Note
Go to the end to download the full example code.
Using the ctapipe Provenance service#
The provenance functionality is used automatically when you use most of
ctapipe functionality (particularly ctapipe.core.Tool
and functions
in ctapipe.io
and ctapipe.utils
), so normally you don’t have to
work with it directly. It tracks both input and output files, as well as
details of the machine and software environment on which a Tool
executed.
Here we show some very low-level functions of this system:
16 from pprint import pprint
17
18 from ctapipe.core import Provenance
Activities#
The basis of Provenance is an activity, which is generally an executable or step in a script. Activities can be nested (e.g. with sub-activities), as shown below, but normally this is not required:
29 p = Provenance() # note this is a singleton, so only ever one global provenence object
30 p.clear()
31 p.start_activity()
32 p.add_input_file("test.txt")
33
34 p.start_activity("sub")
35 p.add_input_file("subinput.txt")
36 p.add_input_file("anothersubinput.txt")
37 p.add_output_file("suboutput.txt")
38 p.finish_activity("sub")
39
40 p.start_activity("sub2")
41 p.add_input_file("sub2input.txt")
42 p.finish_activity("sub2")
43
44 p.finish_activity()
47 p.finished_activity_names
['sub', 'sub2', '/home/docs/checkouts/readthedocs.org/user_builds/ctapipe/envs/stable/bin/python']
Activities have associated input and output entities (files or other objects)
55 [(x["activity_name"], x["input"]) for x in p.provenance]
[('sub', [{'url': '/home/docs/checkouts/readthedocs.org/user_builds/ctapipe/checkouts/stable/examples/core/subinput.txt', 'role': None}, {'url': '/home/docs/checkouts/readthedocs.org/user_builds/ctapipe/checkouts/stable/examples/core/anothersubinput.txt', 'role': None}]), ('sub2', [{'url': '/home/docs/checkouts/readthedocs.org/user_builds/ctapipe/checkouts/stable/examples/core/sub2input.txt', 'role': None}]), ('/home/docs/checkouts/readthedocs.org/user_builds/ctapipe/envs/stable/bin/python', [{'url': '/home/docs/checkouts/readthedocs.org/user_builds/ctapipe/checkouts/stable/examples/core/test.txt', 'role': None}])]
Activities track when they were started and finished:
62 [(x["activity_name"], x["duration_min"]) for x in p.provenance]
[('sub', 0.0037166666667509674), ('sub2', 0.0037999999999449585), ('/home/docs/checkouts/readthedocs.org/user_builds/ctapipe/envs/stable/bin/python', 0.01130000000003406)]
Full provenance#
The provenance object is a list of activities, and for each lots of details are collected:
73 p.provenance[0]
{'activity_name': 'sub', 'activity_uuid': 'e843244b-aec3-49e3-ad34-89967e09cf7f', 'start': {'time_utc': '2024-05-15T13:13:08.580'}, 'stop': {'time_utc': '2024-05-15T13:13:08.803'}, 'system': {'ctapipe_version': '0.21.1', 'ctapipe_resources_version': 'not installed', 'eventio_version': '1.12.1', 'ctapipe_svc_path': None, 'executable': '/home/docs/checkouts/readthedocs.org/user_builds/ctapipe/envs/stable/bin/python', 'platform': {'architecture_bits': '64bit', 'architecture_linkage': '', 'machine': 'x86_64', 'processor': 'x86_64', 'node': 'build-24386221-project-702899-ctapipe', 'version': '#29~22.04.1-Ubuntu SMP Tue Jun 20 19:12:11 UTC 2023', 'system': 'Linux', 'release': '5.19.0-1028-aws', 'libcver': ('glibc', '2.35'), 'n_cpus': 2, 'boot_time': '2024-05-15T12:18:41.000'}, 'python': {'version_string': '3.10.13 (main, Feb 1 2024, 16:44:52) [GCC 11.4.0]', 'version': ('3', '10', '13'), 'compiler': 'GCC 11.4.0', 'implementation': 'CPython', 'packages': [{'name': 'Babel', 'version': '2.15.0'}, {'name': 'Jinja2', 'version': '3.1.4'}, {'name': 'MarkupSafe', 'version': '2.1.5'}, {'name': 'PyYAML', 'version': '6.0.1'}, {'name': 'Pygments', 'version': '2.18.0'}, {'name': 'QtPy', 'version': '2.4.1'}, {'name': 'Send2Trash', 'version': '1.8.3'}, {'name': 'Sphinx', 'version': '7.3.7'}, {'name': 'accessible-pygments', 'version': '0.0.5'}, {'name': 'alabaster', 'version': '0.7.16'}, {'name': 'anyio', 'version': '4.3.0'}, {'name': 'argon2-cffi', 'version': '23.1.0'}, {'name': 'argon2-cffi-bindings', 'version': '21.2.0'}, {'name': 'arrow', 'version': '1.3.0'}, {'name': 'astropy', 'version': '6.1.0'}, {'name': 'astropy-iers-data', 'version': '0.2024.5.13.0.30.12'}, {'name': 'asttokens', 'version': '2.4.1'}, {'name': 'async-lru', 'version': '2.0.4'}, {'name': 'attrs', 'version': '23.2.0'}, {'name': 'beautifulsoup4', 'version': '4.12.3'}, {'name': 'bleach', 'version': '6.1.0'}, {'name': 'blosc2', 'version': '2.6.2'}, {'name': 'bokeh', 'version': '3.4.1'}, {'name': 'certifi', 'version': '2024.2.2'}, {'name': 'cffi', 'version': '1.16.0'}, {'name': 'charset-normalizer', 'version': '3.3.2'}, {'name': 'comm', 'version': '0.2.2'}, {'name': 'contourpy', 'version': '1.2.1'}, {'name': 'corsikaio', 'version': '0.4.0'}, {'name': 'ctapipe', 'version': '0.21.1'}, {'name': 'cycler', 'version': '0.12.1'}, {'name': 'debugpy', 'version': '1.8.1'}, {'name': 'decorator', 'version': '5.1.1'}, {'name': 'defusedxml', 'version': '0.7.1'}, {'name': 'docutils', 'version': '0.21.2'}, {'name': 'eventio', 'version': '1.12.1'}, {'name': 'exceptiongroup', 'version': '1.2.1'}, {'name': 'executing', 'version': '2.0.1'}, {'name': 'fastjsonschema', 'version': '2.19.1'}, {'name': 'ffmpeg-python', 'version': '0.2.0'}, {'name': 'fonttools', 'version': '4.51.0'}, {'name': 'fqdn', 'version': '1.5.1'}, {'name': 'future', 'version': '1.0.0'}, {'name': 'graphviz', 'version': '0.20.3'}, {'name': 'h11', 'version': '0.14.0'}, {'name': 'httpcore', 'version': '1.0.5'}, {'name': 'httpx', 'version': '0.27.0'}, {'name': 'idna', 'version': '3.7'}, {'name': 'imagesize', 'version': '1.4.1'}, {'name': 'iminuit', 'version': '2.25.2'}, {'name': 'ipykernel', 'version': '6.29.4'}, {'name': 'ipython', 'version': '8.24.0'}, {'name': 'ipywidgets', 'version': '8.1.2'}, {'name': 'isoduration', 'version': '20.11.0'}, {'name': 'jedi', 'version': '0.19.1'}, {'name': 'joblib', 'version': '1.4.2'}, {'name': 'json5', 'version': '0.9.25'}, {'name': 'jsonpointer', 'version': '2.4'}, {'name': 'jsonschema', 'version': '4.22.0'}, {'name': 'jsonschema-specifications', 'version': '2023.12.1'}, {'name': 'jupyter', 'version': '1.0.0'}, {'name': 'jupyter-console', 'version': '6.6.3'}, {'name': 'jupyter-events', 'version': '0.10.0'}, {'name': 'jupyter-lsp', 'version': '2.2.5'}, {'name': 'jupyter_client', 'version': '8.6.1'}, {'name': 'jupyter_core', 'version': '5.7.2'}, {'name': 'jupyter_server', 'version': '2.14.0'}, {'name': 'jupyter_server_terminals', 'version': '0.5.3'}, {'name': 'jupyterlab', 'version': '4.1.8'}, {'name': 'jupyterlab_pygments', 'version': '0.3.0'}, {'name': 'jupyterlab_server', 'version': '2.27.1'}, {'name': 'jupyterlab_widgets', 'version': '3.0.10'}, {'name': 'kiwisolver', 'version': '1.4.5'}, {'name': 'latexcodec', 'version': '3.0.0'}, {'name': 'llvmlite', 'version': '0.42.0'}, {'name': 'matplotlib', 'version': '3.8.4'}, {'name': 'matplotlib-inline', 'version': '0.1.7'}, {'name': 'mistune', 'version': '3.0.2'}, {'name': 'msgpack', 'version': '1.0.8'}, {'name': 'nbclient', 'version': '0.10.0'}, {'name': 'nbconvert', 'version': '7.16.4'}, {'name': 'nbformat', 'version': '5.10.4'}, {'name': 'nbsphinx', 'version': '0.9.4'}, {'name': 'ndindex', 'version': '1.8'}, {'name': 'nest-asyncio', 'version': '1.6.0'}, {'name': 'notebook', 'version': '7.1.3'}, {'name': 'notebook_shim', 'version': '0.2.4'}, {'name': 'numba', 'version': '0.59.1'}, {'name': 'numexpr', 'version': '2.10.0'}, {'name': 'numpy', 'version': '1.26.4'}, {'name': 'numpydoc', 'version': '1.7.0'}, {'name': 'overrides', 'version': '7.7.0'}, {'name': 'packaging', 'version': '24.0'}, {'name': 'pandas', 'version': '2.2.2'}, {'name': 'pandocfilters', 'version': '1.5.1'}, {'name': 'parso', 'version': '0.8.4'}, {'name': 'pexpect', 'version': '4.9.0'}, {'name': 'pillow', 'version': '10.3.0'}, {'name': 'pip', 'version': '24.0'}, {'name': 'platformdirs', 'version': '4.2.2'}, {'name': 'prometheus_client', 'version': '0.20.0'}, {'name': 'prompt-toolkit', 'version': '3.0.43'}, {'name': 'psutil', 'version': '5.9.8'}, {'name': 'ptyprocess', 'version': '0.7.0'}, {'name': 'pure-eval', 'version': '0.2.2'}, {'name': 'py-cpuinfo', 'version': '9.0.0'}, {'name': 'pybtex', 'version': '0.24.0'}, {'name': 'pybtex-docutils', 'version': '1.0.3'}, {'name': 'pycparser', 'version': '2.22'}, {'name': 'pydata-sphinx-theme', 'version': '0.15.2'}, {'name': 'pyerfa', 'version': '2.0.1.4'}, {'name': 'pypandoc', 'version': '1.13'}, {'name': 'pyparsing', 'version': '3.1.2'}, {'name': 'python-dateutil', 'version': '2.9.0.post0'}, {'name': 'python-json-logger', 'version': '2.0.7'}, {'name': 'pytz', 'version': '2024.1'}, {'name': 'pyzmq', 'version': '26.0.3'}, {'name': 'qtconsole', 'version': '5.5.2'}, {'name': 'readthedocs-sphinx-ext', 'version': '2.2.5'}, {'name': 'referencing', 'version': '0.35.1'}, {'name': 'requests', 'version': '2.31.0'}, {'name': 'rfc3339-validator', 'version': '0.1.4'}, {'name': 'rfc3986-validator', 'version': '0.1.1'}, {'name': 'rpds-py', 'version': '0.18.1'}, {'name': 'scikit-learn', 'version': '1.4.2'}, {'name': 'scipy', 'version': '1.13.0'}, {'name': 'setuptools', 'version': '69.5.1'}, {'name': 'setuptools-scm', 'version': '8.1.0'}, {'name': 'six', 'version': '1.16.0'}, {'name': 'sniffio', 'version': '1.3.1'}, {'name': 'snowballstemmer', 'version': '2.2.0'}, {'name': 'soupsieve', 'version': '2.5'}, {'name': 'sphinx-automodapi', 'version': '0.17.0'}, {'name': 'sphinx-gallery', 'version': '0.16.0'}, {'name': 'sphinx_design', 'version': '0.5.0'}, {'name': 'sphinxcontrib-applehelp', 'version': '1.0.8'}, {'name': 'sphinxcontrib-bibtex', 'version': '2.6.2'}, {'name': 'sphinxcontrib-devhelp', 'version': '1.0.6'}, {'name': 'sphinxcontrib-htmlhelp', 'version': '2.0.5'}, {'name': 'sphinxcontrib-jsmath', 'version': '1.0.1'}, {'name': 'sphinxcontrib-qthelp', 'version': '1.0.7'}, {'name': 'sphinxcontrib-serializinghtml', 'version': '1.1.10'}, {'name': 'stack-data', 'version': '0.6.3'}, {'name': 'tables', 'version': '3.9.2'}, {'name': 'tabulate', 'version': '0.9.0'}, {'name': 'terminado', 'version': '0.18.1'}, {'name': 'threadpoolctl', 'version': '3.5.0'}, {'name': 'tinycss2', 'version': '1.3.0'}, {'name': 'tomli', 'version': '2.0.1'}, {'name': 'tornado', 'version': '6.4'}, {'name': 'tqdm', 'version': '4.66.4'}, {'name': 'traitlets', 'version': '5.14.3'}, {'name': 'types-python-dateutil', 'version': '2.9.0.20240316'}, {'name': 'typing_extensions', 'version': '4.11.0'}, {'name': 'tzdata', 'version': '2024.1'}, {'name': 'uri-template', 'version': '1.3.0'}, {'name': 'urllib3', 'version': '2.2.1'}, {'name': 'wcwidth', 'version': '0.2.13'}, {'name': 'webcolors', 'version': '1.13'}, {'name': 'webencodings', 'version': '0.5.1'}, {'name': 'websocket-client', 'version': '1.8.0'}, {'name': 'wheel', 'version': '0.40.0'}, {'name': 'widgetsnbextension', 'version': '4.0.10'}, {'name': 'xyzservices', 'version': '2024.4.0'}, {'name': 'zstandard', 'version': '0.22.0'}]}, 'environment': {'CONDA_DEFAULT_ENV': None, 'CONDA_PREFIX': None, 'CONDA_PYTHON_EXE': None, 'CONDA_EXE': None, 'CONDA_PROMPT_MODIFIER': None, 'CONDA_SHLVL': None, 'PATH': '/home/docs/checkouts/readthedocs.org/user_builds/ctapipe/envs/stable/bin:/home/docs/.asdf/shims:/home/docs/.asdf/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin', 'LD_LIBRARY_PATH': None, 'DYLD_LIBRARY_PATH': None, 'USER': None, 'HOME': '/home/docs', 'SHELL': None}, 'arguments': ['/home/docs/checkouts/readthedocs.org/user_builds/ctapipe/checkouts/stable/examples/core/provenance.py'], 'start_time_utc': '2024-05-15T13:13:08.803'}, 'input': [{'url': '/home/docs/checkouts/readthedocs.org/user_builds/ctapipe/checkouts/stable/examples/core/subinput.txt', 'role': None}, {'url': '/home/docs/checkouts/readthedocs.org/user_builds/ctapipe/checkouts/stable/examples/core/anothersubinput.txt', 'role': None}], 'output': [{'url': '/home/docs/checkouts/readthedocs.org/user_builds/ctapipe/checkouts/stable/examples/core/suboutput.txt', 'role': None}], 'status': 'sub', 'duration_min': 0.0037166666667509674}
This can be better represented in JSON:
80 print(p.as_json(indent=2))
[
{
"activity_name": "sub",
"activity_uuid": "e843244b-aec3-49e3-ad34-89967e09cf7f",
"start": {
"time_utc": "2024-05-15T13:13:08.580"
},
"stop": {
"time_utc": "2024-05-15T13:13:08.803"
},
"system": {
"ctapipe_version": "0.21.1",
"ctapipe_resources_version": "not installed",
"eventio_version": "1.12.1",
"ctapipe_svc_path": null,
"executable": "/home/docs/checkouts/readthedocs.org/user_builds/ctapipe/envs/stable/bin/python",
"platform": {
"architecture_bits": "64bit",
"architecture_linkage": "",
"machine": "x86_64",
"processor": "x86_64",
"node": "build-24386221-project-702899-ctapipe",
"version": "#29~22.04.1-Ubuntu SMP Tue Jun 20 19:12:11 UTC 2023",
"system": "Linux",
"release": "5.19.0-1028-aws",
"libcver": [
"glibc",
"2.35"
],
"n_cpus": 2,
"boot_time": "2024-05-15T12:18:41.000"
},
"python": {
"version_string": "3.10.13 (main, Feb 1 2024, 16:44:52) [GCC 11.4.0]",
"version": [
"3",
"10",
"13"
],
"compiler": "GCC 11.4.0",
"implementation": "CPython",
"packages": [
{
"name": "Babel",
"version": "2.15.0"
},
{
"name": "Jinja2",
"version": "3.1.4"
},
{
"name": "MarkupSafe",
"version": "2.1.5"
},
{
"name": "PyYAML",
"version": "6.0.1"
},
{
"name": "Pygments",
"version": "2.18.0"
},
{
"name": "QtPy",
"version": "2.4.1"
},
{
"name": "Send2Trash",
"version": "1.8.3"
},
{
"name": "Sphinx",
"version": "7.3.7"
},
{
"name": "accessible-pygments",
"version": "0.0.5"
},
{
"name": "alabaster",
"version": "0.7.16"
},
{
"name": "anyio",
"version": "4.3.0"
},
{
"name": "argon2-cffi",
"version": "23.1.0"
},
{
"name": "argon2-cffi-bindings",
"version": "21.2.0"
},
{
"name": "arrow",
"version": "1.3.0"
},
{
"name": "astropy",
"version": "6.1.0"
},
{
"name": "astropy-iers-data",
"version": "0.2024.5.13.0.30.12"
},
{
"name": "asttokens",
"version": "2.4.1"
},
{
"name": "async-lru",
"version": "2.0.4"
},
{
"name": "attrs",
"version": "23.2.0"
},
{
"name": "beautifulsoup4",
"version": "4.12.3"
},
{
"name": "bleach",
"version": "6.1.0"
},
{
"name": "blosc2",
"version": "2.6.2"
},
{
"name": "bokeh",
"version": "3.4.1"
},
{
"name": "certifi",
"version": "2024.2.2"
},
{
"name": "cffi",
"version": "1.16.0"
},
{
"name": "charset-normalizer",
"version": "3.3.2"
},
{
"name": "comm",
"version": "0.2.2"
},
{
"name": "contourpy",
"version": "1.2.1"
},
{
"name": "corsikaio",
"version": "0.4.0"
},
{
"name": "ctapipe",
"version": "0.21.1"
},
{
"name": "cycler",
"version": "0.12.1"
},
{
"name": "debugpy",
"version": "1.8.1"
},
{
"name": "decorator",
"version": "5.1.1"
},
{
"name": "defusedxml",
"version": "0.7.1"
},
{
"name": "docutils",
"version": "0.21.2"
},
{
"name": "eventio",
"version": "1.12.1"
},
{
"name": "exceptiongroup",
"version": "1.2.1"
},
{
"name": "executing",
"version": "2.0.1"
},
{
"name": "fastjsonschema",
"version": "2.19.1"
},
{
"name": "ffmpeg-python",
"version": "0.2.0"
},
{
"name": "fonttools",
"version": "4.51.0"
},
{
"name": "fqdn",
"version": "1.5.1"
},
{
"name": "future",
"version": "1.0.0"
},
{
"name": "graphviz",
"version": "0.20.3"
},
{
"name": "h11",
"version": "0.14.0"
},
{
"name": "httpcore",
"version": "1.0.5"
},
{
"name": "httpx",
"version": "0.27.0"
},
{
"name": "idna",
"version": "3.7"
},
{
"name": "imagesize",
"version": "1.4.1"
},
{
"name": "iminuit",
"version": "2.25.2"
},
{
"name": "ipykernel",
"version": "6.29.4"
},
{
"name": "ipython",
"version": "8.24.0"
},
{
"name": "ipywidgets",
"version": "8.1.2"
},
{
"name": "isoduration",
"version": "20.11.0"
},
{
"name": "jedi",
"version": "0.19.1"
},
{
"name": "joblib",
"version": "1.4.2"
},
{
"name": "json5",
"version": "0.9.25"
},
{
"name": "jsonpointer",
"version": "2.4"
},
{
"name": "jsonschema",
"version": "4.22.0"
},
{
"name": "jsonschema-specifications",
"version": "2023.12.1"
},
{
"name": "jupyter",
"version": "1.0.0"
},
{
"name": "jupyter-console",
"version": "6.6.3"
},
{
"name": "jupyter-events",
"version": "0.10.0"
},
{
"name": "jupyter-lsp",
"version": "2.2.5"
},
{
"name": "jupyter_client",
"version": "8.6.1"
},
{
"name": "jupyter_core",
"version": "5.7.2"
},
{
"name": "jupyter_server",
"version": "2.14.0"
},
{
"name": "jupyter_server_terminals",
"version": "0.5.3"
},
{
"name": "jupyterlab",
"version": "4.1.8"
},
{
"name": "jupyterlab_pygments",
"version": "0.3.0"
},
{
"name": "jupyterlab_server",
"version": "2.27.1"
},
{
"name": "jupyterlab_widgets",
"version": "3.0.10"
},
{
"name": "kiwisolver",
"version": "1.4.5"
},
{
"name": "latexcodec",
"version": "3.0.0"
},
{
"name": "llvmlite",
"version": "0.42.0"
},
{
"name": "matplotlib",
"version": "3.8.4"
},
{
"name": "matplotlib-inline",
"version": "0.1.7"
},
{
"name": "mistune",
"version": "3.0.2"
},
{
"name": "msgpack",
"version": "1.0.8"
},
{
"name": "nbclient",
"version": "0.10.0"
},
{
"name": "nbconvert",
"version": "7.16.4"
},
{
"name": "nbformat",
"version": "5.10.4"
},
{
"name": "nbsphinx",
"version": "0.9.4"
},
{
"name": "ndindex",
"version": "1.8"
},
{
"name": "nest-asyncio",
"version": "1.6.0"
},
{
"name": "notebook",
"version": "7.1.3"
},
{
"name": "notebook_shim",
"version": "0.2.4"
},
{
"name": "numba",
"version": "0.59.1"
},
{
"name": "numexpr",
"version": "2.10.0"
},
{
"name": "numpy",
"version": "1.26.4"
},
{
"name": "numpydoc",
"version": "1.7.0"
},
{
"name": "overrides",
"version": "7.7.0"
},
{
"name": "packaging",
"version": "24.0"
},
{
"name": "pandas",
"version": "2.2.2"
},
{
"name": "pandocfilters",
"version": "1.5.1"
},
{
"name": "parso",
"version": "0.8.4"
},
{
"name": "pexpect",
"version": "4.9.0"
},
{
"name": "pillow",
"version": "10.3.0"
},
{
"name": "pip",
"version": "24.0"
},
{
"name": "platformdirs",
"version": "4.2.2"
},
{
"name": "prometheus_client",
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Storing provenance info in output files#
already this can be stored in something like an HDF5 file header, which allows hierarchies.
Try to flatted the data so it can be stored in a key=value header in a FITS file (using the FITS extended keyword convention to allow >8 character keywords), or as a table
95 def flatten_dict(y):
96 out = {}
97
98 def flatten(x, name=""):
99 if isinstance(x, dict):
100 for a in x:
101 flatten(x[a], name + a + ".")
102 elif isinstance(x, list):
103 i = 0
104 for a in x:
105 flatten(a, name + str(i) + ".")
106 i += 1
107 else:
108 out[name[:-1]] = x
109
110 flatten(y)
111 return out
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'16:44:52) [GCC 11.4.0]',
'activity.2.system.start_time_utc': '2024-05-15T13:13:08.580'}
Total running time of the script: (0 minutes 0.764 seconds)