From 50cca59bbc75d0eecb53d9dd76fd4c9c32f72d55 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 1 Jun 2026 17:11:50 +0000 Subject: [PATCH 1/2] ci(pre-commit.ci): autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/compilerla/conventional-pre-commit: v4.2.0 → v4.4.0](https://github.com/compilerla/conventional-pre-commit/compare/v4.2.0...v4.4.0) - [github.com/psf/black-pre-commit-mirror: 25.9.0 → 26.5.1](https://github.com/psf/black-pre-commit-mirror/compare/25.9.0...26.5.1) - [github.com/abravalheri/validate-pyproject: v0.24.1 → v0.25](https://github.com/abravalheri/validate-pyproject/compare/v0.24.1...v0.25) --- .pre-commit-config.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 09df4a8..f1bdac5 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -7,7 +7,7 @@ default_install_hook_types: [pre-commit, commit-msg] repos: - repo: https://github.com/compilerla/conventional-pre-commit - rev: v4.2.0 + rev: v4.4.0 hooks: - id: conventional-pre-commit stages: [commit-msg] @@ -23,12 +23,12 @@ repos: - id: check-yaml - repo: https://github.com/psf/black-pre-commit-mirror - rev: 25.9.0 + rev: 26.5.1 hooks: - id: black - repo: https://github.com/abravalheri/validate-pyproject - rev: v0.24.1 + rev: v0.25 hooks: - id: validate-pyproject From 33fae50a71fdf9b0446770dc64ea347030344393 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 1 Jun 2026 17:12:02 +0000 Subject: [PATCH 2/2] style(pre-commit.ci): auto fixes [...] --- setup.py | 6 ++---- src/matchmaps/_compute_mr_diff.py | 2 +- src/matchmaps/_compute_ncs_diff.py | 2 +- src/matchmaps/_compute_realspace_diff.py | 2 +- src/matchmaps/_diagnostic_plots.py | 3 +-- src/matchmaps/_utils.py | 6 ++---- tests/test_validate_inputs.py | 2 +- 7 files changed, 9 insertions(+), 14 deletions(-) diff --git a/setup.py b/setup.py index b407b85..15ad419 100644 --- a/setup.py +++ b/setup.py @@ -1,14 +1,12 @@ import sys -sys.stderr.write( - """ +sys.stderr.write(""" =============================== Unsupported installation method =============================== matchmaps does not support installation with `python setup.py install`. Please use `python -m pip install .` instead. -""" -) +""") sys.exit(1) diff --git a/src/matchmaps/_compute_mr_diff.py b/src/matchmaps/_compute_mr_diff.py index c762283..2c7f132 100644 --- a/src/matchmaps/_compute_mr_diff.py +++ b/src/matchmaps/_compute_mr_diff.py @@ -274,7 +274,7 @@ def main(): if not os.path.exists(args.input_dir): raise ValueError(f"Input directory '{args.input_dir}' does not exist") - (input_dir, output_dir, ligands, mtzoff, mtzon, pdboff) = _validate_inputs( + input_dir, output_dir, ligands, mtzoff, mtzon, pdboff = _validate_inputs( args.input_dir, args.output_dir, args.ligands, diff --git a/src/matchmaps/_compute_ncs_diff.py b/src/matchmaps/_compute_ncs_diff.py index 6b387cf..59fe752 100644 --- a/src/matchmaps/_compute_ncs_diff.py +++ b/src/matchmaps/_compute_ncs_diff.py @@ -174,7 +174,7 @@ def compute_ncs_difference_map( def main(): args = matchmaps_ncs_parser.parse_args() - (input_dir, output_dir, ligands, mtz, pdb) = _validate_inputs( + input_dir, output_dir, ligands, mtz, pdb = _validate_inputs( args.input_dir, args.output_dir, args.ligands, diff --git a/src/matchmaps/_compute_realspace_diff.py b/src/matchmaps/_compute_realspace_diff.py index 757ec5a..33869e6 100755 --- a/src/matchmaps/_compute_realspace_diff.py +++ b/src/matchmaps/_compute_realspace_diff.py @@ -279,7 +279,7 @@ def compute_realspace_difference_map( def main(): args = matchmaps_parser.parse_args() - (input_dir, output_dir, ligands, mtzoff, mtzon, pdboff) = _validate_inputs( + input_dir, output_dir, ligands, mtzoff, mtzon, pdboff = _validate_inputs( args.input_dir, args.output_dir, args.ligands, diff --git a/src/matchmaps/_diagnostic_plots.py b/src/matchmaps/_diagnostic_plots.py index a26ed5b..50c015f 100644 --- a/src/matchmaps/_diagnostic_plots.py +++ b/src/matchmaps/_diagnostic_plots.py @@ -10,7 +10,6 @@ from matchmaps._parsers import matchmaps_diagnose_parser from matchmaps._utils import _validate_inputs, _validate_column_dtypes - # to do list: # [ x ] write function for making plot # [ ] write main function which directs command-line arguments into the plot @@ -132,7 +131,7 @@ def cc_datasets( def main(): args = matchmaps_diagnose_parser.parse_args() - (input_dir, output_dir, _, mtzoff, mtzon) = _validate_inputs( + input_dir, output_dir, _, mtzoff, mtzon = _validate_inputs( args.input_dir, args.output_dir, None, diff --git a/src/matchmaps/_utils.py b/src/matchmaps/_utils.py index 7ea8a8e..93eb5ca 100644 --- a/src/matchmaps/_utils.py +++ b/src/matchmaps/_utils.py @@ -254,14 +254,12 @@ def _handle_special_positions(pdboff, output_dir): ) else: - raise NotImplementedError( - """ + raise NotImplementedError(""" Input model contains a non-water atom on a special position, which is not allowed in rigid-body refinement. You may attempt to exclude this atom via a custom atom selection to the `--rbr-selections` argument, but this feature is not currently tested. Alternatively, you can remove this atom from your structure altogether and try again. -""" - ) +""") # if pdboff.suffix in ('.cif', '.CIF'): # pdboff_nospecialpositions = output_dir / (pdboff.name.lower().removesuffix(".cif") + "_nospecialpositions.pdb") diff --git a/tests/test_validate_inputs.py b/tests/test_validate_inputs.py index b42c767..d9af13e 100644 --- a/tests/test_validate_inputs.py +++ b/tests/test_validate_inputs.py @@ -35,7 +35,7 @@ ), ) def test_validate_inputs(inputs): - (input_dir, output_dir, ligands, mtzoff, mtzon, pdboff) = _validate_inputs(*inputs) + input_dir, output_dir, ligands, mtzoff, mtzon, pdboff = _validate_inputs(*inputs) assert isinstance(input_dir, Path) assert isinstance(output_dir, Path)