calkit-python 0.38.2__tar.gz → 0.38.4__tar.gz

{calkit_python-0.38.2 → calkit_python-0.38.4}/.pre-commit-config.yaml

@@ -4,6 +4,7 @@ repos:
     hooks:
       - id: check-case-conflict
       - id: check-merge-conflict
+        exclude: ^docs/overleaf\.md$
       - id: end-of-file-fixer
       - id: trailing-whitespace
       - id: check-yaml

{calkit_python-0.38.2 → calkit_python-0.38.4}/AGENTS.md

@@ -18,3 +18,6 @@ Wrap prose at natural breakpoints in phrases or punctuation to keep max
 line length below 80 characters.
 
 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.

{calkit_python-0.38.2 → calkit_python-0.38.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: calkit-python
-Version: 0.38.2
+Version: 0.38.4
 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'
@@ -209,6 +209,11 @@ all scientific or analytical computing projects.
 
 <!-- INCLUDE: docs/quickstart.md +1 -->
 
+<!-- prettier-ignore -->
+!!! note
+    `ck` is an abbreviated alias for the `calkit` executable.
+    All `calkit` commands can be run as `ck` instead, e.g., `ck save -am "..."`.
+
 ### From an existing project
 
 If you want to use Calkit with an existing project,

{calkit_python-0.38.2 → calkit_python-0.38.4}/README.md

@@ -150,6 +150,11 @@ all scientific or analytical computing projects.
 
 <!-- INCLUDE: docs/quickstart.md +1 -->
 
+<!-- prettier-ignore -->
+!!! note
+    `ck` is an abbreviated alias for the `calkit` executable.
+    All `calkit` commands can be run as `ck` instead, e.g., `ck save -am "..."`.
+
 ### From an existing project
 
 If you want to use Calkit with an existing project,

calkit_python-0.38.4/calkit/__init__.py

@@ -0,0 +1,83 @@
+from importlib.metadata import version as _version
+
+__version__ = _version("calkit-python")
+
+from .core import *  # noqa: F403, I001
+
+# Lazy-load submodules to speed up imports
+_SUBMODULES = {
+    "git",
+    "dvc",
+    "cloud",
+    "fs",
+    "jupyter",
+    "config",
+    "models",
+    "office",
+    "templates",
+    "conda",
+    "calc",
+    "check",
+    "github",
+    "invenio",
+    "releases",
+    "licenses",
+    "overleaf",
+    "julia",
+    "notebooks",
+    "environments",
+    "pipeline",
+    "matlab",
+    "datasets",
+    "detect",
+    "docker",
+    "gui",
+    "magics",
+    "ops",
+    "server",
+}
+
+
+def __getattr__(name: str):
+    if name in _SUBMODULES:
+        import importlib
+
+        mod = importlib.import_module(f"calkit.{name}")
+        globals()[name] = mod
+        return mod
+    if name == "declare_notebook":
+        from .notebooks import declare_notebook
+
+        globals()["declare_notebook"] = declare_notebook
+        return declare_notebook
+    raise AttributeError(f"module 'calkit' has no attribute {name!r}")
+
+
+def _jupyter_labextension_paths():
+    return [{"src": "labextension", "dest": "calkit"}]
+
+
+def _jupyter_server_extension_points():
+    return [{"module": "calkit"}]
+
+
+def _load_jupyter_server_extension(server_app):
+    """Registers the API handler to receive HTTP requests from the frontend
+    extension.
+
+    Parameters
+    ----------
+    server_app: jupyterlab.labapp.LabApp
+        JupyterLab application instance
+    """
+    import os
+
+    from .jupyterlab.routes import setup_route_handlers
+
+    # Change to root_dir so all handlers work in the correct directory context
+    root_dir = server_app.root_dir
+    os.chdir(root_dir)
+    server_app.log.info(f"Changed working directory to {root_dir}")
+    setup_route_handlers(server_app.web_app)
+    name = "calkit"
+    server_app.log.info(f"Registered {name} server extension")

{calkit_python-0.38.2 → calkit_python-0.38.4}/calkit/check.py

@@ -3,8 +3,6 @@
 import os
 from typing import Callable
 
-import git
-from git.exc import InvalidGitRepositoryError
 from pydantic import BaseModel, computed_field
 
 import calkit
@@ -176,6 +174,9 @@ 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

{calkit_python-0.38.2 → calkit_python-0.38.4}/calkit/cli/check.py

@@ -11,22 +11,11 @@ import subprocess
 from typing import Annotated, Callable
 
 import dotenv
-import git
 import typer
 
 import calkit
-import calkit.environments
-import calkit.matlab
-import calkit.pipeline
-from calkit.check import check_reproducibility
 from calkit.cli import raise_error, warn
 from calkit.core import get_md5
-from calkit.environments import (
-    get_all_conda_lock_fpaths,
-    get_all_docker_lock_fpaths,
-    get_all_venv_lock_fpaths,
-    get_env_lock_fpath,
-)
 
 check_app = typer.Typer(no_args_is_help=True)
 
@@ -249,6 +238,8 @@ def check_repro(
     ] = ".",
 ) -> None:
     """Check the reproducibility of a project."""
+    from calkit.check import check_reproducibility
+
     res = check_reproducibility(wdir=wdir, log_func=typer.echo)
     calkit.echo(res.to_pretty())
 
@@ -268,6 +259,13 @@ def check_environment(
     ] = False,
 ) -> str | None:
     """Check that an environment is up-to-date."""
+    from calkit.environments import (
+        get_all_conda_lock_fpaths,
+        get_all_docker_lock_fpaths,
+        get_all_venv_lock_fpaths,
+        get_env_lock_fpath,
+    )
+
     dotenv.load_dotenv(dotenv_path=".env", verbose=verbose)
     ck_info = calkit.load_calkit_info(process_includes="environments")
     envs = ck_info.get("environments", {})
@@ -353,8 +351,8 @@ def check_environment(
             raise_error("venv environments require a prefix")
         if "path" not in env:
             raise_error("venv environments require a path")
-        prefix = env["prefix"]
-        path = env["path"]
+        prefix = os.path.expandvars(env["prefix"])
+        path = os.path.expandvars(env["path"])
         lock_fpath = get_env_lock_fpath(
             env=env, env_name=env_name, as_posix=False
         )
@@ -457,6 +455,10 @@ def check_environments(
     if not envs:
         typer.echo("No environments defined in calkit.yaml")
         return
+    # Set any project-level environmental variables before checking
+    # environments
+    dotenv.load_dotenv(dotenv_path=".env", verbose=verbose)
+    calkit.set_env_vars(ck_info=ck_info, cli=True)
     failures = []
     for env_name, env in envs.items():
         if env.get("kind") in calkit.environments.KINDS_NO_CHECK:
@@ -1290,6 +1292,8 @@ 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()
     if not repo.ignored(".env"):
         typer.echo("Adding .env to .gitignore")

{calkit_python-0.38.2 → calkit_python-0.38.4}/calkit/cli/cloud.py

@@ -8,7 +8,6 @@ import webbrowser
 from typing import Annotated
 
 import typer
-from requests.exceptions import HTTPError
 
 import calkit
 from calkit.cli import raise_error
@@ -47,6 +46,8 @@ def login(
     First try a GET request to the /user endpoint to check if the user is
     already logged in. If not, perform OAuth device flow.
     """
+    from requests.exceptions import HTTPError
+
     try:
         calkit.cloud.get("/user")
         calkit.echo("Authenticated successfully ✅")

{calkit_python-0.38.2 → calkit_python-0.38.4}/calkit/cli/config.py

@@ -6,15 +6,11 @@ import glob
 import os
 import subprocess
 
-import git
 import typer
-from git.exc import InvalidGitRepositoryError
 from typing_extensions import Annotated
 
 import calkit
-from calkit import config
 from calkit.cli.core import raise_error
-from calkit.dvc import configure_remote, get_remotes, set_remote_auth
 
 config_app = typer.Typer(no_args_is_help=True)
 
@@ -22,6 +18,8 @@ config_app = typer.Typer(no_args_is_help=True)
 @config_app.command(name="set")
 def set_config_value(key: str, value: str):
     """Set a value in the config."""
+    from calkit import config
+
     keys = config.Settings.model_fields.keys()
     if key not in keys:
         raise_error(
@@ -38,6 +36,8 @@ def set_config_value(key: str, value: str):
 @config_app.command(name="get")
 def get_config_value(key: str) -> None:
     """Get and print a value from the config."""
+    from calkit import config
+
     cfg = config.read().model_dump()
     if key not in cfg:
         raise_error(
@@ -53,6 +53,8 @@ def get_config_value(key: str) -> None:
 @config_app.command(name="unset")
 def unset_config_value(key: str):
     """Unset a value in the config, returning it to default."""
+    from calkit import config
+
     model_fields = config.Settings.model_fields
     if key not in model_fields:
         raise_error(
@@ -90,6 +92,11 @@ 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
+
     try:
         remote_name = configure_remote(use_ck=not http)
         set_remote_auth(remote_name=remote_name)
@@ -119,6 +126,8 @@ def setup_remote_auth():
     """Store a Calkit cloud token in the local DVC config for all Calkit
     remotes.
     """
+    from calkit.dvc import get_remotes, set_remote_auth
+
     try:
         remotes = get_remotes()
     except Exception:
@@ -132,6 +141,8 @@ def setup_remote_auth():
 @config_app.command(name="list")
 def list_config_keys():
     """List keys in the config."""
+    from calkit import config
+
     cfg = config.read()
     for key in cfg.model_dump():
         typer.echo(key)
@@ -140,6 +151,8 @@ def list_config_keys():
 @config_app.command(name="github-ssh")
 def config_github_ssh():
     """Walk through the process of adding an SSH key to GitHub."""
+    import git
+
     typer.echo("Checking if you can already connect to GitHub via SSH")
     # First check if we can already connect to GitHub
     ssh_test_cmd = ["ssh", "-T", "git@github.com"]

calkit_python-0.38.4/calkit/cli/core.py

@@ -0,0 +1,85 @@
+"""Core CLI functionality."""
+
+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",
+    incomplete: str,
+) -> list:
+    """Return pipeline stage names for shell tab-completion."""
+    if not os.path.isfile("calkit.yaml"):
+        return []
+    try:
+        import ruamel.yaml
+        from click.shell_completion import CompletionItem
+
+        ryaml = ruamel.yaml.YAML()
+        with open("calkit.yaml") as f:
+            info = ryaml.load(f) or {}
+        stages = info.get("pipeline", {}).get("stages", {})
+        return [
+            CompletionItem(name)
+            for name in stages
+            if name.startswith(incomplete)
+        ]
+    except Exception:
+        return []
+
+
+def print_sep(name: str):
+    width = 66
+    txt_width = len(name) + 2
+    buffer_width = (width - txt_width) // 2
+    buffer = "-" * buffer_width
+    line = f"{buffer} {name} {buffer}"
+    if len(line) == (width - 1):
+        line += "-"
+    typer.echo(line)
+
+
+def run_cmd(cmd: list[str]):
+    if os.name == "nt":
+        subprocess.call(cmd)
+    else:
+        import pty
+
+        pty.spawn(cmd, lambda fd: os.read(fd, 1024))
+
+
+def raise_error(txt: str):
+    typer.echo(typer.style("Error: " + str(txt), fg="red"), err=True)
+    raise typer.Exit(1)
+
+
+def warn(txt: str, prefix: str = "Warning: "):
+    typer.echo(typer.style(prefix + str(txt), fg="yellow"))

{calkit_python-0.38.2 → calkit_python-0.38.4}/calkit/cli/import_.py

@@ -9,16 +9,10 @@ import os
 from copy import deepcopy
 from typing import Annotated
 
-import git
-import requests
 import typer
-from tqdm import tqdm
 
 import calkit
-import calkit.invenio
 from calkit.cli import raise_error
-from calkit.dvc import run_dvc_command
-from calkit.models.core import _ImportedFromProject
 
 import_app = typer.Typer(no_args_is_help=True)
 
@@ -72,12 +66,19 @@ def import_dataset(
                 "remote instead of ck://."
             ),
         ),
-    ] = not calkit.dvc.USE_CK_REMOTE_BY_DEFAULT,
+    ] = False,
 ):
     """Import a dataset.
 
     Currently only supports datasets kept in DVC, not Git.
     """
+    import git
+    import requests
+    from tqdm import tqdm
+
+    from calkit.dvc import run_dvc_command
+    from calkit.models.core import _ImportedFromProject
+
     # Ensure we don't already have a dataset at this path
     path_split = src_path.split("/")
     owner_name = path_split[0]
@@ -260,6 +261,8 @@ 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 "
@@ -368,6 +371,11 @@ def import_from_zenodo(
     ] = False,
 ):
     """Import files from a Zenodo record."""
+    import git
+    import requests
+
+    from calkit.dvc import run_dvc_command
+
     # Ensure destination directory either doesn't exist or is empty
     if os.path.isdir(dest_dir):
         if os.listdir(dest_dir):

{calkit_python-0.38.2 → calkit_python-0.38.4}/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)
@@ -134,9 +140,29 @@ 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:
             continue
         typer.echo(name)
+
+
+@list_app.command(name="remotes")
+def list_remotes():
+    """List Git and DVC remotes."""
+    import git
+
+    try:
+        repo = git.Repo()
+        for remote in repo.remotes:
+            typer.echo(f"(Git) {remote.name}: {remote.url}")
+    except Exception as e:
+        warn(f"Could not list Git remotes: {e}")
+    # Now DVC remotes
+    try:
+        dvc_remotes = calkit.dvc.get_remotes()
+        for name, url in dvc_remotes.items():
+            typer.echo(f"(DVC) {name}: {url}")
+    except Exception as e:
+        warn(f"Could not list DVC remotes: {e}")