Synthetics Bugs

.github/workflows/run-tests.yml

@@ -5,9 +5,9 @@ name: Run tests
 
 on:
   push:
-    branches: [ develop, master ]
+    branches: [ develop, main ]
   pull_request:
-    branches: [ develop ]
+    branches: [ develop, main ]
 
 jobs:
   build:
@@ -16,18 +16,17 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.6", "3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         python -m pip install .[test]
     - name: Test with pytest
-      run: |
-        python run_tests.py
+      run: pytest

AUTHORS.md

@@ -10,6 +10,6 @@ The following people have contributed to the project (in alphabetical order):
 - [Thomas Martin](https://github.com/ThomasMGeo), Colorado, USA
 - [Steve Purves](https://github.com/stevejpurves), Curvenote, Spain
 - [Patrick Reinhard](https://github.com/patrick-reinhard), Shell, The Netherlands
-- [DC Slagel](https://github.com/dcslagel), Shell, The Netherlands
+- [DC Slagel](https://github.com/dcslagel), Code Farm, Colorado, USA
 - [Miguel de la Varga](https://github.com/Leguark), Germany
 - [Wenting Xiong](https://github.com/wenting-x), Shell, The Netherlands

CODE_OF_CONDUCT.md

@@ -0,0 +1,79 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to make participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, sex characteristics, gender identity and expression,
+level of experience, education, socio-economic status, nationality, personal
+appearance, race, religion, or sexual identity and orientation.
+
+## Our standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+  advances
+* Racist or racially biased remarks, attacks, or content.
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Our responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies within all project spaces, and it also applies when
+an individual is representing the project or its community in public spaces.
+Examples of representing a project or community include using an official
+project e-mail address, posting via an official social media account, or acting
+as an appointed representative at an online or offline event. Representation of
+a project may be further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting any of the following people:
+
+- Matt Hall, [[email protected]](mailto:[email protected])
+- Evan Bianco, [[email protected]](mailto:[email protected])
+
+All complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant](https://www.contributor-covenant.org/), version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq

pyproject.toml

@@ -1,11 +1,62 @@
 [build-system]
-requires = [
-    "setuptools>=48",
-    "setuptools_scm[toml] >= 4, <6",
-    "setuptools_scm_git_archive",
-    "wheel >= 0.29.0",
+requires = ["hatchling", "hatch-vcs"]
+build-backend = "hatchling.build"
+
+[project]
+name = "welly"
+dynamic = ["version"]
+authors = [{ name = "The Welly Authors", email = "[email protected]" }]
+description = "Tools for making and managing well data."
+readme = "README.md"
+readme-content-type = "text/markdown"
+homepage = "https://github.com/agilescientific/welly"
+classifiers = [
+    "Intended Audience :: Science/Research",
+    "Development Status :: 4 - Beta",
+    "Natural Language :: English",
+    "Programming Language :: Python :: 3.6",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "License :: OSI Approved :: Apache Software License",
+    "Operating System :: OS Independent"
+]
+dependencies = [
+    "numpy",
+    "scipy",
+    "pandas",
+    "matplotlib",
+    "lasio",
+    "striplog",
+    "tqdm",
+    "wellpathpy",
+    "requests"
+]
+
+[project.optional-dependencies]
+docs = ["sphinx", "sphinxcontrib-apidoc", "myst_nb", "furo"]
+test = ["pytest", "pytest-cov", "pytest-mpl"]
+dev = ["build", "pytest", "pytest-cov", "pytest-mpl", "sphinx", "sphinxcontrib-apidoc", "myst_nb", "furo"]
+
+[tool.hatch.metadata]
+packages = ["welly"]
+
+[tool.hatch.version]
+source = "vcs"
+
+[tool.hatch.build.hooks.vcs]
+version-file = "_version.py"
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+addopts = [
+  "--cov=welly",
+  "--cov-config=pyproject.toml",
+  "--mpl",
+  "--mpl-baseline-path=tests/baseline",
 ]
-build-backend = "setuptools.build_meta"
+testpaths = ["tests"]
 
 [tool.setuptools_scm]
 write_to = "welly/_version.py"

tests/test_plots.py

@@ -9,6 +9,7 @@
 
 https://pypi.python.org/pypi/pytest-mpl/0.3
 """
+import matplotlib.pyplot as plt
 import pytest
 
 from welly import Well
@@ -114,7 +115,8 @@ def test_synthetic_plot():
     test_params = {'dt': 0.004}
     s = Synthetic(data, params=test_params)
 
-    fig = s.plot().get_figure()
+    fig, ax = plt.subplots(figsize=(2, 10))
+    s.plot(ax)
 
     return fig
 
@@ -127,7 +129,8 @@ def test_well_synthetic_plot():
     w = Well.from_las(FNAME)
     w.make_synthetic()
 
-    fig = w.data['Synthetic'].plot().get_figure()
+    fig, ax = plt.subplots(figsize=(2, 10))
+    w.data['Synthetic'].plot(ax)
 
     return fig
 

tests/test_synthetic.py

@@ -1,6 +1,6 @@
 # -*- coding: utf 8 -*-
 """
-Define a suite a tests for the Curve module.
+Define a suite a tests for the Synthetic class.
 """
 import numpy as np
 
@@ -17,3 +17,18 @@ def test_synthetic():
 
     assert s.dt == 0.004
     assert s.name == 'Synthetic'
+
+
+def test_synthetic_as_curve():
+    """
+    Test synthetic to curve.
+    """
+    data = np.array([4, 2, 0, -4, -2, 1, 3, 6, 3, 1, -2, -5, -1, 0])
+    params = {'dt': 0.004}
+    s = Synthetic(data, params=params)
+
+    crv = s.as_curve(0, 500, 0.1, mnemonic="SYNTH_CRV")
+
+    assert crv.index[0] == 0
+    assert round((crv.index[1]-crv.index[0]),2) == 0.1
+    assert crv.mnemonic == 'SYNTH_CRV'

tests/test_well.py

@@ -5,6 +5,8 @@
 import os
 from pathlib import Path
 
+import pandas as pd
+
 import welly
 from welly import Well
 
@@ -148,3 +150,11 @@ def test_iter_well(well):
     for curve in well:
         assert curve == well.data['CALI']
         break
+
+def test_df_object_cols(df):
+
+    df["Test object"] = "54"
+    df["test_str"] = '1z'
+    well = Well.from_df(df)
+    assert all(well.df()["Test object"] == 54)
+    assert all(well.df()["test_str"] == "1z")

welly/__init__.py

@@ -3,6 +3,8 @@
 welly
 ==================
 """
+import sys
+
 from .project import Project
 from .well import Well
 from .header import Header
@@ -12,6 +14,7 @@
 from .crs import CRS
 from . import tools
 from . import quality
+from . import defaults
 
 
 def read_las(path, **kwargs):
@@ -66,17 +69,10 @@ def read_df(df, **kwargs):
           ]
 
 
-from pkg_resources import get_distribution, DistributionNotFound
-
-try:
-    VERSION = get_distribution(__name__).version
-except DistributionNotFound:
-    try:
-        from ._version import version as VERSION
-    except ImportError:
-        raise ImportError(
-            "Failed to find (autogenerated) _version.py. "
-            "This might be because you are installing from GitHub's tarballs, "
-            "use the PyPI ones."
-            )
-__version__ = VERSION
+if sys.version_info >= (3, 8):
+    from importlib import metadata
+else:
+    import importlib_metadata as metadata
+
+__version__ = metadata.version(__name__)
+