calkit-python 0.41.14__tar.gz → 0.41.16__tar.gz

{calkit_python-0.41.14 → calkit_python-0.41.16}/.gitignore

@@ -12,6 +12,8 @@ tsconfig.tsbuildinfo
 lib
 node_modules
 .yarn
+*.eslintcache
+*.stylelintcache
 calkit/labextension
 coverage
 junit.xml

{calkit_python-0.41.14 → calkit_python-0.41.16}/.pre-commit-config.yaml

@@ -23,5 +23,3 @@ repos:
     hooks:
       - id: prettier
         exclude: calkit
-        args:
-          - --config=package.json

{calkit_python-0.41.14 → calkit_python-0.41.16}/.prettierignore

@@ -2,7 +2,6 @@ node_modules
 **/node_modules
 **/lib
 **/package.json
-!/package.json
 calkit
 .mypy_cache
 .pytest_cache

calkit_python-0.41.16/.prettierrc.json

@@ -0,0 +1,6 @@
+{
+  "singleQuote": false,
+  "trailingComma": "all",
+  "arrowParens": "always",
+  "endOfLine": "auto"
+}

{calkit_python-0.41.14 → calkit_python-0.41.16}/AGENTS.md

@@ -43,3 +43,6 @@ The only exception here is if splitting up a function makes it easier to
 write meaningful unit tests.
 If a function is only used inside one other function, nest it inside the
 caller at the top.
+
+No spaces on either side of en or em dashes used for ranges or pauses in prose,
+respectively.

{calkit_python-0.41.14 → calkit_python-0.41.16}/Makefile

@@ -53,19 +53,21 @@ import-profile: ## Profile the import time of the CLI.
 
 .PHONY: jlab-dev
 jlab-dev: ## Develop the JupyterLab extension.
-	uv run jlpm run watch
+	cd jupyterlab-ext && uv run jlpm run watch
 
 .PHONY: jlab
 jlab: ## Build the JupyterLab extension.
-	uv run jlpm run build:prod
+	cd jupyterlab-ext && uv run jlpm run build:prod
 
-.PHONY: test-frontend
-test-frontend: ## Run frontend unit tests with Jest.
-	@echo "🚀 Running frontend unit tests"
-	@uv run jlpm test
+.PHONY: test-jlab
+test-jlab: ## Run JupyterLab extension unit tests with Jest.
+	@echo "🚀 Running JupyterLab extension unit tests"
+	@cd jupyterlab-ext && uv run jlpm test
 
-.PHONY: test-ui
-test-ui: ## Run the JupyterLab UI integration tests.
+.PHONY: test-jlab-ui
+test-jlab-ui: ## Run the JupyterLab UI integration tests.
 	@echo "🚀 Running JupyterLab UI tests with Playwright"
-	@uv run npm run build
-	@uv run --directory=ui-tests jlpm playwright test -u --reporter=list
+	@cd jupyterlab-ext && uv run jlpm run build:prod
+	@uv run --directory=jupyterlab-ext/ui-tests jlpm install
+	@uv run --directory=jupyterlab-ext/ui-tests jlpm playwright install
+	@uv run --directory=jupyterlab-ext/ui-tests jlpm playwright test -u --reporter=list

{calkit_python-0.41.14 → calkit_python-0.41.16}/PKG-INFO

@@ -1,6 +1,6 @@
 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 → calkit_python-0.41.16}/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_python-0.41.14 → calkit_python-0.41.16}/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_python-0.41.14 → calkit_python-0.41.16}/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_python-0.41.14 → calkit_python-0.41.16}/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_python-0.41.14 → calkit_python-0.41.16}/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_python-0.41.14 → calkit_python-0.41.16}/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_python-0.41.14 → calkit_python-0.41.16}/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_python-0.41.14 → calkit_python-0.41.16}/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_python-0.41.14 → calkit_python-0.41.16}/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_python-0.41.14 → calkit_python-0.41.16}/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_python-0.41.14 → calkit_python-0.41.16}/calkit/labextension/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 → calkit_python-0.41.16}/calkit/labextension/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",
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     },
     "extension": true,
-    "outputDir": "calkit/labextension",
+    "outputDir": "../calkit/labextension",
     "schemaDir": "schema"
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-    "trailingComma": "all",
-    "arrowParens": "always",
-    "endOfLine": "auto"
-  },
   "stylelint": {
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