nsheff
commented
3 years ago Wow this is strange.
This works:python3 -c "import peppy; p = peppy.Project('asset_pep/refgenie_build_cfg.yaml')"
import peppy
p = peppy.Project("asset_pep/refgenie_build_cfg.yaml")This does not work: python3 -c "import looper; import peppy; p = peppy.Project('asset_pep/refgenie_build_cfg.yaml')"
import looper
import peppy
p = peppy.Project("asset_pep/refgenie_build_cfg.yaml") ...: import looper
...: import peppy
...: p = peppy.Project("asset_pep/refgenie_build_cfg.yaml")
---------------------------------------------------------------------------
RecursionError Traceback (most recent call last)
<ipython-input-1-58741ae6196d> in <module>
1 import looper
2 import peppy
----> 3 p = peppy.Project("asset_pep/refgenie_build_cfg.yaml")
~/.local/lib/python3.8/site-packages/peppy/project.py in __init__(self, cfg, amendments, sample_table_index, subsample_table_index, defer_samples_creation)
57 if isinstance(cfg, str):
58 self[CONFIG_FILE_KEY] = cfg
---> 59 self.parse_config_file(cfg, amendments)
60 else:
61 self[CONFIG_FILE_KEY] = None
~/.local/lib/python3.8/site-packages/peppy/project.py in parse_config_file(self, cfg_path, amendments)
127 if not os.path.exists(cfg_path) and not is_url(cfg_path):
128 raise OSError(f"Project config file path does not exist: {cfg_path}")
--> 129 config = load_yaml(cfg_path)
130 assert isinstance(
131 config, Mapping
~/.local/lib/python3.8/site-packages/peppy/utils.py in load_yaml(filepath)
130 return oyaml.safe_load(text)
131 else:
--> 132 return read_yaml_file(filepath)
133
134
~/.local/lib/python3.8/site-packages/peppy/utils.py in read_yaml_file(filepath)
117 filepath = os.path.abspath(filepath)
118 with open(filepath, "r") as f:
--> 119 data = oyaml.safe_load(f)
120 return data
121
/apps/software/standard/core/anaconda/2020.11-py3.8/lib/python3.8/site-packages/yaml/__init__.py in safe_load(stream)
160 to be safe for untrusted input.
161 """
--> 162 return load(stream, SafeLoader)
163
164 def safe_load_all(stream):
/apps/software/standard/core/anaconda/2020.11-py3.8/lib/python3.8/site-packages/yaml/__init__.py in load(stream, Loader)
112 loader = Loader(stream)
113 try:
--> 114 return loader.get_single_data()
115 finally:
116 loader.dispose()
/apps/software/standard/core/anaconda/2020.11-py3.8/lib/python3.8/site-packages/yaml/constructor.py in get_single_data(self)
49 node = self.get_single_node()
50 if node is not None:
---> 51 return self.construct_document(node)
52 return None
53
/apps/software/standard/core/anaconda/2020.11-py3.8/lib/python3.8/site-packages/yaml/constructor.py in construct_document(self, node)
58 self.state_generators = []
59 for generator in state_generators:
---> 60 for dummy in generator:
61 pass
62 self.constructed_objects = {}
/apps/software/standard/core/anaconda/2020.11-py3.8/lib/python3.8/site-packages/yaml/constructor.py in construct_yaml_map(self, node)
411 data = {}
412 yield data
--> 413 value = self.construct_mapping(node)
414 data.update(value)
415
~/.local/lib/python3.8/site-packages/peppy/utils.py in my_construct_mapping(self, node, deep)
146 # ordered by default.
147 def my_construct_mapping(self, node, deep=False):
--> 148 data = self.construct_mapping_org(node, deep)
149 return {
150 (str(key) if isinstance(key, float) or isinstance(key, int) else key): data[key]
~/.local/lib/python3.8/site-packages/yacman/yacman.py in my_construct_mapping(self, node, deep)
29 # ordered by default.
30 def my_construct_mapping(self, node, deep=False):
---> 31 data = self.construct_mapping_org(node, deep)
32 return {
33 (str(key) if isinstance(key, float) or isinstance(key, int) else key): data[key]
... last 1 frames repeated, from the frame below ...
~/.local/lib/python3.8/site-packages/yacman/yacman.py in my_construct_mapping(self, node, deep)
29 # ordered by default.
30 def my_construct_mapping(self, node, deep=False):
---> 31 data = self.construct_mapping_org(node, deep)
32 return {
33 (str(key) if isinstance(key, float) or isinstance(key, int) else key): data[key]
RecursionError: maximum recursion depth exceeded
Not sure if this is related to:
When on the cluster, I get this error. The same command works on my local computer on the same file....
Relevant versions appear to match. Both are
Python 3.8.5.on rivanna:
local:
having trouble tracking this down; why can't looper run on rivanna...