plkx
commented
3 years ago Fixes for all of these can be found in other Issues/threads.
The pandas issue is easily resolved as described in https://github.com/mordred-descriptor/mordred/issues/80#issuecomment-718042620
PANDAS through version 1.1.3 can then be used.
The NETWORKX issue is resolved as described here: https://github.com/mordred-descriptor/mordred/issues/80#issuecomment-725330942
NETWORKX through version 2.5 can then be used.
You must install YAML.
Best Regards,
plkx
Summary
It's really easy to install with conda 👍 but there are missing instructions about compatible module versions.
Here is what I needed to complete "python -m mordred.tests" without errors. conda install networkx=2.3 conda install pandas=0.25-3 conda install pyyaml
Now it's all fine, thanks for a great software !
Below is a sample of errors I had while running: python -m mordred.tests
Yaml (not installed or "conda install yaml")
====================================================================== ERROR: Failure: ModuleNotFoundError (No module named 'yaml')
Traceback (most recent call last): File "/home/dgomes/miniconda3/envs/mordred/lib/python3.7/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/home/dgomes/miniconda3/envs/mordred/lib/python3.7/site-packages/nose/loader.py", line 417, in loadTestsFromName addr.filename, addr.module) File "/home/dgomes/miniconda3/envs/mordred/lib/python3.7/site-packages/nose/importer.py", line 47, in importFromPath return self.importFromDir(dir_path, fqname) File "/home/dgomes/miniconda3/envs/mordred/lib/python3.7/site-packages/nose/importer.py", line 94, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/home/dgomes/miniconda3/envs/mordred/lib/python3.7/imp.py", line 234, in load_module return load_source(name, filename, file) File "/home/dgomes/miniconda3/envs/mordred/lib/python3.7/imp.py", line 171, in load_source module = _load(spec) File "", line 696, in _load
File "", line 677, in _load_unlocked
File "", line 728, in exec_module
File "", line 219, in _call_with_frames_removed
File "/home/dgomes/miniconda3/envs/mordred/lib/python3.7/site-packages/mordred/tests/test_by_references.py", line 4, in
import yaml
ModuleNotFoundError: No module named 'yaml'
Networkx 2.5
====================================================================== FAIL: mordred.tests.test_mordred_main.test_sdf_3D
Traceback (most recent call last): File "/home/dgomes/miniconda3/envs/mordred/lib/python3.7/site-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/home/dgomes/miniconda3/envs/mordred/lib/python3.7/site-packages/mordred/tests/test_mordred_main.py", line 176, in test_sdf3D eq(stderr, "") AssertionError: "[ERROR] Benzene: module 'networkx' has no attribute 'biconnected_component_subgraphs' (SpAbs_Dt/SpAbs/mordred._matrix_attributes.Eigen(mordred.DetourMatrix.DetourMatrixCache())/mordred.DetourMatrix.DetourMatrixCache())\n" != ''
PANDAS 1.0.1
http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated yield ok_, np.isnan(f.ix[1, 1]) ./home/dgomes/miniconda3/envs/mordred/lib/python3.7/site-packages/mordred/tests/test_pandas.py:26: FutureWarning: .ix is deprecated. Please use .loc for label based indexing or .iloc for positional indexing