calkit-python 0.37.4__tar.gz → 0.37.6__tar.gz

{calkit_python-0.37.4 → calkit_python-0.37.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: calkit-python
-Version: 0.37.4
+Version: 0.37.6
 Summary: Reproducibility simplified.
 Project-URL: Homepage, https://calkit.org
 Project-URL: Issues, https://github.com/calkit/calkit/issues

calkit_python-0.37.6/calkit/cli/dev.py

@@ -0,0 +1,47 @@
+"""CLI for Calkit developers, hidden from the typical help menu."""
+
+from __future__ import annotations
+
+import subprocess
+import sys
+from typing import Annotated
+
+import typer
+
+import calkit
+
+dev_app = typer.Typer(no_args_is_help=True)
+
+
+@dev_app.command(
+    name="python",
+    add_help_option=False,
+    context_settings={
+        "ignore_unknown_options": True,
+        "allow_extra_args": True,
+    },
+)
+def run_python(
+    ctx: typer.Context,
+    help: Annotated[bool, typer.Option("-h", "--help")] = False,
+):
+    """Start an Python shell in Calkit's environment."""
+    subprocess.run([sys.executable] + sys.argv[3:])
+
+
+@dev_app.command(
+    name="ipython",
+    add_help_option=False,
+    context_settings={
+        "ignore_unknown_options": True,
+        "allow_extra_args": True,
+    },
+)
+def run_ipython(
+    ctx: typer.Context,
+    help: Annotated[bool, typer.Option("-h", "--help")] = False,
+):
+    """Start an IPython shell in Calkit's environment."""
+    from IPython import start_ipython
+
+    start_ipython(argv=sys.argv[3:], user_ns={"calkit": calkit})

{calkit_python-0.37.4 → calkit_python-0.37.6}/calkit/cli/main/core.py

@@ -47,6 +47,7 @@ from calkit.cli.check import (
 from calkit.cli.cloud import cloud_app
 from calkit.cli.config import config_app
 from calkit.cli.describe import describe_app
+from calkit.cli.dev import dev_app
 from calkit.cli.import_ import import_app
 from calkit.cli.latex import latex_app
 from calkit.cli.list import list_app
@@ -84,6 +85,7 @@ app.add_typer(latex_app, name="latex", help="Work with LaTeX.")
 app.add_typer(overleaf_app, name="overleaf", help="Interact with Overleaf.")
 app.add_typer(cloud_app, name="cloud", help="Interact with a Calkit Cloud.")
 app.add_typer(slurm_app, name="slurm", help="Work with SLURM.")
+app.add_typer(dev_app, name="dev", help="Developer tools.", hidden=True)
 
 
 def _to_shell_cmd(cmd: list[str]) -> str:

{calkit_python-0.37.4 → calkit_python-0.37.6}/calkit/cli/notebooks.py

@@ -586,9 +586,9 @@ def execute_notebook(
         run_in_env(cmd, env_name=env_name, no_check=no_check, verbose=verbose)
     if not no_replace:
         # Replace original notebook outputs with those from executed version
-        with open(fpath_out_exec, "r") as f:
+        with open(fpath_out_exec, "r", encoding="utf-8") as f:
             executed_nb = json.load(f)
-        with open(path, "r") as f:
+        with open(path, "r", encoding="utf-8") as f:
             original_nb = json.load(f)
         for orig_cell, exec_cell in zip(
             original_nb.get("cells", []), executed_nb.get("cells", [])
@@ -600,7 +600,7 @@ def execute_notebook(
                 and "execution_count" in exec_cell
             ):
                 orig_cell["execution_count"] = exec_cell["execution_count"]
-        with open(path, "w") as f:
+        with open(path, "w", encoding="utf-8") as f:
             json.dump(original_nb, f, indent=1)
     for to_fmt in to:
         if to_fmt != "notebook":

{calkit_python-0.37.4 → calkit_python-0.37.6}/calkit/invenio.py

@@ -34,6 +34,9 @@ def get_token(service: ServiceName = DEFAULT_SERVICE) -> str:
 
 
 def get_base_url(service: ServiceName = DEFAULT_SERVICE) -> str:
+    override = os.getenv(f"CALKIT_INVENIO_BASE_URL_{service.upper()}")
+    if override:
+        return override
     current_env = calkit.config.get_env()
     if service == "zenodo":
         if (

{calkit_python-0.37.4 → calkit_python-0.37.6}/calkit/jupyter.py

@@ -3,6 +3,7 @@
 from __future__ import annotations
 
 import subprocess
+import sys
 
 from pydantic import BaseModel
 
@@ -15,7 +16,9 @@ class Server(BaseModel):
 
 def get_servers() -> list[Server]:
     out = (
-        subprocess.check_output(["jupyter", "server", "list"])
+        subprocess.check_output(
+            [sys.executable, "-m", "jupyter", "server", "list"]
+        )
         .decode()
         .strip()
         .split("\n")
@@ -33,6 +36,8 @@ def start_server(wdir=None, no_browser=False):
     """Start a Jupyter server."""
     subprocess.Popen(
         [
+            sys.executable,
+            "-m",
             "jupyter",
             "lab",
             "-y",
@@ -45,4 +50,4 @@ def start_server(wdir=None, no_browser=False):
 def stop_server(url: str):
     # Extract the port from the URL
     port = url.split(":")[2][:4]
-    subprocess.call(["jupyter", "server", "stop", port])
+    subprocess.call([sys.executable, "-m", "jupyter", "server", "stop", port])

{calkit_python-0.37.4 → calkit_python-0.37.6}/calkit/tests/cli/test_new.py

@@ -1,6 +1,7 @@
 """Tests for ``cli.new``."""
 
 import os
+import re
 import subprocess
 
 import git
@@ -548,7 +549,65 @@ def test_new_julia_env(tmp_dir):
     assert not os.path.isfile("envs/empty/Manifest.toml")
 
 
-def test_new_release(tmp_dir):
+def test_new_release(tmp_dir, monkeypatch, httpserver):
+    # Set up a mock Zenodo API so the test doesn't depend on the real sandbox
+    record_id = "test-record-abc123"
+    doi = "10.5072/zenodo.test123"
+    # Point the Zenodo base URL at the local mock server and provide a dummy
+    # token so no real credentials are needed.  Both env vars are inherited
+    # by every subprocess started by this test.
+    monkeypatch.setenv(
+        "CALKIT_INVENIO_BASE_URL_ZENODO",
+        httpserver.url_for("").rstrip("/"),
+    )
+    monkeypatch.setenv("ZENODO_TOKEN", "test-token")
+    # POST /records – create a new draft record
+    httpserver.expect_request(
+        re.compile(r"^/records$"), method="POST"
+    ).respond_with_json({"id": record_id, "pids": {}})
+    # POST /records/{id}/draft/files – initiate a file upload slot
+    httpserver.expect_request(
+        re.compile(rf"^/records/{record_id}/draft/files$"), method="POST"
+    ).respond_with_json({"entries": []})
+    # PUT /records/{id}/draft/files/{filename}/content – stream file bytes
+    httpserver.expect_request(
+        re.compile(rf"^/records/{record_id}/draft/files/.+/content$"),
+        method="PUT",
+    ).respond_with_data("", status=200)
+    # POST /records/{id}/draft/files/{filename}/commit – finalise upload
+    httpserver.expect_request(
+        re.compile(rf"^/records/{record_id}/draft/files/.+/commit$"),
+        method="POST",
+    ).respond_with_json({"key": "file", "status": "completed"})
+    # POST /records/{id}/draft/pids/doi – reserve a DOI for a draft
+    httpserver.expect_request(
+        re.compile(rf"^/records/{record_id}/draft/pids/doi$"), method="POST"
+    ).respond_with_json({"pids": {"doi": {"identifier": doi}}})
+    # GET /records/{id}/draft/files – list files already in the draft
+    # (used by --reupload to decide which files to delete first)
+    httpserver.expect_request(
+        re.compile(rf"^/records/{record_id}/draft/files$"), method="GET"
+    ).respond_with_json({"entries": []})
+    # POST /records/{id}/draft/actions/publish – publish the draft
+    httpserver.expect_request(
+        re.compile(rf"^/records/{record_id}/draft/actions/publish$"),
+        method="POST",
+    ).respond_with_json(
+        {"id": record_id, "pids": {"doi": {"identifier": doi}}}
+    )
+    # GET /records/{id} – fetch the published record for post-test assertions
+    httpserver.expect_request(
+        re.compile(rf"^/records/{record_id}$"), method="GET"
+    ).respond_with_json(
+        {
+            "metadata": {
+                "license": {"id": "cc-by-4.0"},
+                "related_identifiers": [
+                    {"identifier": ("https://github.com/calkit/test-project")}
+                ],
+            }
+        }
+    )
     subprocess.check_call(
         [
             "calkit",
@@ -661,7 +720,10 @@ def test_new_release(tmp_dir):
     # )
 
 
-def test_new_release_is_runnable(tmp_dir):
+def test_new_release_is_runnable(tmp_dir, monkeypatch):
+    # Provide a dummy Zenodo token so `new_release` can pass its early
+    # token-validation step even in dry-run mode.
+    monkeypatch.setenv("ZENODO_TOKEN", "test-token")
     subprocess.check_call(["calkit", "init"])
     with open("calkit.yaml", "w") as f:
         calkit.ryaml.dump(

{calkit_python-0.37.4 → calkit_python-0.37.6}/docs/cli-reference.md

@@ -42,6 +42,7 @@
 | [`overleaf`](#command-group-overleaf)         | Interact with Overleaf.                                            |
 | [`cloud`](#command-group-cloud)               | Interact with a Calkit Cloud.                                      |
 | [`slurm`](#command-group-slurm)               | Work with SLURM.                                                   |
+| [`dev`](#command-group-dev)                   | Developer tools.                                                   |
 
 ## Top-level command details
 
@@ -2757,3 +2758,38 @@ Options:
 | Option           | Type    | Required | Default | Description                         |
 | ---------------- | ------- | -------- | ------- | ----------------------------------- |
 | `--follow`, `-f` | boolean | no       | False   | Follow the log output like tail -f. |
+
+<a id="command-group-dev"></a>
+
+### `calkit dev`
+
+Developer tools.
+
+| Command                              | Description                                     |
+| ------------------------------------ | ----------------------------------------------- |
+| [`python`](#subcommand-dev-python)   | Start an Python shell in Calkit's environment.  |
+| [`ipython`](#subcommand-dev-ipython) | Start an IPython shell in Calkit's environment. |
+
+<a id="subcommand-dev-python"></a>
+
+#### `calkit dev python`
+
+Start an Python shell in Calkit's environment.
+
+Usage:
+
+```text
+calkit dev python [OPTIONS]
+```
+
+<a id="subcommand-dev-ipython"></a>
+
+#### `calkit dev ipython`
+
+Start an IPython shell in Calkit's environment.
+
+Usage:
+
+```text
+calkit dev ipython [OPTIONS]
+```

{calkit_python-0.37.4 → calkit_python-0.37.6}/pyproject.toml

@@ -85,6 +85,7 @@ dev = [
   "mkdocs-material",
   "mkdocs-mermaid2-plugin",
   "pytest-env>=1.1.5",
+  "pytest-httpserver>=1.0.0",
   "pytest-xdist>=3.8.0",
   "pypdf>=6.4.2",
   "mkdocs-glightbox>=0.5.2",

{calkit_python-0.37.4 → calkit_python-0.37.6}/uv.lock

@@ -798,6 +798,7 @@ dev = [
     { name = "pytest-asyncio" },
     { name = "pytest-cov" },
     { name = "pytest-env" },
+    { name = "pytest-httpserver" },
     { name = "pytest-jupyter", extra = ["server"] },
     { name = "pytest-test-utils" },
     { name = "pytest-xdist" },
@@ -861,6 +862,7 @@ dev = [
     { name = "pytest-asyncio" },
     { name = "pytest-cov" },
     { name = "pytest-env", specifier = ">=1.1.5" },
+    { name = "pytest-httpserver", specifier = ">=1.0.0" },
     { name = "pytest-jupyter", extras = ["server"], specifier = ">=0.6.0" },
     { name = "pytest-test-utils" },
     { name = "pytest-xdist", specifier = ">=3.8.0" },
@@ -2398,14 +2400,14 @@ wheels = [
 
 [[package]]
 name = "gitpython"
-version = "3.1.46"
+version = "3.1.47"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "gitdb" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/df/b5/59d16470a1f0dfe8c793f9ef56fd3826093fc52b3bd96d6b9d6c26c7e27b/gitpython-3.1.46.tar.gz", hash = "sha256:400124c7d0ef4ea03f7310ac2fbf7151e09ff97f2a3288d64a440c584a29c37f", size = 215371, upload-time = "2026-01-01T15:37:32.073Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/c1/bd/50db468e9b1310529a19fce651b3b0e753b5c07954d486cba31bbee9a5d5/gitpython-3.1.47.tar.gz", hash = "sha256:dba27f922bd2b42cb54c87a8ab3cb6beb6bf07f3d564e21ac848913a05a8a3cd", size = 216978, upload-time = "2026-04-22T02:44:44.059Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/6a/09/e21df6aef1e1ffc0c816f0522ddc3f6dcded766c3261813131c78a704470/gitpython-3.1.46-py3-none-any.whl", hash = "sha256:79812ed143d9d25b6d176a10bb511de0f9c67b1fa641d82097b0ab90398a2058", size = 208620, upload-time = "2026-01-01T15:37:30.574Z" },
+    { url = "https://files.pythonhosted.org/packages/f2/c5/a1bc0996af85757903cf2bf444a7824e68e0035ce63fb41d6f76f9def68b/gitpython-3.1.47-py3-none-any.whl", hash = "sha256:489f590edfd6d20571b2c0e72c6a6ac6915ee8b8cd04572330e3842207a78905", size = 209547, upload-time = "2026-04-22T02:44:41.271Z" },
 ]
 
 [[package]]
@@ -5465,6 +5467,18 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/61/af/99b52a8524983bfece35e51e65a0b517b22920c023e57855c95e744e19e4/pytest_env-1.5.0-py3-none-any.whl", hash = "sha256:89a15686ac837c9cd009a8a2d52bd55865e2f23c82094247915dae4540c87161", size = 10122, upload-time = "2026-02-17T18:31:37.496Z" },
 ]
 
+[[package]]
+name = "pytest-httpserver"
+version = "1.1.5"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "werkzeug" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/50/17/ad187f46998814014f7cda309de700b87c0eb4b2e111e18bc8c819be7116/pytest_httpserver-1.1.5.tar.gz", hash = "sha256:dc3d82e1fe00e491829d8939c549bf4bd9b39a260f87113c619b9d517c2f8ff1", size = 70974, upload-time = "2026-02-14T13:27:23.412Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/ec/df/0bdf90b84c6a586a9fd2b509523a3ab26b1cc1b1dba2fb62a32e4411ea9e/pytest_httpserver-1.1.5-py3-none-any.whl", hash = "sha256:ee83feb587ab652c0c6729598db2820e9048233bac8df756818b7845a1621d0a", size = 23330, upload-time = "2026-02-14T13:27:22.119Z" },
+]
+
 [[package]]
 name = "pytest-jupyter"
 version = "0.11.0"
@@ -6786,6 +6800,18 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/34/db/b10e48aa8fff7407e67470363eac595018441cf32d5e1001567a7aeba5d2/websocket_client-1.9.0-py3-none-any.whl", hash = "sha256:af248a825037ef591efbf6ed20cc5faa03d3b47b9e5a2230a529eeee1c1fc3ef", size = 82616, upload-time = "2025-10-07T21:16:34.951Z" },
 ]
 
+[[package]]
+name = "werkzeug"
+version = "3.1.8"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "markupsafe" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/dd/b2/381be8cfdee792dd117872481b6e378f85c957dd7c5bca38897b08f765fd/werkzeug-3.1.8.tar.gz", hash = "sha256:9bad61a4268dac112f1c5cd4630a56ede601b6ed420300677a869083d70a4c44", size = 875852, upload-time = "2026-04-02T18:49:14.268Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/93/8c/2e650f2afeb7ee576912636c23ddb621c91ac6a98e66dc8d29c3c69446e1/werkzeug-3.1.8-py3-none-any.whl", hash = "sha256:63a77fb8892bf28ebc3178683445222aa500e48ebad5ec77b0ad80f8726b1f50", size = 226459, upload-time = "2026-04-02T18:49:12.72Z" },
+]
+
 [[package]]
 name = "wrapt"
 version = "2.1.1"