Refactor workflow initialization to remove hard dependency on topoaa

examples/run_tests.py

@@ -47,34 +47,34 @@
 # keys are the examples folder, and values are the configuration files
 # the whitespaces below are anti-pythonic but facilitate reading :-)
 examples = (
-    ("docking-antibody-antigen"    , "docking-antibody-antigen-ranairCDR-test.cfg"),  # noqa: E203, E501
-    ("docking-antibody-antigen"    , "docking-antibody-antigen-ranairCDR-clt-test.cfg"),  # noqa: E203, E501
-    ("docking-antibody-antigen"    , "docking-antibody-antigen-CDR-accessible-test.cfg"),  # noqa: E203, E501
-    ("docking-antibody-antigen"    , "docking-antibody-antigen-CDR-accessible-clt-test.cfg"),  # noqa: E203, E501
-    ("docking-antibody-antigen"    , "docking-antibody-antigen-CDR-NMR-CSP-test.cfg"),  # noqa: E203, E501
-    ("docking-protein-DNA"         , "docking-protein-DNA-test.cfg"),  # noqa: E203, E501
-    ("docking-protein-DNA"         , "docking-protein-DNA-mdref-test.cfg"),  # noqa: E203, E501
-    ("docking-protein-homotrimer"  , "docking-protein-homotrimer-test.cfg"),  # noqa: E203, E501
-    ("docking-protein-glycan"      , "docking-protein-glycan-test.cfg"),  # noqa: E203, E501
-    ("docking-protein-glycan"      , "docking-protein-glycan-ilrmsd-test.cfg"),  # noqa: E203, E501
-    ("docking-protein-glycan"      , "docking-flexref-protein-glycan-test.cfg"),  # noqa: E203, E501
-    ("docking-protein-ligand-shape", "docking-protein-ligand-shape-test.cfg"),  # noqa: E203, E501
-    ("docking-protein-ligand"      , "docking-protein-ligand-test.cfg"),  # noqa: E203, E501
-    ("docking-protein-peptide"     , "docking-protein-peptide-test.cfg"),  # noqa: E203, E501
-    ("docking-protein-peptide"     , "docking-protein-peptide-mdref-test.cfg"),  # noqa: E203, E501
-    ("docking-protein-protein"     , "docking-protein-protein-test.cfg"),  # noqa: E203, E501
-    ("docking-protein-protein"     , "docking-protein-protein-cltsel-test.cfg"),  # noqa: E203, E501
-    ("docking-protein-protein"     , "docking-protein-protein-mdref-test.cfg"),  # noqa: E203, E501
-    ("docking-multiple-ambig"      , "docking-multiple-tbls-test.cfg"),  # noqa: E203, E501
-    ("docking-protein-protein"     , "docking-exit-test.cfg"),  # noqa: E203, E501
-    ("refine-complex"              , "refine-complex-test.cfg"),  # noqa: E203, E501
-    ("scoring"                     , "emscoring-test.cfg"),  # noqa: E203, E501
-    ("scoring"                     , "mdscoring-test.cfg"),  # noqa: E203, E501
-    ("scoring"                     , "emscoring-mdscoring-test.cfg"),  # noqa: E203, E501
-    ("analysis"                    , "topoaa-caprieval-test.cfg"),  # noqa: E203, E501
-    ("analysis"                    , "topoaa-ilrmsdmatrix-clustrmsd-test.cfg"),  # noqa: E203, E501
-    ("analysis"                    , "alascan-test.cfg"),  # noqa: E203, E501
-    ("analysis"                    , "contmap-test.cfg"),  # noqa: E203, E501
+    ("docking-antibody-antigen"    , "docking-antibody-antigen-ranairCDR-test.cfg"),
+    ("docking-antibody-antigen"    , "docking-antibody-antigen-ranairCDR-clt-test.cfg"),
+    ("docking-antibody-antigen"    , "docking-antibody-antigen-CDR-accessible-test.cfg"),
+    ("docking-antibody-antigen"    , "docking-antibody-antigen-CDR-accessible-clt-test.cfg"),
+    ("docking-antibody-antigen"    , "docking-antibody-antigen-CDR-NMR-CSP-test.cfg"),
+    ("docking-protein-DNA"         , "docking-protein-DNA-test.cfg"),
+    ("docking-protein-DNA"         , "docking-protein-DNA-mdref-test.cfg"),
+    ("docking-protein-homotrimer"  , "docking-protein-homotrimer-test.cfg"),
+    ("docking-protein-glycan"      , "docking-protein-glycan-test.cfg"),
+    ("docking-protein-glycan"      , "docking-protein-glycan-ilrmsd-test.cfg"),
+    ("docking-protein-glycan"      , "docking-flexref-protein-glycan-test.cfg"),
+    ("docking-protein-ligand-shape", "docking-protein-ligand-shape-test.cfg"),
+    ("docking-protein-ligand"      , "docking-protein-ligand-test.cfg"),
+    ("docking-protein-peptide"     , "docking-protein-peptide-test.cfg"),
+    ("docking-protein-peptide"     , "docking-protein-peptide-mdref-test.cfg"),
+    ("docking-protein-protein"     , "docking-protein-protein-test.cfg"),
+    ("docking-protein-protein"     , "docking-protein-protein-cltsel-test.cfg"),
+    ("docking-protein-protein"     , "docking-protein-protein-mdref-test.cfg"),
+    ("docking-multiple-ambig"      , "docking-multiple-tbls-test.cfg"),
+    ("docking-protein-protein"     , "docking-exit-test.cfg"),
+    ("refine-complex"              , "refine-complex-test.cfg"),
+    ("scoring"                     , "emscoring-test.cfg"),
+    ("scoring"                     , "mdscoring-test.cfg"),
+    ("scoring"                     , "emscoring-mdscoring-test.cfg"),
+    ("analysis"                    , "topoaa-caprieval-test.cfg"),
+    ("analysis"                    , "topoaa-ilrmsdmatrix-clustrmsd-test.cfg"),
+    ("analysis"                    , "alascan-test.cfg"),
+    ("analysis"                    , "contmap-test.cfg"),
     )
 
 
@@ -160,7 +160,7 @@ def main(examples, break_on_errors=True):
                 rmtree("run2", ignore_errors=True)
                 run_subprocess_cmd("haddock3-copy -r run1-test -m 0 4 -o run2")
                 run_subprocess_cmd(
-                    "haddock3 docking-extend-run-exit-test.cfg --extend-run run2",  # noqa: E501
+                    "haddock3 docking-extend-run-exit-test.cfg --extend-run run2",
                     )
 
                 # test exit with --restart
@@ -178,20 +178,20 @@ def main(examples, break_on_errors=True):
 
                 # perform a haddock3 re-scoring command
                 run_subprocess_cmd(
-                    "haddock3-re score -e 1.1 -w 1 -d 0.3 -b 1 -a 1 run1-re/2_caprieval",  # noqa : E501
+                    "haddock3-re score -e 1.1 -w 1 -d 0.3 -b 1 -a 1 run1-re/2_caprieval",
                     )
 
                 # perform a haddock3 re-clustfcc command
                 run_subprocess_cmd(
-                    "haddock3-re clustfcc -f 0.5 -s 0.7 -t 2 run1-re/1_clustfcc",  # noqa : E501
+                    "haddock3-re clustfcc -f 0.5 -s 0.7 -t 2 run1-re/1_clustfcc",
                     )
 
                 # FIXME: Make this runs properly function
                 # perform a haddock3 re-clustrmsd command
 
                 # perform haddock3 --extend-run on re-run
                 # run_subprocess_cmd(
-                #     "haddock3 docking-re-extend-run-test.cfg --extend-run run1-re",  # noqa : E501
+                #     "haddock3 docking-re-extend-run-test.cfg --extend-run run1-re",
                 #     )
 
                 # perform haddock3 --restart on re-run

integration_tests/test_alascan.py

@@ -17,7 +17,7 @@ def alascan_module():
     """Return a default alascan module."""
     with tempfile.TemporaryDirectory(dir=".") as tmpdir:
         alascan = AlascanModule(
-            order=0, path=".", initial_params=DEFAULT_ALASCAN_CONFIG
+            order=1, path=Path("."), initial_params=DEFAULT_ALASCAN_CONFIG
         )
         alascan.params["int_cutoff"] = 3.5
         yield alascan

integration_tests/test_caprieval.py

@@ -16,7 +16,7 @@
 def caprieval_module():
     with tempfile.TemporaryDirectory() as tmpdir:
         yield CaprievalModule(
-            order=0,
+            order=1,
             path=Path(tmpdir),
             init_params=DEFAULT_CAPRIEVAL_CONFIG,
         )

integration_tests/test_contactmap.py

@@ -18,7 +18,7 @@ def contactmap():
     """Return contmap module."""
     with tempfile.TemporaryDirectory() as tmpdir:
         preset_contactmap = CMapModule(
-            order=0,
+            order=1,
             path=Path(tmpdir),
             initial_params=CONTMAP_CONF,
             )

integration_tests/test_ilrmsdmatrix.py

@@ -22,7 +22,7 @@ def ilrmsdmatrix_module():
     """Provide a parametrized IL-RMSD matrix module."""
     with tempfile.TemporaryDirectory() as tmpdir:
         ilrmsdmatrix = IlrmsdmatrixModule(
-            order=0, path=tmpdir, initial_params=DEFAULT_ILRMSD_CONFIG
+            order=1, path=Path(tmpdir), initial_params=DEFAULT_ILRMSD_CONFIG
             )
         yield ilrmsdmatrix
 

integration_tests/test_rigidbody.py

@@ -16,7 +16,7 @@
 def rigidbody_module():
     with tempfile.TemporaryDirectory() as tmpdir:
         rigidbody = RigidbodyModule(
-            order=0, path=Path(tmpdir), initial_params=DEFAULT_RIGIDBODY_CONFIG
+            order=1, path=Path(tmpdir), initial_params=DEFAULT_RIGIDBODY_CONFIG
         )
         yield rigidbody
 

integration_tests/test_rmsdmatrix.py

@@ -13,9 +13,9 @@
 
 @pytest.fixture
 def rmsdmatrix_module():
-    with tempfile.TemporaryDirectory() as tmpdir:
+    with tempfile.TemporaryDirectory(".") as tmpdir:
         ilrmsdmatrix = rmsdmatrixModule(
-            order=0, path=tmpdir, initial_params=DEFAULT_RMSD_CONFIG
+            order=1, path=Path(tmpdir), initial_params=DEFAULT_RMSD_CONFIG
         )
         yield ilrmsdmatrix
 

integration_tests/test_topoaa.py

@@ -1,31 +1,57 @@
 import tempfile
-from pathlib import Path
-
 import pytest
+from pathlib import Path
+from shutil import copyfile
 
-from haddock.modules.topology.topoaa import DEFAULT_CONFIG as DEFAULT_TOPOAA_CONFIG
-from haddock.modules.topology.topoaa import HaddockModule as TopoaaModule
+from haddock.core.defaults import DATA_DIRNAME
+from haddock.libs.libio import working_directory
+from haddock.modules.topology.topoaa import (
+    DEFAULT_CONFIG as DEFAULT_TOPOAA_CONFIG,
+    HaddockModule as TopoaaModule,
+    )
 
 from . import CNS_EXEC, DATA_DIR, has_cns
 
 
 @pytest.fixture
-def topoaa_module():
+def molecules():
+    return [
+        Path(DATA_DIR, "docking-protein-protein/data/e2aP_1F3G.pdb"),
+        Path(DATA_DIR, "docking-protein-protein/data/hpr_ensemble.pdb"),
+        ]
+
+
+@pytest.fixture
+def prepare_topoaa_run(molecules):
     with tempfile.TemporaryDirectory() as tmpdir:
-        topoaa = TopoaaModule(
-            order=0, path=tmpdir, initial_params=DEFAULT_TOPOAA_CONFIG
+        with working_directory(tmpdir):
+            modulename_path = Path("0_topoaa")
+            modulename_path.mkdir(parents=True)
+            input_dir_path = Path(DATA_DIRNAME, modulename_path)
+            input_dir_path.mkdir(parents=True)
+            mol_copies = [
+                copyfile(mol, Path(input_dir_path, mol.name))
+                for mol in molecules
+                ]
+            yield modulename_path, mol_copies
+
+
+@pytest.fixture
+def topoaa_module(prepare_topoaa_run):
+    modulename_path = prepare_topoaa_run[0]
+    mol_copies = prepare_topoaa_run[1]
+    topoaa = TopoaaModule(
+        order=0,
+        path=modulename_path,
+        initial_params=DEFAULT_TOPOAA_CONFIG,
         )
-        topoaa.__init__(path=tmpdir, order=0)
-        topoaa.params["molecules"] = [
-            Path(DATA_DIR, "docking-protein-protein/data/e2aP_1F3G.pdb"),
-            Path(DATA_DIR, "docking-protein-protein/data/hpr_ensemble.pdb"),
-        ]
-        topoaa.params["mol1"] = {"prot_segid": "A"}
-        topoaa.params["mol2"] = {"prot_segid": "B"}
+    topoaa.params["molecules"] = mol_copies
+    topoaa.params["mol1"] = {"prot_segid": "A"}
+    topoaa.params["mol2"] = {"prot_segid": "B"}
 
-        topoaa.params["cns_exec"] = CNS_EXEC
+    topoaa.params["cns_exec"] = CNS_EXEC
 
-        yield topoaa
+    yield topoaa
 
 
 @has_cns

src/haddock/clis/__init__.py

@@ -1,8 +1,8 @@
 """
 Command-line interfaces.
 
-HADDOCK3 has a series of command-line interfaces (CLIs), from which the most important
-one is ``haddock3``. You can ask help to the CLIs with the ``-h`` flag::
-
+HADDOCK3 has a series of command-line interfaces (CLIs), from which the most
+important one is ``haddock3``.
+You can ask help to the CLIs with the ``-h`` flag:
     haddock3 -h
 """