Merge pull request #85 from sebhmg/develop

merge release branch to develop
MiraGeoscience · Jan 15, 2025 · 230a225 · 230a225
2 parents 1e4b708 + 251c298
commit 230a225
Show file tree

Hide file tree

Showing 40 changed files with 461 additions and 33 deletions.
diff --git a/.github/workflows/python_deploy_dev.yml b/.github/workflows/python_deploy_dev.yml
@@ -21,7 +21,7 @@ jobs:
       JFROG_ARTIFACTORY_URL: ${{ secrets.JFROG_ARTIFACTORY_URL }}
       JFROG_ARTIFACTORY_TOKEN: ${{ secrets.JFROG_ARTIFACTORY_TOKEN }}
   call-workflow-pypi-publish:
-    name: Publish development pypi package (JFrog Artifactory and TestPyPI)
+    name: Publish development pypi package (JFrog Artifactory, TestPyPI)
     uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-publish_pypi_package.yml@main
     with:
       package-manager: 'poetry'

diff --git a/.github/workflows/python_deploy_prod.yml b/.github/workflows/python_deploy_prod.yml
@@ -33,7 +33,7 @@ jobs:
       JFROG_ARTIFACTORY_URL: ${{ secrets.JFROG_ARTIFACTORY_URL }}
       JFROG_ARTIFACTORY_TOKEN: ${{ secrets.JFROG_ARTIFACTORY_TOKEN }}
   call-workflow-pypi-release:
-    name: Publish production PyPI package (JFrog Artifactory and PyPI)
+    name: Publish production PyPI package (JFrog Artifactory, PyPI)
     if: ${{ github.event_name == 'release' || github.event.inputs.publish-pypi == 'true' }}
     uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-release_pypi_assets.yml@main
     with:

diff --git a/.idea/copyright/GMG.xml b/.idea/copyright/GMG.xml
diff --git a/.idea/copyright/MiraGeoscience.xml b/.idea/copyright/MiraGeoscience.xml
diff --git a/.idea/copyright/profiles_settings.xml b/.idea/copyright/profiles_settings.xml
diff --git a/.idea/scopes/sources.xml b/.idea/scopes/sources.xml
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -17,12 +17,12 @@ repos:
     -   id: poetry-check
         args: [--lock]
 -   repo: https://github.com/hadialqattan/pycln
-    rev: v2.4.0
+    rev: v2.5.0
     hooks:
     -   id: pycln
         args: [--config=pyproject.toml]
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.0
+    rev: v0.9.0
     hooks:
     -   id: ruff
         args:
@@ -31,29 +31,50 @@ repos:
 #        -   --unsafe-fixes
     -   id: ruff-format
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.12.0
+    rev: v1.14.1
     hooks:
     -   id: mypy
         additional_dependencies: [
 #            numpy==1.26.*,  # TODO: fix mypy errors related to numpy
             tomli, # to read config from pyproject.toml
             types-six,
             types-toml,
+            types-PyYAML
         ]
         files: ^(omf/fileio/geoh5\.py$|omf/scripts/|tests/)
         exclude: ^docs/
 -   repo: https://github.com/codingjoe/relint
-    rev: 3.2.0
+    rev: 3.3.1
     hooks:
     -   id: relint
         args: [-W]  # to fail on warnings
         files: ^(omf/fileio/geoh5\.py$|omf/scripts/|tests/)
 -   repo: https://github.com/MiraGeoscience/pre-commit-hooks
-    rev: v1.0.1
+    rev: v1.0.2
     hooks:
-#    -   id: check-copyright  # no copyright nor license notice: differ to upstream repo
-#        files: ^(omf/fileio/geoh5\.py$|omf/scripts/|tests/)
+    -   id: check-copyright
+        files: (^package\.rst|^LICENSE|^README(|-dev)\.rst|\.py|\.pyi)$
+        # do not check sources from the original omf package
+        exclude: |
+            (?x)(
+                ^\..*|
+                ^docs/.*|
+                omf/(
+                fileio/__init__|
+                fileio/fileio|
+                fileio/utils|
+                base|
+                data|
+                lineset|
+                pointset|
+                serializers|
+                surface|
+                texture|
+                volume)\.py|
+                tests/doc_example_test\.py
+            )$
     -   id: prepare-commit-msg
+    -   id: check-commit-msg
 -   repo: local
     hooks:
     -   id: pylint

diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,7 @@
 MIT License
 
 Copyright (c) 2017 Global Mining Standards and Guidelines Group
+Copyright (c) 2022-2025 Mira Geoscience
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/README.rst b/README.rst
@@ -63,7 +63,7 @@ This library makes use of the `properties <https://github.com/seequent/propertie
 open-source project, which is designed and publicly supported by
 `Seequent <https://seequent.com>`_.
 
-Connection to the geoh5 format makes use of `geoh5py <https://geoh5py.readthedocs.io/>`_
+Connection to the geoh5 format makes use of `geoh5py <https://mirageoscience-geoh5py.readthedocs-hosted.com/>`_
 publicly supported by `Mira Geoscience <https://mirageoscience.com/>`_
 
 Installation
@@ -89,7 +89,8 @@ License
 ^^^^^^^
 MIT License
 
-Copyright (c) 2024 Mira Geoscience
+Copyright (c) 2017 Global Mining Standards and Guidelines Group
+Copyright (c) 2022-2025 Mira Geoscience
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/meta.yaml b/meta.yaml
@@ -15,7 +15,7 @@ build:
 
 requirements:
   host:
-    - python >=3.10.0,<3.11
+    - python >=3.10.0,<4.0.0
     - poetry-core >=1.0.0
     - setuptools
     - pip
@@ -26,7 +26,7 @@ requirements:
     - pypng 0.20220715.*
     - six >=1.16.0
     - vectormath >=0.2.0
-    - geoh5py >=0.9.1a0.dev0,<0.11.0a0.dev0
+    - geoh5py >=0.10.0b1,<0.11.0a.dev
 
 about:
   license: MIT

diff --git a/omf/__init__.py b/omf/__init__.py
@@ -1,5 +1,19 @@
 """omf: API library for Open Mining Format file interchange format"""
 
+# ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+#  Copyright (c) 2022-2025 Mira Geoscience Ltd.                                '
+#                                                                              '
+#  This file is part of mira-omf package.                                      '
+#                                                                              '
+#  mira-omf is distributed under the terms and conditions of the MIT License   '
+#  (see LICENSE file at the root of this source code package).                 '
+#                                                                              '
+# ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+
+# ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+#  Copyright (c) 2017 Global Mining Standards and Guidelines Group             '
+# ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+
 import logging
 import sys
 
@@ -31,9 +45,12 @@
 
 
 __version__ = "3.4.0-alpha.1"
-__author__ = "Global Mining Standards and Guidelines Group"
+__author__ = "Global Mining Standards and Guidelines Group, Mira Geoscience Ltd."
 __license__ = "MIT License"
-__copyright__ = "Copyright 2017 Global Mining Standards and Guidelines Group"
+__copyright__ = (
+    "Copyright 2017 Global Mining Standards and Guidelines Group, "
+    "Copyright 2022-2025 Mira Geoscience Ltd."
+)
 
 
 def _create_logger():

diff --git a/omf/base.py b/omf/base.py
@@ -1,5 +1,15 @@
 """base.py: OMF Project and base classes for its components"""
 
+# ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+#  Copyright (c) 2017 Global Mining Standards and Guidelines Group             '
+#                                                                              '
+#  This file is part of mira-omf package.                                      '
+#                                                                              '
+#  mira-omf is distributed under the terms and conditions of the MIT License   '
+#  (see LICENSE file at the root of this source code package).                 '
+#                                                                              '
+# ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+
 from __future__ import annotations
 
 import datetime

diff --git a/omf/data.py b/omf/data.py
@@ -1,5 +1,15 @@
 """data.py: different ProjectElementData classes"""
 
+# ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+#  Copyright (c) 2017 Global Mining Standards and Guidelines Group             '
+#                                                                              '
+#  This file is part of mira-omf package.                                      '
+#                                                                              '
+#  mira-omf is distributed under the terms and conditions of the MIT License   '
+#  (see LICENSE file at the root of this source code package).                 '
+#                                                                              '
+# ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+
 import numpy as np
 import properties
 

diff --git a/omf/fileio/__init__.py b/omf/fileio/__init__.py
@@ -1,3 +1,13 @@
+# ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+#  Copyright (c) 2017 Global Mining Standards and Guidelines Group             '
+#                                                                              '
+#  This file is part of mira-omf package.                                      '
+#                                                                              '
+#  mira-omf is distributed under the terms and conditions of the MIT License   '
+#  (see LICENSE file at the root of this source code package).                 '
+#                                                                              '
+# ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+
 from .fileio import OMFReader, OMFWriter
 from .geoh5 import GeoH5Writer
 from .utils import compare_elements
diff --git a/omf/fileio/fileio.py b/omf/fileio/fileio.py
@@ -1,5 +1,15 @@
 """fileio.py: OMF Writer and Reader for serializing to and from .omf files"""
 
+# ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+#  Copyright (c) 2017 Global Mining Standards and Guidelines Group             '
+#                                                                              '
+#  This file is part of mira-omf package.                                      '
+#                                                                              '
+#  mira-omf is distributed under the terms and conditions of the MIT License   '
+#  (see LICENSE file at the root of this source code package).                 '
+#                                                                              '
+# ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+
 from __future__ import annotations
 
 import json

diff --git a/omf/fileio/geoh5.py b/omf/fileio/geoh5.py
@@ -1,3 +1,13 @@
+# ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+#  Copyright (c) 2022-2025 Mira Geoscience Ltd.                                '
+#                                                                              '
+#  This file is part of mira-omf package.                                      '
+#                                                                              '
+#  mira-omf is distributed under the terms and conditions of the MIT License   '
+#  (see LICENSE file at the root of this source code package).                 '
+#                                                                              '
+# ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+
 # pylint: disable=too-many-lines
 
 from __future__ import annotations

diff --git a/omf/fileio/utils.py b/omf/fileio/utils.py
@@ -1,3 +1,13 @@
+# ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+#  Copyright (c) 2017 Global Mining Standards and Guidelines Group             '
+#                                                                              '
+#  This file is part of mira-omf package.                                      '
+#                                                                              '
+#  mira-omf is distributed under the terms and conditions of the MIT License   '
+#  (see LICENSE file at the root of this source code package).                 '
+#                                                                              '
+# ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+
 from numpy import testing
 
 

diff --git a/omf/lineset.py b/omf/lineset.py
@@ -1,5 +1,15 @@
 """lineset.py: LineSet element and geometry"""
 
+# ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+#  Copyright (c) 2017 Global Mining Standards and Guidelines Group             '
+#                                                                              '
+#  This file is part of mira-omf package.                                      '
+#                                                                              '
+#  mira-omf is distributed under the terms and conditions of the MIT License   '
+#  (see LICENSE file at the root of this source code package).                 '
+#                                                                              '
+# ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+
 import numpy as np
 import properties
 

diff --git a/omf/pointset.py b/omf/pointset.py
@@ -1,5 +1,15 @@
 """pointset.py: PointSet element and geometry"""
 
+# ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+#  Copyright (c) 2017 Global Mining Standards and Guidelines Group             '
+#                                                                              '
+#  This file is part of mira-omf package.                                      '
+#                                                                              '
+#  mira-omf is distributed under the terms and conditions of the MIT License   '
+#  (see LICENSE file at the root of this source code package).                 '
+#                                                                              '
+# ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+
 import properties
 
 from .base import ProjectElement, ProjectElementGeometry

diff --git a/omf/scripts/__init__.py b/omf/scripts/__init__.py
@@ -0,0 +1,9 @@
+# ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+#  Copyright (c) 2025 Mira Geoscience Ltd.                                     '
+#                                                                              '
+#  This file is part of mira-omf package.                                      '
+#                                                                              '
+#  mira-omf is distributed under the terms and conditions of the MIT License   '
+#  (see LICENSE file at the root of this source code package).                 '
+#                                                                              '
+# ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
diff --git a/omf/scripts/geoh5_to_omf.py b/omf/scripts/geoh5_to_omf.py
@@ -1,3 +1,13 @@
+# ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+#  Copyright (c) 2025 Mira Geoscience Ltd.                                     '
+#                                                                              '
+#  This file is part of mira-omf package.                                      '
+#                                                                              '
+#  mira-omf is distributed under the terms and conditions of the MIT License   '
+#  (see LICENSE file at the root of this source code package).                 '
+#                                                                              '
+# ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+
 import argparse
 import logging
 import sys

diff --git a/omf/scripts/omf_to_geoh5.py b/omf/scripts/omf_to_geoh5.py
@@ -1,3 +1,13 @@
+# ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+#  Copyright (c) 2025 Mira Geoscience Ltd.                                     '
+#                                                                              '
+#  This file is part of mira-omf package.                                      '
+#                                                                              '
+#  mira-omf is distributed under the terms and conditions of the MIT License   '
+#  (see LICENSE file at the root of this source code package).                 '
+#                                                                              '
+# ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+
 import argparse
 import logging
 import sys

diff --git a/omf/serializers.py b/omf/serializers.py
@@ -1,5 +1,15 @@
 """serializers.py: array and image serializers/deserializers for OMF file IO"""
 
+# ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+#  Copyright (c) 2017 Global Mining Standards and Guidelines Group             '
+#                                                                              '
+#  This file is part of mira-omf package.                                      '
+#                                                                              '
+#  mira-omf is distributed under the terms and conditions of the MIT License   '
+#  (see LICENSE file at the root of this source code package).                 '
+#                                                                              '
+# ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+
 import zlib
 from io import BytesIO