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Merge dev into main to update the documentation and add doc-generating shell scripts #40

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merged 2 commits into from
Apr 4, 2023

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@WenjieDu WenjieDu commented Apr 4, 2023

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@WenjieDu WenjieDu merged commit 3ac3185 into main Apr 4, 2023
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coveralls commented Apr 4, 2023

Pull Request Test Coverage Report for Build 4605384128

  • 0 of 0 changed or added relevant lines in 0 files are covered.
  • 7 unchanged lines in 4 files lost coverage.
  • Overall coverage remained the same at 84.787%

Files with Coverage Reduction New Missed Lines %
pypots/imputation/base.py 1 78.16%
pypots/classification/base.py 2 77.63%
pypots/clustering/crli.py 2 88.15%
pypots/tests/test_clustering.py 2 94.0%
Totals Coverage Status
Change from base Build 4577653180: 0.0%
Covered Lines: 2625
Relevant Lines: 3096

💛 - Coveralls

MaciejSkrabski added a commit to MaciejSkrabski/PyPOTS that referenced this pull request 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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