Fixed issues with installing environment in higher-level packages

CHANGELOG.md

@@ -4,6 +4,13 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
 
 ## [Unreleased]
+### Removed
+- `geom.is_duplicate_conformer()` and `irmsd` dependency. (Broken `numpy` reference in solved `irmsd` version).
+- `Algorithm.IRMSD` conformer-group identity algorithm.
+
+
+### Fixed
+- Dependencies listed in `pixi.toml` instead of `pyproject.toml`
 
 ## [0.0.22] - 2026-08-28
 ### Added

CONTRIBUTING.md

@@ -67,7 +67,7 @@ Conversions are standalone module-level functions, not methods on the Pydantic m
 
 ### Current module map
 
-- `automol.geom` — the `Geometry` core model (`core.py`), plus `properties.py` (center of mass, distance matrix/keys, adjacency matrix), `transform.py`, `comparison.py` (e.g. `is_duplicate_conformer`, via `irmsd`), and `view.py` (`View`, 3D visualization, py3Dmol-based).
+- `automol.geom` — the `Geometry` core model (`core.py`), plus `properties.py` (center of mass, distance matrix/keys, adjacency matrix), `transform.py`, `comparison.py`, and `view.py` (`View`, 3D visualization, py3Dmol-based).
 - `automol.rd` — RDKit bridge (`rd/mol.py`) for `Geometry` ↔ RDKit mol conversion.
 - `automol.ident` — `Algorithm`/`Identity` for InChI/SMILES generation from a `Geometry`.
 - `automol.utils` — shared low-level helpers: `constants.py`, `types.py`, `exc.py`, `utils/element/`.

docs/source/geometry.md

@@ -108,30 +108,6 @@ subset of atoms by index, leaving the rest untouched:
 geom.transform.translate(water, [1.0, 0.0, 0.0], keys=[0])  # move only atom 0
 ```
 
-## Duplicate conformer detection
-
-`is_duplicate_conformer` checks whether a `Geometry` is geometrically
-identical to any geometry in a list, using
-[irmsd](https://pypi.org/project/irmsd/)'s interatomic RMSD after optimal
-alignment (translation, rotation, and atom matching) — so a rotated or
-translated copy still counts as a match, while a genuinely different
-conformer doesn't:
-
-```python
-rotated_water = geom.transform.rotate(water, Rotation.from_euler("z", 60, degrees=True))
-geom.is_duplicate_conformer(water, [rotated_water])  # True
-
-geom.is_duplicate_conformer(water, [])  # False — nothing to compare against
-```
-
-Candidates with a different atom count are never considered a match.
-`rthr` (default `0.125`, matching irmsd's own default) sets the iRMSD
-threshold, in Angstroms, below which two geometries count as identical —
-lower it for stricter matching:
-
-```python
-geom.is_duplicate_conformer(water, [rotated_water], rthr=1e-6)  # stricter
-```
 
 ## Next steps
 

pixi.toml

@@ -6,8 +6,6 @@ preview = ["pixi-build"]
 [dependencies]
 python = ">=3.12,<3.14"
 automol = { path = "." }
-ipython = ">=9.15.0,<10"
-pynauty = ">=2.8.8.1,<3"
 
 [package]
 name = "automol"
@@ -50,7 +48,6 @@ dev = { features = ["dev", "docs"], solve-group = "default"}
 
 [pypi-dependencies]
 stereomolgraph = ">=0.0.22b0"
-irmsd = "==0.1.1"
 xyzrender = ">=0.3.1, <0.4"
 
 [feature.dev.tasks]

pyproject.toml

@@ -7,15 +7,17 @@ authors = [
 ]
 requires-python = ">= 3.12"
 dependencies = [
+    "ipython>=9.17.1",
     "numpy>=2.0",
     "pint>=0.24",
     "py3dmol>=2.5",
     "pydantic>=2.5",
+    "pynauty>=2.8.8.1",
     "pyparsing>=3.3.2",
     "rdkit>=2025",
     "scipy>=1.13",
     "stereomolgraph>=0.0.22b0",
-    "irmsd>=0.1.1",
+    "xyzrender>=0.3.8",
 ]
 
 [build-system]

src/automol/geom/__init__.py

@@ -16,7 +16,6 @@
     inertia_axes,
     inertia_moments,
     inertia_tensor,
-    is_duplicate_conformer,
     kabsch_align,
     mass_weight_vector,
     normal_mode_projection,
@@ -64,7 +63,6 @@
     "inertia_moments",
     "inertia_tensor",
     "io",
-    "is_duplicate_conformer",
     "kabsch_align",
     "mass_weight_vector",
     "normal_mode_projection",

src/automol/geom/analysis.py

@@ -1,11 +1,9 @@
 """Geometric, structural, and vibrational analysis of a geometry."""
 
-from collections.abc import Sequence
 from itertools import permutations
 from math import factorial
 from typing import TYPE_CHECKING, Literal
 
-import irmsd
 import numpy as np
 import numpy.typing as npt
 from pynauty import Graph, autgrp, canon_label
@@ -746,50 +744,6 @@ def harmonic_zpv(
 
 
 # Comparison
-def is_duplicate_conformer(
-    geo: "Geometry",
-    geos: Sequence["Geometry"],
-    *,
-    rthr: float = RMSD_THRESHOLD,
-) -> list[bool]:
-    """Check whether a geometry is an identical conformer to one in a list.
-
-    Two geometries are considered identical conformers if, after optimal
-    alignment (translation, rotation, and atom matching), their interatomic
-    RMSD is below `rthr`. Candidates with a different atom count are never
-    considered a match.
-
-    Parameters
-    ----------
-    geo
-        Geometry to check.
-    geos
-        Candidate geometries to compare against.
-    rthr
-        iRMSD threshold, in Angstroms, below which two geometries are
-        considered identical conformers.
-
-    Returns
-    -------
-        List the same length as `geos`, with `True` at each position where `geo`
-        matches the corresponding candidate, `False` otherwise.
-    """
-    mol = irmsd.Molecule(symbols=geo.symbols, positions=geo.coordinates)
-
-    matches = []
-    for candidate in geos:
-        if len(candidate.symbols) != len(geo.symbols):
-            matches.append(False)
-            continue
-        candidate_mol = irmsd.Molecule(
-            symbols=candidate.symbols, positions=candidate.coordinates
-        )
-        value, _, _ = irmsd.get_irmsd_molecule(mol, candidate_mol)
-        matches.append(value <= rthr)
-
-    return matches
-
-
 def bond_graph(geo: "Geometry") -> Graph:
     """Build a pynauty graph representing geo's bond connectivity.