phenoworks-sdk 0.1.0__tar.gz

phenoworks_sdk-0.1.0/.gitignore

@@ -0,0 +1,14 @@
+# Built from mkdocs/ with MkDocs; keep the source in version control.
+/docs/
+# Local configuration and analysis outputs.
+.env
+.env.*
+!.env.example
+/results/
+/dist/
+/build/
+.venv/
+__pycache__/
+*.py[cod]
+.pytest_cache/
+.ruff_cache/

phenoworks_sdk-0.1.0/LICENSE

@@ -0,0 +1,202 @@
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phenoworks_sdk-0.1.0/PKG-INFO

@@ -0,0 +1,186 @@
+Metadata-Version: 2.5
+Name: phenoworks-sdk
+Version: 0.1.0
+Summary: A Python package for interacting with PhenoWorks projects, datasets, pipelines, and artifacts.
+Project-URL: Homepage, https://github.com/OpenSciML/phenoworks
+Project-URL: Repository, https://github.com/OpenSciML/phenoworks/tree/main/packages/phenoworks-sdk
+Project-URL: Documentation, https://github.com/OpenSciML/phenoworks/tree/main/packages/phenoworks-sdk/mkdocs
+Project-URL: Issues, https://github.com/OpenSciML/phenoworks/issues
+Author-email: haruiz <henryruiz22@gmail.com>
+License-Expression: Apache-2.0
+License-File: LICENSE
+Requires-Python: >=3.11
+Requires-Dist: httpx<1,>=0.27
+Provides-Extra: authoring
+Requires-Dist: lgopy; extra == 'authoring'
+Provides-Extra: cli
+Requires-Dist: pydantic<3,>=2.8; extra == 'cli'
+Requires-Dist: rich>=13; extra == 'cli'
+Requires-Dist: typer>=0.12.3; extra == 'cli'
+Provides-Extra: dev
+Requires-Dist: pydantic<3,>=2.8; extra == 'dev'
+Requires-Dist: pytest>=8.3; extra == 'dev'
+Requires-Dist: rich>=13; extra == 'dev'
+Requires-Dist: typer>=0.12.3; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# PhenoWorks SDK
+
+PhenoWorks SDK is a Python package for working with PhenoWorks from scripts,
+notebooks, and the command line. It connects to your PhenoWorks server using an
+API key and gives you access to projects, datasets, pipelines, and analysis
+outputs with the permissions of your account.
+
+Use it to:
+
+- Browse projects and studies, and find datasets by modality.
+- Upload files and manage datasets, assets, plots, and annotations.
+- Submit pipelines, monitor their progress, and retrieve previous runs.
+- Download artifacts for downstream analysis and machine-learning workflows.
+- Discover analysis blocks and manage account-level installations.
+
+The package provides `PhenoWorksClient`, `AsyncPhenoWorksClient`, and the optional
+`phenoworks` CLI. The Python client requires Python 3.11 or later and HTTPX.
+
+## Installation
+
+From the PhenoWorks repository root, install the Python package:
+
+```bash
+pip install ./packages/phenoworks-sdk
+```
+
+To include the CLI:
+
+```bash
+pip install './packages/phenoworks-sdk[cli]'
+```
+
+These commands install from this checkout. See the
+[installation guide](mkdocs/getting-started.md) for uv workspace usage.
+
+## Connect to PhenoWorks
+
+Create an API key in your account settings and configure your server connection:
+
+```bash
+export PHENOWORKS_API_URL="https://your-phenoworks-server"
+export PHENOWORKS_API_KEY="YOUR_API_KEY"
+```
+
+Then list the projects available to your account:
+
+```python
+from phenoworks_sdk import PhenoWorksClient
+
+with PhenoWorksClient() as client:
+    projects = client.projects.list()
+    for project in projects:
+        print(project["id"], project["name"])
+```
+
+You can also pass `base_url` and `api_key` directly to the client. Keep real keys
+out of committed code and shared notebooks.
+
+## Find datasets by modality
+
+Replace the example project ID with one from your account:
+
+```python
+from phenoworks_sdk import PhenoWorksClient
+
+with PhenoWorksClient() as client:
+    datasets = client.datasets.filter_by_modality("thermal", project_id=7)
+    for dataset in datasets:
+        print(dataset["id"], dataset["name"])
+```
+
+This filters datasets by their declared `supported_modalities`. It does not
+verify that matching assets have been uploaded.
+
+## Run a pipeline and download results
+
+Save a valid pipeline definition as `pipeline.json`, using analysis blocks
+available to your account. Replace `42` with the dataset you want to process.
+
+```python
+import json
+from pathlib import Path
+
+from phenoworks_sdk import PhenoWorksClient
+
+with PhenoWorksClient() as client:
+    definition = json.loads(Path("pipeline.json").read_text(encoding="utf-8"))
+    run = client.run_pipeline(dataset_id=42, json_pipeline=definition)
+    print("Pipeline:", run.pipeline_id, "Operation:", run.operation_id)
+    run.wait(timeout=3600)
+
+    for artifact in run.artifacts():
+        if artifact["status"] == "ready":
+            destination = Path("results") / f"artifact-{artifact['id']}"
+            client.artifacts.download(artifact["id"], destination)
+```
+
+Inspect each artifact's type, format, and metadata to select the output needed
+for your analysis. Downloads require a local filename and refuse to overwrite
+existing files unless `overwrite=True` is supplied.
+
+To retrieve a previous run, use `client.pipeline_run(pipeline_id=123)` inside a
+client context. This reconnects to the existing run without submitting work.
+See [pipelines and artifacts](mkdocs/pipelines.md) for discovery, waiting,
+error handling, and downloads.
+
+## Command-line usage
+
+The CLI uses the same server URL and API key environment variables:
+
+```bash
+phenoworks auth me
+phenoworks datasets filter-by-modality thermal --param project_id=7
+phenoworks pipelines run --dataset-id 42 --file pipeline.json --wait
+phenoworks artifacts list --param pipeline_id=123
+phenoworks artifacts download 789 --output ./results/features.csv
+```
+
+Use IDs and filenames from your own account. Run `phenoworks --help` to explore
+commands. The [CLI guide](mkdocs/cli.md) covers uploads, JSON payloads, and
+migration from the backend CLI.
+
+## Documentation
+
+- [Installation and authentication](mkdocs/getting-started.md)
+- [Dataset discovery](mkdocs/datasets.md)
+- [Pipelines and artifacts](mkdocs/pipelines.md)
+- [File uploads and recovery](mkdocs/uploads.md)
+- [Async clients and MCP integration](mkdocs/async.md)
+- [Python API reference](mkdocs/reference.md)
+- [Development and compatibility](mkdocs/development.md)
+
+To preview the documentation from the SDK package directory:
+
+```bash
+uv run --group docs mkdocs serve
+```
+
+Markdown sources live in `mkdocs/`; `mkdocs build --strict` generates the site in
+`docs/`. Generated HTML is ignored by Git.
+
+## Development
+
+Run tests and build the package from the repository root:
+
+```bash
+uv run --package phenoworks-sdk --extra dev pytest packages/phenoworks-sdk/tests
+uv build --package phenoworks-sdk
+```
+
+Version 0.1 targets the API in this PhenoWorks checkout. Most SDK tests use mock
+HTTP responses; the optional live-server test requires explicit configuration.
+See the [development guide](mkdocs/development.md) before running it.
+
+Contributions follow the PhenoWorks [contribution guidelines](https://github.com/OpenSciML/phenoworks/blob/main/CONTRIBUTING.md).
+Report vulnerabilities using the project's [security policy](https://github.com/OpenSciML/phenoworks/blob/main/SECURITY.md).
+
+## License
+
+Licensed under [Apache 2.0](LICENSE).

phenoworks_sdk-0.1.0/README.md

@@ -0,0 +1,160 @@
+# PhenoWorks SDK
+
+PhenoWorks SDK is a Python package for working with PhenoWorks from scripts,
+notebooks, and the command line. It connects to your PhenoWorks server using an
+API key and gives you access to projects, datasets, pipelines, and analysis
+outputs with the permissions of your account.
+
+Use it to:
+
+- Browse projects and studies, and find datasets by modality.
+- Upload files and manage datasets, assets, plots, and annotations.
+- Submit pipelines, monitor their progress, and retrieve previous runs.
+- Download artifacts for downstream analysis and machine-learning workflows.
+- Discover analysis blocks and manage account-level installations.
+
+The package provides `PhenoWorksClient`, `AsyncPhenoWorksClient`, and the optional
+`phenoworks` CLI. The Python client requires Python 3.11 or later and HTTPX.
+
+## Installation
+
+From the PhenoWorks repository root, install the Python package:
+
+```bash
+pip install ./packages/phenoworks-sdk
+```
+
+To include the CLI:
+
+```bash
+pip install './packages/phenoworks-sdk[cli]'
+```
+
+These commands install from this checkout. See the
+[installation guide](mkdocs/getting-started.md) for uv workspace usage.
+
+## Connect to PhenoWorks
+
+Create an API key in your account settings and configure your server connection:
+
+```bash
+export PHENOWORKS_API_URL="https://your-phenoworks-server"
+export PHENOWORKS_API_KEY="YOUR_API_KEY"
+```
+
+Then list the projects available to your account:
+
+```python
+from phenoworks_sdk import PhenoWorksClient
+
+with PhenoWorksClient() as client:
+    projects = client.projects.list()
+    for project in projects:
+        print(project["id"], project["name"])
+```
+
+You can also pass `base_url` and `api_key` directly to the client. Keep real keys
+out of committed code and shared notebooks.
+
+## Find datasets by modality
+
+Replace the example project ID with one from your account:
+
+```python
+from phenoworks_sdk import PhenoWorksClient
+
+with PhenoWorksClient() as client:
+    datasets = client.datasets.filter_by_modality("thermal", project_id=7)
+    for dataset in datasets:
+        print(dataset["id"], dataset["name"])
+```
+
+This filters datasets by their declared `supported_modalities`. It does not
+verify that matching assets have been uploaded.
+
+## Run a pipeline and download results
+
+Save a valid pipeline definition as `pipeline.json`, using analysis blocks
+available to your account. Replace `42` with the dataset you want to process.
+
+```python
+import json
+from pathlib import Path
+
+from phenoworks_sdk import PhenoWorksClient
+
+with PhenoWorksClient() as client:
+    definition = json.loads(Path("pipeline.json").read_text(encoding="utf-8"))
+    run = client.run_pipeline(dataset_id=42, json_pipeline=definition)
+    print("Pipeline:", run.pipeline_id, "Operation:", run.operation_id)
+    run.wait(timeout=3600)
+
+    for artifact in run.artifacts():
+        if artifact["status"] == "ready":
+            destination = Path("results") / f"artifact-{artifact['id']}"
+            client.artifacts.download(artifact["id"], destination)
+```
+
+Inspect each artifact's type, format, and metadata to select the output needed
+for your analysis. Downloads require a local filename and refuse to overwrite
+existing files unless `overwrite=True` is supplied.
+
+To retrieve a previous run, use `client.pipeline_run(pipeline_id=123)` inside a
+client context. This reconnects to the existing run without submitting work.
+See [pipelines and artifacts](mkdocs/pipelines.md) for discovery, waiting,
+error handling, and downloads.
+
+## Command-line usage
+
+The CLI uses the same server URL and API key environment variables:
+
+```bash
+phenoworks auth me
+phenoworks datasets filter-by-modality thermal --param project_id=7
+phenoworks pipelines run --dataset-id 42 --file pipeline.json --wait
+phenoworks artifacts list --param pipeline_id=123
+phenoworks artifacts download 789 --output ./results/features.csv
+```
+
+Use IDs and filenames from your own account. Run `phenoworks --help` to explore
+commands. The [CLI guide](mkdocs/cli.md) covers uploads, JSON payloads, and
+migration from the backend CLI.
+
+## Documentation
+
+- [Installation and authentication](mkdocs/getting-started.md)
+- [Dataset discovery](mkdocs/datasets.md)
+- [Pipelines and artifacts](mkdocs/pipelines.md)
+- [File uploads and recovery](mkdocs/uploads.md)
+- [Async clients and MCP integration](mkdocs/async.md)
+- [Python API reference](mkdocs/reference.md)
+- [Development and compatibility](mkdocs/development.md)
+
+To preview the documentation from the SDK package directory:
+
+```bash
+uv run --group docs mkdocs serve
+```
+
+Markdown sources live in `mkdocs/`; `mkdocs build --strict` generates the site in
+`docs/`. Generated HTML is ignored by Git.
+
+## Development
+
+Run tests and build the package from the repository root:
+
+```bash
+uv run --package phenoworks-sdk --extra dev pytest packages/phenoworks-sdk/tests
+uv build --package phenoworks-sdk
+```
+
+Version 0.1 targets the API in this PhenoWorks checkout. Most SDK tests use mock
+HTTP responses; the optional live-server test requires explicit configuration.
+See the [development guide](mkdocs/development.md) before running it.
+
+Contributions follow the PhenoWorks [contribution guidelines](https://github.com/OpenSciML/phenoworks/blob/main/CONTRIBUTING.md).
+Report vulnerabilities using the project's [security policy](https://github.com/OpenSciML/phenoworks/blob/main/SECURITY.md).
+
+## License
+
+Licensed under [Apache 2.0](LICENSE).

phenoworks_sdk-0.1.0/mkdocs/async.md

@@ -0,0 +1,62 @@
+# Async clients and shared services
+
+Use `AsyncPhenoWorksClient` when your application already uses an event loop.
+Configure your server and API key as described in [getting started](getting-started.md),
+then await API calls. Replace the example IDs with IDs from your account.
+
+```python
+from phenoworks_sdk import AsyncPhenoWorksClient
+
+
+async def analyze():
+    async with AsyncPhenoWorksClient() as client:
+        run = client.pipeline_run(pipeline_id=123)
+        await run.wait()
+        return await run.artifacts()
+```
+
+HTTP requests and pipeline polling are asynchronous. Local
+file reads/writes and progress callbacks execute synchronously in bounded chunks.
+Keep callbacks short. Async resource methods have the same names and arguments
+as their synchronous counterparts.
+
+Call `await analyze()` in an async application or notebook, or
+`asyncio.run(analyze())` in a script after importing `asyncio`.
+
+## Forward credentials in a service
+
+Pass `auth_token="..."` instead of `api_key` to use an existing bearer token.
+For a shared service such as MCP, use explicit forwarding mode:
+
+```python
+from phenoworks_sdk import AsyncPhenoWorksClient
+
+async def find_thermal(caller_api_key: str) -> list[dict]:
+    async with AsyncPhenoWorksClient(
+        base_url="https://your-phenoworks-server", forward_auth_headers=True
+    ) as client:
+        return await client.datasets.filter_by_modality(
+            "thermal", headers={"X-API-Key": caller_api_key}
+        )
+```
+
+In forwarding mode, each request supplies the caller's credential. Environment
+credentials are ignored. Resource methods, `request()`, `get()`, `post()`, `stream()`, and
+`download()` accept request-specific `headers`. They replace fixed authentication
+rather than merging with it, and never mutate shared transport headers. High-level
+run/upload helpers retain their owning client's credentials; use fixed per-user
+clients for those helpers. Do not share a fixed user client between callers.
+
+## Downloads and progress
+
+Async download progress callbacks may be synchronous or awaitable.
+`save_stream()` consumes an already-open SDK response, atomically saves it, and
+returns `path`, `size_bytes`, and `sha256`. MCP uses this helper while retaining
+control of destination paths and progress messages.
+
+## PhenoWorks MCP
+
+PhenoWorks MCP uses the async SDK for API authentication, HTTP requests, and
+streaming downloads. MCP retains responsibility for tool schemas, caller
+context, progress messages, and destination paths. It communicates with the
+same backend API as a Python SDK client.