diff --git a/docs/changelog.md b/docs/changelog.md index 4ca30298..948b99f7 100644 --- a/docs/changelog.md +++ b/docs/changelog.md @@ -13,6 +13,9 @@ behavior they verify rather than listed separately. ### Added +- Install the legacy Kwik GUI dependencies with the optional `phy[kwik]` + extra. The supported legacy environment uses Python 3.10 or 3.11 and NumPy + 1.23 without constraining regular Template GUI installations. - Select the first eligible clusters in the Similarity View with `Control+Space`. The default is 15 clusters; **Select > Select N Similar** changes the number and remembers it across sessions. diff --git a/docs/installation.md b/docs/installation.md index fb5011c9..16888469 100644 --- a/docs/installation.md +++ b/docs/installation.md @@ -161,14 +161,17 @@ phy template-gui /path/to/output/params.py ## Legacy Kwik support The Template GUI is the recommended workflow for current template-based sorters. -The legacy Kwik GUI needs additional packages. Install them in a separate -uv-managed environment because `klustakwik2` needs NumPy, setuptools, and Cython -available while it builds: +The legacy Kwik GUI requires Python 3.10 or 3.11 because its unmaintained +dependencies are not compatible with current NumPy releases. Install it in a +separate uv-managed environment. The `kwik` extra supplies the tested legacy +dependency versions, while `klustakwik2` still needs NumPy, setuptools, and +Cython available while it builds: ```bash -uv venv --python 3.12 phy-kwik-env -uv pip install --python phy-kwik-env phy klusta cython +uv venv --python 3.11 phy-kwik-env +uv pip install --python phy-kwik-env "numpy>=1.23,<1.24" "setuptools<81" six cython uv pip install --python phy-kwik-env --no-build-isolation klustakwik2 +uv pip install --python phy-kwik-env "phy[kwik]" ``` Activate the environment using the command printed by `uv venv`. It can then be diff --git a/pyproject.toml b/pyproject.toml index 9cac0665..22d79f8b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -22,6 +22,7 @@ classifiers = [ "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", ] requires-python = ">=3.10" @@ -34,7 +35,7 @@ dependencies = [ "joblib", "matplotlib", "mtscomp", - "numpy", + "numpy>=1.23", "pillow", "pip", "PyQt5>=5.15.11,<5.16", @@ -55,6 +56,13 @@ Repository = "https://github.com/cortex-lab/phy" Documentation = "https://phy.readthedocs.io/en/latest/" [project.optional-dependencies] +kwik = [ + "klusta", + "klustakwik2", + "numpy>=1.23,<1.24", + "setuptools<81", + "six", +] dev = [ "Cython>=3.0", "pytest", @@ -108,6 +116,12 @@ phy = [ [tool.uv] required-version = ">=0.11.8,<0.13" +conflicts = [ + [ + { extra = "kwik" }, + { group = "dev" }, + ], +] required-environments = [ "sys_platform == 'win32' and platform_machine == 'AMD64'", ] diff --git a/uv.lock b/uv.lock index a1c16972..3835a7b4 100644 --- a/uv.lock +++ b/uv.lock @@ -2,14 +2,20 @@ version = 1 revision = 3 requires-python = ">=3.10" resolution-markers = [ - "(python_full_version >= '3.11' and platform_machine != 'AMD64') or (python_full_version >= '3.11' and sys_platform != 'win32')", - "python_full_version >= '3.11' and platform_machine == 'AMD64' and sys_platform == 'win32'", + "(python_full_version >= '3.12' and platform_machine != 'AMD64') or (python_full_version >= '3.12' and sys_platform != 'win32')", + "(python_full_version == '3.11.*' and platform_machine != 'AMD64') or (python_full_version == '3.11.*' and sys_platform != 'win32')", + "python_full_version >= '3.12' and platform_machine == 'AMD64' and sys_platform == 'win32'", + "python_full_version == '3.11.*' and platform_machine == 'AMD64' and sys_platform == 'win32'", "(python_full_version < '3.11' and platform_machine != 'AMD64') or (python_full_version < '3.11' and sys_platform != 'win32')", "python_full_version < '3.11' and platform_machine == 'AMD64' and sys_platform == 'win32'", ] required-markers = [ "platform_machine == 'AMD64' and sys_platform == 'win32'", ] +conflicts = [[ + { package = "phy", extra = "kwik" }, + { package = "phy", group = "dev" }, +]] [[package]] name = "annotated-doc" @@ -170,7 +176,7 @@ name = "click" version = "8.4.2" source = { registry = "https://pypi.org/simple" } dependencies = [ - { name = "colorama", marker = "sys_platform == 'win32'" }, + { name = "colorama", marker = "sys_platform == 'win32' or (extra == 'extra-3-phy-kwik' and extra == 'group-3-phy-dev')" }, ] sdist = { url = "https://files.pythonhosted.org/packages/76/d4/81420972a676e8ffea40450d8c8c92943e7218a78fe9b64359836cc9876b/click-8.4.2.tar.gz", hash = "sha256:9a6cea6e60b17ebe0a44c5cc636d94f09bd66142c1cd7d8b4cd731c4917a15f6", size = 338000, upload-time = "2026-06-24T17:45:15.148Z" } wheels = [ @@ -221,8 +227,9 @@ name = "contourpy" version = "1.3.2" 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= "1.3.0" source = { registry = "https://pypi.org/simple" } dependencies = [ - { name = "typing-extensions" }, + { name = "typing-extensions", marker = "python_full_version < '3.11' or (extra == 'extra-3-phy-kwik' and extra == 'group-3-phy-dev')" }, ] sdist = { url = "https://files.pythonhosted.org/packages/0b/9f/a65090624ecf468cdca03533906e7c69ed7588582240cfe7cc9e770b50eb/exceptiongroup-1.3.0.tar.gz", hash = "sha256:b241f5885f560bc56a59ee63ca4c6a8bfa46ae4ad651af316d4e81817bb9fd88", size = 29749, upload-time = "2025-05-10T17:42:51.123Z" } wheels = [ @@ -605,8 +612,9 @@ name = "h5py" version = "3.16.0" source = { registry = "https://pypi.org/simple" } dependencies = [ - { name = "numpy", version = "2.2.6", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11'" }, - { name = "numpy", version = "2.4.3", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" }, + { name = "numpy", version = "1.23.5", source = { 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dependencies = [ - { name = "zipp" }, + { name = "zipp", marker = "python_full_version < '3.12' or (extra == 'extra-3-phy-kwik' and extra == 'group-3-phy-dev')" }, ] sdist = { url = "https://files.pythonhosted.org/packages/76/66/650a33bd90f786193e4de4b3ad86ea60b53c89b669a5c7be931fac31cdb0/importlib_metadata-8.7.0.tar.gz", hash = "sha256:d13b81ad223b890aa16c5471f2ac3056cf76c5f10f82d6f9292f0b415f389000", size = 56641, upload-time = "2025-04-27T15:29:01.736Z" } wheels = [ @@ -694,14 +702,13 @@ name = "ipykernel" version = "7.3.0" source = { registry = "https://pypi.org/simple" } dependencies = [ - { name = "appnope", marker = "sys_platform == 'darwin'" }, + { name = "appnope", marker = "sys_platform == 'darwin' or (extra == 'extra-3-phy-kwik' and extra == 'group-3-phy-dev')" }, { name = "comm" }, { name = "debugpy" }, - { name = "ipython", version = "8.37.0", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11'" }, - { name = "ipython", version = 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