Investigate upstream issue with netcdf4==1.7.1 on Linux. Pin netcdf4 for now

.copier-answers.yml

@@ -1,5 +1,5 @@
 # Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
-_commit: 86fa907
+_commit: 0bdf6b4
 _src_path: gh:blakeNaccarato/copier-python
 actions_runner: ubuntu-22.04
 active: true

.vscode/tasks.json

@@ -43,17 +43,21 @@
       ]
     },
     {
-      "id": "version",
+      "id": "dependency",
       "type": "promptString",
-      "description": "version",
-      "default": "0.0.1"
+      "description": "Show tree of packages requesting this dependency."
     },
-    // * -------------------------------------------------------------------------- * //
     {
       "id": "templateOptions",
       "description": "Template options.",
       "type": "pickString",
       "options": ["", "-Stay", "-Stay -Prompt", "-Recopy -Prompt"]
+    },
+    {
+      "id": "changeType",
+      "description": "Change type.",
+      "type": "pickString",
+      "options": ["breaking", "deprecation", "change"]
     }
   ],
   "tasks": [
@@ -288,6 +292,20 @@
     // * -------------------------------------------------------------------------- * //
     // * OTHER TASKS * //
 
+    {
+      "label": "task: Generate changelog entry",
+      "type": "shell",
+      "command": ". scripts/Initialize-Shell.ps1; python -m boilercv_tools add-change ${input:changeType}",
+      "icon": { "id": "request-changes" },
+      "problemMatcher": []
+    },
+    {
+      "label": "task: Show tree of packages requesting a dependency",
+      "type": "shell",
+      "command": ". scripts/Initialize-Shell.ps1; pipdeptree --reverse --packages ${input:dependency}",
+      "icon": { "id": "versions" },
+      "problemMatcher": []
+    },
     {
       "label": "task: Run pytest with coverage",
       "type": "shell",

changelog/215.change.md

@@ -0,0 +1 @@
+Investigate upstream issue with `netcdf4==1.7.1` on Linux. Pin `netcdf4` for now

docs/pyproject.toml

@@ -37,6 +37,9 @@ dependencies = [
     "shapely>=2.0.3",
     "sympy>=1.12",
     "trackpy>=0.6.2",
+    # ? https://nvd.nist.gov/vuln/detail/CVE-2024-37891
+    # ? via sphinx
+    "urllib3>=2.2.2",
 ]
 
 [tool.fawltydeps]
@@ -65,6 +68,9 @@ ignore_unused = [
     "sphinxcontrib-bibtex",
     "sphinxcontrib-mermaid",
     "sphinxcontrib-towncrier",
+    # ? https://nvd.nist.gov/vuln/detail/CVE-2024-37891
+    # ? via sphinx
+    "urllib3",
 ]
 [tool.fawltydeps.custom_mapping]
 ipykernel = ["IPython"]

pyproject.toml

@@ -21,8 +21,8 @@ dependencies = [
     "sympy>=1.12",
     "xarray[accel,io,parallel]>=2023.7.0",
     # ? https://github.com/softboiler/boilercv/issues/213
-    "netcdf4>=1.7.0",
-    "netcdf4!=1.7.1 ; sys_platform == 'linux'",
+    "netcdf4>=1.6.5",
+    "netcdf4!=1.7.1.post1 ; sys_platform == 'linux'",
 ]
 [project.optional-dependencies]
 # * Minimal CV flavor needed, but allow `boilercv` to coexist with different flavors

requirements/dev.in

@@ -10,6 +10,7 @@ fawltydeps==0.15.0
 flit==3.9.0
 keyring==25.2.1
 pandas-stubs~=2.2.2
+pipdeptree==2.23.0
 pre-commit==3.7.1
 pyright==1.1.367
 ruff==0.4.8

requirements/requirements.txt

@@ -27,7 +27,7 @@ billiard==4.2.0
 bleach==6.1.0
 blosc2==2.7.0
 boilercine @ git+https://github.com/blakeNaccarato/boilercine@046ee0146394bebf5693fe0c18bbcea3d3e64fe5
-bokeh==3.4.1
+bokeh==3.4.2
 bottleneck==1.4.0
 cachetools==5.3.3
 cachier @ git+https://github.com/blakeNaccarato/cachier@0892f53dc8fd9fb8a7f959305a1a9ec692876dc0
@@ -52,7 +52,7 @@ configobj==5.0.8
 contourpy==1.2.1
 copier==9.2.0
 copykitten==1.1.1
-coverage==7.5.3
+coverage==7.5.4
 cryptography==42.0.8
 cycler==0.12.1
 cyclopts==2.7.0
@@ -89,7 +89,7 @@ executing==2.0.1
 fasteners==0.19
 fastjsonschema==2.20.0
 fawltydeps==0.15.0
-filelock==3.15.3
+filelock==3.15.4
 fiona==1.9.6
 flatten-dict==0.4.2
 flit-core==3.9.0
@@ -106,14 +106,14 @@ geopandas==0.14.3
 gitdb==4.0.11
 gitpython==3.1.43
 gmpy2==2.1.5
-google-api-core==2.19.0
+google-api-core==2.19.1
 google-auth-oauthlib==1.2.0
 google-auth==2.30.0
 google-cloud-core==2.4.1
 google-cloud-storage==2.17.0
 google-crc32c==1.5.0
 google-resumable-media==2.7.1
-googleapis-common-protos==1.63.1
+googleapis-common-protos==1.63.2
 grandalf==0.8
 greenlet==3.0.3
 gto==1.7.1
@@ -125,7 +125,7 @@ identify==2.5.36
 idna==3.7
 imageio==2.34.1
 imagesize==1.4.1
-importlib-metadata==7.2.0
+importlib-metadata==8.0.0
 incremental==22.10.0
 iniconfig==2.0.0
 ipykernel==6.29.4
@@ -176,7 +176,7 @@ nbconvert==7.7.3
 nbformat==5.10.4
 ndindex==1.8
 nest-asyncio==1.6.0
-netcdf4==1.7.0
+netcdf4==1.6.5
 networkx==3.3
 nodeenv==1.9.1
 nptyping==2.5.0
@@ -196,27 +196,29 @@ packaging==24.1
 pandas-stubs==2.2.2.240514
 pandas==2.2.2
 pandocfilters==1.5.1
-param==2.1.0
+param==2.1.1
 parso==0.8.4
 partd==1.4.2
 pathspec==0.12.1
 pathtools==0.1.2
 pexpect==4.9.0
 pillow==10.3.0
 pip-requirements-parser==32.0.1
+pip==24.1
+pipdeptree==2.23.0
 pipx==1.6.0
 platformdirs==3.11.0
 ploomber-core==0.2.25
 ploomber-engine==0.0.30
 pluggy==1.5.0
 plumbum==1.8.3
 pooch==1.8.2
-portalocker==2.8.2
+portalocker==2.10.0
 posthog==3.5.0
 pre-commit==3.7.1
 prompt-toolkit==3.0.47
 proto-plus==1.24.0
-protobuf==4.25.3
+protobuf==5.27.2
 psutil==6.0.0
 ptyprocess==0.7.0
 pure-eval==0.2.2
@@ -232,7 +234,7 @@ pycparser==2.22
 pyct==0.5.0
 pydantic-core==2.18.2
 pydantic==2.7.1
-pydata-sphinx-theme==0.15.3
+pydata-sphinx-theme==0.15.4
 pydot==2.0.0
 pygit2==1.15.0
 pygments==2.18.0
@@ -279,7 +281,7 @@ seaborn==0.13.2
 secretstorage==3.3.3
 semver==3.0.2
 setproctitle==1.3.3
-setuptools==70.1.0
+setuptools==70.1.1
 shapely==2.0.3
 shellingham==1.5.4
 shiboken6==6.7.1
@@ -342,8 +344,8 @@ urllib3==2.2.2
 userpath==1.9.2
 uvicorn==0.30.1
 vine==5.1.0
-virtualenv==20.26.2
-voluptuous==0.14.2
+virtualenv==20.26.3
+voluptuous==0.15.0
 watchdog==4.0.1
 watchfiles==0.22.0
 wcwidth==0.2.13

scripts/boilercv_tools/__main__.py

@@ -1,14 +1,16 @@
 """CLI for tools."""
 
-import tomllib
 from collections.abc import Collection
 from pathlib import Path
 from re import finditer, sub
 from shlex import join, split
+from tomllib import loads
 
 from cyclopts import App
 
+from boilercv_tools import add_changes
 from boilercv_tools.sync import PYTEST, check_compilation, escape
+from boilercv_tools.types import ChangeType
 
 APP = App(help_format="markdown")
 """CLI."""
@@ -24,6 +26,12 @@ def compile(high: bool = False):  # noqa: A001
     log(check_compilation(high))
 
 
+@APP.command
+def add_change(change: ChangeType = "change"):
+    """Add change."""
+    add_changes.add_change(change)
+
+
 @APP.command
 def get_actions():
     """Get actions used by this repository.
@@ -59,7 +67,7 @@ def sync_local_dev_configs():
     shadowing. Concurrent test runs are disabled in the local pytest configuration which
     slows down the usual local, granular test workflow.
     """
-    config = tomllib.loads(Path("pyproject.toml").read_text("utf-8"))
+    config = loads(Path("pyproject.toml").read_text("utf-8"))
     pytest = config["tool"]["pytest"]["ini_options"]
     pytest["addopts"] = disable_concurrent_tests(pytest["addopts"])
     PYTEST.write_text(

scripts/boilercv_tools/add_changes.py

@@ -0,0 +1,131 @@
+"""Add changes."""
+
+from dataclasses import dataclass
+from json import loads
+from re import sub
+from shlex import quote, split
+from subprocess import run
+from textwrap import dedent
+from typing import Any, NamedTuple
+from urllib.parse import urlparse
+
+from dulwich.repo import Repo
+
+from boilercv_tools.types import ChangeType
+
+
+def add_change(typ: ChangeType = "change"):
+    """Add change."""
+    owner, repo, issue = get_issue_from_active_branch()
+    change = get_change(owner, repo, issue)
+    content = quote(f"{change.name}\n")
+    run(
+        split(  # noqa: S603
+            f"""towncrier create --content {content} {change.id}.{typ}.md"""
+        ),
+        check=True,
+    )
+
+
+class Issue(NamedTuple):
+    """Issue."""
+
+    owner: str
+    """Owner."""
+    repo: str
+    """Repository."""
+    issue: int
+    """Issue."""
+
+
+def get_issue_from_active_branch() -> Issue:
+    """Get issue associated with active branch."""
+    repository = Repo(".")
+    owner, repo = (
+        urlparse(repository.get_config().get(("remote", "origin"), "url"))
+        .path.decode("utf-8")
+        .removesuffix(".git")
+        .strip("/")
+        .split("/")
+    )
+    (_, ref), _ = repository.refs.follow(b"HEAD")
+    issue = ref.decode("utf-8").split("/")[-1].split("=")[0].split("-")[0]
+    return Issue(owner, repo, issue)
+
+
+@dataclass
+class Change:
+    """Change."""
+
+    id: int
+    """ID."""
+    name: str
+    """Name."""
+
+
+def get_change(owner: str, repo: str, issue: int) -> Change:
+    """Get related issue title."""
+    first = 1
+    if nodes := get_connected_prs(owner, repo, issue, first):
+        subject = nodes[0]["subject"]
+        return Change(id=subject["number"], name=subject["title"])
+    return Change(id=issue, name=query_gh_issue(owner, repo, issue)["title"])
+
+
+def get_connected_prs(
+    owner: str, repo: str, issue: int, first: int
+) -> list[dict[str, Any]]:
+    """Get first PR connected to an issue."""
+    return query_gh_issue(
+        owner,
+        repo,
+        issue,
+        query=f"""
+            timelineItems(itemTypes: CONNECTED_EVENT, first: {first}) {{
+                nodes {{
+                    ... on ConnectedEvent {{
+                        subject {{ ... on PullRequest {{ number title }} }}
+                    }}
+                }}
+            }}""",
+    )["timelineItems"]["nodes"]
+
+
+def query_gh_issue(
+    owner: str, repo: str, issue: int, query: str = "title"
+) -> dict[str, Any]:
+    """Query GitHub for an issue."""
+    result = run(
+        [  # noqa: S603, S607
+            "gh",
+            "api",
+            "graphql",
+            "-f",
+            sanitize(f"""query= {{
+                repository(owner:"{owner}", name:"{repo}") {{
+                    issue(number: {issue}) {{ {sanitize(query)} }}
+                }}
+            }}"""),
+        ],
+        capture_output=True,
+        text=True,
+        check=False,
+    )
+    if result.returncode:
+        raise RuntimeError(result.stderr)
+    data = loads(result.stdout)["data"].get("repository")
+    if not data:
+        raise RuntimeError("Query does not return a repository.")
+    if data := data.get("issue"):
+        return data
+    else:
+        raise RuntimeError("Query does not return an issue.")
+
+
+def sanitize(query: str) -> str:
+    """Sanitize query."""
+    return sub(r"\s+", " ", f"{dedent(query)}").strip().replace("\n", "")
+
+
+if __name__ == "__main__":
+    add_change()

scripts/boilercv_tools/types.py

@@ -16,6 +16,8 @@
 """Allowable operator."""
 ops: tuple[Op, ...] = (" @ ", "==")
 """Allowable operators."""
+ChangeType: TypeAlias = Literal["breaking", "deprecation", "change"]
+"""Type of change to add to changelog."""
 
 
 class Dep(TypedDict):