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Update README Add a to-do to improve plotting function Add py3.13 to env list Remove irrelevant to-do Refactor fit_model and import data (on-going) Raise error if assortative==False in ACD Remove fit_model Change the position where the class get instantiated; add test Refactoring data import for DynCRep (not working) Finish refactoring data import (now it does work) Remove unnecessary elif's Fix tests in notebooks and cv (not finished) Refactor read covariates Implement Jean-Claude's feedback Black repo Apply 1 suggestion(s) to 1 file(s) Co-authored-by: Jean-Claude Passy <[email protected]> Fix typo in README Add optional kwargs to fit functions Fix tests Remove `load_algorithm_data` from `main` Fix tests Refactor fit methods to data gdata Fix tests Refactor model selection (MTCOV still not working) Fix MTCOV case Fix tests for notebooks and data loaders Remove dead code Fix one more notebook Fix some validation tests Fix one more notebook (hopefully last one) Fix DynCRep validation test Format files Create tutorial about JCRep and assortative Move cv of models into package; refactored the `model_selection` submod Add random test, add (and skip) test from file Refactor `ACD` to make it fit the desired logic (on-going) Fix inputs (but add bug) Fix bug (still a lot to refactor) Out-comment termcolor pkg Add `preprocess_data_for_fit` function Remove redundant code from the init; update tests Remove randomize and initialize functions from `acd` (using super() now) Work on init from file (not finished) Finish test on init from file Remove dependencies in super() Add ACD to main Create `update_real` and `log_real` for ACD Remove unnecessary `self`s Create test for main `ACD` Move `dyncrep` syn to `synthetic` Move `gen_syn` content to `synthetic` Black all Add logger Improve logs Add more flags to CLI, improve logs for out_inference `False` Update saving of config file Fix tests Fix some pylint warnings Add tests for `syn_acd` Add more tests for `syn_acd` Refactor tests Solve some mypy issues Solve more mypy issues Add type hints to `acd` Add check for keys in theta in acd Remove dead code Fix assert inside fixtures Add tutorial outputs to gitignore Update gitignore Fix more mypy issues Fix too many values to unpack problem Create `model_selection` module Make it depend on the parameters refactor run_cv Add 'MTCOV' (broken due to some wrong copy) Fix `MTCOV` Add comments Update docs Add `ACD` to model selection Ignore cv outputs Refactor cv scripts, create template Changes approved by Hadiseh Create single run, and run full cv methods Works for CRep and JointCRep Comment out so Bamboo does not break Create fill cv script that iterates over parameter grid Fix wrong instantiation time, it now happens after param grid creation The full cv works for 4 models Fix code based on Hadiseh's comments Add missing type hints Add missing type hints Create parameter search submod Create labeling submod Add metrics submod Create masking submod Add dyncrep cv class Correct missing imports Create likelihood submod Fix missing imports Create validation test for cv module Add more tests for the cv module Check to-do list Fix too large T's Add cv tests for dyncrep Create validation tests for cv Create tests for CRep's cv Create validation test for CRep's cv using current implementation Create validation tests for JointCRep Create validation test for ACD's cv Create validation test for MTCOV's cv Create validation test for DynCRep Refactor tests for cv Add numerical parameters as an input to cv Remove `demo.py` Black scripts Remove extra_params dependency for CRep Remove them from JointCRep Remove them from DynCRep Remove them from MTCOV Remove them from ACD Fix undefined attributes Remove `ModelFitParams` Fix validation test for ACD Update tutorials about DnyCRep and JointCRep Update CRep tutorial Fix tests for CRep Organize numeric params alphabetically Update docstrings Add checks for changes in config file Fix MTCOV tutorial Update docstrings; add DynCRep tutorial Update docstrings Fix tests Create cross-validation and ACD tutorial Move cv of models into package; refactored the `model_selection` submod Add random test, add (and skip) test from file Refactor `ACD` to make it fit the desired logic (on-going) Fix inputs (but add bug) Fix bug (still a lot to refactor) Out-comment termcolor pkg Add `preprocess_data_for_fit` function Remove redundant code from the init; update tests Remove randomize and initialize functions from `acd` (using super() now) Work on init from file (not finished) Finish test on init from file Remove dependencies in super() Add ACD to main Create `update_real` and `log_real` for ACD Remove unnecessary `self`s Create test for main `ACD` Move `dyncrep` syn to `synthetic` Move `gen_syn` content to `synthetic` Black all Add logger Improve logs Add more flags to CLI, improve logs for out_inference `False` Update saving of config file Fix tests Fix some pylint warnings Add tests for `syn_acd` Add more tests for `syn_acd` Refactor tests Solve some mypy issues Solve more mypy issues Add type hints to `acd` Add check for keys in theta in acd Remove dead code Fix assert inside fixtures Add tutorial outputs to gitignore Update gitignore Fix more mypy issues Fix too many values to unpack problem Create `model_selection` module Make it depend on the parameters refactor run_cv Add 'MTCOV' (broken due to some wrong copy) Fix `MTCOV` Add comments Update docs Add `ACD` to model selection Ignore cv outputs Refactor cv scripts, create template Changes approved by Hadiseh Create single run, and run full cv methods Works for CRep and JointCRep Comment out so Bamboo does not break Create fill cv script that iterates over parameter grid Fix wrong instantiation time, it now happens after param grid creation The full cv works for 4 models Fix code based on Hadiseh's comments Add missing type hints Add missing type hints Create parameter search submod Create labeling submod Add metrics submod Create masking submod Add dyncrep cv class Correct missing imports Create likelihood submod Fix missing imports Create validation test for cv module Add more tests for the cv module Check to-do list Fix too large T's Add cv tests for dyncrep Create validation tests for cv Create tests for CRep's cv Create validation test for CRep's cv using current implementation Create validation tests for JointCRep Create validation test for ACD's cv Create validation test for MTCOV's cv Create validation test for DynCRep Refactor tests for cv Add numerical parameters as an input to cv Remove `demo.py` Black scripts Remove extra_params dependency for CRep Remove them from JointCRep Remove them from DynCRep Remove them from MTCOV Remove them from ACD Fix undefined attributes Remove `ModelFitParams` Fix validation test for ACD Update tutorials about DnyCRep and JointCRep Update CRep tutorial Fix tests for CRep Organize numeric params alphabetically Update docstrings Add checks for changes in config file Fix MTCOV tutorial Update docstrings; add DynCRep tutorial Update docstrings Add draft of tutorial Remove duplicated code in cv functions; update draft Generate new GT data Change print statements Update tutorial Update docstrings Update docstrings Change the way I get the logger Update tutorial; generate new data FIx tests Update tutorial Fix tests again Update tutorial; run black on pkg and notebooks Update tutorial Replace sktensor by tensorly (on-going) More replacing Replace all the sparse cases Fix tests Remove skt and tensorly; runs with sparse Fix tests Remove comments; remove sparse Add sparse again Skip test for sparse data in DynCrep Add comments Add tests for JointCRep when force_dense=True Add tests for ACD when force_dense=False Fix tests Add draft of tutorial Add updated tutorial Split `syn_rep` Create base for syn Fix tests Refactor plotting function into base Fix bug in sbm Create syn_mtcov Update tutorial; keeping JCRep and assortative Fix structure of tutorial; remove old unused parts Add tests for synthetic mtcov Add `conv` init Fix bug on tests; JCRep was not converging Black files Fix tests Work on tutorial; add suggestions about improv. suggested by Martina Create plotting function for matrices; generate initial w Improve tutorial; remove quantitative assessment Improve tutorial, black notebook, remove logs Add test for new notebook Update test for syn Update parameters Fix typo in tutorial Update tutorial Remove dead code Rename package to probinet Fix left pgm instances Delete more instances of pgm Remove pgm calls Redefine entrypoint to run_probinet; fix relative paths Add more details about entrypoint to README Add message about sphinx installation Add more info about arguments of CLI Fix tests Rename submodules inside synthetic Ignore outputs dir at top level Add ipynb checkpoints to gitignore Remove outputs from model_selection Move content of metrics into evaluate Create vis module; rename output module, rename functions inside it Fix tests Fix tests; add comments to compute M Remove evaluate.py Remove unused `properties` Rename functions inside preproc; delete repeated transposing funct Remove unnecessary notebooks Fix tests; refactor model; create utils Correct docstrings; fix tests Add more details about installation to the README Fix docstrings Add section about tutorials Update index Add path to tutorials Rename function to build incidence Fix tests Fix more tests Black files Fix more tests; remove deprecated timeout call for nbs Refactor expression into eta validation Refactor expression into validate undirected Create custom type for graph data Remove more to-do's Change variable name inside config file Fix tests in notebook Rename adj file Rename to dynamic and highschool network Rename more files Fix missing imports Fix tests Fix typos in notebook Add fix_w to check_fit_params in CRep Remove error raised if no best loglik Add logs about convergence at INFO Refactor to avoid if-else for different data types Remove some to-do's about data pkg Add more tests; fix assortative False for ACD Remove unneeded message variable Fix tests Skip test to check parallel jobs in Bamboo Fix dyncrep tests after refactoring Fix mypy/pylint errors Fix tests Add tests for link prediction Remove unused variable Remove duplicate code from synthetic Fix docstrings; fix single dispatch Correct docstrings Black files Skip reciprocity if network is undirected Fix tests for synthetic MTCOV Change definition of docstrings Black files Remove dead code Add references page; add 5 references Add missing ref, add cites to notebook Add them to all notebooks Remove some citations to avoid duplicates Fix overflow of references Fix for real Stop trying to make it split the api and tutorials on the left Fix missing reference for CRep notebook Fix wrongly imported logging Add some new types Add more types Add more types Add GraphDataType where missing Add missing imports Fix some mypy errors Refactor compute_community_detection_metric Fix more mypy errors Add missing docstrings Fix conflicts in rebasing Black files Rename custom type to use Sequence Add out folder as constant where missing Fix notebook Fix tests Fix tests Remove unnecessary Optional Remove unused imports Format files Remove floats as custom types
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