deriva-ml 1.14.34__tar.gz → 1.14.36__tar.gz

{deriva_ml-1.14.34 → deriva_ml-1.14.36}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: deriva-ml
-Version: 1.14.34
+Version: 1.14.36
 Summary: Utilities to simplify use of Dervia and Pandas to create reproducable ML pipelines
 Author-email: ISRD <isrd-dev@isi.edu>
 Requires-Python: >=3.10

{deriva_ml-1.14.34 → deriva_ml-1.14.36}/pyproject.toml

@@ -27,6 +27,9 @@ deriva-ml-table-comments-utils = "deriva_ml.schema_setup.table_comments_utils:ma
 deriva-ml-create-schema = "deriva_ml.schema_setup.create_schema:main"
 deriva-ml-alter-annotation = "deriva_ml.schema_setup.alter_annotation:main"
 deriva-ml-run-notebook = "deriva_ml.run_notebook:main"
+deriva-ml-install-kernel = "deriva_ml.install_kernel:main"
+bump-version = "deriva_ml.bump_version:main"
+
 deriva-ml-check-catalog-schema = "deriva_ml.schema.check_schema:main"
 
 [project.optional-dependencies]
@@ -77,8 +80,8 @@ addopts = "-v  --import-mode=importlib"
 [tool.ruff]
 line-length = 120
 target-version = "py310"
-select = ["E", "F", "I", "PTH"]
-ignore = []
+lint.select = ["E", "F", "I", "PTH"]
+lint.ignore = []
 
 [tool.ruff.format]
 # Like Black, use double quotes for strings.

deriva_ml-1.14.36/src/deriva_ml/bump_version.py

@@ -0,0 +1,142 @@
+#!/usr/bin/env python3
+"""
+Release helper: seed initial semver tag if none exists, otherwise bump with bump-my-version.
+
+Usage:
+  python release.py [patch|minor|major]
+
+Env vars:
+  START   - initial version if no tag exists (default: 0.1.0)
+  PREFIX  - tag prefix (default: v)
+"""
+
+from __future__ import annotations
+
+import argparse
+import os
+import shutil
+import subprocess
+import sys
+from typing import Sequence
+
+
+def run(
+    cmd: Sequence[str], check: bool = True, capture: bool = False, quiet: bool = False
+) -> subprocess.CompletedProcess:
+    if not quiet:
+        print(f"$ {' '.join(cmd)}")
+    return subprocess.run(
+        cmd,
+        check=check,
+        capture_output=capture,
+        text=True,
+    )
+
+
+def in_git_repo() -> bool:
+    try:
+        run(["git", "rev-parse", "--is-inside-work-tree"], capture=True)
+        return True
+    except subprocess.CalledProcessError:
+        return False
+
+
+def has_commits() -> bool:
+    try:
+        run(["git", "log", "-1"], capture=True)
+        return True
+    except subprocess.CalledProcessError:
+        return False
+
+
+def latest_semver_tag(prefix: str) -> str | None:
+    # Use git's matcher to keep parity with Bash: prefix + x.y.z
+    pattern = f"{prefix}[0-9]*.[0-9]*.[0-9]*"
+    try:
+        cp = run(["git", "describe", "--tags", "--abbrev=0", "--match", pattern], capture=True, quiet=True)
+        tag = cp.stdout.strip()
+        return tag or None
+    except subprocess.CalledProcessError:
+        return None
+
+
+def seed_initial_tag(tag: str) -> None:
+    print(f"No existing semver tag found. Seeding initial tag: {tag}")
+    run(["git", "tag", tag, "-m", f"Initial release {tag}"])
+    # Push tags (ignore failure to keep parity with bash's simple flow)
+    run(["git", "push", "--tags"])
+
+
+def require_tool(name: str) -> None:
+    if shutil.which(name) is None:
+        print(f"Error: required tool '{name}' not found on PATH.", file=sys.stderr)
+        sys.exit(1)
+
+
+def main() -> int:
+    parser = argparse.ArgumentParser(
+        description="Set a new version tag for the current repository, and push to remote."
+    )
+    parser.add_argument(
+        "bump", nargs="?", default="patch", choices=["patch", "minor", "major"], help="Which semver part to bump."
+    )
+    args = parser.parse_args()
+
+    start = os.environ.get("START", "0.1.0")
+    prefix = os.environ.get("PREFIX", "v")
+
+    # Sanity checks
+    require_tool("git")
+    require_tool("uv")
+
+    if not in_git_repo():
+        print("Not a git repo.", file=sys.stderr)
+        return 1
+
+    # Ensure tags visible in shallow clones
+    try:
+        run(["git", "fetch", "--tags", "--quiet"], check=False)
+    except Exception:
+        pass  # non-fatal
+
+    if not has_commits():
+        print("No commits found. Commit something before tagging.", file=sys.stderr)
+        return 1
+
+    # Find latest semver tag with prefix
+    tag = latest_semver_tag(prefix)
+
+    if not tag:
+        seed_initial_tag(f"{prefix}{start}")
+        print(f"Seeded {prefix}{start}. Done.")
+        return 0
+
+    print(f"Bumping version: {args.bump}")
+
+    # Bump using bump-my-version via uv
+    # Mirrors: uv run bump-my-version bump $BUMP --verbose
+    try:
+        run(["uv", "run", "bump-my-version", "bump", args.bump, "--verbose"])
+    except subprocess.CalledProcessError as e:
+        print(e.stdout or "", end="")
+        print(e.stderr or "", end="", file=sys.stderr)
+        return e.returncode
+
+    # Push commits and tags
+    print("Pushing changes to remote repository...")
+    run(["git", "push", "--follow-tags"])
+
+    # Retrieve new version tag
+    try:
+        cp = run(["git", "describe", "--tags", "--abbrev=0"], capture=True)
+        new_tag = cp.stdout.strip()
+        print(f"New version tag: {new_tag}")
+    except subprocess.CalledProcessError:
+        print("Warning: unable to determine new tag via git describe.", file=sys.stderr)
+
+    print("Release process complete!")
+    return 0
+
+
+if __name__ == "__main__":
+    sys.exit(main())

{deriva_ml-1.14.34 → deriva_ml-1.14.36}/src/deriva_ml/execution/workflow.py

@@ -100,9 +100,6 @@ class Workflow(BaseModel):
             - DERIVA_ML_WORKFLOW_CHECKSUM: Override the computed checksum
 
         Args:
-            name: Human-readable name for the workflow.
-            workflow_type: Type of workflow (must be a vocabulary term).
-            description: Optional description of workflow purpose.
 
         Returns:
             Workflow: New workflow instance with detected Git information.
@@ -240,6 +237,7 @@ class Workflow(BaseModel):
         """
 
         server, session = Workflow._get_notebook_session()
+
         if server and session:
             relative_path = session["notebook"]["path"]
             # Join the notebook directory with the relative path
@@ -321,8 +319,8 @@ class Workflow(BaseModel):
                 # Being called from the command line interpreter.
                 filename = Path.cwd() / Path("REPL")
             # Get the caller's filename, which is two up the stack from here.
-        else:
-            raise DerivaMLException("Looking for caller failed")  # Stack is too shallow
+            else:
+                raise DerivaMLException("Looking for caller failed")  # Stack is too shallow
         return filename, is_notebook
 
     @staticmethod

deriva_ml-1.14.36/src/deriva_ml/install_kernel.py

@@ -0,0 +1,46 @@
+# your_pkg/install_kernel.py
+import sys
+import re
+from importlib import metadata
+from ipykernel.kernelspec import install as install_kernel
+
+def _dist_name_for_this_package() -> str:
+    """
+    Try to resolve the distribution name that provides this package.
+    Works in editable installs and wheels.
+    """
+    # Top-level package name of this module (your_pkg)
+    top_pkg = __name__.split(".")[0]
+
+    # Map top-level packages -> distributions
+    pkg_to_dists = metadata.packages_distributions()
+    dists = pkg_to_dists.get(top_pkg) or []
+
+    # Fall back to project name in METADATA when mapping isn't available
+    dist_name = dists[0] if dists else metadata.metadata(top_pkg).get("Name", top_pkg)
+    return dist_name
+
+def _normalize_kernel_name(name: str) -> str:
+    """
+    Jupyter kernel directory names should be simple: lowercase, [-a-z0-9_].
+    """
+    name = name.strip().lower()
+    name = re.sub(r"[^a-z0-9._-]+", "-", name)
+    return name
+
+def main() -> None:
+    dist_name = _dist_name_for_this_package()               # e.g., "deriva-model-template"
+    kernel_name = _normalize_kernel_name(dist_name)         # e.g., "deriva-model-template"
+    display_name = f"Python ({dist_name})"
+
+    # Install into the current environment's prefix (e.g., .venv/share/jupyter/kernels/..)
+    install_kernel(
+        user=False,                 # write under sys.prefix (the active env)
+        kernel_name=kernel_name,
+        display_name=display_name,
+        prefix=sys.prefix,
+    )
+    print(f"Installed Jupyter kernel '{kernel_name}' with display name '{display_name}' under {sys.prefix!s}")
+
+if __name__ == "__main__":
+    main()

{deriva_ml-1.14.34 → deriva_ml-1.14.36}/src/deriva_ml.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: deriva-ml
-Version: 1.14.34
+Version: 1.14.36
 Summary: Utilities to simplify use of Dervia and Pandas to create reproducable ML pipelines
 Author-email: ISRD <isrd-dev@isi.edu>
 Requires-Python: >=3.10

{deriva_ml-1.14.34 → deriva_ml-1.14.36}/src/deriva_ml.egg-info/SOURCES.txt

@@ -3,7 +3,6 @@ LICENSE
 README.md
 mkdocs.yml
 pyproject.toml
-release.sh
 uv.lock
 .github/release-drafter.yml
 .github/workflows/publish-docs.yml
@@ -42,8 +41,10 @@ docs/user-guide/install.md
 docs/user-guide/notebooks.md
 docs/user-guide/overview.md
 src/deriva_ml/__init__.py
+src/deriva_ml/bump_version.py
 src/deriva_ml/demo_catalog.py
 src/deriva_ml/feature.py
+src/deriva_ml/install_kernel.py
 src/deriva_ml/run_notebook.py
 src/deriva_ml.egg-info/PKG-INFO
 src/deriva_ml.egg-info/SOURCES.txt

{deriva_ml-1.14.34 → deriva_ml-1.14.36}/src/deriva_ml.egg-info/entry_points.txt

@@ -1,6 +1,8 @@
 [console_scripts]
+bump-version = deriva_ml.bump_version:main
 deriva-ml-alter-annotation = deriva_ml.schema_setup.alter_annotation:main
 deriva-ml-check-catalog-schema = deriva_ml.schema.check_schema:main
 deriva-ml-create-schema = deriva_ml.schema_setup.create_schema:main
+deriva-ml-install-kernel = deriva_ml.install_kernel:main
 deriva-ml-run-notebook = deriva_ml.run_notebook:main
 deriva-ml-table-comments-utils = deriva_ml.schema_setup.table_comments_utils:main