Robustness and polish fixes

src/raven_python/gapfilling/fill.py

@@ -15,6 +15,7 @@
 """
 from __future__ import annotations
 
+import math
 from collections.abc import Iterable
 from dataclasses import dataclass
 
@@ -76,13 +77,25 @@ def _solve_min_templates(
     prob = working.problem
     indicators: dict[str, object] = {}
     extra = []
+    # Big-M for the indicator constraints. A template reaction with an infinite
+    # bound would otherwise put an infinite coefficient into the MILP; clamp it to
+    # the largest finite bound magnitude in the model (>= any flux it can carry).
+    finite_bounds = [
+        abs(b)
+        for r in working.reactions
+        for b in (r.lower_bound, r.upper_bound)
+        if math.isfinite(b)
+    ]
+    big_m = max(finite_bounds) if finite_bounds else 1000.0
     for rid in template_ids:
         rxn = working.reactions.get_by_id(rid)
         y = prob.Variable(f"_gf_keep_{rid}", type="binary")
         indicators[rid] = y
         # Flux is confined to [lb*y, ub*y]: zero unless the reaction is kept (y=1).
-        extra.append(prob.Constraint(rxn.flux_expression - rxn.upper_bound * y, ub=0, name=f"_gf_ub_{rid}"))
-        extra.append(prob.Constraint(rxn.flux_expression - rxn.lower_bound * y, lb=0, name=f"_gf_lb_{rid}"))
+        ub = rxn.upper_bound if math.isfinite(rxn.upper_bound) else big_m
+        lb = rxn.lower_bound if math.isfinite(rxn.lower_bound) else -big_m
+        extra.append(prob.Constraint(rxn.flux_expression - ub * y, ub=0, name=f"_gf_ub_{rid}"))
+        extra.append(prob.Constraint(rxn.flux_expression - lb * y, lb=0, name=f"_gf_lb_{rid}"))
     working.add_cons_vars(list(indicators.values()) + extra)
 
     if allow_net_production:  # relax steady state to Sv >= 0 (mets may accumulate)

src/raven_python/io/excel.py

@@ -104,7 +104,7 @@ def export_to_excel(
         ws.append([
             None, f"{m.name}[{m.compartment}]", m.name, None,
             _miriam_string(m.annotation, exclude=("smiles",)),
-            None if inchi else m.formula, inchi, m.compartment, m.id, m.charge,
+            m.formula, inchi, m.compartment, m.id, m.charge,
         ])
 
     # --- COMPS ---

src/raven_python/reconstruction/kegg/download.py

@@ -69,7 +69,14 @@ def _resolve_auth(
             f"No credentials given and {path} does not exist. Create it (chmod 600) "
             f"with a line:\n    machine {host} login YOUR_USER password YOUR_PASS"
         )
-    creds = netrc.netrc(str(path)).authenticators(host)
+    try:
+        creds = netrc.netrc(str(path)).authenticators(host)
+    except (netrc.NetrcParseError, OSError) as exc:
+        raise ValueError(
+            f"Could not read credentials from {path}: {exc}. Ensure it is a valid "
+            f".netrc (chmod 600) with a line:\n"
+            f"    machine {host} login YOUR_USER password YOUR_PASS"
+        ) from exc
     if not creds:
         raise ValueError(
             f"No credentials for '{host}' in {path}. Add a line:\n"

src/raven_python/visualization/__init__.py

@@ -1 +1,15 @@
 """Pathway-map and omics-overlay visualisation (stub — not yet implemented)."""
+from __future__ import annotations
+
+
+def __getattr__(name: str):
+    # PEP 562: accessing any attribute of this stub package fails with a clear,
+    # actionable message rather than a bare AttributeError. Dunder lookups
+    # (``__path__`` etc.) fall through to normal handling.
+    if name.startswith("__"):
+        raise AttributeError(name)
+    raise NotImplementedError(
+        f"raven_python.visualization.{name!r} is not implemented yet. Pathway-map "
+        "and omics-overlay visualisation is on the roadmap; until then export the "
+        "model via raven_python.io and use an external viewer such as Escher."
+    )

tests/test_gapfilling.py

@@ -54,6 +54,16 @@ def test_fill_gaps_connects_blocked_reaction(draft_and_template):
     assert "r_unneeded" not in res.added_reactions  # irrelevant template rxn not added
 
 
+def test_fill_gaps_handles_infinite_template_bound(draft_and_template):
+    # A template reaction with an unbounded (inf) bound must not put an infinite
+    # coefficient into the big-M MILP; it is clamped to a finite surrogate.
+    draft, template = draft_and_template
+    template.reactions.get_by_id("r2").upper_bound = float("inf")
+    res = connect_blocked_reactions(draft, template)
+    assert "r1" in res.newly_connected
+    assert "r2" in res.added_reactions
+
+
 def test_fill_gaps_returns_working_model_that_unblocks(draft_and_template):
     draft, template = draft_and_template
     res = connect_blocked_reactions(draft, template)

tests/test_io_excel.py

@@ -76,7 +76,7 @@ def test_mets_sheet(model, tmp_path):
     assert atp["ID"] == "ATP[c]"
     assert atp["NAME"] == "ATP"
     assert atp["InChI"] == "InChI=1S/X"
-    assert atp["COMPOSITION"] is None  # suppressed when InChI present
+    assert atp["COMPOSITION"] == "C10H16N5O13P3"  # formula kept even when InChI present
     assert atp["CHARGE"] == -4
     assert atp["MIRIAM"] == "kegg.compound/C00002"  # smiles excluded
 

tests/test_reconstruction_kegg_download.py

@@ -57,6 +57,14 @@ def test_resolve_auth_host_absent(tmp_path):
         _resolve_auth("ftp.kegg.net", netrc_path=netrc_file)
 
 
+def test_resolve_auth_malformed_netrc(tmp_path):
+    netrc_file = tmp_path / ".netrc"
+    netrc_file.write_text("this is not a valid netrc line\n")
+    netrc_file.chmod(0o600)
+    with pytest.raises(ValueError, match="Could not read credentials"):
+        _resolve_auth("ftp.kegg.net", netrc_path=netrc_file)
+
+
 # --------------------------------------------------------------------------- #
 # Extract / arrange
 # --------------------------------------------------------------------------- #

tests/test_visualization.py

@@ -0,0 +1,9 @@
+"""The visualization subpackage is a documented stub (not yet implemented)."""
+import pytest
+
+
+def test_visualization_stub_raises_not_implemented():
+    import raven_python.visualization as viz
+
+    with pytest.raises(NotImplementedError, match="not implemented yet"):
+        viz.draw_pathway()  # attribute access triggers __getattr__ and raises