OpenChemistry/avogadrolibs

codespell finds common misspellings in code and comments. It's now part of avogadrolibs' pre-commit checks (#3102), but 31 typos from before it was added are still in the code. They're listed below. This issue fixes them, so that pre-commit run codespell --all-files passes. The configuration in .codespellrc matters. Out of the box, codespell reports about 2,600 "typos" in this repository, and almost all of them are correct: Chemistry and file formats: CONECT (a PDB record), Te and Nd (tellurium and neodymium), SER (serine), $CONTRL (a GAMESS input group), lj/cut/coul (a LAMMPS pair style), &OT (a CP2K section). "Correcting" these would break Avogadro's file readers and the input files it writes. Translations: about 2,500 hits are in i18n/*.po, which are Bosnian, Catalan and other languages, not English typos. Citations and test data: e.g. "An imbedded [sic] family…", "J. Numer. Anal.", "Formate anion". .codespellrc skips or ignores all of these, with a comment explaining each word.

clang-tidy is a C++ linter. avogadrolibs already has a .clang-tidy configuration, but nobody works through its warnings regularly, so a backlog has built up. This issue covers checks whose fixes are mechanical: clang-tidy applies them itself with --fix, and the result means exactly what the old code did. One PR per checkbox, please. Comment below with the box you're taking so two people don't pick the same one. Keep each PR to what clang-tidy produces. The diff should be clang-tidy's own fixes, formatted, and nothing else. A reviewer can then confirm it by re-running the same command. If you need to hand-edit something, say so in the PR and explain why. Please don't touch avogadro/qtplugins/qtaim/ (due for a larger rewrite) or avogadro/qtplugins/surfaces/surfaces.cpp (other changes in progress). Checks Counts are from a scan of the current code. readability-container-size-empty v.size() == 0 → v.empty(), s == "" → s.empty(), and so on. avogadro/core: 22 in 9 files avogadro/io: 2

Clazy is a static analyzer for Qt code. It flags patterns that compile fine but are slow, fragile or quietly wrong. Running it on avogadrolibs turns up a set of small, mechanical fixes, listed below. The biggest group is old-style connections, which name signals and slots as strings: // Old: checked only at run time. A typo or a wrong argument list // prints a warning to the console and the connection never happens. connect(ui.showHydrogens, SIGNAL(toggled(bool)), this, SLOT(updatePreview())); // New: checked by the compiler. connect(ui.showHydrogens, &QCheckBox::toggled, this, &MyDialog::updatePreview); This isn't only cosmetic. Two string connections in avogadrolibs had been silently doing nothing, one of them since 2017. Converting the rest lets the compiler catch any others. One PR per checkbox, please. Comment below with the box you're taking so two people don't pick the same one. Please don't touch avogadro/qtplugins/qtaim/; it's due for a larger rewrite. Part 1: new-style signa

Avogadro fuzzes its file readers nightly with libFuzzer under AddressSanitizer and UndefinedBehaviorSanitizer: random variations of real files are fed to each parser to find crashes, hangs and memory errors. Several readers aren't fuzzed yet, even though sample files for them are already in avogadrodata. Adding a target needs no C++, only two CMake and workflow lists. One PR per format, please. Comment below with the format you're taking so two people don't pick the same one. Every format in a section needs the same edits. Formats avogadrolibs/tests/io gro (GROMACS): table entry gro, 15 seeds in data/gro/ mol (MDL Molfile): table entry mol=sdf. data/sdf/ holds the three .mol files. This shares a parser with the existing sdf target, so it mainly adds the single-molecule path. dcd (CHARMM/NAMD trajectory, binary): table entry dcd, 1 seed in data/dcd/. Talk to a maintainer first: the DCD header reader has known unaligned reads, so UBSan will likely fail this target straight away. It m

Avogadro can be driven over JSON-RPC (see https://avogadro.cc/source/develop/rpc.md). Plugins opt in by registering command names and answering them in handleCommand(). Today only 8 of 79 plugins do: bonding, crystal, spacegroup, resetview, navigator, surfaces, vibrations (extensions) and aligntool (tool). This is a list of simple 'wiring' tasks to add commands to different C++ classes The recipe avogadro/qtplugins/bonding/bonding.cpp is the reference implementation. Read it first; every Tier 1 item below is the same three edits. 1. Header (myplugin.h) — add the two overrides: bool handleCommand(const QString& command, const QVariantMap& options) override; void registerCommands() override; 2. Register (myplugin.cpp) — one line per command, description translated: void MyPlugin::registerCommands() { emit registerCommand("addHydrogens", tr("Add hydrogens to the molecule.")); } 3. Dispatch — guard on the molecule, then call the existing slot: bool MyPlugi