hpcflow 0.1.9__py3-none-any.whl → 0.2.0a271__py3-none-any.whl

hpcflow/__init__.py

@@ -1,12 +1,3 @@
-"""`hpcflow.__init__.py`"""
-
 from hpcflow._version import __version__
-from hpcflow.api import (
-    make_workflow,
-    submit_workflow,
-    clean,
-    get_stats,
-    save_stats,
-    kill,
-    cloud_connect,
-)
+
+_app_name = "hpcFlow"

hpcflow/__pyinstaller/__init__.py

@@ -0,0 +1,5 @@
+from pathlib import Path
+
+
+def get_hook_dirs():
+    return [str(Path(__file__).parent.resolve())]

hpcflow/__pyinstaller/hook-hpcflow.py

@@ -0,0 +1,40 @@
+from PyInstaller.utils.hooks import collect_data_files
+
+from hpcflow.sdk import sdk_classes
+
+
+# most of the modules in `sdk_classes` are imported on-demand via the app object:
+hiddenimports = [
+    *sdk_classes.values(),
+    "hpcflow.sdk.data",
+    "hpcflow.data.demo_data_manifest",
+    "hpcflow.data.scripts",
+    "hpcflow.data.jinja_templates",
+    "hpcflow.data.template_components",
+    "hpcflow.data.workflows",
+    "hpcflow.tests.data",
+    "hpcflow.sdk.core.test_utils",
+    "hpcflow.sdk.utils.patches",
+    "click.testing",
+    "requests",  # for GitHub fsspec file system
+    "fsspec.implementations.github",  # for GitHub fsspec file system
+]
+
+datas = (
+    collect_data_files("hpcflow.sdk.data")
+    + collect_data_files("hpcflow.data.demo_data_manifest")
+    + collect_data_files(
+        "hpcflow.data.scripts", include_py_files=True, excludes=("**/__pycache__",)
+    )
+    + collect_data_files(
+        "hpcflow.data.jinja_templates",
+        include_py_files=True,
+        excludes=("**/__pycache__",),
+    )
+    + collect_data_files("hpcflow.data.template_components")
+    + collect_data_files("hpcflow.data.workflows")
+    + collect_data_files(
+        "hpcflow.tests", include_py_files=True, excludes=("**/__pycache__",)
+    )
+    + collect_data_files("hpcflow.tests.data")
+)

hpcflow/_version.py

@@ -1 +1 @@
-__version__ = '0.1.9'
+__version__ = "0.2.0a271"

hpcflow/app.py

@@ -0,0 +1,43 @@
+from __future__ import annotations
+from hpcflow import __version__, _app_name
+from hpcflow.sdk import app as sdk_app
+from hpcflow.sdk.config import ConfigOptions
+
+
+# provide access to app attributes:
+__getattr__ = sdk_app.get_app_attribute
+
+# ensure docs/help can see dynamically loaded attributes:
+__all__ = sdk_app.get_app_module_all()
+__dir__ = sdk_app.get_app_module_dir()
+
+# set app-level config options:
+config_options = ConfigOptions(
+    directory_env_var="HPCFLOW_CONFIG_DIR",
+    default_directory="~/.hpcflow",
+)
+
+# load built in template components (in this case, for demonstration purposes):
+template_components = sdk_app.BaseApp.load_builtin_template_component_data(
+    "hpcflow.data.template_components"
+)
+
+# initialise the App object:
+app: sdk_app.BaseApp = sdk_app.BaseApp(
+    name=_app_name,
+    version=__version__,
+    module=__name__,
+    docs_import_conv="hf",
+    description="Computational workflow management",
+    gh_org="hpcflow",
+    gh_repo="hpcflow",
+    config_options=config_options,
+    template_components=template_components,
+    scripts_dir="data.scripts",  # relative to root package
+    jinja_templates_dir="data.jinja_templates",  # relative to root package
+    programs_dir="data.programs",  # relative to root package
+    workflows_dir="data.workflows",  # relative to root package
+    demo_data_dir="hpcflow.data.demo_data",
+    demo_data_manifest_dir="hpcflow.data.demo_data_manifest",
+    docs_url="https://hpcflow.github.io/docs/stable",
+)  #: |app|

hpcflow/cli.py

@@ -1,464 +1,4 @@
-"""`hpcflow.cli.py`
+from hpcflow.app import cli
 
-Module that exposes a command line interface for `hpcflow`.
-
-"""
-import socket
-import os
-from pathlib import Path
-from pprint import pprint
-from datetime import datetime
-from random import randint
-
-import click
-
-from hpcflow import __version__
-from hpcflow import api
-
-
-def get_process_stamp():
-    return '{} {} {}'.format(
-        datetime.now(),
-        socket.gethostname(),
-        os.getpid(),
-    )
-
-
-def validate_cloud_provider(ctx, param, value):
-
-    good_providers = ['dropbox']
-    if value not in good_providers:
-        msg = ('`provider` must be one of: {}'.format(good_providers))
-        raise click.BadParameter(msg)
-
-    return value
-
-
-def validate_task_ranges(ctx, param, value):
-    """Validate the task range.
-
-    Parameters
-    ----------
-    ctx
-    param
-    value : str
-        Stringified comma-separated list, where each element indicates the
-        tasks to submit for that channel of the Workflow. List elements can be
-        one of:
-            all
-                submit all tasks in the given channel.
-            n[-m[:s]]
-                submit a range of tasks from task `n` to task `m`
-                (inclusively), with an optional step size of `s`.
-            <empty>
-                submit no tasks from the given channel.
-
-    Returns
-    -------
-    task_ranges : list of tuple
-        (start, stop, step)
-
-    """
-
-    if value is None:
-        return
-
-    if ',' in value:
-        value = value.split(',')
-    else:
-        value = [value]
-
-    task_ranges = []
-    for i in value:
-
-        if i.strip() == 'all':
-            task_ranges.append([1, -1, 1])
-            continue
-
-        elif i.strip() == '':
-            task_ranges.append([])
-            continue
-
-        task_step = 1
-
-        msg = ('Could not understand task range. It should be specified in '
-               'the format: `n[-m[:s]]` where `n` is the starting task ID, `m` is '
-               ' the ending task ID, and `s` is the task step size.')
-
-        if '-' in i:
-            # Task range
-            task_start, task_stop = i.split('-')
-
-            if ':' in task_stop:
-                # With step size:
-                task_stop, task_step = task_stop.split(':')
-
-                try:
-                    task_step = int(task_step)
-                except ValueError:
-                    raise click.BadParameter(msg)
-
-            try:
-                task_start = int(task_start)
-                task_stop = int(task_stop)
-            except ValueError:
-                raise click.BadParameter(msg)
-
-        else:
-            # Single task
-            try:
-                task = int(i)
-                task_start = task
-                task_stop = task
-            except ValueError:
-                raise click.BadParameter(msg)
-
-        if task_start > task_stop:
-            msg = ('Task starting ID must be smaller than or equal to '
-                   'task ending ID.')
-            raise click.BadParameter(msg)
-
-        task_range = [task_start, task_stop, task_step]
-        task_ranges.append(task_range)
-
-    task_ranges = task_ranges[0]  # For now - no channels.
-    return task_ranges
-
-
-@click.group()
-@click.version_option(version=__version__)
-def cli():
-    pass
-
-
-@cli.command()
-@click.option('--yes', '-y', is_flag=True)
-@click.option('--config-dir', type=click.Path(exists=True))
-def clean(directory=None, yes=True, config_dir=None):
-    """Clean the directory of all content generated by `hpcflow`."""
-    msg = ('Do you want to remove all `hpc-flow`-generated files '
-           'from {}?')
-    if directory:
-        msg = msg.format(directory)
-    else:
-        msg = msg.format('the current directory')
-    if yes or click.confirm(msg):
-        api.clean(dir_path=directory, config_dir=config_dir)
-
-
-@cli.command()
-@click.option('--directory', '-d')
-@click.option('--json-file')
-@click.option('--json')
-@click.option('--config-dir', type=click.Path(exists=True))
-@click.argument('profiles', nargs=-1, type=click.Path(exists=True))
-def make(directory=None, profiles=None, json_file=None, json=None, config_dir=None):
-    """Generate a new Workflow."""
-    print('hpcflow.cli.make', flush=True)
-
-    workflow_id = api.make_workflow(
-        dir_path=directory,
-        profile_list=profiles,
-        json_file=json_file,
-        json_str=json,
-        config_dir=config_dir,
-        clean=False,
-    )
-    print('Generated new Workflow with ID {}'.format(workflow_id))
-
-
-@cli.command()
-@click.option('--directory', '-d')
-@click.option('--config-dir', type=click.Path(exists=True))
-@click.argument('cmd_group_sub_id', type=click.INT)
-@click.argument('task_idx', type=click.INT)
-@click.argument('iter_idx', type=click.INT)
-def write_runtime_files(cmd_group_sub_id, task_idx, iter_idx, directory=None,
-                        config_dir=None):
-    print('hpcflow.cli.write_runtime_files', flush=True)
-    api.write_runtime_files(
-        cmd_group_sub_id,
-        task_idx,
-        iter_idx,
-        dir_path=directory,
-        config_dir=config_dir,
-    )
-
-
-@cli.command()
-@click.option('--directory', '-d')
-@click.option('--config-dir', type=click.Path(exists=True))
-@click.argument('cmd_group_sub_id', type=click.INT)
-@click.argument('task_idx', type=click.INT)
-@click.argument('iter_idx', type=click.INT)
-def set_task_start(cmd_group_sub_id, task_idx, iter_idx, directory=None, config_dir=None):
-    print('hpcflow.cli.set_task_start', flush=True)
-    api.set_task_start(cmd_group_sub_id, task_idx, iter_idx, directory, config_dir)
-
-
-@cli.command()
-@click.option('--directory', '-d')
-@click.option('--config-dir', type=click.Path(exists=True))
-@click.argument('cmd_group_sub_id', type=click.INT)
-@click.argument('task_idx', type=click.INT)
-@click.argument('iter_idx', type=click.INT)
-def set_task_end(cmd_group_sub_id, task_idx, iter_idx, directory=None, config_dir=None):
-    print('hpcflow.cli.set_task_end', flush=True)
-    api.set_task_end(cmd_group_sub_id, task_idx, iter_idx, directory, config_dir)
-
-
-@cli.command()
-@click.option('--directory', '-d')
-@click.option('--config-dir', type=click.Path(exists=True))
-@click.argument('cmd_group_sub_id', type=click.INT)
-@click.argument('task_idx', type=click.INT)
-@click.argument('iter_idx', type=click.INT)
-def archive(cmd_group_sub_id, task_idx, iter_idx, directory=None, config_dir=None):
-    print('hpcflow.cli.archive', flush=True)
-    api.archive(
-        cmd_group_sub_id,
-        task_idx,
-        iter_idx,
-        dir_path=directory,
-        config_dir=config_dir,
-    )
-
-
-@cli.command()
-@click.option('--directory', '-d')
-@click.option('--config-dir', type=click.Path(exists=True))
-@click.argument('cmd_group_sub_id', type=click.INT)
-@click.argument('task_idx', type=click.INT)
-@click.argument('iter_idx', type=click.INT)
-def get_scheduler_stats(cmd_group_sub_id, task_idx, iter_idx, directory=None,
-                        config_dir=None):
-    print('hpcflow.cli.get_scheduler_stats', flush=True)
-    api.get_scheduler_stats(
-        cmd_group_sub_id,
-        task_idx,
-        iter_idx,
-        dir_path=directory,
-        config_dir=config_dir,
-    )
-
-
-@cli.command()
-@click.option('--directory', '-d')
-@click.option('--workflow-id', '-w', type=click.INT)
-@click.option('--config-dir', type=click.Path(exists=True))
-def root_archive(workflow_id, directory=None, config_dir=None):
-    print('hpcflow.cli.root_archive', flush=True)
-    api.root_archive(
-        workflow_id,
-        dir_path=directory,
-        config_dir=config_dir,
-    )
-
-
-@cli.command()
-def stat():
-    """Show the status of running tasks and the number completed tasks."""
-    print('hpcflow.cli.stat')
-
-
-@cli.command()
-@click.option('--directory', '-d')
-@click.option('--workflow-id', '-w', type=click.INT)
-@click.option('--config-dir', type=click.Path(exists=True))
-def show_stats(directory=None, workflow_id=None, config_dir=None):
-    'Show task statistics, formatted as a table.'
-    stats_fmt = api.get_formatted_stats(directory, workflow_id, config_dir=config_dir)
-    print(stats_fmt)
-
-
-@cli.command()
-@click.option('--directory', '-d')
-@click.option('--workflow-id', '-w', type=click.INT)
-@click.option('--config-dir', type=click.Path(exists=True))
-@click.argument('save_path', type=click.Path(exists=False, dir_okay=False))
-def save_stats(save_path, directory=None, workflow_id=None, config_dir=None):
-    'Save task statistics as a JSON file.'
-    api.save_stats(save_path, directory, workflow_id, config_dir=config_dir)
-
-
-@cli.command()
-@click.option('--directory', '-d')
-@click.option('--workflow-id', '-w', type=click.INT)
-@click.option('--config-dir', type=click.Path(exists=True))
-def kill(directory=None, workflow_id=None, config_dir=None):
-    api.kill(directory, workflow_id, config_dir=config_dir)
-
-
-@cli.command()
-@click.option('--directory', '-d')
-@click.option('--workflow-id', '-w', type=click.INT)
-@click.option('--config-dir', type=click.Path(exists=True))
-@click.option('--json-file')
-@click.option('--json')
-@click.option('--task-ranges', '-t',
-              help=('Task ranges are specified as a comma-separated list whose'
-                    ' elements are one of: "n[-m[:s]]", "all" or "" (empty)'),
-              callback=validate_task_ranges)
-@click.argument('profiles', nargs=-1, type=click.Path(exists=True))
-def submit(directory=None, workflow_id=None, task_ranges=None, profiles=None,
-           json_file=None, json=None, config_dir=None):
-    """Submit(and optionally generate) a Workflow."""
-
-    print('hpcflow.cli.submit', flush=True)
-
-    existing_ids = api.get_workflow_ids(directory, config_dir)
-    submit_args = {
-        'dir_path': directory,
-        'task_range': task_ranges,
-        'config_dir': config_dir,
-    }
-
-    if workflow_id:
-        # Submit an existing Workflow.
-
-        if not existing_ids:
-            msg = 'There are no existing Workflows in the directory {}'
-            raise ValueError(msg.format(directory))
-
-        submit_args['workflow_id'] = workflow_id
-
-        if workflow_id not in existing_ids:
-            msg = ('The Workflow ID "{}" does not match an existing Workflow '
-                   'in the directory {}. Existing Workflow IDs are {}')
-            raise ValueError(msg.format(workflow_id, directory, existing_ids))
-
-        submission_id = api.submit_workflow(**submit_args)
-
-    else:
-        # First generate a Workflow, and then submit it.
-
-        make_workflow = True
-        if existing_ids:
-            # Check user did not want to submit existing Workflow:
-            msg = 'Previous workflows exist with IDs: {}. Add new workflow?'
-            make_workflow = click.confirm(msg.format(existing_ids))
-
-            # TODO: if `make_workflow=False`, show existing IDs and offer to
-            # submit one?
-
-        if make_workflow:
-            workflow_id = api.make_workflow(
-                dir_path=directory,
-                profile_list=profiles,
-                json_file=json_file,
-                json_str=json,
-                config_dir=config_dir,
-            )
-            print('Generated new Workflow with ID {}'.format(workflow_id))
-
-            submit_args['workflow_id'] = workflow_id
-            submission_id = api.submit_workflow(**submit_args)
-
-        else:
-            print('Exiting.')
-            return
-
-    print('Submitted Workflow (ID {}) with submission '
-          'ID {}'.format(workflow_id, submission_id))
-
-
-@cli.command()
-@click.option('--name', '-n', required=True)
-@click.option('--value', '-v', required=True)
-@click.option('--config-dir', type=click.Path(exists=True))
-def update_config(name, value, config_dir=None):
-    api.update_config(name, value, config_dir=config_dir)
-
-
-@cli.command()
-@click.option('--provider', '-p', required=True)
-@click.option('--config-dir', type=click.Path(exists=True))
-def cloud_connect(provider, config_dir=None):
-    api.cloud_connect(provider, config_dir=config_dir)
-
-
-@cli.group()
-def dummy():
-    'Dummy commands for testing/documentation.'
-
-
-@dummy.command('makeSomething')
-@click.option('--name', default='infile')
-@click.option('--num', type=click.INT, default=2)
-@click.argument('extension', nargs=-1, default=None)
-def dummy_make_something(name, num, extension):
-
-    if not extension:
-        extension = ['.txt' for i in range(num)]
-    elif len(extension) != num:
-        raise click.BadParameter(
-            'Number of specified extensions argument must match `num` parameter.')
-
-    for i in range(num):
-        out_path = Path('{}_{}{}'.format(name, i + 1, extension[i]))
-        with out_path.open('w') as handle:
-            handle.write('{}\n'.format(randint(0, 1e6)))
-            handle.write('{} Generated by `makeSomething --name {} --num {} {}`.'.format(
-                get_process_stamp(),
-                name,
-                num,
-                ' '.join(['"{}"'.format(j) for j in extension])
-            ))
-
-
-@dummy.command('doSomething')
-@click.option('--infile1', '-i1', type=click.Path(exists=True), required=True)
-@click.option('--infile2', '-i2', type=click.Path(exists=True), required=True)
-@click.option('--value', '-v')
-@click.option('--out', '-o')
-def dummy_do_something(infile1, infile2, value=None, out=None):
-
-    with Path(infile1).open('r') as handle:
-        file_id_1 = int(handle.readline().strip())
-    with Path(infile2).open('r') as handle:
-        file_id_2 = int(handle.readline().strip())
-
-    if out is None:
-        out = 'outfile.txt'
-    out_path = Path(out)
-    with out_path.open('a') as handle:
-        handle.write('{}\n'.format(randint(0, 1e6)))
-        handle.write('{} Generated by `doSomething --infile1 {} --infile2 {}`.\n'.format(
-            get_process_stamp(), infile1, infile2))
-        if value:
-            handle.write('{} Value: {}\n'.format(get_process_stamp(), value))
-        handle.write('{} Original file ID: {}: {}\n'.format(
-            get_process_stamp(), infile1, file_id_1))
-        handle.write('{} Original file ID: {}: {}\n'.format(
-            get_process_stamp(), infile2, file_id_2))
-
-
-@dummy.command('splitSomething')
-@click.argument('infile', type=click.Path(exists=True))
-@click.option('--num', '-n', type=click.INT, default=2)
-def dummy_split_something(infile, num):
-
-    with Path(infile).open('r') as handle:
-        file_id = int(handle.readline().strip())
-    for i in range(num):
-        out_path = Path('outfile_{}.txt'.format(i + 1))
-        with out_path.open('w') as handle:
-            handle.write('{}\n'.format(randint(0, 1e6)))
-            handle.write('{} Generated by `splitSomething {}`.\n'.format(
-                get_process_stamp(), infile))
-            handle.write('{} Original file ID: {}: {}\n'.format(
-                get_process_stamp(), infile, file_id))
-
-
-@dummy.command('processSomething')
-@click.argument('infile', type=click.Path(exists=True))
-def dummy_process_something(infile):
-
-    with Path(infile).open('a') as handle:
-        handle.write('\n{} Modified by `processSomething {}`.\n'.format(
-            get_process_stamp(), infile
-        ))
-
-
-if __name__ == '__main__':
+if __name__ == "__main__":
     cli()

hpcflow/data/demo_data_manifest/__init__.py

@@ -0,0 +1,3 @@
+"""
+Manifest for demonstration data.
+"""

hpcflow/data/demo_data_manifest/demo_data_manifest.json

@@ -0,0 +1,6 @@
+{
+    "text_file.txt": {
+        "in_zip": "text_file.zip"
+    },
+    "zip_file.zip": {}
+}

hpcflow/data/jinja_templates/test/test_template.txt

@@ -0,0 +1,8 @@
+Hola, {{ name }}!
+
+This is a template, with a loop. Here are your specified fruits:
+
+{%- for fruit_i in fruits %}
+- {{ fruit_i -}}
+{% endfor %}
+

hpcflow/data/programs/hello_world/README.md

@@ -0,0 +1 @@
+This directory contains binary programs that are used to test the `Action.program` attribute. These binary programs are generated by the `generate_test_programs.yml` GitHub actions workflow (from `hello_world.c`), and are organised into sub-directories named by the `resources.platform` (e.g. "win", "linux", "macos") attribute.

hpcflow/data/programs/hello_world/hello_world.c

@@ -0,0 +1,87 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "cJSON.h"
+
+void hello_world()
+{
+    printf("hello, world\n");
+}
+
+void hello_world_ins_outs(const char *inputs_path, const char *outputs_path)
+{
+    printf("hello, world\n");
+
+    // Read input JSON
+    FILE *fp = fopen(inputs_path, "r");
+    if (!fp)
+    {
+        perror("Failed to open input file");
+        exit(1);
+    }
+
+    fseek(fp, 0, SEEK_END);
+    long len = ftell(fp);
+    fseek(fp, 0, SEEK_SET);
+
+    char *data = malloc(len + 1);
+    fread(data, 1, len, fp);
+    data[len] = '\0';
+    fclose(fp);
+
+    cJSON *json = cJSON_Parse(data);
+    if (!json)
+    {
+        fprintf(stderr, "Error parsing JSON input\n");
+        free(data);
+        exit(1);
+    }
+
+    double p1 = cJSON_GetObjectItem(json, "p1")->valuedouble;
+    double p2 = cJSON_GetObjectItem(json, "p2")->valuedouble;
+    double p3 = cJSON_GetObjectItem(json, "p3")->valuedouble;
+    double p4 = p1 + p2 + p3;
+
+    cJSON_Delete(json);
+    free(data);
+
+    // Create output JSON
+    cJSON *output_json = cJSON_CreateObject();
+    cJSON_AddNumberToObject(output_json, "p4", p4);
+
+    char *out_string = cJSON_Print(output_json);
+
+    fp = fopen(outputs_path, "w");
+    if (!fp)
+    {
+        perror("Failed to open output file");
+        cJSON_Delete(output_json);
+        free(out_string);
+        exit(1);
+    }
+
+    fprintf(fp, "%s\n", out_string);
+    fclose(fp);
+
+    cJSON_Delete(output_json);
+    free(out_string);
+}
+
+int main(int argc, char *argv[])
+{
+    if (argc == 1)
+    {
+        hello_world();
+    }
+    else if (argc == 3)
+    {
+        hello_world_ins_outs(argv[1], argv[2]);
+    }
+    else
+    {
+        fprintf(stderr, "Usage: %s [input.json output.json]\n", argv[0]);
+        return 1;
+    }
+
+    return 0;
+}