chore: Sync dependency lockfiles from pyproject.toml

.claude/commands/swp/test/audit.md

@@ -19,11 +19,12 @@ Detects anti-patterns BEFORE they cause test failures.
 
 | ID | Pattern | Severity | Count (baseline) |
 |----|---------|----------|------------------|
-| swp-test-001 | `assert X is not None` (trivial) | warning | 133 |
+| swp-test-001 | `assert X is not None` (trivial) | warning | 74 |
 | swp-test-002 | `patch.object` without `wraps=` | warning | 76 |
 | swp-test-003 | Assert without error message | info | - |
 | swp-test-004 | `plt.subplots()` (verify cleanup) | info | 59 |
 | swp-test-006 | `len(x) > 0` without type check | info | - |
+| swp-test-009 | `isinstance(X, object)` (disguised trivial) | warning | 0 |
 
 ### Good Patterns to Track (Adoption Metrics)
 
@@ -77,6 +78,15 @@ mcp__ast-grep__find_code(
     language="python",
     max_results=30
 )
+
+# 5. Disguised trivial assertion (swp-test-009)
+# isinstance(X, object) is equivalent to X is not None
+mcp__ast-grep__find_code(
+    project_folder="/path/to/SolarWindPy",
+    pattern="isinstance($OBJ, object)",
+    language="python",
+    max_results=50
+)
 ```
 
 **FALLBACK: CLI ast-grep (requires local `sg` installation)**
@@ -163,6 +173,7 @@ This skill is for **routine audits** - quick pattern detection before/during tes
 | Anti-Pattern | Fix | TEST_PATTERNS.md Section |
 |--------------|-----|-------------------------|
 | `assert X is not None` | `assert isinstance(X, Type)` | #6 Return Type Verification |
+| `isinstance(X, object)` | `isinstance(X, SpecificType)` | #6 Return Type Verification |
 | `patch.object(i, m)` | `patch.object(i, m, wraps=i.m)` | #1 Mock-with-Wraps |
 | Missing `plt.close()` | Add at test end | #15 Resource Cleanup |
 | Default parameter values | Use distinctive values (77, 2.5) | #2 Parameter Passthrough |

docs/requirements.txt

@@ -1,5 +1,5 @@
 #
-# This file is autogenerated by pip-compile with Python 3.12
+# This file is autogenerated by pip-compile with Python 3.11
 # by the following command:
 #
 #    pip-compile --allow-unsafe --extra=docs --output-file=docs/requirements.txt pyproject.toml

pyproject.toml

@@ -117,6 +117,9 @@ analysis = [
 "Bug Tracker" = "https://github.com/blalterman/SolarWindPy/issues"
 "Source" = "https://github.com/blalterman/SolarWindPy"
 
+[tool.setuptools.package-data]
+solarwindpy = ["core/data/*.csv"]
+
 [tool.pip-tools]
 # pip-compile configuration for lockfile generation
 generate-hashes = false  # Set to true for security-critical deployments

requirements-dev.lock

@@ -1,5 +1,5 @@
 #
-# This file is autogenerated by pip-compile with Python 3.12
+# This file is autogenerated by pip-compile with Python 3.11
 # by the following command:
 #
 #    pip-compile --allow-unsafe --extra=dev --output-file=requirements-dev.lock pyproject.toml

setup.cfg

@@ -10,7 +10,7 @@ tests_require =
 
 [flake8]
 extend-select = D402, D413, D205, D406
-ignore = E501, W503, D100, D101, D102, D103, D104, D105, D200, D202, D209, D214, D215, D300, D302, D400, D401, D403, D404, D405, D409, D412, D414
+ignore = E231, E501, W503, D100, D101, D102, D103, D104, D105, D200, D202, D209, D214, D215, D300, D302, D400, D401, D403, D404, D405, D409, D412, D414
 enable = W605
 docstring-convention = numpy
 max-line-length = 88

solarwindpy.yml

@@ -22,94 +22,29 @@ name: solarwindpy
 channels:
 - conda-forge
 dependencies:
-- alabaster
 - astropy
 - astropy-iers-data
-- babel
-- black
-- python-blosc2
 - bottleneck
-- certifi
-- cfgv
-- charset-normalizer
-- click
 - contourpy
-- coverage[toml]
 - cycler
-- distlib
-- doc8
 - docstring-inheritance
-- docutils
-- filelock
-- flake8
-- flake8-docstrings
 - fonttools
 - h5py
-- identify
-- idna
-- imagesize
-- iniconfig
-- jinja2
 - kiwisolver
-- latexcodec
 - llvmlite
-- markupsafe
 - matplotlib
-- mccabe
-- msgpack-python
-- mypy_extensions
-- ndindex
-- nodeenv
 - numba
 - numexpr
 - numpy
-- numpydoc
 - packaging
 - pandas
-- pathspec
 - pillow
-- platformdirs
-- pluggy
-- pre-commit
-- psutil
-- py-cpuinfo
-- pybtex
-- pybtex-docutils
-- pycodestyle
-- pydocstyle
-- pyenchant
 - pyerfa
-- pyflakes
-- pygments
 - pyparsing
-- pytest
-- pytest-cov
 - python-dateutil
-- pytokens
 - pytz
 - pyyaml
-- requests
-- restructuredtext_lint
-- roman-numerals
-- roman-numerals-py
 - scipy
 - six
-- snowballstemmer
-- sphinx
-- sphinx-rtd-theme
-- sphinxcontrib-applehelp
-- sphinxcontrib-bibtex
-- sphinxcontrib-devhelp
-- sphinxcontrib-htmlhelp
-- sphinxcontrib-jquery
-- sphinxcontrib-jsmath
-- sphinxcontrib-qthelp
-- sphinxcontrib-serializinghtml
-- sphinxcontrib-spelling
-- stevedore
-- pytables
 - tabulate
-- typing-extensions
 - tzdata
-- urllib3
-- virtualenv

solarwindpy/core/__init__.py

@@ -8,6 +8,7 @@
 from .spacecraft import Spacecraft
 from .units_constants import Units, Constants
 from .alfvenic_turbulence import AlfvenicTurbulence
+from .abundances import ReferenceAbundances
 
 __all__ = [
     "Base",
@@ -20,4 +21,5 @@
     "Units",
     "Constants",
     "AlfvenicTurbulence",
+    "ReferenceAbundances",
 ]

solarwindpy/core/abundances.py

@@ -0,0 +1,103 @@
+__all__ = ["ReferenceAbundances"]
+
+import numpy as np
+import pandas as pd
+from collections import namedtuple
+from pathlib import Path
+
+Abundance = namedtuple("Abundance", "measurement,uncertainty")
+
+
+class ReferenceAbundances:
+    """Elemental abundances from Asplund et al. (2009).
+
+    Provides both photospheric and meteoritic abundances.
+
+    References
+    ----------
+    Asplund, M., Grevesse, N., Sauval, A. J., & Scott, P. (2009).
+    The Chemical Composition of the Sun.
+    Annual Review of Astronomy and Astrophysics, 47(1), 481–522.
+    https://doi.org/10.1146/annurev.astro.46.060407.145222
+    """
+
+    def __init__(self):
+        self.load_data()
+
+    @property
+    def data(self):
+        r"""Elemental abundances in dex scale:
+
+        log ε_X = log(N_X/N_H) + 12
+
+        where N_X is the number density of species X.
+        """
+        return self._data
+
+    def load_data(self):
+        """Load Asplund 2009 data from package CSV."""
+        path = Path(__file__).parent / "data" / "asplund2009.csv"
+        data = pd.read_csv(path, skiprows=4, header=[0, 1], index_col=[0, 1]).astype(
+            np.float64
+        )
+        self._data = data
+
+    def get_element(self, key, kind="Photosphere"):
+        r"""Get measurements for element stored at `key`.
+
+        Parameters
+        ----------
+        key : str or int
+            Element symbol ('Fe') or atomic number (26).
+        kind : str, default "Photosphere"
+            Which abundance source: "Photosphere" or "Meteorites".
+        """
+        if isinstance(key, str):
+            level = "Symbol"
+        elif isinstance(key, int):
+            level = "Z"
+        else:
+            raise ValueError(f"Unrecognized key type ({type(key)})")
+
+        out = self.data.loc[:, kind].xs(key, axis=0, level=level)
+        assert out.shape[0] == 1
+        return out.iloc[0]
+
+    @staticmethod
+    def _convert_from_dex(case):
+        m = case.loc["Ab"]
+        u = case.loc["Uncert"]
+        mm = 10.0 ** (m - 12.0)
+        uu = mm * np.log(10) * u
+        return mm, uu
+
+    def abundance_ratio(self, numerator, denominator):
+        r"""Calculate abundance ratio N_X/N_Y with uncertainty.
+
+        Parameters
+        ----------
+        numerator, denominator : str or int
+            Element symbols ('Fe', 'O') or atomic numbers.
+
+        Returns
+        -------
+        Abundance
+            namedtuple with (measurement, uncertainty).
+        """
+        top = self.get_element(numerator)
+        tu = top.Uncert
+        if np.isnan(tu):
+            tu = 0
+
+        if denominator != "H":
+            bottom = self.get_element(denominator)
+            bu = bottom.Uncert
+            if np.isnan(bu):
+                bu = 0
+
+            rat = 10.0 ** (top.Ab - bottom.Ab)
+            uncert = rat * np.log(10) * np.sqrt((tu**2) + (bu**2))
+        else:
+            rat, uncert = self._convert_from_dex(top)
+
+        return Abundance(rat, uncert)

solarwindpy/core/data/asplund2009.csv

@@ -0,0 +1,90 @@
+Chemical composition of the Sun from Table 1 in [1].
+
+[1] Asplund, M., Grevesse, N., Sauval, A. J., & Scott, P. (2009). The Chemical Composition of the Sun. Annual Review of Astronomy and Astrophysics, 47(1), 481–522. https://doi.org/10.1146/annurev.astro.46.060407.145222
+
+Kind,,Meteorites,Meteorites,Photosphere,Photosphere
+,,Ab,Uncert,Ab,Uncert
+Z,Symbol,,,,
+1,H,8.22 , 0.04,12.00,
+2,He,1.29,,10.93 , 0.01
+3,Li,3.26 , 0.05,1.05 , 0.10
+4,Be,1.30 , 0.03,1.38 , 0.09
+5,B,2.79 , 0.04,2.70 , 0.20
+6,C,7.39 , 0.04,8.43 , 0.05
+7,N,6.26 , 0.06,7.83 , 0.05
+8,O,8.40 , 0.04,8.69 , 0.05
+9,F,4.42 , 0.06,4.56 , 0.30
+10,Ne,-1.12,,7.93 , 0.10
+11,Na,6.27 , 0.02,6.24 , 0.04
+12,Mg,7.53 , 0.01,7.60 , 0.04
+13,Al,6.43 , 0.01,6.45 , 0.03
+14,Si,7.51 , 0.01,7.51 , 0.03
+15,P,5.43 , 0.04,5.41 , 0.03
+16,S,7.15 , 0.02,7.12 , 0.03
+17,Cl,5.23 , 0.06,5.50 , 0.30
+18,Ar,-0.05,,6.40 , 0.13
+19,K,5.08 , 0.02,5.03 , 0.09
+20,Ca,6.29 , 0.02,6.34 , 0.04
+21,Sc,3.05 , 0.02,3.15 , 0.04
+22,Ti,4.91 , 0.03,4.95 , 0.05
+23,V,3.96 , 0.02,3.93 , 0.08
+24,Cr,5.64 , 0.01,5.64 , 0.04
+25,Mn,5.48 , 0.01,5.43 , 0.04
+26,Fe,7.45 , 0.01,7.50 , 0.04
+27,Co,4.87 , 0.01,4.99 , 0.07
+28,Ni,6.20 , 0.01,6.22 , 0.04
+29,Cu,4.25 , 0.04,4.19 , 0.04
+30,Zn,4.63 , 0.04,4.56 , 0.05
+31,Ga,3.08 , 0.02,3.04 , 0.09
+32,Ge,3.58 , 0.04,3.65 , 0.10
+33,As,2.30 , 0.04,,
+34,Se,3.34 , 0.03,,
+35,Br,2.54 , 0.06,,
+36,Kr,-2.27,,3.25 , 0.06
+37,Rb,2.36 , 0.03,2.52 , 0.10
+38,Sr,2.88 , 0.03,2.87 , 0.07
+39,Y,2.17 , 0.04,2.21 , 0.05
+40,Zr,2.53 , 0.04,2.58 , 0.04
+41,Nb,1.41 , 0.04,1.46 , 0.04
+42,Mo,1.94 , 0.04,1.88 , 0.08
+44,Ru,1.76 , 0.03,1.75 , 0.08
+45,Rh,1.06 , 0.04,0.91 , 0.10
+46,Pd,1.65 , 0.02,1.57 , 0.10
+47,Ag,1.20 , 0.02,0.94 , 0.10
+48,Cd,1.71 , 0.03,,
+49,In,0.76 , 0.03,0.80 , 0.20
+50,Sn,2.07 , 0.06,2.04 , 0.10
+51,Sb,1.01 , 0.06,,
+52,Te,2.18 , 0.03,,
+53,I,1.55 , 0.08,,
+54,Xe,-1.95,,2.24 , 0.06
+55,Cs,1.08 , 0.02,,
+56,Ba,2.18 , 0.03,2.18 , 0.09
+57,La,1.17 , 0.02,1.10 , 0.04
+58,Ce,1.58 , 0.02,1.58 , 0.04
+59,Pr,0.76 , 0.03,0.72 , 0.04
+60,Nd,1.45 , 0.02,1.42 , 0.04
+62,Sm,0.94 , 0.02,0.96 , 0.04
+63,Eu,0.51 , 0.02,0.52 , 0.04
+64,Gd,1.05 , 0.02,1.07 , 0.04
+65,Tb,0.32 , 0.03,0.30 , 0.10
+66,Dy,1.13 , 0.02,1.10 , 0.04
+67,Ho,0.47 , 0.03,0.48 , 0.11
+68,Er,0.92 , 0.02,0.92 , 0.05
+69,Tm,0.12 , 0.03,0.10 , 0.04
+70,Yb,0.92 , 0.02,0.84 , 0.11
+71,Lu,0.09 , 0.02,0.10 , 0.09
+72,Hf,0.71 , 0.02,0.85 , 0.04
+73,Ta,-0.12 , 0.04,,
+74,W,0.65 , 0.04,0.85 , 0.12
+75,Re,0.26 , 0.04,,
+76,Os,1.35 , 0.03,1.40 , 0.08
+77,Ir,1.32 , 0.02,1.38 , 0.07
+78,Pt,1.62 , 0.03,,
+79,Au,0.80 , 0.04,0.92 , 0.10
+80,Hg,1.17 , 0.08,,
+81,Tl,0.77 , 0.03,0.90 , 0.20
+82,Pb,2.04 , 0.03,1.75 , 0.10
+83,Bi,0.65 , 0.04,,
+90,Th,0.06 , 0.03,0.02 , 0.10
+92,U,-0.54 , 0.03,,