fix: numpy Python 3.13 pin + codex skill dir (#1154 #1160)

#1154: scope numpy>=2.0 constraint to python_version>='3.13' only.
numpy 1.26.4 ships no cp313 wheel so uv sync falls back to a source
build requiring a C compiler. The marker avoids forcing numpy 2.x on
3.10-3.12 users who have working 1.x environments.

#1160: codex platform skill now installs to .codex/skills/graphify/
instead of .agents/skills/graphify/. The hook already wrote to .codex/
so the skill destination was inconsistent. Propagates automatically
through install/uninstall (both read _PLATFORM_CONFIG dynamically).
Updated all codex-specific test assertions.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
This commit is contained in:
Safi
2026-06-07 12:11:34 +01:00
co-authored by Claude Sonnet 4.6
parent 079b34da78
commit f146be3ea2
4 changed files with 303 additions and 104 deletions
+1 -1
View File
@@ -415,7 +415,7 @@ _PLATFORM_CONFIG: dict[str, dict] = {
},
"codex": {
"skill_file": "skill-codex.md",
"skill_dst": Path(".agents") / "skills" / "graphify" / "SKILL.md",
"skill_dst": Path(".codex") / "skills" / "graphify" / "SKILL.md",
"claude_md": False,
"skill_refs": "codex",
},
+2 -2
View File
@@ -52,7 +52,7 @@ mcp = ["mcp"]
neo4j = ["neo4j"]
pdf = ["pypdf", "markdownify"]
watch = ["watchdog"]
svg = ["matplotlib"]
svg = ["matplotlib", "numpy>=2.0; python_version >= '3.13'"]
leiden = ["graspologic; python_version < '3.13'"]
office = ["python-docx", "openpyxl"]
google = ["openpyxl"]
@@ -71,7 +71,7 @@ sql = ["tree-sitter-sql"]
# avoids breaking the default `uv tool install graphifyy` for everyone (#1104).
dm = ["tree-sitter-dm"]
terraform = ["tree-sitter-hcl"]
all = ["mcp", "neo4j", "pypdf", "markdownify", "watchdog", "graspologic; python_version < '3.13'", "python-docx", "openpyxl", "faster-whisper; python_version >= '3.11'", "yt-dlp", "matplotlib", "openai", "tiktoken", "boto3", "anthropic", "tree-sitter-sql", "jieba", "tree-sitter-dm", "tree-sitter-hcl"]
all = ["mcp", "neo4j", "pypdf", "markdownify", "watchdog", "graspologic; python_version < '3.13'", "python-docx", "openpyxl", "faster-whisper; python_version >= '3.11'", "yt-dlp", "matplotlib", "numpy>=2.0; python_version >= '3.13'", "openai", "tiktoken", "boto3", "anthropic", "tree-sitter-sql", "jieba", "tree-sitter-dm", "tree-sitter-hcl"]
[project.scripts]
graphify = "graphify.__main__:main"
+9 -9
View File
@@ -8,7 +8,7 @@ import pytest
PLATFORMS = {
"claude": (".claude/skills/graphify/SKILL.md",),
"codex": (".agents/skills/graphify/SKILL.md",),
"codex": (".codex/skills/graphify/SKILL.md",),
"opencode": (".config/opencode/skills/graphify/SKILL.md",),
"kilo": (
".config/kilo/skills/graphify/SKILL.md",
@@ -41,7 +41,7 @@ def test_install_default_claude(tmp_path):
def test_install_codex(tmp_path):
_install(tmp_path, "codex")
assert (tmp_path / ".agents" / "skills" / "graphify" / "SKILL.md").exists()
assert (tmp_path / ".codex" / "skills" / "graphify" / "SKILL.md").exists()
def test_install_opencode(tmp_path):
@@ -87,10 +87,10 @@ def test_install_project_codex_writes_skill_and_agents(tmp_path, monkeypatch):
monkeypatch.setattr(sys, "argv", ["graphify", "install", "--project", "--platform", "codex"])
with patch("graphify.__main__.Path.home", return_value=home):
main()
assert (project / ".agents" / "skills" / "graphify" / "SKILL.md").exists()
assert (project / ".codex" / "skills" / "graphify" / "SKILL.md").exists()
assert (project / "AGENTS.md").exists()
assert (project / ".codex" / "hooks.json").exists()
assert not (home / ".agents" / "skills" / "graphify" / "SKILL.md").exists()
assert not (home / ".codex" / "skills" / "graphify" / "SKILL.md").exists()
def test_claude_subcommand_project_install_and_uninstall_are_project_scoped(tmp_path, monkeypatch):
@@ -124,14 +124,14 @@ def test_codex_subcommand_project_install_and_uninstall_are_project_scoped(tmp_p
home = tmp_path / "home"
project = tmp_path / "project"
project.mkdir()
user_skill = home / ".agents" / "skills" / "graphify" / "SKILL.md"
user_skill = home / ".codex" / "skills" / "graphify" / "SKILL.md"
user_skill.parent.mkdir(parents=True)
user_skill.write_text("user skill")
monkeypatch.chdir(project)
with patch("graphify.__main__.Path.home", return_value=home):
monkeypatch.setattr(sys, "argv", ["graphify", "codex", "install", "--project"])
main()
assert (project / ".agents" / "skills" / "graphify" / "SKILL.md").exists()
assert (project / ".codex" / "skills" / "graphify" / "SKILL.md").exists()
assert (project / "AGENTS.md").exists()
assert (project / ".codex" / "hooks.json").exists()
assert user_skill.exists()
@@ -140,7 +140,7 @@ def test_codex_subcommand_project_install_and_uninstall_are_project_scoped(tmp_p
main()
assert user_skill.exists()
assert not (project / ".agents" / "skills" / "graphify" / "SKILL.md").exists()
assert not (project / ".codex" / "skills" / "graphify" / "SKILL.md").exists()
assert not (project / "AGENTS.md").exists()
hooks_path = project / ".codex" / "hooks.json"
assert hooks_path.exists()
@@ -339,7 +339,7 @@ def test_uninstall_project_removes_project_skill_only(tmp_path, monkeypatch):
home = tmp_path / "home"
project = tmp_path / "project"
project.mkdir()
user_skill = home / ".agents" / "skills" / "graphify" / "SKILL.md"
user_skill = home / ".codex" / "skills" / "graphify" / "SKILL.md"
user_skill.parent.mkdir(parents=True)
user_skill.write_text("user skill")
monkeypatch.chdir(project)
@@ -349,7 +349,7 @@ def test_uninstall_project_removes_project_skill_only(tmp_path, monkeypatch):
monkeypatch.setattr(sys, "argv", ["graphify", "uninstall", "--project", "--platform", "codex"])
main()
assert user_skill.exists()
assert not (project / ".agents" / "skills" / "graphify" / "SKILL.md").exists()
assert not (project / ".codex" / "skills" / "graphify" / "SKILL.md").exists()
assert not (project / "AGENTS.md").exists()
Generated
+291 -92
View File
@@ -5,9 +5,12 @@ resolution-markers = [
"python_full_version >= '3.14' and sys_platform == 'win32'",
"python_full_version >= '3.14' and sys_platform == 'emscripten'",
"python_full_version >= '3.14' and sys_platform != 'emscripten' and sys_platform != 'win32'",
"python_full_version >= '3.11' and python_full_version < '3.14' and sys_platform == 'win32'",
"python_full_version >= '3.11' and python_full_version < '3.14' and sys_platform == 'emscripten'",
"python_full_version >= '3.11' and python_full_version < '3.14' and sys_platform != 'emscripten' and sys_platform != 'win32'",
"python_full_version == '3.13.*' and sys_platform == 'win32'",
"python_full_version >= '3.11' and python_full_version < '3.13' and sys_platform == 'win32'",
"python_full_version == '3.13.*' and sys_platform == 'emscripten'",
"python_full_version >= '3.11' and python_full_version < '3.13' and sys_platform == 'emscripten'",
"python_full_version == '3.13.*' and sys_platform != 'emscripten' and sys_platform != 'win32'",
"python_full_version >= '3.11' and python_full_version < '3.13' and sys_platform != 'emscripten' and sys_platform != 'win32'",
"python_full_version < '3.11'",
]
@@ -98,7 +101,7 @@ name = "autograd"
version = "1.8.0"
source = { registry = "https://pypi.org/simple" }
dependencies = [
{ name = "numpy", marker = "python_full_version < '3.14'" },
{ name = "numpy", version = "1.26.4", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.13'" },
]
sdist = { url = "https://files.pythonhosted.org/packages/67/1c/3c24ec03c8ba4decc742b1df5a10c52f98c84ca8797757f313e7bdcdf276/autograd-1.8.0.tar.gz", hash = "sha256:107374ded5b09fc8643ac925348c0369e7b0e73bbed9565ffd61b8fd04425683", size = 2562146, upload-time = "2025-05-05T12:49:02.502Z" }
wheels = [
@@ -512,7 +515,7 @@ resolution-markers = [
"python_full_version < '3.11'",
]
dependencies = [
{ name = "numpy", marker = "python_full_version < '3.11'" },
{ name = "numpy", version = "1.26.4", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11'" },
]
sdist = { url = "https://files.pythonhosted.org/packages/66/54/eb9bfc647b19f2009dd5c7f5ec51c4e6ca831725f1aea7a993034f483147/contourpy-1.3.2.tar.gz", hash = "sha256:b6945942715a034c671b7fc54f9588126b0b8bf23db2696e3ca8328f3ff0ab54", size = 13466130, upload-time = "2025-04-15T17:47:53.79Z" }
wheels = [
@@ -582,12 +585,16 @@ resolution-markers = [
"python_full_version >= '3.14' and sys_platform == 'win32'",
"python_full_version >= '3.14' and sys_platform == 'emscripten'",
"python_full_version >= '3.14' and sys_platform != 'emscripten' and sys_platform != 'win32'",
"python_full_version >= '3.11' and python_full_version < '3.14' and sys_platform == 'win32'",
"python_full_version >= '3.11' and python_full_version < '3.14' and sys_platform == 'emscripten'",
"python_full_version >= '3.11' and python_full_version < '3.14' and sys_platform != 'emscripten' and sys_platform != 'win32'",
"python_full_version == '3.13.*' and sys_platform == 'win32'",
"python_full_version >= '3.11' and python_full_version < '3.13' and sys_platform == 'win32'",
"python_full_version == '3.13.*' and sys_platform == 'emscripten'",
"python_full_version >= '3.11' and python_full_version < '3.13' and sys_platform == 'emscripten'",
"python_full_version == '3.13.*' and sys_platform != 'emscripten' and sys_platform != 'win32'",
"python_full_version >= '3.11' and python_full_version < '3.13' and sys_platform != 'emscripten' and sys_platform != 'win32'",
]
dependencies = [
{ name = "numpy", marker = "python_full_version >= '3.11'" },
{ name = "numpy", version = "1.26.4", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11' and python_full_version < '3.13'" },
{ name = "numpy", version = "2.4.6", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.13'" },
]
sdist = { url = "https://files.pythonhosted.org/packages/58/01/1253e6698a07380cd31a736d248a3f2a50a7c88779a1813da27503cadc2a/contourpy-1.3.3.tar.gz", hash = "sha256:083e12155b210502d0bca491432bb04d56dc3432f95a979b429f2848c3dbe880", size = 13466174, upload-time = "2025-07-26T12:03:12.549Z" }
wheels = [
@@ -847,7 +854,8 @@ name = "ctranslate2"
version = "4.7.1"
source = { registry = "https://pypi.org/simple" }
dependencies = [
{ name = "numpy", marker = "python_full_version >= '3.11'" },
{ name = "numpy", version = "1.26.4", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11' and python_full_version < '3.13'" },
{ name = "numpy", version = "2.4.6", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.13'" },
{ name = "pyyaml", marker = "python_full_version >= '3.11'" },
{ name = "setuptools", marker = "python_full_version >= '3.11'" },
]
@@ -914,7 +922,8 @@ name = "datasketch"
version = "1.10.0"
source = { registry = "https://pypi.org/simple" }
dependencies = [
{ name = "numpy" },
{ name = "numpy", version = "1.26.4", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.13'" },
{ name = "numpy", version = "2.4.6", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.13'" },
{ name = "scipy", version = "1.15.3", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11'" },
{ name = "scipy", version = "1.17.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" },
]
@@ -1106,10 +1115,10 @@ name = "gensim"
version = "4.4.0"
source = { registry = "https://pypi.org/simple" }
dependencies = [
{ name = "numpy", marker = "python_full_version < '3.14'" },
{ name = "numpy", version = "1.26.4", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.13'" },
{ name = "scipy", version = "1.15.3", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11'" },
{ name = "scipy", version = "1.17.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11' and python_full_version < '3.14'" },
{ name = "smart-open", marker = "python_full_version < '3.14'" },
{ name = "scipy", version = "1.17.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11' and python_full_version < '3.13'" },
{ name = "smart-open", marker = "python_full_version < '3.13'" },
]
sdist = { url = "https://files.pythonhosted.org/packages/1a/80/fe9d2e1ace968041814dbcfce4e8499a643a36c41267fa4b6c4f54cce420/gensim-4.4.0.tar.gz", hash = "sha256:a3f5b626da5518e79a479140361c663089fe7998df8ba52d56e1ded71ac5bdf5", size = 23260095, upload-time = "2025-10-18T02:06:45.962Z" }
wheels = [
@@ -1137,7 +1146,7 @@ wheels = [
[[package]]
name = "graphifyy"
version = "0.8.31"
version = "0.8.33"
source = { editable = "." }
dependencies = [
{ name = "datasketch" },
@@ -1183,6 +1192,7 @@ all = [
{ name = "matplotlib" },
{ name = "mcp" },
{ name = "neo4j" },
{ name = "numpy", version = "2.4.6", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.13'" },
{ name = "openai" },
{ name = "openpyxl" },
{ name = "pypdf" },
@@ -1241,11 +1251,15 @@ pdf = [
{ name = "markdownify" },
{ name = "pypdf" },
]
postgres = [
{ name = "psycopg", extra = ["binary"] },
]
sql = [
{ name = "tree-sitter-sql" },
]
svg = [
{ name = "matplotlib" },
{ name = "numpy", version = "2.4.6", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.13'" },
]
terraform = [
{ name = "tree-sitter-hcl" },
@@ -1300,6 +1314,8 @@ requires-dist = [
{ name = "neo4j", marker = "extra == 'all'" },
{ name = "neo4j", marker = "extra == 'neo4j'" },
{ name = "networkx", specifier = ">=3.4" },
{ name = "numpy", marker = "python_full_version >= '3.13' and extra == 'all'", specifier = ">=2.0" },
{ name = "numpy", marker = "python_full_version >= '3.13' and extra == 'svg'", specifier = ">=2.0" },
{ name = "openai", marker = "extra == 'all'" },
{ name = "openai", marker = "extra == 'gemini'" },
{ name = "openai", marker = "extra == 'kimi'" },
@@ -1308,6 +1324,7 @@ requires-dist = [
{ name = "openpyxl", marker = "extra == 'all'" },
{ name = "openpyxl", marker = "extra == 'google'" },
{ name = "openpyxl", marker = "extra == 'office'" },
{ name = "psycopg", extras = ["binary"], marker = "extra == 'postgres'" },
{ name = "pypdf", marker = "extra == 'all'" },
{ name = "pypdf", marker = "extra == 'pdf'" },
{ name = "python-docx", marker = "extra == 'all'" },
@@ -1354,7 +1371,7 @@ requires-dist = [
{ name = "yt-dlp", marker = "extra == 'all'" },
{ name = "yt-dlp", marker = "extra == 'video'" },
]
provides-extras = ["mcp", "neo4j", "pdf", "watch", "svg", "leiden", "office", "google", "video", "kimi", "ollama", "bedrock", "anthropic", "gemini", "openai", "chinese", "sql", "dm", "terraform", "all"]
provides-extras = ["mcp", "neo4j", "pdf", "watch", "svg", "leiden", "office", "google", "postgres", "video", "kimi", "ollama", "bedrock", "anthropic", "gemini", "openai", "chinese", "sql", "dm", "terraform", "all"]
[package.metadata.requires-dev]
dev = [
@@ -1381,26 +1398,26 @@ name = "graspologic"
version = "3.4.4"
source = { registry = "https://pypi.org/simple" }
dependencies = [
{ name = "anytree", marker = "python_full_version < '3.14'" },
{ name = "beartype", marker = "python_full_version < '3.14'" },
{ name = "future", marker = "python_full_version < '3.14'" },
{ name = "gensim", marker = "python_full_version < '3.14'" },
{ name = "graspologic-native", marker = "python_full_version < '3.14'" },
{ name = "hyppo", marker = "python_full_version < '3.14'" },
{ name = "joblib", marker = "python_full_version < '3.14'" },
{ name = "matplotlib", marker = "python_full_version < '3.14'" },
{ name = "anytree", marker = "python_full_version < '3.13'" },
{ name = "beartype", marker = "python_full_version < '3.13'" },
{ name = "future", marker = "python_full_version < '3.13'" },
{ name = "gensim", marker = "python_full_version < '3.13'" },
{ name = "graspologic-native", marker = "python_full_version < '3.13'" },
{ name = "hyppo", marker = "python_full_version < '3.13'" },
{ name = "joblib", marker = "python_full_version < '3.13'" },
{ name = "matplotlib", marker = "python_full_version < '3.13'" },
{ name = "networkx", version = "3.4.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11'" },
{ name = "networkx", version = "3.6.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11' and python_full_version < '3.14'" },
{ name = "numpy", marker = "python_full_version < '3.14'" },
{ name = "pot", marker = "python_full_version < '3.14'" },
{ name = "networkx", version = "3.6.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11' and python_full_version < '3.13'" },
{ name = "numpy", version = "1.26.4", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.13'" },
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{ name = "statsmodels", marker = "python_full_version < '3.14'" },
{ name = "typing-extensions", marker = "python_full_version < '3.14'" },
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@@ -1535,18 +1552,18 @@ name = "hyppo"
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source = { registry = "https://pypi.org/simple" }
dependencies = [
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{ name = "future", marker = "python_full_version < '3.14'" },
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