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Resources","sub_category":"Soil and Land","monthly_downloads":3767,"total_dependent_repos":2,"total_dependent_packages":3,"readme":"# PYGEF\n\n[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)\n[![PyPi Version](https://img.shields.io/pypi/v/pygef.svg)](https://pypi.org/project/pygef)\n[![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2Fcemsbv%2Fpygef%2Fmaster%2Fpyproject.toml)](https://github.com/cemsbv/pygef/blob/master/pyproject.toml)\n[![Coverage Status](https://coveralls.io/repos/github/cemsbv/pygef/badge.svg?branch=master)](https://coveralls.io/github/cemsbv/pygef?branch=master)\n\nSimple parser for \\*.GEF and BRO XML files. These are files used for soil\nproperty measurements.\n\nIf you find a file that doesn't work with pygef, please make an issue about it or a PR :)\n\n## Installation\n\nLatest stable version:\n\n```sh\npip install pygef\n```\n\nCutting-edge version (might break):\n\n```sh\npip install git+https://github.com/cemsbv/pygef.git\n```\n\n## CPT files\n\n```python\n\u003e\u003e \u003e from pygef import read_cpt\n\u003e\u003e \u003e  # read gef and xml files\n\u003e\u003e \u003e cpt_data = read_cpt(\"./my-cpt.xml\")\n\u003e\u003e \u003e cpt_data\nCPTData: {'bro_id': 'CPT000000099543',\n          'cone_diameter': 44,\n          'cone_surface_area': 1500,\n          'cone_surface_quotient': 0.67,\n          'cone_to_friction_sleeve_distance': 100,\n          'cone_to_friction_sleeve_surface_area': 22530,\n          'cone_to_friction_sleeve_surface_quotient': 1.0,\n          ...\n              'zlm_pore_pressure_u3_after': None,\n'zlm_pore_pressure_u3_before': None}\n\u003e\u003e \u003e  # access the underlying polars DataFrame under the `data` attribute\n\u003e\u003e \u003e cpt_data.data.head()\nshape: (5, 9)\n┌────────────┬───────┬───────────┬────────────┬─────┬────────────┬────────────┬────────────┬────────────┐\n│ penetratio ┆ depth ┆ elapsedTi ┆ coneResist ┆ ... ┆ inclinatio ┆ inclinatio ┆ localFrict ┆ frictionRa │\n│ nLength    ┆ ---   ┆ me        ┆ ance       ┆     ┆ nNS        ┆ nResultant ┆ ion        ┆ tio        │\n│ ---        ┆ f64   ┆ ---       ┆ ---        ┆     ┆ ---        ┆ ---        ┆ ---        ┆ ---        │\n│ f64        ┆       ┆ f64       ┆ f64        ┆     ┆ i64        ┆ i64        ┆ f64        ┆ f64        │\n╞════════════╪═══════╪═══════════╪════════════╪═════╪════════════╪════════════╪════════════╪════════════╡\n│ 0.0        ┆ 0.0   ┆ -9.99999\ne ┆ -9.99999e5 ┆ ... ┆ -999999    ┆ -999999    ┆ -9.99999e5 ┆ -9.99999e5 │\n│            ┆       ┆ 5         ┆            ┆     ┆            ┆            ┆            ┆            │\n├╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┤\n│ 0.02       ┆ 0.02  ┆ 11.0      ┆ 2.708      ┆ ... ┆ 0          ┆ 0          ┆ 0.03       ┆ 0.6        │\n├╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┤\n│ 0.04       ┆ 0.039 ┆ 13.0      ┆ 4.29       ┆ ... ┆ 0          ┆ 0          ┆ 0.039      ┆ 0.8        │\n├╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┤\n│ 0.06       ┆ 0.059 ┆ 15.0      ┆ 5.124      ┆ ... ┆ 0          ┆ 0          ┆ 0.045      ┆ 0.9        │\n├╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┤\n│ 0.08       ┆ 0.079 ┆ 17.0      ┆ 5.45       ┆ ... ┆ 0          ┆ 0          ┆ 0.049      ┆ 1.0        │\n└────────────┴───────┴───────────┴────────────┴─────┴────────────┴────────────┴────────────┴────────────┘\n```\n\n## Bore files\n\n```python\n\u003e\u003e \u003e from pygef import read_bore\n\u003e\u003e \u003e  # read gef and xml files\n\u003e\u003e \u003e bore_data = read_bore(\"./my-bore.xml\")\n\u003e\u003e \u003e bore_data\nBoreData: {'bore_hole_completed': True,\n           'bore_rock_reached': False,\n           'data': (13, 8),\n           'delivered_location': Location(srs_name='urn:ogc:def:crs:EPSG::28992', x=158322.139, y=444864.706),\n           'delivered_vertical_position_datum': 'nap',\n           'delivered_vertical_position_offset': 10.773,\n           'delivered_vertical_position_reference_point': 'maaiveld',\n           'description_procedure': 'ISO14688d1v2019c2020',\n           'final_bore_depth': 12.0,\n           'final_sample_depth': 12.0,\n           'research_report_date': datetime.date(2021, 10, 19)}\n\u003e\u003e \u003e  # access the underlying polars DataFrame under the `data` attribute\n\u003e\u003e \u003e bore_data.data.head()\nshape: (5, 8)\n┌────────────┬────────────┬────────────┬──────────┬────────────┬────────────┬────────────┬─────────┐\n│ upper_boun ┆ lower_boun ┆ geotechnic ┆ color    ┆ dispersed_ ┆ organic_ma ┆ sand_media ┆ soil_di │\n│ dary       ┆ dary       ┆ al_soil_na ┆ ---      ┆ inhomogeni ┆ tter_conte ┆ n_class    ┆ st      │\n│ ---        ┆ ---        ┆ me         ┆ str      ┆ ty         ┆ nt_class   ┆ ---        ┆ ---     │\n│ f64        ┆ f64        ┆ ---        ┆          ┆ ---        ┆ ---        ┆ str        ┆ list[f6 │\n│            ┆            ┆ str        ┆          ┆ bool       ┆ str        ┆            ┆ 4]      │\n╞════════════╪════════════╪════════════╪══════════╪════════════╪════════════╪════════════╪═════════╡\n│ 0.0        ┆ 1.0        ┆ zwakGrindi ┆ donkergr ┆ false      ┆ nietOrgani ┆ middelgrof ┆ [0.2,   │\n│            ┆            ┆ gZand      ┆ ijs      ┆            ┆ sch        ┆ 420\ntot630u ┆ 0.0,    │\n│            ┆            ┆            ┆          ┆            ┆            ┆ m          ┆ ...     │\n│            ┆            ┆            ┆          ┆            ┆            ┆            ┆ 0.0]    │\n├╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌┤\n│ 1.0        ┆ 1.1        ┆ zwakGrindi ┆ donkergr ┆ false      ┆ nietOrgani ┆ middelgrof ┆ [0.2,   │\n│            ┆            ┆ gZand      ┆ ijs      ┆            ┆ sch        ┆ 420\ntot630u ┆ 0.0,    │\n│            ┆            ┆            ┆          ┆            ┆            ┆ m          ┆ ...     │\n│            ┆            ┆            ┆          ┆            ┆            ┆            ┆ 0.0]    │\n├╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌┤\n│ 1.1        ┆ 2.0        ┆ zwakZandig ┆ standaar ┆ false      ┆ nietOrgani ┆ null       ┆ [0.0,   │\n│            ┆            ┆ eKleiMetGr ┆ dBruin   ┆            ┆ sch        ┆            ┆ 0.1,    │\n│            ┆            ┆ ind        ┆          ┆            ┆            ┆            ┆ ...     │\n│            ┆            ┆            ┆          ┆            ┆            ┆            ┆ 0.0]    │\n├╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌┤\n│ 2.0        ┆ 3.0        ┆ zwakZandig ┆ standaar ┆ false      ┆ nietOrgani ┆ null       ┆ [0.0,   │\n│            ┆            ┆ eKlei      ┆ dGrijs   ┆            ┆ sch        ┆            ┆ 0.0,    │\n│            ┆            ┆            ┆          ┆            ┆            ┆            ┆ ...     │\n│            ┆            ┆            ┆          ┆            ┆            ┆            ┆ 0.0]    │\n├╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌┤\n│ 3.0        ┆ 4.0        ┆ zwakZandig ┆ donkergr ┆ false      ┆ nietOrgani ┆ null       ┆ [0.0,   │\n│            ┆            ┆ eKlei      ┆ ijs      ┆            ┆ sch        ┆            ┆ 0.0,    │\n│            ┆            ┆            ┆          ┆            ┆            ┆            ┆ ...     │\n│            ┆            ┆            ┆          ┆            ┆            ┆            ┆ 0.0]    │\n└────────────┴────────────┴────────────┴──────────┴────────────┴────────────┴────────────┴─────────┘\n```\n\n## Plotting\n\nTo use the plotting functionality pygef needs to be installed with the `[plot]`\nfeature.\n\n```sh\npip install pygef[plot]\n```\n\n```python\nfrom pygef import read_cpt, read_bore\nfrom pygef.plotting import plot_cpt, plot_bore\n\n# plot cpt file\nplot_cpt(read_cpt(\"myfile.xml\"))\n\n# plot a bore file\nplot_bore(read_bore(\"myfile.xml\"))\n```\n\n## Documentation\n\nBuild the docs:\n\n```bash\npython -m pip install --upgrade pip setuptools\npip install -r requirements.txt\npip install .\n\nsphinx-build -b html docs public\n```\n\n## Format\n\nWe format our code with black and isort.\n\n```bash\nblack --config \"pyproject.toml\" .\nisort --settings-path \"pyproject.toml\" .\n```\n\n## Lint\n\nTo maintain code quality we use the GitHub super-linter.\n\nTo run the linters locally, run the following bash script from the root\ndirectory:\n\n```bash\ndocker run \\\n--env VALIDATE_ALL_CODEBASE=true \\\n--env DEFAULT_BRANCH=master \\\n--env RUN_LOCAL=true \\\n--env FIX_PYTHON_ISORT=true \\\n--env FIX_PYTHON_BLACK=true \\\n--env FIX_YAML_PRETTIER=true \\\n--env VALIDATE_BASH=false \\\n--env VALIDATE_BIOME_FIX=false \\\n--env VALIDATE_BIOME_FORMAT=false \\\n--env VALIDATE_BIOME_LINT=false \\\n--env VALIDATE_CSS=false \\\n--env VALIDATE_CSS_PRETTIER=false \\\n--env VALIDATE_GRAPHQL=false \\\n--env VALIDATE_GRAPHQL_PRETTIER=false \\\n--env VALIDATE_HTML=false \\\n--env VALIDATE_HTML_PRETTIER=false \\\n--env VALIDATE_JAVASCRIPT_ES=false \\\n--env VALIDATE_JAVASCRIPT_PRETTIER=false \\\n--env VALIDATE_JSCPD=false \\\n--env VALIDATE_JSONC=false \\\n--env VALIDATE_JSONC_PRETTIER=false \\\n--env VALIDATE_JSON_ES=false \\\n--env VALIDATE_JSON_PRETTIER=false \\\n--env VALIDATE_JSX=false \\\n--env VALIDATE_JSX_PRETTIER=false \\\n--env VALIDATE_MARKDOWN=false \\\n--env VALIDATE_MARKDOWN_PRETTIER=false \\\n--env VALIDATE_NATURAL_LANGUAGE=false \\\n--env VALIDATE_PYTHON_PYLINT=false \\\n--env VALIDATE_PYTHON_RUFF=false \\\n--env VALIDATE_PYTHON_RUFF_FORMAT=false \\\n--env VALIDATE_TSX=false \\\n--env VALIDATE_TYPESCRIPT_ES=false \\\n--env VALIDATE_TYPESCRIPT_PRETTIER=false \\\n--env VALIDATE_VUE=false \\\n--env VALIDATE_VUE_PRETTIER=false \\\n--env VALIDATE_YAML=false \\\n--env LINTER_RULES_PATH=/ \\\n--env PYTHON_BLACK_CONFIG_FILE=pyproject.toml \\\n--env PYTHON_ISORT_CONFIG_FILE=pyproject.toml \\\n--env PYTHON_MYPY_CONFIG_FILE=pyproject.toml \\\n--env PYTHON_FLAKE8_CONFIG_FILE=.flake8 \\\n-v $(pwd):/tmp/lint ghcr.io/super-linter/super-linter:v8\n```\n\n## UnitTest\n\nTest the software with the use of coverage:\n\n```bash\npython -m pip install --upgrade pip setuptools\npip install -r requirements.txt\npip install -e .[test] .[map] .[plot]\n\ncoverage run -m pytest\n```\n\n## Requirements\n\nRequirements are autogenerated by `pip-compile` with python 3.9\n\n```bash\npip-compile --extra=plot --extra=test --extra=docs --extra=lint --extra=map --output-file=requirements.txt pyproject.toml\n```\n\nTo update the requirements within the defined ranges, run:\n\n```bash\npip-compile --upgrade --extra=plot --extra=test --extra=docs --extra=lint --extra=map --output-file=requirements.txt pyproject.toml\n```\n","funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["animations","profile","measures","composable","conversion","archiving","contributing","stress-test","generate","synchronous"],"project_url":"https://ost.ecosyste.ms/api/v1/projects/46157","html_url":"https://ost.ecosyste.ms/projects/46157"}