idmtools-cli 0.0.0.dev0__tar.gz → 0.0.3__tar.gz

idmtools_cli-0.0.3/.bumpversion.cfg

@@ -0,0 +1,28 @@
+[bumpversion]
+current_version = 3.0.0+nightly
+commit = False
+tag = False
+parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(?P<release>\+\w+)?(\.(?P<build>\d+))?
+serialize = 
+	{major}.{minor}.{patch}{release}.{build}
+	{major}.{minor}.{patch}{release}
+	{major}.{minor}.{patch}
+
+[bumpversion:part:release]
+optional_value = prod
+first_value = prod
+values = 
+	prod
+	+nightly
+
+[bumpversion:file:./idmtools_cli/__init__.py]
+search = __version__ = "{current_version}"
+replace = __version__ = "{new_version}"
+serialize = {major}.{minor}.{patch}{release}
+	{major}.{minor}.{patch}
+
+[bumpversion:file:./pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"
+serialize = {major}.{minor}.{patch}{release}
+	{major}.{minor}.{patch}

idmtools_cli-0.0.3/LICENSE.TXT

@@ -0,0 +1,3 @@
+idmtools is licensed under the Creative Commons Attribution-Noncommercial-ShareAlike 4.0 License.
+
+To view a copy of this license, visit https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode

idmtools_cli-0.0.3/MANIFEST.in

@@ -0,0 +1,4 @@
+include idmtools_cli/cli/common_project_templates.json
+include README.md
+include LICENSE.TXT
+prune tests

idmtools_cli-0.0.3/Makefile

@@ -0,0 +1,2 @@
+PACKAGE_NAME=idmtools_cli
+include $(abspath ../dev_scripts/package_general.mk)

idmtools_cli-0.0.3/PKG-INFO

@@ -0,0 +1,208 @@
+Metadata-Version: 2.4
+Name: idmtools_cli
+Version: 0.0.3
+Summary: CLI for IDM-Tools
+Author-email: Sharon Chen <schen@idmod.org>, Clinton Collins <ccollins@idmod.org>, Zhaowei Du <zdu@idmod.org>, Mary Fisher <mfisher@idmod.org>, Clark Kirkman IV <ckirkman@idmod.org>, Benoit Raybaud <braybaud@idmod.org>
+Project-URL: Homepage, https://github.com/InstituteforDiseaseModeling/idmtools
+Keywords: modeling,IDM,cli
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE.TXT
+Requires-Dist: click~=8.1.7
+Requires-Dist: click-plugins
+Requires-Dist: colorama~=0.4.6
+Requires-Dist: cookiecutter~=2.6.0
+Requires-Dist: idmtools<1.0.0,>=0.0.0
+Requires-Dist: tabulate<0.10,>=0.8.9
+Requires-Dist: pyperclip~=1.8
+Requires-Dist: yaspin<3.1.0,>=1.2.0
+Provides-Extra: test
+Requires-Dist: idmtools[test]; extra == "test"
+Dynamic: license-file
+
+![Staging: idmtools-cli](https://github.com/InstituteforDiseaseModeling/idmtools/workflows/Staging:%20idmtools-cli/badge.svg?branch=dev)
+
+# idmtools-cli
+
+<!-- START doctoc generated TOC please keep comment here to allow auto update -->
+<!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE -->
+**Table of Contents**
+
+  - [Installing](#installing)
+- [Development tips](#development-tips)
+- [Using the CLI](#using-the-cli)
+  - [Version command](#version-command)
+  - [Experiment commands for Local Platform](#experiment-commands-for-local-platform)
+    - [Status](#status)
+    - [Delete](#delete)
+  - [Simulation commands for Local Platform](#simulation-commands-for-local-platform)
+  - [Status](#status-1)
+  - [GitRepo commands](#gitrepo-commands)
+    - [View](#view)
+    - [Repos](#repos)
+    - [Releases](#releases)
+    - [Peep](#peep)
+    - [Download](#download)
+
+<!-- END doctoc generated TOC please keep comment here to allow auto update -->
+
+## Installing
+
+```bash
+pip install idmtools-cli --index-url=https://packages.idmod.org/api/pypi/pypi-production/simple
+```
+
+# Development tips
+
+There is a Makefile file available for most common development tasks. Here is a list of commands
+```bash
+clean       -   Clean up temproary files
+lint        -   Lint package and tests
+test        -   Run All tests
+coverage    -   Run tests and generate coverage report that is shown in browser
+```
+On Windows, you can use `pymake` instead of `make`
+
+# Using the CLI
+
+The CLI requires the workers service to already be running.
+`idmtools`
+
+## Version command
+
+To determine version of idmtools and related plugins, use the version cli command.
+
+
+```
+> idmtools version
+```
+
+Example output
+```bash
+emodpy                               Version: 1.3.0                           
+  Plugins:
+    EMODTask                  
+idmtools                             Version: 1.4.0+nightly.0                 
+  Plugins:
+    CommandTask               
+idmtools-cli                         Version: 1.4.0+nightly.0                 
+idmtools-models                      Version: 1.4.0+nightly.0                 
+  Plugins:
+    JSONConfiguredPythonTask  
+    JSONConfiguredRTask       
+    JSONConfiguredTask        
+    PythonTask                
+    RTask                     
+    ScriptWrapperTask         
+    TemplatedScriptTask       
+idmtools-platform-comps              Version: 1.4.0+nightly.0                 
+  Plugins:
+    COMPSPlatform             
+    SSMTPlatform                        
+idmtools-platform-slurm              Version: 1.0.0+nightly                   
+  Plugins:
+    SlurmPlatform             
+```
+
+
+## Experiment commands for Local Platform
+
+### Status
+
+You can check the status of experiments use the follow command. It will also summarize the simulations under
+the experiment as a progress bar with green section for completed tasks, yellow for in progress, red for failed, and
+white for queued. 
+
+```
+> idmtools experiment --platform Local status --help
+```
+ 
+
+In addition, we used in conjunction with a console that supports auto-highlighting of hyperlinks, you will be able to
+easily open up the asset directories by clicking on the data path URLs.
+
+You can also perform filtering on the experiments
+```bash
+> idmtools experiment --platform Local status --tag type PythonExperiment
+> idmtools experiment --platform Local status --id 8EHU147Z
+```
+
+### Delete
+
+You can delete experiments and their child simulations using the following command. Optionally you can also delete
+the associated data directories as well by using the *--data* option.
+
+```
+>idmtools experiment --platform Local delete <experiment_id>
+```
+
+## Simulation commands for Local Platform
+
+## Status 
+
+You can check the status of simulations use the follow command.
+
+```
+>idmtools simulation --platform Local status
+```
+
+You can also filter by a either id, experiment id, status, and tags or any combination of the aforementioned
+
+```bash
+> idmtools simulation --platform Local status --experiment-id EFX6JXBV
+> idmtools simulation --platform Local status --id XDT0VMVV
+> idmtools simulation --platform Local status --tag a 5 --tag b
+> idmtools simulation --platform Local status --experiment-id --status failed
+```
+
+
+## GitRepo commands
+
+### View
+
+You can check idmtools available examples. You can use --raw to determine to display in detailed or simplified format
+
+```
+> idmtools gitrepo view
+```
+
+### Repos
+
+You can list all public repos for a GitHub owner. You can use --owner to specify an owner and --page for pagination
+--owner default to 'institutefordiseasemodeling'
+--page default to 1
+
+```
+> idmtools gitrepo repos
+```
+
+### Releases
+
+You can list all releases of a repo by providing --owner and --repo
+--owner default to 'institutefordiseasemodeling' and --repo default to 'idmtools'
+
+```
+> idmtools gitrepo releasess
+```
+
+### Peep
+
+You can list all current files/dirs of a repo folder by providing --url
+
+```
+> idmtools gitrepo peep
+```
+
+### Download
+
+You can download files from a public repo to a specified local folder (default to current folder). By default, it will 
+download idmtools examples. You can also download any files from any public repo by using --url (multiple is supported)
+
+```
+> idmtools gitrepo download
+```

idmtools_cli-0.0.3/README.md

@@ -0,0 +1,181 @@
+![Staging: idmtools-cli](https://github.com/InstituteforDiseaseModeling/idmtools/workflows/Staging:%20idmtools-cli/badge.svg?branch=dev)
+
+# idmtools-cli
+
+<!-- START doctoc generated TOC please keep comment here to allow auto update -->
+<!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE -->
+**Table of Contents**
+
+  - [Installing](#installing)
+- [Development tips](#development-tips)
+- [Using the CLI](#using-the-cli)
+  - [Version command](#version-command)
+  - [Experiment commands for Local Platform](#experiment-commands-for-local-platform)
+    - [Status](#status)
+    - [Delete](#delete)
+  - [Simulation commands for Local Platform](#simulation-commands-for-local-platform)
+  - [Status](#status-1)
+  - [GitRepo commands](#gitrepo-commands)
+    - [View](#view)
+    - [Repos](#repos)
+    - [Releases](#releases)
+    - [Peep](#peep)
+    - [Download](#download)
+
+<!-- END doctoc generated TOC please keep comment here to allow auto update -->
+
+## Installing
+
+```bash
+pip install idmtools-cli --index-url=https://packages.idmod.org/api/pypi/pypi-production/simple
+```
+
+# Development tips
+
+There is a Makefile file available for most common development tasks. Here is a list of commands
+```bash
+clean       -   Clean up temproary files
+lint        -   Lint package and tests
+test        -   Run All tests
+coverage    -   Run tests and generate coverage report that is shown in browser
+```
+On Windows, you can use `pymake` instead of `make`
+
+# Using the CLI
+
+The CLI requires the workers service to already be running.
+`idmtools`
+
+## Version command
+
+To determine version of idmtools and related plugins, use the version cli command.
+
+
+```
+> idmtools version
+```
+
+Example output
+```bash
+emodpy                               Version: 1.3.0                           
+  Plugins:
+    EMODTask                  
+idmtools                             Version: 1.4.0+nightly.0                 
+  Plugins:
+    CommandTask               
+idmtools-cli                         Version: 1.4.0+nightly.0                 
+idmtools-models                      Version: 1.4.0+nightly.0                 
+  Plugins:
+    JSONConfiguredPythonTask  
+    JSONConfiguredRTask       
+    JSONConfiguredTask        
+    PythonTask                
+    RTask                     
+    ScriptWrapperTask         
+    TemplatedScriptTask       
+idmtools-platform-comps              Version: 1.4.0+nightly.0                 
+  Plugins:
+    COMPSPlatform             
+    SSMTPlatform                        
+idmtools-platform-slurm              Version: 1.0.0+nightly                   
+  Plugins:
+    SlurmPlatform             
+```
+
+
+## Experiment commands for Local Platform
+
+### Status
+
+You can check the status of experiments use the follow command. It will also summarize the simulations under
+the experiment as a progress bar with green section for completed tasks, yellow for in progress, red for failed, and
+white for queued. 
+
+```
+> idmtools experiment --platform Local status --help
+```
+ 
+
+In addition, we used in conjunction with a console that supports auto-highlighting of hyperlinks, you will be able to
+easily open up the asset directories by clicking on the data path URLs.
+
+You can also perform filtering on the experiments
+```bash
+> idmtools experiment --platform Local status --tag type PythonExperiment
+> idmtools experiment --platform Local status --id 8EHU147Z
+```
+
+### Delete
+
+You can delete experiments and their child simulations using the following command. Optionally you can also delete
+the associated data directories as well by using the *--data* option.
+
+```
+>idmtools experiment --platform Local delete <experiment_id>
+```
+
+## Simulation commands for Local Platform
+
+## Status 
+
+You can check the status of simulations use the follow command.
+
+```
+>idmtools simulation --platform Local status
+```
+
+You can also filter by a either id, experiment id, status, and tags or any combination of the aforementioned
+
+```bash
+> idmtools simulation --platform Local status --experiment-id EFX6JXBV
+> idmtools simulation --platform Local status --id XDT0VMVV
+> idmtools simulation --platform Local status --tag a 5 --tag b
+> idmtools simulation --platform Local status --experiment-id --status failed
+```
+
+
+## GitRepo commands
+
+### View
+
+You can check idmtools available examples. You can use --raw to determine to display in detailed or simplified format
+
+```
+> idmtools gitrepo view
+```
+
+### Repos
+
+You can list all public repos for a GitHub owner. You can use --owner to specify an owner and --page for pagination
+--owner default to 'institutefordiseasemodeling'
+--page default to 1
+
+```
+> idmtools gitrepo repos
+```
+
+### Releases
+
+You can list all releases of a repo by providing --owner and --repo
+--owner default to 'institutefordiseasemodeling' and --repo default to 'idmtools'
+
+```
+> idmtools gitrepo releasess
+```
+
+### Peep
+
+You can list all current files/dirs of a repo folder by providing --url
+
+```
+> idmtools gitrepo peep
+```
+
+### Download
+
+You can download files from a public repo to a specified local folder (default to current folder). By default, it will 
+download idmtools examples. You can also download any files from any public repo by using --url (multiple is supported)
+
+```
+> idmtools gitrepo download
+```

idmtools_cli-0.0.3/idmtools_cli/__init__.py

@@ -0,0 +1,12 @@
+"""iidmtools_cli version definition file."""
+try:
+    from importlib.metadata import version, PackageNotFoundError
+except ImportError:
+    # Python < 3.8
+    from importlib_metadata import version, PackageNotFoundError
+
+try:
+    __version__ = version("idmtools-cli")  # Use your actual package name
+except PackageNotFoundError:
+    # Package not installed, use fallback
+    __version__ = "0.0.0+unknown"

idmtools_cli-0.0.3/idmtools_cli/cli/__init__.py

@@ -0,0 +1 @@
+"""Package init file."""

idmtools_cli-0.0.3/idmtools_cli/cli/common_project_templates.json

@@ -0,0 +1,19 @@
+[{
+  "name": "reproducible-science",
+  "url": "gh:mkrapp/cookiecutter-reproducible-science",
+  "description": "A boilerplate for reproducible and transparent science with close resemblances to the philosophy of Cookiecutter Data Science: A logical, reasonably standardized, but flexible project structure for doing and sharing data science work.",
+  "info": "https://github.com/mkrapp/cookiecutter-reproducible-science"
+  },
+  {
+  "name": "docker-science",
+  "url": "git@github.com:docker-science/cookiecutter-docker-science.git",
+  "description": "This project is a tiny template for machine learning projects developed in Docker environments. In machine learning tasks, projects glow uniquely to fit target tasks, but in the initial state, most directory structure and targets in Makefile are common. Cookiecutter Docker Science generates initial directories which fits simple machine learning tasks.",
+  "info": "https://docker-science.github.io/"
+  },
+  {
+  "name": "data-science",
+  "url": "https://github.com/drivendata/cookiecutter-data-science",
+  "description": "A logical, reasonably standardized, but flexible project structure for doing and sharing data science work.",
+  "info": "https://docker-science.github.io/"
+  }
+  ]

idmtools_cli-0.0.3/idmtools_cli/cli/config_file.py

@@ -0,0 +1,199 @@
+"""Defines the config cli group and commands."""
+import configparser
+import dataclasses
+import os
+import re
+import click
+from click import secho
+from colorama import Fore, Style
+from idmtools.registry.platform_specification import PlatformPlugins
+from idmtools_cli.cli.entrypoint import cli
+
+IGNORED_PLATFORMS = ["Test", "Slurm", "File", "Container", "SSMT", "TestExecute", "Process"]
+AVAILABLE_PLATFORMS = PlatformPlugins().get_plugin_map()
+for platform in IGNORED_PLATFORMS:
+    if platform in AVAILABLE_PLATFORMS:
+        del AVAILABLE_PLATFORMS[platform]
+HIDDEN_FIELD_REGEX = re.compile('^_.+$')
+FIELD_BLACKLIST = ['platform_type_map', 'supported_types', 'plugin_key', 'docker_image']
+
+
+@cli.group()
+@click.option("--config_path", prompt="Path to the idmtools.ini file",
+              help="Path to the idmtools.ini file",
+              default=os.path.join(os.getcwd(), "idmtools.ini"),
+              type=click.Path(dir_okay=False, file_okay=True, exists=False, writable=True, resolve_path=True))
+@click.option("--global-config/--no-global-config", default=False, help="Allow generating config in the platform default global location")
+@click.pass_context
+def config(ctx, config_path, global_config):
+    """
+    Contains commands related to the creation of idmtools.ini.
+
+    With the config command, you can :
+     - Generate an idmtools.ini file in the current directory
+     - Add a configuration block
+    """
+    ctx.ensure_object(dict)
+    if global_config:
+        from idmtools import IdmConfigParser
+        config_path = IdmConfigParser.get_global_configuration_name()
+
+    # Create a config parser and read the file if it exist
+    # The comment prefixes and allow_no_value is a truck to keep the comments even while editing
+    cp = configparser.ConfigParser(comment_prefixes='/', allow_no_value=True)
+    if os.path.exists(config_path):
+        cp.read_file(open(config_path))
+
+    # Store the config parser in the context
+    ctx.obj["cp"] = cp
+    ctx.obj["path"] = config_path
+
+
+def slugify(value):
+    """
+    Slugify the option.
+
+    This means upper-casing and replacing spaces with "-"
+
+    Args:
+        value: Item to slugify
+
+    Returns:
+        Slugified string
+    """
+    value = value.upper()
+    value = value.replace(" ", "_")
+    return value
+
+
+def validate_block_name(context, value):
+    """
+    Validate if a block name exists, and if so, should we overwrite it.
+
+    Args:
+        context: Context object
+        value: Value to check
+
+    Returns:
+        Slugified value name
+    """
+    cp = context.obj["cp"]
+    value = slugify(value)
+    if value in cp.sections():
+        secho(f"The {value} block already exists in the selected ini file.", fg="bright_yellow")
+        click.confirm(click.style("Do you want to continue and overwrite the existing block?", fg="bright_yellow"), default=False, abort=True)
+
+        # Remove the block from the config parser
+        del cp[value]
+
+    context.obj['cp'] = cp
+
+    return value
+
+
+@config.command()
+@click.option("--block_name", prompt="New block name",
+              help="Name of the new block in the file",
+              callback=lambda c, p, v: validate_block_name(c, v),
+              type=click.STRING)
+@click.option('--platform', default='COMPS', type=click.Choice(AVAILABLE_PLATFORMS.keys()), prompt="Platform type")
+@click.pass_context
+def block(ctx, block_name, platform):
+    """
+    Command to create/replace a block in the selected idmtools.ini.
+
+    Args:
+        ctx: Context containing the path of idmtools.ini and the associated configparser
+        block_name:  Name of the block to create/replace
+        platform:  Selected platform
+    """
+    config_path = ctx.obj['path']
+    print("\n" + Style.BRIGHT + "-" * 50)
+    print("idmtools.ini Utility")
+    print(f"- INI Location: {config_path}")
+    print(f"- Selected block: {block_name}")
+    print(f"- Selected platform: {platform}")
+    print("-" * 50 + Style.NORMAL + "\n")
+
+    # Retrieve the platform and its associated fields
+    platform_obj = AVAILABLE_PLATFORMS[platform]
+    fields = dataclasses.fields(platform_obj.get_type())
+
+    # Dictionary to store user choices and field defaults
+    # Store both to allow the fields callback functions to access the previous user choices regardless of defaults
+    values = {"type": platform}
+    defaults = {}
+
+    # Ask about each field
+    # The field needs to contain a `help` section in the metadata to be considered
+    for field in filter(lambda f: "help" in f.metadata, fields):
+
+        # Display the help message
+        print(f"{Fore.CYAN}{field.metadata['help']}{Fore.RESET}")
+
+        # Retrieve the metadata
+        md = dict(field.metadata)
+
+        # If a callback exists -> execute it
+        if "callback" in md:
+            md.update(md["callback"](values, field))
+
+        # Create the default
+        field_default = md.get("default", field.default if field.default is not None else '')
+        defaults[field.name] = field.default
+
+        # Handle the choices if any
+        prompt_type = click.Choice(md["choices"]) if "choices" in md else field.type
+
+        # Retrieve the validation function if any
+        if "validate" in md:
+            validation = md["validate"]
+        else:
+            validation = lambda v: (True, None)  # noqa: E731
+
+        # Prompt the user
+        while True:
+            user_input = click.prompt(field.name, type=prompt_type, default=field_default, prompt_suffix=f": {Fore.GREEN}")
+
+            # Call the validation
+            result, msg = validation(user_input)
+
+            # If positive, get out
+            if result:
+                break
+
+            # Else display the error message
+            secho(msg, fg="bright_red")
+
+        # Store the value
+        values[field.name] = user_input if user_input != "" else None
+        print(Fore.RESET)
+
+    # Remove the default values from the values
+    for k, d in defaults.items():
+        if values[k] == d:
+            del values[k]
+
+    # Display a validation prompt
+    print("The following block will be added to the file:\n")
+    longest_param = max(len(p) for p in values)
+    block_parameters = "\n".join(f"{param.ljust(longest_param)} = {value}" for param, value in values.items())
+    block_headers = f"[{block_name}]"
+    block = block_headers + "\n" + block_parameters
+    secho(f"{block}\n", fg="bright_blue")
+
+    # If we decide to go ahead -> write to file
+    if click.confirm("Do you want to write this block to the file?", default=True):
+        # First re-write the content of the config parser
+        cp = ctx.obj["cp"]
+        with open(config_path, 'w') as fp:
+            cp.write(fp)
+            fp.writelines("\n" + block)
+
+        secho("Block written successfully!", fg="bright_green")
+    else:
+        secho("Aborted...", fg="bright_red")
+
+
+if __name__ == '__main__':
+    config(["block", '--block_name', 'test'])