This changes the CSV output file to list one model ligand per line,
instead of one reference ligand.

OST only reads the first model (_atom_site.pdbx_PDB_model_num) of an
mmCIF file. This commit clarifies it in the doc, and adds a warning to
the output if models are ignored.

Silences a Sphinx warning.

Avoid confusion, as the editors don't come with context managers.

All counts were reset to 0 by a call to NextMolecule(). Now we are
displaying the data straight from the entity. Assumes an empty
entity at the start.

Added script-level info on progress; warnings upon crazy chain mappings;
silenced Verbose logging about selections; generally increased verbosity.

This may cause trouble for downstream applications when called on the same
entity several times. The result may be a generic property that marks a
terminal residue which is not terminal anymore because the entity has been
updated. This leads to a crash in the parameterization stage.

Now we always have a warning on the deprecated doc with a link to the
new implementation; and a note on the new implementation which starts
with "this is the new implementation" rather than "XXX is deprecated".

The breadcrumbs now correctly indicate the module hierarchy and can be
used to determine imports. All the documentation for ost.* is now rooted
on the base `ost` module for more clarity.

ost.mol.alg submodules are now documented in separate pages. This should
make it clearer what to import.

This way we avoid making networkx a hard dependency on mol.alg.

parasail produces slightly different alignments for one test case

Use np.isnan instead of scipy.isnan. Starting from scipy 1.12
(or earlier), scipy.isnan was definitely deprecated. This made the
SpearmanCorrel function silently return None which triggered a failing
unit test that was reported by Andrius Merkys.