res2df 1.3.8__tar.gz → 1.3.10__tar.gz

res2df-1.3.10/.github/dependabot.yml

@@ -0,0 +1,7 @@
+---
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

{res2df-1.3.8 → res2df-1.3.10}/.github/workflows/codecov.yml

@@ -23,7 +23,7 @@ jobs:
         sudo apt-get update
         sudo apt-get install libegl1
 
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
 
     - name: Setup Python
       uses: actions/setup-python@v6
@@ -43,8 +43,8 @@ jobs:
     - name: Generate coverage report and upload
       run: |
         pytest tests --disable-warnings --cov=res2df --cov-report=xml
-        # Uninstall packages that res2df supports not being installed:
-        uv pip uninstall ert opm
+        # Uninstall package that res2df supports not being installed:
+        uv pip uninstall ert
         # Run tests again in cov-append-mode:
         pytest tests --disable-warnings --cov=res2df --cov-report=xml --cov-append
         bash <(curl -s https://codecov.io/bash)

{res2df-1.3.8 → res2df-1.3.10}/.github/workflows/publish.yml

@@ -16,7 +16,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0
 

{res2df-1.3.8 → res2df-1.3.10}/.github/workflows/res2df.yml

@@ -21,7 +21,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.11', '3.12']
+        python-version: ['3.11', '3.12', '3.13']
         include:
           # For one of the Python versions we
           # install the extra dependency ert
@@ -37,7 +37,7 @@ jobs:
           sudo apt-get install libegl1
 
       - name: Checkout commit locally
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
 
       - name: Checkout tags
         # This seems necessary for setuptools_scm to be able to infer
@@ -78,6 +78,7 @@ jobs:
 
       - name: Build documentation
         run: |
+          sudo apt-get install graphviz
           sphinx-build -W -b html docs build/sphinx/html
 
       - name: Update GitHub pages

{res2df-1.3.8 → res2df-1.3.10}/.github/workflows/style.yml

@@ -1,11 +1,11 @@
 name: Style
 
 on:
- push:
-   branches:
-     - master
-     - 'version-**'
- pull_request:
+  push:
+    branches:
+      - master
+      - 'version-**'
+  pull_request:
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -20,10 +20,10 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.12']
+        python-version: ['3.13']
 
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         fetch-depth: 0
 

{res2df-1.3.8 → res2df-1.3.10}/.github/workflows/typing.yml

@@ -1,11 +1,15 @@
 name: Typing
 
 on:
- push:
-   branches:
-     - master
-     - 'version-**'
- pull_request:
+  push:
+    branches:
+      - master
+      - 'version-**'
+  pull_request:
+
+  schedule:
+    # Run CI every night and check that tests are working with latest dependencies
+    - cron: '0 0 * * *'
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -20,10 +24,10 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.12']
+        python-version: ['3.13']
 
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         fetch-depth: 0
 

{res2df-1.3.8 → res2df-1.3.10}/.pre-commit-config.yaml

@@ -11,7 +11,7 @@ repos:
   - id: trailing-whitespace
 
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.0
+    rev: v0.14.8
     hooks:
     - id: ruff-check
       args: [ --fix ]

res2df-1.3.10/PKG-INFO

@@ -0,0 +1,94 @@
+Metadata-Version: 2.4
+Name: res2df
+Version: 1.3.10
+Summary: Convert reservoir simulator input and output to DataFrames
+Author-email: Håvard Berland <havb@equinor.com>
+License-Expression: GPL-3.0-only
+Project-URL: Homepage, https://github.com/equinor/res2df
+Project-URL: Repository, https://github.com/equinor/res2df
+Project-URL: Documentation, https://equinor.github.io/res2df/
+Keywords: energy,subsurface,reservoir,scientific,engineering
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Software Development :: Libraries
+Classifier: Topic :: Utilities
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Natural Language :: English
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: resdata>=5.0.0-b0
+Requires-Dist: resfo
+Requires-Dist: networkx
+Requires-Dist: numpy
+Requires-Dist: opm>=2020.10.2
+Requires-Dist: pandas
+Requires-Dist: pyarrow
+Requires-Dist: pyyaml>=5.1
+Requires-Dist: treelib
+Provides-Extra: tests
+Requires-Dist: pytest; extra == "tests"
+Requires-Dist: pytest-cov; extra == "tests"
+Requires-Dist: pytest-mock; extra == "tests"
+Requires-Dist: pytest-timeout; extra == "tests"
+Provides-Extra: style
+Requires-Dist: pre-commit; extra == "style"
+Provides-Extra: types
+Requires-Dist: mypy; extra == "types"
+Requires-Dist: types-PyYAML; extra == "types"
+Requires-Dist: types-python-dateutil; extra == "types"
+Requires-Dist: types-setuptools; extra == "types"
+Requires-Dist: types-networkx; extra == "types"
+Requires-Dist: pandas-stubs; extra == "types"
+Provides-Extra: docs
+Requires-Dist: sphinx-autoapi; extra == "docs"
+Requires-Dist: ipython; extra == "docs"
+Requires-Dist: rstcheck; extra == "docs"
+Requires-Dist: setuptools; extra == "docs"
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: sphinx-argparse; extra == "docs"
+Requires-Dist: sphinx-autodoc-typehints; extra == "docs"
+Requires-Dist: sphinx_rtd_theme; extra == "docs"
+Provides-Extra: ert
+Requires-Dist: ert>=10.2.0b13; extra == "ert"
+Dynamic: license-file
+
+[![Publish to PyPI](https://github.com/equinor/res2df/actions/workflows/publish.yml/badge.svg)](https://github.com/equinor/res2df/actions/workflows/publish.yml)
+[![PyPI version](https://img.shields.io/pypi/v/res2df.svg)](https://pypi.org/project/res2df/)
+[![codecov](https://codecov.io/gh/equinor/res2df/graph/badge.svg?token=3sZBGGu5VG)](https://codecov.io/gh/equinor/res2df)
+[![Python 3.11-3.13](https://img.shields.io/badge/python-3.11%20|%203.12%20|%203.13-blue.svg)](https://www.python.org)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
+[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
+
+# res2df
+
+res2df is a Pandas DataFrame wrapper around resdata and opm.io, which
+are used to access binary files outputted by reservoir simulators,
+or its input files --- or any other tool outputting to the same data format.
+
+The reverse operation, from a Pandas DataFrame to reservoir simulator include files
+(commonly given the extension ".inc", ".grdecl" etc.) is provided for some of the
+modules.
+
+The package consists of a module pr. datatype, e.g. one module for summary
+files (.UNSMRY), one for completion data etc.
+
+There is a command line frontend for almost all functionality, called
+`res2csv`, which converts the reservoir data to DataFrames, and then dumps
+the dataframes to files in CSV format, and a similar `csv2res` for the
+reverse operation.
+
+For documentation, see <https://equinor.github.io/res2df/>
+
+## License
+
+This library is released under GPLv3.
+
+## Copyright
+
+The code is Copyright Equinor ASA 2019-2021.
+
+Contributions without copyright transfer are welcome.

{res2df-1.3.8 → res2df-1.3.10}/README.md

@@ -1,7 +1,7 @@
 [![Publish to PyPI](https://github.com/equinor/res2df/actions/workflows/publish.yml/badge.svg)](https://github.com/equinor/res2df/actions/workflows/publish.yml)
 [![PyPI version](https://img.shields.io/pypi/v/res2df.svg)](https://pypi.org/project/res2df/)
 [![codecov](https://codecov.io/gh/equinor/res2df/graph/badge.svg?token=3sZBGGu5VG)](https://codecov.io/gh/equinor/res2df)
-[![Python 3.11-3.12](https://img.shields.io/badge/python-3.11%20|%203.12-blue.svg)](https://www.python.org)
+[![Python 3.11-3.13](https://img.shields.io/badge/python-3.11%20|%203.12%20|%203.13-blue.svg)](https://www.python.org)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 

{res2df-1.3.8 → res2df-1.3.10}/docs/conf.py

@@ -39,10 +39,11 @@ version = release
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    "autoapi.sphinx",
+    "autoapi.extension",
     "sphinx.ext.autodoc",
     "sphinx.ext.autosummary",
     "sphinx.ext.githubpages",
+    "sphinx.ext.inheritance_diagram",
     "sphinx.ext.mathjax",
     "sphinx.ext.napoleon",
     "sphinx.ext.viewcode",
@@ -50,12 +51,30 @@ extensions = [
     "sphinxarg.ext",
 ]
 
-autoapi_modules: dict = {"res2df": None}
+autoapi_dirs = ["../src/res2df"]
+autoapi_root = "res2df"
+autoapi_type = "python"
+autoapi_add_toctree_entry = False
+autoapi_own_page_level = "module"
+
+autoapi_options = [
+    "members",
+    "undoc-members",
+    "show-inheritance",
+    "show-module-summary",
+]
 
-autodoc_default_options = {"members": None}
+autodoc_default_options = {
+    "members": True,
+    "imported-members": False,
+}
 
 autosummary_generate = True
 
+suppress_warnings = [
+    "docutils",
+]
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 
@@ -188,3 +207,27 @@ epub_exclude_files = ["search.html"]
 
 
 # -- Extension configuration -------------------------------------------------
+
+
+def skip_unwanted_members(app, what, name, obj, skip, options):
+    short_name = name.split(".")[-1]
+
+    if "vfp" in name and short_name.startswith("_"):
+        return False
+
+    if ".constants." in name or name.endswith(".constants"):
+        return True
+
+    if short_name == "logger":
+        return True
+
+    if what == "data" and (
+        short_name.isupper() or short_name.replace("_", "").isupper()
+    ):
+        return True
+
+    return skip
+
+
+def setup(app):
+    app.connect("autoapi-skip-member", skip_unwanted_members)

{res2df-1.3.8 → res2df-1.3.10}/docs/index.rst

@@ -23,7 +23,7 @@ data format.
    :maxdepth: 10
    :caption: Python API
 
-   res2df/res2df
+   res2df/res2df/index
 
 Indices and tables
 ==================

{res2df-1.3.8 → res2df-1.3.10}/pyproject.toml

@@ -6,14 +6,15 @@ requires = [
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools_scm]
-write_to = "src/res2df/version.py"
+version_file = "src/res2df/version.py"
 
 [project]
 name = "res2df"
 description = "Convert reservoir simulator input and output to DataFrames"
 readme = "README.md"
 requires-python = ">=3.11"
-license = { file = "LICENSE" }
+license = "GPL-3.0-only"
+license-files = ["LICENSE"]
 authors = [
     { name = "Håvard Berland", email = "havb@equinor.com" }
 ]
@@ -26,8 +27,8 @@ classifiers = [
     "Topic :: Utilities",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Natural Language :: English",
-    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
 ]
 
 dynamic = ["version"]
@@ -61,7 +62,7 @@ types = [
     "pandas-stubs",
 ]
 docs = [
-    "autoapi",
+    "sphinx-autoapi",
     "ipython",
     "rstcheck",
     "setuptools",
@@ -104,8 +105,8 @@ extra_checks = true
 
 [[tool.mypy.overrides]]
 module = [
+    "ert",
     "opm.*",
-    "resfo",
     "pyarrow", # should be removed for pyarrow > 21.0.0
     "resdata.*",
 ]
@@ -138,6 +139,7 @@ select = [
   "PD",  # pandas-vet
   "RUF",  # ruff specific rules
   "UP",  # pyupgrade
+  "ANN",  # flake8-annotations
 ]
 preview = true
 ignore = [
@@ -159,7 +161,8 @@ ignore = [
 
 [tool.ruff.lint.extend-per-file-ignores]
 "src/res2df/__init__.py" = ["PLC0414"]
-"tests/*" = ["RUF005"]
+"tests/*" = ["RUF005", "ANN"]
+"docs/*" = ["ANN"]
 
 [tool.ruff.lint.pylint]
 max-args = 20

res2df-1.3.10/src/res2df/__init__.py

@@ -0,0 +1,68 @@
+from . import compdat as compdat
+from . import csv2res as csv2res
+from . import equil as equil
+from . import faults as faults
+from . import fipreports as fipreports
+from . import grid as grid
+from . import gruptree as gruptree
+from . import nnc as nnc
+from . import pillars as pillars
+from . import pvt as pvt
+from . import res2csv as res2csv
+from . import rft as rft
+from . import satfunc as satfunc
+from . import summary as summary
+from . import trans as trans
+from . import vfp as vfp
+from . import wcon as wcon
+from . import wellcompletiondata as wellcompletiondata
+from . import wellconnstatus as wellconnstatus
+from .__version__ import __version__ as __version__
+from .res2csvlogger import getLogger_res2csv as getLogger_res2csv
+from .resdatafiles import ResdataFiles as ResdataFiles
+
+SUBMODULES: list[str] = [
+    "compdat",
+    "equil",
+    "faults",
+    "fipreports",
+    "grid",
+    "gruptree",
+    "nnc",
+    "pillars",
+    "pvt",
+    "rft",
+    "satfunc",
+    "summary",
+    "trans",
+    "vfp",
+    "wellcompletiondata",
+    "wellconnstatus",
+    "wcon",
+]
+
+
+__all__ = [
+    "ResdataFiles",
+    "__version__",
+    "compdat",
+    "csv2res",
+    "equil",
+    "faults",
+    "fipreports",
+    "getLogger_res2csv",
+    "grid",
+    "gruptree",
+    "nnc",
+    "pillars",
+    "pvt",
+    "res2csv",
+    "rft",
+    "satfunc",
+    "summary",
+    "trans",
+    "vfp",
+    "wcon",
+    "wellcompletiondata",
+    "wellconnstatus",
+]

{res2df-1.3.8 → res2df-1.3.10}/src/res2df/__version__.py

@@ -1,5 +1,5 @@
 try:
-    from .version import version  # type: ignore
+    from .version import version
 
     __version__ = version
 except ImportError:

{res2df-1.3.8 → res2df-1.3.10}/src/res2df/common.py

@@ -11,28 +11,24 @@ import shlex
 import signal
 import sys
 from collections import defaultdict
+from collections.abc import Mapping
 from importlib import resources
 from pathlib import Path
 from typing import Any, cast
 
 import dateutil.parser
 import numpy as np
+import opm.io.deck
 import pandas as pd
 import pyarrow as pa
+
+# This import is seemingly not used, but necessary for some attributes
+# to be included in DeckItem objects.
+from opm.io.deck import DeckKeyword  # noqa: F401
 from pyarrow import (
     feather,  # necessary as this module is not loaded unless explicitly imported
 )
 
-try:
-    import opm.io.deck
-
-    # This import is seemingly not used, but necessary for some attributes
-    # to be included in DeckItem objects.
-    from opm.io.deck import DeckKeyword  # noqa: F401
-except ImportError:
-    # Allow parts of res2df to work without OPM:
-    pass
-
 from .__version__ import __version__
 from .constants import MAGIC_STDOUT
 
@@ -189,9 +185,9 @@ def datetime_to_ecldate(timestamp: str | datetime.datetime | datetime.date) -> s
 
 
 def keyworddata_to_df(
-    deck,
+    deck: "opm.opmcommon_python.Deck",
     keyword: str,
-    renamer: dict[str, str | list[str]] | None = None,
+    renamer: Mapping[str, str | list[str]] | None = None,
     recordcountername: str | None = None,
     emptyrecordcountername: str | None = None,
 ) -> pd.DataFrame:
@@ -275,7 +271,7 @@ def parse_opmio_deckrecord(
     keyword: str,
     itemlistname: str = "items",
     recordindex: int | None = None,
-    renamer: dict[str, str] | dict[str, str | list[str]] | None = None,
+    renamer: Mapping[str, str | list[str]] | None = None,
 ) -> dict[str, Any]:
     """
     Parse an opm.io.DeckRecord belonging to a certain keyword
@@ -344,8 +340,9 @@ def parse_opmio_deckrecord(
     if renamer:
         renamed_dict: dict[str, Any] = {}
         for key, value in rec_dict.items():
-            if key in renamer and not isinstance(renamer[key], list):
-                renamed_dict[renamer[key]] = value  # type: ignore
+            renamed_key = renamer.get(key)
+            if isinstance(renamed_key, str):
+                renamed_dict[renamed_key] = value
             else:
                 renamed_dict[key] = value
         return renamed_dict
@@ -470,7 +467,7 @@ def handle_wanted_keywords(
 
 def fill_reverse_parser(
     parser: argparse.ArgumentParser, modulename: str, defaultoutputfile: str
-):
+) -> argparse.ArgumentParser:
     """A standardized submodule parser for the command line utility
        to produce :term:`include files <include file>` from a CSV file.
 
@@ -543,6 +540,7 @@ def df2res(
     """
     from_module = inspect.stack()[1]
     calling_module = inspect.getmodule(from_module[0])
+    assert calling_module is not None
     if dataframe.empty:
         raise ValueError("Empty dataframe")
     if (
@@ -580,7 +578,7 @@ def df2res(
         if not_supported:
             logger.warning(
                 "Requested keyword(s) not supported by %s: %s",
-                calling_module.__name__,  # type: ignore
+                calling_module.__name__,
                 not_supported,
             )
         # Warn if some requested keywords are not in frame:
@@ -601,7 +599,7 @@ def df2res(
     string = ""
     res2df_header = (
         "Output file printed by "
-        + calling_module.__name__  # type: ignore
+        + calling_module.__name__
         + " "
         + __version__
         + "\n"
@@ -631,7 +629,7 @@ def generic_deck_table(
     dframe: pd.DataFrame,
     keyword: str,
     comment: str | None = None,
-    renamer: dict[str, str] | None = None,
+    renamer: Mapping[str, str] | None = None,
     drop_trailing_columns: bool = True,
 ) -> str:
     """Construct string contents of a :term:`.DATA file` table.
@@ -855,7 +853,7 @@ def is_color(input_string: str) -> bool:
     return bool(re.match(regex, input_string))
 
 
-def parse_lyrfile(filename: str) -> list[dict[str, Any]] | None:
+def parse_lyrfile(filename: str | Path) -> list[dict[str, Any]] | None:
     """Return a list of dicts representation of the lyr file.
 
     The lyr file contains data of the following format,
@@ -927,7 +925,9 @@ def parse_lyrfile(filename: str) -> list[dict[str, Any]] | None:
     return lyrlist
 
 
-def convert_lyrlist_to_zonemap(lyrlist: list[dict[str, Any]]) -> dict[int, str]:
+def convert_lyrlist_to_zonemap(
+    lyrlist: list[dict[str, Any]] | None,
+) -> dict[int, str] | None:
     """Returns a layer to zone map as a dictionary
 
     Args:
@@ -949,7 +949,7 @@ def convert_lyrlist_to_zonemap(lyrlist: list[dict[str, Any]]) -> dict[int, str]:
     return zonemap
 
 
-def get_wells_matching_template(template: str, wells: list):
+def get_wells_matching_template(template: str, wells: list[str]) -> list[str]:
     """Returns the wells in the list that is matching the template
     containing wilcard characters. The wildcard charachters supported
     are * to match zero or more charachters and ? to match a single

{res2df-1.3.8 → res2df-1.3.10}/src/res2df/compdat.py

@@ -11,16 +11,14 @@
 """
 
 import argparse
-import contextlib
 import datetime
 import logging
+from typing import Any
 
 import numpy as np
+import opm.io.deck
 import pandas as pd
 
-with contextlib.suppress(ImportError):
-    import opm.io.deck
-
 from .common import (
     get_wells_matching_template,
     merge_zones,
@@ -97,6 +95,7 @@ def deck2dfs(
     complumprecords = []
     welspecs = {}
     date = start_date  # DATE column will always be there, but can contain NaN/None
+    rec_data: dict[str, Any]
     for idx, kword in enumerate(deck):
         if kword.name in ["DATES", "START"]:
             for rec in kword:
@@ -752,7 +751,7 @@ def expand_complump_in_welopen_df(
                 exp_welopens.append(cell_row)
 
     dframe = pd.DataFrame(exp_welopens)
-    return dframe.astype(object).where(pd.notna(dframe), None)
+    return dframe.astype(object).where(pd.notna(dframe), None)  # type: ignore[call-overload]
 
 
 def expand_wlist_in_welopen_df(
@@ -786,7 +785,7 @@ def expand_wlist_in_welopen_df(
             # Explicit wellname was used, no expansion to happen:
             exp_welopens.append(row)
     dframe = pd.DataFrame(exp_welopens)
-    return dframe.astype(object).where(pd.notna(dframe), None)
+    return dframe.astype(object).where(pd.notna(dframe), None)  # type: ignore[call-overload]
 
 
 def applywelopen(
@@ -845,7 +844,7 @@ def applywelopen(
                 "The WLIST dataframe must be expanded through expand_wlist()"
             )
 
-    welopen_df = welopen_df.astype(object).where(pd.notna(welopen_df), None)
+    welopen_df = welopen_df.astype(object).where(pd.notna(welopen_df), None)  # type: ignore[call-overload]
     if wlist_df is not None:
         welopen_df = expand_wlist_in_welopen_df(welopen_df, wlist_df)
     if complump_df is not None:
@@ -951,7 +950,7 @@ def fill_parser(parser: argparse.ArgumentParser) -> argparse.ArgumentParser:
     return parser
 
 
-def compdat_main(args):
+def compdat_main(args: argparse.Namespace) -> None:
     """Entry-point for module, for command line utility"""
     logger = getLogger_res2csv(__name__, vars(args))
     resdatafiles = ResdataFiles(args.DATAFILE)

{res2df-1.3.8 → res2df-1.3.10}/src/res2df/csv2res.py

@@ -34,7 +34,7 @@ def get_parser() -> argparse.ArgumentParser:
         version=f"%(prog)s {__version__}",
     )
 
-    subparsers = parser.add_subparsers(  # type: ignore
+    subparsers = parser.add_subparsers(
         required=True,
         dest="subcommand",
         parser_class=argparse.ArgumentParser,