Merge remote-tracking branch 'origin/main' into swap-hac4ui

.github/workflows/pages.yml

@@ -26,15 +26,7 @@ jobs:
       # needs to install hd3 so the command-line pages are
       # rendered properly
       - name: Install HADDOCK3
-        run: |
-          pwd
-          ls -lsa
-          mkdir bin
-          touch bin/cns
-          cd src/fcc/src
-          chmod u+x Makefile
-          ./Makefile 2>%1 >/dev/null || true
-          cd -
+        run: pip install -v .
 
       - name: Generate docs
         run: |

examples/peptide-cyclisation/cyclise-peptide-full.cfg

@@ -19,7 +19,7 @@ run_dir = "run1-cyclise-full"
 # and comment the lines under the HPC execution
 mode = "local"
 ncores = 10
-less_io = true
+debug = false
 concat = 1
 
 # molecules to be docked

examples/peptide-cyclisation/cyclise-peptide-test.cfg

@@ -19,7 +19,7 @@ run_dir = "run1-cyclise-test"
 # and comment the lines under the HPC execution
 mode = "local"
 ncores = 10
-less_io = true
+debug = false
 concat = 1
 
 # molecules to be docked

integration_tests/test_caprieval.py

@@ -330,11 +330,11 @@ def test_caprieval_default(
     )
 
 
-def test_caprieval_less_io(
+def test_caprieval_nodebug(
     caprieval_module, model_list, expected_ss_data, expected_clt_data
 ):
     caprieval_module.previous_io = MockPreviousIO(path=caprieval_module.path)
-    caprieval_module.params["less_io"] = True
+    caprieval_module.params["debug"] = False
 
     caprieval_module.run()
 

integration_tests/test_emref.py

@@ -67,6 +67,7 @@ def output(self):
 def test_emref_defaults(emref_module, calc_fnat):
 
     emref_module.previous_io = MockPreviousIO(path=emref_module.path)
+    emref_module.params["debug"] = True
 
     emref_module.run()
 
@@ -91,6 +92,8 @@ def test_emref_fle(emref_module, calc_fnat):
     emref_module.params["fle_end_1 "] = 77
     emref_module.params["fle_seg_1  "] = "B"
 
+    emref_module.params["debug"] = True
+
     emref_module.run()
 
     assert Path(emref_module.path, "emref_1.pdb").exists()
@@ -118,6 +121,8 @@ def test_emref_mutliple_fle(emref_module, calc_fnat):
     emref_module.params["fle_end_2 "] = 47
     emref_module.params["fle_seg_2  "] = "B"
 
+    emref_module.params["debug"] = True
+
     emref_module.run()
 
     assert Path(emref_module.path, "emref_1.pdb").exists()

integration_tests/test_flexref.py

@@ -74,7 +74,6 @@ def test_flexref_defaults(flexref_module, calc_fnat):
     flexref_module.run()
 
     assert Path(flexref_module.path, "flexref_1.pdb").exists()
-    assert Path(flexref_module.path, "flexref_1.out.gz").exists()
 
     fnat = calc_fnat(
         model=Path(flexref_module.path, "flexref_1.pdb"),
@@ -94,6 +93,7 @@ def test_flexref_fle(flexref_module, calc_fnat):
     flexref_module.params["fle_end_1 "] = 77
     flexref_module.params["fle_seg_1  "] = "B"
     flexref_module.params["log_level"] = "verbose"
+    flexref_module.params["debug"] = True
 
     flexref_module.run()
 
@@ -124,6 +124,8 @@ def test_flexref_mutliple_fle(flexref_module, calc_fnat):
     flexref_module.params["fle_end_2 "] = 47
     flexref_module.params["fle_seg_2  "] = "B"
 
+    flexref_module.params["debug"] = True
+
     flexref_module.run()
 
     assert Path(flexref_module.path, "flexref_1.pdb").exists()

integration_tests/test_mdref.py

@@ -67,7 +67,7 @@ def output(self):
 def test_mdref_defaults(mdref_module, calc_fnat):
 
     mdref_module.previous_io = MockPreviousIO(path=mdref_module.path)
-
+    mdref_module.params["debug"] = True
     mdref_module.run()
 
     assert Path(mdref_module.path, "mdref_1.pdb").exists()
@@ -91,6 +91,8 @@ def test_mdref_fle(mdref_module, calc_fnat):
     mdref_module.params["fle_end_1 "] = 77
     mdref_module.params["fle_seg_1  "] = "B"
 
+    mdref_module.params["debug"] = True
+
     mdref_module.run()
 
     assert Path(mdref_module.path, "mdref_1.pdb").exists()
@@ -118,6 +120,8 @@ def test_mdref_mutliple_fle(mdref_module, calc_fnat):
     mdref_module.params["fle_end_2 "] = 47
     mdref_module.params["fle_seg_2  "] = "B"
 
+    mdref_module.params["debug"] = True
+
     mdref_module.run()
 
     assert Path(mdref_module.path, "mdref_1.pdb").exists()

integration_tests/test_restraints.py

@@ -88,6 +88,7 @@ def test_restraints_rigidbody(rigidbody_module):
     rigidbody_module.params["unambig_fname"] = Path(GOLDEN_DATA, "unambig.tbl")
     rigidbody_module.params["hbond_fname"] = Path(GOLDEN_DATA, "hbond.tbl")
     rigidbody_module.params["mode"] = "local"
+    rigidbody_module.params["debug"] = True
 
     rigidbody_module.run()
 

integration_tests/test_rigidbody.py

@@ -83,6 +83,7 @@ def test_rigidbody_local(rigidbody_module):
     rigidbody_module.params["mol_fix_origin_1"] = True
     rigidbody_module.params["mol_fix_origin_2"] = False
     rigidbody_module.params["mode"] = "local"
+    rigidbody_module.params["debug"] = True
 
     rigidbody_module.run()
 
@@ -108,6 +109,7 @@ def test_rigidbody_mpi(rigidbody_module):
     rigidbody_module.params["mol_fix_origin_2"] = False
     rigidbody_module.params["mode"] = "mpi"
     rigidbody_module.params["ncores"] = 1
+    rigidbody_module.params["debug"] = True
 
     rigidbody_module.run()
 
@@ -122,15 +124,14 @@ def test_rigidbody_mpi(rigidbody_module):
         assert Path(rigidbody_module.path, f"rigidbody_{i}.inp").stat().st_size > 0
 
 
-def test_rigidbody_less_io(rigidbody_module):
+def test_rigidbody_debug(rigidbody_module):
 
     sampling = 2
     rigidbody_module.previous_io = MockPreviousIO(path=rigidbody_module.path)
     rigidbody_module.params["sampling"] = sampling
     rigidbody_module.params["cmrest"] = True
     rigidbody_module.params["mol_fix_origin_1"] = True
     rigidbody_module.params["mol_fix_origin_2"] = False
-    rigidbody_module.params["less_io"] = True
 
     rigidbody_module.run()
 

integration_tests/test_topoaa.py

@@ -29,6 +29,7 @@ def test_topoaa_module_protein(topoaa_module):
     topoaa_module.params["mol1"] = {"prot_segid": "A"}
     topoaa_module.params["mol2"] = {"prot_segid": "B"}
     topoaa_module.params["cns_exec"] = CNS_EXEC
+    topoaa_module.params["debug"] = True
 
     topoaa_module.run()
 
@@ -71,6 +72,7 @@ def test_topoaa_module_ligand(topoaa_module):
     topoaa_module.params["delenph"] = False
     topoaa_module.params["preprocess"] = False
     topoaa_module.params["cns_exec"] = CNS_EXEC
+    topoaa_module.params["debug"] = True
 
     topoaa_module.run()
 
@@ -94,6 +96,7 @@ def test_topoaa_cyclic(topoaa_module):
     topoaa_module.params["disulphide_dist"] = 4.0
     topoaa_module.params["mol1"] = {"cyclicpept": True}
     topoaa_module.params["cns_exec"] = CNS_EXEC
+    topoaa_module.params["debug"] = True
 
     topoaa_module.run()
 

src/haddock/libs/libcns.py

@@ -273,7 +273,7 @@ def prepare_cns_input(
     ambig_fname: FilePath = "",
     native_segid: bool = False,
     default_params_path: Optional[Path] = None,
-    less_io: Optional[bool] = True,
+    debug: Optional[bool] = False,
     seed: Optional[int] = None,
 ) -> Union[Path, str]:
     """
@@ -372,7 +372,7 @@ def prepare_cns_input(
 
     inp = default_params + input_str + seed_str + output + segid_str + recipe_str
 
-    if less_io:
+    if not debug:
         return inp
     else:
         inp_file = Path(f"{identifier}_{model_number}.inp")

src/haddock/modules/analysis/caprieval/__init__.py

@@ -112,7 +112,7 @@ def _run(self) -> None:
         exec_mode = get_analysis_exec_mode(self.params["mode"])
         Engine = get_engine(exec_mode, self.params)
 
-        less_io = self.params["less_io"] and self.params["mode"] == "local"
+        _less_io = self.params["mode"] == "local" and not self.params["debug"]
 
         # Each model is a job; this is not the most efficient way
         #  but by assigning each model to an individual job
@@ -133,14 +133,14 @@ def _run(self) -> None:
                     path=Path("."),
                     reference=reference,
                     params=self.params,
-                    less_io=less_io,
+                    debug=not _less_io,
                 )
             )
 
         engine = Engine(jobs)
         engine.run()
 
-        if less_io and isinstance(engine, Scheduler):
+        if _less_io and isinstance(engine, Scheduler):
             jobs = engine.results
             extract_data_from_capri_class(
                 capri_objects=jobs,
@@ -151,7 +151,10 @@ def _run(self) -> None:
 
         else:
             self.log(
-                msg="DEPRECATION NOTICE: This execution mode (less_io=False) will no longer be supported in the next version.",
+                msg=(
+                    "DEPRECATION NOTICE: This execution mode (debug=True) "
+                    "will no longer be supported in the next version."
+                    ),
                 level="warning",
             )
             jobs = merge_data(jobs)

src/haddock/modules/analysis/caprieval/capri.py

@@ -179,7 +179,7 @@ def __init__(
         path: Path,
         reference: PDBPath,
         params: ParamMap,
-        less_io: Optional[bool] = False,
+        debug: Optional[bool] = False,
     ) -> None:
         """
         Initialize the class.
@@ -225,7 +225,7 @@ def __init__(
         self.output = self.output_ss_fname
         self.identificator = identificator
         self.core_model_idx = identificator
-        self.less_io = less_io
+        self.debug = debug
 
     def calc_irmsd(self, cutoff: float = 5.0) -> None:
         """Calculate the I-RMSD.
@@ -654,7 +654,7 @@ def run(self) -> Union[None, "CAPRI"]:
             log.debug(f"id {self.identificator}, calculating global RMSD")
             self.calc_global_rmsd()
 
-        if not self.less_io:
+        if self.debug:
             self.make_output()
         else:
             # The scheduler will use the return of the `run` method as the output of the tasks

src/haddock/modules/defaults.yaml

@@ -138,14 +138,15 @@ offline:
     generated files, therefore completely isolating haddock3 from any web call.
   group: "execution"
   explevel: easy
-less_io:
+debug:
   default: false
   type: boolean
-  title: Reduce the amount of I/O operations.
-  short: Reduce the amount of I/O operations.
-  long: This option will reduce the amount of I/O operations by writing
-    less files to disk. This can be useful for example when running on
-    a network file system where I/O operations are slow.
+  title: Write intermediate and stdout files.
+  short: Write intermediate and stdout files.
+  long: When set to true, this option will increase the amount of I/O 
+    operations by writing intermediate input, output and error files on disk.
+    Turning it to false can be useful for example when running on a network
+    file system where I/O operations are slow.
   group: "execution"
   explevel: easy
   incompatible:

src/haddock/modules/refinement/emref/__init__.py

@@ -99,7 +99,7 @@ def _run(self) -> None:
                     "emref",
                     ambig_fname=ambig_fname,
                     native_segid=True,
-                    less_io=self.params["less_io"],
+                    debug=self.params["debug"],
                     seed=model.seed if isinstance(model, PDBFile) else None,
                 )
                 out_file = f"emref_{idx}.out"

src/haddock/modules/refinement/flexref/__init__.py

@@ -113,7 +113,7 @@ def _run(self) -> None:
                     "flexref",
                     ambig_fname=ambig_fname,
                     native_segid=True,
-                    less_io=self.params["less_io"],
+                    debug=self.params["debug"],
                     seed=model.seed if isinstance(model, PDBFile) else None,
                 )
 

src/haddock/modules/refinement/mdref/__init__.py

@@ -112,7 +112,7 @@ def _run(self) -> None:
                     "mdref",
                     ambig_fname=ambig_fname,
                     native_segid=True,
-                    less_io=self.params["less_io"],
+                    debug=self.params["debug"],
                     seed=model.seed if isinstance(model, PDBFile) else None,
                 )
                 out_file = f"mdref_{idx}.out"

src/haddock/modules/sampling/rigidbody/__init__.py

@@ -114,7 +114,7 @@ def prepare_cns_input_sequential(
                     ambig_fname=ambig_fname,
                     default_params_path=self.toppar_path,
                     native_segid=True,
-                    less_io=self.params["less_io"],
+                    debug=self.params["debug"],
                     seed=seed,
                 )
                 _l.append((combination, rigidbody_input, ambig_fname, seed))
@@ -150,7 +150,7 @@ def prepare_cns_input_parallel(
                     ambig_fname=ambig_fname,
                     native_segid=True,
                     default_params_path=self.toppar_path,
-                    less_io=self.params["less_io"],
+                    debug=self.params["debug"],
                     seed=seed,
                 )
 

src/haddock/modules/scoring/emscoring/__init__.py

@@ -56,7 +56,7 @@ def _run(self) -> None:
                 self.params,
                 "emscoring",
                 native_segid=True,
-                less_io=self.params["less_io"],
+                debug=self.params["debug"],
                 seed=model.seed if isinstance(model, PDBFile) else None,
             )
 

src/haddock/modules/scoring/mdscoring/__init__.py

@@ -56,7 +56,7 @@ def _run(self) -> None:
                 self.params,
                 "mdscoring",
                 native_segid=True,
-                less_io=self.params["less_io"],
+                debug=self.params["debug"],
                 seed=model.seed if isinstance(model, PDBFile) else None,
             )
 

src/haddock/modules/topology/topoaa/__init__.py

@@ -254,7 +254,7 @@ def _run(self) -> None:
                     self.params,
                     parameters_for_this_molecule,
                     default_params_path=self.toppar_path,
-                    write_to_disk=not self.params["less_io"],
+                    write_to_disk=self.params["debug"],
                 )
 
                 self.log("Topology CNS input created")

tests/test_libcns.py

@@ -127,7 +127,7 @@ def test_prepare_cns_input(pdbfile):
         ambig_fname="",
         native_segid=False,
         default_params_path=None,
-        less_io=True,
+        debug=False,
         seed=pdbfile.seed,
     )