From 68eb4db7251f7f2d94844a80cd703e8a578d36ad Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?H=C3=A5vard=20Berland?= Date: Thu, 7 Dec 2023 12:33:27 +0100 Subject: [PATCH] Use ruff in pre-commit, update versions Fix whatever ruff finds fixable. --- .github/workflows/fmu-ensemble.yml | 3 +- .pre-commit-config.yaml | 17 ++-- HISTORY.rst | 2 - docs/advancedusage.rst | 2 - docs/conf.py | 152 +++++++++++++++-------------- docs/usage.rst | 16 +-- test_requirements.txt | 1 + tests/data/README.md | 2 +- tests/test_observations.py | 1 - 9 files changed, 100 insertions(+), 96 deletions(-) diff --git a/.github/workflows/fmu-ensemble.yml b/.github/workflows/fmu-ensemble.yml index 8a0ac573..5aee9693 100644 --- a/.github/workflows/fmu-ensemble.yml +++ b/.github/workflows/fmu-ensemble.yml @@ -50,8 +50,7 @@ jobs: - name: 🕵️ Check code style run: | - black --check src/ tests/test_*.py setup.py - flake8 src tests/*.py + pre-commit run --all-files - name: 🤖 Run tests run: | diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 714a6217..c9399055 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,6 @@ repos: - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v2.5.0 + rev: v4.5.0 hooks: - id: no-commit-to-branch args: ['--branch', 'master'] @@ -12,12 +12,15 @@ repos: - id: mixed-line-ending - id: trailing-whitespace -- repo: https://github.com/ambv/black - rev: 20.8b1 +- repo: https://github.com/psf/black + rev: 23.11.0 hooks: - id: black -- repo: https://gitlab.com/pycqa/flake8 - rev: 3.8.4 - hooks: - - id: flake8 +- repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.1.7 + hooks: + - id: ruff + args: [ --fix ] + +exclude: "tests/data/testensemble-reek001" diff --git a/HISTORY.rst b/HISTORY.rst index 237da99f..5eb24045 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -19,5 +19,3 @@ work from at leastL: * Smørbukk Sør webportal * Post-processing library made for webportal (2017/2018) https://github.com/Statoil/fmu_postprocessing * PyPostFMU https://git.equinor.com/FDIL/pypostfmu - - diff --git a/docs/advancedusage.rst b/docs/advancedusage.rst index 7164baab..6dff3f93 100644 --- a/docs/advancedusage.rst +++ b/docs/advancedusage.rst @@ -334,5 +334,3 @@ ensemble only for that particular datatype: 0 LowerReek 1105.552718 6.070259e+08 1599.113406 109885776.0 1 MidReek 966.315122 9.608399e+08 1586.559663 161875872.0 2 UpperReek 592.824625 1.028779e+09 1571.164775 148655376.0 - - diff --git a/docs/conf.py b/docs/conf.py index 5eb7c6a7..5f7838a6 100755 --- a/docs/conf.py +++ b/docs/conf.py @@ -1,5 +1,4 @@ #!/usr/bin/env python -# -*- coding: utf-8 -*- # # Documentation build configuration file, created by # sphinx-quickstart on Tue Jul 9 22:26:36 2013. @@ -20,46 +19,50 @@ # directory, add these directories to sys.path here. If the directory is # relative to the documentation root, use os.path.abspath to make it # absolute, like shown here. -sys.path.insert(0, os.path.abspath('src')) +sys.path.insert(0, os.path.abspath("src")) # Get the project root dir, which is the parent dir of this cwd = os.getcwd() -project_root = os.path.dirname(cwd) + '/src' +project_root = os.path.dirname(cwd) + "/src" # Insert the project root dir as the first element in the PYTHONPATH. # This lets us ensure that the source package is imported, and that its # version is used. sys.path.insert(0, project_root) -print('SYS!', sys.path) +print("SYS!", sys.path) -import fmu.ensemble +import fmu.ensemble # noqa: E402 # -- General configuration --------------------------------------------- # If your documentation needs a minimal Sphinx version, state it here. -#needs_sphinx = '1.0' +# needs_sphinx = '1.0' # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones. -extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode', - 'sphinx.ext.napoleon', 'sphinx.ext.mathjax'] +extensions = [ + "sphinx.ext.autodoc", + "sphinx.ext.viewcode", + "sphinx.ext.napoleon", + "sphinx.ext.mathjax", +] # Add any paths that contain templates here, relative to this directory. -templates_path = ['_templates'] +templates_path = ["_templates"] # The suffix of source filenames. -source_suffix = '.rst' +source_suffix = ".rst" # The encoding of source files. -#source_encoding = 'utf-8-sig' +# source_encoding = 'utf-8-sig' # The master toctree document. -master_doc = 'index' +master_doc = "index" # General information about the project. -project = u'fmu-ensemble' -copyright = u"Equinor" +project = "fmu-ensemble" +copyright = "Equinor" # The version info for the project you're documenting, acts as replacement # for |version| and |release|, also used in various other places throughout @@ -72,131 +75,131 @@ # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. -#language = None +# language = None # There are two options for replacing |today|: either, you set today to # some non-false value, then it is used: -#today = '' +# today = '' # Else, today_fmt is used as the format for a strftime call. -#today_fmt = '%B %d, %Y' +# today_fmt = '%B %d, %Y' # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. -exclude_patterns = ['_build'] +exclude_patterns = ["_build"] # Sort members by input order in classes -autodoc_member_order = 'bysource' -autodoc_default_flags = ['members', 'show_inheritance'] +autodoc_member_order = "bysource" +autodoc_default_flags = ["members", "show_inheritance"] # The reST default role (used for this markup: `text`) to use for all # documents. -#default_role = None +# default_role = None # If true, '()' will be appended to :func: etc. cross-reference text. -#add_function_parentheses = True +# add_function_parentheses = True # If true, the current module name will be prepended to all description # unit titles (such as .. function::). -#add_module_names = True +# add_module_names = True # If true, sectionauthor and moduleauthor directives will be shown in the # output. They are ignored by default. -#show_authors = False +# show_authors = False # The name of the Pygments (syntax highlighting) style to use. -pygments_style = 'sphinx' +pygments_style = "sphinx" # A list of ignored prefixes for module index sorting. -#modindex_common_prefix = [] +# modindex_common_prefix = [] # If true, keep warnings as "system message" paragraphs in the built # documents. -#keep_warnings = False +# keep_warnings = False # -- Options for HTML output ------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. -html_theme = 'sphinx_rtd_theme' +html_theme = "sphinx_rtd_theme" # Theme options are theme-specific and customize the look and feel of a # theme further. For a list of options available for each theme, see the # documentation. -#html_theme_options = {} +# html_theme_options = {} # Add any paths that contain custom themes here, relative to this directory. -#html_theme_path = [] +# html_theme_path = [] # The name for this set of Sphinx documents. If None, it defaults to # " v documentation". -#html_title = None +# html_title = None # A shorter title for the navigation bar. Default is the same as # html_title. -#html_short_title = None +# html_short_title = None # The name of an image file (relative to this directory) to place at the # top of the sidebar. -html_logo = '_static/equinor-logo2.jpg' +html_logo = "_static/equinor-logo2.jpg" # The name of an image file (within the static path) to use as favicon # of the docs. This file should be a Windows icon file (.ico) being # 16x16 or 32x32 pixels large. -#html_favicon = None +# html_favicon = None # Add any paths that contain custom static files (such as style sheets) # here, relative to this directory. They are copied after the builtin # static files, so a file named "default.css" will overwrite the builtin # "default.css". -html_static_path = ['_static'] +html_static_path = ["_static"] # If not '', a 'Last updated on:' timestamp is inserted at every page # bottom, using the given strftime format. -#html_last_updated_fmt = '%b %d, %Y' +# html_last_updated_fmt = '%b %d, %Y' # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. -#html_use_smartypants = True +# html_use_smartypants = True # Custom sidebar templates, maps document names to template names. -#html_sidebars = {} +# html_sidebars = {} # Additional templates that should be rendered to pages, maps page names # to template names. -#html_additional_pages = {} +# html_additional_pages = {} # If false, no module index is generated. -#html_domain_indices = True +# html_domain_indices = True # If false, no index is generated. -#html_use_index = True +# html_use_index = True # If true, the index is split into individual pages for each letter. -#html_split_index = False +# html_split_index = False # If true, links to the reST sources are added to the pages. -#html_show_sourcelink = True +# html_show_sourcelink = True # If true, "Created using Sphinx" is shown in the HTML footer. # Default is True. -#html_show_sphinx = True +# html_show_sphinx = True # If true, "(C) Copyright ..." is shown in the HTML footer. # Default is True. -#html_show_copyright = True +# html_show_copyright = True # If true, an OpenSearch description file will be output, and all pages # will contain a tag referring to it. The value of this option # must be the base URL from which the finished HTML is served. -#html_use_opensearch = '' +# html_use_opensearch = '' # This is the file name suffix for HTML files (e.g. ".xhtml"). -#html_file_suffix = None +# html_file_suffix = None # Output file base name for HTML help builder. -htmlhelp_basename = 'fmu-ensemble-doc' +htmlhelp_basename = "fmu-ensemble-doc" # -- Options for LaTeX output ------------------------------------------ @@ -204,10 +207,8 @@ latex_elements = { # The paper size ('letterpaper' or 'a4paper'). #'papersize': 'letterpaper', - # The font size ('10pt', '11pt' or '12pt'). #'pointsize': '10pt', - # Additional stuff for the LaTeX preamble. #'preamble': '', } @@ -216,30 +217,34 @@ # (source start file, target name, title, author, documentclass # [howto/manual]). latex_documents = [ - ('index', 'fmu-ensemble.tex', - u'fmu-ensemble Documentation', - u'Jan C. Rivenaes', 'manual'), + ( + "index", + "fmu-ensemble.tex", + "fmu-ensemble Documentation", + "Jan C. Rivenaes", + "manual", + ), ] # The name of an image file (relative to this directory) to place at # the top of the title page. -#latex_logo = None +# latex_logo = None # For "manual" documents, if this is true, then toplevel headings # are parts, not chapters. -#latex_use_parts = False +# latex_use_parts = False # If true, show page references after internal links. -#latex_show_pagerefs = False +# latex_show_pagerefs = False # If true, show URL addresses after external links. -#latex_show_urls = False +# latex_show_urls = False # Documents to append as an appendix to all manuals. -#latex_appendices = [] +# latex_appendices = [] # If false, no module index is generated. -#latex_domain_indices = True +# latex_domain_indices = True # -- Options for manual page output ------------------------------------ @@ -247,13 +252,11 @@ # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ - ('index', 'fmu-ensemble', - u'fmu-ensemble Documentation', - [u'Jan C. Rivenaes'], 1) + ("index", "fmu-ensemble", "fmu-ensemble Documentation", ["Jan C. Rivenaes"], 1) ] # If true, show URL addresses after external links. -#man_show_urls = False +# man_show_urls = False # -- Options for Texinfo output ---------------------------------------- @@ -262,22 +265,25 @@ # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ - ('index', 'fmu-ensemble', - u'fmu-ensemble Documentation', - u'Jan C. Rivenaes', - 'fmu-ensemble', - 'One line description of project.', - 'Miscellaneous'), + ( + "index", + "fmu-ensemble", + "fmu-ensemble Documentation", + "Jan C. Rivenaes", + "fmu-ensemble", + "One line description of project.", + "Miscellaneous", + ), ] # Documents to append as an appendix to all manuals. -#texinfo_appendices = [] +# texinfo_appendices = [] # If false, no module index is generated. -#texinfo_domain_indices = True +# texinfo_domain_indices = True # How to display URL addresses: 'footnote', 'no', or 'inline'. -#texinfo_show_urls = 'footnote' +# texinfo_show_urls = 'footnote' # If true, do not generate a @detailmenu in the "Top" node's menu. -#texinfo_no_detailmenu = False +# texinfo_no_detailmenu = False diff --git a/docs/usage.rst b/docs/usage.rst index 70c3f824..3ffd9b5a 100644 --- a/docs/usage.rst +++ b/docs/usage.rst @@ -46,7 +46,7 @@ into Python's memory first. ens # the output should be something like # - + You name your ensemble in the first argument. This name is used when you combine the ensemble with other ensembles into an ``EnsembleSet``. The path is where on the filesystem your realizations roots are. The realization root is also called @@ -69,7 +69,7 @@ When an ensemble is loaded into memory, you can ask for certain properties, # Obtain a Pandas Dataframe of the parameters ens.parameters - # Unique realizations indices with parameters.txt + # Unique realizations indices with parameters.txt ens.parameters['REAL'].unique() # List of parameters available: @@ -78,7 +78,7 @@ When an ensemble is loaded into memory, you can ask for certain properties, Loading multiple ensembles ^^^^^^^^^^^^^^^^^^^^^^^^^^ -If you have multiple ensembles in the typical ``realization-*/iter-*`` +If you have multiple ensembles in the typical ``realization-*/iter-*`` directory structure, you can load all these ensembles in one go: .. code-block:: python @@ -159,7 +159,7 @@ containing the summary data you requested. Each row is the values for a specific realization at a specific time. Pandas DataFrames can be written to disk as CSV files quite easily using e.g. ``smry.to_csv('summaryvectors.csv', index=False)``. For `time_index` you -may also try `yearly`, `daily` or `raw`. Check the function +may also try `yearly`, `daily` or `raw`. Check the function documentation for further possibilities. If you replace `get_smry` with `load_smry` the same dataframe will also be @@ -202,10 +202,10 @@ You can then ask to get a "volumetric rate" for `FOPT` at various time indices, yearly will give you yearly volumes, monthly will give monthly volumes etc. The data is returned as `FOPR` but you must be careful not to mix its meaning with the original `FOPR`. It is also possible to supply a -custom time index (with arbitrary time between each index), but where the +custom time index (with arbitrary time between each index), but where the volumetric rates are scaled to correspond to daily/monthly/yearly rates. These will sum up to the cumulative given correct integration (with -time interval length weigthing). +time interval length weigthing). .. code-block:: python @@ -330,7 +330,7 @@ ensemble and returned as a DataFrame. The current implementation can be slow for large grid model and/or ensembles with many realizations. .. code-block:: python - + # Find of the report number corresponding to the date you are interested to extract from ens.get_unrst_report_dates() # Extract the mean of following properties at the report step 4 @@ -370,7 +370,7 @@ Examples: # Extract the subset for a specific sensitivity. vens = ens.filter('parameters.txt', key='DRAINAGE_STRATEGY', value='Depletion', inplace=False) - + # Remove all realizations where a specific output file # (that we have tried to internalize) is missing ens.filter('geo_oil_1.csv') diff --git a/test_requirements.txt b/test_requirements.txt index 9013e502..c25a5a9d 100644 --- a/test_requirements.txt +++ b/test_requirements.txt @@ -1,5 +1,6 @@ black>=21.4b0 flake8>=2.6.0 +pre-commit pylint pytest>=2.9.2 pytest-cov diff --git a/tests/data/README.md b/tests/data/README.md index 6d76e5c5..79ed394c 100644 --- a/tests/data/README.md +++ b/tests/data/README.md @@ -3,5 +3,5 @@ Test data folder testensemble-reek001 is copied from /scratch/fmu/havb/2_r001_reek and then stripped for all RMS input/output, all Eclipse input/output except UNSMRY and most other noisy data from the Ert run. Can be used to verify -loading of ensembles, processing the STATUS file, parameters.txt, +loading of ensembles, processing the STATUS file, parameters.txt, UNSMRY and volumetrics text files from RMS diff --git a/tests/test_observations.py b/tests/test_observations.py index 2702062a..7bbfd7b4 100644 --- a/tests/test_observations.py +++ b/tests/test_observations.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 -*- """Testing observations in fmu-ensemble.""" import os