From cde8a76f23a828eca6b9254c782ed7d31d6f0411 Mon Sep 17 00:00:00 2001 From: "Haoyu (Daniel) YANG" Date: Sun, 15 Sep 2024 21:38:30 +0800 Subject: [PATCH 1/4] Remove reverse readline, test again NP1 and recover NumPy 1 dependency support (#203) * test monty fix for reverse readline * ensure pip env consistency * remove reverse readline * remove monty pin * test NP1 * use readlines * revert numpy version pin to > 1.26 to support NP1 --- .github/workflows/test.yml | 3 --- chgnet/utils/vasp_utils.py | 42 +++++++++++++++++--------------------- pyproject.toml | 4 +--- 3 files changed, 20 insertions(+), 29 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 70dc8cc7..95b4a9a7 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -34,9 +34,6 @@ jobs: pip install uv uv pip install -e .[test,logging] --resolution=${{ matrix.version.resolution }} --system - # TODO: remove pin once reverse readline fixed - uv pip install monty==2024.7.12 --system - - name: Run Tests run: pytest --capture=no --cov --cov-report=xml env: diff --git a/chgnet/utils/vasp_utils.py b/chgnet/utils/vasp_utils.py index 96943d3c..82ee659c 100644 --- a/chgnet/utils/vasp_utils.py +++ b/chgnet/utils/vasp_utils.py @@ -5,7 +5,7 @@ import warnings from typing import TYPE_CHECKING -from monty.io import reverse_readfile +from monty.io import zopen from monty.os.path import zpath from pymatgen.io.vasp.outputs import Oszicar, Vasprun @@ -58,13 +58,11 @@ def parse_vasp_dir( exception_on_bad_xml=False, ) - charge, mag_x, mag_y, mag_z, header, all_lines = [], [], [], [], [], [] + charge, mag_x, mag_y, mag_z, header = [], [], [], [], [] - for line in reverse_readfile(outcar_path): - clean = line.strip() - all_lines.append(clean) + with zopen(outcar_path, encoding="utf-8") as file: + all_lines = [line.strip() for line in file.readlines()] - all_lines.reverse() # For single atom systems, VASP doesn't print a total line, so # reverse parsing is very difficult # for SOC calculations only @@ -79,23 +77,21 @@ def parse_vasp_dir( if clean.startswith("# of ion"): header = re.split(r"\s{2,}", clean.strip()) header.pop(0) - else: - m = re.match(r"\s*(\d+)\s+(([\d\.\-]+)\s+)+", clean) - if m: - tokens = [float(token) for token in re.findall(r"[\d\.\-]+", clean)] - tokens.pop(0) - if read_charge: - charge.append(dict(zip(header, tokens))) - elif read_mag_x: - mag_x.append(dict(zip(header, tokens))) - elif read_mag_y: - mag_y.append(dict(zip(header, tokens))) - elif read_mag_z: - mag_z.append(dict(zip(header, tokens))) - elif clean.startswith("tot"): - if ion_step_count == (len(mag_x_all) + 1): - mag_x_all.append(mag_x) - read_charge = read_mag_x = read_mag_y = read_mag_z = False + elif re.match(r"\s*(\d+)\s+(([\d\.\-]+)\s+)+", clean): + tokens = [float(token) for token in re.findall(r"[\d\.\-]+", clean)] + tokens.pop(0) + if read_charge: + charge.append(dict(zip(header, tokens))) + elif read_mag_x: + mag_x.append(dict(zip(header, tokens))) + elif read_mag_y: + mag_y.append(dict(zip(header, tokens))) + elif read_mag_z: + mag_z.append(dict(zip(header, tokens))) + elif clean.startswith("tot"): + if ion_step_count == (len(mag_x_all) + 1): + mag_x_all.append(mag_x) + read_charge = read_mag_x = read_mag_y = read_mag_z = False if clean == "total charge": read_charge = True read_mag_x = read_mag_y = read_mag_z = False diff --git a/pyproject.toml b/pyproject.toml index ce44d983..ae3a444c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,9 +9,7 @@ license = { text = "Modified BSD" } dependencies = [ "ase>=3.23.0", "cython>=3", - # "monty==2024.7.12", # TODO: restore once readline fixed - # "numpy>=1.26", # TODO: remove after test - "numpy>=2.0.0", + "numpy>=1.26", "nvidia-ml-py3>=7.352.0", "pymatgen>=2024.9.10", "torch>=2.4.1", From bf87bf2e741e867a674f34778a1e4763bcbef99b Mon Sep 17 00:00:00 2001 From: Janosh Riebesell Date: Sun, 15 Sep 2024 20:51:46 -0400 Subject: [PATCH 2/4] Drop Python 3.9 support (#204) * bump min supported python to 3.10 following numpy and pymatgen https://github.com/numpy/numpy/pull/26222 https://github.com/materialsproject/pymatgen/pull/4009 * pass strict=True to zip() added in python 3.10 safer, since it errors if iterables have different lengths * fix UP038 Use `X | Y` in `isinstance` call instead of `(X, Y)` --- .github/workflows/release.yml | 2 +- .pre-commit-config.yaml | 2 +- README.md | 2 +- chgnet/graph/converter.py | 4 +++- chgnet/graph/graph.py | 2 +- chgnet/model/composition_model.py | 2 +- chgnet/model/dynamics.py | 2 +- chgnet/model/functions.py | 3 ++- chgnet/model/model.py | 16 ++++++++++++---- chgnet/trainer/trainer.py | 2 +- chgnet/utils/vasp_utils.py | 8 ++++---- examples/crystaltoolkit_relax_viewer.ipynb | 4 ++-- pyproject.toml | 6 +++--- 13 files changed, 33 insertions(+), 22 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index fb6e5602..7178ce2a 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -44,7 +44,7 @@ jobs: strategy: matrix: os: [ubuntu-latest, macos-14, windows-latest] - python-version: ["39", "310", "311", "312"] + python-version: ["310", "311", "312"] runs-on: ${{ matrix.os }} steps: - name: Check out repo diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index ed544705..a0de1493 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -4,7 +4,7 @@ default_install_hook_types: [pre-commit, commit-msg] repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.6.4 + rev: v0.6.5 hooks: - id: ruff args: [--fix] diff --git a/README.md b/README.md index 1773c1ed..72b41be7 100755 --- a/README.md +++ b/README.md @@ -8,7 +8,7 @@ ![GitHub repo size](https://img.shields.io/github/repo-size/CederGroupHub/chgnet?logo=github&logoColor=white&label=Repo%20Size) [![PyPI](https://img.shields.io/pypi/v/chgnet?logo=pypi&logoColor=white)](https://pypi.org/project/chgnet?logo=pypi&logoColor=white) [![Docs](https://img.shields.io/badge/API-Docs-blue?logo=readthedocs&logoColor=white)](https://chgnet.lbl.gov) -[![Requires Python 3.9+](https://img.shields.io/badge/Python-3.9+-blue.svg?logo=python&logoColor=white)](https://python.org/downloads) +[![Requires Python 3.10+](https://img.shields.io/badge/Python-3.10+-blue.svg?logo=python&logoColor=white)](https://python.org/downloads) diff --git a/chgnet/graph/converter.py b/chgnet/graph/converter.py index 3fb98f15..89276a98 100644 --- a/chgnet/graph/converter.py +++ b/chgnet/graph/converter.py @@ -215,7 +215,9 @@ def _create_graph_legacy( Graph data structure used to create Crystal_Graph object """ graph = Graph([Node(index=idx) for idx in range(n_atoms)]) - for ii, jj, img, dist in zip(center_index, neighbor_index, image, distance): + for ii, jj, img, dist in zip( + center_index, neighbor_index, image, distance, strict=True + ): graph.add_edge(center_index=ii, neighbor_index=jj, image=img, distance=dist) return graph diff --git a/chgnet/graph/graph.py b/chgnet/graph/graph.py index 7e373f2c..084dfbb6 100644 --- a/chgnet/graph/graph.py +++ b/chgnet/graph/graph.py @@ -309,7 +309,7 @@ def line_graph_adjacency_list(self, cutoff) -> tuple[list[list[int]], list[int]] # We will need to find directed edges with center = center1 # and create angles with DE1, then do the same for center2 and DE2 for center, dir_edge in zip( - u_edge.nodes, u_edge.info["directed_edge_index"] + u_edge.nodes, u_edge.info["directed_edge_index"], strict=True ): for directed_edges in self.nodes[center].neighbors.values(): for directed_edge in directed_edges: diff --git a/chgnet/model/composition_model.py b/chgnet/model/composition_model.py index 71f02764..b87ce668 100644 --- a/chgnet/model/composition_model.py +++ b/chgnet/model/composition_model.py @@ -141,7 +141,7 @@ def fit( composition_feas = torch.zeros([num_data, self.max_num_elements]) e = torch.zeros([num_data]) for index, (structure, energy) in enumerate( - zip(structures_or_graphs, energies) + zip(structures_or_graphs, energies, strict=True) ): if isinstance(structure, Structure): atomic_number = torch.tensor( diff --git a/chgnet/model/dynamics.py b/chgnet/model/dynamics.py index c1a8601f..92b7d605 100644 --- a/chgnet/model/dynamics.py +++ b/chgnet/model/dynamics.py @@ -499,7 +499,7 @@ def __init__( """ self.ensemble = ensemble self.thermostat = thermostat - if isinstance(atoms, (Structure, Molecule)): + if isinstance(atoms, Structure | Molecule): atoms = AseAtomsAdaptor().get_atoms(atoms) # atoms = atoms.to_ase_atoms() diff --git a/chgnet/model/functions.py b/chgnet/model/functions.py index 2eddd1ce..a52da2ad 100644 --- a/chgnet/model/functions.py +++ b/chgnet/model/functions.py @@ -1,5 +1,6 @@ from __future__ import annotations +import itertools from collections.abc import Sequence import torch @@ -83,7 +84,7 @@ def __init__( find_activation(activation), ] if len(hidden_dim) != 1: - for h_in, h_out in zip(hidden_dim[0:-1], hidden_dim[1:]): + for h_in, h_out in itertools.pairwise(hidden_dim): layers.append(nn.Linear(h_in, h_out, bias=bias)) layers.append(find_activation(activation)) layers.append(nn.Dropout(dropout)) diff --git a/chgnet/model/model.py b/chgnet/model/model.py index abca5b21..d42c61c9 100644 --- a/chgnet/model/model.py +++ b/chgnet/model/model.py @@ -379,7 +379,10 @@ def forward( if return_site_energies and self.composition_model is not None: site_energy_shifts = self.composition_model.get_site_energies(graphs) prediction["site_energies"] = [ - i + j for i, j in zip(prediction["site_energies"], site_energy_shifts) + i + j + for i, j in zip( + prediction["site_energies"], site_energy_shifts, strict=True + ) ] return prediction @@ -437,7 +440,12 @@ def _compute( # Message Passing for idx, (atom_layer, bond_layer, angle_layer) in enumerate( - zip(self.atom_conv_layers[:-1], self.bond_conv_layers, self.angle_layers) + zip( + self.atom_conv_layers[:-1], + self.bond_conv_layers, + self.angle_layers, + strict=False, + ) ): # Atom Conv atom_feas = atom_layer( @@ -522,7 +530,7 @@ def _compute( ) # Convert Stress unit from eV/A^3 to GPa scale = 1 / g.volumes * 160.21766208 - stress = [i * j for i, j in zip(stress, scale)] + stress = [i * j for i, j in zip(stress, scale, strict=False)] prediction["s"] = stress # Normalize energy if model is intensive @@ -614,7 +622,7 @@ def predict_graph( m (Tensor) : magnetic moments of sites [num_atoms, 3] in Bohr magneton mu_B """ - if not isinstance(graph, (CrystalGraph, Sequence)): + if not isinstance(graph, CrystalGraph | Sequence): raise TypeError( f"{type(graph)=} must be CrystalGraph or list of CrystalGraphs" ) diff --git a/chgnet/trainer/trainer.py b/chgnet/trainer/trainer.py index 60543ab6..67db99e8 100644 --- a/chgnet/trainer/trainer.py +++ b/chgnet/trainer/trainer.py @@ -830,7 +830,7 @@ def forward( if "m" in self.target_str: mag_preds, mag_targets = [], [] m_mae_size = 0 - for mag_pred, mag_target in zip(prediction["m"], targets["m"]): + for mag_pred, mag_target in zip(prediction["m"], targets["m"], strict=True): # exclude structures without magmom labels if mag_target is not None: mag_preds.append(mag_pred) diff --git a/chgnet/utils/vasp_utils.py b/chgnet/utils/vasp_utils.py index 82ee659c..d17d8a75 100644 --- a/chgnet/utils/vasp_utils.py +++ b/chgnet/utils/vasp_utils.py @@ -81,13 +81,13 @@ def parse_vasp_dir( tokens = [float(token) for token in re.findall(r"[\d\.\-]+", clean)] tokens.pop(0) if read_charge: - charge.append(dict(zip(header, tokens))) + charge.append(dict(zip(header, tokens, strict=True))) elif read_mag_x: - mag_x.append(dict(zip(header, tokens))) + mag_x.append(dict(zip(header, tokens, strict=True))) elif read_mag_y: - mag_y.append(dict(zip(header, tokens))) + mag_y.append(dict(zip(header, tokens, strict=True))) elif read_mag_z: - mag_z.append(dict(zip(header, tokens))) + mag_z.append(dict(zip(header, tokens, strict=True))) elif clean.startswith("tot"): if ion_step_count == (len(mag_x_all) + 1): mag_x_all.append(mag_x) diff --git a/examples/crystaltoolkit_relax_viewer.ipynb b/examples/crystaltoolkit_relax_viewer.ipynb index 60b218ab..363930f5 100644 --- a/examples/crystaltoolkit_relax_viewer.ipynb +++ b/examples/crystaltoolkit_relax_viewer.ipynb @@ -377,7 +377,7 @@ " coords = trajectory.atom_positions[step]\n", " structure.lattice = lattice # update structure in place for efficiency\n", " assert len(structure) == len(coords)\n", - " for site, coord in zip(structure, coords):\n", + " for site, coord in zip(structure, coords, strict=True):\n", " site.coords = coord\n", "\n", " title = make_title(*structure.get_space_group_info())\n", @@ -406,7 +406,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.6" + "version": "3.11.9" } }, "nbformat": 4, diff --git a/pyproject.toml b/pyproject.toml index ae3a444c..a8b66136 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,7 +3,7 @@ name = "chgnet" version = "0.3.8" description = "Pretrained Universal Neural Network Potential for Charge-informed Atomistic Modeling" authors = [{ name = "Bowen Deng", email = "bowendeng@berkeley.edu" }] -requires-python = ">=3.9" +requires-python = ">=3.10" readme = "README.md" license = { text = "Modified BSD" } dependencies = [ @@ -19,7 +19,6 @@ classifiers = [ "Intended Audience :: Science/Research", "License :: OSI Approved :: BSD License", "Operating System :: OS Independent", - "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", @@ -53,7 +52,8 @@ requires = ["Cython", "numpy>=2.0.0", "setuptools>=65", "wheel"] build-backend = "setuptools.build_meta" [tool.ruff] -target-version = "py39" +target-version = "py310" +output-format = "concise" [tool.ruff.lint] select = ["ALL"] From 4b0c56616034bf5e05aad8b917580a402b66122d Mon Sep 17 00:00:00 2001 From: Janosh Riebesell Date: Sun, 15 Sep 2024 21:30:43 -0400 Subject: [PATCH 3/4] v0.4.0 --- .github/release.yml | 4 ++++ pyproject.toml | 2 +- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/release.yml b/.github/release.yml index 4e8b9054..34cd0cd3 100644 --- a/.github/release.yml +++ b/.github/release.yml @@ -18,6 +18,10 @@ changelog: labels: [refactor] - title: ๐Ÿงช Tests labels: [tests] + - title: ๐Ÿงน Linting + labels: [linting] + - title: ๐Ÿท๏ธ Static Typing + labels: [types] # as in static typing - title: ๐Ÿ’ฅ Breaking Changes labels: [breaking] - title: ๐Ÿ”’ Security Fixes diff --git a/pyproject.toml b/pyproject.toml index a8b66136..74d154a6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [project] name = "chgnet" -version = "0.3.8" +version = "0.4.0" description = "Pretrained Universal Neural Network Potential for Charge-informed Atomistic Modeling" authors = [{ name = "Bowen Deng", email = "bowendeng@berkeley.edu" }] requires-python = ">=3.10" From d3e01606f2b09ad7014af39b6eb13b82413a92c3 Mon Sep 17 00:00:00 2001 From: Miles Date: Wed, 16 Oct 2024 06:11:18 -0400 Subject: [PATCH 4/4] Fix `pip install` command in `fine_tuning.ipynb` (#208) * Update fine_tuning.ipynb * fix wrong Returns: section in EquationOfState.fit doc str * change EquationOfState.get_bulk_modulus exception type on bad unit to ValueError --------- Co-authored-by: Janosh Riebesell --- .pre-commit-config.yaml | 6 +++--- chgnet/graph/converter.py | 6 +----- chgnet/model/dynamics.py | 12 ++++++------ examples/fine_tuning.ipynb | 2 +- 4 files changed, 11 insertions(+), 15 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index a0de1493..5f0a13d2 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -4,7 +4,7 @@ default_install_hook_types: [pre-commit, commit-msg] repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.6.5 + rev: v0.6.9 hooks: - id: ruff args: [--fix] @@ -13,7 +13,7 @@ repos: types_or: [python, jupyter] - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.6.0 + rev: v5.0.0 hooks: - id: check-case-conflict - id: check-symlinks @@ -48,7 +48,7 @@ repos: - svelte - repo: https://github.com/pre-commit/mirrors-eslint - rev: v9.10.0 + rev: v9.12.0 hooks: - id: eslint types: [file] diff --git a/chgnet/graph/converter.py b/chgnet/graph/converter.py index 89276a98..9c1ac3bf 100644 --- a/chgnet/graph/converter.py +++ b/chgnet/graph/converter.py @@ -273,11 +273,7 @@ def set_isolated_atom_response( """Set the graph converter's response to isolated atom graph Args: on_isolated_atoms ('ignore' | 'warn' | 'error'): how to handle Structures - with isolated atoms. - Default = 'error'. - - Returns: - None + with isolated atoms. Default = 'error'. """ self.on_isolated_atoms = on_isolated_atoms diff --git a/chgnet/model/dynamics.py b/chgnet/model/dynamics.py index 92b7d605..dd63b26d 100644 --- a/chgnet/model/dynamics.py +++ b/chgnet/model/dynamics.py @@ -814,9 +814,6 @@ def fit( verbose (bool): Whether to print the output of the ASE optimizer. Default = False **kwargs: Additional parameters for the optimizer. - - Returns: - Bulk Modulus (float) """ if isinstance(atoms, Atoms): atoms = AseAtomsAdaptor.get_structure(atoms) @@ -848,7 +845,7 @@ def fit( self.bm.fit() self.fitted = True - def get_bulk_modulus(self, unit: str = "eV/A^3") -> float: + def get_bulk_modulus(self, unit: Literal["eV/A^3", "GPa"] = "eV/A^3") -> float: """Get the bulk modulus of from the fitted Birch-Murnaghan equation of state. Args: @@ -856,7 +853,10 @@ def get_bulk_modulus(self, unit: str = "eV/A^3") -> float: Default = "eV/A^3" Returns: - Bulk Modulus (float) + float: Bulk Modulus + + Raises: + ValueError: If the equation of state is not fitted. """ if self.fitted is False: raise ValueError( @@ -866,7 +866,7 @@ def get_bulk_modulus(self, unit: str = "eV/A^3") -> float: return self.bm.b0 if unit == "GPa": return self.bm.b0_GPa - raise NotImplementedError("unit has to be eV/A^3 or GPa") + raise ValueError("unit has to be eV/A^3 or GPa") def get_compressibility(self, unit: str = "A^3/eV") -> float: """Get the bulk modulus of from the fitted Birch-Murnaghan equation of state. diff --git a/examples/fine_tuning.ipynb b/examples/fine_tuning.ipynb index ac4df485..718c6bae 100644 --- a/examples/fine_tuning.ipynb +++ b/examples/fine_tuning.ipynb @@ -19,7 +19,7 @@ " from chgnet.model import CHGNet\n", "except ImportError:\n", " # install CHGNet (only needed on Google Colab or if you didn't install CHGNet yet)\n", - " !pip install chgnet." + " !pip install chgnet" ] }, {