calkit-python 0.41.15__tar.gz → 0.41.16__tar.gz

{calkit_python-0.41.15 → 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-0.41.15 → 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-0.41.15 → 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-0.41.15 → 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-0.41.15 → calkit_python-0.41.16}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: calkit-python
-Version: 0.41.15
+Version: 0.41.16
 Summary: Reproducibility simplified.
 Project-URL: Homepage, https://calkit.org
 Project-URL: Issues, https://github.com/calkit/calkit/issues

{calkit_python-0.41.15 → 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-0.41.15 → 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-0.41.15 → 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-0.41.15 → 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-0.41.15 → 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",
@@ -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-0.41.15/calkit/labextension/static/remoteEntry.65469af996e7a96aa983.js → calkit_python-0.41.16/calkit/labextension/static/remoteEntry.ac9035764d5b2adbb542.js

@@ -1 +1 @@
-var _JUPYTERLAB;(()=>{"use strict";var e,r,t,a,n,o,i,l,u,f,s,d,c,p,h,b,v,m,y,g,j,w,k,S={4717(e,r,t){var a={"./index":()=>Promise.all([t.e(867),t.e(345),t.e(909)]).then(()=>()=>t(5909)),"./extension":()=>Promise.all([t.e(867),t.e(345),t.e(909)]).then(()=>()=>t(5909)),"./style":()=>t.e(502).then(()=>()=>t(502))},n=(e,r)=>(t.R=r,r=t.o(a,e)?a[e]():Promise.resolve().then(()=>{throw new Error('Module "'+e+'" does not exist in container.')}),t.R=void 0,r),o=(e,r)=>{if(t.S){var a="default",n=t.S[a];if(n&&n!==e)throw new Error("Container initialization failed as it has already been initialized with a different share scope");return t.S[a]=e,t.I(a,r)}};t.d(r,{get:()=>n,init:()=>o})}},P={};function E(e){var r=P[e];if(void 0!==r)return r.exports;var t=P[e]={id:e,exports:{}};return S[e](t,t.exports,E),t.exports}E.m=S,E.c=P,E.n=e=>{var r=e&&e.__esModule?()=>e.default:()=>e;return E.d(r,{a:r}),r},E.d=(e,r)=>{for(var t in 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{calkit_python-0.41.15 → calkit_python-0.41.16/calkit/tests/jupyterlab}/conftest.py

@@ -1,8 +1,7 @@
 import pytest
 
-pytest_plugins = ("pytest_jupyter.jupyter_server",)
-
 
 @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_python-0.41.15 → calkit_python-0.41.16}/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_python-0.41.15 → calkit_python-0.41.16/jupyterlab-ext}/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",
@@ -128,7 +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-0.41.15 → calkit_python-0.41.16}/pyproject.toml

@@ -117,8 +117,8 @@ exclude = [".github"]
 
 [tool.hatch.build.targets.wheel.shared-data]
 "calkit/labextension" = "share/jupyter/labextensions/calkit"
-"install.json" = "share/jupyter/labextensions/calkit/install.json"
-"jupyter-config/server-config" = "etc/jupyter/jupyter_server_config.d"
+"jupyterlab-ext/install.json" = "share/jupyter/labextensions/calkit/install.json"
+"jupyterlab-ext/jupyter-config/server-config" = "etc/jupyter/jupyter_server_config.d"
 
 [tool.hatch.build.hooks.jupyter-builder]
 dependencies = ["hatch-jupyter-builder>=0.5"]
@@ -132,11 +132,13 @@ skip-if-exists = ["calkit/labextension/static/style.js"]
 [tool.hatch.build.hooks.jupyter-builder.build-kwargs]
 build_cmd = "build:prod"
 npm = ["jlpm"]
+path = "jupyterlab-ext"
 
 [tool.hatch.build.hooks.jupyter-builder.editable-build-kwargs]
 build_cmd = "install:extension"
 npm = ["jlpm"]
-source_dir = "src"
+path = "jupyterlab-ext"
+source_dir = "jupyterlab-ext/src"
 build_dir = "calkit/labextension"
 
 [tool.jupyter-releaser.options]
@@ -145,10 +147,10 @@ version_cmd = "hatch version"
 [tool.jupyter-releaser.hooks]
 before-build-npm = [
   "python -m pip install 'jupyterlab>=4.0.0,<5'",
-  "jlpm",
-  "jlpm build:prod",
+  "cd jupyterlab-ext && jlpm",
+  "cd jupyterlab-ext && jlpm build:prod",
 ]
-before-build-python = ["jlpm clean:all"]
+before-build-python = ["cd jupyterlab-ext && jlpm clean:all"]
 
 [tool.check-wheel-contents]
 ignore = ["W002"]
@@ -187,4 +189,4 @@ extend-select = ["I"]  # Import sorting (isort compatibility)
 
 [tool.pytest.ini_options]
 env = ["CALKIT_ENV=test", "CALKIT_TEST_OVERLEAF_TOKEN=none"]
-addopts = "-n auto"
+addopts = "-n auto -p pytest_jupyter.jupyter_server"