calkit-python 0.41.14__py3-none-any.whl → 0.41.16__py3-none-any.whl

calkit/cli/check.py

@@ -180,7 +180,8 @@ def _check_julia_env(
         try:
             subprocess.check_call(
                 cmd,
-                env=os.environ.copy() | {"JULIA_LOAD_PATH": "@:@stdlib"},
+                env=os.environ.copy()
+                | {"JULIA_LOAD_PATH": calkit.julia.load_path()},
             )
         except subprocess.CalledProcessError:
             calkit.environments.save_cache(
@@ -206,7 +207,9 @@ def _check_julia_env(
     cmd = calkit.julia.ensure_startup_file_disabled_in_command(cmd)
     try:
         subprocess.check_call(
-            cmd, env=os.environ.copy() | {"JULIA_LOAD_PATH": "@:@stdlib"}
+            cmd,
+            env=os.environ.copy()
+            | {"JULIA_LOAD_PATH": calkit.julia.load_path()},
         )
     except subprocess.CalledProcessError:
         calkit.environments.save_cache(

calkit/cli/config.py

@@ -4,6 +4,8 @@ from __future__ import annotations
 
 import glob
 import os
+import platform
+import re
 import subprocess
 
 import typer
@@ -233,12 +235,57 @@ def config_github_ssh():
     subprocess.run(keygen_cmd)
     # Start the SSH agent in the background
     typer.echo("Checking that the SSH agent is running")
-    ssh_agent_cmd = subprocess.run(
-        ["ssh-agent", "-s"], capture_output=True, text=True
-    ).stdout
-    p = subprocess.run(ssh_agent_cmd, shell=True)
-    if p.returncode != 0:
-        raise_error("Failed to start ssh-agent")
+    # Note that under git bash / MSYS (MSYSTEM is set) we get a POSIX
+    # ssh-agent on PATH, so we use the POSIX path even on Windows there.
+    native_windows = platform.system() == "Windows" and not os.environ.get(
+        "MSYSTEM"
+    )
+    if native_windows:
+        # On native Windows, OpenSSH's ssh-agent runs as a Windows service
+        # rather than exporting environment variables to the current shell.
+        # The service ships disabled by default, so ensure it's enabled
+        # before starting it (enabling requires administrator privileges).
+        p = subprocess.run(
+            [
+                "powershell",
+                "-NoProfile",
+                "-Command",
+                (
+                    "if ((Get-Service ssh-agent).StartType -eq 'Disabled') "
+                    "{ Set-Service ssh-agent -StartupType Manual }; "
+                    "Start-Service ssh-agent"
+                ),
+            ],
+            capture_output=True,
+            text=True,
+        )
+        if p.returncode != 0:
+            err = (p.stderr.strip() or p.stdout.strip()).lower()
+            if "access" in err and "denied" in err:
+                raise_error(
+                    "Failed to start ssh-agent service: access denied.\n"
+                    "The ssh-agent service is disabled and enabling it "
+                    "requires administrator privileges. Please run the "
+                    "following in an elevated (Run as administrator) "
+                    "PowerShell, then try again:\n\n"
+                    "    Set-Service ssh-agent -StartupType Manual; "
+                    "Start-Service ssh-agent"
+                )
+            raise_error(
+                "Failed to start ssh-agent service: "
+                f"{p.stderr.strip() or p.stdout.strip()}"
+            )
+    else:
+        # On POSIX systems, ssh-agent -s prints shell commands that export
+        # SSH_AUTH_SOCK and SSH_AGENT_PID; parse them into our environment so
+        # the subsequent ssh-add call can find the agent
+        p = subprocess.run(["ssh-agent", "-s"], capture_output=True, text=True)
+        if p.returncode != 0:
+            raise_error("Failed to start ssh-agent")
+        for match in re.finditer(
+            r"(SSH_AUTH_SOCK|SSH_AGENT_PID)=([^;\n]+);", p.stdout
+        ):
+            os.environ[match.group(1)] = match.group(2)
     # Add the SSH key to the ssh-agent
     typer.echo(f"Adding SSH key to ssh-agent: {key_path}")
     cmd = ["ssh-add", key_path]

calkit/cli/main/core.py

@@ -581,6 +581,18 @@ def get_status(
         if pipeline_status and not pipeline_status.has_pipeline:
             typer.echo("This project has no pipeline.")
             return
+        # A failed environment check makes get_status bail out before computing
+        # staleness, leaving stale_stages empty. Don't let that masquerade as an
+        # up-to-date pipeline---say plainly that the status is unknown.
+        elif pipeline_status and pipeline_status.failed_environment_checks:
+            # The failing environments were already named in the warning emitted
+            # right after computing pipeline_status, so keep this explanatory
+            # only rather than repeating the list.
+            typer.echo(
+                "Pipeline status unavailable until the failed environment "
+                "checks above are resolved."
+            )
+            return
         elif pipeline_status and pipeline_status.is_stale:
             typer.echo("Stale stages:")
             for stage_name in pipeline_status.stale_stage_names:
@@ -2586,7 +2598,8 @@ def run_in_env(
             subprocess.check_call(
                 julia_cmd,
                 cwd=wdir,
-                env=os.environ.copy() | {"JULIA_LOAD_PATH": "@:@stdlib"},
+                env=os.environ.copy()
+                | {"JULIA_LOAD_PATH": calkit.julia.load_path()},
             )
         except subprocess.CalledProcessError:
             raise_error("Failed to run in julia environment")

calkit/cli/new.py

@@ -2108,7 +2108,7 @@ def new_julia_env(
         except subprocess.CalledProcessError:
             raise_error(f"Failed to install Julia version {julia_version}")
         cmd = ["julia", f"+{julia_version}", f"--project={env_dir}", "-e"]
-        install_cmd = f'using Pkg; Pkg.activate("{env_dir}");'
+        install_cmd = f'using Pkg; Pkg.activate("{calkit.julia.escape_string(env_dir)}");'
         for package in packages or []:
             install_cmd += f' Pkg.add("{package}");'
         cmd.append(install_cmd)

calkit/cli/notebooks.py

@@ -310,14 +310,18 @@ def check_env_kernel(
                     "still failed."
                 )
         # Don't include version in display_name; IJulia appends it automatically
+        # Escape interpolated values for the Julia string literals---notably the
+        # Windows project path, whose backslashes are otherwise read as invalid
+        # unicode escapes.
+        esc = calkit.julia.escape_string
         julia_cmd = (
             "import IJulia;"
             "kp=IJulia.installkernel("
-            f'"{kernel_name}",'
-            f'"--project={env_dir_abs}",'
+            f'"{esc(kernel_name)}",'
+            f'"--project={esc(env_dir_abs)}",'
             '"--startup-file=no",'
-            f'displayname="{display_name}",'
-            'env=Dict("JULIA_LOAD_PATH" => "@:@stdlib")'
+            f'displayname="{esc(display_name)}",'
+            f'env=Dict("JULIA_LOAD_PATH" => "{esc(calkit.julia.load_path())}")'
             ");"
             "println(kp);"
         )
@@ -474,8 +478,7 @@ def execute_notebook(
         # Create this environment and write it to file
         envs[res.name] = res.env
         ck_info["environments"] = envs
-        with open("calkit.yaml", "w") as f:
-            calkit.ryaml.dump(ck_info, f)
+        calkit.save_calkit_info(ck_info)
     # Detect language from environment
     if language is None:
         detected_language = language_from_notebook(path)
@@ -501,16 +504,20 @@ def execute_notebook(
         raise ValueError(
             "Language must be one of 'python', 'matlab', 'julia', or 'r'"
         )
-    # Try to set kernelspec metadata so execution uses the expected kernel
+    # Try to set kernelspec metadata so execution uses the expected kernel.
+    # Always read/write as UTF-8: notebooks routinely contain non-ASCII (e.g.,
+    # Greek letters such as "ν" in code), and on Windows the default open()
+    # encoding is cp1252, which mangles UTF-8 content into mojibake ("ν" ->
+    # "ν") and breaks execution.
     try:
-        with open(path, "r") as f:
+        with open(path, "r", encoding="utf-8") as f:
             nb_json = json.load(f)
         metadata = nb_json.setdefault("metadata", {})
         kernelspec = metadata.setdefault("kernelspec", {})
         kernelspec["name"] = kernel_name
         kernelspec["display_name"] = display_name
-        kernelspec.setdefault("language", language.lower())
-        with open(path, "w") as f:
+        kernelspec["language"] = language.lower()
+        with open(path, "w", encoding="utf-8") as f:
             json.dump(nb_json, f, indent=1)
     except Exception as e:
         if verbose:

calkit/cli/update.py

@@ -746,7 +746,7 @@ def update_julia_env(
     env_dir = os.path.dirname(spec_path) or "."
     julia_version = env.get("julia")
     julia_bin = ["julia", f"+{julia_version}"] if julia_version else ["julia"]
-    cmds = [f'Pkg.activate("{env_dir}")']
+    cmds = [f'Pkg.activate("{calkit.julia.escape_string(env_dir)}")']
     if add:
         pkg_list = "[" + ", ".join(f'"{p}"' for p in add) + "]"
         cmds.append(f"Pkg.add({pkg_list})")

calkit/core.py

@@ -144,7 +144,9 @@ def load_calkit_info(
     if wdir is not None:
         fpath = os.path.join(wdir, fpath)
     if os.path.isfile(fpath):
-        with open(fpath) as f:
+        # Always read as UTF-8; on Windows the default open() encoding is
+        # cp1252, which mangles non-ASCII content (e.g., Greek letters).
+        with open(fpath, encoding="utf-8") as f:
             info = ryaml.load(f)
     if info is None:
         info = {}
@@ -166,7 +168,7 @@ def load_calkit_info(
                         if wdir is not None:
                             include_fpath = os.path.join(wdir, include_fpath)
                         if os.path.isfile(include_fpath):
-                            with open(include_fpath) as f:
+                            with open(include_fpath, encoding="utf-8") as f:
                                 include_data = ryaml.load(f)
                             info[kind][obj_name] |= include_data
     return info
@@ -180,7 +182,9 @@ def save_calkit_info(
     fpath = "calkit.yaml"
     if wdir is not None:
         fpath = os.path.join(wdir, fpath)
-    with open(fpath, "w") as f:
+    # Always write as UTF-8; on Windows the default open() encoding is cp1252,
+    # which mangles non-ASCII content (e.g., Greek letters) into mojibake.
+    with open(fpath, "w", encoding="utf-8") as f:
         ryaml.dump(info, f)
 
 

calkit/detect.py

@@ -1229,6 +1229,49 @@ def _extract_r_string_assignments(code: str) -> dict[str, str]:
     return assignments
 
 
+def _extract_r_string_vector_assignments(code: str) -> dict[str, list[str]]:
+    """Extract character-vector assignments in R code.
+
+    Captures assignments of the form ``x <- c("a", "b")`` so that a later
+    ``pacman::p_load(char = x)`` can be resolved back to its package list.
+    """
+    assignments = {}
+    pattern = re.compile(
+        r"([A-Za-z_][A-Za-z0-9_.]*)\s*(?:<-|=)\s*c\(([^)]*)\)",
+        flags=re.DOTALL,
+    )
+    for name, body in pattern.findall(code):
+        strings = re.findall(r'["\']([a-zA-Z0-9._]+)["\']', body)
+        if strings:
+            assignments[name] = strings
+    return assignments
+
+
+def _resolve_r_package_args(
+    call_args: str, vector_assignments: dict[str, list[str]]
+) -> set[str]:
+    """Resolve package names from a ``pacman::p_load()`` argument list.
+
+    Handles quoted literals, inline ``c(...)`` vectors, bare (non-standard
+    evaluation) names like ``p_load(dplyr, tidyr)``, and ``char = x`` where
+    ``x`` is a character vector assigned earlier in the script.
+    """
+    packages = set()
+    # Quoted strings are package names, whether passed directly or inside c()
+    packages.update(re.findall(r'["\']([a-zA-Z0-9._]+)["\']', call_args))
+    # char = <var> referencing a character-vector assignment
+    for var in re.findall(r"char\s*=\s*([A-Za-z_][A-Za-z0-9_.]*)", call_args):
+        packages.update(vector_assignments.get(var, []))
+    # Bare names passed positionally; drop keyword arguments (install=, update=,
+    # character.only=, etc.) and their values before collecting identifiers
+    stripped = re.sub(r"[A-Za-z_][A-Za-z0-9_.]*\s*=\s*[^,]+", "", call_args)
+    for token in re.findall(r"[A-Za-z_][A-Za-z0-9_.]*", stripped):
+        # c() is the vector constructor, not a package; TRUE/FALSE are values
+        if token not in {"c", "TRUE", "FALSE", "T", "F"}:
+            packages.add(token)
+    return packages
+
+
 def _extract_julia_string_assignments(code: str) -> dict[str, str]:
     """Extract simple string assignments in Julia code."""
     assignments = {}
@@ -1622,6 +1665,27 @@ def detect_r_dependencies(
     for pattern in patterns:
         matches = re.findall(pattern, code)
         dependencies.update(matches)
+    # requireNamespace()/loadNamespace() take the package as a string and are
+    # commonly used to guard optional installs (e.g. pacman/here bootstrapping)
+    dependencies.update(
+        re.findall(
+            r'(?:require|load)Namespace\s*\(\s*["\']([a-zA-Z0-9._]+)["\']',
+            code,
+        )
+    )
+    # Qualified calls like pkg::fn() or pkg:::fn() reference a package without
+    # ever attaching it, so the package itself is still a dependency
+    dependencies.update(re.findall(r"\b([a-zA-Z][a-zA-Z0-9._]*)\s*:::?", code))
+    # pacman::p_load() loads (and optionally installs) packages dynamically; its
+    # arguments may be bare names, quoted strings, or a character vector passed
+    # via char=, possibly referencing a variable assigned earlier in the script
+    vector_assignments = _extract_r_string_vector_assignments(code)
+    for call_args in re.findall(
+        r"p_load\s*\(((?:[^()]|\([^()]*\))*)\)", code, flags=re.DOTALL
+    ):
+        dependencies.update(
+            _resolve_r_package_args(call_args, vector_assignments)
+        )
     # Filter out base R packages
     base_packages = {
         "base",

calkit/environments.py

@@ -5,6 +5,7 @@ import hashlib
 import json
 import os
 import platform
+import re
 import subprocess
 import tempfile
 from pathlib import Path
@@ -1454,7 +1455,9 @@ def create_julia_project_file_content(
         return content
 
 
-def create_r_description_content(dependencies: list[str]) -> str:
+def create_r_description_content(
+    dependencies: list[str], project_name: str | None = None
+) -> str:
     """Generate R DESCRIPTION file content listing dependencies.
 
     This creates a minimal DESCRIPTION file that renv can work with.
@@ -1463,13 +1466,26 @@ def create_r_description_content(dependencies: list[str]) -> str:
     ----------
     dependencies : list[str]
         List of R package names.
+    project_name : str | None
+        Name for the DESCRIPTION's ``Package`` field. It is sanitized into a
+        valid R package name (letters, numbers and dots, starting with a
+        letter). Falls back to the detected project name, then to
+        ``CalkitProject``.
 
     Returns
     -------
     str
         The DESCRIPTION file content.
     """
-    content = """Package: CalkitProject
+    if project_name is None:
+        project_name = calkit.detect_project_name(prepend_owner=False)
+    # Valid R package names may only contain letters, numbers and dots, and
+    # must start with a letter, so replace anything else (e.g. hyphens) with a
+    # dot and prefix a letter if needed
+    package_name = re.sub(r"[^A-Za-z0-9.]+", ".", project_name).strip(".")
+    if not package_name or not package_name[0].isalpha():
+        package_name = "Calkit." + package_name if package_name else "Calkit"
+    content = f"""Package: {package_name}
 Version: 0.0.1
 Title: Auto-generated R environment
 """

calkit/julia.py

@@ -27,9 +27,36 @@ def get_julia_exe() -> str:
     return "julia"
 
 
+def load_path() -> str:
+    """Return the ``JULIA_LOAD_PATH`` scoping resolution to the active project
+    and stdlib.
+
+    Julia splits ``JULIA_LOAD_PATH`` on the platform path separator---``;`` on
+    Windows and ``:`` elsewhere---so a hardcoded ``:`` leaves ``@stdlib`` off
+    the load path on Windows and even stdlib packages (e.g. ``Pkg``) fail to
+    resolve. ``os.pathsep`` matches Julia's rule on every platform.
+    """
+    return os.pathsep.join(["@", "@stdlib"])
+
+
+def escape_string(value: str) -> str:
+    """Escape ``value`` for embedding in a Julia double-quoted string literal.
+
+    Julia treats ``\\``, ``"`` and ``$`` specially inside double quotes. In
+    particular a Windows path like ``C:\\Users\\...`` is otherwise read as an
+    invalid ``\\U`` unicode escape, so any value interpolated into Julia source
+    (e.g., a ``--project`` path passed via ``julia -e``) must be escaped.
+    """
+    return value.replace("\\", "\\\\").replace('"', '\\"').replace("$", "\\$")
+
+
 def _is_julia_command(arg: str) -> bool:
-    """Whether ``arg`` is a Julia executable (julia or the juliaup launcher)."""
-    base = os.path.basename(arg)
+    """Whether ``arg`` is a Julia executable (julia or the juliaup launcher).
+
+    The comparison is case-insensitive so Windows paths like ``julia.EXE``
+    (e.g. the ``WindowsApps`` execution-alias shim) are recognized.
+    """
+    base = os.path.basename(arg).lower()
     if base.endswith(".exe"):
         base = base[: -len(".exe")]
     return base in ("julia", "julialauncher")

calkit/notebooks.py

@@ -242,11 +242,9 @@ def declare_notebook(
             }
         )
     # Write calkit.yaml
-    fpath = os.path.join(wdir, "calkit.yaml")
     ck_info["pipeline"] = pipeline_dict
     ck_info["notebooks"] = notebooks
-    with open(fpath, "w") as f:
-        calkit.ryaml.dump(ck_info, f)
+    calkit.save_calkit_info(ck_info, wdir=wdir)
     if must_be_rerun:
         raise RuntimeError(
             f"Notebook stage '{stage_name}' was modified while the pipeline "

calkit/pipeline.py

@@ -1011,6 +1011,35 @@ def get_output_storage_map(
     return result
 
 
+def _dump_yaml_if_changed(data, fpath: str, verbose: bool = False) -> bool:
+    """Write ``data`` to ``fpath`` as YAML only if it changes the file.
+
+    ``calkit status`` recompiles the pipeline to DVC on every call, and the VS
+    Code extension polls status continuously. Blindly rewriting an identical
+    file causes two problems: (1) bumping ``dvc.yaml``'s mtime wakes the
+    extension's file watcher, which triggers yet another status poll---an
+    endless loop that keeps re-taking DVC's lock; and (2) the serializer formats
+    slightly differently across platforms and ruamel versions, so the file
+    churns in Git for no real change. Comparison is on the parsed structure, so
+    trivial reformatting is not treated as a change. DVC keys stage staleness on
+    ``dvc.lock`` (not on ``dvc.yaml``'s mtime), so skipping a no-op write is
+    safe. Returns whether the file was written.
+    """
+    if os.path.isfile(fpath):
+        try:
+            with open(fpath) as f:
+                if (calkit.ryaml.load(f) or {}) == data:
+                    return False
+        except Exception:
+            # Unreadable or invalid existing YAML: fall through and overwrite.
+            pass
+    if verbose:
+        typer.echo(f"Writing to {os.path.basename(fpath)}")
+    with open(fpath, "w") as f:
+        calkit.ryaml.dump(data, f)
+    return True
+
+
 def to_dvc(
     ck_info: dict | None = None,
     wdir: str | None = None,
@@ -1099,8 +1128,7 @@ def to_dvc(
                 with open(dvc_yaml_fpath) as f:
                     existing = calkit.ryaml.load(f) or {}
             existing.setdefault("stages", {}).update(wrapper_stages)
-            with open(dvc_yaml_fpath, "w") as f:
-                calkit.ryaml.dump(existing, f)
+            _dump_yaml_if_changed(existing, dvc_yaml_fpath)
         return wrapper_stages
     # Detect stages with the old ``slurm:`` field before model validation
     # because model_validate pops it in place.
@@ -1194,8 +1222,7 @@ def to_dvc(
         for sname in slurm_field_stages:
             stage_data = ck_yaml_data["pipeline"]["stages"][sname]
             stage_data["scheduler"] = stage_data.pop("slurm")
-        with open(ck_yaml_path, "w") as _f:
-            calkit.ryaml.dump(ck_yaml_data, _f)
+        _dump_yaml_if_changed(ck_yaml_data, ck_yaml_path)
     # Validate and initialize scheduler options (SLURM/PBS) for stages
     # whose outer environment is a job scheduler. Env defaults are applied
     # at job-submission time, not here.
@@ -1372,10 +1399,7 @@ def to_dvc(
                 dvc_stages[stage_name] = stage
         dvc_yaml["stages"] = dvc_stages
         dvc_yaml_fpath = os.path.join(wdir, "dvc.yaml") if wdir else "dvc.yaml"
-        with open(dvc_yaml_fpath, "w") as f:
-            if verbose:
-                typer.echo("Writing to dvc.yaml")
-            calkit.ryaml.dump(dvc_yaml, f)
+        _dump_yaml_if_changed(dvc_yaml, dvc_yaml_fpath, verbose=verbose)
         # DVC errors out (FileIsGitIgnored) if dvc.lock is Git-ignored, so make
         # sure it isn't---this keeps both status and pipeline runs working
         calkit.dvc.ensure_dvc_lock_not_ignored(wdir)

calkit/tests/jupyterlab/conftest.py

@@ -0,0 +1,7 @@
+import pytest
+
+
+@pytest.fixture
+def jp_server_config(jp_server_config):
+    # Load the Calkit server extension in the test Jupyter server.
+    return {"ServerApp": {"jpserver_extensions": {"calkit": True}}}

calkit/tests/test_core.py

@@ -43,6 +43,21 @@ def test_detect_project_name(tmp_dir):
     assert calkit.detect_project_name() == "someone-else/some-project"
 
 
+def test_save_calkit_info_preserves_unicode(tmp_dir):
+    # Regression: on Windows, opening calkit.yaml without encoding="utf-8"
+    # writes as cp1252, which either errors or corrupts non-ASCII content
+    # (e.g., the Greek letter "ν") into mojibake ("ν"). ruamel dumps raw
+    # unicode (allow_unicode=True), so the encoding of the file handle matters.
+    info = {"name": "p", "owner": "o", "title": "viscosity ν"}
+    calkit.save_calkit_info(info)
+    # The value must survive the round-trip intact.
+    assert calkit.load_calkit_info()["title"] == "viscosity ν"
+    # Raw bytes must be the UTF-8 encoding of "ν", not cp1252 mojibake.
+    raw = open("calkit.yaml", "rb").read()
+    assert "ν".encode("utf-8") in raw
+    assert "ν".encode("utf-8") not in raw
+
+
 def test_load_calkit_info(tmp_dir, monkeypatch):
     subpath = "some/project"
     os.makedirs(subpath)

calkit/tests/test_detect.py

@@ -863,6 +863,41 @@ data <- read.csv("data.csv")
     assert "tidyr" in deps
     # Base packages should not be included
     assert "base" not in deps
+    # Qualified calls (pkg::fn), requireNamespace/loadNamespace, and
+    # pacman::p_load with a character vector should all be detected
+    pacman_content = """
+if (!requireNamespace("here", quietly = TRUE)) install.packages("here")
+here::i_am("code/master.R")
+loadNamespace("withr")
+pkgs <- c(
+  "haven", "readxl",
+  "dplyr", "ggplot2"
+)
+pacman::p_load(char = pkgs, install = TRUE, character.only = TRUE)
+pacman::p_load(stringr, tidyr)
+pacman::p_load("forcats", c("janitor", "lubridate"))
+"""
+    deps = detect_r_dependencies(code=pacman_content)
+    # Qualified call and the requireNamespace/loadNamespace guards
+    assert "here" in deps
+    assert "pacman" in deps
+    assert "withr" in deps
+    # Vector resolved via char =
+    assert "haven" in deps
+    assert "readxl" in deps
+    assert "ggplot2" in deps
+    # Bare non-standard-evaluation names
+    assert "stringr" in deps
+    assert "tidyr" in deps
+    # Quoted names and inline c() vectors
+    assert "forcats" in deps
+    assert "janitor" in deps
+    assert "lubridate" in deps
+    # The vector constructor and keyword-argument values are not packages
+    assert "c" not in deps
+    assert "TRUE" not in deps
+    assert "install" not in deps
+    assert "character.only" not in deps
 
 
 def test_detect_r_dependencies_from_code():
@@ -1064,6 +1099,20 @@ def test_create_r_description_file(tmp_dir):
     assert "dplyr" in content
     assert "tidyr" in content
     assert "Imports:" in content
+    # The Package field reflects the project name (sanitized to a valid R
+    # package name), not a hard-coded placeholder
+    from calkit.environments import create_r_description_content
+
+    content = create_r_description_content(deps, project_name="AI-Games")
+    assert "Package: AI.Games" in content
+    assert "CalkitProject" not in content
+    # Names that don't start with a letter get a valid prefix
+    content = create_r_description_content(deps, project_name="2023-study")
+    package_line = [
+        ln for ln in content.splitlines() if ln.startswith("Package:")
+    ][0]
+    package_name = package_line.split(":", 1)[1].strip()
+    assert package_name[0].isalpha()
 
 
 def test_create_files_in_subdirectory(tmp_dir):

calkit/tests/test_julia.py

@@ -1,16 +1,40 @@
 """Tests for ``calkit.julia``"""
 
+import os
 from unittest import mock
 
 import pytest
 
 from calkit.julia import (
+    _is_julia_command,
     check_version_in_command,
     ensure_startup_file_disabled_in_command,
+    escape_string,
     get_julia_exe,
+    load_path,
 )
 
 
+def test_escape_string_windows_path():
+    # A Windows path embedded in a Julia string literal must have its
+    # backslashes escaped, otherwise "C:\\Users" is read as an invalid \\U
+    # unicode escape (ParseError).
+    assert escape_string("C:\\Users\\peteb") == "C:\\\\Users\\\\peteb"
+    # Double quotes and dollar signs are the other special characters.
+    assert escape_string('a"b') == 'a\\"b'
+    assert escape_string("a$b") == "a\\$b"
+    # Plain values (e.g. the load path) are unchanged.
+    assert escape_string("@;@stdlib") == "@;@stdlib"
+
+
+def test_load_path_uses_platform_separator():
+    # Julia splits JULIA_LOAD_PATH on the platform path separator, so the
+    # value must use ';' on Windows and ':' elsewhere (== os.pathsep).
+    assert load_path() == f"@{os.pathsep}@stdlib"
+    assert "@" in load_path()
+    assert "@stdlib" in load_path()
+
+
 def test_get_julia_exe(monkeypatch, tmp_path):
     # Prefer julia on the PATH when present
     def which_julia(name):
@@ -44,6 +68,28 @@ def test_get_julia_exe(monkeypatch, tmp_path):
     assert get_julia_exe() == "julia"
 
 
+def test_is_julia_command_case_insensitive():
+    # Windows resolves the execution-alias shim to an uppercase extension
+    # (e.g. ``julia.EXE``); the check must still recognize it.
+    assert _is_julia_command("C:/x/julia.EXE")
+    assert _is_julia_command("C:/x/Julia.Exe")
+    assert _is_julia_command("C:/x/julialauncher.EXE")
+    assert _is_julia_command("/usr/bin/julia")
+    assert _is_julia_command("julialauncher")
+    assert not _is_julia_command("python")
+    assert not _is_julia_command("C:/x/python.exe")
+
+
+def test_disable_startup_file_accepts_uppercase_exe():
+    # Regression: julia.EXE (Windows execution alias) was rejected as not a
+    # Julia command, failing the env check and masking real pipeline status.
+    cmd = ensure_startup_file_disabled_in_command(
+        ["C:/x/julia.EXE", "--version"]
+    )
+    assert cmd[0] == "C:/x/julia.EXE"
+    assert "--startup-file=no" in cmd
+
+
 def test_check_version_in_command():
     cmd = ["julia", "+1.11", "--project", "whatever"]
     # Case 1: juliaup is available

calkit/tests/test_pipeline.py

@@ -521,6 +521,55 @@ def test_to_dvc_unignores_dvc_lock(tmp_dir):
     assert not repo.ignored("dvc.lock")
 
 
+def test_to_dvc_skips_no_op_writes(tmp_dir):
+    # Compiling to DVC happens on every `calkit status` (which the VS Code
+    # extension polls continuously). Rewriting an unchanged dvc.yaml churns Git
+    # across platforms (trivial reformatting) and wakes the extension's dvc.yaml
+    # watcher into another status poll, an endless loop that keeps re-taking
+    # DVC's lock. The write must be skipped unless the parsed content changes.
+    subprocess.check_call(["calkit", "init"])
+    ck_info = {
+        "pipeline": {
+            "stages": {
+                "s1": {
+                    "kind": "command",
+                    "environment": "_system",
+                    "command": "echo a > a.txt",
+                    "outputs": ["a.txt"],
+                }
+            }
+        },
+    }
+    with open("calkit.yaml", "w") as f:
+        calkit.ryaml.dump(ck_info, f)
+    # First compile creates dvc.yaml.
+    calkit.pipeline.to_dvc(ck_info=ck_info, write=True)
+    assert os.path.isfile("dvc.yaml")
+    # Pin an old mtime; a no-op recompile of identical content must leave it.
+    pinned = 1000000000.0
+    os.utime("dvc.yaml", (pinned, pinned))
+    calkit.pipeline.to_dvc(ck_info=ck_info, write=True)
+    assert os.path.getmtime("dvc.yaml") == pinned
+    # A semantically-equal but reformatted/commented file is also left as-is, so
+    # trivial cross-platform reformatting doesn't churn the file in Git.
+    with open("dvc.yaml") as f:
+        original = f.read()
+    with open("dvc.yaml", "w") as f:
+        f.write("# hand-written comment\n" + original)
+    with open("dvc.yaml") as f:
+        reformatted = f.read()
+    os.utime("dvc.yaml", (pinned, pinned))
+    calkit.pipeline.to_dvc(ck_info=ck_info, write=True)
+    with open("dvc.yaml") as f:
+        assert f.read() == reformatted
+    assert os.path.getmtime("dvc.yaml") == pinned
+    # A real change, though, is written.
+    ck_info["pipeline"]["stages"]["s1"]["command"] = "echo b > a.txt"
+    calkit.pipeline.to_dvc(ck_info=ck_info, write=True)
+    with open("dvc.yaml") as f:
+        assert f.read() != reformatted
+
+
 def test_sbatch_stage_to_dvc(tmp_dir):
     """Cover the SLURM stage compilation paths.
 

{calkit_python-0.41.14.data → calkit_python-0.41.16.data}/data/share/jupyter/labextensions/calkit/package.json

@@ -39,7 +39,7 @@
     "clean": "jlpm clean:lib",
     "clean:lib": "rimraf lib tsconfig.tsbuildinfo",
     "clean:lintcache": "rimraf .eslintcache .stylelintcache",
-    "clean:labextension": "rimraf calkit/labextension calkit/_version.py",
+    "clean:labextension": "rimraf ../calkit/labextension ../calkit/_version.py",
     "clean:all": "jlpm clean:lib && jlpm clean:labextension && jlpm clean:lintcache",
     "eslint": "jlpm eslint:check --fix",
     "eslint:check": "eslint . --cache --ext .ts,.tsx",
@@ -128,10 +128,10 @@
       }
     },
     "extension": true,
-    "outputDir": "calkit/labextension",
+    "outputDir": "../calkit/labextension",
     "schemaDir": "schema",
     "_build": {
-      "load": "static/remoteEntry.65469af996e7a96aa983.js",
+      "load": "static/remoteEntry.ac9035764d5b2adbb542.js",
       "extension": "./extension",
       "style": "./style"
     }
@@ -157,20 +157,6 @@
       "project": "tsconfig.json",
       "sourceType": "module"
     },
-    "overrides": [
-      {
-        "files": [
-          "vscode-ext/**/*.ts"
-        ],
-        "parserOptions": {
-          "project": "vscode-ext/tsconfig.json",
-          "sourceType": "module"
-        },
-        "rules": {
-          "@typescript-eslint/naming-convention": "off"
-        }
-      }
-    ],
     "plugins": [
       "@typescript-eslint"
     ],
@@ -205,12 +191,6 @@
       "prefer-arrow-callback": "error"
     }
   },
-  "prettier": {
-    "singleQuote": false,
-    "trailingComma": "all",
-    "arrowParens": "always",
-    "endOfLine": "auto"
-  },
   "stylelint": {
     "extends": [
       "stylelint-config-recommended",

{calkit_python-0.41.14.data → calkit_python-0.41.16.data}/data/share/jupyter/labextensions/calkit/schemas/calkit/package.json.orig

@@ -39,7 +39,7 @@
     "clean": "jlpm clean:lib",
     "clean:lib": "rimraf lib tsconfig.tsbuildinfo",
     "clean:lintcache": "rimraf .eslintcache .stylelintcache",
-    "clean:labextension": "rimraf calkit/labextension calkit/_version.py",
+    "clean:labextension": "rimraf ../calkit/labextension ../calkit/_version.py",
     "clean:all": "jlpm clean:lib && jlpm clean:labextension && jlpm clean:lintcache",
     "eslint": "jlpm eslint:check --fix",
     "eslint:check": "eslint . --cache --ext .ts,.tsx",
@@ -128,7 +128,7 @@
       }
     },
     "extension": true,
-    "outputDir": "calkit/labextension",
+    "outputDir": "../calkit/labextension",
     "schemaDir": "schema"
   },
   "eslintIgnore": [
@@ -152,20 +152,6 @@
       "project": "tsconfig.json",
       "sourceType": "module"
     },
-    "overrides": [
-      {
-        "files": [
-          "vscode-ext/**/*.ts"
-        ],
-        "parserOptions": {
-          "project": "vscode-ext/tsconfig.json",
-          "sourceType": "module"
-        },
-        "rules": {
-          "@typescript-eslint/naming-convention": "off"
-        }
-      }
-    ],
     "plugins": [
       "@typescript-eslint"
     ],
@@ -200,12 +186,6 @@
       "prefer-arrow-callback": "error"
     }
   },
-  "prettier": {
-    "singleQuote": false,
-    "trailingComma": "all",
-    "arrowParens": "always",
-    "endOfLine": "auto"
-  },
   "stylelint": {
     "extends": [
       "stylelint-config-recommended",

calkit_python-0.41.14.data/data/share/jupyter/labextensions/calkit/static/remoteEntry.65469af996e7a96aa983.js → calkit_python-0.41.16.data/data/share/jupyter/labextensions/calkit/static/remoteEntry.ac9035764d5b2adbb542.js

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{calkit_python-0.41.14.dist-info → calkit_python-0.41.16.dist-info}/METADATA

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 Metadata-Version: 2.4
 Name: calkit-python
-Version: 0.41.14
+Version: 0.41.16
 Summary: Reproducibility simplified.
 Project-URL: Homepage, https://calkit.org
 Project-URL: Issues, https://github.com/calkit/calkit/issues

{calkit_python-0.41.14.dist-info → calkit_python-0.41.16.dist-info}/RECORD

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 calkit/cloud.py,sha256=Zd-Az72Gao_DuLnL2TueRQQ95SpD8oFKp0Bahb-PYXc,16802
 calkit/conda.py,sha256=Jb1Fz3jwkk4SZ0NgoWXd4lf50gEC8d8U87ElrYjdiwk,30752
 calkit/config.py,sha256=tkrdAQU1m3__B9efpYgK6IhtLtS3WWFcVpY2zEQpBio,7573
-calkit/core.py,sha256=On8UGUuR0vKBJHdhEvsPJAk5QD9Lzf3LuWl_gmdfUrI,28179
+calkit/core.py,sha256=ferYD6jmvbZ1h1MlNApmuHiMokrLPynWtuU62wudzsc,28534
 calkit/datasets.py,sha256=9lOlOreey2aJGMw6MiV9MDzSHp-fYkCf1k1AZbWTdQE,2235
 calkit/dependencies.py,sha256=y5N_4ctwp9rFZVg82Si9_2x8Yh64Ex-WqP0iiN5NNBE,13276
-calkit/detect.py,sha256=Y70oOw6p-MEIwwxmm-FVZUS9YgPmahcqbQjSHbnLxsc,76416
+calkit/detect.py,sha256=u8dIFX1oFZ-LJexsXB-bM91yi9XtRrRr5ZUGd7LKTuw,79373
 calkit/docker.py,sha256=EEcgbXjs-1ttixAZ-G-hmDlvnqSxYbIZmbzeAza37TI,15706
-calkit/environments.py,sha256=y30tKE0KSRM9ANQwrI15ej2BaXe4s0kUeDm1Vr_BhXA,77230
+calkit/environments.py,sha256=PoAzpD3Esuupn3AGnR8J9ffvjHcxdBH1SQTXLxB1fY0,78060
 calkit/fs.py,sha256=dKWUfi51F1ka7uikn_O__jxvPOUwY05ZmydxE1KaJUA,45459
 calkit/git.py,sha256=rHAWdI13vA35m7q-MhlHj2KHMa42s4ecisTvKbdXKMw,13321
 calkit/github.py,sha256=8_yZ0ej8TKM4qk8iPeGq47R1I4MHdSoJ_Zpr1gRwNEM,1701
 calkit/gui.py,sha256=2UCrMyosc5v4CLlDcHO7oDwW9eLn5_WbNaLaG5bjMTc,23
 calkit/install.py,sha256=n989NLyZSTndj_rEaHceSip5aXP7zZIlG9QwbFs8kTc,7913
 calkit/invenio.py,sha256=aJH04-X9eFzxnrnbrPs71XBeFYBgKYYPiVM2KtyCXEE,4294
-calkit/julia.py,sha256=1025h3vC2WkvwSbatOHpemNX5SexwngwMLIZmkeCOcY,4491
+calkit/julia.py,sha256=4GxUSItNXpYcRlCD9N8dLiuX44-HQaKFcuEudD8At1I,5640
 calkit/jupyter.py,sha256=lE8kKmauHqspY7aPOiNpLGQyw9jSn4taGZScm6aR87I,1157
 calkit/licenses.py,sha256=3ZNBFxwRrfSjx3poG3G07z7GRCKAkdWiZ1AFe1yr8Gg,6853
 calkit/magics.py,sha256=LrwJP7f84AHgKPSzmKmQjxRqzV_ATAUcpt6bHBdyDLQ,12151
 calkit/matlab.py,sha256=wa7tjD5m8Xghwfj9u0oaYbuZ702CScvgk7pItFeTXoU,26061
-calkit/notebooks.py,sha256=obKRJaVf-rrQslcu76yx8lP18QKWGJOD_Irw7yHw9ek,8913
+calkit/notebooks.py,sha256=SGrVF_O5WmghMi7axr2WzHb4xLK7f6OmqTDMxQ5V5EY,8845
 calkit/office.py,sha256=mZqCxkIsmWthBAeJZ5SiGe21fn5zD2zXsy1E6nQIpWE,1291
 calkit/ops.py,sha256=lLlZAFeplU8uLeMavr99d__Iof-YYwKijus74WfLipk,854
 calkit/overleaf.py,sha256=5SI8HwglLVtVlzj7d15Bft_3ZC6AHn3IrAbqMKOAPX0,30170
-calkit/pipeline.py,sha256=qnfwnzze-PxF_2iFAx0zmkEHyfxqGgcFud_nV9txA54,65659
+calkit/pipeline.py,sha256=U28GDnnjU4sQXxiEegEgFXkuW4mvVAwZR2CQVyaH2fY,66853
 calkit/releases.py,sha256=JSmVX2s28WVJ5Lwitwjq5eRgUHZ38k6VbehEK-dR4mg,17478
 calkit/server.py,sha256=GQm1bI5Q1NLFNwQL-iP6j4iWKUpKpP3cLEyfj5IMwe4,22009
 calkit/cli/__init__.py,sha256=pP_1wFuewdUUvEWTtaEcdKblPaSYuTvthQb2Ef08UMo,1921
-calkit/cli/check.py,sha256=eGh9lOuAw7FhJxlZlNcZx3HPBpDSMCRz7FlspeCCObI,49240
+calkit/cli/check.py,sha256=tdiKIODqDn5y3TjfIA7JyunycPfDINpuRSOEIkYbMPY,49307
 calkit/cli/cloud.py,sha256=mMFRRFvo8MrzxQ-B_WTCSI8-erAWnFzgN2Hd0kVvB24,1815
-calkit/cli/config.py,sha256=cTNEM0AmwTPmxWcnXdWp4VdO_073ye74bLcuXSttNsQ,10340
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 calkit/cli/core.py,sha256=oICn4rLv9316X5bThD1Wrcc_qdmBHqye8NE4dIwojmk,3031
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 calkit/cli/describe.py,sha256=g6WWqa4nHSDda1Jt4D1g-VUm1k4bMskBfgKwDAhUokU,1817
@@ -40,14 +40,14 @@ calkit/cli/dev.py,sha256=cu4QsfDiA_KurGx4WJcgA2qgfghMoZutE8kl4IZbUcM,1070
 calkit/cli/import_.py,sha256=5j2ANLq6v7HOku9kJUWylwvQnJfkb_OUKCNOdv1BQXU,18264
 calkit/cli/latex.py,sha256=dhcbVNcR3YjVSD5mo-OBtZN1FhH4mv4mlGnuP19EbjU,6220
 calkit/cli/list.py,sha256=rV3gCVvoZ4CkUYXYfNRow11-AV99b98w7sabcDq08uk,10521
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 calkit/cli/office.py,sha256=jVSTvbl91TCzlglST5O2b8hdApZA_QHw_UiEQFJqxdc,1754
 calkit/cli/overleaf.py,sha256=bS-SkYsSqqhC9YsP-NCzpYJCGS3820w18w_s8JOFihg,25216
 calkit/cli/scheduler.py,sha256=Mn_G2tx78A_wJ3XYE0hRtTkPj376sKTWpSxMZKirHuA,38660
-calkit/cli/update.py,sha256=Ly5kkWqbZg5VSDmcoCOYdKiPDzXfs_kk3au-JJT9cH0,43471
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 calkit/cli/main/__init__.py,sha256=qu1POZPyqs33ZKfasOxv_Wc-EzVcEgK3Dt_vwFL8Bi8,65
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 calkit/cli/main/xr.py,sha256=Bug5qJuiIq0tusmdu30t-ZdyaT_Sy5RwPSTiHvCtIqE,25600
 calkit/dvc/__init__.py,sha256=-B6tilCb_jw7QFmJ2srILez24wDhNKUzIBhZUMt01dE,381
 calkit/dvc/core.py,sha256=p42i_uCzgZD6ClGnLOn88zaiGTwrdSG09quL8Hb8Aas,30908
@@ -74,22 +74,22 @@ calkit/tests/test_calc.py,sha256=h-wOUIRqfyi06LTzhY_rS-a1xChZTkmwdEfBybMUM7E,203
 calkit/tests/test_check.py,sha256=ngRZq1_dSRQoa0oSjcx_QpR94omG9Bpas_h0wqjwrK0,1475
 calkit/tests/test_cloud.py,sha256=yCSuMq0o-i-kN-uWdvbSSBfz6mgKpS_hC3cFA-4DKjs,13542
 calkit/tests/test_conda.py,sha256=t-Oy1mL3Vb5njj_t3LQ8HwMhsmLN64HAzSlebnN1A9s,14204
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 calkit/tests/test_dependencies.py,sha256=HskXLzbvvRJz2TXnKPpPAo9lPhoZGYQFy4BmEF31nvk,11139
-calkit/tests/test_detect.py,sha256=LXQ0agLAGfFth2u36-nXSXu3qIyx7NXOdZc0GYGdVeI,39793
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 calkit/tests/test_docker.py,sha256=27d0K1GOWiCNv_5TkZSob6EaC0EtQ9DSBIDfkEAEzGk,2077
 calkit/tests/test_environments.py,sha256=ms8avkZy70QPD4GSWAFa04O5rhd2oePaBeo0CBgnXAo,40300
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 calkit/tests/test_git.py,sha256=bxPVTn-0DD9mhlarBjEnm6V8XSJHfvm2etl9Z5Pq-qg,15076
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 calkit/tests/test_jupyter.py,sha256=YTL6zI740UM2KUjskSipzvSKxsyQ8rVPFQIX5cb2tMQ,114
 calkit/tests/test_licenses.py,sha256=AxoydeUG1Z6rDVeJJ64YXZ8xCJeyQyJdq6GSkDjlwJE,4001
 calkit/tests/test_magics.py,sha256=1O_hYPLMBVQJj8rLCFV3sU2DejlLLnk6Tv4_Tr-FZHQ,2101
 calkit/tests/test_matlab.py,sha256=7yFKOYDCtxYIkRyFOwTIxlvzx03Pac0FKGIUT4Zx7zA,7589
 calkit/tests/test_notebooks.py,sha256=6xUpHjCbCv08oJkArj-NkTUMlz9zzm8pf1qam3s27M0,2692
-calkit/tests/test_pipeline.py,sha256=SDxZZs3P1yaS2I5zouvScvGSvzpcWuQ0TKZWWih4YAU,84761
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 calkit/tests/test_releases.py,sha256=if6OjeZbUtjyyZ2CMQWhxQPRR8QD2kv5CXkEbOAL9Kc,14199
 calkit/tests/test_templates.py,sha256=RN4RIgmuFlmFYQFgfJUYS-KaLmie8fnWzmfg5Ay1egk,430
 calkit/tests/cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -114,6 +114,7 @@ calkit/tests/dvc/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,
 calkit/tests/dvc/test_core.py,sha256=ywXBEyw1XpoSuu1EnMbFl-ebbdEJjpaBEPG157_3RBY,12914
 calkit/tests/dvc/test_zip.py,sha256=H6L3uJdUpsaNQcOPKnmRxMb5Imr_MaDQFoAnMrZMErU,11212
 calkit/tests/jupyterlab/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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 calkit/tests/jupyterlab/test_routes.py,sha256=TEEyoHiKnzzKOkQsJcMPKdqpKFQ25yBCvVSquqe9nsE,408
 calkit/tests/models/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 calkit/tests/models/test_core.py,sha256=EY-8CRR-Nh6PIjqRfAvyz_An3fkf6Hzk7ed4da02afg,872
@@ -122,23 +123,23 @@ calkit/tests/models/test_pipeline.py,sha256=AJsMAX4928U3_Omt0_8K96U5LU_KoNErgpHe
 calkit/agent_skills/add-pipeline-stage/SKILL.md,sha256=kpYYb-rJsS4B9p1Ub3gL21irCG5ZZ4DvWZpdJeEwPZk,3772
 calkit/agent_skills/conventions/SKILL.md,sha256=nAM2FjSMk6ED56Dr5zh2bL_dhfzDra-h2ZgzHU7ruS4,9524
 calkit/agent_skills/create-pipeline/SKILL.md,sha256=2FGw1iDQVRk5FUq79GP3lPdgvgof2Wi1O9O-abGGtgs,5422
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