calkit-python 0.25.1__tar.gz → 0.25.2__tar.gz

{calkit_python-0.25.1 → calkit_python-0.25.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: calkit-python
-Version: 0.25.1
+Version: 0.25.2
 Summary: Reproducibility simplified.
 Project-URL: Homepage, https://calkit.org
 Project-URL: Issues, https://github.com/calkit/calkit/issues

{calkit_python-0.25.1 → calkit_python-0.25.2}/calkit/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.25.1"
+__version__ = "0.25.2"
 
 from .core import *  # noqa: F403, I001
 from . import git  # noqa: F401

{calkit_python-0.25.1 → calkit_python-0.25.2}/calkit/cli/main.py

@@ -66,7 +66,7 @@ app.add_typer(overleaf_app, name="overleaf", help="Interact with Overleaf.")
 app.add_typer(cloud_app, name="cloud", help="Interact with a Calkit Cloud.")
 
 # Constants for version control auto-ignore
-AUTO_IGNORE_SUFFIXES = [".DS_Store", ".env", ".pyc"]
+AUTO_IGNORE_SUFFIXES = [".DS_Store", ".env", ".pyc", ".synctex.gz"]
 AUTO_IGNORE_PATHS = [os.path.join(".dvc", "config.local")]
 AUTO_IGNORE_PREFIXES = [".venv", "__pycache__"]
 # Constants for version control auto-add to DVC
@@ -675,45 +675,127 @@ def run_local_server():
     )
 
 
-@app.command(
-    name="run",
-    add_help_option=False,
-)
+@app.command(name="run")
 def run(
-    targets: Optional[list[str]] = typer.Argument(default=None),
-    help: Annotated[bool, typer.Option("-h", "--help")] = False,
-    quiet: Annotated[bool, typer.Option("-q", "--quiet")] = False,
-    verbose: Annotated[bool, typer.Option("-v", "--verbose")] = False,
-    force: Annotated[bool, typer.Option("-f", "--force")] = False,
-    interactive: Annotated[bool, typer.Option("-i", "--interactive")] = False,
-    single_item: Annotated[bool, typer.Option("-s", "--single-item")] = False,
+    targets: Optional[list[str]] = typer.Argument(
+        default=None, help="Stages to run."
+    ),
+    quiet: Annotated[
+        bool, typer.Option("-q", "--quiet", help="Be quiet.")
+    ] = False,
+    verbose: Annotated[
+        bool, typer.Option("-v", "--verbose", help="Print verbose output.")
+    ] = False,
+    force: Annotated[
+        bool,
+        typer.Option(
+            "-f",
+            "--force",
+            help="Run even if stages or inputs have not changed.",
+        ),
+    ] = False,
+    interactive: Annotated[
+        bool,
+        typer.Option(
+            "-i",
+            "--interactive",
+            help="Ask for confirmation before running each stage.",
+        ),
+    ] = False,
+    single_item: Annotated[
+        bool,
+        typer.Option(
+            "-s",
+            "--single-item",
+            help="Run only a single stage without any dependents.",
+        ),
+    ] = False,
     pipeline: Annotated[
         Optional[str], typer.Option("-p", "--pipeline")
     ] = None,
     all_pipelines: Annotated[
-        bool, typer.Option("-P", "--all-pipelines")
+        bool,
+        typer.Option(
+            "-P", "--all-pipelines", help="Run all pipelines in the repo."
+        ),
+    ] = False,
+    recursive: Annotated[
+        bool,
+        typer.Option(
+            "-R", "--recursive", help="Run pipelines in subdirectories."
+        ),
     ] = False,
-    recursive: Annotated[bool, typer.Option("-R", "--recursive")] = False,
     downstream: Annotated[
-        Optional[list[str]], typer.Option("--downstream")
+        Optional[list[str]],
+        typer.Option(
+            "--downstream",
+            help="Start from the specified stage and run all downstream.",
+        ),
     ] = None,
     force_downstream: Annotated[
-        bool, typer.Option("--force-downstream")
+        bool,
+        typer.Option(
+            "--force-downstream",
+            help=(
+                "Force downstream stages to run even if "
+                "they are still up-to-date."
+            ),
+        ),
+    ] = False,
+    pull: Annotated[
+        bool,
+        typer.Option("--pull", help="Try automatically pulling missing data."),
     ] = False,
-    pull: Annotated[bool, typer.Option("--pull")] = False,
-    allow_missing: Annotated[bool, typer.Option("--allow-missing")] = False,
-    dry: Annotated[bool, typer.Option("--dry")] = False,
-    keep_going: Annotated[bool, typer.Option("--keep-going", "-k")] = False,
-    ignore_errors: Annotated[bool, typer.Option("--ignore-errors")] = False,
-    glob: Annotated[bool, typer.Option("--glob")] = False,
-    no_commit: Annotated[bool, typer.Option("--no-commit")] = False,
-    no_run_cache: Annotated[bool, typer.Option("--no-run-cache")] = False,
+    allow_missing: Annotated[
+        bool,
+        typer.Option("--allow-missing", help="Skip stages with missing data."),
+    ] = False,
+    dry: Annotated[
+        bool,
+        typer.Option("--dry", help="Only print commands that would execute."),
+    ] = False,
+    keep_going: Annotated[
+        bool,
+        typer.Option(
+            "--keep-going",
+            "-k",
+            help=(
+                "Continue executing, skipping stages with failed "
+                "inputs from other stages."
+            ),
+        ),
+    ] = False,
+    ignore_errors: Annotated[
+        bool,
+        typer.Option("--ignore-errors", help="Ignore errors from stages."),
+    ] = False,
+    glob: Annotated[
+        bool,
+        typer.Option("--glob", help="Match stages with glob-style patterns."),
+    ] = False,
+    no_commit: Annotated[
+        bool, typer.Option("--no-commit", help="Do not save to the run cache.")
+    ] = False,
+    no_run_cache: Annotated[
+        bool, typer.Option("--no-run-cache", help="Ignore the run cache.")
+    ] = False,
+    save_after_run: Annotated[
+        bool,
+        typer.Option("--save", "-S", help="Save the project after running."),
+    ] = False,
+    save_message: Annotated[
+        str | None,
+        typer.Option(
+            "--save-message", "-m", help="Commit message for saving."
+        ),
+    ] = None,
 ):
     """Check dependencies and run the pipeline."""
     os.environ["CALKIT_PIPELINE_RUNNING"] = "1"
     dotenv.load_dotenv(dotenv_path=".env", verbose=verbose)
     # First check any system-level dependencies exist
-    typer.echo("Checking system-level dependencies")
+    if not quiet:
+        typer.echo("Checking system-level dependencies")
     try:
         calkit.check_system_deps()
     except Exception as e:
@@ -722,7 +804,8 @@ def run(
     # Compile the pipeline
     ck_info = calkit.load_calkit_info()
     if ck_info.get("pipeline", {}):
-        typer.echo("Compiling DVC pipeline")
+        if not quiet:
+            typer.echo("Compiling DVC pipeline")
         try:
             calkit.pipeline.to_dvc(ck_info=ck_info, write=True)
         except Exception as e:
@@ -733,7 +816,6 @@ def run(
     args = targets
     # Extract any boolean args
     for name in [
-        "help",
         "quiet",
         "verbose",
         "force",
@@ -762,6 +844,12 @@ def run(
         os.environ.pop("CALKIT_PIPELINE_RUNNING", None)
         raise_error("DVC pipeline failed")
     os.environ.pop("CALKIT_PIPELINE_RUNNING", None)
+    if save_after_run or save_message is not None:
+        if save_message is None:
+            save_message = "Run pipeline"
+        if not quiet:
+            typer.echo("Saving the project after successful run")
+        save(save_all=True, message=save_message)
 
 
 @app.command(name="manual-step", help="Execute a manual step.")

{calkit_python-0.25.1 → calkit_python-0.25.2}/calkit/models/pipeline.py

@@ -132,16 +132,19 @@ class PythonScriptStage(Stage):
 class LatexStage(Stage):
     kind: Literal["latex"] = "latex"
     target_path: str
-    silent: bool = False
+    verbose: bool = False
     force: bool = False
+    synctex: bool = True
 
     @property
     def dvc_cmd(self) -> str:
         cmd = f"{self.xenv_cmd} -- latexmk -cd -interaction=nonstopmode"
-        if self.silent:
+        if not self.verbose:
             cmd += " -silent"
         if self.force:
             cmd += " -f"
+        if self.synctex:
+            cmd += " -synctex=1"
         cmd += f" -pdf {self.target_path}"
         return cmd
 

{calkit_python-0.25.1 → calkit_python-0.25.2}/calkit/pipeline.py

@@ -44,9 +44,13 @@ def to_dvc(
     except Exception as e:
         raise ValueError(f"Pipeline is not defined properly: {e}")
     dvc_stages = {}
-    # First, create stages for checking/exporting all environments
+    # First, create stages for checking/exporting all environments used in the
+    # pipeline
+    used_envs = set([stage.environment for stage in pipeline.stages.values()])
     env_lock_fpaths = {}
     for env_name, env in ck_info.get("environments", {}).items():
+        if env_name not in used_envs:
+            continue
         env_fpath = env.get("path")
         lock_fpath = get_env_lock_fpath(
             env=env, env_name=env_name, as_posix=True

{calkit_python-0.25.1 → calkit_python-0.25.2}/calkit/tests/cli/test_new.py

@@ -548,7 +548,7 @@ def test_new_latex_stage(tmp_dir):
     pipeline = calkit.dvc.read_pipeline()
     assert pipeline["stages"]["build-paper"]["cmd"] == (
         "calkit xenv -n tex --no-check -- "
-        "latexmk -cd -interaction=nonstopmode -pdf paper.tex"
+        "latexmk -cd -interaction=nonstopmode -silent -synctex=1 -pdf paper.tex"
     )
     assert set(pipeline["stages"]["build-paper"]["deps"]) == set(
         ["paper.tex", ".calkit/env-locks/tex.json"]

{calkit_python-0.25.1 → calkit_python-0.25.2}/calkit/tests/models/test_pipeline.py

@@ -46,8 +46,8 @@ def test_wordtopdfstage():
 
 def test_latexstage():
     s = LatexStage(environment="tex", target_path="my-paper.tex")
-    assert " -silent " not in s.dvc_cmd
-    s.silent = True
     assert " -silent " in s.dvc_cmd
+    s.verbose = True
+    assert " -silent " not in s.dvc_cmd
     assert "my-paper.tex" in s.dvc_deps
     assert "my-paper.pdf" in s.dvc_outs

{calkit_python-0.25.1 → calkit_python-0.25.2}/calkit/tests/test_pipeline.py

@@ -21,7 +21,7 @@ def test_to_dvc():
             "stages": {
                 "get-data": {
                     "kind": "python-script",
-                    "environment": "my-env",
+                    "environment": "py",
                     "script_path": "something/my-cool-script.py",
                     "outputs": [
                         "my-output.out",

{calkit_python-0.25.1 → calkit_python-0.25.2}/docs/notebooks.md

@@ -38,7 +38,7 @@ we can focus on three rules:
    `nbstripout --install` in the project directory.
 1. A notebook must run in one of the project's [environments](environments.md).
 1. Notebooks should be incorporated into the project's
-   [pipeline](pipeline/index.md), notebooks are no exception.
+   [pipeline](pipeline/index.md).
    It's fine to do some ad hoc work interactively to get the notebook
    working properly, but
    "official" outputs should be generated by calling `calkit run`.