Removing analysis steps on run restart

CHANGELOG.md

@@ -1,5 +1,6 @@
 # Changelog
 
+- 2026-04-10: Removing analysis modules downstream when restarting - Issue #1495
 - 2026-04-08: Improved docstring in modules
 - 2026-04-08: Increased NOE restraints array size in scoring modules - Issue #1501
 - 2026-03-09: Automated type casting for optional argument seed in haddock3-restraints random_removal - Issue #1485

src/haddock/clis/cli_analyse.py

@@ -30,7 +30,7 @@
 from haddock import log
 from haddock.clis.cli_unpack import main as haddock3_unpack
 from haddock.clis.cli_clean import main as haddock3_clean
-from haddock.core.defaults import INTERACTIVE_RE_SUFFIX
+from haddock.core.defaults import INTERACTIVE_RE_SUFFIX, ANA_FOLDER
 from haddock.core.typing import (
     Any,
     ArgumentParser,
@@ -63,7 +63,6 @@
 from haddock.modules.analysis.caprieval import HaddockModule
 
 
-ANA_FOLDER = "analysis"  # name of the analysis folder
 INTER_STR = INTERACTIVE_RE_SUFFIX  # suffix of interactive analysis folders
 
 
@@ -758,9 +757,15 @@ def main(
     # get the module folders from the run_dir input
     sel_steps = get_module_steps_folders(Path("./"), modules)
     if inter:
-        sel_steps = [st for st in sel_steps if st.endswith(INTER_STR)]
+        sel_steps = [
+            st for st in sel_steps
+            if st.endswith(INTERACTIVE_RE_SUFFIX)
+            ]
     else:
-        sel_steps = [st for st in sel_steps if not st.endswith(INTER_STR)]
+        sel_steps = [
+            st for st in sel_steps
+            if not st.endswith(INTERACTIVE_RE_SUFFIX)
+            ]
     log.info(f"selected steps: {', '.join(sel_steps)}")
 
     # analysis

src/haddock/clis/cli_traceback.py

@@ -17,16 +17,14 @@
 import pandas as pd
 
 from haddock import log
+from haddock.core.defaults import TRACEBACK_FOLDER
 from haddock.core.typing import Any, FilePath
 from haddock.libs import libcli
 from haddock.libs.libontology import ModuleIO, PDBFile
 from haddock.libs.libplots import make_traceback_plot
 from haddock.modules import get_module_steps_folders
 
 
-TRACK_FOLDER = "traceback"  # name of the traceback folder
-
-
 def get_steps_without_pdbs(run_dir, all_steps):
     """
     Get the modules that do not produce PDB files.
@@ -270,7 +268,7 @@ def main(run_dir: FilePath, offline: bool = False) -> None:
         log.info(f"Steps to trace back: {', '.join(sel_step)}")
 
     # creating traceback folder
-    outdir = Path(run_dir, TRACK_FOLDER)
+    outdir = Path(run_dir, TRACEBACK_FOLDER)
     try:
         outdir.mkdir(exist_ok=False)
         log.info(f"Created directory: {str(outdir.resolve())}")
@@ -350,18 +348,18 @@ def main(run_dir: FilePath, offline: bool = False) -> None:
     # ordering the dataframe
     df_output = order_traceback_df(df_output, sel_step)
     # dumping the dataframe
-    track_filename = Path(run_dir, TRACK_FOLDER, "traceback.tsv")
+    track_filename = Path(run_dir, TRACEBACK_FOLDER, "traceback.tsv")
     log.info(
         f"Output dataframe {track_filename} " f"created with shape {df_output.shape}"
     )
     df_output.to_csv(track_filename, sep="\t", index=False)
 
     # taking (and writing) a subset of the dataframe
-    consensus_filename = Path(run_dir, TRACK_FOLDER, "consensus.tsv")
+    consensus_filename = Path(run_dir, TRACEBACK_FOLDER, "consensus.tsv")
     rank_data_subset = subset_traceback(df_output, consensus_filename)
 
     # plotting the traceback dataframe
-    plot_filename = Path(run_dir, TRACK_FOLDER, "traceback.html")
+    plot_filename = Path(run_dir, TRACEBACK_FOLDER, "traceback.html")
     make_traceback_plot(rank_data_subset, plot_filename, offline=offline)
     return
 

src/haddock/core/defaults.py

@@ -34,6 +34,12 @@
 INTERACTIVE_RE_SUFFIX = "interactive"
 """Suffix added to interactive haddock3-re runs."""
 
+ANA_FOLDER = "analysis"
+"""Name of the analysis folder."""
+
+TRACEBACK_FOLDER = "traceback"
+"""Name of the traceback folder."""
+
 MODULE_DEFAULT_YAML = "defaults.yaml"
 """Default name of the yaml default parameters file."""
 

src/haddock/gear/prepare_run.py

@@ -6,9 +6,7 @@
 import json
 import os
 import shutil
-import string
 import sys
-import tarfile
 from contextlib import contextmanager, suppress
 from copy import copy, deepcopy
 from functools import lru_cache, wraps
@@ -59,7 +57,7 @@
     config_optional_general_parameters_dict,
 )
 from haddock.gear.preprocessing import process_pdbs, read_additional_residues
-from haddock.gear.restart_run import remove_folders_after_number
+from haddock.gear.restart_run import preprocess_restart_from
 from haddock.gear.validations import (
     v_rundir,
     validate_defaults_yaml,
@@ -330,9 +328,7 @@ def setup_run(
         check_mandatory_argments_are_present(general_params)
 
     if restarting_from:
-        remove_folders_after_number(general_params[RUNDIR], restart_from)
-        _data_dir = Path(general_params[RUNDIR], "data")
-        remove_folders_after_number(_data_dir, restart_from)
+        preprocess_restart_from(general_params[RUNDIR], restart_from)
 
     if restarting_from or starting_from_copy:
         # get run files in folder
@@ -397,7 +393,7 @@ def setup_run(
     enhanced_haddock_params = deepcopy(general_params)
     enhanced_haddock_params.update(modules_params)
     config_files["enhanced_haddock_params"] = enhanced_haddock_params
-    config_saves = save_configuration_files(config_files, data_dir)  # noqa : F841
+    _config_saves = save_configuration_files(config_files, data_dir)  # noqa : F841
 
     if scratch_rest0:
         copy_molecules_to_data_dir(

src/haddock/gear/restart_run.py

@@ -2,7 +2,9 @@
 from argparse import ArgumentParser, ArgumentTypeError
 from functools import partial
 from pathlib import Path
+from shutil import rmtree
 
+from haddock.core.defaults import ANA_FOLDER, TRACEBACK_FOLDER
 from haddock.libs.libutil import non_negative_int, remove_folder
 from haddock.modules import get_module_steps_folders
 
@@ -62,6 +64,31 @@ def remove_folders_after_number(run_dir: Path, num: int) -> None:
         if int(folder.split('_')[0]) >= num
         ]
     # Loop over folders to remove
-    for torm_folder in from_num_folders:
-        remove_folder(Path(run_dir, torm_folder))
+    for toremove_folder in from_num_folders:
+        remove_folder(Path(run_dir, toremove_folder))
     return
+
+
+def preprocess_restart_from(rundir: str, restart_from: int) -> None:
+    """Remove all folders and files that are downstream of restart index.
+
+    Also remove analyses directories and traceback.
+
+    Parameters
+    ----------
+    rundir : str
+        Workflow run directory
+    module_index : int
+        Index of module to restart from
+    """
+    # Remove modules data after index
+    remove_folders_after_number(rundir, restart_from)
+    # Remove data for corresponding modules
+    _data_dir = Path(rundir, "data")
+    remove_folders_after_number(_data_dir, restart_from)
+    # Remove analysis folders after index
+    _analysis_dir = Path(rundir, ANA_FOLDER)
+    remove_folders_after_number(_analysis_dir, restart_from)
+    # Remove traceback directory
+    _traceback_dir = Path(rundir, TRACEBACK_FOLDER)
+    rmtree(_traceback_dir, ignore_errors=True)

tests/test_gear_restart.py

@@ -1,9 +1,13 @@
 """Test gear.restart_run."""
 import argparse
-
+import os
 import pytest
+import tempfile
+
+from pathlib import Path
 
 from haddock.gear import restart_run
+from haddock.core.defaults import ANA_FOLDER, TRACEBACK_FOLDER
 
 
 def test_has_help():
@@ -65,3 +69,38 @@ def test_restart_cli_error(n):
         ap.parse_args(f'--restart {n}'.split())
     assert exit.type == SystemExit
     assert exit.value.code == 2
+
+
+def test_preprocess_restart_from():
+    """Test removal of downstream directories."""
+    with tempfile.TemporaryDirectory() as tmpdir:
+        # Build mimic of previous run directories
+        module_dirs = ["topoaa", "rigidbody", "caprieval"]
+        for module_index, module_name in enumerate(module_dirs):
+            os.makedirs(f"{tmpdir}/data/{module_index}_{module_name}")
+            os.makedirs(f"{tmpdir}/{module_index}_{module_name}")
+            if module_name == "caprieval":
+                os.makedirs(
+                    f"{tmpdir}/{ANA_FOLDER}/{module_index}_{module_name}_analysis"
+                    )
+        os.makedirs(f"{tmpdir}/{TRACEBACK_FOLDER}")
+
+        # Test restart preprocessing function
+        restart_run.preprocess_restart_from(Path(tmpdir), 2)
+
+        # Verify they were removed
+        expected_to_be_removed = [
+            f"{tmpdir}/{TRACEBACK_FOLDER}",
+            f"{tmpdir}/{ANA_FOLDER}/2_caprieval_analysis",
+            f"{tmpdir}/2_caprieval",
+        ]
+        expected_to_stay_there = [
+            f"{tmpdir}/1_rigidbody",
+            f"{tmpdir}/data/1_rigidbody",
+            f"{tmpdir}/0_topoaa",
+            f"{tmpdir}/data/0_topoaa",
+        ]
+        for should_not_exist in expected_to_be_removed:
+            assert not os.path.exists(should_not_exist)
+        for should_exist in expected_to_stay_there:
+            assert os.path.exists(should_exist)