Initial commit transfering files over from original automlst.engine project

.devcontainer/devcontainer.json

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+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/python
+{
+	"name": "Python 3",
+	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
+	"image": "mcr.microsoft.com/devcontainers/python:1-3.12-bullseye",
+
+	// Features to add to the dev container. More info: https://containers.dev/features.
+	// "features": {},
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Use 'postCreateCommand' to run commands after the container is created.
+	"postCreateCommand": "pip3 install --user -r requirements.txt && pip3 install -e .",
+	"customizations": {
+		"vscode": {
+			"extensions": [
+				"mechatroner.rainbow-csv"
+			]
+		}
+	},
+	// Configure tool-specific properties.
+	// "customizations": {},
+
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+	// "remoteUser": "root"
+
+	"containerEnv": {
+		"PIP_EXTRA_INDEX_URL": "https://git.reslate.systems/api/packages/ydeng/pypi/simple"
+	}
+}

.gitignore

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+# File created using '.gitignore Generator' for Visual Studio Code: https://bit.ly/vscode-gig
+# Created by https://www.toptal.com/developers/gitignore/api/visualstudiocode,linux,python
+# Edit at https://www.toptal.com/developers/gitignore?templates=visualstudiocode,linux,python
+
+### Linux ###
+*~
+
+# temporary files which can be created if a process still has a handle open of a deleted file
+.fuse_hidden*
+
+# KDE directory preferences
+.directory
+
+# Linux trash folder which might appear on any partition or disk
+.Trash-*
+
+# .nfs files are created when an open file is removed but is still being accessed
+.nfs*
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+### Python Patch ###
+# Poetry local configuration file - https://python-poetry.org/docs/configuration/#local-configuration
+poetry.toml
+
+# ruff
+.ruff_cache/
+
+# LSP config files
+pyrightconfig.json
+
+### VisualStudioCode ###
+.vscode/*
+!.vscode/settings.json
+!.vscode/tasks.json
+!.vscode/launch.json
+!.vscode/extensions.json
+!.vscode/*.code-snippets
+
+# Local History for Visual Studio Code
+.history/
+
+# Built Visual Studio Code Extensions
+*.vsix
+
+### VisualStudioCode Patch ###
+# Ignore all local history of files
+.history
+.ionide
+
+# End of https://www.toptal.com/developers/gitignore/api/visualstudiocode,linux,python
+
+# Custom rules (everything added below won't be overriden by 'Generate .gitignore File' if you use 'Update' option)
+

.vscode/settings.json

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+{
+    "python.analysis.autoImportCompletions": true
+}

Jenkinsfile

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+pipeline {
+    agent {
+        kubernetes {
+            cloud 'rsys-devel'
+            defaultContainer 'pip'
+            inheritFrom 'pip'
+        }
+    }
+    stages {
+        stage("install") {
+            steps {
+                sh 'python -m pip install -r requirements.txt'
+            }
+        }
+        stage("unit tests") {
+            steps {
+                sh returnStatus: true, script: "python -m pytest --junitxml=test_results.xml --cov=src --cov-report xml:coverage.xml"
+                xunit checksName: '', tools: [JUnit(excludesPattern: '', pattern: 'test_results.xml', stopProcessingIfError: true)]
+                recordCoverage(tools: [[parser: 'COBERTURA', pattern: 'coverage.xml']])
+            }
+        }
+        stage("build") {
+            steps {
+                sh "python -m build"
+            }
+        }
+        stage("archive") {
+            steps {
+                archiveArtifacts artifacts: 'dist/*.tar.gz, dist/*.whl', fingerprint: true, followSymlinks: false, onlyIfSuccessful: true
+            }
+        }
+        stage("publish") {
+            environment {
+                CREDS = credentials('4d6f64be-d26d-4f95-8de3-b6a9b0beb311')
+            }
+            steps {
+                sh returnStatus: true, script: 'python -m twine upload --repository-url https://git.reslate.systems/api/packages/${CREDS_USR}/pypi -u ${CREDS_USR} -p ${CREDS_PSW} --non-interactive --disable-progress-bar --verbose dist/*'
+            }
+        }
+    }
+}

pyproject.toml

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+[build-system]
+requires = ["setuptools>=64", "setuptools_scm>=8"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "automlst.cli"
+dynamic = ["version"]
+
+dependencies = [
+    "automlst-engine"
+]
+requires-python = ">=3.11"
+description = "A CLI tool to rapidly fetch fetch MLST profiles given sequences for various diseases."
+
+[project.scripts]
+automlst = "automlst.cli.program:run"
+
+[tool.setuptools_scm]
+
+[tool.pyright]
+extraPaths = ["src"]
+exclude = [
+    "**/node_modules",
+    "**/__pycache__"
+]
+executionEnvironments = [
+    {root = "src"}
+]
+
+[tool.setuptools]
+package-dir = {"" = "src"}
+
+[tool.pytest.ini_options]
+testpaths = [
+    "tests"
+]
+pythonpath = [
+    "src"
+]
+addopts = [
+    "--import-mode=importlib",
+]
+asyncio_mode = "auto"
+
+[tool.pylint.main]
+source-roots = "src"
+
+[tool.pylint.format]
+# Maximum number of characters on a single line.
+max-line-length = 88
+

requirements.txt

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+pytest
+pytest-asyncio
+pytest-cov
+build
+twine
+setuptools_scm
+automlst-engine

src/automlst/cli/info.py

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+from argparse import ArgumentParser
+import asyncio
+from automlst.engine.remote.databases.bigsdb import BIGSdbIndex
+
+def setup_parser(parser: ArgumentParser):
+    parser.description = "Fetches the latest BIGSdb MLST database definitions."
+    parser.add_argument(
+        "--retrieve-bigsdbs", "-l",
+        action="store_true",
+        dest="list_dbs",
+        required=False,
+        default=False,
+        help="Lists all known BIGSdb MLST databases (fetched from known APIs and cached)."
+    )
+
+    parser.add_argument(
+        "--retrieve-bigsdb-schemas", "-lschemas",
+        nargs="+",
+        action="extend",
+        dest="list_bigsdb_schemas",
+        required=False,
+        default=[],
+        type=str,
+        help="Lists the known schema IDs for a given BIGSdb sequence definition database name. The name, and then the ID of the schema is given."
+    )
+
+    parser.set_defaults(func=run_asynchronously)
+
+async def run(args):
+    async with BIGSdbIndex() as bigsdb_index:
+        if args.list_dbs:
+            known_seqdef_dbs = await bigsdb_index.get_known_seqdef_dbs(force=False)
+            print("\n".join(known_seqdef_dbs.keys()))
+
+        for bigsdb_schema_name in args.list_bigsdb_schemas:
+            schemas = await bigsdb_index.get_schemas_for_seqdefdb(bigsdb_schema_name)
+            for schema_desc, schema_id in schemas.items():
+                print(f"{schema_desc}: {schema_id}")
+
+def run_asynchronously(args):
+    asyncio.run(run(args))
+

src/automlst/cli/meta.py

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+def get_module_base_name(name):
+    return name.split(".")[-1]

src/automlst/cli/program.py

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+import argparse
+import asyncio
+import datetime
+from os import path
+import os
+
+from automlst.cli import info, st
+from automlst.cli.meta import get_module_base_name
+from automlst.engine.data.genomics import NamedString
+from automlst.engine.local.abif import read_abif
+from automlst.engine.local.csv import write_mlst_profiles_as_csv
+from automlst.engine.local.fasta import read_fasta
+from automlst.engine.remote.databases.bigsdb import BIGSdbIndex
+
+root_parser = argparse.ArgumentParser()
+subparsers = root_parser.add_subparsers(required=True)
+
+info.setup_parser(subparsers.add_parser(get_module_base_name(info.__name__)))
+st.setup_parser(subparsers.add_parser(get_module_base_name(st.__name__)))
+
+
+def run():
+    args = root_parser.parse_args()
+    args.func(args)
+
+if __name__ == "__main__":
+    run()

src/automlst/cli/st.py

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+
+from argparse import ArgumentParser
+import asyncio
+import datetime
+from automlst.engine.local.csv import write_mlst_profiles_as_csv
+from automlst.engine.local.fasta import read_multiple_fastas
+from automlst.engine.remote.databases.bigsdb import BIGSdbIndex
+
+
+def setup_parser(parser: ArgumentParser):
+    parser.description = "Returns MLST exact profile matches."
+    parser.add_argument(
+        "fastas",
+        nargs="+",
+        action='extend',
+        default=[],
+        type=str,
+        help="The FASTA files to process. Multiple can be listed."
+    )
+
+    parser.add_argument(
+        "seqdefdb",
+        help="The BIGSdb seqdef database to use for typing."
+    )
+
+    parser.add_argument(
+        "schema",
+        type=int,
+        help="The BIGSdb seqdef database schema ID (integer) to use for typing."
+    )
+
+    parser.add_argument(
+        "out",
+        default=f'./{datetime.datetime.now().strftime(r"%Y%m%d%H%M%S")}',
+        help="The output CSV name (.csv will be appended)."
+    )
+
+    parser.add_argument(
+        "--exact", "-ex",
+        action="store_true",
+        dest="exact",
+        required=False,
+        default=False,
+        help="Should run exact matching rather than returning all similar ones"
+    )
+
+    parser.add_argument(
+        "--stop-on-fail", "-sof",
+        action="store_true",
+        dest="stop_on_fail",
+        required=False,
+        default=False,
+        help="Should the algorithm stop in the case there are no matches (or partial matches when expecting exact matches)."
+    )
+    parser.set_defaults(func=run_asynchronously)
+
+async def run(args):
+    async with BIGSdbIndex() as bigsdb_index:
+        gen_strings = read_multiple_fastas(args.fastas)
+        async with await bigsdb_index.build_profiler_from_seqdefdb(args.seqdefdb, args.schema) as mlst_profiler:
+            mlst_profiles = mlst_profiler.profile_multiple_strings(gen_strings, exact=args.exact)
+            failed = await write_mlst_profiles_as_csv(mlst_profiles, args.out)
+            if len(failed) > 0:
+                print(f"A total of {len(failed)} IDs failed:\n{"\n".join(failed)}")
+            print(f"Completed fetching MLSTs for {len(args.fastas)} sequences.")
+
+def run_asynchronously(args):
+    asyncio.run(run(args))
+