module-qc-database-tools 0.0.1__tar.gz

module_qc_database_tools-0.0.1/.env.template

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+INSTITUTION="LBNL_PIXEL_MODULES"
+ITKDB_ACCESS_CODE1="accesscode1"
+ITKDB_ACCESS_CODE2="accesscode2"

module_qc_database_tools-0.0.1/.gitignore

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+# Our stuff
+.DS_Store
+output/
+*~
+*.swp
+plots/
+module-qc-tools/
+outputs/
+
+# 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/
+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/
+cover/
+
+# 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/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .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.
+#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/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# setuptools_scm / hatch-vcs
+src/*/_version.py

module_qc_database_tools-0.0.1/.gitlab-ci.yml

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+stages:
+  - autoupdate
+  - check
+  - test
+  - build
+  - deploy
+
+variables:
+  # see https://docs.gitlab.com/ee/ci/caching/#cache-python-dependencies
+  PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip"
+
+cache:
+  paths:
+    - .cache/pip
+    - venv/
+
+image: python:3.7-buster
+before_script:
+  # want to set up a virtualenv to cache
+  - apt-get install -y --no-install-recommends git
+  - python -V
+  - git config --global credential.helper 'cache'
+  - |
+    echo "protocol=https
+    host=gitlab.cern.ch
+    username=gitlab-ci-token
+    password=${CI_JOB_TOKEN}
+    " | git credential approve
+  - python -m venv venv
+  - source venv/bin/activate
+  - python -m pip install -U pip pipx
+  - python -m pipx ensurepath
+  - python -m pip freeze --local
+
+pre-commit:
+  stage: check
+  variables:
+    PRE_COMMIT_HOME: "$CI_PROJECT_DIR/.cache/pre-commit"
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "push"
+  script:
+    - python -m pip install pre-commit
+    - python -m pip freeze --local
+    - pre-commit run --hook-stage manual --all-files
+  cache:
+    key:
+      files:
+        - .pre-commit-config.yaml
+    paths:
+      - .cache/pre-commit
+
+pre-commit-autoupdate:
+  stage: autoupdate
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "schedule"
+      when: always
+    - if:
+        $CI_PIPELINE_SOURCE == "push" && $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
+      when: manual
+      # manual jobs need allow_failure? https://gitlab.com/gitlab-org/gitlab/-/issues/233876
+      allow_failure: true
+  script:
+    - python -m pip install pre-commit
+    - python -m pip freeze --local
+    - ci/pre-commit-update.sh
+
+  cache:
+    key:
+      files:
+        - .pre-commit-config.yaml
+    paths:
+      - .cache/pre-commit
+
+lint:
+  stage: check
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "push"
+  script:
+    - pipx run hatch run lint
+
+tests:
+  stage: test
+  image: $IMAGE
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "push"
+  script:
+    - pipx run hatch run +py=${PYTHON_VERSION} dev:test
+  parallel:
+    matrix:
+      - IMAGE: "python:3.7-buster"
+        PYTHON_VERSION: "3.7"
+      - IMAGE: "python:3.8-buster"
+        PYTHON_VERSION: "3.8"
+      - IMAGE: "python:3.9-buster"
+        PYTHON_VERSION: "3.9"
+      - IMAGE: "python:3.10-buster"
+        PYTHON_VERSION: "3.10"
+      - IMAGE: "python:3.11-buster"
+        PYTHON_VERSION: "3.11"
+
+package:
+  stage: build
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "push"
+  script:
+    - pipx run hatch run build-check
+  artifacts:
+    paths:
+      - dist/
+    expire_in: 1 day
+
+.deploy_package:
+  stage: deploy
+  dependencies:
+    - package
+  script:
+    - pipx run twine upload --verbose dist/*whl dist/*gz
+
+deploy_package_gitlab:
+  extends: .deploy_package
+  rules:
+    - if:
+        $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH && $CI_PIPELINE_SOURCE == "push"
+  variables:
+    TWINE_REPOSITORY_URL: "https://gitlab.cern.ch/api/v4/projects/${CI_PROJECT_ID}/packages/pypi"
+    TWINE_USERNAME: "gitlab-ci-token"
+    TWINE_PASSWORD: "${CI_JOB_TOKEN}"
+
+deploy_package_pypi:
+  extends: .deploy_package
+  only:
+    - tags
+  variables:
+    TWINE_REPOSITORY: pypi
+    TWINE_USERNAME: __token__
+    TWINE_PASSWORD: $PYPI_TOKEN

module_qc_database_tools-0.0.1/.pre-commit-config.yaml

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+ci:
+  autoupdate_commit_msg: "chore: update pre-commit hooks"
+  autofix_commit_msg: "style: pre-commit fixes"
+
+exclude: |
+  (?x)^(
+    add_attachment.py|
+    add_comment.py|
+    generatePlots.py|
+    getContentSummary.py|
+    getInventory.py|
+    registerComponent.py|
+    tests/integration/cassettes/.*.json
+  )$
+
+repos:
+  - repo: https://github.com/psf/black
+    rev: "23.3.0"
+    hooks:
+      - id: black-jupyter
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v4.4.0"
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
+        exclude: mkdocs.yml
+      - id: check-yaml
+        name: check-yaml (unsafe)
+        files: mkdocs.yml
+        args: ["--unsafe"]
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: name-tests-test
+        args: ["--pytest-test-first"]
+      - id: requirements-txt-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: "v1.10.0"
+    hooks:
+      - id: rst-backticks
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
+
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v3.0.0-alpha.6"
+    hooks:
+      - id: prettier
+        types_or: [yaml, markdown, html, css, scss, javascript, json]
+        args: [--prose-wrap=always]
+
+  - repo: https://github.com/asottile/blacken-docs
+    rev: "1.13.0"
+    hooks:
+      - id: blacken-docs
+        additional_dependencies: [black==22.8.0]
+
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.0.261
+    hooks:
+      - id: ruff
+        args: ["--fix", "--show-fixes"]
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.4
+    hooks:
+      - id: codespell
+        exclude: |
+          (?x)^(
+            .*\.json |
+            .*\.pem
+          )$
+
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: "v0.9.0.2"
+    hooks:
+      - id: shellcheck
+
+  - repo: local
+    hooks:
+      - id: disallow-caps
+        name: Disallow improper capitalization
+        language: pygrep
+        entry: PyBind|Numpy|Cmake|CCache|Github|PyTest
+        exclude: .pre-commit-config.yaml

module_qc_database_tools-0.0.1/PKG-INFO

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+Metadata-Version: 2.1
+Name: module-qc-database-tools
+Version: 0.0.1
+Summary: Python wrapper to interface with LocalDB and Production DB for common tasks for pixel modules.
+Project-URL: Homepage, https://gitlab.cern.ch/atlas-itk/pixel/module/module-qc-database-tools
+Project-URL: Bug Tracker, https://gitlab.cern.ch/atlas-itk/pixel/module/module-qc-database-tools/issues
+Project-URL: Source, https://gitlab.cern.ch/atlas-itk/pixel/module/module-qc-database-tools
+Author-email: Jay Chan <jay.chan@cern.ch>
+Maintainer-email: Giordon Stark <kratsg@gmail.com>, Elisabetta Pianori <elisabetta.pianori@cern.ch>, Lingxin Meng <lingxin.meng@cern.ch>
+Classifier: Development Status :: 1 - Planning
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.7
+Requires-Dist: importlib-resources>=1.4.0; python_version < '3.9'
+Requires-Dist: itkdb>=0.4.0
+Requires-Dist: pandas
+Requires-Dist: typer
+Description-Content-Type: text/markdown
+
+# Module QC Database Tools v0.0.1
+
+The package to regisiter ITkPixV1.1 modules, and generate YARR configs from ITk
+production database using `itkdb` API.
+
+## Set-Up and First-time Installation
+
+A minimum of python version 3.7+ is required.
+
+### Virtual Python Environment
+
+Creating the python virtual environment the standard way used the python version
+available on the operating system. For CentOS 7 this is version 3.6. If using
+CentOS 7, you can install python 3.8 following these
+[instructions](https://tecadmin.net/install-python-3-8-centos/).
+
+After installing python 3.8, create the virtual environment:
+
+```
+$ python3 -m venv venv
+$ source venv/bin/activate
+```
+
+For future use:
+
+```
+$ source venv/bin/activate
+```
+
+Alternatively, [anaconda](https://docs.anaconda.com/anaconda/install/index.html)
+or [miniconda](https://docs.conda.io/en/latest/miniconda.html) can also be
+installed.
+
+For future use:
+
+```
+$ conda activate
+```
+
+### Install
+
+```
+$ python -m pip install module-qc-database-tools
+```
+
+### Environment Variables
+
+If not already set elsewhere (e.g. `~/.bashrc`), copy `.env.template` to `.env`
+and update the values of the shell variables. Essentially, the following
+variables regarding the production database should be available, shown below as
+an example of environmental variables in `~/.bashrc`:
+
+```bash
+export INSTITUTION="LBNL_PIXEL_MODULES"
+export ITKDB_ACCESS_CODE1="accesscode1"
+export ITKDB_ACCESS_CODE2="accesscode2"
+```
+
+## Module registration
+
+Under construction...
+
+## Generate YARR configuration
+
+This script has been tested on python 3.7+.
+
+To generate YARR configuration for a given module, run `generateYARRConfig` or
+`mqdbt generate-yarr-config`:
+
+```
+$ generateYARRConfig -sn [ATLAS SN] -o [outdir]
+$ mqdbt generate-yarr-config -sn [ATLAS SN] -o [outdir]
+
+Parameters:
+-sn, --sn, required=True: ATLAS serial number of the module
+-ch, --chipTemplate, default="configs/YARR/chip_template.json": provide the path of a chip config template to generate the new chip configs from
+-o, --outdir, required=True: Path to output directory config folder will be placed in
+```
+
+For example, to generate the YARR configs for the module `20UPGR91301046` with
+all power configs:
+
+```
+$ generateYARRConfig -sn 20UPGR91301046 -o ~/module_data/.
+$ mqdbt generate-yarr-config -sn 20UPGR91301046 -o ~/module_data/.
+```
+
+The time needed to generate warm and cold L2 configs for a quad module is about
+4 seconds.

module_qc_database_tools-0.0.1/README.md

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+# Module QC Database Tools v0.0.1
+
+The package to regisiter ITkPixV1.1 modules, and generate YARR configs from ITk
+production database using `itkdb` API.
+
+## Set-Up and First-time Installation
+
+A minimum of python version 3.7+ is required.
+
+### Virtual Python Environment
+
+Creating the python virtual environment the standard way used the python version
+available on the operating system. For CentOS 7 this is version 3.6. If using
+CentOS 7, you can install python 3.8 following these
+[instructions](https://tecadmin.net/install-python-3-8-centos/).
+
+After installing python 3.8, create the virtual environment:
+
+```
+$ python3 -m venv venv
+$ source venv/bin/activate
+```
+
+For future use:
+
+```
+$ source venv/bin/activate
+```
+
+Alternatively, [anaconda](https://docs.anaconda.com/anaconda/install/index.html)
+or [miniconda](https://docs.conda.io/en/latest/miniconda.html) can also be
+installed.
+
+For future use:
+
+```
+$ conda activate
+```
+
+### Install
+
+```
+$ python -m pip install module-qc-database-tools
+```
+
+### Environment Variables
+
+If not already set elsewhere (e.g. `~/.bashrc`), copy `.env.template` to `.env`
+and update the values of the shell variables. Essentially, the following
+variables regarding the production database should be available, shown below as
+an example of environmental variables in `~/.bashrc`:
+
+```bash
+export INSTITUTION="LBNL_PIXEL_MODULES"
+export ITKDB_ACCESS_CODE1="accesscode1"
+export ITKDB_ACCESS_CODE2="accesscode2"
+```
+
+## Module registration
+
+Under construction...
+
+## Generate YARR configuration
+
+This script has been tested on python 3.7+.
+
+To generate YARR configuration for a given module, run `generateYARRConfig` or
+`mqdbt generate-yarr-config`:
+
+```
+$ generateYARRConfig -sn [ATLAS SN] -o [outdir]
+$ mqdbt generate-yarr-config -sn [ATLAS SN] -o [outdir]
+
+Parameters:
+-sn, --sn, required=True: ATLAS serial number of the module
+-ch, --chipTemplate, default="configs/YARR/chip_template.json": provide the path of a chip config template to generate the new chip configs from
+-o, --outdir, required=True: Path to output directory config folder will be placed in
+```
+
+For example, to generate the YARR configs for the module `20UPGR91301046` with
+all power configs:
+
+```
+$ generateYARRConfig -sn 20UPGR91301046 -o ~/module_data/.
+$ mqdbt generate-yarr-config -sn 20UPGR91301046 -o ~/module_data/.
+```
+
+The time needed to generate warm and cold L2 configs for a quad module is about
+4 seconds.