Merge dev into main to update the documentation and add doc-generating shell scripts
#40
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Pull Request Test Coverage Report for Build 4605384128
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MaciejSkrabski
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Apr 11, 2023
* feat: enable auto reply on PRs created by new contributors; * feat: simplify requirements to speed up the installation process of PyPOTS; * feat: remove torch_geometric from the setup file as well to speed up installation; * doc: update README to add the usage example; * feat: print all outputs during test with pytest; * feat: add MANIFEST.in to remove the test dir from the released package; * fix: the bug of separating the code-coverage report; * fix: capture the error caused by singular matrix existence in VaDER; * doc: update the documentation; * doc: add the doc of all implemented modules; * fix: add the dependencies of PyPOTS into the doc building requirement file; * doc: update README; * feat: add the lazy-loading strategy for BaseDataset; * doc: update README; * feat: add limitations on lib dependencies; * feat: add class Logger to help present logs better; * feat: replace print with logger; * feat: add the func create_dir_if_not_exist() in pypots.utils.files; * fix: TypeError when using logger with mistake; * refactor: update the logger; * feat: add the test cases for logging; * feat: add the attribute __all__ into __init__ files; * doc: update README; * feat: add the file lazy-loading strategy for classes derived from BaseDataset; * doc: fix the reference ; * fix: update the dependencies; * doc: update README to add pypots installation with conda; * feat: separate the input data assembling functions of training, validating, and testing stages; * doc: update the reference info; * fix: imputation models applying MIT do not need use DatasetForMIT on val_set; * fix: only import h5py when needed; * feat: move check_input() to BaseDataset; * fix: correct mistaken operator from & to ^; * fix: turn imputation to numpy.ndarray in the validation stage; * feat: update the data given and input logic to support loading dataset from files; * fix: bugs in Dataset classes' functions with lazy-loading strategy; * fix: update the dependencies; * feat: add testing cases for lazy-loading datasets; * doc: update README; * feat: v0.0.10 is ready; * fix: running testing cases for forecasting models and lazy-loading datasets; * fix: running testing cases for logging; * fix: try to fix the BlockingIOError, see below message for details; BlockingIOError: [Errno 35] Unable to create file (unable to lock file, errno = 35, error message = 'Resource temporarily unavailable') This may be caused by the program creates h5 files for multiple times; * refactor: test scripts; * fix: use annotation @pytest.mark.xdist_group to help pytest-dist execute tasks sequentially; Some test tasks need to be executed sequentially, but we're using pytest-dist to accelerate the testing precess. To solve this problem, refer to pytest-dev/pytest-xdist#385 (comment). And please note that it need pytest-dist >= v2.5.0. * fix: fix some warnings while running VaDER; * fix: move dataset saving into test steps; * fix: the error file name of test_data.py; * doc: update the documentation; * doc: update the documentation; * Merge `dev` into `main` to update the documentation and add doc-generating shell scripts (WenjieDu#40) * doc: update the documentation; * doc: update the documentation; * refactor: preprocessing functions of specific dataset now move to module load_preprocessing; * fix: solve the problem of circular import; moved the functions of parsing delta to util.py. * refactor: don't save data into h5 files if the datasets already exit; * feat: add issue templates of bug report, feature request, and model addition; * Add issue templates (WenjieDu#41) * doc: update the documentation; * doc: update the documentation; * refactor: preprocessing functions of specific dataset now move to module load_preprocessing; * fix: solve the problem of circular import; moved the functions of parsing delta to util.py. * refactor: don't save data into h5 files if the datasets already exit; * feat: add issue templates of bug report, feature request, and model addition; * feat: turn the given device (str or torch.device) into torch.device; * feat: enable save training logs into `tb_file_saving_path` in BaseModel, need to be inherited in model implementations; tb_file_saving_pathi is the path to save the tensorboard file, which contains the loss values recorded during training. * feat: enable set num_workers of DataLoader and typing annotation; * feat: add typing annotations in the functions in `data` and `utils`; * feat: add python version 3.11 of all three platforms in the testing workflow; * fix: numpy.float is deprecated; * Decrease testing python version 3.11 to 3.10, and remove fixed dependency versions (WenjieDu#43) * fix: remove fixed dependency versions; * fix: lower python version from 3.11 to 3.10; * fix: lower python version from 3.11 to 3.10; * feat: add pytorch-scatter; * fix: fine with python 3.10, try to upgrade to 3.11 again; * fix: remove pyg dependencies to see if conda parsing error with python3.11 is caused by pyg; * fix: decrease python version back to 3.10; * feat: add daily testing workflow; * feat: make imputation models val_X_intact and val_indicating_mask should be included in val_set; * fix: invalid attribute; * fix: invalid `cron` attribute, 7 is not standard, should use 0 to represent Sunday; * doc: update README, split the table of the available algos according to the task; * refactor: move gene_incomplete_random_walk_dataset and gene_physionet2012 to data.generating, delete tests/unified_data_for_test; * fix: correct the mistaken path to environment_for_pip_test.txt; * fix: fix error the caused by renaming file `test_logging` to `test_utils`, and rename the workflow name from `Tests` to `CI`; * feat: remove `pull_request` trigger to avoid duplicate CI running; --------- Co-authored-by: Wenjie Du <wenjay.du@gmail.com>
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