MSFragger speclib incomaptible with alphaPeptDeep

[GeorgWa]

Describe the bug Loading a MSFragger lib and predicting spectra works on the main branch of alphaBase but fails on the development branch of alphaBase.

To Reproduce

%reload_ext autoreload
%autoreload 2
import logging
logging.getLogger().setLevel(logging.INFO)

from alphabase.spectral_library.reader import LibraryReaderBase

lib_location = '/Users/georgwallmann/Documents/data/alphadia_benchmarking/libraries/patricia_hela/21min_Evosep_HeLa_BR14_48fractions_diaPASEF_py_diAID_2.tsv'

# create dense library from diann psm file
target_lib = LibraryReaderBase()
target_lib.add_modification_mapping(
    {'Oxidation@M':['M(Oxidation)'],
     'Dimethyl@K':['K(Dimethyl)'],
     'Dimethyl@R':['R(Dimethyl)'],
     'Dimethyl@Any N-term':['(Dimethyl)']
    }
)
psm = target_lib.import_file(lib_location)

from peptdeep.pretrained_models import ModelManager
from alphabase.peptide.fragment import get_charged_frag_types

model_mgr = ModelManager(device='cpu')

model_mgr.nce = 25
model_mgr.instrument = 'orbitrap'

target_lib.precursor_df['instrument'] = model_mgr.instrument
target_lib.precursor_df['nce'] = model_mgr.nce

frag_types = get_charged_frag_types(
    ['b','y'],
    2
)

res = model_mgr.predict_all(
    target_lib.precursor_df,
    predict_items=['ms2'],
    frag_types = frag_types,
)
target_lib._precursor_df = res['precursor_df']
target_lib._fragment_mz_df = res['fragment_mz_df']
target_lib._fragment_intensity_df = res['fragment_intensity_df']

Additional context

Error Message

```python --------------------------------------------------------------------------- RemoteTraceback Traceback (most recent call last) RemoteTraceback: """ Traceback (most recent call last): File "/Users/georgwallmann/miniconda3/envs/alpha/lib/python3.9/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, **kwds)) File "/Users/georgwallmann/Documents/git/alphapeptdeep/peptdeep/pretrained_models.py", line 887, in _predict_func_for_mp return self.predict_all( File "/Users/georgwallmann/Documents/git/alphapeptdeep/peptdeep/pretrained_models.py", line 1065, in predict_all fragment_mz_df = create_fragment_mz_dataframe( File "/Users/georgwallmann/Documents/git/alphabase/alphabase/peptide/fragment.py", line 913, in create_fragment_mz_dataframe return create_fragment_mz_dataframe( File "/Users/georgwallmann/Documents/git/alphabase/alphabase/peptide/fragment.py", line 975, in create_fragment_mz_dataframe return mask_fragments_for_charge_greater_than_precursor_charge( File "/Users/georgwallmann/Documents/git/alphabase/alphabase/peptide/fragment.py", line 502, in mask_fragments_for_charge_greater_than_precursor_charge fragment_df.loc[ File "/Users/georgwallmann/miniconda3/envs/alpha/lib/python3.9/site-packages/pandas/core/indexing.py", line 815, in __setitem__ indexer = self._get_setitem_indexer(key) File "/Users/georgwallmann/miniconda3/envs/alpha/lib/python3.9/site-packages/pandas/core/indexing.py", line 698, in _get_setitem_indexer return self._convert_tuple(key) File "/Users/georgwallmann/miniconda3/envs/alpha/lib/python3.9/site-packages/pandas/core/indexing.py", line 897, in _convert_tuple keyidx = [self._convert_to_indexer(k, axis=i) for i, k in enumerate(key)] File "/Users/georgwallmann/miniconda3/envs/alpha/lib/python3.9/site-packages/pandas/core/indexing.py", line 897, in keyidx = [self._convert_to_indexer(k, axis=i) for i, k in enumerate(key)] File "/Users/georgwallmann/miniconda3/envs/alpha/lib/python3.9/site-packages/pandas/core/indexing.py", line 1394, in _convert_to_indexer key = check_bool_indexer(labels, key) File "/Users/georgwallmann/miniconda3/envs/alpha/lib/python3.9/site-packages/pandas/core/indexing.py", line 2567, in check_bool_indexer return check_array_indexer(index, result) File "/Users/georgwallmann/miniconda3/envs/alpha/lib/python3.9/site-packages/pandas/core/indexers/utils.py", line 553, in check_array_indexer raise IndexError( IndexError: Boolean index has wrong length: 51864 instead of 3084552 """ The above exception was the direct cause of the following exception: IndexError Traceback (most recent call last) [/Users/georgwallmann/Downloads/create_msfragger_lib.ipynb](https://file+.vscode-resource.vscode-cdn.net/Users/georgwallmann/Downloads/create_msfragger_lib.ipynb) Cell 4 in 1 [10](vscode-notebook-cell:/Users/georgwallmann/Downloads/create_msfragger_lib.ipynb#W3sZmlsZQ%3D%3D?line=9) target_lib.precursor_df['nce'] = model_mgr.nce [12](vscode-notebook-cell:/Users/georgwallmann/Downloads/create_msfragger_lib.ipynb#W3sZmlsZQ%3D%3D?line=11) frag_types = get_charged_frag_types( [13](vscode-notebook-cell:/Users/georgwallmann/Downloads/create_msfragger_lib.ipynb#W3sZmlsZQ%3D%3D?line=12) ['b','y'], [14](vscode-notebook-cell:/Users/georgwallmann/Downloads/create_msfragger_lib.ipynb#W3sZmlsZQ%3D%3D?line=13) 2 [15](vscode-notebook-cell:/Users/georgwallmann/Downloads/create_msfragger_lib.ipynb#W3sZmlsZQ%3D%3D?line=14) ) ---> [17](vscode-notebook-cell:/Users/georgwallmann/Downloads/create_msfragger_lib.ipynb#W3sZmlsZQ%3D%3D?line=16) res = model_mgr.predict_all( [18](vscode-notebook-cell:/Users/georgwallmann/Downloads/create_msfragger_lib.ipynb#W3sZmlsZQ%3D%3D?line=17) target_lib.precursor_df, [19](vscode-notebook-cell:/Users/georgwallmann/Downloads/create_msfragger_lib.ipynb#W3sZmlsZQ%3D%3D?line=18) predict_items=['ms2'], [20](vscode-notebook-cell:/Users/georgwallmann/Downloads/create_msfragger_lib.ipynb#W3sZmlsZQ%3D%3D?line=19) frag_types = frag_types, [21](vscode-notebook-cell:/Users/georgwallmann/Downloads/create_msfragger_lib.ipynb#W3sZmlsZQ%3D%3D?line=20) ) [22](vscode-notebook-cell:/Users/georgwallmann/Downloads/create_msfragger_lib.ipynb#W3sZmlsZQ%3D%3D?line=21) target_lib._precursor_df = res['precursor_df'] [23](vscode-notebook-cell:/Users/georgwallmann/Downloads/create_msfragger_lib.ipynb#W3sZmlsZQ%3D%3D?line=22) target_lib._fragment_mz_df = res['fragment_mz_df'] File [~/Documents/git/alphapeptdeep/peptdeep/pretrained_models.py:1098](https://file+.vscode-resource.vscode-cdn.net/Users/georgwallmann/Downloads/~/Documents/git/alphapeptdeep/peptdeep/pretrained_models.py:1098), in ModelManager.predict_all(self, precursor_df, predict_items, frag_types, multiprocessing, min_required_precursor_num_for_mp, process_num, mp_batch_size) 1096 else: 1097 logging.info(f"Using multiprocessing with {process_num} processes ...") -> 1098 return self.predict_all_mp( 1099 precursor_df, 1100 predict_items=predict_items, 1101 process_num = process_num, 1102 mp_batch_size=mp_batch_size, 1103 ) File [~/Documents/git/alphapeptdeep/peptdeep/pretrained_models.py:937](https://file+.vscode-resource.vscode-cdn.net/Users/georgwallmann/Downloads/~/Documents/git/alphapeptdeep/peptdeep/pretrained_models.py:937), in ModelManager.predict_all_mp(self, precursor_df, predict_items, frag_types, process_num, mp_batch_size) 934 self.verbose = False 936 with mp.get_context('spawn').Pool(process_num) as p: --> 937 for ret_dict in process_bar( 938 p.imap_unordered( 939 self._predict_func_for_mp, 940 mp_param_generator(df_groupby) 941 ), 942 get_batch_num_mp(df_groupby) 943 ): 944 precursor_df_list.append(ret_dict['precursor_df']) 945 if fragment_mz_df_list is not None: File [~/Documents/git/alphapeptdeep/peptdeep/utils.py:27](https://file+.vscode-resource.vscode-cdn.net/Users/georgwallmann/Downloads/~/Documents/git/alphapeptdeep/peptdeep/utils.py:27), in process_bar(iterator, len_iter) 25 with tqdm.tqdm(total=len_iter) as bar: 26 i = 0 ---> 27 for i,iter in enumerate(iterator): 28 yield iter 29 bar.update() File [~/miniconda3/envs/alpha/lib/python3.9/multiprocessing/pool.py:870](https://file+.vscode-resource.vscode-cdn.net/Users/georgwallmann/Downloads/~/miniconda3/envs/alpha/lib/python3.9/multiprocessing/pool.py:870), in IMapIterator.next(self, timeout) 868 if success: 869 return value --> 870 raise value IndexError: Boolean index has wrong length: 51864 instead of 3084552 ```

Conda Env

``` # packages in environment at /Users/georgwallmann/miniconda3/envs/alpha: # # Name Version Build Channel alabaster 0.7.12 pypi_0 pypi alphabase 0.2.0 dev_0 alphadia 1.2.0 dev_0 alphapept 0.4.8 pypi_0 pypi alpharaw 0.1.0 dev_0 alphatims 1.0.6 dev_0 altair 4.2.0 pypi_0 pypi anyio 3.6.1 pyhd8ed1ab_1 conda-forge appnope 0.1.3 pyhd8ed1ab_0 conda-forge argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge argon2-cffi-bindings 21.2.0 py39hb18efdd_2 conda-forge arrow 1.2.3 pypi_0 pypi asteval 0.9.28 pypi_0 pypi asttokens 2.0.8 pyhd8ed1ab_0 conda-forge astunparse 1.6.3 pyhd8ed1ab_0 conda-forge attrs 22.1.0 pyh71513ae_1 conda-forge autodocsumm 0.2.9 pypi_0 pypi babel 2.10.3 pyhd8ed1ab_0 conda-forge backcall 0.2.0 pyh9f0ad1d_0 conda-forge backports 1.0 py_2 conda-forge backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge beautifulsoup4 4.11.1 pyha770c72_0 conda-forge biopython 1.79 pypi_0 pypi bleach 5.0.1 pyhd8ed1ab_0 conda-forge blinker 1.5 pypi_0 pypi bokeh 2.4.3 pyhd8ed1ab_3 conda-forge boto3 1.26.37 pypi_0 pypi botocore 1.29.37 pypi_0 pypi bravado 11.0.3 pypi_0 pypi bravado-core 5.17.1 pypi_0 pypi brotli 1.0.9 h1c322ee_7 conda-forge brotli-bin 1.0.9 h1c322ee_7 conda-forge brotlipy 0.7.0 py39hb18efdd_1004 conda-forge bump2version 1.0.1 pypi_0 pypi bumpversion 0.6.0 pypi_0 pypi bzip2 1.0.8 h3422bc3_4 conda-forge c-ares 1.18.1 h3422bc3_0 conda-forge ca-certificates 2023.05.30 hca03da5_0 cachetools 5.2.0 pypi_0 pypi certifi 2023.7.22 py39hca03da5_0 cffi 1.15.1 py39h04d3946_0 conda-forge chardet 5.1.0 pypi_0 pypi charset-normalizer 2.1.1 pyhd8ed1ab_0 conda-forge click 8.1.3 pypi_0 pypi cloudpickle 2.2.0 pyhd8ed1ab_0 conda-forge clr-loader 0.2.6 pypi_0 pypi colorama 0.4.5 pyhd8ed1ab_0 conda-forge colorcet 3.0.1 pyhd8ed1ab_0 conda-forge commonmark 0.9.1 pypi_0 pypi conda 22.9.0 py39h2804cbe_1 conda-forge conda-package-handling 1.9.0 py39h02fc5c5_0 conda-forge contextlib2 21.6.0 pypi_0 pypi contourpy 1.0.5 py39haaf3ac1_0 conda-forge coverage 7.2.0 pypi_0 pypi coverage-badge 1.1.0 pypi_0 pypi cryptography 38.0.4 py39he2a39a8_0 conda-forge cycler 0.11.0 pyhd8ed1ab_0 conda-forge dask-core 2022.10.0 pyhd8ed1ab_0 conda-forge datashader 0.14.2 pyh6c4a22f_0 conda-forge datashape 0.5.4 py_1 conda-forge debugpy 1.6.3 py39h3c22d25_0 conda-forge decorator 5.1.1 pyhd8ed1ab_0 conda-forge defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge docutils 0.19 pypi_0 pypi easygui 0.98.3 pypi_0 pypi entrypoints 0.4 pyhd8ed1ab_0 conda-forge execnb 0.1.4 pyhd8ed1ab_0 conda-forge executing 1.1.1 pyhd8ed1ab_0 conda-forge fastcore 1.5.27 pypi_0 pypi filelock 3.8.0 pypi_0 pypi flit-core 3.7.1 pyhd8ed1ab_0 conda-forge fmt 9.1.0 hffc8910_0 conda-forge fonttools 4.37.4 py39h02fc5c5_0 conda-forge fqdn 1.5.1 pypi_0 pypi freetype 2.12.1 hd633e50_0 conda-forge fsspec 2022.8.2 pyhd8ed1ab_0 conda-forge furo 2022.12.7 pypi_0 pypi future 0.18.2 pypi_0 pypi ghapi 1.0.3 pyhd8ed1ab_1 conda-forge gitdb 4.0.9 pypi_0 pypi gitpython 3.1.29 pypi_0 pypi h5py 3.7.0 pypi_0 pypi hdf5 1.12.2 nompi_h33dac16_100 conda-forge hilbertcurve 2.0.5 pypi_0 pypi holoviews 1.15.1 pyhd8ed1ab_0 conda-forge huggingface-hub 0.10.1 pypi_0 pypi hvplot 0.8.1 pyhd8ed1ab_0 conda-forge icu 70.1 h6b3803e_0 conda-forge idna 3.4 pyhd8ed1ab_0 conda-forge imageio 2.27.0 pypi_0 pypi imagesize 1.4.1 pypi_0 pypi imbalanced-learn 0.11.0 pypi_0 pypi importlib-metadata 4.11.4 py39h2804cbe_0 conda-forge importlib_resources 5.10.0 pyhd8ed1ab_0 conda-forge iniconfig 1.1.1 pyhd3eb1b0_0 ipykernel 6.16.0 pyh736e0ef_0 conda-forge ipympl 0.9.3 pypi_0 pypi ipython 8.5.0 pyhd1c38e8_1 conda-forge ipython_genutils 0.2.0 py_1 conda-forge ipywidgets 7.6.5 pyhd3eb1b0_1 isoduration 20.11.0 pypi_0 pypi jedi 0.18.1 pyhd8ed1ab_2 conda-forge jinja2 3.1.2 pyhd8ed1ab_1 conda-forge jmespath 1.0.1 pypi_0 pypi joblib 1.2.0 pyhd8ed1ab_0 conda-forge jpeg 9e he4db4b2_2 conda-forge json5 0.9.5 pyh9f0ad1d_0 conda-forge jsonpointer 2.3 pypi_0 pypi jsonref 1.0.1 pypi_0 pypi jsonschema 4.16.0 pyhd8ed1ab_0 conda-forge jupyter_client 7.4.2 pyhd8ed1ab_0 conda-forge jupyter_core 4.11.1 py39h2804cbe_0 conda-forge jupyter_server 1.21.0 pyhd8ed1ab_0 conda-forge jupyterlab 3.4.8 pyhd8ed1ab_0 conda-forge jupyterlab_pygments 0.2.2 pyhd8ed1ab_0 conda-forge jupyterlab_server 2.16.0 pyhd8ed1ab_0 conda-forge jupyterlab_widgets 1.0.0 pyhd3eb1b0_1 kiwisolver 1.4.4 py39hab5e169_0 conda-forge krb5 1.19.3 he492e65_0 conda-forge lazy-loader 0.2 pypi_0 pypi lcms2 2.12 had6a04f_0 conda-forge lerc 4.0.0 h9a09cb3_0 conda-forge libarchive 3.5.2 hdd7f49f_3 conda-forge libblas 3.9.0 16_osxarm64_openblas conda-forge libbrotlicommon 1.0.9 h1c322ee_7 conda-forge libbrotlidec 1.0.9 h1c322ee_7 conda-forge libbrotlienc 1.0.9 h1c322ee_7 conda-forge libcblas 3.9.0 16_osxarm64_openblas conda-forge libcurl 7.86.0 h1c293e1_1 conda-forge libcxx 14.0.6 h2692d47_0 conda-forge libdeflate 1.14 h1a8c8d9_0 conda-forge libedit 3.1.20191231 hc8eb9b7_2 conda-forge libev 4.33 h642e427_1 conda-forge libffi 3.4.2 h3422bc3_5 conda-forge libgfortran 5.0.0 11_3_0_hd922786_25 conda-forge libgfortran5 11.3.0 hdaf2cc0_25 conda-forge libiconv 1.17 he4db4b2_0 conda-forge liblapack 3.9.0 16_osxarm64_openblas conda-forge libllvm11 11.1.0 hfa12f05_4 conda-forge libmamba 1.1.0 he1bf84c_2 conda-forge libmambapy 1.1.0 py39h6901ea2_2 conda-forge libnghttp2 1.47.0 h519802c_1 conda-forge libopenblas 0.3.21 openmp_hc731615_3 conda-forge libpng 1.6.38 h76d750c_0 conda-forge libsodium 1.0.18 h27ca646_1 conda-forge libsolv 0.7.22 h1280f1d_0 conda-forge libsqlite 3.39.4 h76d750c_0 conda-forge libssh2 1.10.0 h7a5bd25_3 conda-forge libtiff 4.4.0 hfa0b094_4 conda-forge libwebp-base 1.2.4 h57fd34a_0 conda-forge libxcb 1.13 h9b22ae9_1004 conda-forge libxml2 2.10.3 h87b0503_0 conda-forge libzlib 1.2.13 h03a7124_4 conda-forge line-profiler 3.5.1 pypi_0 pypi llvm-openmp 14.0.6 hc6e5704_0 llvmlite 0.39.1 py39h8ca5d33_0 conda-forge lmfit 1.1.0 pypi_0 pypi locket 1.0.0 pyhd8ed1ab_0 conda-forge lxml 4.9.1 pypi_0 pypi lz4-c 1.9.3 hbdafb3b_1 conda-forge lzo 2.10 h642e427_1000 conda-forge mamba 1.1.0 py39ha55b623_2 conda-forge markdown 3.4.1 pyhd8ed1ab_0 conda-forge markdown-it-py 2.1.0 pypi_0 pypi markupsafe 2.1.1 py39hb18efdd_1 conda-forge matplotlib-base 3.5.3 py39hc377ac9_0 matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge matplotlib-venn 0.11.7 pypi_0 pypi maturin 0.13.7 py39ha6e5c4f_0 mdit-py-plugins 0.3.3 pypi_0 pypi mdurl 0.1.2 pypi_0 pypi mistune 2.0.4 pyhd8ed1ab_0 conda-forge mmh3 3.0.0 pypi_0 pypi monotonic 1.6 pypi_0 pypi msgpack 1.0.4 pypi_0 pypi multipledispatch 0.6.0 py_0 conda-forge munkres 1.1.4 pyh9f0ad1d_0 conda-forge myst-parser 0.18.1 pypi_0 pypi nb_conda_kernels 2.3.1 py39h2804cbe_1 conda-forge nbclassic 0.4.5 pyhd8ed1ab_0 conda-forge nbclient 0.7.0 pyhd8ed1ab_0 conda-forge nbconvert 7.2.1 pyhd8ed1ab_0 conda-forge nbconvert-core 7.2.1 pyhd8ed1ab_0 conda-forge nbconvert-pandoc 7.2.1 pyhd8ed1ab_0 conda-forge nbdev 2.2.10 pyhd8ed1ab_0 conda-forge nbformat 5.7.0 pyhd8ed1ab_0 conda-forge nbsphinx 0.8.10 pypi_0 pypi ncurses 6.3 h07bb92c_1 conda-forge neptune 1.6.1 pypi_0 pypi nest-asyncio 1.5.6 pyhd8ed1ab_0 conda-forge networkx 3.1 pypi_0 pypi notebook 6.5.1 pyha770c72_0 conda-forge notebook-shim 0.1.0 pyhd8ed1ab_0 conda-forge numba 0.56.4 py39h78102c4_0 numexpr 2.8.3 pypi_0 pypi numpy 1.23.3 py39hcb4b507_0 conda-forge oauthlib 3.2.2 pypi_0 pypi openjpeg 2.5.0 h5d4e404_1 conda-forge openssl 3.0.10 h1a28f6b_0 packaging 21.3 pyhd8ed1ab_0 conda-forge pandas 1.5.0 pypi_0 pypi pandoc 2.12 hca03da5_0 pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge panel 0.14.0 pyhd8ed1ab_0 conda-forge param 1.12.2 pyh6c4a22f_0 conda-forge parso 0.8.3 pyhd8ed1ab_0 conda-forge partd 1.3.0 pyhd8ed1ab_0 conda-forge peptdeep 0.1.7 dev_0 pexpect 4.8.0 pyh9f0ad1d_2 conda-forge pickleshare 0.7.5 py_1003 conda-forge pillow 9.2.0 py39he45c975_2 conda-forge pip 22.3 pyhd8ed1ab_0 conda-forge pkgutil-resolve-name 1.3.10 pyhd8ed1ab_0 conda-forge pluggy 1.0.0 py39hca03da5_1 pprofile 2.1.0 pypi_0 pypi progressbar 2.5 pypi_0 pypi prometheus_client 0.15.0 pyhd8ed1ab_0 conda-forge prompt-toolkit 3.0.31 pyha770c72_0 conda-forge protobuf 3.20.3 pypi_0 pypi psutil 5.9.2 py39h02fc5c5_0 conda-forge pthread-stubs 0.4 h27ca646_1001 conda-forge ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge py 1.11.0 pyhd3eb1b0_0 py-lmd 1.0.0 pypi_0 pypi py-rs-playground 0.1.0 pypi_0 pypi pyarrow 9.0.0 pypi_0 pypi pybind11-abi 4 hd8ed1ab_3 conda-forge pycosat 0.6.3 py39hb18efdd_1010 conda-forge pycparser 2.21 pyhd8ed1ab_0 conda-forge pyct 0.4.6 py_0 conda-forge pyct-core 0.4.6 py_0 conda-forge pydeck 0.8.0b4 pypi_0 pypi pydivsufsort 0.0.6 pypi_0 pypi pygments 2.13.0 pyhd8ed1ab_0 conda-forge pygount 1.5.1 pypi_0 pypi pyjwt 2.6.0 pypi_0 pypi pympler 1.0.1 pypi_0 pypi pyopenssl 22.1.0 pyhd8ed1ab_0 conda-forge pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge pyrsistent 0.18.1 py39hb18efdd_1 conda-forge pysocks 1.7.1 pyha2e5f31_6 conda-forge pyteomics 4.5.5 pypi_0 pypi pytest 7.1.2 py39hca03da5_0 python 3.9.13 h96fcbfb_0_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python-fastjsonschema 2.16.2 pyhd8ed1ab_0 conda-forge python_abi 3.9 2_cp39 conda-forge pythonnet 3.0.1 pypi_0 pypi pytz 2022.4 pyhd8ed1ab_0 conda-forge pytz-deprecation-shim 0.1.0.post0 pypi_0 pypi pyviz_comms 2.2.1 pyhd8ed1ab_1 conda-forge pywavelets 1.4.1 pypi_0 pypi pyyaml 6.0 py39hb18efdd_4 conda-forge pyzmq 24.0.1 py39h0553236_0 conda-forge pyzstd 0.15.3 pypi_0 pypi readline 8.1.2 h46ed386_0 conda-forge regex 2022.9.13 pypi_0 pypi reproc 14.2.3 h3422bc3_0 conda-forge reproc-cpp 14.2.3 hbdafb3b_0 conda-forge requests 2.28.1 pyhd8ed1ab_1 conda-forge requests-oauthlib 1.3.1 pypi_0 pypi rfc3339-validator 0.1.4 pypi_0 pypi rfc3987 1.3.8 pypi_0 pypi rich 12.6.0 pypi_0 pypi rocket-fft 0.1.5 pypi_0 pypi ruamel_yaml 0.15.80 py39h9eb174b_1007 conda-forge s3transfer 0.6.0 pypi_0 pypi scikit-image 0.20.0 pypi_0 pypi scikit-learn 1.3.0 py39h46d7db6_0 scipy 1.9.1 py39h737da60_0 conda-forge seaborn 0.12.0 py39hca03da5_0 semver 2.13.0 pypi_0 pypi send2trash 1.8.0 pyhd8ed1ab_0 conda-forge setuptools 65.5.0 pyhd8ed1ab_0 conda-forge simplejson 3.18.0 pypi_0 pypi six 1.16.0 pyh6c4a22f_0 conda-forge smmap 5.0.0 pypi_0 pypi sniffio 1.3.0 pyhd8ed1ab_0 conda-forge snowballstemmer 2.2.0 pypi_0 pypi soupsieve 2.3.2.post1 pyhd8ed1ab_0 conda-forge sphinx 5.3.0 pypi_0 pypi sphinx-basic-ng 1.0.0b1 pypi_0 pypi sphinxcontrib-applehelp 1.0.2 pypi_0 pypi sphinxcontrib-devhelp 1.0.2 pypi_0 pypi sphinxcontrib-htmlhelp 2.0.0 pypi_0 pypi sphinxcontrib-jsmath 1.0.1 pypi_0 pypi sphinxcontrib-qthelp 1.0.3 pypi_0 pypi sphinxcontrib-serializinghtml 1.1.5 pypi_0 pypi sqlalchemy 1.4.42 pypi_0 pypi sqlite 3.39.4 h2229b38_0 conda-forge stack_data 0.5.1 pyhd8ed1ab_0 conda-forge streamlit 1.13.0 pypi_0 pypi svgelements 1.9.1 pypi_0 pypi swagger-spec-validator 3.0.3 pypi_0 pypi tables 3.7.0 pypi_0 pypi tbb 2021.5.0 h525c30c_0 terminado 0.16.0 pyhd1c38e8_0 conda-forge threadpoolctl 3.1.0 pyh8a188c0_0 conda-forge tifffile 2023.3.21 pypi_0 pypi tinycss2 1.1.1 pyhd8ed1ab_0 conda-forge tk 0.1.0 pypi_0 pypi tokenizers 0.13.1 pypi_0 pypi toml 0.10.2 pypi_0 pypi tomli 2.0.1 pyhd8ed1ab_0 conda-forge toolz 0.12.0 pyhd8ed1ab_0 conda-forge torch 1.12.1 pypi_0 pypi torchaudio 0.14.0.dev20221025 pypi_0 pypi torchvision 0.15.0.dev20221026 pypi_0 pypi tornado 6.2 py39h9eb174b_0 conda-forge tqdm 4.64.1 pyhd8ed1ab_0 conda-forge traitlets 5.4.0 pyhd8ed1ab_0 conda-forge transformers 4.23.1 pypi_0 pypi typing_extensions 4.4.0 pyha770c72_0 conda-forge tzdata 2022.5 pypi_0 pypi tzlocal 4.2 pypi_0 pypi uncertainties 3.1.7 pypi_0 pypi unicodedata2 14.0.0 py39hb18efdd_1 conda-forge uri-template 1.2.0 pypi_0 pypi urllib3 1.26.11 pyhd8ed1ab_0 conda-forge validators 0.20.0 pypi_0 pypi vulture 2.7 pypi_0 pypi wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge webcolors 1.12 pypi_0 pypi webencodings 0.5.1 py_1 conda-forge websocket-client 1.4.1 pyhd8ed1ab_0 conda-forge wheel 0.37.1 pyhd8ed1ab_0 conda-forge widgetsnbextension 3.5.2 py39hca03da5_0 xarray 2022.10.0 pyhd8ed1ab_0 conda-forge xorg-libxau 1.0.9 h27ca646_0 conda-forge xorg-libxdmcp 1.1.3 h27ca646_0 conda-forge xxhash 3.2.0 pypi_0 pypi xz 5.2.6 h57fd34a_0 conda-forge yaml 0.2.5 h3422bc3_2 conda-forge yaml-cpp 0.7.0 hb7217d7_2 conda-forge zeromq 4.3.4 hbdafb3b_1 conda-forge zipp 3.9.0 pyhd8ed1ab_0 conda-forge zstd 1.5.2 h8128057_4 conda-forge ```

I'm using the dev branch of alphaPeptDeep. I placed a notebook and library at pool-mann-projects\0_Georg\for_people\Feng.

[jalew188]

@GeorgWa Thanks. I guess this is because we introduce some new features in alphabase==1.1.0, and alphapeptdeep==1.1.0 supports the new features. I will test it today