amina-cli 0.1.0__tar.gz

amina_cli-0.1.0/.gitignore

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+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# Virtual environments
+.venv/
+venv/
+ENV/
+env/
+
+# uv
+.uv/
+uv.lock
+
+# IDE
+.idea/
+.vscode/
+*.swp
+*.swo
+*~
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Testing
+.pytest_cache/
+.coverage
+htmlcov/
+coverage_html_agent/
+coverage_agent.xml
+.tox/
+.nox/
+
+# Test reference outputs with machine-specific paths
+tests/toolkit/unit/test_ipsae/dunbrack_reference/test_inputs/*.pml
+tests/toolkit/unit/test_ipsae/dunbrack_reference/test_inputs/*.txt
+
+# Gateway test outputs (generated during manual testing)
+tests/cli/modal_gateway_tests/test_outputs/
+
+# Modal tool test outputs
+tests/toolkit/modal_tool_tests/test_reports/
+
+# Jupyter
+.ipynb_checkpoints/
+
+# Local config
+.env
+.env.local
+*.local
+.claude/settings.local.json
+
+# Logs
+*.log
+logs/
+
+# Build artifacts
+*.whl
+
+# Modal
+.modal/

amina_cli-0.1.0/LICENSE

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+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
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amina_cli-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: amina-cli
+Version: 0.1.0
+Summary: CLI for AminoAnalytica protein engineering platform
+Project-URL: Homepage, https://aminoanalytica.com
+Project-URL: Documentation, https://docs.aminoanalytica.com
+Author-email: AminoAnalytica <support@aminoanalytica.com>
+License: Apache-2.0
+License-File: LICENSE
+Keywords: bioinformatics,cli,esmfold,protein,protein-design,proteinmpnn,structure-prediction
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.11
+Requires-Dist: httpx>=0.27.0
+Requires-Dist: pydantic>=2.0
+Requires-Dist: rich>=13.0.0
+Requires-Dist: supabase>=2.0.0
+Requires-Dist: typer>=0.9.0
+Provides-Extra: dev
+Requires-Dist: pytest; extra == 'dev'
+Requires-Dist: pytest-asyncio; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# Amina CLI
+
+Command-line interface for the [AminoAnalytica](https://aminoanalytica.com) protein engineering platform.
+
+Run protein structure prediction, sequence design, and analysis tools directly from your terminal.
+
+## Installation
+
+```bash
+pip install amina-cli
+```
+
+## Quick Start
+
+```bash
+# Set your API key (get one at https://app.aminoanalytica.com/settings/api)
+amina auth set-key "ami_your_api_key"
+
+# List available tools
+amina tools
+
+# Run ESMFold structure prediction
+amina run esmfold --sequence "MKFLILLFNILCLFPVLAADNH" -o ./results/
+
+# Run ProteinMPNN sequence design
+amina run proteinmpnn --pdb ./structure.pdb --num-sequences 10 -o ./results/
+```
+
+## Available Tools
+
+### Folding
+- `esmfold` - Predict protein structure from sequence
+- `boltz2` - Structure prediction with Boltz-2
+- `openfold3` - OpenFold3 structure prediction
+
+### Design
+- `proteinmpnn` - Design sequences for a backbone structure
+- `rfdiffusion` - Generate novel protein backbones
+- `esm-if1` - Inverse folding with ESM-IF1
+
+### Analysis
+- `simple-rmsd` - Calculate RMSD between structures
+- `hydrophobicity` - Analyze hydrophobic properties
+- `surface-charge` - Electrostatic surface analysis
+
+### Utilities
+- `pdb-cleaner` - Clean and prepare PDB files
+- `pdb-to-fasta` - Extract sequences from structures
+
+Run `amina tools` for the complete list.
+
+## Usage
+
+```bash
+# Get help
+amina --help
+amina run --help
+amina run esmfold --help
+
+# Check tool parameters
+amina tools esmfold
+
+# Run with custom job name
+amina run esmfold --sequence "MKTV..." --job-name my_protein -o ./output/
+```
+
+## Authentication
+
+Get an API key from your [account settings](https://app.aminoanalytica.com/settings/api).
+
+```bash
+# Set API key
+amina auth set-key "ami_your_api_key"
+
+# Check auth status
+amina auth status
+
+# Remove stored key
+amina auth logout
+```
+
+## Output
+
+Results are downloaded to your specified output directory:
+
+```
+./results/
+├── esmfold_XXXX_structure.pdb      # Predicted structure
+├── esmfold_XXXX_plddt_scores.csv   # Per-residue confidence
+└── esmfold_XXXX_plddt_plot.png     # Confidence visualization
+```
+
+## Requirements
+
+- Python 3.11+
+- API key from [AminoAnalytica](https://app.aminoanalytica.com)
+
+## Links
+
+- [Website](https://aminoanalytica.com)
+- [Documentation](https://docs.aminoanalytica.com)
+- [Get API Key](https://app.aminoanalytica.com/settings/api)
+
+## License
+
+Apache 2.0

amina_cli-0.1.0/README.md

@@ -0,0 +1,106 @@
+# Amina CLI
+
+Command-line interface for the [AminoAnalytica](https://aminoanalytica.com) protein engineering platform.
+
+Run protein structure prediction, sequence design, and analysis tools directly from your terminal.
+
+## Installation
+
+```bash
+pip install amina-cli
+```
+
+## Quick Start
+
+```bash
+# Set your API key (get one at https://app.aminoanalytica.com/settings/api)
+amina auth set-key "ami_your_api_key"
+
+# List available tools
+amina tools
+
+# Run ESMFold structure prediction
+amina run esmfold --sequence "MKFLILLFNILCLFPVLAADNH" -o ./results/
+
+# Run ProteinMPNN sequence design
+amina run proteinmpnn --pdb ./structure.pdb --num-sequences 10 -o ./results/
+```
+
+## Available Tools
+
+### Folding
+- `esmfold` - Predict protein structure from sequence
+- `boltz2` - Structure prediction with Boltz-2
+- `openfold3` - OpenFold3 structure prediction
+
+### Design
+- `proteinmpnn` - Design sequences for a backbone structure
+- `rfdiffusion` - Generate novel protein backbones
+- `esm-if1` - Inverse folding with ESM-IF1
+
+### Analysis
+- `simple-rmsd` - Calculate RMSD between structures
+- `hydrophobicity` - Analyze hydrophobic properties
+- `surface-charge` - Electrostatic surface analysis
+
+### Utilities
+- `pdb-cleaner` - Clean and prepare PDB files
+- `pdb-to-fasta` - Extract sequences from structures
+
+Run `amina tools` for the complete list.
+
+## Usage
+
+```bash
+# Get help
+amina --help
+amina run --help
+amina run esmfold --help
+
+# Check tool parameters
+amina tools esmfold
+
+# Run with custom job name
+amina run esmfold --sequence "MKTV..." --job-name my_protein -o ./output/
+```
+
+## Authentication
+
+Get an API key from your [account settings](https://app.aminoanalytica.com/settings/api).
+
+```bash
+# Set API key
+amina auth set-key "ami_your_api_key"
+
+# Check auth status
+amina auth status
+
+# Remove stored key
+amina auth logout
+```
+
+## Output
+
+Results are downloaded to your specified output directory:
+
+```
+./results/
+├── esmfold_XXXX_structure.pdb      # Predicted structure
+├── esmfold_XXXX_plddt_scores.csv   # Per-residue confidence
+└── esmfold_XXXX_plddt_plot.png     # Confidence visualization
+```
+
+## Requirements
+
+- Python 3.11+
+- API key from [AminoAnalytica](https://app.aminoanalytica.com)
+
+## Links
+
+- [Website](https://aminoanalytica.com)
+- [Documentation](https://docs.aminoanalytica.com)
+- [Get API Key](https://app.aminoanalytica.com/settings/api)
+
+## License
+
+Apache 2.0

amina_cli-0.1.0/pyproject.toml

@@ -0,0 +1,49 @@
+[project]
+name = "amina-cli"
+version = "0.1.0"
+description = "CLI for AminoAnalytica protein engineering platform"
+readme = "README.md"
+license = {text = "Apache-2.0"}
+requires-python = ">=3.11"
+authors = [
+    {name = "AminoAnalytica", email = "support@aminoanalytica.com"}
+]
+keywords = ["protein", "bioinformatics", "cli", "esmfold", "proteinmpnn", "protein-design", "structure-prediction"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Environment :: Console",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: Apache Software License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+dependencies = [
+    "typer>=0.9.0",      # CLI framework (built on click)
+    "httpx>=0.27.0",     # Async HTTP client for Modal workers
+    "rich>=13.0.0",      # Beautiful terminal output (included with typer)
+    "pydantic>=2.0",     # Data validation
+    "supabase>=2.0.0",   # Supabase client for file operations
+]
+
+[project.scripts]
+amina = "amina_cli.main:app"
+
+[project.urls]
+Homepage = "https://aminoanalytica.com"
+Documentation = "https://docs.aminoanalytica.com"
+
+[project.optional-dependencies]
+dev = [
+    "pytest",
+    "pytest-asyncio",
+]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/amina_cli"]

amina_cli-0.1.0/src/amina_cli/__init__.py

@@ -0,0 +1,12 @@
+"""
+Amina CLI - Command-line interface for AminoAnalytica protein engineering platform.
+
+Installation:
+    pip install amina-cli
+
+Quick start:
+    amina auth set-key "ami_your_api_key"
+    amina run esmfold --sequence "MKFLILLFNILCLFPVLAADNH"
+"""
+
+__version__ = "0.1.0"