sequenzo 0.1.19__cp39-cp39-macosx_10_9_universal2.whl → 0.1.20__cp39-cp39-macosx_10_9_universal2.whl

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Files changed (23) hide show
  1. sequenzo/big_data/clara/utils/get_weighted_diss.c +157 -157
  2. sequenzo/big_data/clara/utils/get_weighted_diss.cpython-39-darwin.so +0 -0
  3. sequenzo/clustering/hierarchical_clustering.py +1 -1
  4. sequenzo/dissimilarity_measures/get_distance_matrix.py +1 -1
  5. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  6. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +157 -157
  7. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cpython-39-darwin.so +0 -0
  8. sequenzo/dissimilarity_measures/utils/seqconc.c +157 -157
  9. sequenzo/dissimilarity_measures/utils/seqconc.cpython-39-darwin.so +0 -0
  10. sequenzo/dissimilarity_measures/utils/seqdss.c +157 -157
  11. sequenzo/dissimilarity_measures/utils/seqdss.cpython-39-darwin.so +0 -0
  12. sequenzo/dissimilarity_measures/utils/seqdur.c +157 -157
  13. sequenzo/dissimilarity_measures/utils/seqdur.cpython-39-darwin.so +0 -0
  14. sequenzo/dissimilarity_measures/utils/seqlength.c +157 -157
  15. sequenzo/dissimilarity_measures/utils/seqlength.cpython-39-darwin.so +0 -0
  16. sequenzo/multidomain/dat.py +11 -3
  17. sequenzo/multidomain/idcd.py +0 -2
  18. sequenzo/multidomain/linked_polyad.py +0 -1
  19. {sequenzo-0.1.19.dist-info → sequenzo-0.1.20.dist-info}/METADATA +29 -1
  20. {sequenzo-0.1.19.dist-info → sequenzo-0.1.20.dist-info}/RECORD +23 -23
  21. {sequenzo-0.1.19.dist-info → sequenzo-0.1.20.dist-info}/WHEEL +0 -0
  22. {sequenzo-0.1.19.dist-info → sequenzo-0.1.20.dist-info}/licenses/LICENSE +0 -0
  23. {sequenzo-0.1.19.dist-info → sequenzo-0.1.20.dist-info}/top_level.txt +0 -0
sequenzo/multidomain/dat.py CHANGED
@@ -1,3 +1,11 @@
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+ '''
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+ Author: Yuqi Liang dawson1900@live.com
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+ Date: 2025-09-25 08:46:49
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+ LastEditors: Yuqi Liang dawson1900@live.com
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+ LastEditTime: 2025-10-07 20:38:10
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+ FilePath: /Sequenzo-main/sequenzo/multidomain/dat.py
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+ Description: 这是默认设置,请设置`customMade`, 打开koroFileHeader查看配置 进行设置: https://github.com/OBKoro1/koro1FileHeader/wiki/%E9%85%8D%E7%BD%AE
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+ '''
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  """
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  @Author : Yuqi Liang 梁彧祺
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  @File : dat.py
@@ -60,11 +68,11 @@ if __name__ == '__main__':
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  time_cols = [col for col in children_df.columns if col.startswith("age_")]
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- seq_left = SequenceData(data=left_df, time_type="age", time=time_cols, states=[0, 1],
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+ seq_left = SequenceData(data=left_df, time=time_cols, states=[0, 1],
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  labels=["At home", "Left home"])
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- seq_child = SequenceData(data=children_df, time_type="age", time=time_cols, states=[0, 1],
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+ seq_child = SequenceData(data=children_df, time=time_cols, states=[0, 1],
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  labels=["No child", "Child"])
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- seq_marr = SequenceData(data=married_df, time_type="age", time=time_cols, states=[0, 1],
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+ seq_marr = SequenceData(data=married_df, time=time_cols, states=[0, 1],
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  labels=["Not married", "Married"])
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  domains_seq_list = [seq_left, seq_child, seq_marr]
sequenzo/multidomain/idcd.py CHANGED
@@ -75,7 +75,6 @@ def _generate_combined_sequence_from_csv(csv_paths: List[str],
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  def create_idcd_sequence_from_csvs(
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  csv_paths: List[str],
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  time_cols: List[str],
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- time_type: str = "year",
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  id_col: str = "id",
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  domain_state_labels: List[Dict] = None
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  ) -> SequenceData:
@@ -86,7 +85,6 @@ def create_idcd_sequence_from_csvs(
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  Parameters:
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  - csv_paths: List of paths to domain CSVs
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  - time_cols: List of time column names to use
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- - time_type: 'year' or 'age'
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  - id_col: ID column name
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  - domain_state_labels: List of dictionaries mapping raw state values to labels for each domain
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sequenzo/multidomain/linked_polyad.py CHANGED
@@ -190,7 +190,6 @@ def linked_polyadic_sequence_analysis(seqlist: List[SequenceData],
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  seq_shuffled = SequenceData(
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  data=shuffled,
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  time=merged_seqdata.time,
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- time_type=merged_seqdata.time_type,
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  states=merged_seqdata.states,
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  labels=merged_seqdata.labels,
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  id_col="__id__"
{sequenzo-0.1.19.dist-info → sequenzo-0.1.20.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: sequenzo
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- Version: 0.1.19
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+ Version: 0.1.20
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  Summary: A fast, scalable and intuitive Python package for social sequence analysis.
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  Author-email: Yuqi Liang <yuqi.liang.1900@gmail.com>, Xinyi Li <1836724126@qq.com>, Jan Heinrich Ernst Meyerhoff-Liang <jan.meyerhoff1@gmail.com>
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  License: BSD 3-Clause License
@@ -181,6 +181,34 @@ If you have some issues with the installation, it might because you have both Py
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  pip3 install sequenzo
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  ```
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+ ### ⚠️ Having Installation or Import Issues?
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+
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+ **Error:** `ImportError: numpy.core.multiarray failed to import`
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+
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+ **Most likely cause:** NumPy version mismatch (you have NumPy 1.x, but need 2.x)
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+
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+ **Quick Fix** (copy-paste these commands):
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+ ```bash
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+ # Check your NumPy version first
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+ python -c "import numpy; print(f'NumPy: {numpy.__version__}')"
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+
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+ # If you see 1.x.x, upgrade to 2.x:
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+ pip install --upgrade "numpy>=2.0.0"
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+ pip uninstall sequenzo -y
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+ pip install --no-cache-dir sequenzo
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+ ```
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+
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+ 📖 **Still having issues?**
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+ 1. Run our diagnostic tool to identify the problem:
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+ ```bash
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+ curl -O https://raw.githubusercontent.com/Liang-Team/Sequenzo/main/diagnose.py
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+ python diagnose.py
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+ ```
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+ 2. See our detailed guides:
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+ - **[QUICK_FIX.md](QUICK_FIX.md)** - Simple step-by-step solutions
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+ - **[TROUBLESHOOTING.md](TROUBLESHOOTING.md)** - Comprehensive troubleshooting
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+ - **[docs/WHY_IMPORT_FAILS.md](docs/WHY_IMPORT_FAILS.md)** - Technical explanation
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+
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  ### Optional R Integration
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  Sequenzo now checks the system environment variables before running ward.D hierarchical clustering.
{sequenzo-0.1.19.dist-info → sequenzo-0.1.20.dist-info}/RECORD RENAMED
@@ -8,14 +8,14 @@ sequenzo/big_data/clara/visualization.py,sha256=EpSmtAxRHVqcXlcXvSGiUuBjEETR7zK_
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  sequenzo/big_data/clara/utils/__init__.py,sha256=2_o1tz8HFZVKFy8w8oJWdWlVKtwGjGY3z4PQylHKjt0,726
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  sequenzo/big_data/clara/utils/aggregatecases.py,sha256=ul97pbnRlwxbFbX_0M4j-Bkyxkp7zMAKatSo4eanO24,2899
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  sequenzo/big_data/clara/utils/davies_bouldin.py,sha256=4Y6VFjqopG3CaftQ8tDxQPjxxupJ6Hgv-yTXwCvgN7w,3037
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- sequenzo/big_data/clara/utils/get_weighted_diss.c,sha256=iNxIWGvWU9OIrN8ivnmMdlN9Jz1FyQZn76H1lakIVoY,466603
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- sequenzo/big_data/clara/utils/get_weighted_diss.cpython-39-darwin.so,sha256=6qiAXq_DF41S5YL4i4ktWpFrRiN1axKMuSYdCfgBMCU,104280
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+ sequenzo/big_data/clara/utils/get_weighted_diss.c,sha256=5aT6x2c37XtBMisiKniHMDv7FRUFveeb2sAJ0IVXb6o,466603
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+ sequenzo/big_data/clara/utils/get_weighted_diss.cpython-39-darwin.so,sha256=aNSKyAm-5FOXBum7RTaPkpXwAZnl__2GER0HatAlyhY,104280
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  sequenzo/big_data/clara/utils/get_weighted_diss.pyx,sha256=UYR-u8MDQEuWID3inKhSpBsuxu7qTFmEwLrjNPBMmUw,430
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  sequenzo/big_data/clara/utils/wfcmdd.py,sha256=-1H6CbTteTW-CeuQ_ehVDhnKH3ozcCkUobxoCSRIpYg,7074
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  sequenzo/clustering/KMedoids.py,sha256=asktGP0KKgP4TsOH4bSYEWfE8yY5b9BfKa1d54KzaXI,7147
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  sequenzo/clustering/__init__.py,sha256=duEY0Hq0-7Kc_lv0uFDK3D8IEXby-7Z0Rjff0EgO0KM,875
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  sequenzo/clustering/clustering_c_code.cpython-39-darwin.so,sha256=Fj5RvS-gmqEooFTeW6wUe4SEhMPyFmr0S0-Pajl1hGk,362760
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- sequenzo/clustering/hierarchical_clustering.py,sha256=b0ZkWoj9PGPqzVoRUaOIIM6AC-Udi2_Fcgi7AzAWE4c,61590
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+ sequenzo/clustering/hierarchical_clustering.py,sha256=3O2ipqqPMQ0O74H2YpLc2mmldWNFtiQI7Bs16hyXoDk,61572
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  sequenzo/clustering/src/KMedoid.cpp,sha256=Bb4LaRes004T9vyCmUknRS0NUaNr4ZoEpWvtkYGq-jw,9299
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  sequenzo/clustering/src/PAM.cpp,sha256=UFXdTy1wMWheYa-fUoi8ASQPmn0Ew-AO7fqVQVxn_E8,8357
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  sequenzo/clustering/src/PAMonce.cpp,sha256=C9HqGBRenmF2tnQofALjjU1As02dTw2oqEnuvdhoJIk,7943
@@ -48,8 +48,8 @@ sequenzo/datasets/polyadic_seqc1.csv,sha256=ydZ-U8NTszR4lNBN4hhsH_dHfq0w5VZSMM7t
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  sequenzo/datasets/polyadic_seqp1.csv,sha256=sydXCR0JBKJlbMxJyGa46cic9XQstUpYFOtHaLmkp_0,7681
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  sequenzo/dissimilarity_measures/__init__.py,sha256=qkWAQ1sBpS2aayO-FSA8Zha7rQ_vjs0_KIHEB60bVg4,958
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  sequenzo/dissimilarity_measures/c_code.cpython-39-darwin.so,sha256=s6h-gzYX6kK55Hf5KXr-39QXd-QyEEvwxf_Z6YLJpoY,345992
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- sequenzo/dissimilarity_measures/get_distance_matrix.py,sha256=6C8x06IDZ3wZeEr-JN-Sce5rxMQLXXoyJNrlsQXn8Pk,29903
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- sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py,sha256=A2ohhpJw-dznmjfsjctVnO5BOzajRBm3Ffj-oPYEvJ4,9551
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+ sequenzo/dissimilarity_measures/get_distance_matrix.py,sha256=dNZtqg0aN3vAz5r1sTgjS3jwLAzcXGbG4MGWeBEvhag,29886
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+ sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py,sha256=Yed91VyNHkzeYxIduCTVF8hmJiAmltPH4R0lhvKQoKk,9533
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  sequenzo/dissimilarity_measures/src/DHDdistance.cpp,sha256=RbWbSaELxlJiw5ST_JaD-wPx_sD7PGV2VdK4qEhOcxE,4714
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  sequenzo/dissimilarity_measures/src/LCPdistance.cpp,sha256=VCqRm_mbI2IOm6KiO7SACHDOpZXBTkDdyr1Fo39zJVE,3231
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  sequenzo/dissimilarity_measures/src/OMdistance.cpp,sha256=0HxjF4VFXkCtrV2zV7Kb_URVMWrjgt_W-4ugf1O7cDo,8726
@@ -155,28 +155,28 @@ sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_vsx_register
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  sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_wasm_register.hpp,sha256=Am-0VbiA-S1zX2YXxKPgHc4dxWDDHS6_bL2ox5x7aMA,2437
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  sequenzo/dissimilarity_measures/utils/__init__.py,sha256=aZMQJGgJq4GsL1x-pQPLmL7KrJ78cHMH46GVmVE8pJ0,407
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  sequenzo/dissimilarity_measures/utils/get_LCP_length_for_2_seq.py,sha256=bJjbEQcjENSAdLv2IMRUWJC4avldwCfHrtSEnlDEACY,1470
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- sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c,sha256=CPqcIv1CUGX3Gncya0FzYOI6YbjO9WfYn2sdngv68jM,578883
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- sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cpython-39-darwin.so,sha256=CC0vxK8b5D9RM8KXnAJA0W4qdrRhlqwQUChkeHyZ2hc,145144
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+ sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c,sha256=zgwDsrmq5C1Cu8xfE6MhgMswjyVBKT7cuG6363gxAOg,578883
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+ sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cpython-39-darwin.so,sha256=wf9zaEPtuG8nGUn3s_N6HnWYl9grwCDvQTi_u6xRvUI,145144
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- sequenzo/dissimilarity_measures/utils/seqconc.c,sha256=Ph_H9_VA6nr-t_rEcQZotqHv73XD_GjqY_8CYCVM3EA,488207
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- sequenzo/dissimilarity_measures/utils/seqconc.cpython-39-darwin.so,sha256=PMVU4ZZpmuKYGu-7lerqwDmtKzV7nu2kq83WhvE1Ovk,123440
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+ sequenzo/dissimilarity_measures/utils/seqconc.c,sha256=We9O9bWeJy3Ofo86wOBef0Z3jqVeP6LdjSzXf2OiE4U,488207
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+ sequenzo/dissimilarity_measures/utils/seqconc.cpython-39-darwin.so,sha256=7IHpqPsh1boxBfYMJIzABDu9DCD3AxbGypXr_mHx9nk,123440
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- sequenzo/dissimilarity_measures/utils/seqdss.c,sha256=3V-oGn1OjIA3VBbJMUw8tIGIkBNKoyshP08YaItKeQ8,599803
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- sequenzo/dissimilarity_measures/utils/seqdss.cpython-39-darwin.so,sha256=IkuD0sL-d39xHPVZprVqn5ZF0PBn7jU_Da7ZgbKmTCA,153192
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+ sequenzo/dissimilarity_measures/utils/seqdss.c,sha256=y_YRfezFLgPTSypdlbJVgjZxyXJR850SqqKbst1jYqI,599803
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+ sequenzo/dissimilarity_measures/utils/seqdss.cpython-39-darwin.so,sha256=rgkmlvJ5e4Auer337GdqdOR5cWLSYxkXt4fwFanYXcc,153192
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- sequenzo/dissimilarity_measures/utils/seqdur.c,sha256=8Uiwb3c0xiwUbJ8tmrgLNt5g8ZyWOLkb6gQzNZ-wAR4,524109
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- sequenzo/dissimilarity_measures/utils/seqdur.cpython-39-darwin.so,sha256=xfmC7MY_Nkk06jihqVMi1FeoPPiH3NRDwlNccsB82r0,126136
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+ sequenzo/dissimilarity_measures/utils/seqdur.c,sha256=a789kTfPw0Ha-9NhPcXMccrcyWhJ2hslY-bgaQjNb-U,524109
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+ sequenzo/dissimilarity_measures/utils/seqdur.cpython-39-darwin.so,sha256=xPFIoh-MK10aLatsi5M1GYC4EvPTWcs5_rgTA1R_7lY,126136
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- sequenzo/dissimilarity_measures/utils/seqlength.c,sha256=Xsx_UVoSxa5BnxCSYls_VwfvBUwVDf0ZmnZrv2DujzY,476176
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- sequenzo/dissimilarity_measures/utils/seqlength.cpython-39-darwin.so,sha256=14vNpZUcsgQSg8UMQGQ3CfZ1lO4dMdSYm0YnDUV8I8k,121904
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+ sequenzo/dissimilarity_measures/utils/seqlength.c,sha256=-4MWhvXmDOrPe1fq1MgATCLPYyW74OjCEOzxxYQWOo8,476176
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+ sequenzo/dissimilarity_measures/utils/seqlength.cpython-39-darwin.so,sha256=cPFcPAOmdRbr-LpxZMxybo0ruVUb8I0IcNOtIgcp9Q8,121904
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  sequenzo/multidomain/association_between_domains.py,sha256=V4I_ILAAwf3cfz2i0HdLF8otAqPtF2LfjcCKo1IkfHA,10855
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  sequenzo/multidomain/combt.py,sha256=aE1OsCE5huJI6VqInBpBjT6WjAIZlgFHFtUwSZt9XLU,22079
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- sequenzo/multidomain/dat.py,sha256=OwSSi9AiuWBF4LP_HOi79MRngvRCqe4o-eahWrrKTPw,3155
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- sequenzo/multidomain/idcd.py,sha256=EGY__QnS6WEE07zaqWeKaFbFiZPzxALmYV_5shJ6uTA,4588
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- sequenzo/multidomain/linked_polyad.py,sha256=2G_WfKt_o_pdqg68bmQis738h76GiBVjHusnUNAys64,13666
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+ sequenzo/multidomain/dat.py,sha256=ljhc3kbAl8t8tpNh06eu4lAbR36PFUQCkxXBBtx81lo,3477
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+ sequenzo/multidomain/idcd.py,sha256=kKSGJfL_c0pBPbbDdR1BJ08GIIErGFj5ft7ieHyhnT8,4526
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+ sequenzo/multidomain/linked_polyad.py,sha256=l2ysDmhKeuHXq2xMVGb-WOq7AStnLd99NZ363gmh3lA,13614
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  sequenzo/prefix_tree/__init__.py,sha256=YxMzr5UwM22DmpMDMAmKYI-vjhikDI8Gft_cJ9h1gYo,1126
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  sequenzo/prefix_tree/system_level_indicators.py,sha256=tGnzRRqwzJbGv-vjOMAzdh6arN6QJkdsybe0Yif57ug,17507
@@ -208,8 +208,8 @@ sequenzo/visualization/utils/utils.py,sha256=9Z1L3PVL-Z41fvCW4tLJ5DaUVHO6C6PAJYl
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  sequenzo/with_event_history_analysis/__init__.py,sha256=B2EZhtJ7NEzO8piDwfSbh0l87fQ0ZuesPO5GNJEXKPo,730
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  sequenzo/with_event_history_analysis/sequence_analysis_multi_state_model.py,sha256=wtsKnq-82bJhRH78cy49Nzo3yGJKoFD4RckoZ7D-SS8,37301
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  sequenzo/with_event_history_analysis/sequence_history_analysis.py,sha256=vv5y2u9cpzhmNJX_fSYgLmFOncPvB7DVhWujljII1vA,10902
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- sequenzo-0.1.19.dist-info/licenses/LICENSE,sha256=URRMyLHVeGF2kyDLC1xbRKBBIjDHJyWqF4nWpzfBX10,1497
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- sequenzo-0.1.19.dist-info/METADATA,sha256=q5gIoiMbMlVxPRzkhFj6XB5zyuJ-DMU-AjyohJr0tis,14189
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- sequenzo-0.1.19.dist-info/WHEEL,sha256=Q9x5RaJ3mFaLYQ0AssqccH-ZQbedr2DD19gIJkZDXGM,112
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- sequenzo-0.1.19.dist-info/top_level.txt,sha256=yM8eczbPzqB1bRHMYLptvjjQ3p5tYhY6VjgWHUIi9vw,9
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- sequenzo-0.1.19.dist-info/RECORD,,
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+ sequenzo-0.1.20.dist-info/licenses/LICENSE,sha256=URRMyLHVeGF2kyDLC1xbRKBBIjDHJyWqF4nWpzfBX10,1497
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+ sequenzo-0.1.20.dist-info/METADATA,sha256=lQcoAZFNwlZhOI3M8nd9z0TSGe3z7Ogcs70Baj78tns,15147
213
+ sequenzo-0.1.20.dist-info/WHEEL,sha256=Q9x5RaJ3mFaLYQ0AssqccH-ZQbedr2DD19gIJkZDXGM,112
214
+ sequenzo-0.1.20.dist-info/top_level.txt,sha256=yM8eczbPzqB1bRHMYLptvjjQ3p5tYhY6VjgWHUIi9vw,9
215
+ sequenzo-0.1.20.dist-info/RECORD,,