From 61cd7dbea418bab4b7e5b931c2cdd98596f77d29 Mon Sep 17 00:00:00 2001 From: cal3502 Date: Mon, 29 Jun 2026 13:18:50 -0400 Subject: [PATCH 01/36] Added the instanovo parser, need to add test and fix ruff errors --- urgap/unodes/instanovo/__init__.py | 1 + urgap/unodes/instanovo/instanovo_1_2_2.py | 149 ++++++++++++++++++++++ 2 files changed, 150 insertions(+) create mode 100644 urgap/unodes/instanovo/__init__.py create mode 100644 urgap/unodes/instanovo/instanovo_1_2_2.py diff --git a/urgap/unodes/instanovo/__init__.py b/urgap/unodes/instanovo/__init__.py new file mode 100644 index 0000000..8f7a5b3 --- /dev/null +++ b/urgap/unodes/instanovo/__init__.py @@ -0,0 +1 @@ +"""Init Instanovo Unode.""" \ No newline at end of file diff --git a/urgap/unodes/instanovo/instanovo_1_2_2.py b/urgap/unodes/instanovo/instanovo_1_2_2.py new file mode 100644 index 0000000..0f749da --- /dev/null +++ b/urgap/unodes/instanovo/instanovo_1_2_2.py @@ -0,0 +1,149 @@ +"""Urgap Instanovo_1_2_2 wrapper.""" + +import importlib.util +import logging +import os +import sys + +from pathlib import Path + +import urgap + + +class Instanovo(urgap.unode.UNodeBase): + """Urgap wrapper for the Instanovo de-novosearch engine. + + Instanovo is a de novo peptide sequencing program that sequences peptides from an mgf file into an csv file. + This requires a gpu to run, or else the program will not be able to complete and continue going forever. See publication provided under META_INFO[ + "citation"] for further info. + """ + + META_INFO = { + "name": "Instanovo", + "wrapper_version": {"major": 1, "minor": 2, "patch": 2}, + "versions": [ + {"version": "1.2.2", "exe_path": "$instanovo"}, + ], + "parameters_not_triggering_rerun": [], + "input_uftypes": { + urgap.uftypes.proteomics.converter.PYMZML_MGF: {"min": 1, "max": 1}, + urgap.uftypes.proteomics.denovosearch.INSTANOVO_YAML: {"min": 1, "max": 1}, + }, + "output_uftypes": { + urgap.uftypes.proteomics.denovosearch.INSTANOVO_CSV : {"min": 1, "max": 1}, + }, + "engine": None, + "engine_type": ("identification",), + "citation": """Eloff, K., Kalogeropoulos, K., Mabona, A. et al. InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments. + at Mach Intell 7, 565-579 (2025). https://doi.org/10.1038/s42256-025-01019-5""", + } + + def __init__(self, *args: str, **kwargs: str) -> None: + """Initialize Instanovo_1_2_2 class.""" + super().__init__(*args, **kwargs) + + def find_instanovo_configs(self) -> Path: + """Locate the instanovo package's built-in configs directory. + + Returns: + Path: Resolved path to the instanovo/configs directory. + + Raises: + FileNotFoundError: If the instanovo/configs directory could not + be located via the package spec or sys.path. + """ + # try to find the package spec first (works if package is installed/importable) + spec = importlib.util.find_spec("instanovo") + if spec and spec.submodule_search_locations: + pkg_path = Path(spec.submodule_search_locations[0]) + cfg = pkg_path / "configs" + if cfg.exists(): + return cfg.resolve() + + # fallback: scan sys.path entries for a possible instanovo/configs folder + for entry in map(Path, sys.path): + candidate = entry / "instanovo" / "configs" + if candidate.exists(): + return candidate.resolve() + + msg = "Could not locate instanovo/configs on this system" + raise FileNotFoundError(msg) + + def preflight( + self, + utrace: urgap.UTrace, + ) -> urgap.UTrace: + """Preflight routine for Instanovo_1 wrapper. + + During preflight, + - parameters are formatted + - mods are mapped and formatted + - param file is written + + Args: + utrace: Combination of urun_dict, ufile_list and unode.meta. + + Returns: + UTrace object, combination of urun_dict, ufile_list and unode.meta. + """ + input_params = utrace.urun_dict.parameters[ + f"{self.META_INFO['unode_full_identifier']}" + ] + mgf_file = utrace.input_files.get_path_objects_by_uftype( + urgap.uftypes.proteomics.converter.PYMZML_MGF, + )[0] + param_file = utrace.input_files.get_path_objects_by_uftype( + urgap.uftypes.proteomics.denovosearch.INSTANOVO_YAML, + )[0] + + output_csv = utrace.output_files.get_path_objects_by_uftype( + urgap.uftypes.proteomics.denovosearch.INSTANOVO_CSV, + )[0] + + # Get the directory containing YOUR custom config file + config_dir = Path(param_file).parent.resolve() + + # InstaNovo executes from its built-in configs directory, so we need + # to calculate the relative path from there to your custom config directory + instanovo_configs_dir = self.find_instanovo_configs() + + # Calculate relative path from InstaNovo's configs dir to your config dir + relative_config_path = os.path.relpath(config_dir, instanovo_configs_dir) + model_used = input_params["model_used"] + if model_used not in ["transformer", "diffusion"]: + logging.error( + "Unknown search mode %s. Search mode has to be either " + "'transformer' or 'diffusion'", + model_used, + ) + utrace.urun_dict.command_list = [ + str(self.exe_path), + f"{model_used}", + "predict", + "--data-path", + mgf_file, + "--output-path", + output_csv, + "--config-path", + relative_config_path, + "--config-name", + param_file.stem, + ] + return utrace + + def postflight( + self, + utrace: urgap.UTrace, + ) -> urgap.UTrace: + """Postflight routine for Instanovo_1 wrapper. + + During postflight the Instanovo native .csv output file is converted into the + pre-defined urgap output file, which is of csv format. + + Args: + utrace: Combination of urun_dict, ufile_list and unode.meta. + + Returns: + UTrace object, combination of urun_dict, ufile_list and unode.meta. + """ + return utrace From bc4aa7c39a0d2deae61c27cb04e7975c8e50f3e4 Mon Sep 17 00:00:00 2001 From: cal3502 Date: Tue, 30 Jun 2026 09:05:55 -0400 Subject: [PATCH 02/36] Added instanovo parser with tests --- .../wrappers/test_instanovo.py | 103 ++++++++++++++++++ urgap/unodes/instanovo/instanovo_1_2_2.py | 18 +-- 2 files changed, 112 insertions(+), 9 deletions(-) create mode 100644 tests/integrationtests/wrappers/test_instanovo.py diff --git a/tests/integrationtests/wrappers/test_instanovo.py b/tests/integrationtests/wrappers/test_instanovo.py new file mode 100644 index 0000000..08da583 --- /dev/null +++ b/tests/integrationtests/wrappers/test_instanovo.py @@ -0,0 +1,103 @@ +"""Integration test for Instanovo.""" + +from pathlib import Path + +import pytest + +import urgap + + +def test_instanovo_node_init() -> None: + """Test that the Instanovo node can be initialized.""" + instanovo_node = urgap.init_node("Instanovo:1.2.2") + assert instanovo_node is not None + + +def test_instanovo_ufile_construction(tmp_path: Path) -> None: + """Test that UFiles can be constructed with correct uftypes.""" + mgf_file = tmp_path / "test.pymzml.mgf" + yaml_file = tmp_path / "default.yaml" + mgf_file.touch() + yaml_file.touch() + + ufiles = urgap.UFileList( + [ + urgap.UFile( + uri=f"file://{mgf_file.parent}?uftype={urgap.uftypes.proteomics.converter.PYMZML_MGF}" + f"#{mgf_file.name}", + ), + urgap.UFile( + uri=f"file://{yaml_file.parent}?uftype={urgap.uftypes.proteomics.denovosearch.INSTANOVO_YAML}" + f"#{yaml_file.name}", + ), + ], + ) + + assert len(ufiles) == 2 + mgf_ufiles = ufiles.get_path_objects_by_uftype(urgap.uftypes.proteomics.converter.PYMZML_MGF) + yaml_ufiles = ufiles.get_path_objects_by_uftype(urgap.uftypes.proteomics.denovosearch.INSTANOVO_YAML) + assert len(mgf_ufiles) == 1 + assert len(yaml_ufiles) == 1 + + +def test_instanovo_urun_dict_transformer() -> None: + """Test that a URunDict with transformer mode can be constructed.""" + urun_dict = urgap.URunDict( + { + "parameters": { + "Instanovo:1.2.2": { + "model_used": "transformer", + }, + }, + "unode_parameters": { + "storage_base_uri": "file:///tmp", + }, + }, + ) + params = urun_dict.parameters["Instanovo:1.2.2"] + assert params["model_used"] == "transformer" + + +def test_instanovo_urun_dict_diffusion() -> None: + """Test that a URunDict with diffusion mode can be constructed.""" + urun_dict = urgap.URunDict( + { + "parameters": { + "Instanovo:1.2.2": { + "model_used": "diffusion", + }, + }, + "unode_parameters": { + "storage_base_uri": "file:///tmp", + }, + }, + ) + params = urun_dict.parameters["Instanovo:1.2.2"] + assert params["model_used"] == "diffusion" + + +def test_instanovo_invalid_model_mode() -> None: + """Test that an invalid model_used value is not one of the accepted modes.""" + invalid_mode = "invalid_mode" + valid_modes = ["transformer", "diffusion"] + assert invalid_mode not in valid_modes + + +@pytest.mark.parametrize("model_used", ["transformer", "diffusion"]) +def test_instanovo_urun_dict_model_used(model_used: str) -> None: + """Test that model_used is correctly stored in URunDict parameters.""" + urun_dict = urgap.URunDict( + { + "parameters": { + "Instanovo:1.2.2": { + "model_used": model_used, + }, + }, + "unode_parameters": { + "storage_base_uri": "file:///tmp", + }, + }, + ) + params = urun_dict.parameters["Instanovo:1.2.2"] + assert params["model_used"] == model_used + assert params["model_used"] in ["transformer", "diffusion"] diff --git a/urgap/unodes/instanovo/instanovo_1_2_2.py b/urgap/unodes/instanovo/instanovo_1_2_2.py index 0f749da..1ab2107 100644 --- a/urgap/unodes/instanovo/instanovo_1_2_2.py +++ b/urgap/unodes/instanovo/instanovo_1_2_2.py @@ -12,7 +12,7 @@ class Instanovo(urgap.unode.UNodeBase): """Urgap wrapper for the Instanovo de-novosearch engine. - + Instanovo is a de novo peptide sequencing program that sequences peptides from an mgf file into an csv file. This requires a gpu to run, or else the program will not be able to complete and continue going forever. See publication provided under META_INFO[ "citation"] for further info. @@ -44,10 +44,10 @@ def __init__(self, *args: str, **kwargs: str) -> None: def find_instanovo_configs(self) -> Path: """Locate the instanovo package's built-in configs directory. - + Returns: Path: Resolved path to the instanovo/configs directory. - + Raises: FileNotFoundError: If the instanovo/configs directory could not be located via the package spec or sys.path. @@ -74,15 +74,15 @@ def preflight( utrace: urgap.UTrace, ) -> urgap.UTrace: """Preflight routine for Instanovo_1 wrapper. - + During preflight, - parameters are formatted - mods are mapped and formatted - param file is written - + Args: utrace: Combination of urun_dict, ufile_list and unode.meta. - + Returns: UTrace object, combination of urun_dict, ufile_list and unode.meta. """ @@ -136,13 +136,13 @@ def postflight( utrace: urgap.UTrace, ) -> urgap.UTrace: """Postflight routine for Instanovo_1 wrapper. - + During postflight the Instanovo native .csv output file is converted into the pre-defined urgap output file, which is of csv format. - + Args: utrace: Combination of urun_dict, ufile_list and unode.meta. - + Returns: UTrace object, combination of urun_dict, ufile_list and unode.meta. """ From 598f0d9974feb01c17970bad356d01b0aaf8dea4 Mon Sep 17 00:00:00 2001 From: cal3502 Date: Tue, 30 Jun 2026 09:08:31 -0400 Subject: [PATCH 03/36] Added relevant uftypes --- urgap/uftypes/proteomics.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/urgap/uftypes/proteomics.py b/urgap/uftypes/proteomics.py index 8bb8a1e..026d409 100644 --- a/urgap/uftypes/proteomics.py +++ b/urgap/uftypes/proteomics.py @@ -28,6 +28,9 @@ proteomics.denovosearch = types.SimpleNamespace() proteomics.denovosearch.NOVOR_CSV = ".novor.csv" +urgap.uftypes.proteomics.denovosearch.INSTANOVO_YAML = ".instanovo.yaml" +urgap.uftypes.proteomics.denovosearch.INSTANOVO_CSV = ".instanovo.csv" + proteomics.converter = types.SimpleNamespace() proteomics.converter.ANY = "proteomics.converter.ANY" From 8c717219ab20e49c5fd74c9aa54c0aad10347d16 Mon Sep 17 00:00:00 2001 From: cal3502 Date: Tue, 30 Jun 2026 09:25:50 -0400 Subject: [PATCH 04/36] Updated pyproject to include Instanovo --- pyproject.toml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 5f7fb20..48af259 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -10,7 +10,8 @@ requires-python = ">=3.11" dependencies = [ "urgap[all]", "pymzml>=2.5.0", - "pyiohat>=1.9.0" + "pyiohat>=1.9.0", + "instanovo>=1.2.2" ] [project.optional-dependencies] From 2ba6bb8cbee34b6119ae3baaaf759ce6e9ca26a8 Mon Sep 17 00:00:00 2001 From: cal3502 Date: Tue, 30 Jun 2026 09:30:05 -0400 Subject: [PATCH 05/36] Fixed ruff errors --- urgap/unodes/instanovo/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/urgap/unodes/instanovo/__init__.py b/urgap/unodes/instanovo/__init__.py index 8f7a5b3..d37be57 100644 --- a/urgap/unodes/instanovo/__init__.py +++ b/urgap/unodes/instanovo/__init__.py @@ -1 +1 @@ -"""Init Instanovo Unode.""" \ No newline at end of file +"""Init Instanovo Unode.""" From 4449490a8f62a469809edfbd236950efae133195 Mon Sep 17 00:00:00 2001 From: cal3502 Date: Tue, 30 Jun 2026 10:00:31 -0400 Subject: [PATCH 06/36] Updated pyproject to include flowkit to fix a dependency error --- pyproject.toml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 48af259..0a5b180 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -11,7 +11,8 @@ dependencies = [ "urgap[all]", "pymzml>=2.5.0", "pyiohat>=1.9.0", - "instanovo>=1.2.2" + "instanovo>=1.2.2", + "flowkit>=1.0.0" ] [project.optional-dependencies] From 11d414b371fe39ab2eff1bb45543ee6ecb2d156c Mon Sep 17 00:00:00 2001 From: cal3502 Date: Tue, 30 Jun 2026 10:12:02 -0400 Subject: [PATCH 07/36] Removoed flowkit due to package discrepencies --- pyproject.toml | 1 - 1 file changed, 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 0a5b180..062bc22 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,7 +12,6 @@ dependencies = [ "pymzml>=2.5.0", "pyiohat>=1.9.0", "instanovo>=1.2.2", - "flowkit>=1.0.0" ] [project.optional-dependencies] From 12f78ad6143f2316e230d07ab283ea07fbd60da1 Mon Sep 17 00:00:00 2001 From: cal3502 Date: Tue, 30 Jun 2026 10:41:42 -0400 Subject: [PATCH 08/36] Removed Instanovo due to package discrepencies --- pyproject.toml | 1 - 1 file changed, 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 062bc22..a903869 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -11,7 +11,6 @@ dependencies = [ "urgap[all]", "pymzml>=2.5.0", "pyiohat>=1.9.0", - "instanovo>=1.2.2", ] [project.optional-dependencies] From 5bd3b68968c429c9d0867a397d6008b6621d0aae Mon Sep 17 00:00:00 2001 From: cal3502 Date: Tue, 30 Jun 2026 10:46:10 -0400 Subject: [PATCH 09/36] Updated Uftypes --- urgap/uftypes/proteomics.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/urgap/uftypes/proteomics.py b/urgap/uftypes/proteomics.py index 026d409..afa8b1c 100644 --- a/urgap/uftypes/proteomics.py +++ b/urgap/uftypes/proteomics.py @@ -28,8 +28,8 @@ proteomics.denovosearch = types.SimpleNamespace() proteomics.denovosearch.NOVOR_CSV = ".novor.csv" -urgap.uftypes.proteomics.denovosearch.INSTANOVO_YAML = ".instanovo.yaml" -urgap.uftypes.proteomics.denovosearch.INSTANOVO_CSV = ".instanovo.csv" +proteomics.denovosearch.INSTANOVO_YAML = ".instanovo.yaml" +proteomics.denovosearch.INSTANOVO_CSV = ".instanovo.csv" proteomics.converter = types.SimpleNamespace() From 3c43a74d08a2094de6e08832a0915137d364331e Mon Sep 17 00:00:00 2001 From: cal3502 Date: Tue, 30 Jun 2026 11:08:13 -0400 Subject: [PATCH 10/36] Added tests to test instanovo --- .../wrappers/test_instanovo.py | 67 +++++++++++++++++++ 1 file changed, 67 insertions(+) diff --git a/tests/integrationtests/wrappers/test_instanovo.py b/tests/integrationtests/wrappers/test_instanovo.py index 08da583..055091b 100644 --- a/tests/integrationtests/wrappers/test_instanovo.py +++ b/tests/integrationtests/wrappers/test_instanovo.py @@ -6,6 +6,10 @@ import urgap +import os +import subprocess +import time + def test_instanovo_node_init() -> None: """Test that the Instanovo node can be initialized.""" @@ -101,3 +105,66 @@ def test_instanovo_urun_dict_model_used(model_used: str) -> None: params = urun_dict.parameters["Instanovo:1.2.2"] assert params["model_used"] == model_used assert params["model_used"] in ["transformer", "diffusion"] + + +def test_instanovo_program_starts() -> None: + """Test that the instanovo CLI binary exists and starts executing.""" + proc = subprocess.Popen( + ["instanovo", "--help"], + stdout=subprocess.PIPE, + stderr=subprocess.PIPE, + ) + try: + time.sleep(2) + assert proc.poll() is None or proc.returncode == 0 + finally: + if proc.poll() is None: + proc.terminate() + proc.wait(timeout=5) + + +def test_instanovo_predict_process_starts(tmp_path: Path) -> None: + """Test that `instanovo predict` actually launches (not completes). + + Builds the config-path the same way Instanovo.preflight() does: relative + to instanovo's built-in configs directory, resolved via importlib. + """ + mgf_file = tmp_path / "test.pymzml.mgf" + output_csv = tmp_path / "output.instanovo.csv" + config_dir = tmp_path / "config" + config_dir.mkdir() + config_file = config_dir / "default.yaml" + mgf_file.touch() + config_file.write_text("model_used: transformer\n") + + instanovo_node = urgap.init_node("Instanovo:1.2.2") + instanovo_configs_dir = instanovo_node.find_instanovo_configs() + relative_config_path = os.path.relpath(config_dir, instanovo_configs_dir) + + model_used = "transformer" + proc = subprocess.Popen( + [ + "instanovo", + model_used, + "predict", + "--data-path", + str(mgf_file), + "--output-path", + str(output_csv), + "--config-path", + relative_config_path, + "--config-name", + config_file.stem, + ], + stdout=subprocess.PIPE, + stderr=subprocess.PIPE, + ) + try: + time.sleep(3) + # 127 = command not found; anything else (still running, or failing + # later on bad/empty data) confirms the process actually started. + assert proc.poll() is None or proc.returncode != 127 + finally: + if proc.poll() is None: + proc.terminate() + proc.wait(timeout=5) \ No newline at end of file From 42234aeba3e37038bb7d134f1d4ed7820498f129 Mon Sep 17 00:00:00 2001 From: cal3502 Date: Tue, 30 Jun 2026 11:43:53 -0400 Subject: [PATCH 11/36] Changed Instanovo pytest to better check that the unode is actually able to run --- tests/data/instanovo_params/default.yaml | 116 + tests/data/mgfs/BSA1.mgf | 133179 +++++++++++++++ .../wrappers/test_instanovo.py | 110 +- 3 files changed, 133350 insertions(+), 55 deletions(-) create mode 100644 tests/data/instanovo_params/default.yaml create mode 100644 tests/data/mgfs/BSA1.mgf diff --git a/tests/data/instanovo_params/default.yaml b/tests/data/instanovo_params/default.yaml new file mode 100644 index 0000000..f498000 --- /dev/null +++ b/tests/data/instanovo_params/default.yaml @@ -0,0 +1,116 @@ +# Data paths and output location +data_path: # type: .mgf, .mzml or any other filetype supported by SpectrumDataFrame +instanovo_model: instanovo-v1.2.0 # type: model id or path to a *.ckpt file +instanovo_plus_model: instanovoplus-v1.1.0 # type: model id or path to a *.ckpt file +output_path: # type: .csv +knapsack_path: # type: directory + +# Data type only used if data_path is a directory. +data_type: # .csv, .mgf, .mzml, .mzxml + +# Inference mode +denovo: True +num_beams: 5 # 1 defaults to greedy search with basic filtering +max_length: 40 +max_charge: 10 # Must be <= model max charge +isotope_error_range: [0, 1] +subset: 1.0 # Subset of dataset to perform inference on, useful for debugging. Represented as a float between 0 and 1. +use_knapsack: False +save_all_predictions: True + +# Encoder output saving +save_encoder_outputs: False +encoder_output_path: # type: .parquet +encoder_output_reduction: mean # mean, max, sum, full +# Note: Full encoder output reduction is not yet implemented. + +# Refine mode +refine: false +refinement_path: # type: .csv +prediction_refine_col: predictions_tokenised +prediction_confidence_col: log_probs +refinement_id_col: spectrum_id +dataset_id_col: spectrum_id +refine_all: False # If True, all predictions will be refined +refine_threshold: 0.9 # Only predictions with a confidence score less than this will be refined + +# Prediction columns +prediction_tokenised_col: predictions_tokenised +prediction_col: predictions +log_probs_col: log_probs +token_log_probs_col: token_log_probs + +# These two only work in greedy search +# Residues whose log probability will be set to -inf +suppressed_residues: ["(+25.98)"] # legacy +# Stop model from predicting n-terminal modifications anywhere along the sequence +disable_terminal_residues_anywhere: True + +# Run config +num_workers: 16 +batch_size: 128 +pin_memory: False +prefetch_factor: +force_cpu: False +fp16: True +mps: False +force_fp32: False + +# Logging +log_interval: 50 +use_basic_logging: True + +# Metrics config, does not affect saved results +filter_precursor_ppm: 20 +filter_confidence: 1e-4 +filter_fdr_threshold: 0.05 + +# Dataset specific configs +residue_remapping: + "M(ox)": "M[UNIMOD:35]" # Oxidation or Hydroxylation + "M(+15.99)": "M[UNIMOD:35]" + "S(p)": "S[UNIMOD:21]" # Phosphorylation + "T(p)": "T[UNIMOD:21]" + "Y(p)": "Y[UNIMOD:21]" + "S(+79.97)": "S[UNIMOD:21]" + "T(+79.97)": "T[UNIMOD:21]" + "Y(+79.97)": "Y[UNIMOD:21]" + "Q(+0.98)": "Q[UNIMOD:7]" # Deamidation + "N(+0.98)": "N[UNIMOD:7]" + "Q(+.98)": "Q[UNIMOD:7]" + "N(+.98)": "N[UNIMOD:7]" + "C(+57.02)": "C[UNIMOD:4]" # Carboxyamidomethylation + "R(+0.984016)": "R[UNIMOD:7]" # Arginine citrullination + "P(+15.994915)": "P[UNIMOD:35]" # Proline hydroxylation + "(+42.01)": "[UNIMOD:1]" # Acetylation + "(+43.01)": "[UNIMOD:5]" # Carbamylation + "(-17.03)": "[UNIMOD:385]" # Loss of ammonia + +column_map: + "Modified sequence": "modified_sequence" + "MS/MS m/z": "precursor_mz" + # "m/z": "precursor_mz" + "Mass": "precursor_mass" + "Charge": "precursor_charge" + "Mass values": "mz_array" + "Mass spectrum": "mz_array" + "Intensity": "intensity_array" + "Raw intensity spectrum": "intensity_array" + "Scan number": "scan_number" + +# A list of columns that (if found) will be retained in output csv +index_columns: + - "id" + - "experiment_name" + - "evidence_index" + - "scan_number" + - "spectrum_id" + - "global_index" + - "spectrum_index" + - "file_index" + - "sample" + - "file" + - "index" + - "fileno" + - "precursor_mz" + - "precursor_charge" diff --git a/tests/data/mgfs/BSA1.mgf b/tests/data/mgfs/BSA1.mgf new file mode 100644 index 0000000..fb44de5 --- /dev/null +++ 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"diffusion"]) + def test_instanovo_urun_dict_model_used(model_used: str) -> None: """Test that model_used is correctly stored in URunDict parameters.""" urun_dict = urgap.URunDict( @@ -107,64 +110,61 @@ def test_instanovo_urun_dict_model_used(model_used: str) -> None: assert params["model_used"] in ["transformer", "diffusion"] -def test_instanovo_program_starts() -> None: - """Test that the instanovo CLI binary exists and starts executing.""" - proc = subprocess.Popen( - ["instanovo", "--help"], - stdout=subprocess.PIPE, - stderr=subprocess.PIPE, +def test_instanovo_starts(tmp_dir, caplog): + urd = urgap.URunDict( + { + "parameters": { + "Instanovo:1.2.2": { + "model_used": "transformer", + }, + }, + "unode_parameters": { + "storage_base_uri": f"file://{tmp_dir}", + }, + }, + ) + ufiles = urgap.UFileList( + [ + urgap.UFile( + uri=f"file://" + f"{urgap._test_folder}/data?uftype={urgap.uftypes.proteomics.converter.PYMZML_MGF}" + f"#mgfs/BSA1.mgf" + ), + urgap.UFile( + uri=f"file://" + f"{urgap._test_folder}/data?uftype={urgap.uftypes.proteomics.denovosearch.INSTANOVO_YAML}" + f"#instanovo_params/default.yaml" + ), + ], ) - try: - time.sleep(2) - assert proc.poll() is None or proc.returncode == 0 - finally: - if proc.poll() is None: - proc.terminate() - proc.wait(timeout=5) - - -def test_instanovo_predict_process_starts(tmp_path: Path) -> None: - """Test that `instanovo predict` actually launches (not completes). - - Builds the config-path the same way Instanovo.preflight() does: relative - to instanovo's built-in configs directory, resolved via importlib. - """ - mgf_file = tmp_path / "test.pymzml.mgf" - output_csv = tmp_path / "output.instanovo.csv" - config_dir = tmp_path / "config" - config_dir.mkdir() - config_file = config_dir / "default.yaml" - mgf_file.touch() - config_file.write_text("model_used: transformer\n") instanovo_node = urgap.init_node("Instanovo:1.2.2") - instanovo_configs_dir = instanovo_node.find_instanovo_configs() - relative_config_path = os.path.relpath(config_dir, instanovo_configs_dir) - model_used = "transformer" - proc = subprocess.Popen( - [ - "instanovo", - model_used, - "predict", - "--data-path", - str(mgf_file), - "--output-path", - str(output_csv), - "--config-path", - relative_config_path, - "--config-name", - config_file.stem, - ], - stdout=subprocess.PIPE, - stderr=subprocess.PIPE, + thread = threading.Thread( + target=instanovo_node.run, + kwargs={"urun_dict": urd, "ufiles": ufiles}, + daemon=True, ) try: - time.sleep(3) - # 127 = command not found; anything else (still running, or failing - # later on bad/empty data) confirms the process actually started. - assert proc.poll() is None or proc.returncode != 127 + with caplog.at_level(logging.INFO): + thread.start() + + deadline = time.monotonic() + 10 + launched = False + while time.monotonic() < deadline: + if "Executing command list: " in caplog.text: + launched = True + break + time.sleep(0.2) + + assert "Running execute ..." in caplog.text + assert launched, "instanovo command was never launched" + assert ( + "instanovo diffusion predict" in caplog.text + or "instanovo transformer predict" in caplog.text + ) finally: - if proc.poll() is None: - proc.terminate() - proc.wait(timeout=5) \ No newline at end of file + for proc in psutil.process_iter(["cmdline"]): + cmdline = " ".join(proc.info["cmdline"] or []) + if "instanovo" in cmdline and "predict" in cmdline: + proc.terminate() \ No newline at end of file From cd765a6eb143380a8141ce6d3edb9a0b7e0e936b Mon Sep 17 00:00:00 2001 From: cal3502 Date: Tue, 7 Jul 2026 13:05:57 -0400 Subject: [PATCH 12/36] Changes to test file to check the command line and unode to allow command line parameters --- .../wrappers/test_instanovo.py | 196 ++++++++++-------- urgap/unodes/instanovo/instanovo_1_2_2.py | 71 +++++-- 2 files changed, 158 insertions(+), 109 deletions(-) diff --git a/tests/integrationtests/wrappers/test_instanovo.py b/tests/integrationtests/wrappers/test_instanovo.py index 65cb809..91a5bc6 100644 --- a/tests/integrationtests/wrappers/test_instanovo.py +++ b/tests/integrationtests/wrappers/test_instanovo.py @@ -12,159 +12,173 @@ import logging import threading import psutil - -def test_instanovo_node_init() -> None: - """Test that the Instanovo node can be initialized.""" - instanovo_node = urgap.init_node("Instanovo:1.2.2") - assert instanovo_node is not None +from unittest.mock import patch -def test_instanovo_ufile_construction(tmp_path: Path) -> None: - """Test that UFiles can be constructed with correct uftypes.""" - mgf_file = tmp_path / "test.pymzml.mgf" - yaml_file = tmp_path / "default.yaml" - mgf_file.touch() - yaml_file.touch() +def test_instanovo_command_construction_yaml_no_model(tmp_path: Path) -> None: + """Test that command_list is built correctly with no model_used, using a yaml config file.""" + urun_dict = urgap.URunDict( + { + "parameters": { + "Instanovo:1.2.2": {}, + }, + "unode_parameters": { + "storage_base_uri": f"file://{tmp_path}", + }, + }, + ) ufiles = urgap.UFileList( [ urgap.UFile( - uri=f"file://{mgf_file.parent}?uftype={urgap.uftypes.proteomics.converter.PYMZML_MGF}" - f"#{mgf_file.name}", + uri=f"file://{urgap._test_folder}/data?uftype=" + f"{urgap.uftypes.proteomics.converter.PYMZML_MGF}#mgfs/BSA1.mgf", ), urgap.UFile( - uri=f"file://{yaml_file.parent}?uftype={urgap.uftypes.proteomics.denovosearch.INSTANOVO_YAML}" - f"#{yaml_file.name}", + uri=f"file://{urgap._test_folder}/data?uftype=" + f"{urgap.uftypes.proteomics.denovosearch.INSTANOVO_YAML}#instanovo_params/default.yaml", ), ], ) - assert len(ufiles) == 2 - mgf_ufiles = ufiles.get_path_objects_by_uftype(urgap.uftypes.proteomics.converter.PYMZML_MGF) - yaml_ufiles = ufiles.get_path_objects_by_uftype(urgap.uftypes.proteomics.denovosearch.INSTANOVO_YAML) - assert len(mgf_ufiles) == 1 - assert len(yaml_ufiles) == 1 + instanovo_node = urgap.init_node("Instanovo:1.2.2") + + with patch("subprocess.run") as mock_run: + mock_run.return_value.returncode = 0 + mock_run.return_value.stdout = "" + with pytest.raises(FileNotFoundError): + instanovo_node.run(ufiles, urun_dict) + actual_cmd = [str(c) for c in mock_run.call_args[0][0]] -def test_instanovo_urun_dict_transformer() -> None: - """Test that a URunDict with transformer mode can be constructed.""" + assert actual_cmd[0].endswith("instanovo") + assert actual_cmd[1] == "predict" + assert actual_cmd[2] == "--data-path" + assert actual_cmd[3].endswith("BSA1.mgf") + assert actual_cmd[4] == "--output-path" + assert actual_cmd[6] == "--config-path" + assert actual_cmd[8] == "--config-name" + assert actual_cmd[9] == "default" + assert len(actual_cmd) == 10 + + +def test_instanovo_command_construction_with_model_and_cli_params(tmp_path: Path) -> None: + """Test that command_list includes model_used and CLI overrides when no yaml file is provided.""" urun_dict = urgap.URunDict( { "parameters": { "Instanovo:1.2.2": { "model_used": "transformer", + "num_beams": 5, }, }, "unode_parameters": { - "storage_base_uri": "file:///tmp", + "storage_base_uri": f"file://{tmp_path}", }, }, ) - params = urun_dict.parameters["Instanovo:1.2.2"] - assert params["model_used"] == "transformer" - -def test_instanovo_urun_dict_diffusion() -> None: - """Test that a URunDict with diffusion mode can be constructed.""" - urun_dict = urgap.URunDict( - { - "parameters": { - "Instanovo:1.2.2": { - "model_used": "diffusion", - }, - }, - "unode_parameters": { - "storage_base_uri": "file:///tmp", - }, - }, + ufiles = urgap.UFileList( + [ + urgap.UFile( + uri=f"file://{urgap._test_folder}/data?uftype=" + f"{urgap.uftypes.proteomics.converter.PYMZML_MGF}#mgfs/BSA1.mgf", + ), + ], ) - params = urun_dict.parameters["Instanovo:1.2.2"] - assert params["model_used"] == "diffusion" + instanovo_node = urgap.init_node("Instanovo:1.2.2") + + with patch("subprocess.run") as mock_run: + mock_run.return_value.returncode = 0 + mock_run.return_value.stdout = "" + with pytest.raises(FileNotFoundError): + instanovo_node.run(ufiles, urun_dict) -def test_instanovo_invalid_model_mode() -> None: - """Test that an invalid model_used value is not one of the accepted modes.""" - invalid_mode = "invalid_mode" - valid_modes = ["transformer", "diffusion"] - assert invalid_mode not in valid_modes + actual_cmd = [str(c) for c in mock_run.call_args[0][0]] + assert actual_cmd[0].endswith("instanovo") + assert actual_cmd[1] == "transformer" + assert actual_cmd[2] == "predict" + assert actual_cmd[3] == "--data-path" + assert actual_cmd[4].endswith("BSA1.mgf") + assert actual_cmd[5] == "--output-path" + assert actual_cmd[7] == "num_beams=5" + assert len(actual_cmd) == 8 -@pytest.mark.parametrize("model_used", ["transformer", "diffusion"]) -def test_instanovo_urun_dict_model_used(model_used: str) -> None: - """Test that model_used is correctly stored in URunDict parameters.""" +def test_instanovo_invalid_model_used_logs_error(tmp_path: Path, caplog) -> None: + """An unrecognized model_used should log an error.""" urun_dict = urgap.URunDict( { "parameters": { "Instanovo:1.2.2": { - "model_used": model_used, + "model_used": "not_a_real_mode", }, }, "unode_parameters": { - "storage_base_uri": "file:///tmp", + "storage_base_uri": f"file://{tmp_path}", }, }, ) - params = urun_dict.parameters["Instanovo:1.2.2"] - assert params["model_used"] == model_used - assert params["model_used"] in ["transformer", "diffusion"] + ufiles = urgap.UFileList( + [ + urgap.UFile( + uri=f"file://{urgap._test_folder}/data?uftype=" + f"{urgap.uftypes.proteomics.converter.PYMZML_MGF}#mgfs/BSA1.mgf", + ), + ], + ) + + instanovo_node = urgap.init_node("Instanovo:1.2.2") + + with patch("subprocess.run") as mock_run: + mock_run.return_value.returncode = 0 + mock_run.return_value.stdout = "" + with caplog.at_level(logging.ERROR): + with pytest.raises(FileNotFoundError): + instanovo_node.run(ufiles, urun_dict) + + assert "Unknown search mode" in caplog.text -def test_instanovo_starts(tmp_dir, caplog): - urd = urgap.URunDict( + +def test_instanovo_param_file_and_cli_params_raises(tmp_path: Path) -> None: + """Providing both a yaml config file and non-model_used CLI parameters should raise ValueError.""" + urun_dict = urgap.URunDict( { "parameters": { "Instanovo:1.2.2": { "model_used": "transformer", + "num_beams": 5, }, }, "unode_parameters": { - "storage_base_uri": f"file://{tmp_dir}", + "storage_base_uri": f"file://{tmp_path}", }, }, ) + ufiles = urgap.UFileList( [ urgap.UFile( - uri=f"file://" - f"{urgap._test_folder}/data?uftype={urgap.uftypes.proteomics.converter.PYMZML_MGF}" - f"#mgfs/BSA1.mgf" + uri=f"file://{urgap._test_folder}/data?uftype=" + f"{urgap.uftypes.proteomics.converter.PYMZML_MGF}#mgfs/BSA1.mgf", ), urgap.UFile( - uri=f"file://" - f"{urgap._test_folder}/data?uftype={urgap.uftypes.proteomics.denovosearch.INSTANOVO_YAML}" - f"#instanovo_params/default.yaml" + uri=f"file://{urgap._test_folder}/data?uftype=" + f"{urgap.uftypes.proteomics.denovosearch.INSTANOVO_YAML}#instanovo_params/default.yaml", ), ], ) instanovo_node = urgap.init_node("Instanovo:1.2.2") - thread = threading.Thread( - target=instanovo_node.run, - kwargs={"urun_dict": urd, "ufiles": ufiles}, - daemon=True, - ) - try: - with caplog.at_level(logging.INFO): - thread.start() - - deadline = time.monotonic() + 10 - launched = False - while time.monotonic() < deadline: - if "Executing command list: " in caplog.text: - launched = True - break - time.sleep(0.2) - - assert "Running execute ..." in caplog.text - assert launched, "instanovo command was never launched" - assert ( - "instanovo diffusion predict" in caplog.text - or "instanovo transformer predict" in caplog.text - ) - finally: - for proc in psutil.process_iter(["cmdline"]): - cmdline = " ".join(proc.info["cmdline"] or []) - if "instanovo" in cmdline and "predict" in cmdline: - proc.terminate() \ No newline at end of file + with pytest.raises(ValueError) as excinfo: + instanovo_node.run(ufiles, urun_dict) + + assert ( + "Both a config yaml file and command-line parameters in the " + "urun_dict were provided for Instanovo. Please provide only one." + in str(excinfo.value) + ) \ No newline at end of file diff --git a/urgap/unodes/instanovo/instanovo_1_2_2.py b/urgap/unodes/instanovo/instanovo_1_2_2.py index 1ab2107..9574e05 100644 --- a/urgap/unodes/instanovo/instanovo_1_2_2.py +++ b/urgap/unodes/instanovo/instanovo_1_2_2.py @@ -27,7 +27,7 @@ class Instanovo(urgap.unode.UNodeBase): "parameters_not_triggering_rerun": [], "input_uftypes": { urgap.uftypes.proteomics.converter.PYMZML_MGF: {"min": 1, "max": 1}, - urgap.uftypes.proteomics.denovosearch.INSTANOVO_YAML: {"min": 1, "max": 1}, + urgap.uftypes.proteomics.denovosearch.INSTANOVO_YAML: {"min": 0, "max": 1}, }, "output_uftypes": { urgap.uftypes.proteomics.denovosearch.INSTANOVO_CSV : {"min": 1, "max": 1}, @@ -85,6 +85,11 @@ def preflight( Returns: UTrace object, combination of urun_dict, ufile_list and unode.meta. + + Raises: + ValueError: If both a config yaml file and command-line + parameters in the urun_dict are provided. Please provide + only one. """ input_params = utrace.urun_dict.parameters[ f"{self.META_INFO['unode_full_identifier']}" @@ -92,43 +97,73 @@ def preflight( mgf_file = utrace.input_files.get_path_objects_by_uftype( urgap.uftypes.proteomics.converter.PYMZML_MGF, )[0] - param_file = utrace.input_files.get_path_objects_by_uftype( + + param_files = utrace.input_files.get_path_objects_by_uftype( urgap.uftypes.proteomics.denovosearch.INSTANOVO_YAML, - )[0] + ) output_csv = utrace.output_files.get_path_objects_by_uftype( urgap.uftypes.proteomics.denovosearch.INSTANOVO_CSV, )[0] - # Get the directory containing YOUR custom config file - config_dir = Path(param_file).parent.resolve() + # command-line overrides, e.g. {"num_beams": 5, "max_length": 30} + cli_params_dict = {k: v for k, v in input_params.items() if k != "model_used"} - # InstaNovo executes from its built-in configs directory, so we need - # to calculate the relative path from there to your custom config directory - instanovo_configs_dir = self.find_instanovo_configs() + param_file_provided = len(param_files) == 1 + cli_params_provided = bool(cli_params_dict) - # Calculate relative path from InstaNovo's configs dir to your config dir - relative_config_path = os.path.relpath(config_dir, instanovo_configs_dir) - model_used = input_params["model_used"] - if model_used not in ["transformer", "diffusion"]: + if param_file_provided and cli_params_provided: + msg = ( + "Both a config yaml file and command-line parameters in the " + "urun_dict were provided for Instanovo. Please provide only one." + ) + raise ValueError(msg) + + model_used = input_params.get("model_used") + if model_used is not None and model_used not in ["transformer", "diffusion"]: logging.error( "Unknown search mode %s. Search mode has to be either " "'transformer' or 'diffusion'", model_used, ) + utrace.urun_dict.command_list = [ str(self.exe_path), - f"{model_used}", + ] + + if model_used is not None: + utrace.urun_dict.command_list.append(f"{model_used}") + + utrace.urun_dict.command_list += [ "predict", "--data-path", mgf_file, "--output-path", output_csv, - "--config-path", - relative_config_path, - "--config-name", - param_file.stem, ] + + if param_file_provided: + param_file = param_files[0] + # Get the directory containing YOUR custom config file + config_dir = Path(param_file).parent.resolve() + + # InstaNovo executes from its built-in configs directory, so we need + # to calculate the relative path from there to your custom config directory + instanovo_configs_dir = self.find_instanovo_configs() + + # Calculate relative path from InstaNovo's configs dir to your config dir + relative_config_path = os.path.relpath(config_dir, instanovo_configs_dir) + + utrace.urun_dict.command_list += [ + "--config-path", + relative_config_path, + "--config-name", + param_file.stem, + ] + else: + for key, value in cli_params_dict.items(): + utrace.urun_dict.command_list.append(f"{key}={value}") + return utrace def postflight( @@ -146,4 +181,4 @@ def postflight( Returns: UTrace object, combination of urun_dict, ufile_list and unode.meta. """ - return utrace + return utrace \ No newline at end of file From e037938108d0c6de65380b83438a5f4826771d72 Mon Sep 17 00:00:00 2001 From: cal3502 Date: Mon, 13 Jul 2026 14:06:15 -0400 Subject: [PATCH 13/36] Changed dependencies and added a section of the Read Me for instructions on how to install Instanovo --- README.md | 7 +++++++ pyproject.toml | 4 ++-- 2 files changed, 9 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 3d5e5f4..f085da5 100644 --- a/README.md +++ b/README.md @@ -5,3 +5,10 @@ This repository contains unodes, resources, and tests for the following engines: - PymzMLToMGF - ThermoRawFileParser + +# Unode Resources Installation Instructions + +# Instanovo + +In order to avoid dependency conflicts with other parts of urgap, Python must be verion 3.10 and the urgap[cloud] dependency must not be installed. After installation of urgap, Instanovo can be installed with +"pip install instanovo". \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index a903869..98c9661 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,9 +6,9 @@ build-backend = "hatchling.build" name = "urgap-proteomics" version = "0.0.1" description = "Urgap proteomics specific extension" -requires-python = ">=3.11" +requires-python = ">=3.10" dependencies = [ - "urgap[all]", + "urgap", "pymzml>=2.5.0", "pyiohat>=1.9.0", ] From 030cd03fbf9b4ba9985877109112341752a041d1 Mon Sep 17 00:00:00 2001 From: cal3502 Date: Mon, 13 Jul 2026 14:11:36 -0400 Subject: [PATCH 14/36] Changes to ruff formatting --- .../wrappers/test_instanovo.py | 18 ++++++------------ urgap/unodes/instanovo/instanovo_1_2_2.py | 2 +- 2 files changed, 7 insertions(+), 13 deletions(-) diff --git a/tests/integrationtests/wrappers/test_instanovo.py b/tests/integrationtests/wrappers/test_instanovo.py index 91a5bc6..0b6019a 100644 --- a/tests/integrationtests/wrappers/test_instanovo.py +++ b/tests/integrationtests/wrappers/test_instanovo.py @@ -1,19 +1,14 @@ """Integration test for Instanovo.""" +import logging + from pathlib import Path +from unittest.mock import patch import pytest import urgap -import os -import subprocess -import time -import logging -import threading -import psutil -from unittest.mock import patch - def test_instanovo_command_construction_yaml_no_model(tmp_path: Path) -> None: """Test that command_list is built correctly with no model_used, using a yaml config file.""" @@ -136,9 +131,8 @@ def test_instanovo_invalid_model_used_logs_error(tmp_path: Path, caplog) -> None with patch("subprocess.run") as mock_run: mock_run.return_value.returncode = 0 mock_run.return_value.stdout = "" - with caplog.at_level(logging.ERROR): - with pytest.raises(FileNotFoundError): - instanovo_node.run(ufiles, urun_dict) + with caplog.at_level(logging.ERROR), pytest.raises(FileNotFoundError): + instanovo_node.run(ufiles, urun_dict) assert "Unknown search mode" in caplog.text @@ -181,4 +175,4 @@ def test_instanovo_param_file_and_cli_params_raises(tmp_path: Path) -> None: "Both a config yaml file and command-line parameters in the " "urun_dict were provided for Instanovo. Please provide only one." in str(excinfo.value) - ) \ No newline at end of file + ) diff --git a/urgap/unodes/instanovo/instanovo_1_2_2.py b/urgap/unodes/instanovo/instanovo_1_2_2.py index 9574e05..e57ad41 100644 --- a/urgap/unodes/instanovo/instanovo_1_2_2.py +++ b/urgap/unodes/instanovo/instanovo_1_2_2.py @@ -181,4 +181,4 @@ def postflight( Returns: UTrace object, combination of urun_dict, ufile_list and unode.meta. """ - return utrace \ No newline at end of file + return utrace From 8202048e12bfee9b0375dacb759d34e98a1a149d Mon Sep 17 00:00:00 2001 From: cal3502 Date: Mon, 13 Jul 2026 14:23:36 -0400 Subject: [PATCH 15/36] Changed dependencies to install urgap[dev] to have the github actions work, theis will not cause dependency issues with Instanovo --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 98c9661..8a83daa 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -8,7 +8,7 @@ version = "0.0.1" description = "Urgap proteomics specific extension" requires-python = ">=3.10" dependencies = [ - "urgap", + "urgap[dev]", "pymzml>=2.5.0", "pyiohat>=1.9.0", ] From 317cb35ff951a898aa71f77b80b4fe9904a97583 Mon Sep 17 00:00:00 2001 From: cal3502 Date: Mon, 13 Jul 2026 14:28:42 -0400 Subject: [PATCH 16/36] Changed dependencies to install both urgap and urgap[dev] --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index 8a83daa..6e25995 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -8,6 +8,7 @@ version = "0.0.1" description = "Urgap proteomics specific extension" requires-python = ">=3.10" dependencies = [ + "urgap", "urgap[dev]", "pymzml>=2.5.0", "pyiohat>=1.9.0", From c1128075fe6ea344ac8666d70bbf3bfa950a645a Mon Sep 17 00:00:00 2001 From: cal3502 Date: Mon, 13 Jul 2026 14:42:56 -0400 Subject: [PATCH 17/36] Changes to dependencies and github actions in order to properly run tests --- .github/workflows/main.yaml | 2 +- pyproject.toml | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index 5d3be16..053e657 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -58,7 +58,7 @@ jobs: run: | pip install uv uv pip install pytest pytest-asyncio --system - uv pip install . --system + uv pip install ".[dev]" --system - name: Set up Java 17 uses: actions/setup-java@v4 with: diff --git a/pyproject.toml b/pyproject.toml index 6e25995..68c4b97 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,7 +9,6 @@ description = "Urgap proteomics specific extension" requires-python = ">=3.10" dependencies = [ "urgap", - "urgap[dev]", "pymzml>=2.5.0", "pyiohat>=1.9.0", ] @@ -18,7 +17,7 @@ dependencies = [ dev = [ "pytest", "pytest-asyncio>=0.23", - "urgap[dev]", + "urgap[all]", ] From 46b6bf8abde574e2262b035ffaf1af9d4f33d609 Mon Sep 17 00:00:00 2001 From: cal3502 Date: Mon, 13 Jul 2026 14:45:39 -0400 Subject: [PATCH 18/36] Removed pycaches --- tests/__pycache__/__init__.cpython-39.pyc | Bin 169 -> 0 bytes .../conftest.cpython-39-pytest-8.4.2.pyc | Bin 7737 -> 0 bytes ...ermorawfileparser.cpython-39-pytest-8.4.2.pyc | Bin 2352 -> 0 bytes 3 files changed, 0 insertions(+), 0 deletions(-) delete mode 100644 tests/__pycache__/__init__.cpython-39.pyc delete mode 100644 tests/__pycache__/conftest.cpython-39-pytest-8.4.2.pyc delete mode 100644 tests/integrationtests/wrappers/__pycache__/test_thermorawfileparser.cpython-39-pytest-8.4.2.pyc diff --git a/tests/__pycache__/__init__.cpython-39.pyc b/tests/__pycache__/__init__.cpython-39.pyc deleted file mode 100644 index cc9a100f92e37451d956dc02fd0d9e7b1e58fdfd..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 169 zcmYe~<>g`kf)|givUq{?V-N=!FakLaKwQiLBvKfn7*ZI688n%y*fR6-GE4OQG#PKP z$H%ASC&$OHWGG?+DgqO~Z1jsW5{pt(^ox@93yShfQuA|D^-GJ=6AScnQp+=oVS<^- m#rh?w#U;i1@$s2J6XWCc3My}L*yQG?l;)(`fvo=w#0&uT#VhLo diff --git a/tests/__pycache__/conftest.cpython-39-pytest-8.4.2.pyc b/tests/__pycache__/conftest.cpython-39-pytest-8.4.2.pyc deleted file mode 100644 index 2c00381f36b7137688b4de0fa9a602dcb752838a..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 7737 zcmcIp+ix7#d7t}UxFnZ1Nt9%HE!(nI7D-8t<3v>)%eusFBF2ztC!RW;4)+YnS?}r zb7sz&Ip=)myZpY3!twF4fxqAV=4$izXAI*v)H(cTqw@hS_4lS>2t$}H!#DYEwQb8V zjke>vX8y+WJ$_U03w$s7MZTB(65q>yneSu%7~d;?h4173INvAy3EZvLWV`BDc}=@D z)t>gJ`|Hp6GyL7GKg;(ye=e#<$9B!;@x2rKMl=`93rDz*4gaL@L;?3x(Mr|}?)9FX|Y(Al~M&i^9BT)EAzUEl~}^wF@@7Jh1)aMogGWtdrr^VH-)!pVXwmW@9svrD-%^)k=>{k zuhlkErEBMvmi3y9R3}Y@s_C>A);e*rj-mVANa@9L4S#o|cGO;tWKC~`8ej0#cDPkb zQazY_XzuxsZ`}EWR^=sX(Ss#>yEm*w4`*{*i0Wp za;=p6SZ{ZyYIg9t#4mhA_DPmK}8ZDs)aaN=xphYG~t!}!oxTb=|lCx zT1d97g+}Jkgv`7wiK}%tD|T9;UQ1;=^VF8oQ9E<7StPTv>aKQV+K80OoJQDc)$Poo z!)7kT61KAf2x^CkcxK2+to7pBlG+GmB$i}j2@`dcwxgx4Tn{@-t>|H_27_@!Eorb* zEj7|)jh+@eThhf6bGVd;#_`^qA4q)#*trGFM3ZS)LnHmzMtozb>1wbO&O{GIXC z+BJV+3X-6Zct#y-z2LDJv%<)i113`XzJ8ng_bhQ~ZbgdC4wN<GOIF|KgmifTb<~Zl&Q=djYk-S+g$^J%cxEowEjf;F zc$vDD75e&|ncbrV)pCO3wVb9_tn?^dZ)2TY%2wGdoAMO;Bb1Q_jNxL+{t^#F#TV9& zxnuP#VRTLT2oyrXJ9f`*T6>WDzKQqFj=OzQJ59IgH48nb=dM`-Sn$L$jh`6F701v; 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Please provide only one." in str(excinfo.value) - ) + ) \ No newline at end of file From f55b156cd39069e637e99ccf63b7f78775cb847d Mon Sep 17 00:00:00 2001 From: cal3502 Date: Mon, 13 Jul 2026 15:04:18 -0400 Subject: [PATCH 20/36] Changed Instanovo tests to function properly in Github Actions --- tests/integrationtests/wrappers/test_instanovo.py | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/tests/integrationtests/wrappers/test_instanovo.py b/tests/integrationtests/wrappers/test_instanovo.py index 791ed24..39ca179 100644 --- a/tests/integrationtests/wrappers/test_instanovo.py +++ b/tests/integrationtests/wrappers/test_instanovo.py @@ -7,16 +7,17 @@ import pytest import urgap +# 1. Grab a clean reference to the original method to prevent infinite loops +_original_check_deps = urgap.unode_manager.UNodeManager.check_unode_dependencies + def mock_check_dependencies(self, unode: str) -> tuple: """Mock out dependency check to trick the manager into thinking the binary exists.""" - # Call the real implementation first - unode_obj, tmp = self.__class__.check_unode_dependencies(self, unode) + # 2. Call the stored original method safely + unode_obj, tmp = _original_check_deps(self, unode) - # Overwrite the missing path checks so the test passes string validation + # 3. Inject our mock flags tmp[unode]["resource_available"] = True - - # Ensure exe_path resolves to something text-subscriptable instead of None if unode_obj.exe_path is None: unode_obj.exe_path = Path("instanovo") @@ -49,7 +50,7 @@ def test_instanovo_command_construction_yaml_no_model(tmp_path: Path) -> None: ], ) - # Patch the manager dependency and path resolution framework directly + # Patch the manager with our recursion-safe mock wrapper with patch("urgap.unode_manager.UNodeManager.check_unode_dependencies", new=mock_check_dependencies): instanovo_node = urgap.init_node("Instanovo:1.2.2") @@ -97,7 +98,7 @@ def test_instanovo_command_construction_with_model_and_cli_params(tmp_path: Path ], ) - # Patch the manager dependency and path resolution framework directly + # Patch the manager with our recursion-safe mock wrapper with patch("urgap.unode_manager.UNodeManager.check_unode_dependencies", new=mock_check_dependencies): instanovo_node = urgap.init_node("Instanovo:1.2.2") From 327e518e35a328b44f6515d040ac9c6ab5530857 Mon Sep 17 00:00:00 2001 From: cal3502 Date: Mon, 13 Jul 2026 15:08:39 -0400 Subject: [PATCH 21/36] Changed Instanovo tests to function properly in Github Actions --- tests/integrationtests/wrappers/test_instanovo.py | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/tests/integrationtests/wrappers/test_instanovo.py b/tests/integrationtests/wrappers/test_instanovo.py index 39ca179..4d18ce2 100644 --- a/tests/integrationtests/wrappers/test_instanovo.py +++ b/tests/integrationtests/wrappers/test_instanovo.py @@ -7,19 +7,21 @@ import pytest import urgap -# 1. Grab a clean reference to the original method to prevent infinite loops +# Clean reference to prevent infinite recursion loop _original_check_deps = urgap.unode_manager.UNodeManager.check_unode_dependencies def mock_check_dependencies(self, unode: str) -> tuple: """Mock out dependency check to trick the manager into thinking the binary exists.""" - # 2. Call the stored original method safely unode_obj, tmp = _original_check_deps(self, unode) - # 3. Inject our mock flags + # 1. Force the manager to report that the executable exists tmp[unode]["resource_available"] = True + + # 2. Use patch.object to bypass the read-only property restriction safely if unode_obj.exe_path is None: - unode_obj.exe_path = Path("instanovo") + patcher = patch.object(unode_obj, "exe_path", Path("instanovo")) + patcher.start() return unode_obj, tmp From b83e04125c53076eef943cdad9b95fa8f4408557 Mon Sep 17 00:00:00 2001 From: cal3502 Date: Mon, 13 Jul 2026 15:17:46 -0400 Subject: [PATCH 22/36] Changed Instanovo tests to function properly in Github Actions --- .../wrappers/test_instanovo.py | 42 ++++++++++--------- 1 file changed, 22 insertions(+), 20 deletions(-) diff --git a/tests/integrationtests/wrappers/test_instanovo.py b/tests/integrationtests/wrappers/test_instanovo.py index 4d18ce2..49526dd 100644 --- a/tests/integrationtests/wrappers/test_instanovo.py +++ b/tests/integrationtests/wrappers/test_instanovo.py @@ -7,24 +7,6 @@ import pytest import urgap -# Clean reference to prevent infinite recursion loop -_original_check_deps = urgap.unode_manager.UNodeManager.check_unode_dependencies - - -def mock_check_dependencies(self, unode: str) -> tuple: - """Mock out dependency check to trick the manager into thinking the binary exists.""" - unode_obj, tmp = _original_check_deps(self, unode) - - # 1. Force the manager to report that the executable exists - tmp[unode]["resource_available"] = True - - # 2. Use patch.object to bypass the read-only property restriction safely - if unode_obj.exe_path is None: - patcher = patch.object(unode_obj, "exe_path", Path("instanovo")) - patcher.start() - - return unode_obj, tmp - def test_instanovo_command_construction_yaml_no_model(tmp_path: Path) -> None: """Test that command_list is built correctly with no model_used, using a yaml config file.""" @@ -52,7 +34,18 @@ def test_instanovo_command_construction_yaml_no_model(tmp_path: Path) -> None: ], ) - # Patch the manager with our recursion-safe mock wrapper + # Safely get the original function here, INSIDE the test execution phase + original_check_deps = urgap.unode_manager.UNodeManager.check_unode_dependencies + + def mock_check_dependencies(self, unode: str) -> tuple: + unode_obj, tmp = original_check_deps(self, unode) + tmp[unode]["resource_available"] = True + if unode_obj.exe_path is None: + # Safely mock the read-only property on the instance using patch.object + patcher = patch.object(unode_obj, "exe_path", Path("instanovo")) + patcher.start() + return unode_obj, tmp + with patch("urgap.unode_manager.UNodeManager.check_unode_dependencies", new=mock_check_dependencies): instanovo_node = urgap.init_node("Instanovo:1.2.2") @@ -100,7 +93,16 @@ def test_instanovo_command_construction_with_model_and_cli_params(tmp_path: Path ], ) - # Patch the manager with our recursion-safe mock wrapper + original_check_deps = urgap.unode_manager.UNodeManager.check_unode_dependencies + + def mock_check_dependencies(self, unode: str) -> tuple: + unode_obj, tmp = original_check_deps(self, unode) + tmp[unode]["resource_available"] = True + if unode_obj.exe_path is None: + patcher = patch.object(unode_obj, "exe_path", Path("instanovo")) + patcher.start() + return unode_obj, tmp + with patch("urgap.unode_manager.UNodeManager.check_unode_dependencies", new=mock_check_dependencies): instanovo_node = urgap.init_node("Instanovo:1.2.2") From e8e44817ad594d256a1a9722dc6968a53d2d43f0 Mon Sep 17 00:00:00 2001 From: cal3502 Date: Mon, 13 Jul 2026 15:22:14 -0400 Subject: [PATCH 23/36] Changed Instanovo tests to function properly in Github Actions --- .../wrappers/test_instanovo.py | 44 +++++++++---------- 1 file changed, 22 insertions(+), 22 deletions(-) diff --git a/tests/integrationtests/wrappers/test_instanovo.py b/tests/integrationtests/wrappers/test_instanovo.py index 49526dd..e5d0e98 100644 --- a/tests/integrationtests/wrappers/test_instanovo.py +++ b/tests/integrationtests/wrappers/test_instanovo.py @@ -2,7 +2,7 @@ import logging from pathlib import Path -from unittest.mock import patch +from unittest.mock import patch, PropertyMock import pytest import urgap @@ -34,26 +34,25 @@ def test_instanovo_command_construction_yaml_no_model(tmp_path: Path) -> None: ], ) - # Safely get the original function here, INSIDE the test execution phase original_check_deps = urgap.unode_manager.UNodeManager.check_unode_dependencies def mock_check_dependencies(self, unode: str) -> tuple: unode_obj, tmp = original_check_deps(self, unode) tmp[unode]["resource_available"] = True - if unode_obj.exe_path is None: - # Safely mock the read-only property on the instance using patch.object - patcher = patch.object(unode_obj, "exe_path", Path("instanovo")) - patcher.start() return unode_obj, tmp + # 1. Patch the manager dependency check to pretend the file exists with patch("urgap.unode_manager.UNodeManager.check_unode_dependencies", new=mock_check_dependencies): - instanovo_node = urgap.init_node("Instanovo:1.2.2") + # 2. Patch the class property directly on the class definition to bypass read-only restrictions + with patch("urgap.unodes.instanovo.instanovo_1_2_2.Instanovo.exe_path", new_callable=PropertyMock) as mock_exe: + mock_exe.return_value = Path("instanovo") + instanovo_node = urgap.init_node("Instanovo:1.2.2") - with patch("subprocess.run") as mock_run: - mock_run.return_value.returncode = 0 - mock_run.return_value.stdout = "" - with pytest.raises(FileNotFoundError): - instanovo_node.run(ufiles, urun_dict) + with patch("subprocess.run") as mock_run: + mock_run.return_value.returncode = 0 + mock_run.return_value.stdout = "" + with pytest.raises(FileNotFoundError): + instanovo_node.run(ufiles, urun_dict) actual_cmd = [str(c) for c in mock_run.call_args[0][0]] @@ -98,19 +97,20 @@ def test_instanovo_command_construction_with_model_and_cli_params(tmp_path: Path def mock_check_dependencies(self, unode: str) -> tuple: unode_obj, tmp = original_check_deps(self, unode) tmp[unode]["resource_available"] = True - if unode_obj.exe_path is None: - patcher = patch.object(unode_obj, "exe_path", Path("instanovo")) - patcher.start() return unode_obj, tmp + # 1. Patch the manager dependency check to pretend the file exists with patch("urgap.unode_manager.UNodeManager.check_unode_dependencies", new=mock_check_dependencies): - instanovo_node = urgap.init_node("Instanovo:1.2.2") - - with patch("subprocess.run") as mock_run: - mock_run.return_value.returncode = 0 - mock_run.return_value.stdout = "" - with pytest.raises(FileNotFoundError): - instanovo_node.run(ufiles, urun_dict) + # 2. Patch the class property directly on the class definition to bypass read-only restrictions + with patch("urgap.unodes.instanovo.instanovo_1_2_2.Instanovo.exe_path", new_callable=PropertyMock) as mock_exe: + mock_exe.return_value = Path("instanovo") + instanovo_node = urgap.init_node("Instanovo:1.2.2") + + with patch("subprocess.run") as mock_run: + mock_run.return_value.returncode = 0 + mock_run.return_value.stdout = "" + with pytest.raises(FileNotFoundError): + instanovo_node.run(ufiles, urun_dict) actual_cmd = [str(c) for c in mock_run.call_args[0][0]] From 3103fa20a0da725ece013becf4925cc064b2426f Mon Sep 17 00:00:00 2001 From: cal3502 Date: Mon, 13 Jul 2026 15:27:35 -0400 Subject: [PATCH 24/36] Changed Instanovo tests to properly function in Github Actions --- tests/integrationtests/wrappers/test_instanovo.py | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/tests/integrationtests/wrappers/test_instanovo.py b/tests/integrationtests/wrappers/test_instanovo.py index e5d0e98..3da35b9 100644 --- a/tests/integrationtests/wrappers/test_instanovo.py +++ b/tests/integrationtests/wrappers/test_instanovo.py @@ -41,14 +41,15 @@ def mock_check_dependencies(self, unode: str) -> tuple: tmp[unode]["resource_available"] = True return unode_obj, tmp - # 1. Patch the manager dependency check to pretend the file exists + # Patch the manager dependency check to pretend the binary exists with patch("urgap.unode_manager.UNodeManager.check_unode_dependencies", new=mock_check_dependencies): - # 2. Patch the class property directly on the class definition to bypass read-only restrictions + # Patch the class property directly on the class definition to bypass read-only restrictions with patch("urgap.unodes.instanovo.instanovo_1_2_2.Instanovo.exe_path", new_callable=PropertyMock) as mock_exe: mock_exe.return_value = Path("instanovo") instanovo_node = urgap.init_node("Instanovo:1.2.2") - with patch("subprocess.run") as mock_run: + # Mock Path.exists to return True so the YAML file passes preflight checks + with patch.object(Path, "exists", return_value=True), patch("subprocess.run") as mock_run: mock_run.return_value.returncode = 0 mock_run.return_value.stdout = "" with pytest.raises(FileNotFoundError): @@ -99,14 +100,12 @@ def mock_check_dependencies(self, unode: str) -> tuple: tmp[unode]["resource_available"] = True return unode_obj, tmp - # 1. Patch the manager dependency check to pretend the file exists with patch("urgap.unode_manager.UNodeManager.check_unode_dependencies", new=mock_check_dependencies): - # 2. Patch the class property directly on the class definition to bypass read-only restrictions with patch("urgap.unodes.instanovo.instanovo_1_2_2.Instanovo.exe_path", new_callable=PropertyMock) as mock_exe: mock_exe.return_value = Path("instanovo") instanovo_node = urgap.init_node("Instanovo:1.2.2") - with patch("subprocess.run") as mock_run: + with patch.object(Path, "exists", return_value=True), patch("subprocess.run") as mock_run: mock_run.return_value.returncode = 0 mock_run.return_value.stdout = "" with pytest.raises(FileNotFoundError): From 1e332d63ea75815621185a675a9fcf72eca10a7b Mon Sep 17 00:00:00 2001 From: cal3502 Date: Mon, 13 Jul 2026 15:33:43 -0400 Subject: [PATCH 25/36] Changed Instanovo tests to properly function in Github Actions --- .../integrationtests/wrappers/test_instanovo.py | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/tests/integrationtests/wrappers/test_instanovo.py b/tests/integrationtests/wrappers/test_instanovo.py index 3da35b9..37f495d 100644 --- a/tests/integrationtests/wrappers/test_instanovo.py +++ b/tests/integrationtests/wrappers/test_instanovo.py @@ -43,10 +43,14 @@ def mock_check_dependencies(self, unode: str) -> tuple: # Patch the manager dependency check to pretend the binary exists with patch("urgap.unode_manager.UNodeManager.check_unode_dependencies", new=mock_check_dependencies): - # Patch the class property directly on the class definition to bypass read-only restrictions - with patch("urgap.unodes.instanovo.instanovo_1_2_2.Instanovo.exe_path", new_callable=PropertyMock) as mock_exe: + # Initialize first so urgap safely loads the class into its internal manager lookup map + instanovo_node = urgap.init_node("Instanovo:1.2.2") + + # Now we target the class type directly from the manager's live cache to avoid string path imports + instanovo_cls = urgap.instances.unode_manager.data["all"]["Instanovo:1.2.2"] + + with patch.object(instanovo_cls, "exe_path", new_callable=PropertyMock) as mock_exe: mock_exe.return_value = Path("instanovo") - instanovo_node = urgap.init_node("Instanovo:1.2.2") # Mock Path.exists to return True so the YAML file passes preflight checks with patch.object(Path, "exists", return_value=True), patch("subprocess.run") as mock_run: @@ -101,9 +105,11 @@ def mock_check_dependencies(self, unode: str) -> tuple: return unode_obj, tmp with patch("urgap.unode_manager.UNodeManager.check_unode_dependencies", new=mock_check_dependencies): - with patch("urgap.unodes.instanovo.instanovo_1_2_2.Instanovo.exe_path", new_callable=PropertyMock) as mock_exe: + instanovo_node = urgap.init_node("Instanovo:1.2.2") + instanovo_cls = urgap.instances.unode_manager.data["all"]["Instanovo:1.2.2"] + + with patch.object(instanovo_cls, "exe_path", new_callable=PropertyMock) as mock_exe: mock_exe.return_value = Path("instanovo") - instanovo_node = urgap.init_node("Instanovo:1.2.2") with patch.object(Path, "exists", return_value=True), patch("subprocess.run") as mock_run: mock_run.return_value.returncode = 0 From ccd4ba48004c726201bdf4ae8c84b8c047d7d850 Mon Sep 17 00:00:00 2001 From: cal3502 Date: Mon, 13 Jul 2026 15:50:07 -0400 Subject: [PATCH 26/36] Changed Instanovo tests to properly function in Github Actions --- .../wrappers/test_instanovo.py | 64 ++++++++++++++----- 1 file changed, 49 insertions(+), 15 deletions(-) diff --git a/tests/integrationtests/wrappers/test_instanovo.py b/tests/integrationtests/wrappers/test_instanovo.py index 37f495d..fb42410 100644 --- a/tests/integrationtests/wrappers/test_instanovo.py +++ b/tests/integrationtests/wrappers/test_instanovo.py @@ -41,19 +41,53 @@ def mock_check_dependencies(self, unode: str) -> tuple: tmp[unode]["resource_available"] = True return unode_obj, tmp - # Patch the manager dependency check to pretend the binary exists + # 1. Patch the manager dependency check to pretend the binary is available with patch("urgap.unode_manager.UNodeManager.check_unode_dependencies", new=mock_check_dependencies): - # Initialize first so urgap safely loads the class into its internal manager lookup map - instanovo_node = urgap.init_node("Instanovo:1.2.2") - - # Now we target the class type directly from the manager's live cache to avoid string path imports - instanovo_cls = urgap.instances.unode_manager.data["all"]["Instanovo:1.2.2"] - - with patch.object(instanovo_cls, "exe_path", new_callable=PropertyMock) as mock_exe: + # 2. Patch the class property directly on the class definition + with patch("urgap.unodes.instanovo.instanovo_1_2_2.Instanovo.exe_path", new_callable=PropertyMock) as mock_exe: mock_exe.return_value = Path("instanovo") + instanovo_node = urgap.init_node("Instanovo:1.2.2") - # Mock Path.exists to return True so the YAML file passes preflight checks - with patch.object(Path, "exists", return_value=True), patch("subprocess.run") as mock_run: + # 3. Patch subprocess.run + with patch("subprocess.run") as mock_run: + mock_run.return_value.returncode = 0 + mock_run.return_value.stdout = "" + + # Run inside a try/except block so we stay inside the context manager + try: + instanovo_node.run(ufiles, urun_dict) + except FileNotFoundError: + # We expect this because the mock doesn't produce the output .csv + pass + + # Now mock_run is fully inside scope and populated! + actual_cmd = [str(c) for c in mock_run.call_args[0][0]] + + assert actual_cmd[0].endswith("instanovo") + assert actual_cmd[1] == "predict" + assert actual_cmd[2] == "--data-path" + assert actual_cmd[3].endswith("BSA1.mgf") + assert actual_cmd[4] == "--output-path" + assert actual_cmd[6] == "--config-path" + assert actual_cmd[8] == "--config-name" + assert actual_cmd[9] == "default" + assert len(actual_cmd) == 10 + + original_check_deps = urgap.unode_manager.UNodeManager.check_unode_dependencies + + def mock_check_dependencies(self, unode: str) -> tuple: + unode_obj, tmp = original_check_deps(self, unode) + tmp[unode]["resource_available"] = True + return unode_obj, tmp + + # 1. Patch the manager dependency check to pretend the file exists + with patch("urgap.unode_manager.UNodeManager.check_unode_dependencies", new=mock_check_dependencies): + # 2. Patch the class property directly on the class definition to bypass read-only restrictions + with patch("urgap.unodes.instanovo.instanovo_1_2_2.Instanovo.exe_path", new_callable=PropertyMock) as mock_exe: + mock_exe.return_value = Path("instanovo") + instanovo_node = urgap.init_node("Instanovo:1.2.2") + + with patch("subprocess.run") as mock_run: mock_run.return_value.returncode = 0 mock_run.return_value.stdout = "" with pytest.raises(FileNotFoundError): @@ -104,14 +138,14 @@ def mock_check_dependencies(self, unode: str) -> tuple: tmp[unode]["resource_available"] = True return unode_obj, tmp + # 1. Patch the manager dependency check to pretend the file exists with patch("urgap.unode_manager.UNodeManager.check_unode_dependencies", new=mock_check_dependencies): - instanovo_node = urgap.init_node("Instanovo:1.2.2") - instanovo_cls = urgap.instances.unode_manager.data["all"]["Instanovo:1.2.2"] - - with patch.object(instanovo_cls, "exe_path", new_callable=PropertyMock) as mock_exe: + # 2. Patch the class property directly on the class definition to bypass read-only restrictions + with patch("urgap.unodes.instanovo.instanovo_1_2_2.Instanovo.exe_path", new_callable=PropertyMock) as mock_exe: mock_exe.return_value = Path("instanovo") + instanovo_node = urgap.init_node("Instanovo:1.2.2") - with patch.object(Path, "exists", return_value=True), patch("subprocess.run") as mock_run: + with patch("subprocess.run") as mock_run: mock_run.return_value.returncode = 0 mock_run.return_value.stdout = "" with pytest.raises(FileNotFoundError): From f0e0872305f3a1cb041b02dba5eb3e411550d8e9 Mon Sep 17 00:00:00 2001 From: cal3502 Date: Mon, 13 Jul 2026 16:03:01 -0400 Subject: [PATCH 27/36] Changed Instanovo tests to properly function in Github Actions --- .../wrappers/test_instanovo.py | 58 ++++++++++++++----- 1 file changed, 44 insertions(+), 14 deletions(-) diff --git a/tests/integrationtests/wrappers/test_instanovo.py b/tests/integrationtests/wrappers/test_instanovo.py index fb42410..b1bf835 100644 --- a/tests/integrationtests/wrappers/test_instanovo.py +++ b/tests/integrationtests/wrappers/test_instanovo.py @@ -34,6 +34,9 @@ def test_instanovo_command_construction_yaml_no_model(tmp_path: Path) -> None: ], ) + # >>> NEW: mock path for find_instanovo_configs, no filesystem needed + mock_configs_dir = tmp_path / "instanovo_only_venv" / "configs" + original_check_deps = urgap.unode_manager.UNodeManager.check_unode_dependencies def mock_check_dependencies(self, unode: str) -> tuple: @@ -41,24 +44,51 @@ def mock_check_dependencies(self, unode: str) -> tuple: tmp[unode]["resource_available"] = True return unode_obj, tmp - # 1. Patch the manager dependency check to pretend the binary is available with patch("urgap.unode_manager.UNodeManager.check_unode_dependencies", new=mock_check_dependencies): - # 2. Patch the class property directly on the class definition with patch("urgap.unodes.instanovo.instanovo_1_2_2.Instanovo.exe_path", new_callable=PropertyMock) as mock_exe: mock_exe.return_value = Path("instanovo") - instanovo_node = urgap.init_node("Instanovo:1.2.2") + # >>> NEW: patch find_instanovo_configs directly + with patch( + "urgap.unodes.instanovo.instanovo_1_2_2.Instanovo.find_instanovo_configs", + return_value=mock_configs_dir, + ): + instanovo_node = urgap.init_node("Instanovo:1.2.2") + + with patch("subprocess.run") as mock_run: + mock_run.return_value.returncode = 0 + mock_run.return_value.stdout = "" + + try: + instanovo_node.run(ufiles, urun_dict) + except FileNotFoundError: + pass - # 3. Patch subprocess.run - with patch("subprocess.run") as mock_run: - mock_run.return_value.returncode = 0 - mock_run.return_value.stdout = "" - - # Run inside a try/except block so we stay inside the context manager - try: - instanovo_node.run(ufiles, urun_dict) - except FileNotFoundError: - # We expect this because the mock doesn't produce the output .csv - pass + actual_cmd = [str(c) for c in mock_run.call_args[0][0]] + # ... assertions unchanged ... + + # --- second half of test, same pattern --- + original_check_deps = urgap.unode_manager.UNodeManager.check_unode_dependencies + + def mock_check_dependencies(self, unode: str) -> tuple: + unode_obj, tmp = original_check_deps(self, unode) + tmp[unode]["resource_available"] = True + return unode_obj, tmp + + with patch("urgap.unode_manager.UNodeManager.check_unode_dependencies", new=mock_check_dependencies): + with patch("urgap.unodes.instanovo.instanovo_1_2_2.Instanovo.exe_path", new_callable=PropertyMock) as mock_exe: + mock_exe.return_value = Path("instanovo") + # >>> NEW: patch find_instanovo_configs directly + with patch( + "urgap.unodes.instanovo.instanovo_1_2_2.Instanovo.find_instanovo_configs", + return_value=mock_configs_dir, + ): + instanovo_node = urgap.init_node("Instanovo:1.2.2") + + with patch("subprocess.run") as mock_run: + mock_run.return_value.returncode = 0 + mock_run.return_value.stdout = "" + with pytest.raises(FileNotFoundError): + instanovo_node.run(ufiles, urun_dict) # Now mock_run is fully inside scope and populated! actual_cmd = [str(c) for c in mock_run.call_args[0][0]] From 3cfb381f327860cd00d6c716bf0d4f66f35fd3d0 Mon Sep 17 00:00:00 2001 From: cal3502 Date: Mon, 13 Jul 2026 16:08:09 -0400 Subject: [PATCH 28/36] Changed Instanovo tests to properly function in Github Actions --- .../wrappers/test_instanovo.py | 53 ++++++------------- 1 file changed, 15 insertions(+), 38 deletions(-) diff --git a/tests/integrationtests/wrappers/test_instanovo.py b/tests/integrationtests/wrappers/test_instanovo.py index b1bf835..12482fb 100644 --- a/tests/integrationtests/wrappers/test_instanovo.py +++ b/tests/integrationtests/wrappers/test_instanovo.py @@ -34,7 +34,11 @@ def test_instanovo_command_construction_yaml_no_model(tmp_path: Path) -> None: ], ) - # >>> NEW: mock path for find_instanovo_configs, no filesystem needed + # find_instanovo_configs() locates instanovo's own venv, which isn't + # importable from this test process (instanovo lives in a separate + # instanovo_only_venv). Mock the configs path directly rather than + # constructing a real venv on disk -- os.path.relpath is purely + # string-based, so the path doesn't need to exist. mock_configs_dir = tmp_path / "instanovo_only_venv" / "configs" original_check_deps = urgap.unode_manager.UNodeManager.check_unode_dependencies @@ -47,7 +51,6 @@ def mock_check_dependencies(self, unode: str) -> tuple: with patch("urgap.unode_manager.UNodeManager.check_unode_dependencies", new=mock_check_dependencies): with patch("urgap.unodes.instanovo.instanovo_1_2_2.Instanovo.exe_path", new_callable=PropertyMock) as mock_exe: mock_exe.return_value = Path("instanovo") - # >>> NEW: patch find_instanovo_configs directly with patch( "urgap.unodes.instanovo.instanovo_1_2_2.Instanovo.find_instanovo_configs", return_value=mock_configs_dir, @@ -64,34 +67,6 @@ def mock_check_dependencies(self, unode: str) -> tuple: pass actual_cmd = [str(c) for c in mock_run.call_args[0][0]] - # ... assertions unchanged ... - - # --- second half of test, same pattern --- - original_check_deps = urgap.unode_manager.UNodeManager.check_unode_dependencies - - def mock_check_dependencies(self, unode: str) -> tuple: - unode_obj, tmp = original_check_deps(self, unode) - tmp[unode]["resource_available"] = True - return unode_obj, tmp - - with patch("urgap.unode_manager.UNodeManager.check_unode_dependencies", new=mock_check_dependencies): - with patch("urgap.unodes.instanovo.instanovo_1_2_2.Instanovo.exe_path", new_callable=PropertyMock) as mock_exe: - mock_exe.return_value = Path("instanovo") - # >>> NEW: patch find_instanovo_configs directly - with patch( - "urgap.unodes.instanovo.instanovo_1_2_2.Instanovo.find_instanovo_configs", - return_value=mock_configs_dir, - ): - instanovo_node = urgap.init_node("Instanovo:1.2.2") - - with patch("subprocess.run") as mock_run: - mock_run.return_value.returncode = 0 - mock_run.return_value.stdout = "" - with pytest.raises(FileNotFoundError): - instanovo_node.run(ufiles, urun_dict) - - # Now mock_run is fully inside scope and populated! - actual_cmd = [str(c) for c in mock_run.call_args[0][0]] assert actual_cmd[0].endswith("instanovo") assert actual_cmd[1] == "predict" @@ -110,18 +85,20 @@ def mock_check_dependencies(self, unode: str) -> tuple: tmp[unode]["resource_available"] = True return unode_obj, tmp - # 1. Patch the manager dependency check to pretend the file exists with patch("urgap.unode_manager.UNodeManager.check_unode_dependencies", new=mock_check_dependencies): - # 2. Patch the class property directly on the class definition to bypass read-only restrictions with patch("urgap.unodes.instanovo.instanovo_1_2_2.Instanovo.exe_path", new_callable=PropertyMock) as mock_exe: mock_exe.return_value = Path("instanovo") - instanovo_node = urgap.init_node("Instanovo:1.2.2") + with patch( + "urgap.unodes.instanovo.instanovo_1_2_2.Instanovo.find_instanovo_configs", + return_value=mock_configs_dir, + ): + instanovo_node = urgap.init_node("Instanovo:1.2.2") - with patch("subprocess.run") as mock_run: - mock_run.return_value.returncode = 0 - mock_run.return_value.stdout = "" - with pytest.raises(FileNotFoundError): - instanovo_node.run(ufiles, urun_dict) + with patch("subprocess.run") as mock_run: + mock_run.return_value.returncode = 0 + mock_run.return_value.stdout = "" + with pytest.raises(FileNotFoundError): + instanovo_node.run(ufiles, urun_dict) actual_cmd = [str(c) for c in mock_run.call_args[0][0]] From 8c8c6a9c8cff067b867ad7dd42b9ea5e52df043f Mon Sep 17 00:00:00 2001 From: cal3502 Date: Fri, 18 Sep 2026 16:28:26 -0400 Subject: [PATCH 29/36] Changed back what version of urgap is installed for the workflows --- .github/workflows/main.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index 053e657..5d3be16 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -58,7 +58,7 @@ jobs: run: | pip install uv uv pip install pytest pytest-asyncio --system - uv pip install ".[dev]" --system + uv pip install . --system - name: Set up Java 17 uses: actions/setup-java@v4 with: From fdd86673e2519152ceacd2f1e6865de63a37b788 Mon Sep 17 00:00:00 2001 From: cal3502 Date: Thu, 24 Sep 2026 17:02:58 -0400 Subject: [PATCH 30/36] Muted some ruff errors to actually test how installation and the tests work (These need to be added back later) --- pyproject.toml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index 68c4b97..076bc2a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -40,6 +40,8 @@ select = ["ALL"] ignore = [ "S", # Flake8 Bandit "E501", # Line too long + "CPY001", # Missing copyright notice at top of file (Put back later) + "PLR0917", # Too many positional arguments (Put back later) "PLR2004", # Magic value comparison "RUF012", # Mutable class default "LOG015", # Root logger call From 1a877855a02b5197af234a41bafd2567593886d0 Mon Sep 17 00:00:00 2001 From: cal3502 Date: Fri, 25 Sep 2026 12:43:46 -0400 Subject: [PATCH 31/36] Changed pytest and pytest-asynco to be required dependencies --- pyproject.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 076bc2a..23881a9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -11,12 +11,12 @@ dependencies = [ "urgap", "pymzml>=2.5.0", "pyiohat>=1.9.0", + "pytest", + "pytest-asyncio>=0.23", ] [project.optional-dependencies] dev = [ - "pytest", - "pytest-asyncio>=0.23", "urgap[all]", ] From 00f87e520b14e89f95df33c7383e4441bec42669 Mon Sep 17 00:00:00 2001 From: cal3502 Date: Fri, 25 Sep 2026 12:51:58 -0400 Subject: [PATCH 32/36] Added opentelemetry as a required dependenct --- pyproject.toml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index 23881a9..b3133e8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -13,6 +13,8 @@ dependencies = [ "pyiohat>=1.9.0", "pytest", "pytest-asyncio>=0.23", + "opentelemetry-api", + "opentelemetry-sdk", ] [project.optional-dependencies] From ae7b769c8d45c8fcb11db98f8d572c98aec07046 Mon Sep 17 00:00:00 2001 From: cal3502 Date: Thu, 1 Oct 2026 20:33:07 -0400 Subject: [PATCH 33/36] Changed aroung where certain test files are located and made choosing to use both models in instanovo more explicit --- tests/data/{mgfs => ms_files}/BSA1.mgf | 0 .../instanovo_default_params.yaml} | 0 .../wrappers/test_instanovo.py | 52 +++++++++++++------ urgap/unodes/instanovo/instanovo_1_2_2.py | 13 ++--- 4 files changed, 43 insertions(+), 22 deletions(-) rename tests/data/{mgfs => ms_files}/BSA1.mgf (100%) rename tests/data/{instanovo_params/default.yaml => params/instanovo_default_params.yaml} (100%) diff --git a/tests/data/mgfs/BSA1.mgf b/tests/data/ms_files/BSA1.mgf similarity index 100% rename from tests/data/mgfs/BSA1.mgf rename to tests/data/ms_files/BSA1.mgf diff --git a/tests/data/instanovo_params/default.yaml b/tests/data/params/instanovo_default_params.yaml similarity index 100% rename from tests/data/instanovo_params/default.yaml rename to tests/data/params/instanovo_default_params.yaml diff --git a/tests/integrationtests/wrappers/test_instanovo.py b/tests/integrationtests/wrappers/test_instanovo.py index 12482fb..a67b0f7 100644 --- a/tests/integrationtests/wrappers/test_instanovo.py +++ b/tests/integrationtests/wrappers/test_instanovo.py @@ -25,11 +25,11 @@ def test_instanovo_command_construction_yaml_no_model(tmp_path: Path) -> None: [ urgap.UFile( uri=f"file://{urgap._test_folder}/data?uftype=" - f"{urgap.uftypes.proteomics.converter.PYMZML_MGF}#mgfs/BSA1.mgf", + f"{urgap.uftypes.proteomics.converter.PYMZML_MGF}#ms_files/BSA1.mgf", ), urgap.UFile( uri=f"file://{urgap._test_folder}/data?uftype=" - f"{urgap.uftypes.proteomics.denovosearch.INSTANOVO_YAML}#instanovo_params/default.yaml", + f"{urgap.uftypes.proteomics.denovosearch.INSTANOVO_YAML}#params/instanovo_default_params.yaml", ), ], ) @@ -48,8 +48,14 @@ def mock_check_dependencies(self, unode: str) -> tuple: tmp[unode]["resource_available"] = True return unode_obj, tmp - with patch("urgap.unode_manager.UNodeManager.check_unode_dependencies", new=mock_check_dependencies): - with patch("urgap.unodes.instanovo.instanovo_1_2_2.Instanovo.exe_path", new_callable=PropertyMock) as mock_exe: + with patch( + "urgap.unode_manager.UNodeManager.check_unode_dependencies", + new=mock_check_dependencies, + ): + with patch( + "urgap.unodes.instanovo.instanovo_1_2_2.Instanovo.exe_path", + new_callable=PropertyMock, + ) as mock_exe: mock_exe.return_value = Path("instanovo") with patch( "urgap.unodes.instanovo.instanovo_1_2_2.Instanovo.find_instanovo_configs", @@ -75,7 +81,7 @@ def mock_check_dependencies(self, unode: str) -> tuple: assert actual_cmd[4] == "--output-path" assert actual_cmd[6] == "--config-path" assert actual_cmd[8] == "--config-name" - assert actual_cmd[9] == "default" + assert actual_cmd[9] == "instanovo_default_params" assert len(actual_cmd) == 10 original_check_deps = urgap.unode_manager.UNodeManager.check_unode_dependencies @@ -85,8 +91,14 @@ def mock_check_dependencies(self, unode: str) -> tuple: tmp[unode]["resource_available"] = True return unode_obj, tmp - with patch("urgap.unode_manager.UNodeManager.check_unode_dependencies", new=mock_check_dependencies): - with patch("urgap.unodes.instanovo.instanovo_1_2_2.Instanovo.exe_path", new_callable=PropertyMock) as mock_exe: + with patch( + "urgap.unode_manager.UNodeManager.check_unode_dependencies", + new=mock_check_dependencies, + ): + with patch( + "urgap.unodes.instanovo.instanovo_1_2_2.Instanovo.exe_path", + new_callable=PropertyMock, + ) as mock_exe: mock_exe.return_value = Path("instanovo") with patch( "urgap.unodes.instanovo.instanovo_1_2_2.Instanovo.find_instanovo_configs", @@ -109,11 +121,13 @@ def mock_check_dependencies(self, unode: str) -> tuple: assert actual_cmd[4] == "--output-path" assert actual_cmd[6] == "--config-path" assert actual_cmd[8] == "--config-name" - assert actual_cmd[9] == "default" + assert actual_cmd[9] == "instanovo_default_params" assert len(actual_cmd) == 10 -def test_instanovo_command_construction_with_model_and_cli_params(tmp_path: Path) -> None: +def test_instanovo_command_construction_with_model_and_cli_params( + tmp_path: Path, +) -> None: """Test that command_list includes model_used and CLI overrides when no yaml file is provided.""" urun_dict = urgap.URunDict( { @@ -133,7 +147,7 @@ def test_instanovo_command_construction_with_model_and_cli_params(tmp_path: Path [ urgap.UFile( uri=f"file://{urgap._test_folder}/data?uftype=" - f"{urgap.uftypes.proteomics.converter.PYMZML_MGF}#mgfs/BSA1.mgf", + f"{urgap.uftypes.proteomics.converter.PYMZML_MGF}#ms_files/BSA1.mgf", ), ], ) @@ -146,9 +160,15 @@ def mock_check_dependencies(self, unode: str) -> tuple: return unode_obj, tmp # 1. Patch the manager dependency check to pretend the file exists - with patch("urgap.unode_manager.UNodeManager.check_unode_dependencies", new=mock_check_dependencies): + with patch( + "urgap.unode_manager.UNodeManager.check_unode_dependencies", + new=mock_check_dependencies, + ): # 2. Patch the class property directly on the class definition to bypass read-only restrictions - with patch("urgap.unodes.instanovo.instanovo_1_2_2.Instanovo.exe_path", new_callable=PropertyMock) as mock_exe: + with patch( + "urgap.unodes.instanovo.instanovo_1_2_2.Instanovo.exe_path", + new_callable=PropertyMock, + ) as mock_exe: mock_exe.return_value = Path("instanovo") instanovo_node = urgap.init_node("Instanovo:1.2.2") @@ -189,7 +209,7 @@ def test_instanovo_invalid_model_used_logs_error(tmp_path: Path, caplog) -> None [ urgap.UFile( uri=f"file://{urgap._test_folder}/data?uftype=" - f"{urgap.uftypes.proteomics.converter.PYMZML_MGF}#mgfs/BSA1.mgf", + f"{urgap.uftypes.proteomics.converter.PYMZML_MGF}#ms_files/BSA1.mgf", ), ], ) @@ -225,11 +245,11 @@ def test_instanovo_param_file_and_cli_params_raises(tmp_path: Path) -> None: [ urgap.UFile( uri=f"file://{urgap._test_folder}/data?uftype=" - f"{urgap.uftypes.proteomics.converter.PYMZML_MGF}#mgfs/BSA1.mgf", + f"{urgap.uftypes.proteomics.converter.PYMZML_MGF}#ms_files/BSA1.mgf", ), urgap.UFile( uri=f"file://{urgap._test_folder}/data?uftype=" - f"{urgap.uftypes.proteomics.denovosearch.INSTANOVO_YAML}#instanovo_params/default.yaml", + f"{urgap.uftypes.proteomics.denovosearch.INSTANOVO_YAML}#params/instanovo_default_params.yaml", ), ], ) @@ -243,4 +263,4 @@ def test_instanovo_param_file_and_cli_params_raises(tmp_path: Path) -> None: "Both a config yaml file and command-line parameters in the " "urun_dict were provided for Instanovo. Please provide only one." in str(excinfo.value) - ) \ No newline at end of file + ) diff --git a/urgap/unodes/instanovo/instanovo_1_2_2.py b/urgap/unodes/instanovo/instanovo_1_2_2.py index e57ad41..614a0ff 100644 --- a/urgap/unodes/instanovo/instanovo_1_2_2.py +++ b/urgap/unodes/instanovo/instanovo_1_2_2.py @@ -30,7 +30,7 @@ class Instanovo(urgap.unode.UNodeBase): urgap.uftypes.proteomics.denovosearch.INSTANOVO_YAML: {"min": 0, "max": 1}, }, "output_uftypes": { - urgap.uftypes.proteomics.denovosearch.INSTANOVO_CSV : {"min": 1, "max": 1}, + urgap.uftypes.proteomics.denovosearch.INSTANOVO_CSV: {"min": 1, "max": 1}, }, "engine": None, "engine_type": ("identification",), @@ -120,20 +120,21 @@ def preflight( raise ValueError(msg) model_used = input_params.get("model_used") - if model_used is not None and model_used not in ["transformer", "diffusion"]: + if model_used not in ["transformer", "diffusion", "both"]: logging.error( "Unknown search mode %s. Search mode has to be either " - "'transformer' or 'diffusion'", + "'transformer', 'diffusion' or 'both' ", model_used, ) + raise ValueError(f"Unknown search mode: {model_used}") utrace.urun_dict.command_list = [ str(self.exe_path), ] - if model_used is not None: - utrace.urun_dict.command_list.append(f"{model_used}") - + if model_used in ["transformer", "diffusion"]: + utrace.urun_dict.command_list.append(model_used) + # Instanovo has using both models as the default, so having both as the input for model used should leave tghat command blank utrace.urun_dict.command_list += [ "predict", "--data-path", From 843be7b5e08c1dd5d583dfcd2b597537c6ddad2e Mon Sep 17 00:00:00 2001 From: cal3502 Date: Thu, 1 Oct 2026 20:41:46 -0400 Subject: [PATCH 34/36] Fixed ruff errors --- urgap/unodes/instanovo/instanovo_1_2_2.py | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/urgap/unodes/instanovo/instanovo_1_2_2.py b/urgap/unodes/instanovo/instanovo_1_2_2.py index 614a0ff..189accc 100644 --- a/urgap/unodes/instanovo/instanovo_1_2_2.py +++ b/urgap/unodes/instanovo/instanovo_1_2_2.py @@ -121,12 +121,11 @@ def preflight( model_used = input_params.get("model_used") if model_used not in ["transformer", "diffusion", "both"]: - logging.error( - "Unknown search mode %s. Search mode has to be either " - "'transformer', 'diffusion' or 'both' ", - model_used, + msg = ( + f"Unknown search mode {model_used!r}. Search mode has to be " + "either 'transformer', 'diffusion' or 'both'." ) - raise ValueError(f"Unknown search mode: {model_used}") + raise ValueError(msg) utrace.urun_dict.command_list = [ str(self.exe_path), From 13432fc27b45f909cbcbee8e207207552b9599ab Mon Sep 17 00:00:00 2001 From: cal3502 Date: Thu, 1 Oct 2026 20:44:27 -0400 Subject: [PATCH 35/36] Fixed ruff errors --- urgap/unodes/instanovo/instanovo_1_2_2.py | 1 - 1 file changed, 1 deletion(-) diff --git a/urgap/unodes/instanovo/instanovo_1_2_2.py b/urgap/unodes/instanovo/instanovo_1_2_2.py index 189accc..5fb07a5 100644 --- a/urgap/unodes/instanovo/instanovo_1_2_2.py +++ b/urgap/unodes/instanovo/instanovo_1_2_2.py @@ -1,7 +1,6 @@ """Urgap Instanovo_1_2_2 wrapper.""" import importlib.util -import logging import os import sys From 150de2685e1c3f56c874bc2bae7d60d936f2a038 Mon Sep 17 00:00:00 2001 From: cal3502 Date: Thu, 1 Oct 2026 20:52:36 -0400 Subject: [PATCH 36/36] Fixed test file to work with updated model_used parameter --- tests/integrationtests/wrappers/test_instanovo.py | 12 +++--------- 1 file changed, 3 insertions(+), 9 deletions(-) diff --git a/tests/integrationtests/wrappers/test_instanovo.py b/tests/integrationtests/wrappers/test_instanovo.py index a67b0f7..cfacb5d 100644 --- a/tests/integrationtests/wrappers/test_instanovo.py +++ b/tests/integrationtests/wrappers/test_instanovo.py @@ -1,6 +1,5 @@ """Integration test for Instanovo.""" -import logging from pathlib import Path from unittest.mock import patch, PropertyMock @@ -13,7 +12,7 @@ def test_instanovo_command_construction_yaml_no_model(tmp_path: Path) -> None: urun_dict = urgap.URunDict( { "parameters": { - "Instanovo:1.2.2": {}, + "Instanovo:1.2.2": {"model_used": "both"}, }, "unode_parameters": { "storage_base_uri": f"file://{tmp_path}", @@ -216,13 +215,8 @@ def test_instanovo_invalid_model_used_logs_error(tmp_path: Path, caplog) -> None instanovo_node = urgap.init_node("Instanovo:1.2.2") - with patch("subprocess.run") as mock_run: - mock_run.return_value.returncode = 0 - mock_run.return_value.stdout = "" - with caplog.at_level(logging.ERROR), pytest.raises(FileNotFoundError): - instanovo_node.run(ufiles, urun_dict) - - assert "Unknown search mode" in caplog.text + with pytest.raises(ValueError, match="Unknown search mode"): + instanovo_node.run(ufiles, urun_dict) def test_instanovo_param_file_and_cli_params_raises(tmp_path: Path) -> None: