Description

The following includes additional details to how some features of the packages work with examples that involve internal components. Even though using the package this way is very much possible, cli interface is recomended.

from package_auto_assembler import (VersionHandler, \
    ImportMappingHandler, RequirementsHandler, MetadataHandler, \
        LocalDependaciesHandler, LongDocHandler, SetupDirHandler, \
            ReleaseNotesHandler, MkDocsHandler, PackageAutoAssembler, \
                DependenciesAnalyser)

1. Package versioning

Package versioning within paa is done based on semantic versioning.

major.minor.patch

By default, patch is updated, but the minor and major could also be update based on, for example, commit messages or manually from the log file.

Package auto assembler does try to pull latest version from package storage, but in case of failure uses version logs stored in .paa/tracking.

---

initialize VersionHandler

pv = VersionHandler(
    # required
    versions_filepath = '../tests/package_auto_assembler/other/lsts_package_versions.yml',
    log_filepath = '../tests/package_auto_assembler/other/version_logs.csv',
    # optional
    default_version = "0.0.1")

add new package

pv.add_package(
    package_name = "new_package",
    # optional
    version = "0.0.1"
)

update package version

pv.increment_patch(
    package_name = "new_package"
)
## for not tracked package
pv.increment_patch(
    package_name = "another_new_package",
    # optional
    default_version = "0.0.1"
)

There are no known versions of 'another_new_package', 0.0.1 will be used!

display current versions and logs

pv.get_versions(
    # optional
    versions_filepath = '../tests/package_auto_assembler/other/lsts_package_versions.yml'
)

{'another_new_package': '0.0.1', 'new_package': '0.0.2'}

pv.get_version(
    package_name='new_package'
)

'0.0.2'

pv.get_logs(
    # optional
    log_filepath = '../tests/package_auto_assembler/other/version_logs.csv'
)

	Timestamp	Package	Version
0	2024-07-29 03:26:39	new_package	0.0.1
1	2024-07-29 03:26:40	new_package	0.0.2
2	2024-07-29 03:26:40	another_new_package	0.0.1

flush versions and logs

pv.flush_versions()
pv.flush_logs()

get latest available version with pip

pv.get_latest_pip_version(package_name = 'package-auto-assembler')

'0.3.1'

2. Import mapping

Install and import names of dependencies may vary. The mapping files maps import names to install names so that requirements extraction from .py files is possible. Some of the mapping are packaged and would not need to provided, but in case a dependency used within new package was not inluded, it is possible to augment default mapping through .paa/package_mapping.json.

---

initialize ImportMappingHandler

im = ImportMappingHandler(
    # required
    mapping_filepath = "../env_spec/package_mapping.json"
)

load package mappings

im.load_package_mappings(
    # optional
    mapping_filepath = "../env_spec/package_mapping.json"
)

{'PIL': 'Pillow',
 'bs4': 'beautifulsoup4',
 'fitz': 'PyMuPDF',
 'attr': 'attrs',
 'dotenv': 'python-dotenv',
 'googleapiclient': 'google-api-python-client',
 'google_auth_oauthlib': 'google-auth-oauthlib',
 'sentence_transformers': 'sentence-transformers',
 'flask': 'Flask',
 'stdlib_list': 'stdlib-list',
 'sklearn': 'scikit-learn',
 'yaml': 'pyyaml',
 'package_auto_assembler': 'package-auto-assembler',
 'git': 'gitpython'}

3. Extracting and merging requirements

Maintaining requirements is much simpler, when done automatically based on the .py files.

The actual requirements files is still constructed. Standard libraries are not added, others are added with their versions, if specified. Local files are also used as dependencies, from which imports are extracted as well.

For example:

import os
import pandas
import attr #>=22.2.0
from .components.local_dep import *

produces

pandas
attrs >=22.2.0
yaml

as requirements file, where yaml is extracted from local_dep.py file.

Checking dependecies for vulnerabilities is usefull and it is done with pip audit which is integrated into the paa package and is used by default.

Optional requirements for extras_require could be probided the same way normal requirements are, but each like that contains an import like that should be commented out in a special way, starting with #!, for example:

import os
import pandas
import attr #>=22.2.0
#! import hnswlib #==0.8.0

produces

pandas
attrs >=22.2.0
hnswlib==0.8.0; extra == "hnswlib"

Sometimes automatic translation of import names to install names via package_mapping.json, for packages where these names differ, may not be enough. A manual overwrite can be done with exlusion of some dependencies from automatic extraction pipeline with #- comment next to import and #@ prefix before text that is intended to end up in an equivalent requirements file, for example:

import os
import pandas
import attr #>=22.2.0
import tensorflow #-
#@ tensorflow-gpu

produces

pandas
attrs >=22.2.0
tensorflow-gpu

---

initialize RequirementsHandler

rh = RequirementsHandler(
    # optional/required later
    module_filepath = "../tests/package_auto_assembler/other/example_module.py",
    package_mappings = {'PIL': 'Pillow',
                        'bs4': 'beautifulsoup4',
                        'fitz': 'PyMuPDF',
                        'attr': 'attrs',
                        'dotenv': 'python-dotenv',
                        'googleapiclient': 'google-api-python-client',
                        'sentence_transformers': 'sentence-transformers',
                        'flask': 'Flask',
                        'stdlib_list': 'stdlib-list',
                        'sklearn': 'scikit-learn',
                        'yaml': 'pyyaml'},
    requirements_output_path = "../tests/package_auto_assembler/other/",
    output_requirements_prefix = "requirements_",
    custom_modules_filepath = "../tests/package_auto_assembler/dependancies",
    python_version = '3.8',
    add_header = True
)

list custom modules for a given directory

rh.list_custom_modules(
    # optional
    custom_modules_filepath="../tests/package_auto_assembler/dependancies"
)

['example_local_dependacy_1', 'example_local_dependacy_2']

check if module is a standard python library

rh.is_standard_library(
    # required
    module_name = 'example_local_dependacy_1',
    # optional
    python_version = '3.8'
)

False

rh.is_standard_library(
    # required
    module_name = 'logging',
    # optional
    python_version = '3.8'
)

True

extract requirements from the module file

rh.extract_requirements(
    # optional
    module_filepath = "../tests/package_auto_assembler/other/example_module.py",
    custom_modules = ['example_local_dependacy_2', 'example_local_dependacy_1'],
    package_mappings = {'PIL': 'Pillow',
                        'bs4': 'beautifulsoup4',
                        'fitz': 'PyMuPDF',
                        'attr': 'attrs',
                        'dotenv': 'python-dotenv',
                        'googleapiclient': 'google-api-python-client',
                        'sentence_transformers': 'sentence-transformers',
                        'flask': 'Flask',
                        'stdlib_list': 'stdlib-list',
                        'sklearn': 'scikit-learn',
                        'yaml': 'pyyaml'},
    python_version = '3.8',
    add_header=True
)

(['attrs>=22.2.0'],
 ['torch<=2.4.1', 'fastapi[all]', 'scikit-learn==1.5.1', 'numpy'])

rh.requirements_list

['attrs>=22.2.0']

rh.optional_requirements_list

['torch<=2.4.1', 'fastapi[all]', 'scikit-learn==1.5.1', 'numpy']

audit dependencies

rh.check_vulnerabilities(
    # optional if ran extract_requirements() before
    requirements_list = None,
    raise_error = True
)

No known vulnerabilities found

rh.vulnerabilities

[]

try:
    rh.check_vulnerabilities(
        # optional if ran extract_requirements() before
        requirements_list = ['attrs>=22.2.0', 'pandas', 'hnswlib==0.7.0'],
        raise_error = True
    )
except Exception as e:
    print(f"Error: {e}")

Found 1 known vulnerability in 1 package



Name    Version ID                  Fix Versions
------- ------- ------------------- ------------
hnswlib 0.7.0   GHSA-xwc8-rf6m-xr86

Error: Found vulnerabilities, resolve them or ignore check to move forwards!

rh.vulnerabilities

[{'name': 'hnswlib',
  'version': '0.7.0',
  'id': 'GHSA-xwc8-rf6m-xr86',
  'fix_versions': None}]

save requirements to a file

rh.write_requirements_file(
    # optional/required later
    module_name = 'example_module',
    requirements = ['### example_module.py', 'attrs>=22.2.0'],
    output_path = "../tests/package_auto_assembler/other/",
    prefix = "requirements_"
)

read requirements

rh.read_requirements_file(
    # required
    requirements_filepath = "../tests/package_auto_assembler/other/requirements_example_module.txt"
)

['attrs>=22.2.0']

4. Preparing metadata

Since all of the necessary information for building a package needs to be contained within main component .py file, basic metadata is provided with the use of __package_metadata__ dictionary object, defined within that .py file. It is also used as a trigger for package building within paa pipeline.

Even though some general information shared between packages could be provided through general config, but package specific info should be provided through __package_metadata__. It should support most text fields from setup file, but for others the following fields are available:

• classifiers: adds classifiers to the general ones from config, unless it's Development Status :: then module level definition will overwrite the one from config
• extras_require: a dictionary of optional package that wouldn't be installed during normal installation. The key could be used during installation and the value would be a list of dependencies.
• install_requires : adds requirements to the list read from imports

* Note that providing dependencies this way does not check them through pip-audit or translate them through package mapping

---

initializing MetadataHandler

mh = MetadataHandler(
    # optional/required later
    module_filepath = "../tests/package_auto_assembler/other/example_module.py"
)

check if metadata is available

mh.is_metadata_available(
    # optional
    module_filepath = "../tests/package_auto_assembler/other/example_module.py"
)

True

extract metadata from module

mh.get_package_metadata(
    # optional
    module_filepath = "../tests/package_auto_assembler/other/example_module.py"
)

{'author': 'Kyrylo Mordan',
 'author_email': 'parachute.repo@gmail.com',
 'version': '0.0.1',
 'description': 'A mock handler for simulating a vector database.',
 'keywords': ['python', 'vector database', 'similarity search']}

5. Merging local dependacies into single module

Package auto assembler creates single module packages, meaning that once package is built all of the object are imported from a single place. The packaging tool does allow for local dependecies which are .py files imported from specified dependencies directory and its subfolders. Packaging structure may look like the following:

packaging repo/
└src/
  ├ <package names>.py
  └ components
    ├local_dependecy.py
    └subdir_1
      └local_dependency_2.py 

During packaging process paa merges main module with its local dependies into a single file.

---

initializing LocalDependaciesHandler

ldh = LocalDependaciesHandler(
    # required
    main_module_filepath = "../tests/package_auto_assembler/other/example_module.py",
    dependencies_dir = "../tests/package_auto_assembler/dependancies/",
    # optional
    save_filepath = "./combined_example_module.py"
)

combine main module with dependacies

print(ldh.combine_modules(
    # optional
    main_module_filepath = "../tests/package_auto_assembler/other/example_module.py",
    dependencies_dir = "../tests/package_auto_assembler/dependancies/",
    add_empty_design_choices = False
)[0:1000])

"""
Mock Vector Db Handler

This class is a mock handler for simulating a vector database, designed primarily for testing and development scenarios.
It offers functionalities such as text embedding, hierarchical navigable small world (HNSW) search,
and basic data management within a simulated environment resembling a vector database.
"""

import logging
import json
import time
import attr #>=22.2.0
import sklearn

__design_choices__ = {}

@attr.s
class Shouter:

    """
    A class for managing and displaying formatted log messages.

    This class uses the logging module to create and manage a logger
    for displaying formatted messages. It provides a method to output
    various types of lines and headers, with customizable message and
    line lengths.
    """

    # Formatting settings
    dotline_length = attr.ib(default=50)

    # Logger settings
    logger = attr.ib(default=None)
    logger_name = attr.ib(default='Shouter')
    loggerLvl = attr.ib(default=logging.DEBUG)
    log

ldh.dependencies_names_list

['example_local_dependacy_2', 'example_local_dependacy_1', 'dep_from_bundle_1']

save combined module

ldh.save_combined_modules(
    # optional
    combined_module = ldh.combine_modules(),
    save_filepath = "./combined_example_module.py"
)

6. Prepare README

Package description is based on .ipynb with same name as the .py. By default it is converted to markdown as is, but there is also an option to execute it.

---

import logging
ldh = LongDocHandler(
    # optional/required later
    notebook_path = "../tests/package_auto_assembler/other/example_module.ipynb",
    markdown_filepath = "../example_module.md",
    timeout = 600,
    kernel_name = 'python3',
    # logger
    loggerLvl = logging.DEBUG
)

convert notebook to md without executing

ldh.convert_notebook_to_md(
    # optional
    notebook_path = "../tests/package_auto_assembler/other/example_module.ipynb",
    output_path = "../example_module.md"
)

Converted ../tests/package_auto_assembler/example_module.ipynb to ../example_module.md

convert notebook to md with executing

ldh.convert_and_execute_notebook_to_md(
    # optional
    notebook_path = "../tests/package_auto_assembler/other/example_module.ipynb",
    output_path = "../example_module.md",
    timeout = 600,
    kernel_name = 'python3'
)

Converted and executed ../tests/package_auto_assembler/example_module.ipynb to ../example_module.md

return long description

long_description = ldh.return_long_description(
    # optional
    markdown_filepath = "../example_module.md"
)

7. Assembling setup directory

Packages are created following rather simple sequence of steps. At some point of the process a temporary directory is created to store the following files:

• __init__.py is a simple import from a single module
• <package name>.py is a single module with all of the local dependecies
• cli.py is optional packaged cli tool
• routes.py is optional packaged file with fastapi routes
• streamlit.py is optional packaged streamlit app
• setup.py is a setup file for making a package
• README.md is a package description file based on .ipynb file
• LICENSE is optional license file
• MANIFEST.in is a list of additional files to be included with the package
• mkdocs is a folder with built mkdocs site based on optional extra_docs for the module, module docstring and README.md
• artifacts contains optional files that would be packaged with the module
• tests contains files needed to run tests with pytest
• .paa.tracking contains tracking files from .paa dir to make each release of the package independent of PPR that released it

---

initializing SetupDirHandler

sdh = SetupDirHandler(
    # required
    module_filepath = "../tests/package_auto_assembler/other/example_module.py",
    # optional/ required
    module_name = "example_module",
    metadata = {'author': 'Kyrylo Mordan',
                'version': '0.0.1',
                'description': 'Example module.',
                'long_description' : long_description,
                'keywords': ['python']},
    license_path = "../LICENSE",
    requirements = ['attrs>=22.2.0'],
    classifiers = ['Development Status :: 3 - Alpha',
                   'Intended Audience :: Developers',
                   'Intended Audience :: Science/Research',
                   'Programming Language :: Python :: 3',
                   'Programming Language :: Python :: 3.9',
                   'Programming Language :: Python :: 3.10',
                   'Programming Language :: Python :: 3.11',
                   'License :: OSI Approved :: MIT License',
                   'Topic :: Scientific/Engineering'],
    setup_directory = "./example_setup_dir"
)

create empty setup dir

sdh.flush_n_make_setup_dir(
    # optional
    setup_directory = "./example_setup_dir"
)

copy module to setup dir

sdh.copy_module_to_setup_dir(
    # optional
    module_filepath = "./combined_example_module.py",
    setup_directory = "./example_setup_dir"
)

copy license to setup dir

sdh.copy_module_to_setup_dir(
    # optional
    license_path = "../LICENSE",
    setup_directory = "./example_setup_dir"
)

create init file

sdh.create_init_file(
    # optional
    module_name = "example_module",
    setup_directory = "./example_setup_dir"
)

create setup file

sdh.write_setup_file(
    # optional
    module_name = "example_module",
    metadata = {'author': 'Kyrylo Mordan',
                'version': '0.0.1',
                'description': 'Example Module',
                'keywords': ['python']},
    requirements = ['attrs>=22.2.0'],
    classifiers = ['Development Status :: 3 - Alpha',
                   'Intended Audience :: Developers',
                   'Intended Audience :: Science/Research',
                   'Programming Language :: Python :: 3',
                   'Programming Language :: Python :: 3.9',
                   'Programming Language :: Python :: 3.10',
                   'Programming Language :: Python :: 3.11',
                   'License :: OSI Approved :: MIT License',
                   'Topic :: Scientific/Engineering'],
    setup_directory = "./example_setup_dir"
)

8. Creating release notes from commit messages

Package versioning could be enhanced with release notes. Since the tool is mainly meant for ci/cd, it takes advantage of commit messages to construct a release note for every version.

Commit history is analysed from the last merge, if nothiong found then the next and the next, until at least one of [<package name>] labels are found within commit messages. They are bundled together to for a note, where each commit message or messages deliminated with ; are turned in a list element. Previos notes are used to establish which part of commit history to use as a starting point.

Commit messages could also be used to increment version by something other then a default patch.

• [<package name>][..+] increments patch (default behavior)
• [<package name>][.+.] increments minor
• [<package name>][+..] increments major
• [<package name>][0.1.2] forces specific version 0.1.2

* First release within new packaging repo may struggle to extract release note since commit messages are only analysed from merges in the commit history.

---

rnh = ReleaseNotesHandler(
    # path to existing or new release notes file
    filepath = '../tests/package_auto_assembler/other/release_notes.md',
    # name of label in commit message [example_module] for filter
    label_name = 'example_module',
    # new version to be used in release notes
    version = '0.0.1'
)

No relevant commit messages found!
..trying depth 2 !
No relevant commit messages found!
No messages to clean were provided

overwritting commit messages from example

# commit messages from last merge
rnh.commit_messages

['fixing paa tests',
 'fixing paa tests',
 'fixing paa tests',
 '[package_auto_assembler] increasing default max search depth for commit history to 5',
 'fixing mocker-db release notes',
 'Update package version tracking files',
 'Update README',
 'Update requirements']

example_commit_messages = [
    '[example_module] usage example for initial release notes; bugfixes for RNH',
    '[BUGFIX] missing parameterframe usage example and reduntant png file',
    '[example_module][0.1.2] initial release notes handler',
    'Update README',
    'Update requirements'
]
rnh.commit_messages = example_commit_messages

internal methods that run on intialiazation of ReleaseNotesHandler

# get messages relevant only for label
rnh._filter_commit_messages_by_package()
print("Example filtered_messaged:")
print(rnh.filtered_messages)

# clean messages
rnh._clean_and_split_commit_messages()
print("Example processed_messages:")
print(rnh.processed_messages)

Example filtered_messaged:
['[example_module] usage example for initial release notes; bugfixes for RNH', '[example_module][0.1.2] initial release notes handler']
Example processed_messages:
['usage example for initial release notes', 'bugfixes for RNH', 'initial release notes handler']

get version update from relevant messages

version_update = rnh.extract_latest_version()
print(f"Example version_update: {version_update}")

Example version_update: 0.1.2

get latest version from relevant release notes

latest_version = rnh.extract_latest_version()
print(f"Example latest_version: {latest_version}")

Example latest_version: 0.1.2

augment existing release note with new entries or create new

# augment existing release note with new entries or create new
rnh.create_release_note_entry(
    # optional
    existing_contents=rnh.existing_contents,
    version=rnh.version,
    new_messages=rnh.processed_messages
)
print("Example processed_note_entries:")
print(rnh.processed_note_entries)

Example processed_note_entries:
['# Release notes\n', '\n', '### 0.1.2\n', '\n', '    - usage example for initial release notes\n', '\n', '    - bugfixes for RNH\n', '\n', '    - initial release notes handler\n', '\n', '### 0.0.1\n', '\n', '    - initial version of example_module\n']

saving updated relese notes

rnh.existing_contents

['# Release notes\n',
 '\n',
 '### 0.1.2\n',
 '\n',
 '    - usage example for initial release notes\n',
 '    - bugfixes for RNH\n',
 '    - initial release notes handler\n',
 '### 0.1.2\n',
 '\n',
 '    - usage example for initial release notes\n',
 '\n',
 '    - bugfixes for RNH\n',
 '\n',
 '    - initial release notes handler\n',
 '\n',
 '### 0.0.1\n',
 '\n',
 '    - initial version of example_module\n']

rnh.save_release_notes()

# updated content
rnh.get_release_notes_content()

['# Release notes\n',
 '\n',
 '### 0.1.2\n',
 '\n',
 '    - usage example for initial release notes\n',
 '\n',
 '    - bugfixes for RNH\n',
 '\n',
 '    - initial release notes handler\n',
 '\n',
 '### 0.0.1\n',
 '\n',
 '    - initial version of example_module\n']

9. Analysing package dependencies

Extracting info from installed dependencies can provide important insight into inner workings of a package and help avoid some of the licenses.

Licenses are extracted from package metadata and normalized for analysis. Missing labels are marked with - and not recognized licenses with unknown.

Information about unrecognized license labels could be provided through .paa/package_licenses json file that would contain install package name and corresponding license label.

---

da = DependenciesAnalyser(
    # optional
    package_name = 'mocker-db',
    package_licenses_filepath = '../tests/package_auto_assembler/other/package_licenses.json',
    allowed_licenses = ['mit', 'apache-2.0', 'lgpl-3.0', 'bsd-3-clause', 'bsd-2-clause', '-', 'mpl-2.0']
)

finding installed packages with a list of tags

da.filter_packages_by_tags(tags=['aa-paa-tool'])

[('comparisonframe', '0.0.0'),
 ('mocker-db', '0.0.1'),
 ('package-auto-assembler', '0.0.0'),
 ('proompter', '0.0.0')]

extracting some metadata from the installed package

package_metadata = da.get_package_metadata(
    package_name = 'mocker-db'
)
package_metadata

{'keywords': ['aa-paa-tool'],
 'version': '0.0.1',
 'author': 'Kyrylo Mordan',
 'author_email': 'parachute.repo@gmail.com',
 'classifiers': ['Development Status :: 3 - Alpha',
  'Intended Audience :: Developers',
  'Intended Audience :: Science/Research',
  'Programming Language :: Python :: 3',
  'Programming Language :: Python :: 3.9',
  'Programming Language :: Python :: 3.10',
  'Programming Language :: Python :: 3.11',
  'License :: OSI Approved :: MIT License',
  'Topic :: Scientific/Engineering',
  'PAA-Version :: 0.4.3',
  'PAA-CLI :: False'],
 'paa_version': '0.4.3',
 'paa_cli': 'False',
 'license_label': 'MIT'}

extracting package requirements

package_requirements = da.get_package_requirements(
    package_name = 'mocker-db'
)
package_requirements

['requests',
 'attrs >=22.2.0',
 'httpx',
 'hnswlib ==0.8.0',
 'gridlooper ==0.0.1',
 'dill ==0.3.7',
 'numpy ==1.26.0',
 "sentence-transformers ; extra == 'sentence_transformers'"]

extracting tree of dependencies

extracted_dependencies_tree = da.extract_dependencies_tree(
    package_name = 'mocker-db'
)
extracted_dependencies_tree

{'requests': {'charset-normalizer': [],
  'idna': [],
  'urllib3': [],
  'certifi': []},
 'attrs': {'importlib-metadata': {'zipp': [], 'typing-extensions': []}},
 'httpx': {'anyio': {'idna': [],
   'sniffio': [],
   'exceptiongroup': [],
   'typing-extensions': []},
  'certifi': [],
  'httpcore': {'certifi': [], 'h11': {'typing-extensions': []}},
  'idna': [],
  'sniffio': []},
 'hnswlib': {'numpy': []},
 'gridlooper': {'dill': [],
  'attrs': {'importlib-metadata': {'zipp': [], 'typing-extensions': []}},
  'tqdm': {'colorama': []}},
 'dill': [],
 'numpy': []}

addding license labels to tree of dependencies

extracted_dependencies_tree_license = da.add_license_labels_to_dep_tree(
    dependencies_tree = extracted_dependencies_tree
)
extracted_dependencies_tree_license

{'requests': 'apache-2.0',
 'requests.charset-normalizer': '-',
 'requests.idna': '-',
 'requests.urllib3': '-',
 'requests.certifi': 'mpl-2.0',
 'attrs': '-',
 'attrs.importlib-metadata': '-',
 'attrs.importlib-metadata.zipp': '-',
 'attrs.importlib-metadata.typing-extensions': '-',
 'httpx': '-',
 'httpx.anyio': 'mit',
 'httpx.anyio.idna': '-',
 'httpx.anyio.sniffio': '-',
 'httpx.anyio.exceptiongroup': '-',
 'httpx.anyio.typing-extensions': '-',
 'httpx.certifi': 'mpl-2.0',
 'httpx.httpcore': '-',
 'httpx.httpcore.certifi': 'mpl-2.0',
 'httpx.httpcore.h11': 'mit',
 'httpx.httpcore.h11.typing-extensions': '-',
 'httpx.idna': '-',
 'httpx.sniffio': '-',
 'hnswlib': '-',
 'hnswlib.numpy': 'bsd-3-clause',
 'gridlooper': '-',
 'gridlooper.dill': 'bsd-3-clause',
 'gridlooper.attrs': '-',
 'gridlooper.attrs.importlib-metadata': '-',
 'gridlooper.attrs.importlib-metadata.zipp': '-',
 'gridlooper.attrs.importlib-metadata.typing-extensions': '-',
 'gridlooper.tqdm': '-',
 'gridlooper.tqdm.colorama': '-',
 'dill': 'bsd-3-clause',
 'numpy': 'bsd-3-clause'}

printing extracted tree of dependencies

da.print_flattened_tree(extracted_dependencies_tree_license)

└── requests : apache-2.0
    ├── charset-normalizer : -
    ├── idna : -
    ├── urllib3 : -
    └── certifi : mpl-2.0
└── attrs : -
    └── importlib-metadata : -
        ├── zipp : -
        └── typing-extensions : -
└── httpx : -
    ├── anyio : mit
        ├── idna : -
        ├── sniffio : -
        ├── exceptiongroup : -
        └── typing-extensions : -
    ├── certifi : mpl-2.0
    ├── httpcore : -
        ├── certifi : mpl-2.0
        └── h11 : mit
            └── typing-extensions : -
    ├── idna : -
    └── sniffio : -
└── hnswlib : -
    └── numpy : bsd-3-clause
└── gridlooper : -
    ├── dill : bsd-3-clause
    ├── attrs : -
        └── importlib-metadata : -
            ├── zipp : -
            └── typing-extensions : -
    └── tqdm : -
        └── colorama : -
└── dill : bsd-3-clause
└── numpy : bsd-3-clause

filtering for unexpected licenses in tree of dependencies

allowed_licenses = ['mit', 'apache-2.0', 'lgpl-3.0', 'mpl-2.0', '-']

da.find_unexpected_licenses_in_deps_tree(
    tree_dep_license = extracted_dependencies_tree_license,
    # optional
    allowed_licenses = allowed_licenses,
    raise_error = True
)

{'hnswlib': '', 'gridlooper': ''}
└── dill : bsd-3-clause
└── numpy : bsd-3-clause
└── hnswlib : 
    └── numpy : bsd-3-clause
└── gridlooper : 
    └── dill : bsd-3-clause



---------------------------------------------------------------------------

Exception                                 Traceback (most recent call last)

Cell In[9], line 3
      1 allowed_licenses = ['mit', 'apache-2.0', 'lgpl-3.0', 'mpl-2.0', '-']
----> 3 da.find_unexpected_licenses_in_deps_tree(
      4     tree_dep_license = extracted_dependencies_tree_license,
      5     # optional
      6     allowed_licenses = allowed_licenses,
      7     raise_error = True
      8 )


File ~/miniforge3/envs/testenv/lib/python3.10/site-packages/package_auto_assembler/package_auto_assembler.py:2670, in DependenciesAnalyser.find_unexpected_licenses_in_deps_tree(self, tree_dep_license, allowed_licenses, raise_error)
   2668 if raise_error and out != {}:
   2669     self.print_flattened_tree(flattened_dict = out)
-> 2670     raise Exception("Found unexpected licenses!")
   2671 else:
   2672     self.logger.info("No unexpected licenses found")


Exception: Found unexpected licenses!

10. Adding cli interfaces

The tool allows to make a package with optional cli interfaces. These could be sometimes preferable when a package contains a standalone tool that would be called from script anyway.

All of the cli logic would need to be included within a .py file which should be stored within cli_dir provided in .paa.config. Dependencies from these files are extracted in the similar manner to the main module.

Tools from main .py file could still be imported like the following:

from package_name.package_name import ToBeImported

The code is wired in setup.py via the following automatically assuming that appropriate file with the same name as the package exists within cli_dir location.

...,
entry_points = {'console_scripts': [
    '<package_alias> = package_name.cli:cli']} ,
...

Alias for name could be provided via the following piece of code, defined after imports, otherwise package name would be used.

__cli_metadata__ = {
    "name" : <package_alias>
}

Package-auto-assembler tool itself uses click dependency to build that file, use its cli definition as example.

11. Adding routes and running FastAPI application

The tool allows to make a package with optional routes for FastAPI application and run them. Each packages can have one routes file where its logic should be defined. Package-auto-assembler itself can combine multiple routes from packages and filepaths into one application.

A .py file with the same name of the package should be stored within api_routes_dir provided in .paa.config.

Dependencies from these files are extracted in the similar manner to the main module.

Tools from main .py file could still be imported like the following:

from package_name.package_name import ToBeImported

Api description, middleware and run parameters could be provided via optional .paa.api.config file, which for example would look like:

DESCRIPTION : {
    'version' : 0.0.0
}
MIDDLEWARE : {
    allow_origins : ['*']
}
RUN : {
 host : 0.0.0.0
}

where DESCRIPTION contains parameters for FastAPI, MIDDLEWARE for CORSMiddleware and RUN for uvicorn.run

12. Adding ui and running streamlit application

The tools allows to make a package with optional streamlit application as interface to the packaged code. Each package can have one streamlit file. Package-auto-assembler itself would then be used to run packaged applications from the package.

A .py file with the same name of the package should be stored within streamlit_dir provided in .paa.config.

Dependencies from these files are extracted in the similar manner to the main module.

Tools from main .py file could still be imported like the following:

from package_name import ToBeImported

Config file with server, theme and other settings can be provided via optional .paa.streamlit.config.

13 Adding artifacts to packages

The tool allows to add files to packages that could be accessed from the package or extracted into selected directory.

There are different types of artifacts with a package like this:

• .paa.tracking : includes some tracking files for the purposes of the tool, added to every package
• mkdocs : optional static mkdocs site
• artifacts contains directories, files and links to files copied from artifacts_dir/<package_name> (from .paa.config)
• tests contains optional directory with tests with pytest, copied from tests_dir/<package_name> (from .paa.config)

1. Description of default tracking files

Tracking files are added automatically of artifacts adding was not turned off. At the moment contains:

• .paa.config : config file that specifies how paa show work
• .paa.version: version of package-auto-assembler that was used for packaging
• release_notes.md : latest release notes for the package
• version_logs.csv : logs for version updates for all packages in the packaging repo
• lsts_package_versions.yml : latests versions of all packages in the packaging repo
• package_mapping.json : additional user-provided remapping of package import names to install names
• package_licenses.json : additional user-provided license labels to overwrite detected ones
• notebook.ipynb : optional jupyter notebook that was used for package description`

2. Adding files

User provided artifacts could be provided in two ways:

1. adding directory, file or link to the file under artifacts_dir/<package_name>

   These files would be packaged with the packages, and files from links would be downloaded and packaged as well. To add a link, create a file with .link extension in the name.

2. adding artifact_urls dictionary to __package_metadata__ within module .py file

Example of __package_metadata__ with these additional dictionary would be:

__package_metadata__ = {
    ...,
    "artifact_urls" : {
        'downloaded.md' : 'https://raw.githubusercontent.com/Kiril-Mordan/reusables/refs/heads/main/docs/module_from_raw_file.md',
        'downloaded.png' : 'https://raw.githubusercontent.com/Kiril-Mordan/reusables/refs/heads/main/docs/reuse_logo.png'
    }
}

where key would contain name of the artifact and value its link.

These files would not be downloaded and only links would be packaged. After package installation both kinds of links could be refreshed/donwloaded using cli interface from package-auto-assembler.

3. Accessing packaged artifacts

Artifacts packaged within the package could be accessed in two ways:

1. using package-auto-assembler cli tools to copy a file or files into a selected directory

2. reading packaged artifacts from the package, by the use of similar code that finds path to installed package in your system:

import importlib
import importlib.metadata
import importlib.resources as pkg_resources

installed_package_path = pkg_resources.files('<package_name>')

file_name_path = None
if 'artifacts' in os.listdir(installed_package_path):

    with pkg_resources.path('<package_name>.artifacts', '<file_name>') as path:
        file_name_path = path

14. Preparing module for packaging

1. Preparing code for packaging

To add/edit a python package with package-auto-assembler, its building blocks would need to follow requirements mentioned below.

Note: For basic package only main module would be required. More about role of optional files could be seen here.

• Main module [required]

  Main module is considered to be a <package_name>.py file stored in module_dir (from .paa.config), which can also me called packaging layer. This is where most code of the package would be, unless local dependencies are used.

  Requirements to this file:

  1. starts with module docstring (will be used in package description)
  2. contains __package_metadata__ (a way to provide package metadata)
  3. [optional] import from local dependencies stored only in dependencies_dir
  4. [optional] contains versions of module dependencies (specifying requirements)

• Local dependencies

  Local dependencies are optional modules that other modules from packaging layer would import from, and are not packaged on their own. These are useful for segmenting codebase into smaller independent components. They would be stored in subdirectory of module_dir, specified as dependencies_dir in .paa.config.

  Requirements for these files:

  1. stored only in dependencies_dir or its subdirectories
  2. do not import any other moduled stored locally
  3. [optional] contain versions of module dependencies (specifying requirements)

• Cli interface

  Command line interface could be optionally defined for a package by placing <package_name>.py file into cli_dir (from .paa.config). More about adding cli could be found here.

  Requirements for this file:

  1. imports and uses click to define cli tools
  2. contains __cli_metadata__ (a way to provide alias for cli tools)
  3. [optional] imports from packaging layer and local dependencies only with from <package_name>.<package_name> import ToBeImported
  4. [optional] contains versions of module dependencies (specifying requirements)

• API routes

  Routes for FastAPI application could be optionally defined for a package by placing <package_name>.py file into api_routes_dir (from .paa.config). More about adding api routes could be found here.

  Requirements for this file:

  1. imports from fastapi import APIRouter
  2. defines router = APIRouter(prefix = "/<package-name>")
  3. uses @router.* to define endpoints
  4. [optional] import from packaging layer and local dependencies only with from <package_name>.<package_name> import ToBeImported
  5. [optional] contain versions of module dependencies (specifying requirements)

• Streamlit app

  Streamlit application could be optionally defined for a package by placing <package_name>.py file into streamlit_dir (from .paa.config). More about adding streamlit app could be found here.

  Requirements for this file:

  1. imports streamlit
  2. [optional] import from packaging layer and local dependencies only with from <package_name>.<package_name> import ToBeImported
  3. [optional] contain versions of module dependencies (specifying requirements)

2. Preparing documentation for packaging

• Package description

  Providing package description is a useful way to show what the package is about to the intended audience. By default, main_module docstring would be used for this purpose and stored alongside the package in a README.md file, as shown here.

  Optionally, one could provide additional information that would be appended to the package docstring via <package_name>.ipynb file, placed into example_notebooks_path (from .paa.config). In the early stages of development, this file could both serve as a place where code is developed/tested before a release and a way to show usage examples.

• Additional documentation

  Package description may not be enough to store documentation. A simple mkdocs static site is built by default for every package with for followig tabs:

  • intro contains module docstring and pypi link for github + pypi type of packaging repository
  • description contains optional content from <package_name>.ipynb file, placed into example_notebooks_path (from .paa.config)
  • release notes contains release notes assembled based on commit messages

  Additional documentation can be provided via the following files:

  1. <package_name>.drawio file, placed into drawio_dir (from .paa.config). Each tab would be turned into <package_name>-<tab_name>.png, which if not referenced would be presented as a separate tab;
  2. .png, .ipynb or .md files placed in extra_docs_dir/<package_name> (from .paa.config). Each file would be turned into a separate tab, but just like .png from drawio, if referenced, would not be presented as a separate tab.

  Note: During packaging process files derived from <package_name>.drawio conversion and files from extra_docs_dir/<package_name> would both be placed into .paa/docs with <package_name>-* prefix. Make sure not to name drawio tabs and extra docs with the same names.

3. Preparing files for packaging

Packaging files alongside code and documentation could be achieved by placing files into artifacts_dir/<package_name> directory (from .paa.config). These files could be referenced from within the package and there is an option to provide links instead of physical files. More about adding artifacts to the package could be found here.

Tests that would be used in ci/cd pipeline are expected to be placed into tests_dir<package_name> directory (from .paa.config). These would be copied into the package as well.

15. Making a package

Main wrapper for the package integrates described above components into a class that could be used to build package building pipelines within python scripts.

To simplify usage cli interface is recomended instead.

---

initializing PackageAutoAssembler

paa = PackageAutoAssembler(
    # required
    module_name = "example_module",
    module_filepath  = "../tests/package_auto_assembler/other/example_module.py",
    # optional
    mapping_filepath = "../env_spec/package_mapping.json",
    licenses_filepath = "../tests/package_auto_assembler/other/package_licenses.json",
    allowed_licenses = ['mit', 'apache-2.0', 'lgpl-3.0', 'mpl-2.0', '-'],
    dependencies_dir = "../tests/package_auto_assembler/dependancies/",
    example_notebook_path = "./mock_vector_database.ipynb",
    versions_filepath = '../tests/package_auto_assembler/other/lsts_package_versions.yml',
    log_filepath = '../tests/package_auto_assembler/other/version_logs.csv',
    setup_directory = "./example_module",
    release_notes_filepath = "../tests/package_auto_assembler/other/release_notes.md",
    license_path = "../LICENSE",
    license_label = "mit",
    classifiers = ['Development Status :: 3 - Alpha',
                    'Intended Audience :: Developers',
                    'Intended Audience :: Science/Research',
                    'Programming Language :: Python :: 3',
                    'Programming Language :: Python :: 3.9',
                    'Programming Language :: Python :: 3.10',
                    'Programming Language :: Python :: 3.11',
                    'License :: OSI Approved :: MIT License',
                    'Topic :: Scientific/Engineering'],
    requirements_list = [],
    execute_readme_notebook = True,
    python_version = "3.8",
    version_increment_type = "patch",
    default_version = "0.0.1",
    check_vulnerabilities = True,
    check_dependencies_licenses = False,
    add_requirements_header = True
)

add metadata from module

paa.add_metadata_from_module(
    # optional
    module_filepath  = "../tests/package_auto_assembler/other/example_module.py"
)

Adding metadata ...

add or update version

paa.add_or_update_version(
    # overwrites auto mode (not suggested)
    version_increment_type = "patch",
    version = "1.2.6",
    # optional
    module_name = "example_module",
    versions_filepath = '../tests/package_auto_assembler/lsts_package_versions.yml',
    log_filepath = '../tests/package_auto_assembler/version_logs.csv'
)

Incrementing version ...
No relevant commit messages found!
..trying depth 2 !
No relevant commit messages found!
..trying depth 3 !
No relevant commit messages found!
..trying depth 4 !
No relevant commit messages found!
..trying depth 5 !
No relevant commit messages found!
No messages to clean were provided

add release notes from commit messages

paa.add_or_update_release_notes(
    # optional
    filepath="../tests/package_auto_assembler/release_notes.md",
    version=paa.metadata['version']
)

Updating release notes ...

prepare setup directory

paa.prep_setup_dir()

Preparing setup directory ...

merge local dependacies

paa.merge_local_dependacies(
    # optional
    main_module_filepath = "../tests/package_auto_assembler/other/example_module.py",
    dependencies_dir= "../tests/package_auto_assembler/dependancies/",
    save_filepath = "./example_module/example_module.py"
)

Merging ../tests/package_auto_assembler/other/example_module.py with dependecies from ../tests/package_auto_assembler/dependancies/ into ./example_module/example_module.py

add requirements from module

paa.add_requirements_from_module(
    # optional
    module_filepath = "../tests/package_auto_assembler/other/example_module.py",
    import_mappings = {'PIL': 'Pillow',
                        'bs4': 'beautifulsoup4',
                        'fitz': 'PyMuPDF',
                        'attr': 'attrs',
                        'dotenv': 'python-dotenv',
                        'googleapiclient': 'google-api-python-client',
                        'sentence_transformers': 'sentence-transformers',
                        'flask': 'Flask',
                        'stdlib_list': 'stdlib-list',
                        'sklearn': 'scikit-learn',
                        'yaml': 'pyyaml',
                        'git' : 'gitpython'}
)

Adding requirements from ../tests/package_auto_assembler/other/example_module.py
No known vulnerabilities found

paa.requirements_list

['### example_module.py', 'attrs>=22.2.0']

make README out of example notebook

paa.add_readme(
    # optional
    example_notebook_path = "../tests/package_auto_assembler/other/example_module.ipynb",
    output_path = "./example_module/README.md",
    execute_notebook=False,
)

Adding README from ../tests/package_auto_assembler/other/example_module.ipynb to ./example_module/README.md

prepare setup file

paa.prep_setup_file(
    # optional
    metadata = {'author': 'Kyrylo Mordan',
                'version': '0.0.1',
                'description': 'Example module',
                'keywords': ['python'],
                'license' : 'mit'},
    requirements = ['### example_module.py',
                    'attrs>=22.2.0'],
    classifiers = ['Development Status :: 3 - Alpha',
                    'Intended Audience :: Developers',
                    'Intended Audience :: Science/Research',
                    'Programming Language :: Python :: 3',
                    'Programming Language :: Python :: 3.9',
                    'Programming Language :: Python :: 3.10',
                    'Programming Language :: Python :: 3.11',
                    'License :: OSI Approved :: MIT License',
                    'Topic :: Scientific/Engineering'],
    cli_module_filepath = "../tests/package_auto_assembler/other/cli.py"

)

Preparing setup file for example-module package ...

make package

paa.make_package(
    # optional
    setup_directory = "./example_module"
)

Making package from ./example_module ...





CompletedProcess(args=['python', './example_module/setup.py', 'sdist', 'bdist_wheel'], returncode=0, stdout="running sdist\nrunning egg_info\nwriting example_module.egg-info/PKG-INFO\nwriting dependency_links to example_module.egg-info/dependency_links.txt\nwriting entry points to example_module.egg-info/entry_points.txt\nwriting requirements to example_module.egg-info/requires.txt\nwriting top-level names to example_module.egg-info/top_level.txt\nreading manifest file 'example_module.egg-info/SOURCES.txt'\nwriting manifest file 'example_module.egg-info/SOURCES.txt'\nrunning check\ncreating example_module-0.0.0\ncreating example_module-0.0.0/example_module\ncreating example_module-0.0.0/example_module.egg-info\ncopying files to example_module-0.0.0...\ncopying example_module/__init__.py -> example_module-0.0.0/example_module\ncopying example_module/cli.py -> example_module-0.0.0/example_module\ncopying example_module/example_module.py -> example_module-0.0.0/example_module\ncopying example_module/setup.py -> example_module-0.0.0/example_module\ncopying example_module.egg-info/PKG-INFO -> example_module-0.0.0/example_module.egg-info\ncopying example_module.egg-info/SOURCES.txt -> example_module-0.0.0/example_module.egg-info\ncopying example_module.egg-info/dependency_links.txt -> example_module-0.0.0/example_module.egg-info\ncopying example_module.egg-info/entry_points.txt -> example_module-0.0.0/example_module.egg-info\ncopying example_module.egg-info/requires.txt -> example_module-0.0.0/example_module.egg-info\ncopying example_module.egg-info/top_level.txt -> example_module-0.0.0/example_module.egg-info\ncopying example_module.egg-info/SOURCES.txt -> example_module-0.0.0/example_module.egg-info\nWriting example_module-0.0.0/setup.cfg\nCreating tar archive\nremoving 'example_module-0.0.0' (and everything under it)\nrunning bdist_wheel\nrunning build\nrunning build_py\ncopying example_module/example_module.py -> build/lib/example_module\ncopying example_module/__init__.py -> build/lib/example_module\ncopying example_module/setup.py -> build/lib/example_module\ncopying example_module/cli.py -> build/lib/example_module\ninstalling to build/bdist.linux-x86_64/wheel\nrunning install\nrunning install_lib\ncreating build/bdist.linux-x86_64/wheel\ncreating build/bdist.linux-x86_64/wheel/example_module\ncopying build/lib/example_module/example_module.py -> build/bdist.linux-x86_64/wheel/example_module\ncopying build/lib/example_module/__init__.py -> build/bdist.linux-x86_64/wheel/example_module\ncopying build/lib/example_module/setup.py -> build/bdist.linux-x86_64/wheel/example_module\ncopying build/lib/example_module/cli.py -> build/bdist.linux-x86_64/wheel/example_module\nrunning install_egg_info\nCopying example_module.egg-info to build/bdist.linux-x86_64/wheel/example_module-0.0.0-py3.10.egg-info\nrunning install_scripts\ncreating build/bdist.linux-x86_64/wheel/example_module-0.0.0.dist-info/WHEEL\ncreating 'dist/example_module-0.0.0-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it\nadding 'example_module/__init__.py'\nadding 'example_module/cli.py'\nadding 'example_module/example_module.py'\nadding 'example_module/setup.py'\nadding 'example_module-0.0.0.dist-info/METADATA'\nadding 'example_module-0.0.0.dist-info/WHEEL'\nadding 'example_module-0.0.0.dist-info/entry_points.txt'\nadding 'example_module-0.0.0.dist-info/top_level.txt'\nadding 'example_module-0.0.0.dist-info/RECORD'\nremoving build/bdist.linux-x86_64/wheel\n", stderr='warning: sdist: standard file not found: should have one of README, README.rst, README.txt, README.md\n\n/home/kyriosskia/miniconda3/envs/testenv/lib/python3.10/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.\n!!\n\n        ********************************************************************************\n        Please avoid running ``setup.py`` directly.\n        Instead, use pypa/build, pypa/installer or other\n        standards-based tools.\n\n        See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.\n        ********************************************************************************\n\n!!\n  self.initialize_options()\n')

16. Making simple MkDocs site

Package documentation can be presented in a form of mkdocs static site, which could be either served or deployed to something like github packages.

Main module docstring is used as intro package that contains something like optional pypi and license badges. Package description and realease notes are turned into separate tabs. Png with diagrams for example could be provided and displayed as their own separate tabs as well.

The one for this package can be seen here

It can be packaged with the package and be displayed in web browser like documentation for api via <package-name>\docs when using included api handling capabilities.

---

1. Preparing inputs

package_name = "example_module"

module_content = LongDocHandler().read_module_content(filepath=f"../tests/package_auto_assembler/{package_name}.py")

docstring = LongDocHandler().extract_module_docstring(module_content=module_content)
pypi_link = LongDocHandler().get_pypi_badge(module_name=package_name)


docs_file_paths = {
    "../example_module.md" : "usage-examples.md",
    '../tests/package_auto_assembler/release_notes.md' : 'release_notes.md'
}

mdh = MkDocsHandler(
    # required
    ## name of the package to be displayed
    package_name = package_name,
    ## dictionary of markdown files, with path as keys
    docs_file_paths = docs_file_paths,
    # optional
    ## module docstring to be displayed in the index
    module_docstring = docstring,
    ## pypi badge to be displayed in the index
    pypi_badge = pypi_link,
    ## license badge to be displayed in the index
    license_badge="[![License](https://img.shields.io/github/license/Kiril-Mordan/reusables)](https://github.com/Kiril-Mordan/reusables/blob/main/LICENSE)",
    ## name of the project directory
    project_name = "temp_project")

2. Preparing site

mdh.create_mkdocs_dir()
mdh.move_files_to_docs()
mdh.generate_markdown_for_images()
mdh.create_index()
mdh.create_mkdocs_yml()
mdh.build_mkdocs_site()

Created new MkDocs dir: temp_project
Copied ../example_module.md to temp_project/docs/usage-examples.md
Copied ../tests/package_auto_assembler/release_notes.md to temp_project/docs/release_notes.md
index.md has been created with site_name: example-module
mkdocs.yml has been created with site_name: Example module
Custom CSS created at temp_project/docs/css/extra.css


INFO    -  Cleaning site directory
INFO    -  Building documentation to directory: /home/kyriosskia/Documents/nlp/reusables/example_notebooks/temp_project/site
INFO    -  Documentation built in 0.12 seconds

3. Test-running site

mdh.serve_mkdocs_site()