adagio-cli 0.1.0a1__tar.gz

adagio_cli-0.1.0a1/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Cymis
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

adagio_cli-0.1.0a1/PKG-INFO

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+Metadata-Version: 2.4
+Name: adagio-cli
+Version: 0.1.0a1
+Summary: Command-line runner for Adagio pipeline files.
+Keywords: adagio,bioinformatics,cli,pipelines,qiime2,workflow
+Author: Cymis
+License-Expression: MIT
+License-File: LICENSE
+Classifier: Development Status :: 3 - Alpha
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Dist: cyclopts>=4.5.3
+Requires-Dist: pydantic>=2.12.5
+Requires-Dist: rich>=14.1.0
+Requires-Dist: parsl>=2024.12.16
+Requires-Dist: tomli>=2.2.1 ; python_full_version < '3.11'
+Requires-Python: >=3.10
+Project-URL: Changelog, https://github.com/cymis/adagio-cli/blob/dev/CHANGELOG.md
+Project-URL: Homepage, https://github.com/cymis/adagio-cli
+Project-URL: Issues, https://github.com/cymis/adagio-cli/issues
+Project-URL: Repository, https://github.com/cymis/adagio-cli
+Description-Content-Type: text/markdown
+
+# Adagio CLI
+
+Command-line runner for Adagio pipeline files
+
+## Requirements
+
+- Python 3.10+
+- `uv` (recommended for development)
+- Docker for the default task runtime
+- Apptainer or Singularity when using `kind = "apptainer"` with local `.sif` images
+
+## Installation
+
+Install from PyPI:
+
+```bash
+pip install adagio-cli
+```
+
+Install a prerelease from TestPyPI while validating a release candidate:
+
+```bash
+pip install \
+  --index-url https://test.pypi.org/simple/ \
+  --extra-index-url https://pypi.org/simple \
+  adagio-cli
+```
+
+Install from the current checkout:
+
+```bash
+pip install .
+```
+
+Or with `uv`:
+
+```bash
+uv pip install .
+```
+
+Verify install:
+
+```bash
+adagio --version
+adagio --help
+```
+
+## Usage
+
+### Run a pipeline
+
+Show command help:
+
+```bash
+adagio run --help
+```
+
+Run with a pipeline file:
+
+```bash
+adagio run --pipeline path/to/pipeline.json --cache-dir /path/to/cache
+```
+
+`adagio run` executes each plugin task in its own task environment.
+The default task environment is a Docker image in GHCR derived from the plugin
+name in the pipeline spec, for example `dada2` -> `ghcr.io/cymis/qiime2-plugin-dada2:2026.1`.
+Runtime config can override that per default/plugin/task and switch selected work to
+Apptainer/Singularity with a local `.sif` image path. The cache directory is required
+and is reused across reruns by default so unchanged successful tasks can be replayed.
+
+Equivalent positional form:
+
+```bash
+adagio run path/to/pipeline.json --cache-dir /path/to/cache
+```
+
+Use an arguments file:
+
+```bash
+adagio run --pipeline path/to/pipeline.json --cache-dir /path/to/cache --arguments path/to/arguments.json
+```
+
+Use a runtime config file with defaults, plugin-level overrides, and optional task overrides:
+
+```bash
+adagio run --pipeline path/to/pipeline.json --cache-dir /path/to/cache --config path/to/runtime.toml
+```
+
+Control which dynamic flags are shown in help:
+
+```bash
+adagio run --pipeline path/to/pipeline.json --cache-dir /path/to/cache --show-params required
+# choices: all | missing | required
+```
+
+Disable reuse for a run while still writing outputs into the selected cache directory:
+
+```bash
+adagio run --pipeline path/to/pipeline.json --cache-dir /path/to/cache --no-reuse
+```
+
+The same boolean pair is available as `--reuse` / `--no-reuse`. `--reuse` is the default.
+
+Clear an existing cache directory:
+
+```bash
+adagio cache clear --cache-dir /path/to/cache
+```
+
+### Inspect a pipeline
+
+Print a dependency-ordered summary of the plugin actions in a pipeline:
+
+```bash
+adagio pipeline show path/to/pipeline.json
+```
+
+### Arguments file format
+
+`--arguments` can be downloaded from Adagio directly in the "Run" workflow :
+
+```json
+{
+  "version": 1,
+  "inputs": {
+    "input_name": "/path/to/input.qza"
+  },
+  "parameters": {
+    "param_name": "value"
+  },
+  "outputs": "/path/to/output-dir"
+}
+```
+
+`outputs` may also be a map keyed by output name (WIP: not currently generated by Adagio):
+
+```json
+{
+  "outputs": {
+    "output_a": "/path/to/output-a",
+    "output_b": "/path/to/output-b"
+  }
+}
+```
+
+If outputs are omitted, defaults are generated under `./adagio-outputs`.
+
+### Runtime config format
+
+`--config` accepts TOML. Defaults apply first, then plugin keys, then task keys:
+
+```toml
+version = 1
+
+[defaults]
+platform = "linux/amd64"
+
+[plugins]
+dada2 = { image = "ghcr.io/cymis/qiime2-plugin-dada2:2026.1" }
+demux = { image = "ghcr.io/cymis/qiime2-plugin-demux:2026.1" }
+
+[tasks]
+"dada2.denoise_single" = { image = "registry.internal/custom-dada2:1.0", platform = "linux/amd64" }
+```
+
+`kind`, `image`, and `platform` are all optional on defaults, plugin entries, and task entries.
+`kind` may be `docker` or `apptainer`. `image` remains the environment reference:
+for Docker it is the container image, and for Apptainer it must be a local `.sif` path.
+
+Precedence is `task override > plugin override > defaults > default resolver`.
+
+Task lookup supports graph node `id`, optional task `name` when present in the
+pipeline, and `plugin.action` as a fallback. Plugin lookup uses the pipeline's
+plugin name. If `platform` is omitted all the way through, Adagio uses normal
+Docker platform resolution with no implicit fallback. Anything not listed in the
+config uses the default plugin image resolver.
+
+Concrete Apptainer example:
+
+```toml
+version = 1
+
+[defaults]
+kind = "docker"
+
+[plugins]
+bowtie2 = { kind = "apptainer", image = "/shared/qiime-images/q2-bowtie2-test.sif" }
+```
+
+For `kind = "apptainer"`, Adagio prefers the `apptainer` executable and falls back to
+`singularity`. The current implementation supports only local `.sif` paths and runs
+tasks serially; no scheduler submission or remote image pull behavior is included.
+
+### QAPI generation/submission
+
+Generate and submit plugin metadata from the active QIIME environment:
+
+```bash
+adagio qapi build --action-url http://localhost:81/api/v1
+```
+
+Submit to a protected deployment such as `adagio.run` with a scoped submission token:
+
+```bash
+export ACTION_URL=https://adagio.run/api/v1
+export QAPI_SUBMISSION_TOKEN=<token copied from https://adagio.run/app/profile>
+uv run adagio qapi build
+```
+
+You can also pass `--submission-token`, but the environment variable is safer because it does
+not end up in shell history.
+
+Write payload to disk without submitting:
+
+```bash
+adagio qapi build --output qapi.json --dry-run
+```
+
+Submit selected plugins only:
+
+```bash
+adagio qapi build --plugin dada2 --plugin feature-table
+```
+
+## Development
+
+### Setup
+
+Install runtime and dev dependencies:
+
+```bash
+uv sync --group dev
+```
+
+Run commands inside the project environment:
+
+```bash
+uv run adagio --help
+```
+
+### Linting
+
+```bash
+uv run ruff check .
+uv run ruff format --check .
+uv run ruff format .
+```
+
+### Tests
+
+```bash
+uv run pytest
+```
+
+### Build distributions
+
+```bash
+uv run python -m build
+uv run python -m twine check dist/*
+```
+
+### Running locally during development
+
+```bash
+uv run adagio run --pipeline path/to/pipeline.json --cache-dir /path/to/cache
+```
+
+### Runtime entrypoint (container/integration use)
+
+The `runtime` subcommand is intended for runtime-adapter jobs:
+
+```bash
+uv run adagio runtime --spec spec.json --config runtime.toml --arguments arguments.json --cache-dir /path/to/cache
+```
+
+### Releasing
+
+See [RELEASING.md](RELEASING.md) for the one-time PyPI/GitHub setup, version/tag workflow, and TestPyPI/PyPI publishing steps.

adagio_cli-0.1.0a1/README.md

@@ -0,0 +1,278 @@
+# Adagio CLI
+
+Command-line runner for Adagio pipeline files
+
+## Requirements
+
+- Python 3.10+
+- `uv` (recommended for development)
+- Docker for the default task runtime
+- Apptainer or Singularity when using `kind = "apptainer"` with local `.sif` images
+
+## Installation
+
+Install from PyPI:
+
+```bash
+pip install adagio-cli
+```
+
+Install a prerelease from TestPyPI while validating a release candidate:
+
+```bash
+pip install \
+  --index-url https://test.pypi.org/simple/ \
+  --extra-index-url https://pypi.org/simple \
+  adagio-cli
+```
+
+Install from the current checkout:
+
+```bash
+pip install .
+```
+
+Or with `uv`:
+
+```bash
+uv pip install .
+```
+
+Verify install:
+
+```bash
+adagio --version
+adagio --help
+```
+
+## Usage
+
+### Run a pipeline
+
+Show command help:
+
+```bash
+adagio run --help
+```
+
+Run with a pipeline file:
+
+```bash
+adagio run --pipeline path/to/pipeline.json --cache-dir /path/to/cache
+```
+
+`adagio run` executes each plugin task in its own task environment.
+The default task environment is a Docker image in GHCR derived from the plugin
+name in the pipeline spec, for example `dada2` -> `ghcr.io/cymis/qiime2-plugin-dada2:2026.1`.
+Runtime config can override that per default/plugin/task and switch selected work to
+Apptainer/Singularity with a local `.sif` image path. The cache directory is required
+and is reused across reruns by default so unchanged successful tasks can be replayed.
+
+Equivalent positional form:
+
+```bash
+adagio run path/to/pipeline.json --cache-dir /path/to/cache
+```
+
+Use an arguments file:
+
+```bash
+adagio run --pipeline path/to/pipeline.json --cache-dir /path/to/cache --arguments path/to/arguments.json
+```
+
+Use a runtime config file with defaults, plugin-level overrides, and optional task overrides:
+
+```bash
+adagio run --pipeline path/to/pipeline.json --cache-dir /path/to/cache --config path/to/runtime.toml
+```
+
+Control which dynamic flags are shown in help:
+
+```bash
+adagio run --pipeline path/to/pipeline.json --cache-dir /path/to/cache --show-params required
+# choices: all | missing | required
+```
+
+Disable reuse for a run while still writing outputs into the selected cache directory:
+
+```bash
+adagio run --pipeline path/to/pipeline.json --cache-dir /path/to/cache --no-reuse
+```
+
+The same boolean pair is available as `--reuse` / `--no-reuse`. `--reuse` is the default.
+
+Clear an existing cache directory:
+
+```bash
+adagio cache clear --cache-dir /path/to/cache
+```
+
+### Inspect a pipeline
+
+Print a dependency-ordered summary of the plugin actions in a pipeline:
+
+```bash
+adagio pipeline show path/to/pipeline.json
+```
+
+### Arguments file format
+
+`--arguments` can be downloaded from Adagio directly in the "Run" workflow :
+
+```json
+{
+  "version": 1,
+  "inputs": {
+    "input_name": "/path/to/input.qza"
+  },
+  "parameters": {
+    "param_name": "value"
+  },
+  "outputs": "/path/to/output-dir"
+}
+```
+
+`outputs` may also be a map keyed by output name (WIP: not currently generated by Adagio):
+
+```json
+{
+  "outputs": {
+    "output_a": "/path/to/output-a",
+    "output_b": "/path/to/output-b"
+  }
+}
+```
+
+If outputs are omitted, defaults are generated under `./adagio-outputs`.
+
+### Runtime config format
+
+`--config` accepts TOML. Defaults apply first, then plugin keys, then task keys:
+
+```toml
+version = 1
+
+[defaults]
+platform = "linux/amd64"
+
+[plugins]
+dada2 = { image = "ghcr.io/cymis/qiime2-plugin-dada2:2026.1" }
+demux = { image = "ghcr.io/cymis/qiime2-plugin-demux:2026.1" }
+
+[tasks]
+"dada2.denoise_single" = { image = "registry.internal/custom-dada2:1.0", platform = "linux/amd64" }
+```
+
+`kind`, `image`, and `platform` are all optional on defaults, plugin entries, and task entries.
+`kind` may be `docker` or `apptainer`. `image` remains the environment reference:
+for Docker it is the container image, and for Apptainer it must be a local `.sif` path.
+
+Precedence is `task override > plugin override > defaults > default resolver`.
+
+Task lookup supports graph node `id`, optional task `name` when present in the
+pipeline, and `plugin.action` as a fallback. Plugin lookup uses the pipeline's
+plugin name. If `platform` is omitted all the way through, Adagio uses normal
+Docker platform resolution with no implicit fallback. Anything not listed in the
+config uses the default plugin image resolver.
+
+Concrete Apptainer example:
+
+```toml
+version = 1
+
+[defaults]
+kind = "docker"
+
+[plugins]
+bowtie2 = { kind = "apptainer", image = "/shared/qiime-images/q2-bowtie2-test.sif" }
+```
+
+For `kind = "apptainer"`, Adagio prefers the `apptainer` executable and falls back to
+`singularity`. The current implementation supports only local `.sif` paths and runs
+tasks serially; no scheduler submission or remote image pull behavior is included.
+
+### QAPI generation/submission
+
+Generate and submit plugin metadata from the active QIIME environment:
+
+```bash
+adagio qapi build --action-url http://localhost:81/api/v1
+```
+
+Submit to a protected deployment such as `adagio.run` with a scoped submission token:
+
+```bash
+export ACTION_URL=https://adagio.run/api/v1
+export QAPI_SUBMISSION_TOKEN=<token copied from https://adagio.run/app/profile>
+uv run adagio qapi build
+```
+
+You can also pass `--submission-token`, but the environment variable is safer because it does
+not end up in shell history.
+
+Write payload to disk without submitting:
+
+```bash
+adagio qapi build --output qapi.json --dry-run
+```
+
+Submit selected plugins only:
+
+```bash
+adagio qapi build --plugin dada2 --plugin feature-table
+```
+
+## Development
+
+### Setup
+
+Install runtime and dev dependencies:
+
+```bash
+uv sync --group dev
+```
+
+Run commands inside the project environment:
+
+```bash
+uv run adagio --help
+```
+
+### Linting
+
+```bash
+uv run ruff check .
+uv run ruff format --check .
+uv run ruff format .
+```
+
+### Tests
+
+```bash
+uv run pytest
+```
+
+### Build distributions
+
+```bash
+uv run python -m build
+uv run python -m twine check dist/*
+```
+
+### Running locally during development
+
+```bash
+uv run adagio run --pipeline path/to/pipeline.json --cache-dir /path/to/cache
+```
+
+### Runtime entrypoint (container/integration use)
+
+The `runtime` subcommand is intended for runtime-adapter jobs:
+
+```bash
+uv run adagio runtime --spec spec.json --config runtime.toml --arguments arguments.json --cache-dir /path/to/cache
+```
+
+### Releasing
+
+See [RELEASING.md](RELEASING.md) for the one-time PyPI/GitHub setup, version/tag workflow, and TestPyPI/PyPI publishing steps.

adagio_cli-0.1.0a1/pyproject.toml

@@ -0,0 +1,83 @@
+[project]
+name = "adagio-cli"
+version = "0.1.0a1"
+description = "Command-line runner for Adagio pipeline files."
+readme = "README.md"
+requires-python = ">=3.10"
+authors = [{ name = "Cymis" }]
+license = "MIT"
+license-files = ["LICENSE"]
+keywords = ["adagio", "bioinformatics", "cli", "pipelines", "qiime2", "workflow"]
+classifiers = [
+  "Development Status :: 3 - Alpha",
+  "Environment :: Console",
+  "Intended Audience :: Developers",
+  "Intended Audience :: Science/Research",
+  "License :: OSI Approved :: MIT License",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3 :: Only",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Topic :: Scientific/Engineering :: Bio-Informatics",
+  "Topic :: Software Development :: Libraries :: Python Modules",
+]
+dependencies = [
+  "cyclopts>=4.5.3",
+  "pydantic>=2.12.5",
+  "rich>=14.1.0",
+  "parsl>=2024.12.16",
+  "tomli>=2.2.1; python_version < '3.11'",
+]
+
+[project.urls]
+Homepage = "https://github.com/cymis/adagio-cli"
+Repository = "https://github.com/cymis/adagio-cli"
+Issues = "https://github.com/cymis/adagio-cli/issues"
+Changelog = "https://github.com/cymis/adagio-cli/blob/dev/CHANGELOG.md"
+
+[dependency-groups]
+dev = [
+  "build>=1.2.2",
+  "pytest>=8.4.0",
+  "ruff>=0.13.0",
+  "twine>=6.2.0",
+]
+
+[project.scripts]
+adagio = "adagio.cli.main:main"
+
+[build-system]
+requires = ["uv_build>=0.8.17,<0.9.0"]
+build-backend = "uv_build"
+
+[tool.uv.build-backend]
+module-name = "adagio"
+
+[tool.ruff.format]
+quote-style = "double"
+indent-style = "space"
+docstring-code-format = true
+
+[tool.ruff.lint.isort]
+
+
+known-first-party = ["adagio"]
+section-order = [
+  "future",
+  "standard-library",
+  "third-party",
+  "first-party",
+  "local-folder",
+]
+[tool.mypy]
+plugins = ['pydantic.mypy']
+
+[[tool.mypy.overrides]]
+
+module = ["qiime2.*"]
+ignore_missing_imports = true
+
+[tool.pytest.ini_options]
+addopts = "-ra"
+testpaths = ["tests"]

adagio_cli-0.1.0a1/src/adagio/__init__.py

@@ -0,0 +1,15 @@
+from importlib.metadata import PackageNotFoundError, version
+
+
+def _resolve_version() -> str:
+    for dist_name in ("adagio-cli", "adagio"):
+        try:
+            return version(dist_name)
+        except PackageNotFoundError:
+            continue
+    return "0.0.0"
+
+
+__version__ = _resolve_version()
+
+__all__ = ["__version__"]