diff --git a/integration_tests/test_full_workflow.py b/integration_tests/test_full_workflow.py
index ad351ba1f..51aeb6278 100644
--- a/integration_tests/test_full_workflow.py
+++ b/integration_tests/test_full_workflow.py
@@ -2,8 +2,13 @@
from pathlib import Path
import os
import shutil
-from haddock.libs.libworkflow import WorkflowManager
+
+from haddock.clis.cli import main as cli_main
+from haddock.clis.cli_analyse import main as cli_analyse
+from haddock.clis.cli_re import maincli
from haddock.core.typing import Any
+from haddock.libs.libworkflow import WorkflowManager
+
from integration_tests import GOLDEN_DATA
@@ -66,7 +71,7 @@ def test_interactive_analysis_on_workflow(monkeypatch):
monkeypatch.chdir(tmpdir)
- from haddock.clis.cli import main as cli_main
+
cli_main(
Path("workflow.cfg"),
)
@@ -85,7 +90,7 @@ def test_interactive_analysis_on_workflow(monkeypatch):
# now running interactive re-clustering
clustfcc_dir = f"{run_dir}/2_clustfcc"
- from haddock.clis.cli_re import maincli
+
# faking sys.argv in input to haddock3-re
monkeypatch.setattr("sys.argv",
["haddock3-re", "clustfcc", clustfcc_dir, "-f", "0.7"]
@@ -106,14 +111,15 @@ def test_interactive_analysis_on_workflow(monkeypatch):
assert Path(run_dir, "3_caprieval_interactive/capri_ss.tsv").exists() is True
# now analyse the interactive folders
- from haddock.clis.cli_analyse import main as cli_analyse
- cli_analyse(run_dir,
- [2,3],
- 10,
- format=None,
- scale=None,
- is_cleaned=True,
- inter=True)
+ cli_analyse(
+ run_dir,
+ [2, 3],
+ 10,
+ format=None,
+ scale=None,
+ is_cleaned=True,
+ inter=True,
+ )
exp_clustfcc_dir = Path(run_dir, "analysis", "2_clustfcc_interactive_analysis")
exp_caprieval_dir = Path(run_dir, "analysis", "3_caprieval_interactive_analysis")
assert os.path.isdir(exp_clustfcc_dir) is True
diff --git a/src/haddock/clis/cli_analyse.py b/src/haddock/clis/cli_analyse.py
index a2df10255..1b529d88d 100644
--- a/src/haddock/clis/cli_analyse.py
+++ b/src/haddock/clis/cli_analyse.py
@@ -370,9 +370,9 @@ def get_top_ranked_mapping(
cluster_ranking: ClRank,
clustered_topX: int = 4,
unclustered_topX: int = 10,
- ) -> dict[Path, str]:
+ ) -> dict[Path, Path]:
# Set mapping of generated files
- top_ranked_mapping: dict[Path, str] = {}
+ top_ranked_mapping: dict[Path, Path] = {}
# Read table
capri_df = read_capri_table(capri_filename, comment="#")
@@ -413,15 +413,15 @@ def get_top_ranked_mapping(
struct_gz = Path(f"{struct}.gz")
# copy the structure
if Path(struct).exists():
- top_ranked_mapping[struct] = target_name
+ top_ranked_mapping[struct] = Path(target_name)
elif struct_gz.exists():
- top_ranked_mapping[struct_gz] = target_name
+ top_ranked_mapping[struct_gz] = Path(target_name)
else:
log.warning(f"structure {struct} not found")
return top_ranked_mapping
def zip_top_ranked(
- top_ranked_mapping: dict[Path, str],
+ top_ranked_mapping: dict[Path, Path],
summary_name: str,
gen_archive: bool,
) -> Optional[Path]:
@@ -451,9 +451,9 @@ def zip_top_ranked(
for ori_fpath, new_name in top_ranked_mapping.items():
# If already compressed
if ori_fpath.suffix == ".gz":
- copied_fpath = shutil.copy(ori_fpath, ".")
+ copied_fpath = Path(shutil.copy(ori_fpath, "."))
# unpack the file
- _unpack_gz(copied_fpath.name)
+ _unpack_gz(copied_fpath)
# Rename it
shutil.move(copied_fpath.name.replace(".gz", ""), new_name)
else:
@@ -482,7 +482,7 @@ def zip_top_ranked(
# Create new path
next_filepath = Path(output_fname, str(new_name))
# Hold it in mapping dict
- top_ranked_mapping[ori_fpath] = str(next_filepath)
+ top_ranked_mapping[ori_fpath] = Path(next_filepath)
# Displace file
shutil.move(new_name, top_ranked_mapping[ori_fpath])
log.info(f"Top structures copied into {output_fname}!")
@@ -778,13 +778,12 @@ def main(
offline=offline,
mode=mode,
ncores=ncores,
- #self_contained=self_contained,
- self_contained=True,
+ self_contained=self_contained,
)
except Exception as e:
log.warning(
f"Could not execute the analysis for step {step}. "
- f"The following error occurred {e}"
+ f"The following error occurred: {e}"
)
bad_folder_paths.append(target_path)
else:
diff --git a/src/haddock/libs/libplots.py b/src/haddock/libs/libplots.py
index b85f2bae7..18e3bcd46 100644
--- a/src/haddock/libs/libplots.py
+++ b/src/haddock/libs/libplots.py
@@ -884,7 +884,7 @@ def clt_table_handler(
topX_clusters: int = 10,
clustered_topX: int = 4,
unclustered_topX: int = 10,
- top_ranked_mapping: Optional[dict[Path, str]] = None,
+ top_ranked_mapping: Optional[dict[Path, Path]] = None,
) -> pd.DataFrame:
"""
Create a dataframe including data for tables.
@@ -914,29 +914,30 @@ def clt_table_handler(
clusters_df = clusters_df.round(2)
structs_df = structs_df.round(2)
+ # if the run will be cleaned, the structures are going to be gzipped
if not top_ranked_mapping:
- # if the run will be cleaned, the structures are going to be gzipped
- if is_cleaned and not top_ranked_mapping:
+ if is_cleaned:
# substitute the values in the df by adding .gz at the end
structs_df['model'] = structs_df['model'].replace(
to_replace=r"(\.pdb)$", value=r".pdb.gz", regex=True,
- )
-
- # ss_file is in NN_caprieval/ while report is in
- # analysis/NN_caprieval_analysis/
- # need to correct model paths by prepending ../
- def correct_relative_paths(
- path: str,
- top_ranked_mapping: Optional[dict[Path, str]],
- ) -> str:
- try:
- new_path = top_ranked_mapping[Path(path)]
- except KeyError:
- new_path = f"../{path}"
- return new_path
- structs_df['model'] = structs_df['model'].apply(
- lambda x: correct_relative_paths(x, top_ranked_mapping)
- )
+ )
+ else:
+ # ss_file is in NN_caprieval/ while report is in
+ # analysis/NN_caprieval_analysis/
+ # need to correct model paths by prepending ../
+ def correct_relative_paths(
+ path: str,
+ top_ranked_mapping: Optional[dict[Path, Path]],
+ ) -> str:
+ try:
+ new_path = top_ranked_mapping[path]
+ except (KeyError, TypeError, ):
+ new_path = f"../{path}"
+ return new_path
+
+ structs_df['model'] = structs_df['model'].apply(
+ lambda x: correct_relative_paths(x, top_ranked_mapping)
+ )
is_unclustered = clusters_df["cluster_rank"].unique().tolist() == ["-"]
# If unclustered, we only want to show the top 10 structures in a table.