From 64804fb95cbaafc2145cec28d532a961b28a4a63 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= <24550538+sebhmg@users.noreply.github.com> Date: Fri, 29 May 2026 22:42:58 -0400 Subject: [PATCH 1/8] [GEOPY-2809] pre-commit autoupdate --- .pre-commit-config.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 43577bb..7ba1380 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,6 @@ default_language_version: - python: python3 + python: python3.12 exclude: ^docs/(conf.py|_ext/) default_stages: [pre-commit,pre-push] fail_fast: false @@ -12,7 +12,7 @@ ci: repos: - repo: https://github.com/python-poetry/poetry - rev: 2.2.1 + rev: 2.4.1 hooks: - id: poetry-check args: [--lock, --no-plugins] @@ -22,16 +22,16 @@ repos: - id: pycln args: [--config=pyproject.toml] - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.14.3 + rev: v0.15.15 hooks: - id: ruff-check args: - --fix - --exit-non-zero-on-fix -# - --unsafe-fixes + # - --unsafe-fixes - id: ruff-format - repo: https://github.com/pre-commit/mirrors-mypy - rev: v1.18.2 + rev: v2.1.0 hooks: - id: mypy additional_dependencies: [ @@ -85,7 +85,7 @@ repos: types: [python] exclude: ^docs/ - repo: https://github.com/codespell-project/codespell - rev: v2.4.1 + rev: v2.4.2 hooks: - id: codespell exclude: (\.lock|\.ipynb|^THIRD_PARTY_SOFTWARE\.rst)$ From 9b6f5daf21aadef20a2464f83eb5c0795d4d06ba Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= <24550538+sebhmg@users.noreply.github.com> Date: Fri, 29 May 2026 22:44:40 -0400 Subject: [PATCH 2/8] [GEOPY-2809] remove unnecessary UTF8 BOM --- .gitignore | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index 7d6a7d6..99a8fab 100644 --- a/.gitignore +++ b/.gitignore @@ -1,4 +1,4 @@ -# Byte-compiled / optimized / DLL files +# Byte-compiled / optimized / DLL files __pycache__/ *.py[cod] *$py.class From f931d18817c70bc7ab7328f06465d9e3a697c448 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= <24550538+sebhmg@users.noreply.github.com> Date: Fri, 29 May 2026 22:30:42 -0400 Subject: [PATCH 3/8] [GEOPY-2809] point to geoh5py pre-release and relock --- poetry.lock | 1048 +++++++++++++++++++++++++----------------------- pyproject.toml | 4 +- recipe.yaml | 6 +- 3 files changed, 562 insertions(+), 496 deletions(-) diff --git a/poetry.lock b/poetry.lock index 2b6871e..7302917 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,15 +1,15 @@ -# This file is automatically @generated by Poetry 2.3.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.4.1 and should not be changed by hand. 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">=2.0" -sphinxcontrib-applehelp = "*" -sphinxcontrib-devhelp = "*" -sphinxcontrib-htmlhelp = ">=2.0.0" -sphinxcontrib-jsmath = "*" -sphinxcontrib-qthelp = "*" -sphinxcontrib-serializinghtml = ">=1.1.5" - -[package.extras] -docs = ["sphinxcontrib-websupport"] -lint = ["docutils-stubs", "flake8 (>=3.5.0)", "flake8-bugbear", "flake8-comprehensions", "flake8-simplify", "isort", "mypy (>=0.981)", "sphinx-lint", "types-requests", "types-typed-ast"] -test = ["cython", "html5lib", "pytest (>=4.6)", "typed_ast ; python_version < \"3.8\""] +Jinja2 = ">=3.1" +packaging = ">=23.0" +Pygments = ">=2.17" +requests = ">=2.30.0" +roman-numerals = ">=1.0.0" +snowballstemmer = ">=2.2" +sphinxcontrib-applehelp = ">=1.0.7" +sphinxcontrib-devhelp = ">=1.0.6" +sphinxcontrib-htmlhelp = ">=2.0.6" +sphinxcontrib-jsmath = ">=1.0.1" +sphinxcontrib-qthelp = ">=1.0.6" +sphinxcontrib-serializinghtml = ">=1.1.9" [[package]] name = "sphinxcontrib-applehelp" @@ -1374,14 +1438,14 @@ files = [ [[package]] name = "tomlkit" -version = "0.13.3" +version = "0.15.0" description = "Style preserving TOML library" optional = false -python-versions = ">=3.8" +python-versions = ">=3.9" groups = ["dev"] files = [ - {file = "tomlkit-0.13.3-py3-none-any.whl", hash = "sha256:c89c649d79ee40629a9fda55f8ace8c6a1b42deb912b2a8fd8d942ddadb606b0"}, - {file = "tomlkit-0.13.3.tar.gz", hash = "sha256:430cf247ee57df2b94ee3fbe588e71d362a941ebb545dec29b53961d61add2a1"}, + {file = "tomlkit-0.15.0-py3-none-any.whl", hash = "sha256:4dbc8f0fc024412b57ced8757ac7461305126a648ff8c2c807fcb8e133a78738"}, + {file = "tomlkit-0.15.0.tar.gz", hash = "sha256:7d1a9ecba3086638211b13814ea79c90dd54dd11993564376f3aa92271f5c7a3"}, ] [[package]] @@ -1413,14 +1477,14 @@ typing-extensions = ">=4.12.0" [[package]] name = "urllib3" -version = "2.6.2" +version = "2.7.0" description = "HTTP library with thread-safe connection pooling, file post, and more." optional = false -python-versions = ">=3.9" +python-versions = ">=3.10" groups = ["dev"] files = [ - {file = "urllib3-2.6.2-py3-none-any.whl", hash = "sha256:ec21cddfe7724fc7cb4ba4bea7aa8e2ef36f607a4bab81aa6ce42a13dc3f03dd"}, - {file = "urllib3-2.6.2.tar.gz", hash = "sha256:016f9c98bb7e98085cb2b4b17b87d2c702975664e4f060c6532e64d1c1a5e797"}, + {file = "urllib3-2.7.0-py3-none-any.whl", hash = "sha256:9fb4c81ebbb1ce9531cce37674bbc6f1360472bc18ca9a553ede278ef7276897"}, + {file = "urllib3-2.7.0.tar.gz", hash = "sha256:231e0ec3b63ceb14667c67be60f2f2c40a518cb38b03af60abc813da26505f4c"}, ] [package.extras] @@ -1446,4 +1510,4 @@ numpy = ">=1.7" [metadata] lock-version = "2.1" python-versions = ">=3.12,<3.15" -content-hash = "37935f652d3ba23358f7d69f72c1c52e83fa376b94fc91ec2057e2649e510ea6" +content-hash = "84ab27abc526c9367b087d1d8d40d0f5c9f41bde6ad09210292803e9d2efe1bd" diff --git a/pyproject.toml b/pyproject.toml index 60514c6..fdecbca 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -73,8 +73,8 @@ standard-imghdr = "3.13.*" ## dependencies from Git repositories #------------------------------------ -#geoh5py = {version = ">=0.12.0b5, <0.13.dev", allow-prereleases = true} -geoh5py = {git = "https://github.com/MiraGeoscience/geoh5py.git", rev = "develop"} +geoh5py = {version = ">=0.13.0b1, 0.13.*", allow-prereleases = true} +#geoh5py = {git = "https://github.com/MiraGeoscience/geoh5py.git", rev = "develop"} #geoh5py = {path = "../geoh5py", develop = true} [tool.poetry.group.dev.dependencies] diff --git a/recipe.yaml b/recipe.yaml index 4c6a6a5..fb245cf 100644 --- a/recipe.yaml +++ b/recipe.yaml @@ -29,11 +29,10 @@ requirements: - python ${{ python_min }}.* - poetry-core >=1.8.0 - poetry-dynamic-versioning >=1.9, 1.* - - setuptools run: - python >=${{ python_min }} # Mira packages - - geoh5py >=0.13.0a2, 0.13.* + - geoh5py >=0.13.0b1, 0.13.* # direct dependencies - numpy 2.4.* - properties 0.6.* @@ -44,6 +43,7 @@ requirements: tests: - python: + python_version: ${{ python_min }}.* imports: - ${{ module_name }} - ${{ module_name }}._version @@ -77,4 +77,6 @@ about: extra: recipe-maintainers: - andrewg-mira + - domfournier + - RomFloreani - sebhmg From 716c3c942991afa8ab326ee0248e79f3364e44e1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= <24550538+sebhmg@users.noreply.github.com> Date: Fri, 29 May 2026 23:05:23 -0400 Subject: [PATCH 4/8] [GEOPY-2809] downgrade sphinx for doc tests --- poetry.lock | 74 ++++++++++++++++++++++---------------------------- pyproject.toml | 2 +- 2 files changed, 34 insertions(+), 42 deletions(-) diff --git a/poetry.lock b/poetry.lock index 7302917..e484dce 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2,14 +2,14 @@ [[package]] name = "alabaster" -version = "1.0.0" +version = "0.7.16" description = "A light, configurable Sphinx theme" optional = false -python-versions = ">=3.10" +python-versions = ">=3.9" groups = ["dev"] files = [ - {file = "alabaster-1.0.0-py3-none-any.whl", hash = "sha256:fc6786402dc3fcb2de3cabd5fe455a2db534b371124f1f21de8731783dec828b"}, - {file = "alabaster-1.0.0.tar.gz", hash = "sha256:c00dca57bca26fa62a6d7d0a9fcce65f3e026e9bfe33e9c538fd3fbb2144fd9e"}, + {file = "alabaster-0.7.16-py3-none-any.whl", hash = "sha256:b46733c07dce03ae4e150330b975c75737fa60f0a7c591b6c8bf4928a28e2c92"}, + {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"}, ] [[package]] @@ -352,14 +352,14 @@ profile = ["gprof2dot (>=2022.7.29)"] [[package]] name = "docutils" -version = "0.22.4" +version = "0.19" description = "Docutils -- Python Documentation Utilities" optional = false -python-versions = ">=3.9" +python-versions = ">=3.7" groups = ["dev"] files = [ - {file = "docutils-0.22.4-py3-none-any.whl", hash = "sha256:d0013f540772d1420576855455d050a2180186c91c15779301ac2ccb3eeb68de"}, - {file = "docutils-0.22.4.tar.gz", hash = "sha256:4db53b1fde9abecbb74d91230d32ab626d94f6badfc575d6db9194a49df29968"}, + {file = "docutils-0.19-py3-none-any.whl", hash = "sha256:5e1de4d849fee02c63b040a4a3fd567f4ab104defd8a5511fbbc24a8a017efbc"}, + {file = "docutils-0.19.tar.gz", hash = "sha256:33995a6753c30b7f577febfc2c50411fec6aac7f7ffeb7c4cfe5991072dcf9e6"}, ] [[package]] @@ -1257,18 +1257,6 @@ urllib3 = ">=1.26,<3" socks = ["PySocks (>=1.5.6,!=1.5.7)"] use-chardet-on-py3 = ["chardet (>=3.0.2,<8)"] -[[package]] -name = "roman-numerals" -version = "4.1.0" -description = "Manipulate well-formed Roman numerals" -optional = false -python-versions = ">=3.10" -groups = ["dev"] -files = [ - {file = "roman_numerals-4.1.0-py3-none-any.whl", hash = "sha256:647ba99caddc2cc1e55a51e4360689115551bf4476d90e8162cf8c345fe233c7"}, - {file = "roman_numerals-4.1.0.tar.gz", hash = "sha256:1af8b147eb1405d5839e78aeb93131690495fe9da5c91856cb33ad55a7f1e5b2"}, -] - [[package]] name = "six" version = "1.17.0" @@ -1295,34 +1283,38 @@ files = [ [[package]] name = "sphinx" -version = "9.1.0" +version = "5.3.0" description = "Python documentation generator" optional = false -python-versions = ">=3.12" +python-versions = ">=3.6" groups = ["dev"] files = [ - {file = "sphinx-9.1.0-py3-none-any.whl", hash = "sha256:c84fdd4e782504495fe4f2c0b3413d6c2bf388589bb352d439b2a3bb99991978"}, - {file = "sphinx-9.1.0.tar.gz", hash = "sha256:7741722357dd75f8190766926071fed3bdc211c74dd2d7d4df5404da95930ddb"}, + {file = "Sphinx-5.3.0.tar.gz", hash = "sha256:51026de0a9ff9fc13c05d74913ad66047e104f56a129ff73e174eb5c3ee794b5"}, + {file = "sphinx-5.3.0-py3-none-any.whl", hash = "sha256:060ca5c9f7ba57a08a1219e547b269fadf125ae25b06b9fa7f66768efb652d6d"}, ] [package.dependencies] -alabaster = ">=0.7.14" -babel = ">=2.13" -colorama = {version = ">=0.4.6", markers = "sys_platform == \"win32\""} -docutils = ">=0.21,<0.23" +alabaster = ">=0.7,<0.8" +babel = ">=2.9" +colorama = {version = ">=0.4.5", markers = "sys_platform == \"win32\""} +docutils = ">=0.14,<0.20" imagesize = ">=1.3" -Jinja2 = ">=3.1" -packaging = ">=23.0" -Pygments = ">=2.17" -requests = ">=2.30.0" -roman-numerals = ">=1.0.0" -snowballstemmer = ">=2.2" -sphinxcontrib-applehelp = ">=1.0.7" -sphinxcontrib-devhelp = ">=1.0.6" -sphinxcontrib-htmlhelp = ">=2.0.6" -sphinxcontrib-jsmath = ">=1.0.1" -sphinxcontrib-qthelp = ">=1.0.6" -sphinxcontrib-serializinghtml = ">=1.1.9" +Jinja2 = ">=3.0" +packaging = ">=21.0" +Pygments = ">=2.12" +requests = ">=2.5.0" +snowballstemmer = ">=2.0" +sphinxcontrib-applehelp = "*" +sphinxcontrib-devhelp = "*" +sphinxcontrib-htmlhelp = ">=2.0.0" +sphinxcontrib-jsmath = "*" +sphinxcontrib-qthelp = "*" +sphinxcontrib-serializinghtml = ">=1.1.5" + +[package.extras] +docs = ["sphinxcontrib-websupport"] +lint = ["docutils-stubs", "flake8 (>=3.5.0)", "flake8-bugbear", "flake8-comprehensions", "flake8-simplify", "isort", "mypy (>=0.981)", "sphinx-lint", "types-requests", "types-typed-ast"] +test = ["cython", "html5lib", "pytest (>=4.6)", "typed_ast ; python_version < \"3.8\""] [[package]] name = "sphinxcontrib-applehelp" @@ -1510,4 +1502,4 @@ numpy = ">=1.7" [metadata] lock-version = "2.1" python-versions = ">=3.12,<3.15" -content-hash = "84ab27abc526c9367b087d1d8d40d0f5c9f41bde6ad09210292803e9d2efe1bd" +content-hash = "fb4c4c983079faee394d9002c6aa3d25ef5d4ddff9cf302edda7e0c9284949a5" diff --git a/pyproject.toml b/pyproject.toml index fdecbca..49d1711 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -82,7 +82,7 @@ Pygments = "*" pylint = "*" pytest = "*" pytest-cov = "*" -sphinx = "*" +sphinx = "5.3.*" pyyaml = '*' packaging = '*' From 45e3f1782210c1ffbc27e37eb4e3add7cc062713 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= <24550538+sebhmg@users.noreply.github.com> Date: Fri, 29 May 2026 23:17:18 -0400 Subject: [PATCH 5/8] [GEOPY-2809] split assertion on compressed geoh5 size --- tests/convert_project_test.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/tests/convert_project_test.py b/tests/convert_project_test.py index d4ecc39..9802b64 100644 --- a/tests/convert_project_test.py +++ b/tests/convert_project_test.py @@ -50,7 +50,9 @@ def test_project_compression(random_project: omf.Project, tmp_path: Path): size_med_comp = os.stat(file_med_comp).st_size size_high_comp = os.stat(file_high_comp).st_size - assert size_low_comp > size_med_comp > size_high_comp + assert size_low_comp > size_high_comp + assert size_low_comp > size_med_comp + assert size_med_comp > size_high_comp def test_container_group(random_project: omf.Project, tmp_path: Path): From 40974bb0e567aa40616b08d756b64eb97e3f6e01 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= <24550538+sebhmg@users.noreply.github.com> Date: Fri, 29 May 2026 23:42:33 -0400 Subject: [PATCH 6/8] [GEOPY-2809] was missing "." testing for .geoh5 extension --- omf/fileio/fileio.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/omf/fileio/fileio.py b/omf/fileio/fileio.py index bd214e9..5d6763a 100644 --- a/omf/fileio/fileio.py +++ b/omf/fileio/fileio.py @@ -53,7 +53,7 @@ def __init__(self, project: UidModel, fname: str, compression: int = 5): Binary data is written during project serialization """ - if fname.endswith("geoh5"): + if fname.endswith(".geoh5"): GeoH5Writer(project, fname, compression=compression) else: if not fname.endswith(".omf"): From 32e1255f7614158c8f9536db5cd0bc53c8987c3f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= <24550538+sebhmg@users.noreply.github.com> Date: Sat, 30 May 2026 10:55:54 -0400 Subject: [PATCH 7/8] [GEOPY-2809] temporarily skip test on compression level --- tests/convert_project_test.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/tests/convert_project_test.py b/tests/convert_project_test.py index 9802b64..d9a5e94 100644 --- a/tests/convert_project_test.py +++ b/tests/convert_project_test.py @@ -14,6 +14,7 @@ import os from pathlib import Path +import pytest from geoh5py.groups import ContainerGroup from geoh5py.workspace import Workspace @@ -36,6 +37,7 @@ def test_project_to_geoh5(random_project: omf.Project, tmp_path: Path, caplog): assert len(project.elements) == len(random_project.elements) +@pytest.mark.skip(reason="broken: compression level has no effect. To be fixed") def test_project_compression(random_project: omf.Project, tmp_path: Path): """Test pointset geometry validation""" file_low_comp = str(tmp_path / "project_low_comp.geoh5") From 3ee9a79b89c7c80267391bcb568f064dd9494ad6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= <24550538+sebhmg@users.noreply.github.com> Date: Sat, 30 May 2026 11:02:05 -0400 Subject: [PATCH 8/8] [GEOPY-2809] Revert "[GEOPY-2809] temporarily skip test on compression level" This reverts commit 32e1255f7614158c8f9536db5cd0bc53c8987c3f. --- tests/convert_project_test.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/tests/convert_project_test.py b/tests/convert_project_test.py index d9a5e94..9802b64 100644 --- a/tests/convert_project_test.py +++ b/tests/convert_project_test.py @@ -14,7 +14,6 @@ import os from pathlib import Path -import pytest from geoh5py.groups import ContainerGroup from geoh5py.workspace import Workspace @@ -37,7 +36,6 @@ def test_project_to_geoh5(random_project: omf.Project, tmp_path: Path, caplog): assert len(project.elements) == len(random_project.elements) -@pytest.mark.skip(reason="broken: compression level has no effect. To be fixed") def test_project_compression(random_project: omf.Project, tmp_path: Path): """Test pointset geometry validation""" file_low_comp = str(tmp_path / "project_low_comp.geoh5")