l2o-gpp 0.1.0a1__tar.gz

l2o_gpp-0.1.0a1/.dockerignore

@@ -0,0 +1,18 @@
+**/.git
+**/.gitignore
+**/.vscode
+**/coverage
+**/.env
+**/.aws
+**/.ssh
+**/.DS_Store
+**/venv
+**/env
+**/.venv*
+**/.env*
+**/__pycache__
+**/.pytest_cache
+build/
+dist/
+*.egg-info/
+Dockerfile

l2o_gpp-0.1.0a1/.gitattributes

@@ -0,0 +1 @@
+* text=auto eol=lf

l2o_gpp-0.1.0a1/.gitignore

@@ -0,0 +1,144 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+.reports/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+docs/build/
+docs/source/api/
+jupyter_execute/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#   In our case Pipfile.lock will be inrelevant 'caused of the differents python version / platform we will have
+#   to support.
+Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env*
+.venv*
+env*/
+venv*/
+ENV*/
+env*.bak/
+venv*.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# VS Code (except recommended workspace extensions and settings)
+.vscode/*
+!.vscode/extensions.json
+!.vscode/settings.json
+!.vscode/launch.json
+
+# Ignore EOPF specific data folder on EOPF cluster
+/data

l2o_gpp-0.1.0a1/.gitlab/issue_templates/Action.md

@@ -0,0 +1,35 @@
+<!--
+* Use this issue template for managing project actions.
+
+* The text contained within the HTML comment tags will not be displayed in the GitLab UI.
+  It provides information on the expected contents of the different sections.
+
+* Sections not relevant or applicable to the current action
+  can be left open, stated as not applicable (N/A) or removed.
+-->
+
+## Description
+
+Describe the Action:
+
+**The task** - what must be done
+
+**The end result** - what the output of the action is.
+
+Do not hesitate to use task lists:
+
+- [ ] Task one
+- [ ] Task two
+
+Add a due date and assign (both fields are **mandatory**) inline
+or using the WebGUI.
+
+/due
+
+/assign
+
+## Origin
+
+Minutes of Meeting (MoM) or other source.
+
+/label ~Action

l2o_gpp-0.1.0a1/.gitlab/issue_templates/Bug.md

@@ -0,0 +1,55 @@
+<!--
+
+* Use this issue template for reporting problems or suggesting new features
+  or updates to existing ones.
+
+* The text contained within the HTML comment tags will not be displayed in
+  the GitLab UI. It provides information on the expected contents
+  of the different sections.
+
+* Sections not relevant or applicable to the current issue
+  can be left open, stated as not applicable (N/A) or removed.
+
+-->
+
+## Summary
+
+(Summarize the bug encountered concisely.)
+
+## Steps to reproduce
+
+(How one can reproduce the issue - this is very important.)
+
+## Example Project
+
+(If possible, please create an example project here on the EOPF SDE that exhibits the problematic
+behavior, and link to it here in the bug report.
+If you are using an older version of the EOPF SDE, this will also determine whether the bug has been fixed
+in a more recent version)
+
+## What is the current bug behavior?
+
+(Describe what actually happens.)
+
+## What is the expected correct behavior?
+
+(Describe what you expect see instead.)
+
+## Relevant logs and/or screenshots
+
+(Paste any relevant logs - please use code blocks (```) to format console output, logs, and code, as
+it is very hard to read otherwise.)
+
+## Possible causes and fixes
+
+(If you can, link to the line of code that might be responsible for the problem)
+
+(List of either:
+
+- {file, line number, function name}
+- {permalink (recommended)}
+
+To get a permalink, click on the line in the left part on the concerned file,
+then click on the `permalink` button on top right, finally copy-paste the current URL here.)
+
+/label ~Code

l2o_gpp-0.1.0a1/.gitlab/issue_templates/Documentation.md

@@ -0,0 +1,46 @@
+<!--
+
+* Use this issue template for suggesting new docs or updates to existing docs.
+
+* The text contained within the HTML comment tags will not be displayed in
+  the GitLab UI. It provides information on the expected contents
+  of the different sections.
+
+* Sections not relevant or applicable to the current issue
+  can be left open, stated as not applicable (N/A) or removed.
+
+-->
+
+## Summary
+
+(Summarize the issue encountered concisely.)
+
+## Specification(s)
+
+(Indicate the specification (ECSS, US) not (partially)
+satisfied with the current situation.)
+
+## Impacted document and chapter
+
+(Indicate, as precisely as possible, the location (e.g. document, chapter, ...) where
+the defect has been found.
+Clearly indicate the issue / revision for Word / Pdf documents.
+For the online documentation, please provide the URL.)
+
+## What is the currently observed issue?
+
+(Describe what is actually seen.)
+
+## What is the expected situation?
+
+(Describe what you expect to see.)
+
+## Possible solutions
+
+(Describe possible solutions to obtain the expected situation.)
+
+### Other links/references
+
+(E.g. related GitLab issues / merge requests.)
+
+/label ~Documentation

l2o_gpp-0.1.0a1/.gitlab/issue_templates/Risk.md

@@ -0,0 +1,45 @@
+<!--
+* Use this issue template for managing project risks.
+
+* The text contained within the HTML comment tags will not be displayed in the GitLab UI.
+  It provides information on the expected contents of the different sections.
+
+* Sections not relevant or applicable to the current risk
+  can be left open, stated as not applicable (N/A) or removed.
+-->
+
+## Risk description
+
+Describe the risk.
+
+## Risk consequences
+
+Describe the impact of the risk.
+
+## Risk estimation
+
+| Probability | Severity | Rating |
+| :---:       | :---:    | :---:  |
+|             |          |        |
+
+
+- Assign Probability between Low (1), Medium (2), High (3)
+- Assign Severity between Low (1), Medium (2), High (3)
+- Compute Probability * Severity:
+    - If 1 or 2: assign a "Low" rating
+    - If 3 or 4: assign a "Medium" rating
+    - If 6 or 9: assign a "High" rating
+
+- Add the label corresponding to the Rating: ~Risk::Rating::Low , ~Risk::Rating::Medium , or ~Risk::Rating::High
+
+For example: The risk is estimated to have a Medium probability of occurrence (2) and a Medium severity (2). The overall rating is thus 2 * 2 = 4. Add the ~Risk::Rating::Medium label to the risk.
+
+## Linked mitigation actions
+
+Risks rated High must have related actions. Actions for risks rated Medium or Low are not mandatory but recommended.
+
+<!-- The relate quick action can be used to link directly to the actions:
+/relate #
+-->
+
+/label ~Risk

l2o_gpp-0.1.0a1/.gitlab/merge_request_templates/default.md

@@ -0,0 +1,24 @@
+## What does this Merge Request (MR) do?
+
+<!-- Briefly describe what this MR is about -->
+
+## Related issues
+
+<!-- Link related issues below. -->
+
+## Author's checklist
+
+- [ ] Is the CI pipeline successful?
+- [ ] Has the documentation been updated?
+- [ ] Has the documentation been generated and reviewed locally?<br>
+      Note: The generated documentation is available from branch's
+      CI pipeline as an artifact and can be downloaded to be validated
+      locally.
+- [ ] Has a reviewer been assigned to the MR?
+
+## Reviewer's checklist
+
+- [ ] Is there a test covering / demonstrating the change?
+- [ ] Do the change respect the applicable quality gates?
+- [ ] Has an assignee been assigned to the MR?
+- [ ] Ensure a release milestone is set.

l2o_gpp-0.1.0a1/.gitlab-ci.yml

@@ -0,0 +1,254 @@
+spec:
+  inputs:
+    l2o-corealg-ref:
+      description: Override Gitlab ref where to reinstall l2o-corealg from. Leave default to let workflow rules decide, or set 'DISABLE' to not reinstall.
+      default: "DEFAULT"
+    l2o-vam-ref:
+      description: Override Gitlab ref where to reinstall l2o-vam from. Leave default to let workflow rules decide, or set 'DISABLE' to not reinstall.
+      default: "DEFAULT"
+    l2o-io-ref:
+      description: Override Gitlab ref where to reinstall l2o-io from. Leave default to let workflow rules decide, or set 'DISABLE' to not reinstall.
+      default: "DEFAULT"
+
+---
+
+default:
+  interruptible: true
+  # Speed up CI by using prepared image with all the required tools
+  image: rl2ocean-docker-dev-snapshot.artifacts.dlr.de/pipeline-image:python3.13
+
+stages:
+  - variable checks
+  - test
+  - build
+  - deploy
+  - scan
+
+variables:
+  PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip"
+  SOURCES: src
+  TESTS: tests
+  REPORTS: .reports
+  # Sphinx documentation
+  DOCS_VERSION: ${CI_COMMIT_REF_NAME}
+  DOCS_PACKAGE_NAME: ${CI_PROJECT_NAME}-docs
+  DOCS_PACKAGE_FILENAME: ${DOCS_PACKAGE_NAME}.tar.gz
+  # Default Git ref l2o dependencies are installed from if they are reinstalled from Gitlab in before_script
+  L2O_DEFAULT_REF: "DISABLE"
+
+# Specify when pipelines are created and set some variables accordingly
+workflow:
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "merge_request_event"
+      variables:
+        DOCS_VERSION: $CI_COMMIT_SHORT_SHA
+        L2O_DEFAULT_REF: "main"
+    - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
+      variables:
+        DOCS_VERSION: $CI_COMMIT_BRANCH
+        L2O_DEFAULT_REF: "main"
+    - if: $CI_COMMIT_TAG
+      variables:
+        DOCS_VERSION: $CI_COMMIT_TAG
+        L2O_DEFAULT_REF: "DISABLE"
+
+# Check that required CI group variables are set
+validate-variables:
+  stage: variable checks
+  script:
+    - |
+      mandatoryVars="\
+        JF_DOCKER_REGISTRY \
+        JF_ACCESS_TOKEN \
+        RL_DOCKER_REGISTRY \
+        RL_USER \
+        RL_PASSWORD"
+      found=true
+      for var in ${mandatoryVars}
+      do
+        if [[ -z ${!var} ]]
+        then
+          echo -e "\e[31mERROR: Required variable '${var}' is not set. Please set the variable before running the pipeline\e[0m"
+          found=false
+        fi
+      done
+      if ! ${found}
+      then
+        exit 1
+      fi
+
+# Import job descriptions from a shared component repository to avoid duplicate code across different
+# repositories. The components are stored here: https://gitlab.dlr.de/rl2ocean/gitlab-components
+include:
+  # Python code linter
+  - component: $CI_SERVER_FQDN/$CI_PROJECT_NAMESPACE/gitlab-components/lint@v3.0.0
+    inputs:
+      dirs: ${SOURCES} ${TESTS}
+
+  # Python code formatter
+  - component: $CI_SERVER_FQDN/$CI_PROJECT_NAMESPACE/gitlab-components/format@v3.0.0
+    inputs:
+      dirs: ${SOURCES} ${TESTS}
+
+  # Python type checker
+  - component: $CI_SERVER_FQDN/$CI_PROJECT_NAMESPACE/gitlab-components/typing@v3.0.0
+    inputs:
+      l2o_deps_reinst:
+        - "l2o-corealg@$[[ inputs.l2o-corealg-ref ]]"
+        - "l2o-vam@$[[ inputs.l2o-vam-ref ]]"
+        - "l2o-io@$[[ inputs.l2o-io-ref ]]"
+      l2o_default_ref: ${L2O_DEFAULT_REF}
+
+  # Python code complexity
+  - component: $CI_SERVER_FQDN/$CI_PROJECT_NAMESPACE/gitlab-components/complexity@v3.0.0
+    inputs:
+      dirs: ${SOURCES}
+
+  # Python docstring coverage
+  - component: $CI_SERVER_FQDN/$CI_PROJECT_NAMESPACE/gitlab-components/docstring-coverage@v3.0.0
+    inputs:
+      dirs: ${SOURCES}
+
+  # Python code security scanner
+  - component: $CI_SERVER_FQDN/$CI_PROJECT_NAMESPACE/gitlab-components/code-security@v3.0.0
+    inputs:
+      dirs: ${SOURCES}
+
+  # Python package dependency vulnerability checker
+  - component: $CI_SERVER_FQDN/$CI_PROJECT_NAMESPACE/gitlab-components/deps-security@v3.0.0
+
+  # Python unit tests
+  - component: $CI_SERVER_FQDN/$CI_PROJECT_NAMESPACE/gitlab-components/unit-tests@v3.0.0
+    inputs:
+      l2o_deps_reinst:
+        - "l2o-corealg@$[[ inputs.l2o-corealg-ref ]]"
+        - "l2o-vam@$[[ inputs.l2o-vam-ref ]]"
+        - "l2o-io@$[[ inputs.l2o-io-ref ]]"
+      l2o_default_ref: ${L2O_DEFAULT_REF}
+      reports_dir: ${REPORTS}
+
+  # Build Python package
+  - component: $CI_SERVER_FQDN/$CI_PROJECT_NAMESPACE/gitlab-components/build-package@v3.0.0
+
+  # Deploy Python package to Gitlab package registry
+  - component: $CI_SERVER_FQDN/$CI_PROJECT_NAMESPACE/gitlab-components/deploy-package-gitlab@v3.0.0
+
+  # Deploy Python package to PyPI
+  - component: $CI_SERVER_FQDN/$CI_PROJECT_NAMESPACE/gitlab-components/deploy-package-pypi@v3.0.0
+
+  # Documentation ReST file linter
+  - component: $CI_SERVER_FQDN/$CI_PROJECT_NAMESPACE/gitlab-components/lint-docs@v3.0.0
+
+  # Build PDF documentation
+  - component: $CI_SERVER_FQDN/$CI_PROJECT_NAMESPACE/gitlab-components/build-docs-pdf@v3.0.0
+    inputs:
+      l2o_deps_reinst:
+        - "l2o-corealg@$[[ inputs.l2o-corealg-ref ]]"
+        - "l2o-vam@$[[ inputs.l2o-vam-ref ]]"
+        - "l2o-io@$[[ inputs.l2o-io-ref ]]"
+      l2o_default_ref: ${L2O_DEFAULT_REF}
+      version_string: ${DOCS_VERSION}
+
+  # Build HTML documentation
+  - component: $CI_SERVER_FQDN/$CI_PROJECT_NAMESPACE/gitlab-components/build-docs-html@v3.0.0
+    inputs:
+      l2o_deps_reinst:
+        - "l2o-corealg@$[[ inputs.l2o-corealg-ref ]]"
+        - "l2o-vam@$[[ inputs.l2o-vam-ref ]]"
+        - "l2o-io@$[[ inputs.l2o-io-ref ]]"
+      l2o_default_ref: ${L2O_DEFAULT_REF}
+      version_string: ${DOCS_VERSION}
+
+  # Upload HTML documentation to Gitlab package registry
+  - component: $CI_SERVER_FQDN/$CI_PROJECT_NAMESPACE/gitlab-components/upload-docs@v3.0.0
+    inputs:
+      version_string: ${DOCS_VERSION}
+
+  # Deploy HTML documentation to Gitlab Pages
+  - component: $CI_SERVER_FQDN/$CI_PROJECT_NAMESPACE/gitlab-components/deploy-docs@v3.0.0
+
+# Dockerfile linter
+docker-linter:
+  stage: test
+  image: hadolint/hadolint:latest-debian
+  script:
+    - CHECKSUM=`md5sum Dockerfile | cut -d" " -f1`
+    - hadolint --config .hadolint.yml --format gitlab_codeclimate Dockerfile > hadolint-${CHECKSUM}.json
+  artifacts:
+    name: "$CI_JOB_NAME artifacts from $CI_PROJECT_NAME on $CI_COMMIT_REF_SLUG"
+    expire_in: 1 week
+    when: always
+    reports:
+      codequality:
+        - hadolint-*.json
+
+# Build and upload Docker image
+deploy-image:
+  stage: deploy
+  image:
+    name: martizih/kaniko:debug
+    entrypoint: [""]
+  before_script:
+    # Create Docker config file for kaniko with registry authentication details.
+    - mkdir -p /kaniko/.docker
+    - >-
+      echo "{\"auths\":{
+      \"${JF_DOCKER_REGISTRY}\":{\"auth\":\"${JF_ACCESS_TOKEN}\"},
+      \"${RL_DOCKER_REGISTRY}\":{\"auth\":\"$(printf "%s:%s" "${RL_USER}" "${RL_PASSWORD}" | base64 | tr -d '\n')\"}
+      }}" > /kaniko/.docker/config.json
+  script:
+    # When running on default branch the tag is 'latest'.
+    # All other branches are tagged with the escaped branch name (commit ref slug).
+    - |
+      if [[ "${CI_COMMIT_BRANCH}" == "${CI_DEFAULT_BRANCH}" ]]; then
+        tag="latest"
+        echo "Running on default branch '${CI_DEFAULT_BRANCH}': tag = ${tag}"
+      else
+        tag="${CI_COMMIT_REF_SLUG}"
+        echo "Running on branch '${CI_COMMIT_REF_NAME}': tag = ${tag}"
+      fi
+    - >-
+      /kaniko/executor
+      --context "${CI_PROJECT_DIR}"
+      --dockerfile "${CI_PROJECT_DIR}/Dockerfile"
+      --build-arg CI_COMMIT_SHA
+      --destination "${JF_DOCKER_REGISTRY}/${CI_PROJECT_NAME}:${tag}"
+      --destination "${RL_DOCKER_REGISTRY}/${CI_PROJECT_NAME}:${tag}"
+  rules:
+    - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
+    - if: $CI_COMMIT_TAG
+
+# Scan built Docker image
+scan-image:
+  stage: scan
+  image:
+    name: aquasec/trivy:0.72.0
+    entrypoint: [""]
+  script:
+    # Create Docker config file for trivy with registry authentication details.
+    - mkdir -p ~/.docker
+    - echo "{\"auths\":{\"${JF_DOCKER_REGISTRY}\":{\"auth\":\"${JF_ACCESS_TOKEN}\"}}}" > ~/.docker/config.json
+    # When running on default branch the tag is 'latest'.
+    # All other branches are tagged with the escaped branch name (commit ref slug).
+    - |
+      if [[ "${CI_COMMIT_BRANCH}" == "${CI_DEFAULT_BRANCH}" ]]; then
+        tag="latest"
+        echo "Running on default branch '${CI_DEFAULT_BRANCH}': tag = ${tag}"
+      else
+        tag="${CI_COMMIT_REF_SLUG}"
+        echo "Running on branch '${CI_COMMIT_REF_NAME}': tag = ${tag}"
+      fi
+    - image_name="${JF_DOCKER_REGISTRY}/${CI_PROJECT_NAME}:${tag}"
+    - echo "Image name:" "${image_name}"
+    - >-
+      trivy image "${image_name}"
+      --severity HIGH,CRITICAL
+      --ignore-unfixed
+      --skip-version-check
+      --disable-telemetry
+      --no-progress
+      --exit-code 1
+  allow_failure: true
+  rules:
+    - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
+    - if: $CI_COMMIT_TAG

l2o_gpp-0.1.0a1/.hadolint.yml

@@ -0,0 +1,11 @@
+# Configuration file for hadolint
+failure-threshold: warning
+override:
+  info:
+    # Pin versions in apt-get install
+    - DL3008
+    # Pin versions in pip install
+    - DL3013
+ignored:
+  # Multiple consecutive RUN instructions
+  - DL3059

l2o_gpp-0.1.0a1/.mypy.ini

@@ -0,0 +1,26 @@
+[mypy]
+python_version = 3.13
+mypy_path = $MYPY_CONFIG_FILE_DIR/src
+packages = l2o.gpp
+namespace_packages = True
+explicit_package_bases = True
+warn_unused_configs = True
+warn_redundant_casts = True
+
+[mypy-l2o.*]
+disallow_any_generics = True
+disallow_subclassing_any = True
+disallow_untyped_defs = True
+disallow_incomplete_defs = True
+check_untyped_defs = True
+warn_unused_ignores = True
+no_implicit_reexport = True
+
+[mypy-fsspec]
+ignore_missing_imports = True
+
+[mypy-zarr.*]
+ignore_missing_imports = True
+
+[mypy-jinja2.*]
+ignore_missing_imports = True