diff --git a/.github/workflows/issue_to_jira.yml b/.github/workflows/issue_to_jira.yml index e3a5c066..057d0782 100644 --- a/.github/workflows/issue_to_jira.yml +++ b/.github/workflows/issue_to_jira.yml @@ -1,5 +1,3 @@ -# This workflow will create a JIRA issue upon creation of a GitHub issue - name: Create JIRA issue on: @@ -7,30 +5,8 @@ on: types: [opened] jobs: - new_jira_issue: - runs-on: ubuntu-latest - - steps: - - name: JIRA Login - uses: atlassian/gajira-login@v3.0.1 - env: - JIRA_BASE_URL: ${{ secrets.JIRA_BASE_URL }} - JIRA_USER_EMAIL: ${{ secrets.JIRA_USER_EMAIL }} - JIRA_API_TOKEN: ${{ secrets.JIRA_API_TOKEN }} - - name: Jira Create issue - id: create_jira_issue - uses: atlassian/gajira-create@v3.0.1 - with: - project: GEOPY - issuetype: Story - summary: ${{ github.event.issue.title }} - description: "_from [GitHub issue #${{ github.event.issue.number }}|${{ github.event.issue.html_url }}]_" - # Additional fields in JSON format - fields: '{"components": [{"name": "OMF"}]}' - - name: Post JIRA link - uses: peter-evans/create-or-update-comment@v3 - with: - # The number of the issue or pull request in which to create a comment. - issue-number: ${{ github.event.issue.number }} - # The comment body. - body: "JIRA issue [${{ steps.create_jira_issue.outputs.issue }}] was created." + call-workflow-create-jira-issue: + uses: MiraGeoscience/CI-tools/.github/workflows/reusable-jira-issue_to_jira.yml@main + secrets: inherit + with: + project-key: 'GEOPY' diff --git a/.github/workflows/pr_add_jira_summary.yml b/.github/workflows/pr_add_jira_summary.yml index f0c8a8dd..794bf3f0 100644 --- a/.github/workflows/pr_add_jira_summary.yml +++ b/.github/workflows/pr_add_jira_summary.yml @@ -1,6 +1,3 @@ -# This workflow will comment the PR with the JIRA issue summary -# if a JIRA issue number is detected in the branch name or title - name: Add JIRA issue summary on: @@ -8,57 +5,6 @@ on: types: [opened] jobs: - add_jira_summary: - runs-on: ubuntu-latest - - steps: - - name: Find JIRA issue key - id: find_jira_key - env: - HEAD_REF: ${{ github.head_ref}} - PR_TITLE: ${{ github.event.pull_request.title }} - run: > - echo $HEAD_REF $PR_TITLE - | echo "issue_key=$( - grep -osi "\b\(GA\|GEOPY\|DEVOPS\)[ #-]*[0-9]\+" - | head -n1 - | sed -E "s/([A-Z]+)[-# ]*([0-9]+)/\1-\2/i" - | tr [:lower:] [:upper:] - )" - >> $GITHUB_OUTPUT - - name: Get JIRA summary - id: get_jira_summary - if: ${{ steps.find_jira_key.outputs.issue_key }} - env: - JIRA_BASE_URL: ${{ secrets.JIRA_BASE_URL }} - JIRA_BASIC_AUTH: ${{ secrets.JIRA_BASIC_AUTH }} - run: > - curl -sS -X GET - -H "Authorization: Basic $JIRA_BASIC_AUTH" - -H "Content-Type: application/json" - "$JIRA_BASE_URL/rest/api/2/issue/${{ steps.find_jira_key.outputs.issue_key }}" - | echo "summary=$(jq -r '.fields.summary // empty')" >> $GITHUB_OUTPUT - - name: Extract PR title - id: get_pr_title - env: - PR_TITLE: ${{ github.event.pull_request.title }} - run: | - echo "text=$(echo $PR_TITLE | sed -E "s/^\s*[?[A-Z]+[-# ]*[0-9]+]?[-: ]*(.*)/\1/i")" >> $GITHUB_OUTPUT - - name: Add comment - if: ${{ steps.find_jira_key.outputs.issue_key }} - env: - ISSUE_SUMMARY: ${{ steps.get_jira_summary.outputs.summary }} - TITLE_TEXT: ${{ steps.get_pr_title.outputs.text }} - PR_BODY: ${{ github.event.pull_request.body }} - run: > - jq - --arg ISSUE_ID "${{ steps.find_jira_key.outputs.issue_key }}" - --arg ISSUE_SUMMARY "$(cat <<< $ISSUE_SUMMARY)" - --arg TITLE_TEXT "$(cat <<< ${TITLE_TEXT:-$ISSUE_SUMMARY})" - --arg PR_BODY "$(cat <<< $PR_BODY)" - -c '{"title": ($ISSUE_ID + ": " + $TITLE_TEXT), "body": ("**" + $ISSUE_ID + " - " + $ISSUE_SUMMARY + "**\n" + $PR_BODY)}' <<< {} - | curl -sS -X POST -d @- - -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" - -H "Content-Type: application/json" - "$GITHUB_API_URL/repos/$GITHUB_REPOSITORY/pulls/${{ github.event.pull_request.number }}" - > /dev/null + call-workflow-add-jira-issue-summary: + uses: MiraGeoscience/CI-tools/.github/workflows/reusable-jira-pr_add_jira_summary.yml@main + secrets: inherit diff --git a/.github/workflows/pytest-unix-os.yml b/.github/workflows/pytest-unix-os.yml deleted file mode 100644 index bc621948..00000000 --- a/.github/workflows/pytest-unix-os.yml +++ /dev/null @@ -1,64 +0,0 @@ -name: pytest on Unix OS - -on: - pull_request: - types: [opened, synchronize, reopened, ready_for_review] - branches: - - develop - - main - - release/** - - feature/** - - hotfix/** - push: - branches: - - develop - - main - - release/** - - feature/** - - hotfix/** - -jobs: - pytest: - name: pytest (Unix) - if: github.event_name != 'pull_request' || github.event.pull_request.draft == false - strategy: - fail-fast: false - matrix: - python_ver: ['3.9', '3.10'] - os: [ubuntu-latest] - runs-on: ${{ matrix.os }} - defaults: - run: - shell: bash - env: - POETRY_VIRTUALENVS_CREATE: true - POETRY_VIRTUALENVS_IN_PROJECT: true - steps: - - uses: actions/checkout@v3 - - name: Set up Python version - uses: actions/setup-python@v4 - with: - python-version: ${{ matrix.python_ver }} - - name: Get full Python version - id: full-python-version - run: echo "version=$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")" >> $GITHUB_OUTPUT - - name: Install Poetry - run: | - curl -sSL https://install.python-poetry.org | POETRY_HOME=$HOME/.poetry python - --version 1.3.2 - echo "$HOME/.poetry/bin" >> $GITHUB_PATH - - name: Set up cache - uses: actions/cache@v3 - id: cache - env: - # Increase this value to reset cache if poetry.lock has not changed - CACHE_NUMBER: 1 - with: - path: .venv - key: venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('**/poetry.lock') }}-{{ env.CACHE_NUMBER }} - - name: Ensure cache is healthy - if: steps.cache.outputs.cache-hit == 'true' - run: timeout 10s poetry run pip --version || rm -rf .venv - - name: Install dependencies - run: poetry install -vvv - - name: pytest - run: poetry run pytest --cov --cov-report=xml diff --git a/.github/workflows/pytest-windows.yml b/.github/workflows/pytest-windows.yml deleted file mode 100644 index cc6c1a6f..00000000 --- a/.github/workflows/pytest-windows.yml +++ /dev/null @@ -1,70 +0,0 @@ -name: pytest on Windows - -on: - pull_request: - types: [opened, synchronize, reopened, ready_for_review] - branches: - - develop - - main - - release/** - - feature/** - - hotfix/** - push: - branches: - - develop - - main - - release/** - - feature/** - - hotfix/** - -jobs: - pytest: - name: pytest (Windows) - if: github.event_name != 'pull_request' || github.event.pull_request.draft == false - strategy: - fail-fast: false - matrix: - python_ver: ['3.9', '3.10'] - defaults: - run: - shell: bash - runs-on: windows-latest - env: - POETRY_VIRTUALENVS_CREATE: true - POETRY_VIRTUALENVS_IN_PROJECT: true - steps: - - uses: actions/checkout@v3 - - name: Set up Python version - uses: actions/setup-python@v4 - with: - python-version: ${{ matrix.python_ver }} - - name: Get full Python version - id: full-python-version - run: echo "version=$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")" >> $GITHUB_OUTPUT - - name: Install Poetry - run: | - curl -sSL https://install.python-poetry.org | POETRY_HOME=$HOME/.poetry python - --version 1.3.2 - echo "$HOME/.poetry/bin" >> $GITHUB_PATH - - name: Set up cache - uses: actions/cache@v3 - id: cache - env: - # Increase this value to reset cache if poetry.lock has not changed - CACHE_NUMBER: 1 - with: - path: .venv - key: venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('**/poetry.lock') }}-{{ env.CACHE_NUMBER }} - - name: Ensure cache is healthy - if: steps.cache.outputs.cache-hit == 'true' - run: timeout 10s poetry run pip --version || rm -rf .venv - - name: Install dependencies - run: poetry install -vvv - - name: pytest - run: poetry run pytest --cov --cov-report=xml - - name: Codecov - if: ${{ success() && matrix.python_ver == '3.10' }} - uses: codecov/codecov-action@v4 - with: - name: GitHub - fail_ci_if_error: true - token: ${{ secrets.CODECOV_TOKEN }} diff --git a/.github/workflows/python_analysis.yml b/.github/workflows/python_analysis.yml new file mode 100644 index 00000000..9db19bde --- /dev/null +++ b/.github/workflows/python_analysis.yml @@ -0,0 +1,43 @@ +name: Python analysis + +on: + pull_request: + types: [opened, synchronize, reopened, ready_for_review] + branches: + - develop + - main + - release/** + - feature/** + - hotfix/** + push: + branches: + - develop + - main + - release/** + - feature/** + - hotfix/** + +concurrency: + group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }} + cancel-in-progress: true + +jobs: + call-workflow-static-analysis: + name: Static analysis + uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-static_analysis.yml@main + with: + package-manager: 'poetry' + app-name: 'omf' + python-version: '3.10' + call-workflow-pytest: + name: Pytest + uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-pytest.yml@main + with: + package-manager: 'poetry' + python-versions: '["3.10", "3.11", "3.12"]' + os: '["ubuntu-latest", "windows-latest"]' + cache-number: 1 + codecov-reference-python-version: '3.10' + codecov-reference-os: '["windows-latest"]' + secrets: + CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} diff --git a/.github/workflows/python_deploy_dev.yml b/.github/workflows/python_deploy_dev.yml new file mode 100644 index 00000000..5c681284 --- /dev/null +++ b/.github/workflows/python_deploy_dev.yml @@ -0,0 +1,35 @@ +name: Deploy python package in development + +on: + push: + tags: + - 'v*' # Push events to every version tag (eg. v1.0.0) + +concurrency: + group: ${{ github.workflow }}-${{ github.ref || github.run_id }} + cancel-in-progress: true + +jobs: + call-workflow-conda-publish: + name: Publish development conda package on JFrog Artifactory + uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-publish_conda_package.yml@main + with: + package-name: 'mira-omf' + python-version: '3.10' + virtual-repo-names: '["public-conda-dev"]' + secrets: + 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, TestPyPI) + uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-publish_pypi_package.yml@main + with: + package-manager: 'poetry' + package-name: 'mira-omf' + version-tag: ${{ github.ref_name }} + python-version: '3.10' + virtual-repo-names: '["public-pypi-dev", "test-pypi"]' + secrets: + JFROG_ARTIFACTORY_URL: ${{ secrets.JFROG_ARTIFACTORY_URL }} + JFROG_ARTIFACTORY_TOKEN: ${{ secrets.JFROG_ARTIFACTORY_TOKEN }} + PYPI_TOKEN: ${{ secrets.TEST_PYPI_TOKEN }} diff --git a/.github/workflows/python_deploy_prod.yml b/.github/workflows/python_deploy_prod.yml new file mode 100644 index 00000000..7813ef40 --- /dev/null +++ b/.github/workflows/python_deploy_prod.yml @@ -0,0 +1,46 @@ +name: Deploy python package in production + +on: + release: + types: [published] + workflow_dispatch: + inputs: + release-tag: + description: 'Tag for the existing (draft) release to publish assets from' + required: true + publish-conda: + description: 'Publish Conda package' + required: false + default: true + publish-pypi: + description: 'Publish PyPI package' + required: false + default: true + +concurrency: + group: ${{ github.workflow }}-${{ github.event.release.tag_name || github.event.inputs.release-tag || github.run_id }} + cancel-in-progress: true + +jobs: + call-workflow-conda-release: + name: Publish production Conda package on JFrog Artifactory + uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-release_conda_assets.yml@main + if: ${{ github.event_name == 'release' || github.event.inputs.publish-conda == 'true' }} + with: + virtual-repo-names: '["public-conda-prod"]' + release-tag: ${{ github.event.release.tag_name || github.event.inputs.release-tag }} + secrets: + 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, 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: + package-name: 'mira-omf' + virtual-repo-names: '["public-pypi-prod", "pypi"]' + release-tag: ${{ github.event.release.tag_name || github.event.inputs.release-tag }} + secrets: + JFROG_ARTIFACTORY_URL: ${{ secrets.JFROG_ARTIFACTORY_URL }} + JFROG_ARTIFACTORY_TOKEN: ${{ secrets.JFROG_ARTIFACTORY_TOKEN }} + PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }} diff --git a/.github/workflows/static-analysis.yml b/.github/workflows/static-analysis.yml deleted file mode 100644 index f0760207..00000000 --- a/.github/workflows/static-analysis.yml +++ /dev/null @@ -1,75 +0,0 @@ -name: static analysis - -on: - pull_request: - types: [opened, synchronize, reopened, ready_for_review] - branches: - - develop - - main - - release/** - - feature/** - - hotfix/** - push: - branches: - - develop - - main - - release/** - - feature/** - - hotfix/** - -env: - source_dir: omf - -jobs: - pylint: - name: pylint - if: github.event_name != 'pull_request' || github.event.pull_request.draft == false - runs-on: ubuntu-latest - defaults: - run: - shell: bash - env: - POETRY_VIRTUALENVS_CREATE: true - POETRY_VIRTUALENVS_IN_PROJECT: true - steps: - - uses: actions/checkout@v3 - - name: Set up Python version - uses: actions/setup-python@v4 - with: - python-version: '3.10' - - name: Get full Python version - id: full-python-version - shell: bash - run: echo "version=$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")" >> $GITHUB_OUTPUT - - name: Install Poetry - run: | - curl -sSL https://install.python-poetry.org | POETRY_HOME=$HOME/.poetry python - --version 1.3.2 - echo "$HOME/.poetry/bin" >> $GITHUB_PATH - - name: Set up cache - uses: actions/cache@v3 - id: cache - env: - # Increase this value to reset cache if poetry.lock has not changed - CACHE_NUMBER: 1 - with: - path: .venv - key: venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('**/poetry.lock') }}-{{ env.CACHE_NUMBER }} - - name: Ensure cache is healthy - if: steps.cache.outputs.cache-hit == 'true' - shell: bash - run: timeout 10s poetry run pip --version || rm -rf .venv - - name: Install dependencies - run: poetry install -vvv - - name: capture modified files - if: github.event_name == 'pull_request' - run: >- - git fetch --deepen=500 origin ${{github.base_ref}} - && echo "FILES_PARAM=$( - git diff --diff-filter=AM --name-only refs/remotes/origin/${{github.base_ref}}... -- | grep -E "^(${source_dir}|tests)/.*\.py$" | xargs - )" >> $GITHUB_ENV - - name: Run pylint on modified files - if: github.event_name == 'pull_request' && env.FILES_PARAM - run: poetry run pylint $FILES_PARAM - - name: Run pylint on all files - if: github.event_name == 'push' - run: poetry run pylint $source_dir/fileio/geoh5* tests diff --git a/.idea/copyright/GMG.xml b/.idea/copyright/GMG.xml new file mode 100644 index 00000000..f32445b3 --- /dev/null +++ b/.idea/copyright/GMG.xml @@ -0,0 +1,8 @@ + + + + \ No newline at end of file diff --git a/.idea/copyright/MiraGeoscience.xml b/.idea/copyright/MiraGeoscience.xml new file mode 100644 index 00000000..2d6a4985 --- /dev/null +++ b/.idea/copyright/MiraGeoscience.xml @@ -0,0 +1,8 @@ + + + + \ No newline at end of file diff --git a/.idea/copyright/profiles_settings.xml b/.idea/copyright/profiles_settings.xml new file mode 100644 index 00000000..0313fd03 --- /dev/null +++ b/.idea/copyright/profiles_settings.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + \ No newline at end of file diff --git a/.idea/scopes/sources.xml b/.idea/scopes/sources.xml index ac2cbbb6..f4755295 100644 --- a/.idea/scopes/sources.xml +++ b/.idea/scopes/sources.xml @@ -1,3 +1,3 @@ - - + + \ No newline at end of file diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index ab017d9a..4dc9ef07 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -2,7 +2,7 @@ default_language_version: python: python3 exclude: ^docs/(conf.py|_ext/) -default_stages: [commit,push] +default_stages: [pre-commit,pre-push] fail_fast: false ci: @@ -17,47 +17,64 @@ 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/PyCQA/isort - rev: 5.13.2 +- repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.9.0 hooks: - - id: isort - additional_dependencies: [tomli] # to read config from pyproject.toml -- repo: https://github.com/psf/black - rev: 24.4.2 - hooks: - - id: black -- repo: https://github.com/PyCQA/flake8 - rev: 7.0.0 - hooks: - - id: flake8 - files: ^(omf/fileio/geoh5|tests/) -- repo: https://github.com/asottile/pyupgrade - rev: v3.15.2 - hooks: - - id: pyupgrade - args: [--py39-plus] + - id: ruff + args: + - --fix + - --exit-non-zero-on-fix +# - --unsafe-fixes + - id: ruff-format - repo: https://github.com/pre-commit/mirrors-mypy - rev: v1.10.0 + rev: v1.14.1 hooks: - id: mypy - files: ^(omf/fileio/geoh5|tests/) 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: 3.1.1 + rev: 3.3.1 hooks: - id: relint args: [-W] # to fail on warnings - files: ^omf/fileio/geoh5/ + files: ^(omf/fileio/geoh5\.py$|omf/scripts/|tests/) +- repo: https://github.com/MiraGeoscience/pre-commit-hooks + rev: v1.0.2 + hooks: + - id: check-copyright + files: (^package\.rst|^LICENSE|^README(|-dev)\.rst|\.py|\.pyi)$ + # 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 @@ -66,32 +83,15 @@ repos: language: system require_serial: true # pylint does its own parallelism types: [python] - files: ^(omf/fileio/geoh5|tests/) -# - id: check-copyright # TODO: add missing copyright statements in source files -# name: Check copyright -# entry: python devtools/check-copyright.py -# language: python -# types: [text] -# exclude: (^\.|^docs/) -# files: ^(LICENSE|README(-dev)?.rst|((devtools|omf/fileio/geoh5|tests)/.*\.pyi?))$ - - id: prepare-commit-msg - stages: [prepare-commit-msg] - name: Prepare commit message - entry: python devtools/git_message_hook.py --prepare - language: python - - id: check-commit-msg - stages: [commit-msg] - name: Check commit message - entry: python devtools/git_message_hook.py --check - language: python + exclude: ^docs/ - repo: https://github.com/codespell-project/codespell - rev: v2.2.6 + rev: v2.3.0 hooks: - id: codespell exclude: (\.lock|\.ipynb|^THIRD_PARTY_SOFTWARE\.rst)$ entry: codespell -I .codespellignore - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.6.0 + rev: v5.0.0 hooks: - id: trailing-whitespace exclude: \.mdj$ @@ -99,7 +99,8 @@ repos: exclude_types: [jupyter] - id: check-toml - id: check-yaml -# - id: check-added-large-files # crashing on some configuration. To be investigated + exclude: ^meta.yaml$ + - id: check-added-large-files - id: check-case-conflict - id: check-merge-conflict - id: debug-statements @@ -119,7 +120,7 @@ repos: exclude_types: [jupyter] exclude: ^docs/(.*/)?images/ - repo: https://github.com/rstcheck/rstcheck - rev: v6.2.0 + rev: v6.2.4 hooks: - id: rstcheck exclude: ^THIRD_PARTY_SOFTWARE.rst$ diff --git a/LICENSE b/LICENSE index 79729d2b..3833ab50 100644 --- 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 index eb323f86..415632cb 100644 --- a/README.rst +++ b/README.rst @@ -18,8 +18,6 @@ omf :alt: pytest -Version: 3.2.1 - API library for Open Mining Format, a new standard for mining data backed by the `Global Mining Standards & Guidelines Group `_. @@ -63,7 +61,7 @@ This library makes use of the `properties `_. -Connection to the geoh5 format makes use of `geoh5py `_ +Connection to the geoh5 format makes use of `geoh5py `_ publicly supported by `Mira Geoscience `_ Installation @@ -89,7 +87,8 @@ 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 @@ -112,7 +111,7 @@ SOFTWARE. Third Party Software ^^^^^^^^^^^^^^^^^^^^ -The mira-omf Software may provide links to third party libraries or code (collectively “Third Party Software”) +The mira-omf Software may provide links to third party libraries or code (collectively "Third Party Software") to implement various functions. Third Party Software does not comprise part of the Software. The use of Third Party Software is governed by the terms of such software license(s). Third Party Software notices and/or additional terms and conditions are located in the diff --git a/devtools/check-copyright.py b/devtools/check-copyright.py deleted file mode 100644 index d53a61ed..00000000 --- a/devtools/check-copyright.py +++ /dev/null @@ -1,53 +0,0 @@ -#!/usr/bin/env python3 - -# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -# Copyright (c) 2024 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). ' -# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' - -from __future__ import annotations - -import re -import sys -from datetime import date - -if __name__ == "__main__": - current_year = date.today().year - copyright_re = re.compile( - rf"\bcopyright \(c\) (:?\d{{4}}-|)\b{current_year}\b", re.IGNORECASE - ) - files = sys.argv[1:] - max_lines = 10 - report_files = [] - for f in files: - with open(f, encoding="utf-8") as file: - count = 0 - has_dated_copyright = False - for line in file: - count += 1 - if count >= max_lines and not ( - f.endswith("README.rst") or f.endswith("README-dev.rst") - ): - break - if re.search(copyright_re, line): - has_dated_copyright = True - break - - if not has_dated_copyright: - report_files.append(f) - - if len(report_files) > 0: - for f in report_files: - sys.stderr.write(f"{f}: No copyright or invalid year\n") - sys.exit(1) - -# readonly CURRENT_YEAR=$(date +"%Y") - -# if ! grep -e "Copyright (c) .*$CURRENT_YEAR" $(head -10 $f) 2>&1 1>/dev/null; then -# echo "File '$f' has no copyright or an invalid year" -# exit 1 -# fi diff --git a/devtools/git_message_hook.py b/devtools/git_message_hook.py deleted file mode 100644 index 1633ee58..00000000 --- a/devtools/git_message_hook.py +++ /dev/null @@ -1,224 +0,0 @@ -#!/usr/bin/env python3 - -# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -# Copyright (c) 2024 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). ' -# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' - -"""Some Git pre-commit hooks implementations.""" - -from __future__ import annotations - -import argparse -import re -import shlex -import subprocess -import sys - - -def get_jira_id(text) -> str: - """Detect a JIRA issue ID at the begging of the given text. - - :return: the JIRA issue ID if found, else empty string - """ - - class JiraPattern: - """Internal class that encapsulates the regular expression for the JIRA pattern, - making sure it gets compiled only once.""" - - __pattern = re.compile( - r"(?:GEOPY|DEVOPS|QA|GI|GA|GMS|VPem1D|VPem3D|VPmg|UBCGIF|LICMGR)-\d+" - ) - - @staticmethod - def get(): - """:return: the compiled regular expression for the JIRA pattern""" - return JiraPattern.__pattern - - # use re.match() rather than re.search() to enforce the JIRA reference to be at the beginning - match = re.match(JiraPattern.get(), text.strip()) - return match.group(0) if match else "" - - -def get_branch_name() -> str | None: - """:return: the name of the current branch""" - - git_proc = subprocess.run( - shlex.split("git branch --list"), stdout=subprocess.PIPE, text=True, check=False - ) - - # cannot use HEAD during rebase - # git_proc = subprocess.run( - # shlex.split('git symbolic-ref --short HEAD'), stdout=subprocess.PIPE, universal_newlines=True - # ) - # Note: version above suggested by Atlassian. Could also use: git rev-parse --abbrev-ref HEAD - - if git_proc.returncode != 0: - return None - - current_branch = None - # current branch is prefixed by '*' - for line in git_proc.stdout.splitlines(): - stripped = line.strip() - if stripped and stripped[0] == "*": - current_branch = stripped[1:] - break - assert current_branch is not None - - class RebasingPattern: - """Internal class that encapsulates the regular expression for the rebasing - message pattern, making sure it gets compiled only once.""" - - __pattern = re.compile(r"\(.*\s(\S+)\s*\)") - - @staticmethod - def get(): - """:return: the compiled regular expression for the Rebasing pattern""" - return RebasingPattern.__pattern - - match = re.match(RebasingPattern.get(), current_branch.strip()) - if match: - return match.group(1) - - return current_branch - - -def check_commit_message(filepath: str) -> tuple[bool, str]: - """Check if the branch name or the commit message starts with a reference to JIRA, - and if the message meets the minimum required length for the summary line. - - The JIRA reference has to be at the beginning of the branch name, or of the commit - message. - :return: a tuple telling whether the commit message is valid or not, and an error - message (empty in case the message is valid). - """ - - branch_jira_id = "" - branch_name = get_branch_name() - if branch_name: - branch_jira_id = get_jira_id(branch_name) - - message_jira_id = "" - first_line = None - with open(filepath) as message_file: - for line in message_file: - if not line.startswith("#") and len(line.strip()) > 0: - # test only the first non-comment line that is not empty - # (should we reject messages with empty first line?) - first_line = line - message_jira_id = get_jira_id(first_line) - break - assert first_line is not None - - if not branch_jira_id and not ( - message_jira_id or first_line.strip().lower().startswith("merge") - ): - return ( - False, - "Either the branch name or the commit message must start with a JIRA ID.", - ) - - if branch_jira_id and message_jira_id and branch_jira_id != message_jira_id: - return ( - False, - "Different JIRA ID in commit message %s and in branch name %s." - % (message_jira_id, branch_jira_id), - ) - - stripped_message_line = "" - if first_line: - stripped_message_line = first_line.strip() - if message_jira_id: - stripped_message_line = stripped_message_line[ - len(message_jira_id) + 1 : - ].strip() - - min_required_length = 10 - if len(stripped_message_line) < min_required_length: - return ( - False, - "First line of commit message must be at least %s characters long, " - "beyond the JIRA ID." % min_required_length, - ) - - return True, "" - - -def check_commit_msg(filepath: str) -> None: - """To be used a the Git commit-msg hook. - - Exit with non-0 status if the commit message is deemed invalid. - """ - - (is_valid, error_message) = check_commit_message(filepath) - if not is_valid: - print( - """commit-msg hook: **ERROR** %s - Message has been saved to %s.""" - % (error_message, filepath) - ) - sys.exit(1) - - -def prepare_commit_msg(filepath: str, source: str | None = None) -> None: - """To be used a the Git prepare-commit-msg hook. - - Will add the JIRA ID found in the branch name in case it is missing from the commit - message. - """ - - branch_jira_id = "" - branch_name = get_branch_name() - if branch_name: - branch_jira_id = get_jira_id(branch_name) - - if not branch_jira_id: - return - - if source not in [None, "message", "template"]: - return - - with open(filepath, "r+", encoding="utf-8") as message_file: - message_has_jira_id = False - message_lines = message_file.readlines() - for line_index, line_content in enumerate(message_lines): - if not line_content.startswith("#"): - # test only the first non-comment line - message_jira_id = get_jira_id(line_content) - if not message_jira_id: - message_lines[line_index] = branch_jira_id + ": " + line_content - message_has_jira_id = True - break - - if not message_has_jira_id: - # message is empty or all lines are comments: insert JIRA ID at the very beginning - message_lines.insert(0, branch_jira_id + ": ") - - message_file.seek(0, 0) - message_file.write("".join(message_lines)) - - -if __name__ == "__main__": - parser = argparse.ArgumentParser() - parser.add_argument("msg_file", help="the message file") - group = parser.add_mutually_exclusive_group(required=True) - group.add_argument( - "-p", "--prepare", action="store_true", help="prepare the commit message" - ) - group.add_argument( - "-c", - "--check", - action="store_true", - help="check if the commit message is valid", - ) - parser.add_argument("args", nargs=argparse.REMAINDER) - - args = parser.parse_args() - if args.prepare: - prepare_commit_msg(args.msg_file, *args.args) - elif args.check: - check_commit_msg(args.msg_file) diff --git a/docs/conf.py b/docs/conf.py index a7428b53..e8621612 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -62,9 +62,9 @@ # built documents. # # The short X.Y version. -version = u'3.2.1' +version = u'3.3.0' # The full version, including alpha/beta/rc tags. -release = u'3.2.1' +release = u'3.3.0' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/meta.yaml b/meta.yaml new file mode 100644 index 00000000..b834419f --- /dev/null +++ b/meta.yaml @@ -0,0 +1,39 @@ +{% set name = "mira-omf" %} +{% set version = "3.3.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + path: ../omf + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + +requirements: + host: + - python >=3.10.0,<4.0.0 + - poetry-core >=1.0.0 + - setuptools + - pip + run: + - python >=3.9.0,<3.11 + - numpy >=1.26.0,<1.27.0 + - properties >=0.6 + - pypng 0.20220715.* + - six >=1.16.0 + - vectormath >=0.2.0 + - geoh5py >=0.10.0b1,<0.11.0a.dev + +about: + license: MIT + license_file: + - LICENSE + +extra: + recipe-maintainers: + - SophieCurinier + - sebhmg diff --git a/omf/__init__.py b/omf/__init__.py index 96c6ed10..f7328d6b 100644 --- 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 @@ -29,10 +43,14 @@ from .texture import ImageTexture from .volume import VolumeElement, VolumeGridGeometry -__version__ = "3.2.1" -__author__ = "Global Mining Standards and Guidelines Group" + +__version__ = "3.3.0" +__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 index c0c3ee48..b1a76611 100644 --- 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 @@ -68,9 +78,7 @@ def serialize( return str(self.uid) @classmethod - def deserialize( - cls, uid, trusted=True, registry=None, **kwargs - ): # pylint: disable=arguments-differ + def deserialize(cls, uid, trusted=True, registry=None, **kwargs): # pylint: disable=arguments-differ """Deserialize nested UidModels from flat pointer dictionary""" if registry is None: raise ValueError("no registry provided") @@ -161,8 +169,7 @@ def _validate_data(self): assert self.geometry is not None, "ProjectElement must have a mesh" for i, dat in enumerate(self.data): if ( - dat.location - not in self.geometry._valid_locations # pylint: disable=protected-access + dat.location not in self.geometry._valid_locations # pylint: disable=protected-access ): raise ValueError( f"Invalid location {dat.location} - valid values: " diff --git a/omf/data.py b/omf/data.py index eba5ffdd..3cd34a28 100644 --- 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 @@ -249,9 +259,7 @@ def indices(self, value): def value_dict(self, i): """Return a dictionary of legend entries based on index""" entry = { - legend.name: legend.values[ - self.indices[i] - ] # pylint: disable=unsubscriptable-object + legend.name: legend.values[self.indices[i]] # pylint: disable=unsubscriptable-object for legend in self.legends } # pylint: disable=not-an-iterable return entry @@ -270,11 +278,9 @@ def _validate_indices(self): if np.min(self.indices.array) < -1: # pylint: disable=no-member raise ValueError(f"Indices of DataMap {self.name} must be >= -1") for legend in self.legends: # pylint: disable=not-an-iterable - if np.max(self.indices.array) >= len( - legend.values - ): # pylint: disable=no-member + if np.max(self.indices.array) >= len(legend.values): # pylint: disable=no-member raise ValueError( - "Indices of DataMap {dm} exceed number of available " - "entries in Legend {leg}".format(dm=self.name, leg=legend.name) + f"Indices of DataMap {self.name} exceed number of available " + f"entries in Legend {legend.name}" ) return True diff --git a/omf/fileio/__init__.py b/omf/fileio/__init__.py index ac53c272..0e87312f 100644 --- 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 index d07293a9..bd214e95 100644 --- 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 @@ -9,6 +19,7 @@ from omf.base import UidModel from omf.fileio.geoh5 import GeoH5Writer + __version__ = b"OMF-v0.9.0" diff --git a/omf/fileio/geoh5.py b/omf/fileio/geoh5.py index 5ab5dad0..143525fa 100644 --- 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 @@ -34,6 +44,7 @@ from omf.surface import SurfaceElement, SurfaceGeometry, SurfaceGridGeometry from omf.volume import VolumeElement, VolumeGridGeometry + _logger = logging.getLogger(__package__) @@ -67,7 +78,7 @@ def __init__( file_name: str | Path, compression: int = 5, ): - if not isinstance(file_name, (str, Path)): + if not isinstance(file_name, str | Path): raise TypeError("Input 'file' must be of str or Path.") self.file = file_name @@ -154,9 +165,6 @@ class BaseConversion(ABC): "uid": "uid", "name": "name", } - _geoh5 = None - _parent = None - _mapping = None def __init__( self, @@ -168,7 +176,9 @@ def __init__( if element is None: raise ValueError("Input 'element' cannot be None.") + self._geoh5 = None self.geoh5 = geoh5 + self.compression = compression self._parent = parent @@ -425,7 +435,10 @@ def from_geoh5(self, entity: ObjectBase, **kwargs) -> UidModel: # type: ignore element._backend.update({"uid": uid}) # pylint: disable=W0212 element.data = self.process_dependents( - entity, element, workspace, self.compression # type: ignore + entity, + element, + workspace, + self.compression, # type: ignore ) return element @@ -478,9 +491,12 @@ def from_geoh5(self, entity: RootGroup, **kwargs) -> Project: # type: ignore kwargs = self.collect_attributes(entity, workspace, **kwargs) uid = kwargs.pop("uid") project = self.omf_type(**kwargs) - getattr(project, "_backend").update({"uid": uid}) # pylint: disable=W0212 + project._backend.update({"uid": uid}) # pylint: disable=W0212 project.elements = self.process_dependents( - entity, project, workspace, self.compression # type: ignore + entity, + project, + workspace, + self.compression, # type: ignore ) return project @@ -679,7 +695,10 @@ def collect_h5_attributes( element: ReferencedData, workspace: str | Workspace | Path, **kwargs ) -> dict: with fetch_h5_handle(workspace): - labels = list(element.value_map.map.values()) + if element.value_map is None: + return kwargs + + labels = list(element.value_map().values()) ind = 0 if "Unknown" in labels: ind = 1 @@ -976,8 +995,9 @@ def collect_h5_attributes( with fetch_h5_handle(workspace): geometry = {} for key, alias in cls._attribute_map.items(): - cell_size, count = getattr(entity, f"{alias}_cell_size"), getattr( - entity, f"{alias}_count" + cell_size, count = ( + getattr(entity, f"{alias}_cell_size"), + getattr(entity, f"{alias}_count"), ) tensor = np.ones(count) * np.abs(cell_size) geometry.update({f"tensor_{key}": tensor}) diff --git a/omf/fileio/utils.py b/omf/fileio/utils.py index 743c31c8..c1128530 100644 --- 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 @@ -7,7 +17,7 @@ def compare_elements(elem_a, elem_b): assert elem_a.name == elem_b.name if hasattr(elem_a, "geometry"): - for attr in getattr(elem_a.geometry, "_valid_locations"): + for attr in elem_a.geometry._valid_locations: if getattr(elem_a.geometry, attr, None) is not None: testing.assert_allclose( getattr(elem_a.geometry, attr).array, diff --git a/omf/lineset.py b/omf/lineset.py index d40c81d9..eb90d340 100644 --- 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 index 64f4c140..e957a5ee 100644 --- 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 index e69de29b..d8b6fd73 100644 --- 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 index b2b6a9df..a9412926 100644 --- 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 @@ -6,6 +16,7 @@ from omf.fileio import OMFWriter from omf.fileio.geoh5 import GeoH5Reader + _logger = logging.getLogger(__package__ + "." + Path(__file__).stem) diff --git a/omf/scripts/omf_to_geoh5.py b/omf/scripts/omf_to_geoh5.py index 1ffffad4..a0e285df 100644 --- 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 @@ -6,6 +16,7 @@ from omf.fileio import OMFReader from omf.fileio.geoh5 import GeoH5Writer + _logger = logging.getLogger(__package__ + "." + Path(__file__).stem) diff --git a/omf/serializers.py b/omf/serializers.py index a7fab580..3715d52d 100644 --- a/omf/serializers.py +++ b/omf/serializers.py @@ -1,10 +1,19 @@ """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 import numpy as np -from six import PY2 def array_serializer(arr, open_file, **kwargs): # pylint: disable=unused-argument diff --git a/omf/surface.py b/omf/surface.py index fa8b0a3c..cea30fac 100644 --- a/omf/surface.py +++ b/omf/surface.py @@ -1,5 +1,15 @@ """surface.py: Surface 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 @@ -87,8 +97,8 @@ def _validate_mesh(self): return True if len(self.offset_w) != self.num_nodes: raise ValueError( - "Length of offset_w, {zlen}, must equal number of nodes, " - "{nnode}".format(zlen=len(self.offset_w), nnode=self.num_nodes) + f"Length of offset_w, {len(self.offset_w)}, must equal number of nodes, " + f"{self.num_nodes}" ) return True diff --git a/omf/texture.py b/omf/texture.py index 631406c7..8f00c902 100644 --- a/omf/texture.py +++ b/omf/texture.py @@ -1,5 +1,15 @@ """texture.py: contains ImageTexture definition""" +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# 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 ContentModel diff --git a/omf/volume.py b/omf/volume.py index d399e47e..8982fb14 100644 --- a/omf/volume.py +++ b/omf/volume.py @@ -1,5 +1,15 @@ """volume.py: Volume 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/poetry.lock b/poetry.lock index 6f7b8683..ba4dc764 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,25 +1,36 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.5 and should not be changed by hand. 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"sha256:206f5a15f2af3dbaee80769fb7dc6f249695e940acca08dfb2a4769fe61e538b"}, - {file = "zipp-3.18.1.tar.gz", hash = "sha256:2884ed22e7d8961de1c9a05142eb69a247f120291bc0206a00a7642f09b5b715"}, -] - -[package.extras] -docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] -testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] - [metadata] lock-version = "2.0" -python-versions = "^3.9,<3.11" -content-hash = "952d75dfc5109f72ce2339b75e42bbfb3dfe5f874b9a2ea294f674bb59f7bfad" +python-versions = "^3.10" +content-hash = "79edfb3e198b9e9159d3cb8ada4e9722b5d43949b7f0a67884d18f0f4fc36361" diff --git a/pylintrc b/pylintrc index 7ec2fca1..c7593f0c 100644 --- a/pylintrc +++ b/pylintrc @@ -46,7 +46,9 @@ ignore=CVS # Add files or directories matching the regex patterns to the ignore-list. The # regex matches against paths and can be in Posix or Windows format. -ignore-paths= +### skip source files from upstream repo +ignore-paths=^omf/fileio/(fileio|utils)[.]py$, + ^omf/(base|data|lineset|pointset|serializers|surface|texture|volume)[.]py$ # Files or directories matching the regex patterns are skipped. The regex # matches against base names, not paths. The default value ignores Emacs file diff --git a/pyproject.toml b/pyproject.toml index 1bb1f884..04693982 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "mira-omf" -version = "3.2.1" +version = "3.3.0" description = "API Library for Open Mining Format" license = "MIT" authors = [ @@ -32,12 +32,12 @@ packages = [ ] include = [ - { path = "COPYING", format = ["sdist", "wheel"] }, - { path = "COPYING.LESSER", format = ["sdist", "wheel"] }, - { path = "LICENSE", format = ["sdist", "wheel"] }, - { path = "README.rst", format = ["sdist", "wheel"] }, - { path = "THIRD_PARTY_SOFTWARE.rst", format = ["sdist", "wheel"] }, - { path = "docs/**/THIRD_PARTY_SOFTWARE.rst", format = ["sdist", "wheel"] }, + { path = "COPYING" }, + { path = "COPYING.LESSER" }, + { path = "LICENSE" }, + { path = "README.rst" }, + { path = "THIRD_PARTY_SOFTWARE.rst" }, + { path = "docs/**/THIRD_PARTY_SOFTWARE.rst" }, ] [tool.poetry.scripts] @@ -45,20 +45,19 @@ geoh5_to_omf = 'omf.scripts.geoh5_to_omf:main' omf_to_geoh5 = 'omf.scripts.omf_to_geoh5:main' [tool.poetry.dependencies] -python = "^3.9,<3.11" +python = "^3.10" -numpy = "~1.23.5" # also in geoh5py -properties = "~0.6.0" +numpy = "~1.26.0" # also in geoh5py +properties = "0.6.*" pypng = "^0.20220715" six = "^1.16" -vectormath = "~0.2.0" +vectormath = "0.2.*" ## dependencies from Git repositories #------------------------------------ -geoh5py = {version = "~0.9.0", allow-prereleases = true} -#geoh5py = {git = "https://github.com/MiraGeoscience/geoh5py.git", branch = "release/0.9.0"} -#geoh5py = {url = "https://github.com/MiraGeoscience/geoh5py/archive/refs/heads/release/0.9.0.zip#sha256="} -#geoh5py = {url = "http://localhost:8888/geoh5py.tar.gz#sha256="} +geoh5py = {version = ">=0.10.0b1, <0.11.0a.dev", allow-prereleases = true} +#geoh5py = {git = "https://github.com/MiraGeoscience/geoh5py.git", rev = "release/0.10.0"} +#geoh5py = {path = "../geoh5py", develop = true} [tool.poetry.group.dev.dependencies] Pygments = "*" @@ -66,13 +65,62 @@ pylint = "*" pytest = "*" pytest-cov = "*" sphinx = "^5.3" +pyyaml = '*' +jinja2 = '*' +packaging = '*' tomli = "*" # for tests only -[tool.isort] -profile = "black" +[tool.ruff] +target-version = "py310" + +exclude = [ + "docs/*", + # skip source files from upstream repo + "omf/fileio/fileio.py", + "omf/fileio/utils.py", + "omf/base.py", + "omf/data.py", + "omf/lineset.py", + "omf/pointset.py", + "omf/serializers.py", + "omf/surface.py", + "omf/texture.py", + "omf/volume.py", +] + +[tool.ruff.lint] +ignore = [ + "B028", # no-explicit-stacklevel for warnings.warn() + "E501", # line-too-long - code is reformatted (do not care about comments and docstring) + "F401", # unsused-import - covered by pycln + "RUF005", # collection-literal-concatenation - wrong suggestion with numpy arrays + "RUF012", # TODO +] +select = [ + "A", # flake8-builtins + "B", # flake8-bugbear + "B006", # Do not use mutable data structures for argument defaults + "B9", # flake8-bugbear opiniated warnings + "BLE", # flake8-blind-except + "C4", # flake8-comprehensions + "C9", # mccabe + "E", # pycodestyle errors + "F", # pyflakes + "I", # isort + "RUF", # ruff rules + "TID", # flake8-tidy-imports + "UP", # pyupgrade + "W", # pycodestyle warnings +] + +[tool.ruff.lint.mccabe] +max-complexity = 18 + +[tool.ruff.lint.isort] +lines-after-imports = 2 -[tool.black] -# defaults are just fine +[tool.ruff.format] +# default formatting is just fine [tool.mypy] warn_unused_configs = true diff --git a/tests/__init__.py b/tests/__init__.py index e69de29b..d8b6fd73 100644 --- a/tests/__init__.py +++ b/tests/__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/tests/conftest.py b/tests/conftest.py new file mode 100644 index 00000000..4d71bdda --- /dev/null +++ b/tests/conftest.py @@ -0,0 +1,153 @@ +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# 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). ' +# ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + +from pathlib import Path + +import numpy as np +import pytest + +import omf + + +# pylint: disable=duplicate-code + + +@pytest.fixture +def random_project() -> omf.Project: + tests_dir = Path(__file__).resolve().parent + png_file_path = tests_dir.parent / "docs" / "images" / "PointSetGeometry.png" + proj = omf.Project(name="Test project", description="Just some assorted elements") + + pts = omf.PointSetElement( + name="Random Points", + description="Just random points", + geometry=omf.PointSetGeometry(vertices=np.random.rand(100, 3)), + data=[ + omf.ScalarData( + name="rand data", array=np.random.rand(100), location="vertices" + ), + omf.ScalarData( + name="More rand data", + array=np.random.rand(100), + location="vertices", + ), + ], + textures=[ + omf.ImageTexture( + name="test image", + image=str(png_file_path), + origin=[0, 0, 0], + axis_u=[1, 0, 0], + axis_v=[0, 1, 0], + ), + omf.ImageTexture( + name="test image", + image=str(png_file_path), + origin=[0, 0, 0], + axis_u=[1, 0, 0], + axis_v=[0, 0, 1], + ), + ], + color="green", + ) + + lin = omf.LineSetElement( + name="Random Line", + geometry=omf.LineSetGeometry( + vertices=np.random.rand(100, 3), + segments=np.floor(np.random.rand(50, 2) * 100).astype(int), + ), + data=[ + omf.ScalarData( + name="rand vert data", + array=np.random.rand(100), + location="vertices", + ), + omf.ScalarData( + name="rand segment data", + array=np.random.rand(50), + location="segments", + ), + ], + color="#0000FF", + ) + + surf = omf.SurfaceElement( + name="trisurf", + geometry=omf.SurfaceGeometry( + vertices=np.random.rand(100, 3), + triangles=np.floor(np.random.rand(50, 3) * 100).astype(int), + ), + data=[ + omf.ScalarData( + name="rand vert data", + array=np.random.rand(100), + location="vertices", + ), + omf.ScalarData( + name="rand face data", array=np.random.rand(50), location="faces" + ), + ], + color=[100, 200, 200], + ) + + grid = omf.SurfaceElement( + name="gridsurf", + geometry=omf.SurfaceGridGeometry( + tensor_u=np.ones(10).astype(float), + tensor_v=np.ones(15).astype(float), + origin=[50.0, 50.0, 50.0], + axis_u=[1.0, 0, 0], + axis_v=[0, 0, 1.0], + offset_w=np.random.rand(11, 16).flatten(), + ), + data=[ + omf.ScalarData( + name="rand vert data", + array=np.random.rand(11, 16).flatten(), + location="vertices", + ), + omf.ScalarData( + name="rand face data", + array=np.random.rand(10, 15).flatten(order="f"), + location="faces", + ), + ], + textures=[ + omf.ImageTexture( + name="test image", + image=str(png_file_path), + origin=[2.0, 2.0, 2.0], + axis_u=[5.0, 0, 0], + axis_v=[0, 2.0, 5.0], + ) + ], + ) + + vol = omf.VolumeElement( + name="vol", + geometry=omf.VolumeGridGeometry( + tensor_u=np.ones(10).astype(float), + tensor_v=np.ones(15).astype(float), + tensor_w=np.ones(20).astype(float), + origin=[10.0, 10.0, -10], + ), + data=[ + omf.ScalarData( + name="Random Data", + location="cells", + array=np.random.rand(10, 15, 20).flatten(), + ) + ], + ) + + proj.elements = [pts, lin, surf, grid, vol] + + return proj diff --git a/tests/convert_curve_test.py b/tests/convert_curve_test.py index df0f3866..4094a1c3 100644 --- a/tests/convert_curve_test.py +++ b/tests/convert_curve_test.py @@ -1,12 +1,24 @@ """Tests for PointSet validation""" +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# 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). ' +# ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + +from pathlib import Path + import numpy as np from geoh5py.workspace import Workspace import omf -def test_lineset_to_geoh5(tmp_path): +def test_lineset_to_geoh5(tmp_path: Path): """Test pointset geometry validation""" line = omf.LineSetElement( name="Random Line", diff --git a/tests/convert_grid2d_test.py b/tests/convert_grid2d_test.py index 37418de8..219eff30 100644 --- a/tests/convert_grid2d_test.py +++ b/tests/convert_grid2d_test.py @@ -1,6 +1,17 @@ """Tests for PointSet validation""" +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# 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 logging +from pathlib import Path import numpy as np from geoh5py.workspace import Workspace @@ -8,7 +19,7 @@ import omf -def test_grid2d_to_geoh5(tmp_path, caplog): +def test_grid2d_to_geoh5(tmp_path: Path, caplog): """Test pointset geometry validation""" dip = np.random.uniform(low=0.0, high=90, size=1) diff --git a/tests/convert_pointset_test.py b/tests/convert_pointset_test.py index 1513afa4..3ca2cb98 100644 --- a/tests/convert_pointset_test.py +++ b/tests/convert_pointset_test.py @@ -1,12 +1,24 @@ """Tests for PointSet validation""" +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# 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). ' +# ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + +from pathlib import Path + import numpy as np from geoh5py.workspace import Workspace import omf -def test_pointset_to_geoh5(tmp_path): +def test_pointset_to_geoh5(tmp_path: Path): """Test pointset geometry validation""" colormap = omf.ColorArray( array=[ diff --git a/tests/convert_project_test.py b/tests/convert_project_test.py index 5d1dc712..2feca2fc 100644 --- a/tests/convert_project_test.py +++ b/tests/convert_project_test.py @@ -1,44 +1,49 @@ """Tests for PointSet validation""" +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# 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 logging import os +from pathlib import Path from geoh5py.workspace import Workspace import omf -from .doc_example_test import TestDocEx - -def test_project_to_geoh5(tmp_path, caplog): +def test_project_to_geoh5(random_project: omf.Project, tmp_path: Path, caplog): """Test pointset geometry validation""" - proj = TestDocEx.make_random_project() - file = str(tmp_path / "project.geoh5") - omf.OMFWriter(proj, file) + omf.OMFWriter(random_project, file) warning_records = [r for r in caplog.records if r.levelno == logging.WARNING] assert len(warning_records) == 1 with Workspace(file) as workspace: - assert len(workspace.objects) == len(proj.elements) + assert len(workspace.objects) == len(random_project.elements) project = omf.fileio.geoh5.GeoH5Reader(file).project - assert len(project.elements) == len(proj.elements) + assert len(project.elements) == len(random_project.elements) -def test_project_compression(tmp_path): +def test_project_compression(random_project: omf.Project, tmp_path: Path): """Test pointset geometry validation""" - proj = TestDocEx.make_random_project() - file_low_comp = str(tmp_path / "project_low_comp.geoh5") file_med_comp = str(tmp_path / "project_med_comp.geoh5") file_high_comp = str(tmp_path / "project_high_comp.geoh5") - omf.OMFWriter(proj, file_low_comp, compression=1) - omf.OMFWriter(proj, file_med_comp, compression=5) - omf.OMFWriter(proj, file_high_comp, compression=9) + omf.OMFWriter(random_project, file_low_comp, compression=1) + omf.OMFWriter(random_project, file_med_comp, compression=5) + omf.OMFWriter(random_project, file_high_comp, compression=9) size_low_comp = os.stat(file_low_comp).st_size size_med_comp = os.stat(file_med_comp).st_size diff --git a/tests/convert_surface_test.py b/tests/convert_surface_test.py index 795a459a..407df7c9 100644 --- a/tests/convert_surface_test.py +++ b/tests/convert_surface_test.py @@ -1,12 +1,24 @@ """Tests for PointSet validation""" +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# 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). ' +# ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + +from pathlib import Path + import numpy as np from geoh5py.workspace import Workspace import omf -def test_surface_to_geoh5(tmp_path): +def test_surface_to_geoh5(tmp_path: Path): """Test pointset geometry validation""" surf = omf.SurfaceElement( name="trisurf", diff --git a/tests/convert_volume_test.py b/tests/convert_volume_test.py index 61dcc754..b0a887d4 100644 --- a/tests/convert_volume_test.py +++ b/tests/convert_volume_test.py @@ -1,5 +1,17 @@ """Tests for PointSet validation""" +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# 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). ' +# ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + +from pathlib import Path + import numpy as np from geoh5py.objects import BlockModel from geoh5py.workspace import Workspace @@ -8,7 +20,7 @@ from omf.fileio.geoh5 import block_model_reordering -def test_volume_to_geoh5(tmp_path): +def test_volume_to_geoh5(tmp_path: Path): """Test pointset geometry validation""" dims = [10, 15, 20] vol = omf.VolumeElement( @@ -89,8 +101,8 @@ def test_volume_to_geoh5(tmp_path): ref_b = block_model.get_entity("Reference Data 2")[0] assert all( - key in ref_a.value_map.map and value == ref_a.value_map.map[key] - for key, value in ref_b.value_map.map.items() + key in ref_a.value_map() and value == ref_a.value_map()[key] + for key, value in ref_b.value_map().items() ) omf.fileio.utils.compare_elements(converted_omf, vol) diff --git a/tests/doc_example_test.py b/tests/doc_example_test.py index 3b5f31a4..6131451f 100644 --- a/tests/doc_example_test.py +++ b/tests/doc_example_test.py @@ -1,165 +1,29 @@ -# pylint: disable=duplicate-code - -import os -import unittest - -import numpy as np +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# 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 pathlib import Path import omf -class TestDocEx(unittest.TestCase): - @staticmethod - def make_random_project(): - dirname, _ = os.path.split(os.path.abspath(__file__)) - pngfile = os.path.sep.join( - dirname.split(os.path.sep)[:-1] + ["docs", "images", "PointSetGeometry.png"] - ) - proj = omf.Project( - name="Test project", description="Just some assorted elements" - ) - - pts = omf.PointSetElement( - name="Random Points", - description="Just random points", - geometry=omf.PointSetGeometry(vertices=np.random.rand(100, 3)), - data=[ - omf.ScalarData( - name="rand data", array=np.random.rand(100), location="vertices" - ), - omf.ScalarData( - name="More rand data", - array=np.random.rand(100), - location="vertices", - ), - ], - textures=[ - omf.ImageTexture( - name="test image", - image=pngfile, - origin=[0, 0, 0], - axis_u=[1, 0, 0], - axis_v=[0, 1, 0], - ), - omf.ImageTexture( - name="test image", - image=pngfile, - origin=[0, 0, 0], - axis_u=[1, 0, 0], - axis_v=[0, 0, 1], - ), - ], - color="green", - ) - - lin = omf.LineSetElement( - name="Random Line", - geometry=omf.LineSetGeometry( - vertices=np.random.rand(100, 3), - segments=np.floor(np.random.rand(50, 2) * 100).astype(int), - ), - data=[ - omf.ScalarData( - name="rand vert data", - array=np.random.rand(100), - location="vertices", - ), - omf.ScalarData( - name="rand segment data", - array=np.random.rand(50), - location="segments", - ), - ], - color="#0000FF", - ) - - surf = omf.SurfaceElement( - name="trisurf", - geometry=omf.SurfaceGeometry( - vertices=np.random.rand(100, 3), - triangles=np.floor(np.random.rand(50, 3) * 100).astype(int), - ), - data=[ - omf.ScalarData( - name="rand vert data", - array=np.random.rand(100), - location="vertices", - ), - omf.ScalarData( - name="rand face data", array=np.random.rand(50), location="faces" - ), - ], - color=[100, 200, 200], - ) - - grid = omf.SurfaceElement( - name="gridsurf", - geometry=omf.SurfaceGridGeometry( - tensor_u=np.ones(10).astype(float), - tensor_v=np.ones(15).astype(float), - origin=[50.0, 50.0, 50.0], - axis_u=[1.0, 0, 0], - axis_v=[0, 0, 1.0], - offset_w=np.random.rand(11, 16).flatten(), - ), - data=[ - omf.ScalarData( - name="rand vert data", - array=np.random.rand(11, 16).flatten(), - location="vertices", - ), - omf.ScalarData( - name="rand face data", - array=np.random.rand(10, 15).flatten(order="f"), - location="faces", - ), - ], - textures=[ - omf.ImageTexture( - name="test image", - image=pngfile, - origin=[2.0, 2.0, 2.0], - axis_u=[5.0, 0, 0], - axis_v=[0, 2.0, 5.0], - ) - ], - ) - - vol = omf.VolumeElement( - name="vol", - geometry=omf.VolumeGridGeometry( - tensor_u=np.ones(10).astype(float), - tensor_v=np.ones(15).astype(float), - tensor_w=np.ones(20).astype(float), - origin=[10.0, 10.0, -10], - ), - data=[ - omf.ScalarData( - name="Random Data", - location="cells", - array=np.random.rand(10, 15, 20).flatten(), - ) - ], - ) - - proj.elements = [pts, lin, surf, grid, vol] - - return proj - - -def test_doc_ex(tmp_path): - proj = TestDocEx.make_random_project() - - assert proj.validate() +def test_doc_ex(tmp_path: Path, random_project): + assert random_project.validate() serial_file = str(tmp_path / "out.omf") - omf.OMFWriter(proj, serial_file) + omf.OMFWriter(random_project, serial_file) reader = omf.OMFReader(serial_file) new_proj = reader.get_project() assert new_proj.validate() assert str(new_proj.elements[3].textures[0].uid) == str( - proj.elements[3].textures[0].uid + random_project.elements[3].textures[0].uid ) proj_overview = reader.get_project_overview() diff --git a/tests/script_geoh5_to_omf_test.py b/tests/script_geoh5_to_omf_test.py index df98f2ea..8c6c200f 100644 --- a/tests/script_geoh5_to_omf_test.py +++ b/tests/script_geoh5_to_omf_test.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). ' +# ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + from pathlib import Path from unittest.mock import patch @@ -7,6 +17,7 @@ import omf from omf.scripts import geoh5_to_omf + # pylint: disable=duplicate-code diff --git a/tests/script_omf_to_geoh5_test.py b/tests/script_omf_to_geoh5_test.py index 8ea40236..159607cf 100644 --- a/tests/script_omf_to_geoh5_test.py +++ b/tests/script_omf_to_geoh5_test.py @@ -1,3 +1,14 @@ +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# 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 re from pathlib import Path from unittest.mock import patch @@ -144,7 +155,4 @@ def test_omf_to_geoh5_with_gzip_level_too_high(capsys, tmp_path: Path): assert not output_path.exists() assert captured_exception.value.code == 2 captured_err = capsys.readouterr().err - assert any( - "error: argument --gzip: invalid choice: 10" in line - for line in captured_err.splitlines() - ) + assert re.search(r"error: argument --gzip: invalid choice:", captured_err) diff --git a/tests/version_test.py b/tests/version_test.py index fef69d24..84f1f176 100644 --- a/tests/version_test.py +++ b/tests/version_test.py @@ -1,16 +1,29 @@ """Test the version follows SemVer and is consistent across files.""" +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# 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). ' +# ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + from __future__ import annotations import re from pathlib import Path import tomli as toml +import yaml +from jinja2 import Template +from packaging.version import Version import omf -def get_version(): +def get_pyproject_version(): path = Path(__file__).resolve().parents[1] / "pyproject.toml" with open(str(path), encoding="utf-8") as file: @@ -19,20 +32,25 @@ def get_version(): return pyproject["tool"]["poetry"]["version"] -def get_version_in_readme() -> str | None: - path = Path(__file__).resolve().parents[1] / "README.rst" +def get_conda_recipe_version(): + path = Path(__file__).resolve().parents[1] / "meta.yaml" - version_re = r"^\s*Version:\s*(\S*)\s*$" with open(str(path), encoding="utf-8") as file: - for line in file: - match = re.match(version_re, line) - if match: - return match[1] - return None + content = file.read() + + template = Template(content) + rendered_yaml = template.render() + + recipe = yaml.safe_load(rendered_yaml) + + return recipe["package"]["version"] def test_version_is_consistent(): - assert omf.__version__ == get_version() + assert omf.__version__ == get_pyproject_version() + normalized_conda_version = Version(get_conda_recipe_version()) + normalized_version = Version(omf.__version__) + assert normalized_conda_version == normalized_version def version_base_and_pre() -> tuple[str, str]: @@ -46,16 +64,6 @@ def version_base_and_pre() -> tuple[str, str]: return match[1], match[2] -def test_version_in_readme(): - version_base, prerelease = version_base_and_pre() - version_readme = get_version_in_readme() - assert version_readme is not None - if prerelease is not None and prerelease.startswith("-rc."): - assert version_readme in [omf.__version__, version_base] - else: - assert version_readme == omf.__version__ - - def test_version_is_semver(): semver_re = ( r"^(?P0|[1-9]\d*)\.(?P0|[1-9]\d*)\.(?P0|[1-9]\d*)"