Changelog

Changelog

All notable changes to htpolynet will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]

[2.1.0] - 2026-06-01

Added

  • New htpolynet.repair package implementing a postcure topology-repair stage that sits between cure and postcure. Drivers can do bond-breaking, atom deletion, atom transfer between residues, and re-templating — operations the monotonic cure/cap reaction machinery cannot perform. repair/__init__.py dispatches each postcure_repair config entry by its type: field; repair/topology_surgery.py provides the generic edit primitives (delete_bonds with cascading angle/dihedral/14-pair cleanup, set_atom_attributes, reassign_residue, add_bonds_with_template wrapping make_bonds + map_from_templates + an int-dtype rescue for atom-index columns that pandas float-promotes via NaN-tainted concat); repair/cyanate_cap.py carries the first concrete driver. A new reaction_stage.repair enum value lets repair-stage reactions ride the existing symmetry-expansion and parameterization paths so the cure-template lookup at surgery time uses a properly parameterized linked-product Molecule. The runtime gains cfg.postcure_repair, Dirs.systems_repair, and a do_repair() hook wired into do_workflow between cure and postcure, including a steepest-descent + short NVT relaxation pass to absorb LJ clashes from relocated cap atoms.

  • New triazine_to_cyanate_cap repair type: the BADCy-specific driver in repair/cyanate_cap.py. At finite cure conversion, the topological A2+B3 BADCy model in example 6 leaves artifacts that don’t exist in a real undercured thermoset — free BPA-OH groups and bare triazine C-H sites instead of -O-C#N end-groups. Atom-conservation (the count of unreacted bridge-OH atoms equals the count of dangling crosslinker C atoms across the whole system, exactly) lets the driver dismantle every incomplete triazine (k < full_bond_count bonded BPAs) into three independent -C#N fragments via a within-ring C-N matching; the k fragments already bonded to a BPA become BPA-O-C#N caps in place, and the remaining 3 - k are transferred to the nearest unreacted BPA-OH within cap_search_radius (greedy matching with radius expansion + global-nearest fallback). After the surgery the heavy-atom neighbors of each deleted sacrificial H absorb its lost charge via adjust_charges, keeping the system net-neutral for Ewald. Topology-level outcome on the small test: 19 incomplete TAZ → 57 CYN residues + 1 surviving TAZ + exact heavy-atom conservation, with the C-N bond resolving to GAFF c1-n1 (0.115 nm sp triple) and the BPA-O-C bond to os-c1 (0.132 nm aryl-cyanate ether).

  • Example 6 (6-cyanate-ester.yaml) rebuilt around the topological A2+B3 + postcure-repair architecture. The BPA-O-C#N cyanate-ester core is now represented topologically: BPA (90 → 360 at 4x scale, two reactive phenolic O atoms) reacts with bare 1,3,5-triazine TAZ (60 → 240, three reactive ring C-H atoms; ring N atoms additionally atom-mapped to N1/N2/N3 so the repair driver can refer to them by name) in a simple cure-stage aryl-ether substitution — no in-cure ring closure, no bondcycle_collective bypass needed because the triazine ring is pre-formed in the TAZ monomer rather than constructed via 3-way cyclotrimerization during cure. A new auxiliary CYN building block ([CH:1]#[N:2], hydrogen cyanide; not inserted into the box, exists only as a parameterization template) plus a repair-stage cap_with_cyanate reaction supplies the auto-generated BPA~O1-C1~CYN linked-product template the repair driver splices into the system for every cap. A postcure_repair: [{type: triazine_to_cyanate_cap, ...}] block at the end of the YAML drives the conversion. The header comment block explains the topological model, its tradeoff vs. the previous cyclotrimerization model (no cure-kinetics realism, faithful final-network structure), and how the repair stage restores BADCy residual chemistry.

  • New htpolynet/profiling.py module: a RunProfile with a stage-stack context manager (profiling.stage('name')) and a subprocess-attribution path. Every external command routed through external/command.run (and the two raw subprocess.run sites in external/smiles_input) is timed and classified — gmx-mdrun, gmx-grompp, antechamber, parmchk2, tleap, obabel, rdkit, etc. do_workflow wraps each stage (setup, initialization, densification, precure, cure with one nested frame per iter-K, capping, postcure, final) so subprocess time is attributed to whichever stage was active when the call happened. At end-of-run a formatted table is written to the log (one line per logger.info call, no my_logger asterisk padding) and a machine-readable proj-N/profile.json is dumped beside final.top.

  • New CURE.controls.min_bonds_per_iteration knob (default 10). The bond-search loop now grows the radius until at least this many bonds have been found, falling through to whatever count exists at max_search_radius. The effective floor is clamped against bond_target (remaining bonds needed to reach desired_conversion) and bond_limit (the max_conversion_per_iteration cap), so demanding e.g. min_bonds_per_iteration: 50 near end-of-cure never stalls the build. The post-loop “if nbonds > 0 proceed, else search_failed” branch is preserved — accepting fewer bonds than the floor (when max radius is reached) still triggers relax + equilibrate as before. Empirically on the DGEBA/PACM example, min_bonds_per_iteration=10 cuts the cure iteration count from 41 (with =1) to 15; raising further to =20 saves only one more iteration. The default of 10 was picked off that diminishing-returns curve.

  • The “Radius increased to N nm” log line now also reports the cumulative bond count and the iteration’s min-bonds floor as (X/Y eligible bonds so far). Makes it visible at a glance whether the floor or bond_target is the active constraint as the search radius grows.

  • scripts/run_all_examples.sh — runs every depot example sequentially in its own subdirectory under ./examples-runs/. Discovers the example ID list by parsing htpolynet fetch-example --help (with a 0..4 fallback). Idempotent: skips fetch-example if a YAML is already in the per-example directory. Reports per-example exit status and exits non-zero if any example failed. Pass-through after -- is forwarded to htpolynet run.

  • scripts/run_all_examples.sh --force-reparameterize — convenience flag that forwards --force-parameterization --force-checkin to every htpolynet run call. Each example re-runs antechamber/parmchk/tleap on its monomers and overwrites the user cache (~/.htpolynet/molecules/parameterized/). Appropriate rigor when consecutive examples share monomers but differ in reaction sets — sidesteps the cache-poisoning interaction between e.g. example 0 (no reactions) and example 1 (cure reactions on STY).

  • All five bundled examples (0–4) are now self-contained YAMLs using the RDKit atom-mapping path on each constituent, so the user names reactive atoms by chemical identity (e.g. [CH2:1][CH3:2]) instead of by obabel’s output ordering. The legacy .sh and .tgz siblings have been removed; htpolynet fetch-example N now delivers a single .yaml for any N. Example 4 (DFDA/FDE) additionally gets a reactive_atoms entry for O1/O2 that was missing in its prior shell script (the cap reaction references them). htpolynet fetch-example 1 delivers the YAML directly; usage collapses to htpolynet run 1-polystyrene.yaml. The legacy 1-polystyrene.sh and 1-polystyrene.tgz have been removed. fetch-example now prefers .yaml > .sh > .tgz.

  • Final-stage save now emits final.viz.psf (real bond topology, written via parmed from final.top + final.gro) and final.viz.tcl (drops any bond longer than 3 Å from the display) alongside the existing final.gro / final.top / final.tpx / final.grx. Load with vmd final.viz.psf final.gro -e final.viz.tcl to view a crosslinked network without the “long bonds across PBC” artifact. The TCL uses topo getbondlist both / topo setbondlist both $list — the valid topotools 1.x flag values are type, order, both, none; the earlier all returned an empty list silently and reported “PSF appears to carry no bonds”. The TCL also prints the first bond’s measured length so the user can verify VMD loaded coordinates in Å.

  • New CLI subcommand htpolynet make-viz regenerates final.viz.psf + final.viz.tcl from any final.top + final.gro pair without re-running the full workflow. Defaults assume the current directory has final.top and final.gro (i.e. you’ve cd’d into systems/final-results/); override with -top / -gro / -prefix.

  • VMD viz now ships a sidecar <prefix>.viz.macros.tcl of constituent-keyed atomselect macros, sourced automatically from <prefix>.viz.tcl. Two layers: <NAME> selects every atom of every instance of constituent <NAME> (e.g. GMA picks all 75 bis-GMAs in example 2; DHT picks all 50 linear HTPB chains in example 5), and <NAME>_<NNN> picks one specific instance by global molecule index. The macros are built from final.grx’s molecule / molecule_name columns and compress contiguous atom ranges into VMD index A to B tokens (so e.g. example 5’s 11 KB macros file covers 225 instances). Lets a user highlight chemical entities like bis-GMA or HTPB whose internal residue scheme reflects building blocks (BPA+2×HIE, OB+TB×n+TBO×2) rather than the assembled molecule. The residue-level view is untouched — resname TBO etc. still work — the new macros are additive. htpolynet make-viz gains a -grx flag (auto-detected from the -gro stem) so the macros are also generated when invoked standalone.

  • Two follow-ons to the find_template bystander relaxation, both needed so the small-fragment cure idiom works end-to-end:

    • Molecule.idx_mappers previously asserted that the template and instance had the same bystander count on each side, and built atom-pair mappings by flat-concatenating the per-side bystander lists into one zip. With subset-bystander matching the lists can legitimately differ in length, and the flat concatenation misaligns side-A and side-B bystanders across the zip. Pair each region (bonded residues, side-A bystanders, side-B bystanders, oneaways) in its own zip so a length mismatch in one region doesn’t shift the alignment of others, and drop the exact-count assertion.

    • map_from_templates copies the template’s angle / dihedral / pair tables into the system after mapping template atom indices through temp2inst. For cyanate-ester cure, the template’s CY has more atoms than the post-build system’s CY (the cure-reactive C consumes one H during build, so a system CY has one fewer H on that side than the fresh-from-SMILES cure-template CY does); the template’s H atom that doesn’t exist in the system maps to NaN. Filter rows whose mapped atom indices contain any NaN before concatenating into the system topology — those rows are force-field parameters for atoms that don’t exist in the cured system. No effect on chemistries where all template atoms have system counterparts (examples 1-5).

  • find_template now uses subset semantics on bystanders. A parameterization-stage template T matches a system-instance bond B if every (bystander_resname, bystander_atomname) pair declared by T also appears in B; B is allowed to carry additional bystanders that T doesn’t mention. Oneaway context, atom names, residue names, and the intraresidue flag still require exact equality. When multiple templates match, the one with the most bystanders declared wins, so chain-extension templates produced by bondchain_expand_reactions (which carry specific bystanders) still beat the bare dimer template when their additional context is exactly the in-chain instance’s. This unblocks the “small-fragment cure reactant” idiom in cases like cyanate-ester cure, where CY.C1 is intramolecularly bonded to BPA.O1 in every BCY-embedded instance — the bare CY+CY dimer template carries no BPA bystander, but the BPA bystander is structural context, not bond chemistry, and the subset rule lets the small template match anyway. Verified: example 1’s iter-2 chain-context bond still picks the trimer chain-extension template over the bare dimer template via strict-oneaway discrimination; example 6’s iter-1 CY-CY-in-BCY bond now matches the CY+CY cure template via subset-bystander relaxation.

  • Fixed: tleap-input ordering in external/ambertools.py ran check mymol before loadamberparams <frcmod>, so any GAFF-coverage gap that parmchk2 had already patched (e.g. h5-ce-n2 on cyanate-ester C=N–C=N dimer templates) still showed up in tleap’s output as an early Error!. The run-wrapper’s override needle then fired and aborted the parameterization, even though tleap actually completed and the .top/.crd files were valid. Reordered to load the frcmod before the check so the patched parameters are in scope when the molecule is validated. Unblocks new depot example 6 (cyanate-ester thermoset) whose C=N–C=N open-chain cure dimer falls in a GAFF coverage gap that parmchk2 patches by analogy. Other examples are unaffected — for chemistry where parmchk2 emits no patches, the reorder is a no-op.

  • Fixed: cached monomer .grx files in ~/.htpolynet/molecules/parameterized/ carry reactivity-related attributes (z, sea_idx, bondchain, bondchain_idx) that are YAML-dependent — they reflect the reactions defined for the run that wrote the cache, not anything intrinsic to the monomer. Running example 0 (liquid styrene, no reactions) wrote STY.grx with all-zero z; running example 1 (polystyrene) afterward then loaded that cache and produced 0 candidate atoms in the cure bond search, silently stalling at “Radius increased to N nm (0/10 eligible bonds so far)” all the way out to the max radius. Fix: in the cache-hit branch of _generate_molecule, for monomers (no generator), re-run initialize_monomer_grx_attributes() against the current run’s zrecs so z/sea_idx/bondchain are derived from this YAML rather than inherited from a stale cache. The cache itself can still be written with run-specific z values; only the load-time interpretation is hardened.

  • Fixed: corollary of the monomer-cache-poisoning fix. When STY was first poisoned with z=0 by example 0, the subsequent example-1 run generated and cached the cure-stage dimer (STY~C1-C2~STY.grx) and the cap (STYCC.grx) with empty bondchain data — the dimer’s chain_manager.injest_bond no-ops when neither atom is in a chain, which is exactly what happens when the upstream monomer’s chain_manager was empty at the time. On the next example-1 run, the cached dimer loaded with 0 chains, bondchain_expand_reactions found no 4-atom chains to extend, and zero chain-context templates were generated — so CURE iteration 1 worked (only the dimer template was needed) but iteration 2 raised “you have a bond for which I cannot find a template” because the C1-C2 bond now had a oneaway STY chain partner that no available template captured. Fix: after loading a build product from cache, compare the total chain-atom count carried by the cached chain_manager against the sum across the product’s reactants’ chain_managers; if the cache carries fewer atoms (either zero chains, or a partial chain — e.g. example 2’s hetero-dimer STY~C1-C2~HIE came out length-3 instead of length-4), treat as stale, reset the molecule’s TopoCoord/chain_manager/bond_templates/reaction_bonds/sequence to a blank state, re-parameterize via the normal generate() path, and overwrite the cache. The state reset is needed because the cache-load steps populate TopoCoord (which generate() will then re-merge reactants into) and the half-loaded state ends up float-promoting the globalIdx column on the merged dataframe, crashing the prebonding-mol2 writer. Verified on examples 1 and 2: regenerates the affected dimers, after which bondchain_expand_reactions produces the expected chain-extension templates (3 for example 1, 32 for example 2 — up from 12 before).

  • New depot example 6-cyanate-ester.yaml: bisphenol-A dicyanate ester (BADCy) thermoset. The BCY constituent is assembled at param-stage from a BPA bisphenol-A core plus two single-carbon CY cyanate end-groups (formaldimine, [CH2:1]=[NH:2] — drawn in the sp2 imino-formate active form so the cure-stage triazine-forming C-N bonds have one sacrificial H pre-allocated on each side). Mirrors example 2’s GMA = BPA + 2 HIE build pattern. The cure stage forms C-N bonds between cyanate end-groups on different BCYs via a single cyclize reaction; three such bonds among three monomers close into the 1,3,5-triazine ring (the characteristic crosslink of a cured cyanate ester). The bondcycle_collective ring-suppression check is C-C-specific via the ChainManager, so the heteroatom triazine ring is allowed to close unhindered. Available as htpolynet fetch-example 6. Note: pair with --force-parameterization --force-checkin when extending the YAML to cover atoms not previously named in any reaction (e.g. CY’s N1) — cached build products inherit zrecs-derived z values from the prior YAML’s reactions and won’t pick up newly-added reactivity otherwise.

  • write_top now casts known-int columns (atom indices, function codes, dihedral periodicities, nrexcl, etc.) to pandas’ nullable Int64 before serialization, so they emit as e.g. 2 rather than 2.0. The float form had been silently accepted by gmx grompp but rejected by parmed’s gromacs top reader, which broke the new .viz.psf generation.

  • gmx --version output is now parsed for GPU support: (CUDA, OpenCL, SYCL, disabled) and shown alongside the version line in the startup banner.

  • Consistency check: if the YAML config sets mdrun_options.gpu_id but the installed gmx was built without GPU support, or no GPU devices are visible on the host, the option is dropped and a warning is logged. This prevents the runtime crash that gmx mdrun -gpu_id 0 produces when zero devices are detected.

  • Cache hits during parameterization are now logged at INFO (“Using cached parameterization for <name>”) instead of DEBUG, plus a post-loop summary line tallying reused vs freshly-parameterized molecules and a reminder of the --force-parameterization --force-checkin flags to invalidate stale entries. Pairs with the new “Parameterization caching” section in the user-guide.

  • The -restart flag now emits a prominent runtime warning that resumption is experimental and known to fail at the first cure-stage topology update; the argparse help string is annotated likewise, and docs/source/user-guide/usage.rst carries an expanded warning explaining the root cause (in-memory cure state is not fully reconstructible from cure_state.yaml + on-disk topology files). Pre-cure stages still resume correctly; this section is parked pending a redesign of cure-state persistence.

  • Fixed: htpolynet run -restart failed in CureState.from_yaml with a ConstructorError for the !!python/object: tag, because curecontroller’s loader was yaml.FullLoader (which recent PyYAML tightened to reject Python object tags) while the matching yaml.dump(self) writes those tags. Switched to yaml.Loader to match what checkpoint.py already uses.

  • Fixed: rebuild self.chain_manager from the reloaded coordinates on restart. do_initialization is correctly skipped by the checkpoint decorator on resume, but it’s also where chain_manager was being constructed, so subsequent stages (do_cure) hit AttributeError. do_workflow now reconstructs it from the loaded TopoCoord whenever a checkpoint payload is present.

  • Fixed: htpolynet run -restart could die with shutil.SameFileError when the userlibrary search fell through to projPath and the cwd already lived inside it (so the source file IS the destination). projectfilesystem.py now uses a _safe_copyfile helper that no-ops when src and dst resolve to the same path.

  • Fixed: example 2 HIE constituent’s SMILES used [C:1] (zero implicit H by SMILES bracket-atom rules) instead of [CH:1], so the α-carbon was emitted at valence 3, antechamber typed it c2, and tleap failed with “no angle parameter for o - c2 - os”. Documented the bracket-atom H-count gotcha in docs/source/user-guide/molecular-structure-inputs.rst.

  • Fixed: the RDKit SMILES path now goes through an SDF (molfile) intermediate to obabel rather than PDB. PDB does not carry bond orders, so obabel had to re-infer them and frequently mis-assigned a carbonyl carbon as the alkene sp2 type (C.2 from a C-O single bond rather than C.2+O.2 double-bond pair), which propagated to GAFF as c2 instead of c and broke tleap with “no angle parameter for o - c2 - os” on monomers with ester groups (e.g. HIE in example 2). SDF preserves bond orders, so obabel emits the right sybyl types and antechamber assigns the correct GAFF types.

  • Fixed: SMILES-generated mol2 files were being written to projPath/lib/molecules/inputs/<NAME>.mol2 because Runtime.__init__ runs after pfs._setup_project_dir has chdir’d into the project directory. pfs.checkout() looks in the user library (rootPath/lib/...), so the files were unfindable and molecule generation fell through to a BPA.pdb/STY.pdb assertion. materialize_smiles_inputs is now invoked with an absolute inputs_dir rooted at the user library, and htpolynet run pre-creates lib/molecules/{inputs,parameterized}/ at startup so the library is wired up even when the user’s working directory had no lib/.

  • Constituents in the YAML config may now carry a smiles: key. When present, htpolynet generates lib/molecules/inputs/<NAME>.mol2 itself before parameterization, eliminating the obabel/sed boilerplate that example shell scripts have historically duplicated. Reactive atom names are set via either rename_atoms: {<1-based-index>: <name>} (obabel path, always available) or reactive_atoms: {<smiles-map-num>: <name>} (RDKit path, used when the SMILES contains [*:N] atom-mapping tokens and RDKit is importable). RDKit is an optional extra: pip install 'htpolynet[smiles]'; the container ships it by default.

  • New docker-entrypoint.sh that auto-detects the host owner of the /work bind mount and drops privileges via gosu before invoking htpolynet. Users no longer need to set --user, HOST_UID/HOST_GID, or any other env vars — output files are written with host ownership automatically. The script also writes an /etc/passwd entry for the runtime uid so gosu resolves HOME to /home/htpolynet rather than falling back to /.

  • Entrypoint dispatches by inspecting the first argument: if it resolves to an executable on PATH (bash, python, obabel, …) it is exec’d directly; otherwise it is treated as an htpolynet subcommand. This makes it possible to run docker compose run --rm htpolynet bash 1-polystyrene.sh --run (i.e. drive the example shell scripts that themselves call obabel/htpolynet).

Changed

  • Docker-related files moved from the repo root into a new docker/ subdirectory: docker/Dockerfile, docker/compose.yml, docker/docker-entrypoint.sh. The GH Actions build workflow and the docs curl -O URL are updated to match.

  • Dockerfile installs gosu and uses the new entrypoint script.

  • compose.yml simplified: no user: field; no HOST_UID/HOST_GID substitution. The entrypoint handles uid mapping at runtime.

  • compose.yml bind mount uses ${PWD}:/work:Z so SELinux-enforcing hosts (Fedora, RHEL, openSUSE Tumbleweed, …) relabel the host directory to container_file_t; without this the container is denied writes regardless of POSIX permissions. Harmless on non-SELinux systems.

  • compose.yml sets MPLCONFIGDIR=/tmp/matplotlib in the environment to silence matplotlib’s “not a writable directory” warning.

Fixed

  • _do_pap previously applied the _nonempty_directives guard only to the anneal branch; preequil and postequil ran whenever the section was truthy. That broke for any YAML that defined precure: preequilibration: ... without an explicit precure: postequilibration — _apply_runtime_defaults injects the runtime-default postequilibration block (ps: 0, i.e. “no postequilibration”), TC.equilibrate returns None for ps: 0, and the trailing trace('Density', edr_list, ...) crashes with 'NoneType' object is not iterable. Same guard now wraps all three branches, mirroring the existing anneal pattern, with a comment explaining why the postcure-default ps=0 default behaves as it does.

  • Example 6 (postcure anneal) first cycle segment changed from ps: 20 to ps: 0, matching example 3’s pattern. The earlier value pushed annealing_time[0] to 20 ps while init_t was 0, tripping gmx grompp’s “First time point for annealing > init_t” fatal error at the postcure stage; the leading ps=0 segment exists purely to anchor the annealing protocol at simulation time 0.

  • Topology.rep_ex was shifting the per-copy resnr by c (the copy index) instead of c * residues_per_copy, so when a multi-residue molecule (e.g. the assembled HTPB chains DHT/THT in example 5, ~41 residues each) was replicated N times, the resid ranges of successive copies overlapped almost completely. Single-residue monomers like IPD happened to work because c * 1 == c, which is why no prior example hit this. The collision surfaced downstream in Molecule.idx_mappers (CURE iter-1 topology update): the resid-keyed filter pulled atoms from several distinct instances at once, the atomName merge fanned out, and the same template atom got mapped to multiple instance atoms, tripping the “temp_idx N already claimed” sanity check. Fix: capture resnr_per_copy = max(resnr) before the concat and use it as the shift unit. Existing init.gro/init.top files with corrupted resids must be regenerated (delete proj-* and re-run do_initialization).

  • TopoCoord.bondcycle_collective crashed with AttributeError: 'NoneType' object has no attribute 'added_bonds' when a cure bond’s endpoints weren’t part of any vinyl C-C bondchain (e.g. the urethane O-C linkages between TBO oxygen and IPDI formyl carbon in example 5). The chain-manager’s injest_bond is a no-op when both atoms are outside the chain graph (and create_if_missing=False), so the subsequent chain_of(r.ai) returns None. Such bonds can’t form a C-C bondcycle by chemistry — guard the loop and skip them.

  • Molecule.generate_conformers now reuses existing conformer .gro files instead of regenerating them on every invocation. The check is on file presence in the cwd (molecules/parameterized/), so it kicks in equivalently on -restart and on re-runs in an existing proj dir. Changing count upward still triggers regeneration because the expected files won’t all be present. For example 5 (HTPB chains use 6 gromacs-generated conformers per stereoisomer per long-chain monomer), this skips a substantial amount of work on every restart.

  • Dockerfile: pre-create /home/htpolynet with mode 0777 so named docker volumes mounted there inherit a world-writable initial state. Without this, a fresh htpolynet-home volume came up owned by root and the non-root container user could not create ~/.htpolynet, ~/.config/matplotlib, etc.

  • ParmEd GromacsWarning: The [ pairs ] section contains N exceptions that aren't 1-4 pairs; make sure you know what you're doing! at end of run. CURE can shorten the topological distance between two atoms previously templated as a 1-4 pair down to 1-3 (a new cure bond shortcuts the original 3-bond path), but nothing was pruning those now-invalid pair entries. New Topology.prune_stale_14_pairs() walks the bondlist and drops any [ pairs ] entry whose endpoints aren’t actually 1-4 in the post-cure graph (uses the existing bondlist.partners_of, so it’s O(degree³) per pair — fast). Wired into Runtime.save_data just before write_top; an INFO log line reports the count when any entries get pruned. On the DFA/FDE example 4 build (~23k pairs total) it dropped 40 stale 1-3 pairs.

  • Silent no-op config keys in the depot example YAMLs: initial_search_radius (schema is search_radius) and late_threshhold (schema is late_threshold, no extra h) were being silently swallowed by dict.get(key, default) because the values happened to match defaults. Renamed in all four CURE-bearing examples (1, 2, 3, 4). Behavior unchanged but the docs can now quote the keys honestly.

  • Silent no-op nconformers: keys on FDE and DFA in example 4. The runtime reads conformer settings from a conformers: sub-block (with count, generator, minimize keys); the flat nconformers: line was never read. Dropped.

  • Default CURE.controls.min_bonds_per_iteration is now 10 (was effectively 1, gated by while nbonds == 0). This is silent for users with custom YAMLs that don’t pin the key; rerun behavior shifts toward fewer, larger CURE iterations.

Documentation

  • Container-usage page rewritten around the entrypoint-driven uid mapping; covers SELinux + :Z and the role of the htpolynet-home named volume.

  • Full rewrite of every short-build tutorial against the current self-contained-YAML workflow. Tutorial directory names now match the depot stem: 2-DGEBA-PACM/ → 3-pacm-dgeba-epoxy-thermoset/, 3-VE-STY/ → 2-bisgma-styrene-thermoset/, and a brand-new tutorial 4 (4-dfda-fde-epoxy-thermoset/) was written. All cross-references (ve_* → bgs_*, dgeba_* → pde_*, new dfe_*) renamed accordingly. Each tutorial walks the YAML block-by-block via literalinclude, drops the obsolete run.sh/obabel/sed monomer-prep machinery, and points readers at the new profile.json and min_bonds_per_iteration knob where relevant. Tutorial 0’s results page now ships the final-box.png VMD render.

  • scripts/run_all_examples.sh documented in-script via its header block.

  • Removed the legacy src/htpolynet/resources/cfg/ directory (12 orphaned config snippets with no Python references; pre-example-depot artifacts). Updated the one :download: reference in usage.rst that pointed to a file in there.

[2.0.1] - 2026-05-12

Changed

  • compose.yml: bind-mount source switched from . to ${PWD} so a single shared compose.yml referenced via docker compose -f mounts the caller’s working directory rather than the file’s directory.

  • compose.yml: user: field now reads ${HOST_UID} / ${HOST_GID} instead of ${UID} / ${GID} — bash’s UID is read-only and GID is not exported, so the original form silently fell back to 0 (root) and broke writes into the bind mount under rootless Docker.

  • compose.yml: container now gets a persistent HOME via a named htpolynet-home docker volume — without this, ~/.htpolynet resolved to /.htpolynet (root of the container fs) for the non-root user and the user cache could not be created. The named volume also keeps parameterized monomers/oligomers around across docker compose run --rm invocations.

Fixed

  • Dockerfile header comments: removed duplicated htpolynet token in the example docker run invocations (the ENTRYPOINT already provides it) and added --user $(id -u):$(id -g) so output files are not owned by root.

Documentation

  • Container-usage page now notes that the image is published only to GHCR (a bare docker run htpolynet resolves against Docker Hub and fails) and shows a docker tag shortcut for a local alias.

  • Added a curl -O one-liner for fetching compose.yml directly from the repo.

[2.0.0] - 2026-05-07

Changed

  • Package renamed from HTPolyNet to htpolynet (fully lowercase) for PEP 8 compliance and PyPI consistency.

  • Runtime now logs the HTPolyNet git commit hash at startup, with a warning when uncommitted changes are present.

Added

  • Apptainer/Singularity container support: distributed as a .sif image for reproducible execution on HPC clusters.

  • New gen-slurm-script subcommand generates a ready-to-submit SLURM batch script from an htpolynet YAML config file.

Fixed

  • Chain-expansion bug: bond-chain ChainManager was not rebuilt for monomers on the fetch path, causing bondchain_expand_reactions to produce no chain-extended oligomers in runs that reused cached parameterizations.

[1.0.9] - 2025-01-01

Added

  • minimum_bondcycle_length parameter to allow for cyclic polymerization above a certain threshold length.

Fixed

  • Rings not transferred from monomer templates if they are pre-parameterized.

  • Atom indexes in bondchain structure not remapped after atom deletion.

[1.0.8] - 2024-01-04

Changed

  • Uses chordless_cycles to find rings; ringidx is no longer a unique atom attribute; improved ring-pierce detection.