dyno-phi 0.2.4__tar.gz → 0.3.1__tar.gz

dyno_phi-0.3.1/.gitignore

@@ -0,0 +1,125 @@
+# Python
+__pycache__/
+*.py[cod]
+*.pyo
+*.pyd
+.Python
+
+# Virtual environments
+.venv/
+.venv-install/
+venv/
+env/
+dockq-venv/
+
+# Distribution / packaging
+dist/
+build/
+*.egg-info/
+*.egg
+
+# Testing
+.pytest_cache/
+.coverage
+htmlcov/
+.tox/
+
+# Type checking
+.mypy_cache/
+.dmypy.json
+.pyright/
+
+# Environment files — never commit secrets
+.env
+.env.local
+.env.*.local
+*.env
+
+# GCP service account keys
+*.json
+!pyproject.json
+!.cursor/environment.json
+!tests/fixtures/metrics/ipsae_nonzero_multisubchain.json
+!tests/fixtures/bindcraft/run_metadata.json
+!clients/phi/tests/fixtures/job_types.json
+!clients/phi/tests/fixtures/run_pipelines.json
+!experiments/campaigns/y7_design/config/score_hit_calibration.json
+# Anchored to the repo root so it only blocks a top-level credential dir,
+# not source packages that happen to be named `secrets/`.
+/secrets/
+
+# Team-facing engineering docs live in docs/ (committed).
+# Local-only scratchpads / agent ephemera go in .scratch/.
+.scratch/
+scratch/
+
+# IDE
+.vscode/
+.idea/
+*.swp
+*.swo
+
+# Agent-only Cursor rule — local edit-time tooling, not a committed
+# team artifact. The team-facing version of the same content lives in
+# docs/model-integration-watchlist.md.
+.cursor/rules/model-integration.mdc
+
+# macOS
+.DS_Store
+
+# Alembic auto-generated (keep versions/ tracked)
+alembic/versions/*.pyc
+
+# Terraform state and local overrides
+infrastructure/**/.terraform/
+infrastructure/**/terraform.tfstate
+infrastructure/**/terraform.tfstate.backup
+infrastructure/**/*.tfvars
+!infrastructure/**/terraform.tfvars.example
+# Committed env var files — no secrets here; image_tag is always CI-supplied
+!infrastructure/terraform/staging.tfvars
+!infrastructure/terraform/production.tfvars
+infrastructure/**/.terraform.lock.hcl
+
+# Cloud Build local artifacts
+cloudbuild/*.log
+/runners/capsid-fold-esmfold2-base/source-artifact.zip
+/runners/capsid-fold-esmfold2-base/source-artifact.sha256
+
+# Docker
+.dockerignore.local
+
+*.pdb
+!tests/fixtures/metrics/ipsae_nonzero_multisubchain.pdb
+!examples/bindcraft2/*.pdb
+*.cif
+!examples/bindcraft2/*.cif
+*.csv
+
+# Large binary data / experiment outputs — use GCS, not git
+*.parquet
+*.pq
+*.npz
+
+# Canvas HTML dashboards (generated, not source-controlled)
+canvas/
+
+# Y4 campaign data and validation packages (binary + large CSVs)
+experiments/campaigns/y4_agent_designs/data/
+experiments/campaigns/y4_agent_designs/*.zip
+experiments/campaigns/y4_agent_designs/y4_validation_package_*/
+
+# CXCR3 campaign pipeline scratch — BoltzGen staging, fold inputs, large score tables
+experiments/cxcr3_vhh_design/data/designs/.staging/
+experiments/cxcr3_vhh_design/data/designs/**/.harvested_*
+experiments/cxcr3_vhh_design/data/control_folds/
+experiments/cxcr3_vhh_design/data/control_folds_templated/
+experiments/cxcr3_vhh_design/data/scored/wave1_designs.tsv
+experiments/cxcr3_vhh_design/data/scored/wave1_keep.tsv
+experiments/cxcr3_vhh_design/data/scored/wave1_keep_sequences.tsv
+experiments/cxcr3_vhh_design/data/scored/refold_manifest*.tsv
+
+# Agent-development guide is account/app-specific (DynoPhiAgent). Other
+# contributors run different agents/apps, so keep it local-only, not in the
+# shared repo.
+docs/agent-development.md

dyno_phi-0.3.1/CHANGELOG.md

@@ -0,0 +1,61 @@
+# Changelog
+
+The format follows [Keep a Changelog](https://keepachangelog.com/en/1.1.0/) and the
+package follows [Semantic Versioning](https://semver.org/spec/v2.0.0.html). The
+version is read from `src/phi/_version.py`; a release is the tag `client-v<version>`
+on `dynotx/phi-api`, which `.github/workflows/publish-client.yml` builds and publishes.
+
+## [0.3.1] - 2026-10-17
+
+### Changed
+
+- The CLI is installed with the package: `pip install dyno-phi` puts `phi` on the
+  path. The `[cli]` extra is kept as a no-op alias, so `dyno-phi[cli]` still
+  installs.
+
+## [0.3.0] - 2026-10-17
+
+The first release of the Phi SDK and CLI on PyPI, published from `clients/phi` in
+`dynotx/phi-api`. It was distributed as `phi-client` 0.0.1 from this repository
+over git during the internal preview.
+
+`dyno-phi` 0.2.x on PyPI was an earlier, unrelated client of a retired API. 0.3.0
+replaces it under the same name; nothing from 0.2.x carries over.
+
+### Added
+
+- `PhiClient` and `AsyncPhiClient` with the same resources and signatures:
+  `projects`, `datasets`, `sequences`, `designs`, `jobs`, `job_types`, `runs`,
+  `run_admin`, `artifacts`, `files`, `uploads`, `logs`, `quota`, `tool_configs`,
+  `imports`, `documents`.
+- Typed request and response models, local JSON Schema validation of `params` and
+  `inputs` for every job type (`client.job_types.validate_params`), waiters for
+  jobs and runs, and a typed error taxonomy (`PhiError` and its subclasses).
+- The `phi` CLI behind the `[cli]` extra, every command taking `--json`:
+  `auth`, `projects`, `datasets`, `docs`, `models`, `jobs`, `runs`, `pipeline`,
+  `artifacts`, `export`, `logs`, `quota`, `use`, `quickstart`.
+- Profiles in `~/.config/phi/config.toml`, selected with `--profile` or
+  `PHI_PROFILE`.
+- A Claude Code skill (`skills/phi/SKILL.md`) that drives the CLI.
+
+### Changed from `dyno-phi` 0.2.x
+
+- Environment: `PHI_API` is the base URL and `PHI_KEY` or `PHI_API_KEY` the key
+  (`DYNO_API_BASE_URL` and `DYNO_API_KEY` are not read). `PHI_ORG` names the
+  organization for a static key; a Clerk key carries its own.
+- Command tree: `phi <group> <command>` as listed above. `phi upload`, `phi filter`,
+  `phi research`, `phi notes`, `phi tutorial`, the filter presets and the
+  per-model commands (`phi esmfold`, `phi alphafold`, ...) are gone; a model runs
+  as `phi jobs submit <JOB_TYPE>` and a chain of models as `phi runs submit` or
+  `phi pipeline run`. `phi quickstart` is the walkthrough.
+- State: `.phi/state.json` holds the active project and dataset and the last job
+  and run, nothing else; the API key is never written there.
+- Python 3.12 or newer. The SDK depends on `httpx` and `pydantic` alone; the CLI's
+  dependencies install only with the `[cli]` extra.
+- Web app: results open at `design.dynotx.com`; the dashboard URLs the old client
+  printed no longer exist.
+
+Versioning note: the client stays below 1.0 while the API it speaks to is itself
+pre-1.0 (0.1.x) and the request shapes can still change between releases. 0.3.0
+is the first release on this line only because 0.2.x was already taken on PyPI
+by the earlier client; it is not a continuation of it.

dyno_phi-0.3.1/PKG-INFO

@@ -0,0 +1,209 @@
+Metadata-Version: 2.5
+Name: dyno-phi
+Version: 0.3.1
+Summary: Phi — Python SDK and CLI for the Phi protein design API
+Project-URL: Homepage, https://design.dynotx.com
+Project-URL: Documentation, https://design.dynotx.com/docs
+Project-URL: Source, https://github.com/dynotx/phi-api/tree/main/clients/phi
+Project-URL: Changelog, https://github.com/dynotx/phi-api/blob/main/clients/phi/CHANGELOG.md
+Project-URL: Issues, https://github.com/dynotx/phi-api/issues
+Author: Dyno Therapeutics
+License-Expression: MIT
+Keywords: binder-design,bioinformatics,cli,protein-design,protein-engineering,sdk,structure-prediction
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Typing :: Typed
+Requires-Python: >=3.12
+Requires-Dist: click>=8.1
+Requires-Dist: httpx>=0.27
+Requires-Dist: pydantic>=2.9
+Requires-Dist: pyyaml>=6
+Requires-Dist: rich>=13
+Requires-Dist: typer>=0.12
+Provides-Extra: cli
+Description-Content-Type: text/markdown
+
+# dyno-phi
+
+Python SDK and CLI for the [Phi](https://design.dynotx.com) protein design API.
+The `phi` package exposes synchronous (`PhiClient`) and asynchronous
+(`AsyncPhiClient`) clients and the `phi` CLI, installed together. It is
+published to PyPI from `clients/phi` in
+[`dynotx/phi-api`](https://github.com/dynotx/phi-api).
+
+## Install
+
+The CLI as an isolated tool on your `PATH`:
+
+```bash
+uv tool install dyno-phi
+```
+
+`uv tool` provisions its own Python, which covers the client's **Python 3.12+**
+requirement on stock macOS, where the system Python is 3.9. Re-run with
+`--upgrade` to upgrade. `pip install dyno-phi` into a Python 3.12+ of your own
+does the same. From a `phi-api` checkout, `just install-cli` runs the first
+form and `just install-cli-dev` installs the working tree.
+
+The SDK inside an existing project (the CLI comes with it; the `[cli]` extra
+from 0.3.0 still installs and adds nothing):
+
+```bash
+uv add dyno-phi        # or: pip install dyno-phi
+```
+
+Check the install with `phi --version`. `dyno-phi` 0.2.x was an earlier,
+unrelated client of a retired API; if `phi --version` prints `0.2.x`, that
+client is first on your `PATH` (`which -a phi` lists every match) and
+`pip install --upgrade dyno-phi` in the Python that owns it replaces it.
+Coming from 0.2.x: the key is `PHI_API_KEY` (or `PHI_KEY`) and the base URL
+`PHI_API`, the commands are `phi <group> <command>` as listed under
+[CLI](#cli), and Python 3.12+ is required; see
+[`CHANGELOG.md`](https://github.com/dynotx/phi-api/blob/main/clients/phi/CHANGELOG.md).
+
+If `uv`'s tool directory is behind another `phi` on `PATH`, sourcing uv's shell
+shim is not enough to move it: the shim prepends the directory only when `PATH`
+does not already contain it, and on macOS `path_helper` appends inherited
+entries behind `/etc/paths.d`, so in a shell that inherits a `PATH` naming the
+directory it stays last. Pin the order at the end of `~/.zshrc`:
+
+```zsh
+typeset -U path PATH
+path=("$HOME/.local/bin" $path)
+```
+
+## Authentication
+
+Both the SDK and the CLI read connection settings from the environment, falling
+back to `~/.config/phi/config.toml`:
+
+| Variable | Purpose |
+|---|---|
+| `PHI_API` | Base URL of the API. Its host selects the environment class — `hosted`, `staging`, or `local`. |
+| `PHI_KEY` / `PHI_API_KEY` | API key. |
+| `PHI_ORG` | Organization ID. Required with a static key. |
+
+```bash
+export PHI_API=https://phi-api-staging-917387676927.us-central1.run.app
+export PHI_KEY=...     # static staging key
+export PHI_ORG=dynotx  # literal static tenant, not the Clerk org
+```
+
+With a Clerk key (`ak_...`) the tenant comes from the key, so `PHI_ORG` is
+ignored; it is required only for a static key.
+
+Pass `base_url=`, `api_key=`, and `org=` to the client constructor to override
+the environment.
+
+## 60-second quickstart
+
+```bash
+phi quickstart
+```
+
+Creates the `quickstart` project, folds the Trp-cage mini-protein with `ESMFOLD`,
+waits, and downloads the results. The manual equivalent is:
+
+```bash
+phi jobs submit ESMFOLD --input sequences=@sequence.fasta --wait --out quickstart-output
+```
+
+## SDK usage
+
+Submit a job and wait for it, closing the client on exit:
+
+```python
+from phi import PhiClient
+
+with PhiClient() as client:
+    submitted = client.jobs.submit("ESMFOLD", inputs={"sequences": ["NLYIQWLKDGGPSSGRPPPS"]})
+    job = client.jobs.wait(submitted.job_id)
+    print(job.status, job.outputs)
+```
+
+`AsyncPhiClient` mirrors the same surface for concurrent work:
+
+```python
+import asyncio
+
+from phi import AsyncPhiClient
+
+
+async def fold(sequences: list[str]) -> list[str]:
+    async with AsyncPhiClient() as client:
+        submitted = await asyncio.gather(
+            *(client.jobs.submit("ESMFOLD", inputs={"sequences": [seq]}) for seq in sequences)
+        )
+        jobs = await asyncio.gather(*(client.jobs.wait(job.job_id) for job in submitted))
+    return [job.status for job in jobs]
+
+
+asyncio.run(fold(["NLYIQWLKDGGPSSGRPPPS", "GSHMKELVLALYDYQEKSPRE"]))
+```
+
+Runnable end-to-end scripts live in [`examples/`](examples/): single fold job,
+named pipeline, ad-hoc DAG, artifact download, and concurrent async submission.
+
+### Job types and local validation
+
+`client.job_types` lists the job types the API advertises and the JSON Schema for
+each one's `params` and `inputs`. Schemas are cached on disk per host for 24 hours;
+pass `refresh=True` to refetch.
+
+```python
+client.job_types.validate_params("PROTEINMPNN", {"num_seq_per_target": 8})
+```
+
+`validate_params` and `validate_inputs` raise `PhiValidationError` on a bad key,
+type, enum value, or numeric range. They are a **shallow pre-flight check**:
+top-level keys only, with no descent into nested objects or array items. The
+server validates fully, so a clean pass locally is not a guarantee the request
+will be accepted.
+
+### Knowledge documents
+
+`client.documents` and `AsyncPhiClient.documents` list, read, search, write, and
+review tenant-scoped Markdown documents. Use `iter_documents()` and
+`iter_versions()` to follow cursor pages. Updates take the active digest as
+`if_digest`; a stale value raises `PhiConflictError`. `propose()` creates a draft
+that remains outside active reads and search until a document writer calls
+`activate()`.
+
+## CLI
+
+Every command reads the same environment and accepts `--json` for scripting.
+
+| Group | Commands |
+|---|---|
+| `auth` | `login`, `whoami`, `logout`, `profiles` |
+| `projects` | `list`, `create`, `show`, `update`, `archive` |
+| `datasets` | `list`, `create`, `show`, `update`, `delete`, `copy`, `export`, `sequences` |
+| `docs` | `list`, `read`, `search`, `add`, `update`, `history`, `propose`, `activate`, `sync` |
+| `models` | `list`, `show`, `schema` |
+| `jobs` | `submit`, `list`, `status`, `cancel`, `wait`, `embeddings` |
+| `runs` | `submit`, `estimate`, `list`, `status`, `timeline`, `dag`, `cancel`, `resume` |
+| `pipeline` | `run`, `validate`, `estimate` |
+| `artifacts` | `list`, `download` |
+| `export` | `sequences`, `designs`, `structure`, `pae` |
+| `logs` | `show`, `download`, `settings` |
+| `quota` | (summary), `history` |
+| `use` | Set the active project |
+| `quickstart` | Run the end-to-end ESMFOLD example |
+
+`phi docs sync <dir> --dry-run` safely plans publication from a clean knowledge
+checkout. Without `--dry-run` it publishes only Git-tracked files in the
+authored Markdown layer after the checkout's deny-list guard passes, defaults
+platform documents to internal access, and skips unchanged content and access.
+It does not delete remote-only documents.
+
+## Full reference
+
+See [`docs/sdk-and-cli.md`](https://github.com/dynotx/phi-api/blob/main/docs/sdk-and-cli.md)
+for environment and profile resolution, sync/async parity, the complete CLI
+reference, the error taxonomy and how a release is cut.

dyno_phi-0.3.1/README.md

@@ -0,0 +1,178 @@
+# dyno-phi
+
+Python SDK and CLI for the [Phi](https://design.dynotx.com) protein design API.
+The `phi` package exposes synchronous (`PhiClient`) and asynchronous
+(`AsyncPhiClient`) clients and the `phi` CLI, installed together. It is
+published to PyPI from `clients/phi` in
+[`dynotx/phi-api`](https://github.com/dynotx/phi-api).
+
+## Install
+
+The CLI as an isolated tool on your `PATH`:
+
+```bash
+uv tool install dyno-phi
+```
+
+`uv tool` provisions its own Python, which covers the client's **Python 3.12+**
+requirement on stock macOS, where the system Python is 3.9. Re-run with
+`--upgrade` to upgrade. `pip install dyno-phi` into a Python 3.12+ of your own
+does the same. From a `phi-api` checkout, `just install-cli` runs the first
+form and `just install-cli-dev` installs the working tree.
+
+The SDK inside an existing project (the CLI comes with it; the `[cli]` extra
+from 0.3.0 still installs and adds nothing):
+
+```bash
+uv add dyno-phi        # or: pip install dyno-phi
+```
+
+Check the install with `phi --version`. `dyno-phi` 0.2.x was an earlier,
+unrelated client of a retired API; if `phi --version` prints `0.2.x`, that
+client is first on your `PATH` (`which -a phi` lists every match) and
+`pip install --upgrade dyno-phi` in the Python that owns it replaces it.
+Coming from 0.2.x: the key is `PHI_API_KEY` (or `PHI_KEY`) and the base URL
+`PHI_API`, the commands are `phi <group> <command>` as listed under
+[CLI](#cli), and Python 3.12+ is required; see
+[`CHANGELOG.md`](https://github.com/dynotx/phi-api/blob/main/clients/phi/CHANGELOG.md).
+
+If `uv`'s tool directory is behind another `phi` on `PATH`, sourcing uv's shell
+shim is not enough to move it: the shim prepends the directory only when `PATH`
+does not already contain it, and on macOS `path_helper` appends inherited
+entries behind `/etc/paths.d`, so in a shell that inherits a `PATH` naming the
+directory it stays last. Pin the order at the end of `~/.zshrc`:
+
+```zsh
+typeset -U path PATH
+path=("$HOME/.local/bin" $path)
+```
+
+## Authentication
+
+Both the SDK and the CLI read connection settings from the environment, falling
+back to `~/.config/phi/config.toml`:
+
+| Variable | Purpose |
+|---|---|
+| `PHI_API` | Base URL of the API. Its host selects the environment class — `hosted`, `staging`, or `local`. |
+| `PHI_KEY` / `PHI_API_KEY` | API key. |
+| `PHI_ORG` | Organization ID. Required with a static key. |
+
+```bash
+export PHI_API=https://phi-api-staging-917387676927.us-central1.run.app
+export PHI_KEY=...     # static staging key
+export PHI_ORG=dynotx  # literal static tenant, not the Clerk org
+```
+
+With a Clerk key (`ak_...`) the tenant comes from the key, so `PHI_ORG` is
+ignored; it is required only for a static key.
+
+Pass `base_url=`, `api_key=`, and `org=` to the client constructor to override
+the environment.
+
+## 60-second quickstart
+
+```bash
+phi quickstart
+```
+
+Creates the `quickstart` project, folds the Trp-cage mini-protein with `ESMFOLD`,
+waits, and downloads the results. The manual equivalent is:
+
+```bash
+phi jobs submit ESMFOLD --input sequences=@sequence.fasta --wait --out quickstart-output
+```
+
+## SDK usage
+
+Submit a job and wait for it, closing the client on exit:
+
+```python
+from phi import PhiClient
+
+with PhiClient() as client:
+    submitted = client.jobs.submit("ESMFOLD", inputs={"sequences": ["NLYIQWLKDGGPSSGRPPPS"]})
+    job = client.jobs.wait(submitted.job_id)
+    print(job.status, job.outputs)
+```
+
+`AsyncPhiClient` mirrors the same surface for concurrent work:
+
+```python
+import asyncio
+
+from phi import AsyncPhiClient
+
+
+async def fold(sequences: list[str]) -> list[str]:
+    async with AsyncPhiClient() as client:
+        submitted = await asyncio.gather(
+            *(client.jobs.submit("ESMFOLD", inputs={"sequences": [seq]}) for seq in sequences)
+        )
+        jobs = await asyncio.gather(*(client.jobs.wait(job.job_id) for job in submitted))
+    return [job.status for job in jobs]
+
+
+asyncio.run(fold(["NLYIQWLKDGGPSSGRPPPS", "GSHMKELVLALYDYQEKSPRE"]))
+```
+
+Runnable end-to-end scripts live in [`examples/`](examples/): single fold job,
+named pipeline, ad-hoc DAG, artifact download, and concurrent async submission.
+
+### Job types and local validation
+
+`client.job_types` lists the job types the API advertises and the JSON Schema for
+each one's `params` and `inputs`. Schemas are cached on disk per host for 24 hours;
+pass `refresh=True` to refetch.
+
+```python
+client.job_types.validate_params("PROTEINMPNN", {"num_seq_per_target": 8})
+```
+
+`validate_params` and `validate_inputs` raise `PhiValidationError` on a bad key,
+type, enum value, or numeric range. They are a **shallow pre-flight check**:
+top-level keys only, with no descent into nested objects or array items. The
+server validates fully, so a clean pass locally is not a guarantee the request
+will be accepted.
+
+### Knowledge documents
+
+`client.documents` and `AsyncPhiClient.documents` list, read, search, write, and
+review tenant-scoped Markdown documents. Use `iter_documents()` and
+`iter_versions()` to follow cursor pages. Updates take the active digest as
+`if_digest`; a stale value raises `PhiConflictError`. `propose()` creates a draft
+that remains outside active reads and search until a document writer calls
+`activate()`.
+
+## CLI
+
+Every command reads the same environment and accepts `--json` for scripting.
+
+| Group | Commands |
+|---|---|
+| `auth` | `login`, `whoami`, `logout`, `profiles` |
+| `projects` | `list`, `create`, `show`, `update`, `archive` |
+| `datasets` | `list`, `create`, `show`, `update`, `delete`, `copy`, `export`, `sequences` |
+| `docs` | `list`, `read`, `search`, `add`, `update`, `history`, `propose`, `activate`, `sync` |
+| `models` | `list`, `show`, `schema` |
+| `jobs` | `submit`, `list`, `status`, `cancel`, `wait`, `embeddings` |
+| `runs` | `submit`, `estimate`, `list`, `status`, `timeline`, `dag`, `cancel`, `resume` |
+| `pipeline` | `run`, `validate`, `estimate` |
+| `artifacts` | `list`, `download` |
+| `export` | `sequences`, `designs`, `structure`, `pae` |
+| `logs` | `show`, `download`, `settings` |
+| `quota` | (summary), `history` |
+| `use` | Set the active project |
+| `quickstart` | Run the end-to-end ESMFOLD example |
+
+`phi docs sync <dir> --dry-run` safely plans publication from a clean knowledge
+checkout. Without `--dry-run` it publishes only Git-tracked files in the
+authored Markdown layer after the checkout's deny-list guard passes, defaults
+platform documents to internal access, and skips unchanged content and access.
+It does not delete remote-only documents.
+
+## Full reference
+
+See [`docs/sdk-and-cli.md`](https://github.com/dynotx/phi-api/blob/main/docs/sdk-and-cli.md)
+for environment and profile resolution, sync/async parity, the complete CLI
+reference, the error taxonomy and how a release is cut.

dyno_phi-0.3.1/examples/README.md

@@ -0,0 +1,25 @@
+# phi examples
+
+Runnable SDK scripts. Each reads connection settings from the environment
+(`PHI_API`, `PHI_KEY` or `PHI_API_KEY`, and `PHI_ORG` for a static key) and can
+be run directly:
+
+```bash
+python examples/submit_fold.py
+```
+
+| Script | What it shows |
+|---|---|
+| [`submit_fold.py`](submit_fold.py) | Submit one ESMFOLD job and wait for it to finish. |
+| [`run_pipeline.py`](run_pipeline.py) | Run the named `SCORE_BACKBONES` pipeline seeded from a prior run. |
+| [`compose_dag.py`](compose_dag.py) | Build an ad-hoc ProteinMPNN → ESMFold `PipelineGraph` and submit it as one job. |
+| [`download_results.py`](download_results.py) | List a run's artifacts, download them, and read the manifest. |
+| [`async_concurrent.py`](async_concurrent.py) | Submit several jobs concurrently with `AsyncPhiClient`. |
+
+Scripts that need a project or run identifier take it as an argument, e.g.
+`python examples/compose_dag.py <project_id>`.
+
+Other assets in this directory:
+
+- [`quickstart/`](quickstart/) — the input FASTA used by `phi quickstart`.
+- [`pipelines/`](pipelines/) — graph YAML files for `phi pipeline run -f`.

dyno_phi-0.3.1/examples/async_concurrent.py

@@ -0,0 +1,31 @@
+from __future__ import annotations
+
+import asyncio
+
+from phi import AsyncPhiClient
+
+SEQUENCES = [
+    "NLYIQWLKDGGPSSGRPPPS",
+    "GSHMKELVLALYDYQEKSPRE",
+    "MKTAYIAKQRQISFVKSHFSRQ",
+]
+
+
+async def main(sequences: list[str] = SEQUENCES, batch_id: str = "esmfold-sweep") -> list[str]:
+    async with AsyncPhiClient() as client:
+        # One batch_id ties the sweep together: GET /v1/batches/{batch_id} reads "n of N done".
+        submitted = await asyncio.gather(
+            *(
+                client.jobs.submit("ESMFOLD", inputs={"sequences": [seq]}, batch_id=batch_id)
+                for seq in sequences
+            )
+        )
+        jobs = await asyncio.gather(*(client.jobs.wait(job.job_id) for job in submitted))
+    statuses: list[str] = [job.status for job in jobs]
+    for job in jobs:
+        print(f"{job.job_id}: {job.status}")
+    return statuses
+
+
+if __name__ == "__main__":
+    asyncio.run(main())

dyno_phi-0.3.1/examples/compose_dag.py

@@ -0,0 +1,22 @@
+from __future__ import annotations
+
+import sys
+
+from phi import PhiClient, PipelineGraph
+
+
+def main(project_id: str) -> str:
+    graph = PipelineGraph()
+    design = graph.add("proteinmpnn")
+    fold = graph.add("esmfold")
+    graph.connect(design.sequences, fold.sequences)
+    graph.validate()
+
+    with PhiClient() as client:
+        submitted = client.jobs.submit_graph(graph, project_id=project_id)
+    print(f"{submitted.job_id}: {submitted.status} ({submitted.estimated_credits} credits)")
+    return submitted.job_id
+
+
+if __name__ == "__main__":
+    main(sys.argv[1])

dyno_phi-0.3.1/examples/download_results.py

@@ -0,0 +1,21 @@
+from __future__ import annotations
+
+import json
+import sys
+from pathlib import Path
+
+from phi import PhiClient
+
+
+def main(run_id: str, out_dir: str | Path = "results") -> Path:
+    with PhiClient() as client:
+        artifacts = client.artifacts.list(run_id, suffix=".cif")
+        manifest_path = client.artifacts.download(artifacts, out_dir)
+    manifest = json.loads(manifest_path.read_text())
+    for entry in manifest:
+        print(f"{entry['status']:>10}  {entry['path']}")
+    return manifest_path
+
+
+if __name__ == "__main__":
+    main(sys.argv[1], sys.argv[2] if len(sys.argv) > 2 else "results")

dyno_phi-0.3.1/examples/pipelines/fold_and_analyze.yaml

@@ -0,0 +1,10 @@
+nodes:
+  - id: fold
+    tool: esmfold
+    mode: ""
+  - id: score
+    tool: analysis
+    mode: ""
+edges:
+  - from: fold.sequences
+    to: score.sequences