Merge pull request #66 from WenjieDu/dev

pypots/utils/commands/base.py

@@ -23,6 +23,7 @@ def register_subcommand(parser: ArgumentParser):
 
     @staticmethod
     def execute_command(command: str, verbose: bool = True):
+        logger.info(f"Executing '{command}'...")
         if verbose:
             exec_result = subprocess.Popen(
                 command,
@@ -43,17 +44,14 @@ def execute_command(command: str, verbose: bool = True):
                 stderr=subprocess.PIPE,
                 shell=True,
             )
-            if exec_result.returncode != 0:
-                if len(exec_result.stderr) > 0:
-                    logger.error(exec_result.stderr)
-                if len(exec_result.stdout) > 0:
-                    logger.error(exec_result.stdout)
-                raise RuntimeError()
-        return exec_result.returncode
+
+        if exec_result.returncode != 0:
+            raise RuntimeError(exec_result.stdout, exec_result.stderr)
+        return exec_result
 
     @staticmethod
     def check_if_under_root_dir(strict: bool = True):
-        """ Check if under the root dir of PyPOTS project.
+        """Check if under the root dir of PyPOTS project.
 
         Parameters
         ----------
@@ -85,6 +83,10 @@ def check_if_under_root_dir(strict: bool = True):
 
         return check_result
 
+    @abstractmethod
+    def checkup(self):
+        raise NotImplementedError()
+
     @abstractmethod
     def run(self):
         raise NotImplementedError()

pypots/utils/commands/dev.py

@@ -7,7 +7,7 @@
 
 import os
 import shutil
-from argparse import ArgumentParser, Namespace
+from argparse import Namespace
 
 from pypots.utils.commands.base import BaseCommand
 from pypots.utils.logging import logger
@@ -43,9 +43,10 @@ class DevCommand(BaseCommand):
     """
 
     @staticmethod
-    def register_subcommand(parser: ArgumentParser):
+    def register_subcommand(parser):
         sub_parser = parser.add_parser(
-            "dev", help="CLI tools helping develop PyPOTS code"
+            "dev",
+            help="CLI tools helping develop PyPOTS code",
         )
         sub_parser.add_argument(
             "--build",
@@ -54,18 +55,21 @@ def register_subcommand(parser: ArgumentParser):
             help="Build PyPOTS into a wheel and package the source code into a .tar.gz file for distribution",
         )
         sub_parser.add_argument(
+            "-c",
             "--cleanup",
             dest="cleanup",
             action="store_true",
             help="Delete all caches and building files",
         )
         sub_parser.add_argument(
             "--run_tests",
+            "--run-tests",
             dest="run_tests",
             action="store_true",
             help="Run all test cases",
         )
         sub_parser.add_argument(
+            "--show-coverage",
             "--show_coverage",
             dest="show_coverage",
             action="store_true",
@@ -86,6 +90,7 @@ def register_subcommand(parser: ArgumentParser):
             "matching is case-insensitive.",
         )
         sub_parser.add_argument(
+            "--lint-code",
             "--lint_code",
             dest="lint_code",
             action="store_true",
@@ -109,7 +114,7 @@ def __init__(
         self._show_coverage = show_coverage
         self._lint_code = lint_code
 
-    def check_arguments(self):
+    def checkup(self):
         """Run some checks on the arguments to avoid error usages"""
         self.check_if_under_root_dir()
 
@@ -133,9 +138,8 @@ def check_arguments(self):
 
     def run(self):
         """Execute the given command."""
-
-        # check arguments first
-        self.check_arguments()
+        # run checks first
+        self.checkup()
 
         try:
             if self._cleanup:
@@ -151,7 +155,6 @@ def run(self):
                     if self._show_coverage
                     else pytest_command
                 )
-                logger.info(f"Executing '{command_to_run_test}'...")
                 self.execute_command(command_to_run_test)
                 if self._show_coverage:
                     self.execute_command("coverage report -m")

pypots/utils/commands/doc.py

@@ -7,11 +7,12 @@
 
 import os
 import shutil
-from argparse import ArgumentParser, Namespace
+from argparse import Namespace
+
+from tsdb.data_processing import _download_and_extract
 
 from pypots.utils.commands.base import BaseCommand
 from pypots.utils.logging import logger
-from tsdb.data_processing import _download_and_extract
 
 CLONED_LATEST_PYPOTS = "temp_pypots_latest"
 
@@ -73,43 +74,51 @@ class DocCommand(BaseCommand):
     """
 
     @staticmethod
-    def register_subcommand(parser: ArgumentParser):
+    def register_subcommand(parser):
         sub_parser = parser.add_parser(
-            "doc", help="CLI tools helping build PyPOTS documentation"
+            "doc",
+            help="CLI tools helping build PyPOTS documentation",
+            allow_abbrev=True,
         )
 
         sub_parser.add_argument(
+            "--gene-rst",
             "--gene_rst",
             dest="gene_rst",
             action="store_true",
             help="Generate rst (reStructuredText) documentation according to the latest code on Github",
         )
         sub_parser.add_argument(
+            "-b",
             "--branch",
             type=str,
             default="main",
             choices=["main", "dev"],
             help="Code on which branch will be used for documentation generating",
         )
         sub_parser.add_argument(
+            "--gene-html",
             "--gene_html",
             dest="gene_html",
             action="store_true",
             help="Generate the sphinx documentation into static HTML files",
         )
         sub_parser.add_argument(
+            "--view-doc",
             "--view_doc",
             dest="view_doc",
             action="store_true",
             help="Deploy the generated HTML documentation locally for view",
         )
         sub_parser.add_argument(
+            "-p",
             "--port",
             type=int,
             default=9075,
             help="Use which port to deploy the web server for doc view",  # 9075 looks like "POTS", so use it as default
         )
         sub_parser.add_argument(
+            "-c",
             "--cleanup",
             dest="cleanup",
             action="store_true",
@@ -134,7 +143,7 @@ def __init__(
         self._port = port
         self._cleanup = cleanup
 
-    def check_arguments(self):
+    def checkup(self):
         """Run some checks on the arguments to avoid error usages"""
         self.check_if_under_root_dir()
 
@@ -146,9 +155,8 @@ def check_arguments(self):
 
     def run(self):
         """Execute the given command."""
-
-        # check arguments first
-        self.check_arguments()
+        # run checks first
+        self.checkup()
 
         try:
             if self._cleanup:

pypots/utils/commands/env.py

@@ -0,0 +1,136 @@
+"""
+CLI tools to help initialize environments for running and developing PyPOTS.
+"""
+
+# Created by Wenjie Du <[email protected]>
+# License: GLP-v3
+
+try:
+    # here try importing all dependencies in the scope `basic` defined in `setup.cfg`
+    import torch
+
+    # import numpy
+    # import sklearn
+    # import pandas
+    # import tensorboard
+    # import scipy
+    # import h5py
+    # import tsdb
+    # import pycorruptor
+except ImportError:
+    raise ImportError(
+        "Torch not installed. Using this tool supposes that you've already installed `pypots` "
+        "with at least the scope of `basic` dependencies."
+    )
+
+from argparse import ArgumentParser, Namespace
+
+from setuptools.config import read_configuration
+
+from pypots.utils.commands.base import BaseCommand
+from pypots.utils.logging import logger
+
+
+def env_command_factory(args: Namespace):
+    return EnvCommand(
+        args.install,
+        args.tool,
+    )
+
+
+class EnvCommand(BaseCommand):
+    """CLI tools helping users and developer setup python environments for running and developing PyPOTS.
+
+    Notes
+    -----
+    Using this tool supposes that you've already installed `pypots` with at least the scope of `basic` dependencies.
+    Please refer to file setup.cfg in PyPOTS project's root dir for definitions of different dependency scopes.
+
+    Examples
+    --------
+    $ pypots-cli env --scope full --tool pip
+    $ pypots-cli env --scope full --tool pip
+    $ pypots-cli env --scope dev --tool conda -n
+    """
+
+    @staticmethod
+    def register_subcommand(parser: ArgumentParser):
+        sub_parser = parser.add_parser(
+            "env",
+            help="CLI tools helping users and developer setup python environments for running and developing PyPOTS",
+            allow_abbrev=True,
+        )
+
+        sub_parser.add_argument(
+            "--install",
+            dest="install",
+            type=str,
+            required=True,
+            choices=["dev", "full", "doc", "test", "optional"],
+            help="Install specified dependencies in the current python environment",
+        )
+        sub_parser.add_argument(
+            "--tool",
+            dest="tool",
+            type=str,
+            required=True,
+            choices=["conda", "pip"],
+            help="Setup the environment with pip or conda, have to be specific",
+        )
+
+        sub_parser.set_defaults(func=env_command_factory)
+
+    def __init__(
+        self,
+        install: bool,
+        tool: str,
+    ):
+        self._install = install
+        self._tool = tool
+
+    def checkup(self):
+        """Run some checks on the arguments to avoid error usages"""
+        self.check_if_under_root_dir()
+
+    def run(self):
+        """Execute the given command."""
+        # run checks first
+        self.checkup()
+
+        setup_cfg = read_configuration("setup.cfg")
+
+        logger.info(
+            f"Installing the dependencies in scope `{self._install}` for you..."
+        )
+
+        if self._tool == "conda":
+            assert (
+                self.execute_command("which conda").returncode == 0
+            ), "Conda not installed, cannot set --tool=conda, please check your conda."
+
+            self.execute_command(
+                "conda install pyg pytorch-scatter pytorch-sparse -c pyg"
+            )
+
+            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'", "")
+
+            conda_comm = f"conda install {dependencies} -c conda-forge"
+            self.execute_command(conda_comm)
+
+        else:  # self._tool == "pip"
+            torch_version = torch.__version__
+
+            self.execute_command(
+                f"pip install -e '.[optional]' -f 'https://data.pyg.org/whl/torch-{torch_version}.html'"
+            )
+
+            if self._install != "optional":
+                self.execute_command(f"pip install -e '.[{self._install}]'")
+        logger.info("Installation finished. Enjoy your play with PyPOTS! Bye ;-)")

pypots/utils/commands/pypots_cli.py

@@ -9,6 +9,7 @@
 
 from pypots.utils.commands.dev import DevCommand
 from pypots.utils.commands.doc import DocCommand
+from pypots.utils.commands.env import EnvCommand
 
 
 def main():
@@ -20,6 +21,7 @@ def main():
     # Register commands here
     DevCommand.register_subcommand(commands_parser)
     DocCommand.register_subcommand(commands_parser)
+    EnvCommand.register_subcommand(commands_parser)
 
     # parse all arguments
     args = parser.parse_args()