Curves":
+                double_dot = line.find("..")
+                desc_colon = line.rfind(":")
+
+                # Check that a double_dot is not in the
+                # description string.
+                if double_dot < desc_colon:
+                    name_re = name_with_dots_re
+
+        if section_name == "Parameter":
+            # Search for a value entry with a time-value first.
+            pattern = name_re + unit_re + value_with_time_colon_re + desc_re
+            patterns.append(pattern)
+
+        # Add the regular pattern for all section_names
+        # for the Parameter section this will run after time-value pattern
+        pattern = name_re + unit_re + value_re + desc_re
+        patterns.append(pattern)
+
+        return patterns
+
+    lasio.reader.configure_metadata_patterns = configure_metadata_patterns
+    lasio.reader.patched_configure_metadata_patterns = True
+
+
+def lasio_read(file):
+    """Read a LAS file using lasio.
+
+    Wrapper around lasio.read that patches the reader to handle some
+    edge cases in LAS files.
+    """
+
+    _patch_lasio_reader()
+    return lasio.read(file, mnemonic_case="preserve")

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "las-geoh5"
-version = "0.2.1"
+version = "0.2.2"
 description = "Las/Geoh5 conversion"
 license = "MIT"
 readme = "README.rst"