Add unit-test cases for pypots-cli (#72)

* refactor: move `pypots-cli` from pypots/utils/commands to pypots/cli; * feat: add test cases for pypots-cli; * feat: add test_cli.py into the execution of workflow CI; * fix: raise RuntimeError when enable strict mode in check_if_under_root_dir(); * feat: update environment_for_conda_test.yml; * fix: only run installation command again if necessary; * fix: implement time out with threading; * fix: directly set SPHINX_APIDOC_OPTIONS with os.environ to avoid bugs on Windows platform; * fix: append "+cpu" if torch is not cuda version; * fix: log and ignore error raised when testing on Windows;
WenjieDu · Apr 23, 2023 · 44335be · 44335be
1 parent 5325d25
commit 44335be
Show file tree

Hide file tree

Showing 12 changed files with 288 additions and 56 deletions.
diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
@@ -41,14 +41,15 @@ jobs:
 
             - name: Test with pytest
               run: |
-                  # run tests separately here due to Segmentation Fault in test_clustering when run all in 
+                  # run tests separately here due to Segmentation Fault in test_clustering when run all in
                   # one command with `pytest` on MacOS. Bugs not caught, so this is a trade-off to avoid SF.
-                  python -m pytest -rA pypots/tests/test_classification.py -n auto --cov=pypots --dist=loadgroup 
+                  python -m pytest -rA pypots/tests/test_classification.py -n auto --cov=pypots --dist=loadgroup
                   python -m pytest -rA pypots/tests/test_imputation.py -n auto --cov=pypots --cov-append --dist=loadgroup
                   python -m pytest -rA pypots/tests/test_clustering.py -n auto --cov=pypots --cov-append --dist=loadgroup
                   python -m pytest -rA pypots/tests/test_forecasting.py -n auto --cov=pypots --cov-append --dist=loadgroup
                   python -m pytest -rA pypots/tests/test_data.py -n auto --cov=pypots --cov-append --dist=loadgroup
                   python -m pytest -rA pypots/tests/test_utils.py -n auto --cov=pypots --cov-append --dist=loadgroup
+                  python -m pytest -rA pypots/tests/test_cli.py -n auto --cov=pypots --cov-append --dist=loadgroup
 
             - name: Generate the LCOV report
               run: |
@@ -58,4 +59,4 @@ jobs:
               uses: coverallsapp/github-action@master
               with:
                   github-token: ${{ secrets.GITHUB_TOKEN }}
-                  path-to-lcov: 'coverage.lcov'
+                  path-to-lcov: 'coverage.lcov'
diff --git a/README.md b/README.md
@@ -4,16 +4,16 @@
 **<p align="center">A Python Toolbox for Data Mining on Partially-Observed Time Series</p>**
 
 <p align="center">
-    <img alt="Python version" src="https://img.shields.io/badge/Python->v3.6-yellow?color=88ada6">
-    <img alt="powered by Pytorch" src="https://img.shields.io/static/v1?label=PyTorch&message=%E2%9D%A4%EF%B8%8F&color=bbcdc5&logo=pytorch">
+    <img alt="Python version" src="https://img.shields.io/badge/Python-v3.7--3.10-88ada6?logo=python&logoColor=white">
+    <img alt="powered by Pytorch" src="https://img.shields.io/badge/PyTorch-%E2%9D%A4%EF%B8%8F-bbcdc5?logo=pytorch&logoColor=white">
     <a href="https://pypi.org/project/">
         <img alt="the latest release version" src="https://img.shields.io/github/v/release/wenjiedu/pypots?color=e0eee8&include_prereleases&label=Release">
     </a>
     <a href="https://github.com/WenjieDu/PyPOTS/blob/main/LICENSE">
         <img alt="GPL3 license" src="https://img.shields.io/badge/License-GPL--v3-c0ebd7">
     </a>
     <a href="https://join.slack.com/t/pypots-dev/shared_invite/zt-1gq6ufwsi-p0OZdW~e9UW_IA4_f1OfxA"> 
-        <img alt="Slack Workspace" src="https://img.shields.io/badge/Slack-PyPOTS-grey?logo=slack&color=7bcfa6">
+        <img alt="Slack Workspace" src="https://img.shields.io/badge/Slack-PyPOTS-7bcfa6?logo=slack">
     </a>
     <a href="https://github.com/sponsors/WenjieDu">
         <img alt="GitHub Sponsors" src="https://img.shields.io/github/sponsors/wenjiedu?label=Sponsors&color=7fecad&logo=githubsponsors">
@@ -30,18 +30,19 @@
     <a href="https://coveralls.io/github/WenjieDu/PyPOTS"> 
         <img alt="Coveralls coverage" src="https://img.shields.io/coverallsCoverage/github/WenjieDu/PyPOTS?branch=main&logo=coveralls&color=00e09e&label=Coverage">
     </a>
-    <a href="https://anaconda.org/conda-forge/pypots">
-        <img alt="Conda downloads" src="https://img.shields.io/conda/dn/conda-forge/pypots?label=Conda%20Downloads&color=48c0a3">
-    </a>
-    <a href="https://pypi.org/project/pypots">
-        <img alt="PyPI downloads" src="https://static.pepy.tech/personalized-badge/pypots?period=total&units=international_system&left_color=grey&right_color=teal&left_text=PyPI%20Downloads">
-    </a>
     <a href="https://github.com/WenjieDu/PyPOTS/actions/workflows/testing.yml"> 
-        <img alt="GitHub Testing" src="https://github.com/WenjieDu/PyPOTS/actions/workflows/testing.yml/badge.svg">
+        <img alt="GitHub Testing" src="https://img.shields.io/github/actions/workflow/status/wenjiedu/pypots/testing.yml?logo=github&color=48c0a3&label=CI">
     </a>
     <a href="https://doi.org/10.5281/zenodo.6823221">
-        <img alt="Zenodo DOI" src="https://zenodo.org/badge/DOI/10.5281/zenodo.6823221.svg">
+        <img alt="Zenodo DOI" src="https://img.shields.io/badge/DOI-10.5281/zenodo.6823221-21a675">
+    </a>
+    <a href="https://anaconda.org/conda-forge/pypots">
+        <img alt="Conda downloads" src="https://img.shields.io/conda/dn/conda-forge/pypots?label=Conda%20Downloads&color=057748&logo=anaconda&logoColor=white">
+    </a>
+    <a href="https://pypi.org/project/pypots">
+        <img alt="PyPI downloads" src="https://static.pepy.tech/personalized-badge/pypots?period=total&units=international_system&left_color=grey&right_color=teal&left_text=PyPI%20Downloads&logo=github">
     </a>
+
 </p>
 
 ⦿ `Motivation`: Due to all kinds of reasons like failure of collection sensors, communication error, and unexpected malfunction, missing values are common to see in time series from the real-world environment. This makes partially-observed time series (POTS) a pervasive problem in open-world modeling and prevents advanced data analysis. Although this problem is important, the area of data mining on POTS still lacks a dedicated toolkit. PyPOTS is created to fill in this blank.
@@ -54,6 +55,7 @@ To make various open-source time-series datasets readily available to our users,
 Visit [TSDB](https://github.com/WenjieDu/TSDB) right now to know more about this handy tool 🛠! It now supports a total of 119 open-source datasets.
 <br clear="left">
 
+
 ## ❖ Installation
 PyPOTS now is available on <a href="https://anaconda.org/conda-forge/pypots"><img alt="on Anaconda" align="center" 
 src="https://img.shields.io/badge/Anaconda--lightgreen?style=social&logo=anaconda"></a>❗️ 
@@ -66,8 +68,17 @@ Install the latest release from PyPI:
 or install from the source code with the latest features not officially released in a version:
 > pip install https://github.com/WenjieDu/PyPOTS/archive/main.zip
 
-<details open>
-<summary><b>Below is an example applying SAITS in PyPOTS to impute missing values in the dataset PhysioNet2012:</b></summary>
+
+## ❖ Usage
+PyPOTS tutorials have been released. You can find them [here](https://github.com/WenjieDu/PyPOTS/tree/main/tutorials).
+If you have further questions, please refer to PyPOTS documentation [📑http://pypots.readthedocs.io](http://pypots.readthedocs.io).
+Besides, you can also 
+[raise an issue](https://github.com/WenjieDu/PyPOTS/issues) or
+[ask in our community](https://join.slack.com/t/pypots-dev/shared_invite/zt-1gq6ufwsi-p0OZdW~e9UW_IA4_f1OfxA).
+And please allow us to present you a usage example of imputing missing values in time series with PyPOTS below.
+
+<details>
+<summary><b>Click here to see an example applying SAITS on PhysioNet2012 for imputation:</b></summary>
 
 ``` python
 import numpy as np
@@ -93,6 +104,7 @@ mae = cal_mae(imputation, X_intact, indicating_mask)  # calculate mean absolute
 ```
 </details>
 
+
 ## ❖ Available Algorithms
 PyPOTS supports imputation, classification, clustering, and forecasting tasks on multivariate time series with missing values. The currently available algorithms of four tasks are cataloged in the following table with four partitions. The paper references are all listed at the bottom of this readme file. Please refer to them if you want more details.
 
@@ -160,8 +172,6 @@ Your star is your recognition to PyPOTS, and it matters!
 
 
 ## ❖ Attention 👀
-The documentation and tutorials are under construction. 
-
 ‼️ PyPOTS is currently under developing. If you like it and look forward to its growth, <ins>please give PyPOTS a star 
 and watch it to keep you posted on its progress and to let me know that its development is meaningful</ins>. If you have 
 any feedback, or want to contribute ideas/suggestions or share time-series related algorithms/papers, please join PyPOTS 

diff --git a/pypots/utils/commands/__init__.py → pypots/cli/__init__.py b/pypots/utils/commands/__init__.py → pypots/cli/__init__.py
diff --git a/pypots/utils/commands/base.py → pypots/cli/base.py b/pypots/utils/commands/base.py → pypots/cli/base.py
@@ -76,10 +76,11 @@ def check_if_under_root_dir(strict: bool = True):
         )
 
         if strict:
-            assert check_result, RuntimeError(
-                "Command `pypots-cli dev` can only be run under the root directory of project PyPOTS, "
-                f"but you're running it under the path {os.getcwd()}. Please make a check."
-            )
+            if not check_result:
+                raise RuntimeError(
+                    "Command `pypots-cli dev` can only be run under the root directory of project PyPOTS, "
+                    f"but you're running it under the path {os.getcwd()}. Please make a check."
+                )
 
         return check_result
 

diff --git a/pypots/utils/commands/dev.py → pypots/cli/dev.py b/pypots/utils/commands/dev.py → pypots/cli/dev.py
@@ -9,7 +9,7 @@
 import shutil
 from argparse import Namespace
 
-from pypots.utils.commands.base import BaseCommand
+from pypots.cli.base import BaseCommand
 from pypots.utils.logging import logger
 
 IMPORT_ERROR_MESSAGE = (
@@ -116,7 +116,7 @@ def __init__(
 
     def checkup(self):
         """Run some checks on the arguments to avoid error usages"""
-        self.check_if_under_root_dir()
+        self.check_if_under_root_dir(strict=True)
 
         if self._k is not None:
             assert self._run_tests, (

diff --git a/pypots/utils/commands/doc.py → pypots/cli/doc.py b/pypots/utils/commands/doc.py → pypots/cli/doc.py
@@ -11,7 +11,7 @@
 
 from tsdb.data_processing import _download_and_extract
 
-from pypots.utils.commands.base import BaseCommand
+from pypots.cli.base import BaseCommand
 from pypots.utils.logging import logger
 
 CLONED_LATEST_PYPOTS = "temp_pypots_latest"
@@ -145,7 +145,7 @@ def __init__(
 
     def checkup(self):
         """Run some checks on the arguments to avoid error usages"""
-        self.check_if_under_root_dir()
+        self.check_if_under_root_dir(strict=True)
 
         if self._cleanup:
             assert not self._gene_rst and not self._gene_html and not self._view_doc, (
@@ -191,8 +191,10 @@ def run(self):
 
                 # Generate the docs according to the cloned code
                 logger.info("Generating rst files...")
+                os.environ[
+                    "SPHINX_APIDOC_OPTIONS"
+                ] = "members,undoc-members,show-inheritance,inherited-members"
                 self.execute_command(
-                    "SPHINX_APIDOC_OPTIONS=members,undoc-members,show-inheritance,inherited-members "
                     f"sphinx-apidoc {CLONED_LATEST_PYPOTS} -o {CLONED_LATEST_PYPOTS}/rst"
                 )
 

diff --git a/pypots/utils/commands/env.py → pypots/cli/env.py b/pypots/utils/commands/env.py → pypots/cli/env.py
@@ -27,7 +27,7 @@
 
 from setuptools.config import read_configuration
 
-from pypots.utils.commands.base import BaseCommand
+from pypots.cli.base import BaseCommand
 from pypots.utils.logging import logger
 
 
@@ -90,7 +90,7 @@ def __init__(
 
     def checkup(self):
         """Run some checks on the arguments to avoid error usages"""
-        self.check_if_under_root_dir()
+        self.check_if_under_root_dir(strict=True)
 
     def run(self):
         """Execute the given command."""
@@ -112,23 +112,28 @@ def run(self):
                 "conda install pyg pytorch-scatter pytorch-sparse -c pyg"
             )
 
-            dependencies = ""
-            for i in setup_cfg["options"]["extras_require"][self._install]:
-                dependencies += f"'{i}' "
+            if self._install != "optional":
+                dependencies = ""
+                for i in setup_cfg["options"]["extras_require"][self._install]:
+                    dependencies += f"'{i}' "
 
-            if "torch-geometric" in dependencies:
-                dependencies = dependencies.replace("'torch-geometric'", "")
-                dependencies = dependencies.replace("'torch-scatter'", "")
-                dependencies = dependencies.replace("'torch-sparse'", "")
+                if "torch-geometric" in dependencies:
+                    dependencies = dependencies.replace("'torch-geometric'", "")
+                    dependencies = dependencies.replace("'torch-scatter'", "")
+                    dependencies = dependencies.replace("'torch-sparse'", "")
 
-            conda_comm = f"conda install {dependencies} -c conda-forge"
-            self.execute_command(conda_comm)
+                conda_comm = f"conda install {dependencies} -c conda-forge"
+                self.execute_command(conda_comm)
 
         else:  # self._tool == "pip"
             torch_version = torch.__version__
 
+            if not (torch.cuda.is_available() and torch.cuda.device_count() > 0):
+                if "cpu" not in torch_version:
+                    torch_version = torch_version + "+cpu"
+
             self.execute_command(
-                f"pip install -e '.[optional]' -f 'https://data.pyg.org/whl/torch-{torch_version}.html'"
+                f"python -m pip install -e '.[optional]' -f https://data.pyg.org/whl/torch-{torch_version}.html"
             )
 
             if self._install != "optional":

diff --git a/pypots/utils/commands/pypots_cli.py → pypots/cli/pypots_cli.py b/pypots/utils/commands/pypots_cli.py → pypots/cli/pypots_cli.py
@@ -7,9 +7,9 @@
 
 from argparse import ArgumentParser
 
-from pypots.utils.commands.dev import DevCommand
-from pypots.utils.commands.doc import DocCommand
-from pypots.utils.commands.env import EnvCommand
+from pypots.cli.dev import DevCommand
+from pypots.cli.doc import DocCommand
+from pypots.cli.env import EnvCommand
 
 
 def main():

diff --git a/pypots/tests/environment_for_conda_test.yml b/pypots/tests/environment_for_conda_test.yml
@@ -1,10 +1,13 @@
 name: pypots-test
+
 channels:
     - conda-forge
     - pytorch
     - pyg
     - nodefaults
+
 dependencies:
+    # basic
     - conda-forge::python
     - conda-forge::pip
     - conda-forge::scipy
@@ -13,12 +16,24 @@ dependencies:
     - conda-forge::pandas <2.0.0
     - conda-forge::h5py
     - conda-forge::tensorboard
-    - conda-forge::pytest-cov
-    - conda-forge::pytest-xdist
-    - conda-forge::coverage
     - conda-forge::pycorruptor
     - conda-forge::tsdb
     - pytorch::pytorch >=1.10.0
+
+    # optional
     - pyg::pyg
     - pyg::pytorch-scatter
-    - pyg::pytorch-sparse
+    - pyg::pytorch-sparse
+
+    # test
+    - conda-forge::pytest-cov
+    - conda-forge::pytest-xdist
+
+    # doc
+    - conda-forge::sphinx
+    - conda-forge::sphinxcontrib-bibtex
+    - conda-forge::furo
+
+    # dev
+    - conda-forge::black
+    - conda-forge::flake8