calkit-python 0.38.3__tar.gz → 0.39.0__tar.gz

{calkit_python-0.38.3 → calkit_python-0.39.0}/AGENTS.md

@@ -21,3 +21,7 @@ Agents should never make commits to Git.
 
 Prefer tests that include multiple scenarios to comprehensively test
 a feature in one function over many different test functions.
+
+Do not write docstrings in test functions.
+
+For prose, only use one space after punctuation.

{calkit_python-0.38.3 → calkit_python-0.39.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: calkit-python
-Version: 0.38.3
+Version: 0.39.0
 Summary: Reproducibility simplified.
 Project-URL: Homepage, https://calkit.org
 Project-URL: Issues, https://github.com/calkit/calkit/issues
@@ -26,9 +26,9 @@ Requires-Dist: arithmeval
 Requires-Dist: bibtexparser
 Requires-Dist: checksumdir
 Requires-Dist: docx2pdf
-Requires-Dist: dvc==3.66.1
+Requires-Dist: dvc==3.67.1
 Requires-Dist: fastapi
-Requires-Dist: fsspec>=2026.2.0
+Requires-Dist: fsspec>=2026.4.0
 Requires-Dist: gitpython
 Requires-Dist: json2latex>=0.0.3
 Requires-Dist: jupyterlab>=4.4.5
@@ -45,10 +45,10 @@ Requires-Dist: python-dotenv>=1
 Requires-Dist: pywin32; platform_system == 'Windows'
 Requires-Dist: requests
 Requires-Dist: sqlitedict>=2.1.0
-Requires-Dist: texsoup>=0.3.1
+Requires-Dist: texsoup>=0.3.3
 Requires-Dist: toml>=0.10.2
 Requires-Dist: tqdm>=4.67.1
-Requires-Dist: typer==0.24.1
+Requires-Dist: typer==0.25.1
 Requires-Dist: uvicorn
 Provides-Extra: data
 Requires-Dist: pandas>=2.2.3; extra == 'data'

{calkit_python-0.38.3 → calkit_python-0.39.0}/calkit/check.py

@@ -174,14 +174,13 @@ def check_reproducibility(
     wdir: str = ".", log_func: Callable | None = None
 ) -> ReproCheck:
     """Check the reproducibility of a project."""
-    import git
     from git.exc import InvalidGitRepositoryError
 
     res = dict()
     if log_func is None:
         log_func = print
     try:
-        git.Repo(wdir)
+        calkit.git.get_repo(wdir)
         res["is_git_repo"] = True
     except InvalidGitRepositoryError:
         res["is_git_repo"] = False

{calkit_python-0.38.3 → calkit_python-0.39.0}/calkit/cli/check.py

@@ -1292,9 +1292,7 @@ def check_env_vars(
                 dotenv_path=".env", key_to_set=name, value_to_set=value
             )
     # Ensure that .env is ignored by git
-    import git
-
-    repo = git.Repo()
+    repo = calkit.git.get_repo()
     if not repo.ignored(".env"):
         typer.echo("Adding .env to .gitignore")
         with open(".gitignore", "a") as f:

{calkit_python-0.38.3 → calkit_python-0.39.0}/calkit/cli/config.py

@@ -92,7 +92,6 @@ def setup_remote(
     """Setup the Calkit cloud as the default DVC remote and store a token in
     the local config.
     """
-    import git
     from git.exc import InvalidGitRepositoryError
 
     from calkit.dvc import configure_remote, set_remote_auth
@@ -113,7 +112,7 @@ def setup_remote(
     except (ValueError, RuntimeError) as e:
         raise_error(f"Failed to set up DVC remote: {e}")
     if not no_commit:
-        repo = git.Repo()
+        repo = calkit.git.get_repo()
         repo.git.add(".dvc/config")
         if ".dvc/config" in calkit.git.get_staged_files():
             typer.echo("Committing changes to DVC config")

{calkit_python-0.38.3 → calkit_python-0.39.0}/calkit/cli/core.py

@@ -3,15 +3,34 @@
 from __future__ import annotations
 
 import os
+import re
 import subprocess
 from typing import TYPE_CHECKING
 
 import typer
+from typer.core import TyperGroup
 
 if TYPE_CHECKING:
     import click
 
 
+class AliasGroup(TyperGroup):
+    """TyperGroup that resolves command aliases defined with '|' in the name."""
+
+    _CMD_SPLIT_P = re.compile(r" ?[,|] ?")
+
+    def get_command(self, ctx, cmd_name):
+        cmd_name = self._group_cmd_name(cmd_name)
+        return super().get_command(ctx, cmd_name)
+
+    def _group_cmd_name(self, default_name):
+        for cmd in self.commands.values():
+            name = cmd.name
+            if name and default_name in self._CMD_SPLIT_P.split(name):
+                return name
+        return default_name
+
+
 def complete_stage_names(
     ctx: "click.Context",
     param: "click.Parameter",
@@ -27,10 +46,25 @@ def complete_stage_names(
         ryaml = ruamel.yaml.YAML()
         with open("calkit.yaml") as f:
             info = ryaml.load(f) or {}
+        candidates: list[str] = []
         stages = info.get("pipeline", {}).get("stages", {})
+        candidates.extend(stages.keys())
+        for sp_cfg in info.get("subprojects", []):
+            if not isinstance(sp_cfg, dict) or not sp_cfg.get("path"):
+                continue
+            sp_path = sp_cfg["path"]
+            sp_calkit = os.path.join(sp_path, "calkit.yaml")
+            sp_name = os.path.basename(sp_path.rstrip("/"))
+            candidates.append(sp_name)
+            if os.path.isfile(sp_calkit):
+                with open(sp_calkit) as f:
+                    sp_info = ryaml.load(f) or {}
+                sp_stages = sp_info.get("pipeline", {}).get("stages", {})
+                for stage in sp_stages:
+                    candidates.append(f"{sp_name}:{stage}")
         return [
             CompletionItem(name)
-            for name in stages
+            for name in candidates
             if name.startswith(incomplete)
         ]
     except Exception:

{calkit_python-0.38.3 → calkit_python-0.39.0}/calkit/cli/import_.py

@@ -72,7 +72,6 @@ def import_dataset(
 
     Currently only supports datasets kept in DVC, not Git.
     """
-    import git
     import requests
     from tqdm import tqdm
 
@@ -95,7 +94,7 @@ def import_dataset(
         raise_error("A dataset already exists in this project at this path")
     elif overwrite and ds_dest_path in ds_paths:
         datasets = [ds for ds in datasets if ds["path"] != ds_dest_path]
-    repo = git.Repo()
+    repo = calkit.git.get_repo()
     # Obtain, save, and commit the .dvc file for the dataset, or if this is
     # kept in Git, just download the files and commit them here
     typer.echo("Fetching import info")
@@ -261,8 +260,6 @@ def import_environment(
     ] = False,
 ) -> None:
     """Import an environment from another project."""
-    import git
-
     raise_error(
         "This command is not yet implemented; "
         "please thumbs-up this issue if you'd like to see "
@@ -317,7 +314,7 @@ def import_environment(
     ck_info["environments"] = environments
     with open("calkit.yaml", "w") as f:
         calkit.ryaml.dump(ck_info, f)
-    repo = git.Repo()
+    repo = calkit.git.get_repo()
     repo.git.add("calkit.yaml")
     if not no_commit and calkit.git.get_staged_files():
         repo.git.commit(["-m", f"Import environment {src}"])
@@ -371,7 +368,6 @@ def import_from_zenodo(
     ] = False,
 ):
     """Import files from a Zenodo record."""
-    import git
     import requests
 
     from calkit.dvc import run_dvc_command
@@ -440,7 +436,7 @@ def import_from_zenodo(
             for chunk in resp.iter_content(chunk_size=8192):
                 f.write(chunk)
     # Decide if this should be stored in Git or DVC
-    repo = git.Repo()
+    repo = calkit.git.get_repo()
     commit_paths = []
     if storage is None:
         if calkit.get_size(dest_dir) > calkit.DVC_SIZE_THRESH_BYTES:
@@ -508,7 +504,7 @@ def import_from_zenodo(
         json.dump(imports, f, indent=2)
     # Commit if desired
     if not no_commit:
-        repo = git.Repo()
+        repo = calkit.git.get_repo()
         repo.git.add(commit_paths)
         if repo.git.diff(commit_paths + ["--staged"]):
             repo.git.commit(

{calkit_python-0.38.3 → calkit_python-0.39.0}/calkit/cli/list.py

@@ -7,9 +7,9 @@ from typing import Annotated, Literal
 import typer
 
 import calkit
-from calkit.cli import warn
+from calkit.cli import AliasGroup, warn
 
-list_app = typer.Typer(no_args_is_help=True)
+list_app = typer.Typer(cls=AliasGroup, no_args_is_help=True)
 
 
 def _list_objects(
@@ -50,33 +50,37 @@ def _list_objects(
                 typer.echo(f"  {k}: {v}")
 
 
-@list_app.command(name="notebooks")
+@list_app.command(name="notebooks|nb")
 def list_notebooks():
+    """List notebooks in the project."""
     _list_objects("notebooks")
 
 
-@list_app.command(name="figures")
+@list_app.command(name="figures|figs")
 def list_figures():
+    """List figures in the project."""
     _list_objects("figures")
 
 
 @list_app.command(name="datasets")
 def list_datasets():
+    """List datasets in the project."""
     _list_objects("datasets")
 
 
-@list_app.command(name="publications")
+@list_app.command(name="publications|pubs")
 def list_publications():
+    """List publications in the project."""
     _list_objects("publications")
 
 
-@list_app.command(name="references")
+@list_app.command(name="references|refs")
 def list_references():
+    """List reference collections in the project."""
     _list_objects("references")
 
 
-@list_app.command(name="environments")
-@list_app.command(name="envs")
+@list_app.command(name="environments|envs")
 def list_environments():
     """List environments in the project."""
     envs = calkit.load_calkit_info().get("environments", {})
@@ -88,6 +92,7 @@ def list_environments():
 
 @list_app.command(name="templates")
 def list_templates():
+    """List all available Calkit templates."""
     for kind, tpl_dict in calkit.templates.TEMPLATES.items():
         for name in tpl_dict:
             typer.echo(f"{kind}/{name}")
@@ -95,6 +100,7 @@ def list_templates():
 
 @list_app.command(name="procedures")
 def list_procedures():
+    """List procedures in the current project."""
     ck_info = calkit.load_calkit_info()
     for p in ck_info.get("procedures", {}):
         typer.echo(p)
@@ -134,7 +140,7 @@ def list_stages(
         typer.Option("--kind", "-k", help="Filter stages by kind."),
     ] = None,
 ):
-    """List stages."""
+    """List pipeline stages."""
     stages = calkit.load_calkit_info().get("pipeline", {}).get("stages", {})
     for name, stage in stages.items():
         if kinds is not None and stage.get("kind") not in kinds:
@@ -145,10 +151,8 @@ def list_stages(
 @list_app.command(name="remotes")
 def list_remotes():
     """List Git and DVC remotes."""
-    import git
-
     try:
-        repo = git.Repo()
+        repo = calkit.git.get_repo()
         for remote in repo.remotes:
             typer.echo(f"(Git) {remote.name}: {remote.url}")
     except Exception as e: