dh-cli 0.1.9__tar.gz

dh_cli-0.1.9/.gitignore

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+##### Specific to Dayhoff #####
+
+# Pixi (managed by pixi.toml)
+.pixi/
+pixi.lock
+
+# Folders for heavy things
+/data/**
+!/data/**/
+!/data/**/.gitkeep
+
+/models/**
+!/models/**/
+!/models/**/.gitkeep
+
+/scratch/**
+!/scratch/**/
+!/scratch/**/.gitkeep
+
+**/wandb/**
+!**/wandb/**/.gitkeep
+
+**/artifacts/**
+!**/artifacts/**/.gitkeep
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+**/lightning_logs/**
+!**/lightning_logs/**/.gitkeep
+
+# nohup output
+**/nohup.out
+
+# Files with sensitive information
+key.json
+.env.secret
+workerbee.json
+key_github_actions.json
+
+# Always track DVC files, even in ignored folders
+!*.dvc
+
+# Except in the folder scratch/
+scratch/**/*.dvc
+
+# Dagster records
+pipelines/.dagster/**
+
+.vscode/settings.json
+.venv_studio/
+.venv_workstation/
+.mac_uv_project/
+.aws_uv_project/
+.workstation_uv_project/
+constraints.txt
+.deps_installed_workstation
+pyproject.aws.toml.bak
+
+
+
+
+##### Boilerplate not specific to Dayhoff #####
+
+# Garbage Mac files
+.DS_Store
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+*.pyc
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+# 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
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+# Scrapy stuff:
+.scrapy
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+# Sphinx documentation
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+# PyBuilder
+.pybuilder/
+target/
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+# 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:
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+# 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
+Pipfile.lock
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+# 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
+# pyproject.toml
+
+# pdm
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+.pdm.toml
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+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
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+celerybeat-schedule
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+.venv
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+# PyCharm
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+#  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/
+

dh_cli-0.1.9/LICENSE

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+# PolyForm Noncommercial License 1.0.0
+
+<https://polyformproject.org/licenses/noncommercial/1.0.0>
+
+## Acceptance
+
+In order to get any license under these terms, you must agree to them as
+both strict obligations and conditions to all your licenses.
+
+## Copyright License
+
+The licensor grants you a copyright license for the software to do
+everything you might do with the software that would otherwise infringe
+the licensor's copyright in it for any permitted purpose. However, you
+may only distribute the software according to Distribution License and
+make changes or new works based on the software according to Changes and
+New Works License.
+
+## Distribution License
+
+The licensor grants you an additional copyright license to distribute
+copies of the software. Your license to distribute covers distributing
+the software with changes and new works permitted by Changes and New
+Works License.
+
+## Notices
+
+You must ensure that anyone who gets a copy of any part of the software
+from you also gets a copy of these terms or the URL for them above, as
+well as copies of any plain-text lines beginning with `Required Notice:`
+that the licensor provided with the software. For example:
+
+> Required Notice: Copyright Dayhoff Labs (https://dayhofflabs.com)
+
+## Changes and New Works License
+
+The licensor grants you an additional copyright license to make changes
+and new works based on the software for any permitted purpose.
+
+## Patent License
+
+The licensor grants you a patent license for the software that covers
+patent claims the licensor can license, or becomes able to license, that
+you would infringe by using the software.
+
+## Noncommercial Purposes
+
+Any noncommercial purpose is a permitted purpose.
+
+## Personal Uses
+
+Personal use for research, experiment, and testing for the benefit of
+public knowledge, personal study, private entertainment, hobby projects,
+amateur pursuits, or religious observance, without any anticipated
+commercial application, is use for a permitted purpose.
+
+## Noncommercial Organizations
+
+Use by any charitable organization, educational institution, public
+research organization, public safety or health organization,
+environmental protection organization, or government institution is use
+for a permitted purpose regardless of the source of funding or
+obligations resulting from the funding.
+
+## Fair Use
+
+You may have "fair use" rights for the software under the law. These
+terms do not limit them.
+
+## No Other Rights
+
+These terms do not allow you to sublicense or transfer any of your
+licenses to anyone else, or prevent the licensor from granting licenses
+to anyone else. These terms do not imply any other licenses.
+
+## Patent Defense
+
+If you make any written claim that the software infringes or contributes
+to infringement of any patent, your patent license for the software
+granted under these terms ends immediately. If your company makes such a
+claim, your patent license ends immediately for work on behalf of your
+company.
+
+## Violations
+
+The first time you are notified in writing that you have violated any of
+these terms, or done anything with the software not covered by your
+licenses, your licenses can nonetheless continue if you come into full
+compliance with these terms, and take practical steps to correct past
+violations, within 32 days of receiving notice. Otherwise, all your
+licenses end immediately.
+
+## No Liability
+
+As far as the law allows, the software comes as is, without any warranty
+or condition, and the licensor will not be liable to you for any damages
+arising out of these terms or the use or nature of the software, under
+any kind of legal claim.
+
+## Definitions
+
+The **licensor** is the individual or entity offering these terms, and
+the **software** is the software the licensor makes available under
+these terms.
+
+**You** refers to the individual or entity agreeing to these terms.
+
+**Your company** is any legal entity, sole proprietorship, or other kind
+of organization that you work for, plus all organizations that have
+control over, are under the control of, or are under common control with
+that organization. **Control** means ownership of substantially all the
+assets of an entity, or the power to direct its management and policies
+by vote, contract, or otherwise. Control can be direct or indirect.
+
+**Your licenses** are all the licenses granted to you for the software
+under these terms.
+
+**Use** means anything you do with the software requiring one of your
+licenses.

dh_cli-0.1.9/PKG-INFO

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+Metadata-Version: 2.4
+Name: dh-cli
+Version: 0.1.9
+Summary: Dayhoff Labs developer CLI
+Author-email: Dayhoff Labs <dev@dayhofflabs.com>
+License: # PolyForm Noncommercial License 1.0.0
+        
+        <https://polyformproject.org/licenses/noncommercial/1.0.0>
+        
+        ## Acceptance
+        
+        In order to get any license under these terms, you must agree to them as
+        both strict obligations and conditions to all your licenses.
+        
+        ## Copyright License
+        
+        The licensor grants you a copyright license for the software to do
+        everything you might do with the software that would otherwise infringe
+        the licensor's copyright in it for any permitted purpose. However, you
+        may only distribute the software according to Distribution License and
+        make changes or new works based on the software according to Changes and
+        New Works License.
+        
+        ## Distribution License
+        
+        The licensor grants you an additional copyright license to distribute
+        copies of the software. Your license to distribute covers distributing
+        the software with changes and new works permitted by Changes and New
+        Works License.
+        
+        ## Notices
+        
+        You must ensure that anyone who gets a copy of any part of the software
+        from you also gets a copy of these terms or the URL for them above, as
+        well as copies of any plain-text lines beginning with `Required Notice:`
+        that the licensor provided with the software. For example:
+        
+        > Required Notice: Copyright Dayhoff Labs (https://dayhofflabs.com)
+        
+        ## Changes and New Works License
+        
+        The licensor grants you an additional copyright license to make changes
+        and new works based on the software for any permitted purpose.
+        
+        ## Patent License
+        
+        The licensor grants you a patent license for the software that covers
+        patent claims the licensor can license, or becomes able to license, that
+        you would infringe by using the software.
+        
+        ## Noncommercial Purposes
+        
+        Any noncommercial purpose is a permitted purpose.
+        
+        ## Personal Uses
+        
+        Personal use for research, experiment, and testing for the benefit of
+        public knowledge, personal study, private entertainment, hobby projects,
+        amateur pursuits, or religious observance, without any anticipated
+        commercial application, is use for a permitted purpose.
+        
+        ## Noncommercial Organizations
+        
+        Use by any charitable organization, educational institution, public
+        research organization, public safety or health organization,
+        environmental protection organization, or government institution is use
+        for a permitted purpose regardless of the source of funding or
+        obligations resulting from the funding.
+        
+        ## Fair Use
+        
+        You may have "fair use" rights for the software under the law. These
+        terms do not limit them.
+        
+        ## No Other Rights
+        
+        These terms do not allow you to sublicense or transfer any of your
+        licenses to anyone else, or prevent the licensor from granting licenses
+        to anyone else. These terms do not imply any other licenses.
+        
+        ## Patent Defense
+        
+        If you make any written claim that the software infringes or contributes
+        to infringement of any patent, your patent license for the software
+        granted under these terms ends immediately. If your company makes such a
+        claim, your patent license ends immediately for work on behalf of your
+        company.
+        
+        ## Violations
+        
+        The first time you are notified in writing that you have violated any of
+        these terms, or done anything with the software not covered by your
+        licenses, your licenses can nonetheless continue if you come into full
+        compliance with these terms, and take practical steps to correct past
+        violations, within 32 days of receiving notice. Otherwise, all your
+        licenses end immediately.
+        
+        ## No Liability
+        
+        As far as the law allows, the software comes as is, without any warranty
+        or condition, and the licensor will not be liable to you for any damages
+        arising out of these terms or the use or nature of the software, under
+        any kind of legal claim.
+        
+        ## Definitions
+        
+        The **licensor** is the individual or entity offering these terms, and
+        the **software** is the software the licensor makes available under
+        these terms.
+        
+        **You** refers to the individual or entity agreeing to these terms.
+        
+        **Your company** is any legal entity, sole proprietorship, or other kind
+        of organization that you work for, plus all organizations that have
+        control over, are under the control of, or are under common control with
+        that organization. **Control** means ownership of substantially all the
+        assets of an entity, or the power to direct its management and policies
+        by vote, contract, or otherwise. Control can be direct or indirect.
+        
+        **Your licenses** are all the licenses granted to you for the software
+        under these terms.
+        
+        **Use** means anything you do with the software requiring one of your
+        licenses.
+License-File: LICENSE
+Requires-Python: >=3.11
+Requires-Dist: boto3>=1.36.0
+Requires-Dist: click>=8.0.0
+Requires-Dist: pydantic>=2.0.0
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: questionary>=2.0.1
+Requires-Dist: requests>=2.31.0
+Requires-Dist: toml>=0.10
+Requires-Dist: typer>=0.9.0
+Description-Content-Type: text/markdown
+
+# dh-cli
+
+Developer CLI for [Dayhoff Labs](https://dayhofflabs.com).
+
+## Installation
+
+```bash
+pip install dh-cli
+```
+
+## Usage
+
+```bash
+dh --help
+dh --version
+```
+
+## Commands
+
+| Command | Description |
+|---------|-------------|
+| `dh engine` | Manage compute engines |
+| `dh studio` | Manage development studios |
+| `dh batch` | Submit and monitor batch jobs |
+| `dh aws` | AWS SSO authentication |
+| `dh gcp` | GCP authentication |
+| `dh gh` | GitHub authentication |
+| `dh wget` | Download from data warehouse |
+| `dh wheel` | Build and publish packages |
+| `dh clean` | Delete local git branches |
+
+## Requirements
+
+- Python >= 3.11
+- AWS credentials (for most commands)
+
+## License
+
+[PolyForm Noncommercial 1.0.0](https://polyformproject.org/licenses/noncommercial/1.0.0)

dh_cli-0.1.9/README.md

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+# dh-cli
+
+Developer CLI for [Dayhoff Labs](https://dayhofflabs.com).
+
+## Installation
+
+```bash
+pip install dh-cli
+```
+
+## Usage
+
+```bash
+dh --help
+dh --version
+```
+
+## Commands
+
+| Command | Description |
+|---------|-------------|
+| `dh engine` | Manage compute engines |
+| `dh studio` | Manage development studios |
+| `dh batch` | Submit and monitor batch jobs |
+| `dh aws` | AWS SSO authentication |
+| `dh gcp` | GCP authentication |
+| `dh gh` | GitHub authentication |
+| `dh wget` | Download from data warehouse |
+| `dh wheel` | Build and publish packages |
+| `dh clean` | Delete local git branches |
+
+## Requirements
+
+- Python >= 3.11
+- AWS credentials (for most commands)
+
+## License
+
+[PolyForm Noncommercial 1.0.0](https://polyformproject.org/licenses/noncommercial/1.0.0)

dh_cli-0.1.9/pyproject.toml

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+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "dh-cli"
+version = "0.1.9"
+description = "Dayhoff Labs developer CLI"
+requires-python = ">=3.11"
+readme = "README.md"
+license = {file = "LICENSE"}
+authors = [
+    {name = "Dayhoff Labs", email = "dev@dayhofflabs.com"},
+]
+dependencies = [
+    "boto3>=1.36.0",
+    "click>=8.0.0",
+    "pydantic>=2.0.0",
+    "pyyaml>=6.0",
+    "questionary>=2.0.1",
+    "requests>=2.31.0",
+    "toml>=0.10",
+    "typer>=0.9.0",
+]
+
+[project.scripts]
+dh = "dh_cli.main:app"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/dh_cli"]

dh_cli-0.1.9/src/dh_cli/__init__.py

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+"""Dayhoff Labs developer CLI (dh command)."""

dh_cli-0.1.9/src/dh_cli/batch/__init__.py

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+"""Batch job management CLI for AWS Batch.
+
+This module provides a Click-based CLI for submitting and managing batch jobs
+on AWS Batch, with support for:
+- High-level pipelines (embed-t5, boltz)
+- Generic job submission
+- Job lifecycle management (status, logs, cancel, retry, finalize)
+- Local debugging and shell access
+"""
+
+import click
+
+from .commands.boltz import boltz
+from .commands.cancel import cancel
+from .commands.clean import clean
+from .commands.embed_t5 import embed_t5
+from .commands.finalize import finalize
+from .commands.list_jobs import list_jobs
+from .commands.local import local
+from .commands.logs import logs
+from .commands.retry import retry
+from .commands.status import status
+from .commands.submit import submit
+from .commands.train import train
+
+
+@click.group()
+def batch_cli():
+    """Manage batch jobs on AWS Batch.
+
+    \b
+    Job Management:
+      submit     Submit a custom job from config file
+      status     Show job status
+      cancel     Cancel a running job
+      logs       View job logs
+      retry      Retry failed chunks
+      finalize   Combine results and clean up
+      local      Run a chunk locally for debugging
+      list       List recent jobs
+      clean      Remove old completed job directories
+
+    \b
+    Embedding Pipelines:
+      embed-t5   Generate T5 protein embeddings
+
+    \b
+    Structure Prediction:
+      boltz      Predict protein structures with Boltz
+
+    \b
+    ML Training:
+      train      Submit hatchery ML training jobs
+
+    \b
+    Examples:
+      # Submit an embedding job
+      dh batch embed-t5 /primordial/proteins.fasta --workers 50
+
+      # Submit a structure prediction job
+      dh batch boltz /primordial/complexes/ --workers 100
+
+      # Check job status
+      dh batch status dma-embed-20260109-a3f2
+
+      # View logs for a failed chunk
+      dh batch logs dma-embed-20260109-a3f2 --index 27
+
+      # Retry failed chunks
+      dh batch retry dma-embed-20260109-a3f2
+
+      # Finalize and combine results
+      dh batch finalize dma-embed-20260109-a3f2 --output /primordial/embeddings.h5
+    """
+    pass
+
+
+# Register job management commands
+batch_cli.add_command(submit)
+batch_cli.add_command(status)
+batch_cli.add_command(cancel)
+batch_cli.add_command(logs)
+batch_cli.add_command(retry)
+batch_cli.add_command(finalize)
+batch_cli.add_command(local)
+batch_cli.add_command(list_jobs, name="list")
+batch_cli.add_command(clean)
+
+# Register pipeline commands
+batch_cli.add_command(embed_t5, name="embed-t5")
+batch_cli.add_command(boltz)
+batch_cli.add_command(train)
+
+__all__ = ["batch_cli"]