From 257c8138464b00bdc3c7983f678caf7252f077a1 Mon Sep 17 00:00:00 2001 From: VGPReys Date: Thu, 19 Sep 2024 09:47:45 +0200 Subject: [PATCH 1/5] less_io to debug --- .../peptide-cyclisation/cyclise-peptide-full.cfg | 2 +- .../peptide-cyclisation/cyclise-peptide-test.cfg | 2 +- integration_tests/test_caprieval.py | 4 ++-- integration_tests/test_rigidbody.py | 4 ++-- src/haddock/libs/libcns.py | 4 ++-- .../modules/analysis/caprieval/__init__.py | 9 ++++++--- src/haddock/modules/analysis/caprieval/capri.py | 6 +++--- src/haddock/modules/defaults.yaml | 15 ++++++++------- src/haddock/modules/refinement/emref/__init__.py | 2 +- .../modules/refinement/flexref/__init__.py | 2 +- src/haddock/modules/refinement/mdref/__init__.py | 2 +- .../modules/sampling/rigidbody/__init__.py | 4 ++-- src/haddock/modules/scoring/emscoring/__init__.py | 2 +- src/haddock/modules/scoring/mdscoring/__init__.py | 2 +- src/haddock/modules/topology/topoaa/__init__.py | 2 +- tests/test_libcns.py | 2 +- 16 files changed, 34 insertions(+), 30 deletions(-) diff --git a/examples/peptide-cyclisation/cyclise-peptide-full.cfg b/examples/peptide-cyclisation/cyclise-peptide-full.cfg index 197443eda..13d4bd240 100644 --- a/examples/peptide-cyclisation/cyclise-peptide-full.cfg +++ b/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 diff --git a/examples/peptide-cyclisation/cyclise-peptide-test.cfg b/examples/peptide-cyclisation/cyclise-peptide-test.cfg index ff659b78d..b03976762 100644 --- a/examples/peptide-cyclisation/cyclise-peptide-test.cfg +++ b/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 diff --git a/integration_tests/test_caprieval.py b/integration_tests/test_caprieval.py index ab57cec60..48f87c56d 100644 --- a/integration_tests/test_caprieval.py +++ b/integration_tests/test_caprieval.py @@ -330,11 +330,11 @@ def test_caprieval_default( ) -def test_caprieval_less_io( +def test_caprieval_debug( 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() diff --git a/integration_tests/test_rigidbody.py b/integration_tests/test_rigidbody.py index aef37fe10..34f9da2a1 100644 --- a/integration_tests/test_rigidbody.py +++ b/integration_tests/test_rigidbody.py @@ -122,7 +122,7 @@ 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) @@ -130,7 +130,7 @@ def test_rigidbody_less_io(rigidbody_module): 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.params["debug"] = False rigidbody_module.run() diff --git a/src/haddock/libs/libcns.py b/src/haddock/libs/libcns.py index fae999f10..24d4b13f7 100644 --- a/src/haddock/libs/libcns.py +++ b/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") diff --git a/src/haddock/modules/analysis/caprieval/__init__.py b/src/haddock/modules/analysis/caprieval/__init__.py index 4c38e5aea..4873a86af 100644 --- a/src/haddock/modules/analysis/caprieval/__init__.py +++ b/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 = not self.params["debug"] and self.params["mode"] == "local" # Each model is a job; this is not the most efficient way # but by assigning each model to an individual job @@ -133,7 +133,7 @@ def _run(self) -> None: path=Path("."), reference=reference, params=self.params, - less_io=less_io, + debug=less_io, ) ) @@ -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) diff --git a/src/haddock/modules/analysis/caprieval/capri.py b/src/haddock/modules/analysis/caprieval/capri.py index 90cc4c558..a7eab5fe5 100644 --- a/src/haddock/modules/analysis/caprieval/capri.py +++ b/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] = True, ) -> 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 diff --git a/src/haddock/modules/defaults.yaml b/src/haddock/modules/defaults.yaml index 38f0ba99e..972a19b66 100644 --- a/src/haddock/modules/defaults.yaml +++ b/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: - default: false +debug: + default: true 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: diff --git a/src/haddock/modules/refinement/emref/__init__.py b/src/haddock/modules/refinement/emref/__init__.py index 7c62266d3..acdefc589 100644 --- a/src/haddock/modules/refinement/emref/__init__.py +++ b/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" diff --git a/src/haddock/modules/refinement/flexref/__init__.py b/src/haddock/modules/refinement/flexref/__init__.py index 63ffa8d8b..fca1801a6 100644 --- a/src/haddock/modules/refinement/flexref/__init__.py +++ b/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, ) diff --git a/src/haddock/modules/refinement/mdref/__init__.py b/src/haddock/modules/refinement/mdref/__init__.py index c74653c21..3d651f585 100644 --- a/src/haddock/modules/refinement/mdref/__init__.py +++ b/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" diff --git a/src/haddock/modules/sampling/rigidbody/__init__.py b/src/haddock/modules/sampling/rigidbody/__init__.py index 3eda396cc..e4a3f9fac 100644 --- a/src/haddock/modules/sampling/rigidbody/__init__.py +++ b/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, ) diff --git a/src/haddock/modules/scoring/emscoring/__init__.py b/src/haddock/modules/scoring/emscoring/__init__.py index 5a8ba788a..b23d7d4e5 100644 --- a/src/haddock/modules/scoring/emscoring/__init__.py +++ b/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, ) diff --git a/src/haddock/modules/scoring/mdscoring/__init__.py b/src/haddock/modules/scoring/mdscoring/__init__.py index 1920ba22b..88cdc9bfa 100644 --- a/src/haddock/modules/scoring/mdscoring/__init__.py +++ b/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, ) diff --git a/src/haddock/modules/topology/topoaa/__init__.py b/src/haddock/modules/topology/topoaa/__init__.py index b8b5ed111..a9cbc7a1c 100644 --- a/src/haddock/modules/topology/topoaa/__init__.py +++ b/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") diff --git a/tests/test_libcns.py b/tests/test_libcns.py index 8e9cd3316..c1978dc3c 100644 --- a/tests/test_libcns.py +++ b/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, ) From b0219906a534c3eb8e25085bde3d3a16163c9446 Mon Sep 17 00:00:00 2001 From: VGPReys Date: Thu, 19 Sep 2024 10:18:47 +0200 Subject: [PATCH 2/5] fix capri logics with debug --- integration_tests/test_caprieval.py | 2 +- src/haddock/modules/analysis/caprieval/__init__.py | 6 +++--- src/haddock/modules/analysis/caprieval/capri.py | 6 +++--- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/integration_tests/test_caprieval.py b/integration_tests/test_caprieval.py index 48f87c56d..6764f5faf 100644 --- a/integration_tests/test_caprieval.py +++ b/integration_tests/test_caprieval.py @@ -330,7 +330,7 @@ def test_caprieval_default( ) -def test_caprieval_debug( +def test_caprieval_nodebug( caprieval_module, model_list, expected_ss_data, expected_clt_data ): caprieval_module.previous_io = MockPreviousIO(path=caprieval_module.path) diff --git a/src/haddock/modules/analysis/caprieval/__init__.py b/src/haddock/modules/analysis/caprieval/__init__.py index 4873a86af..92f49e435 100644 --- a/src/haddock/modules/analysis/caprieval/__init__.py +++ b/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 = not self.params["debug"] 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, - debug=less_io, + less_io=_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, diff --git a/src/haddock/modules/analysis/caprieval/capri.py b/src/haddock/modules/analysis/caprieval/capri.py index a7eab5fe5..98efd7e62 100644 --- a/src/haddock/modules/analysis/caprieval/capri.py +++ b/src/haddock/modules/analysis/caprieval/capri.py @@ -179,7 +179,7 @@ def __init__( path: Path, reference: PDBPath, params: ParamMap, - debug: Optional[bool] = True, + less_io: Optional[bool] = True, ) -> 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.debug = debug + self.less_io = less_io 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 self.debug: + if not self.less_io: self.make_output() else: # The scheduler will use the return of the `run` method as the output of the tasks From 5357e081abb8a168e9beaf8750e4f80c25a810fe Mon Sep 17 00:00:00 2001 From: VGPReys Date: Fri, 20 Sep 2024 11:37:50 +0200 Subject: [PATCH 3/5] apply suggestions and set default value of debug to false --- src/haddock/modules/analysis/caprieval/__init__.py | 2 +- src/haddock/modules/analysis/caprieval/capri.py | 6 +++--- src/haddock/modules/defaults.yaml | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/haddock/modules/analysis/caprieval/__init__.py b/src/haddock/modules/analysis/caprieval/__init__.py index 92f49e435..894b8a906 100644 --- a/src/haddock/modules/analysis/caprieval/__init__.py +++ b/src/haddock/modules/analysis/caprieval/__init__.py @@ -133,7 +133,7 @@ def _run(self) -> None: path=Path("."), reference=reference, params=self.params, - less_io=_less_io, + debug=not _less_io, ) ) diff --git a/src/haddock/modules/analysis/caprieval/capri.py b/src/haddock/modules/analysis/caprieval/capri.py index 98efd7e62..47b8f85b0 100644 --- a/src/haddock/modules/analysis/caprieval/capri.py +++ b/src/haddock/modules/analysis/caprieval/capri.py @@ -179,7 +179,7 @@ def __init__( path: Path, reference: PDBPath, params: ParamMap, - less_io: Optional[bool] = True, + 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 diff --git a/src/haddock/modules/defaults.yaml b/src/haddock/modules/defaults.yaml index 972a19b66..5e4210915 100644 --- a/src/haddock/modules/defaults.yaml +++ b/src/haddock/modules/defaults.yaml @@ -139,7 +139,7 @@ offline: group: "execution" explevel: easy debug: - default: true + default: false type: boolean title: Write intermediate and stdout files. short: Write intermediate and stdout files. From a3d62784e74e9d809eee9fff5e256f21f255215c Mon Sep 17 00:00:00 2001 From: VGPReys Date: Fri, 20 Sep 2024 12:33:30 +0200 Subject: [PATCH 4/5] add debug = True in integration tests --- integration_tests/test_emref.py | 5 +++++ integration_tests/test_flexref.py | 4 +++- integration_tests/test_mdref.py | 6 +++++- integration_tests/test_restraints.py | 1 + integration_tests/test_rigidbody.py | 3 ++- integration_tests/test_topoaa.py | 3 +++ 6 files changed, 19 insertions(+), 3 deletions(-) diff --git a/integration_tests/test_emref.py b/integration_tests/test_emref.py index ab7ac0db2..be740fef8 100644 --- a/integration_tests/test_emref.py +++ b/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() diff --git a/integration_tests/test_flexref.py b/integration_tests/test_flexref.py index 9b60d989b..86ef51f64 100644 --- a/integration_tests/test_flexref.py +++ b/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() diff --git a/integration_tests/test_mdref.py b/integration_tests/test_mdref.py index 0102713b3..b6e20913f 100644 --- a/integration_tests/test_mdref.py +++ b/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() diff --git a/integration_tests/test_restraints.py b/integration_tests/test_restraints.py index 7aed72c54..bf2c6c719 100644 --- a/integration_tests/test_restraints.py +++ b/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() diff --git a/integration_tests/test_rigidbody.py b/integration_tests/test_rigidbody.py index 34f9da2a1..25dd0ba67 100644 --- a/integration_tests/test_rigidbody.py +++ b/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() @@ -130,7 +132,6 @@ def test_rigidbody_debug(rigidbody_module): rigidbody_module.params["cmrest"] = True rigidbody_module.params["mol_fix_origin_1"] = True rigidbody_module.params["mol_fix_origin_2"] = False - rigidbody_module.params["debug"] = False rigidbody_module.run() diff --git a/integration_tests/test_topoaa.py b/integration_tests/test_topoaa.py index 4eef9b39a..d516df4fe 100644 --- a/integration_tests/test_topoaa.py +++ b/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() From 1910851dba0db1fdb30ec73d682988cea97d61e1 Mon Sep 17 00:00:00 2001 From: Rodrigo Vargas Honorato Date: Fri, 20 Sep 2024 13:46:12 +0200 Subject: [PATCH 5/5] Update pages.yml --- .github/workflows/pages.yml | 10 +--------- 1 file changed, 1 insertion(+), 9 deletions(-) diff --git a/.github/workflows/pages.yml b/.github/workflows/pages.yml index 561f88626..4fdbc5523 100644 --- a/.github/workflows/pages.yml +++ b/.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: |