From d061a3c15449d72fa5219ed6e5379e3a0abc77b0 Mon Sep 17 00:00:00 2001 From: Ben Darwin Date: Fri, 26 Jan 2024 14:42:08 -0500 Subject: [PATCH 1/4] python311Packages.svgutils: init at 0.3.4 --- .../python-modules/svgutils/default.nix | 40 +++++++++++++++++++ pkgs/top-level/python-packages.nix | 2 + 2 files changed, 42 insertions(+) create mode 100644 pkgs/development/python-modules/svgutils/default.nix diff --git a/pkgs/development/python-modules/svgutils/default.nix b/pkgs/development/python-modules/svgutils/default.nix new file mode 100644 index 000000000000..ea2c7c547e43 --- /dev/null +++ b/pkgs/development/python-modules/svgutils/default.nix @@ -0,0 +1,40 @@ +{ lib +, buildPythonPackage +, fetchFromGitHub +, setuptools +, lxml +, matplotlib +, pytestCheckHook +, nose +}: + +buildPythonPackage rec { + pname = "svgutils"; + version = "0.3.4"; + pyproject = true; + + src = fetchFromGitHub { + owner = "btel"; + repo = "svg_utils"; + rev = "refs/tags/v${version}"; + hash = "sha256-ITvZx+3HMbTyaRmCb7tR0LKqCxGjqDdV9/2taziUD0c="; + }; + + nativeBuildInputs = [ setuptools ]; + + propagatedBuildInputs = [ + lxml + matplotlib + ]; + + nativeCheckInputs = [ pytestCheckHook nose ]; + + pythonImportsCheck = [ "svgutils" ]; + + meta = with lib; { + description = "Python tools to create and manipulate SVG files"; + homepage = "https://github.com/btel/svg_utils"; + license = licenses.mit; + maintainers = with maintainers; [ bcdarwin ]; + }; +} diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index e48f85ef1392..76b62ff373c4 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -14002,6 +14002,8 @@ self: super: with self; { svgelements = callPackage ../development/python-modules/svgelements { }; + svgutils = callPackage ../development/python-modules/svgutils { }; + svgwrite = callPackage ../development/python-modules/svgwrite { }; sv-ttk = callPackage ../development/python-modules/sv-ttk { }; From 43a00710a5fc33db8bc713323aab1ecd98e5e077 Mon Sep 17 00:00:00 2001 From: Ben Darwin Date: Thu, 2 Nov 2023 13:01:03 -0400 Subject: [PATCH 2/4] python311Packages.nipreps-version: init at 1.0.4 --- .../nipreps-versions/default.nix | 46 +++++++++++++++++++ pkgs/top-level/python-packages.nix | 2 + 2 files changed, 48 insertions(+) create mode 100644 pkgs/development/python-modules/nipreps-versions/default.nix diff --git a/pkgs/development/python-modules/nipreps-versions/default.nix b/pkgs/development/python-modules/nipreps-versions/default.nix new file mode 100644 index 000000000000..1c54ab9d905e --- /dev/null +++ b/pkgs/development/python-modules/nipreps-versions/default.nix @@ -0,0 +1,46 @@ +{ lib +, buildPythonPackage +, fetchFromGitHub +, pythonOlder +, flit-scm +, packaging +, setuptools-scm +, pytestCheckHook +}: + +buildPythonPackage rec { + pname = "nipreps-versions"; + version = "1.0.4"; + pyproject = true; + + disabled = pythonOlder "3.7"; + + src = fetchFromGitHub { + owner = "nipreps"; + repo = "version-schemes"; + rev = "refs/tags/${version}"; + hash = "sha256-B2wtLurzgk59kTooH51a2dewK7aEyA0dAm64Wp+tqhM="; + }; + + env.SETUPTOOLS_SCM_PRETEND_VERSION = version; + + nativeBuildInputs = [ + flit-scm + setuptools-scm + ]; + + propagatedBuildInputs = [ + packaging + ]; + + nativeCheckInputs = [ pytestCheckHook ]; + pythonImportsCheck = [ "nipreps_versions" ]; + + meta = with lib; { + description = "Setuptools_scm plugin for nipreps version schemes"; + homepage = "https://github.com/nipreps/version-schemes"; + changelog = "https://github.com/nipreps/version-schemes/blob/${src.rev}/CHANGES.md"; + license = licenses.asl20; + maintainers = with maintainers; [ bcdarwin ]; + }; +} diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index 76b62ff373c4..3a6e8bb74250 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -8363,6 +8363,8 @@ self: super: with self; { ninja = callPackage ../development/python-modules/ninja { inherit (pkgs) ninja; }; + nipreps-versions = callPackage ../development/python-modules/nipreps-versions { }; + nipy = callPackage ../development/python-modules/nipy { }; nipype = callPackage ../development/python-modules/nipype { From cdc7603f70388aa126adcc69c05d3cc6ccb139d7 Mon Sep 17 00:00:00 2001 From: Ben Darwin Date: Thu, 27 Apr 2023 19:01:22 -0400 Subject: [PATCH 3/4] python311Packages.templateflow: init at 23.1.0 --- .../python-modules/templateflow/default.nix | 45 +++++++++++++++++++ pkgs/top-level/python-packages.nix | 2 + 2 files changed, 47 insertions(+) create mode 100644 pkgs/development/python-modules/templateflow/default.nix diff --git a/pkgs/development/python-modules/templateflow/default.nix b/pkgs/development/python-modules/templateflow/default.nix new file mode 100644 index 000000000000..c879b7064d0f --- /dev/null +++ b/pkgs/development/python-modules/templateflow/default.nix @@ -0,0 +1,45 @@ +{ lib +, buildPythonPackage +, fetchFromGitHub +, pythonOlder +, pytestCheckHook +, setuptools-scm +, nipreps-versions +, pybids +, requests +, tqdm +}: + +buildPythonPackage rec { + pname = "templateflow"; + version = "23.1.0"; + pyproject = true; + + disabled = pythonOlder "3.7"; + + src = fetchFromGitHub { + owner = "templateflow"; + repo = "python-client"; + rev = "refs/tags/${version}"; + hash = "sha256-8AdXC1IFGfYZ5cvCAyBz0tD3zia+KBILX0tL9IcO2NA="; + }; + + nativeBuildInputs = [ setuptools-scm ]; + propagatedBuildInputs = [ + nipreps-versions + pybids + requests + tqdm + ]; + + doCheck = false; # most tests try to download data + #pythonImportsCheck = [ "templateflow" ]; # touches $HOME/.cache, hence needs https://github.com/NixOS/nixpkgs/pull/120300 + + meta = with lib; { + homepage = "https://templateflow.org/python-client"; + description = "Python API to query TemplateFlow via pyBIDS"; + changelog = "https://github.com/templateflow/python-client/releases/tag/${version}"; + license = licenses.asl20; + maintainers = with maintainers; [ bcdarwin ]; + }; +} diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index 3a6e8bb74250..d40c4626b625 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -14146,6 +14146,8 @@ self: super: with self; { tempita = callPackage ../development/python-modules/tempita { }; + templateflow = callPackage ../development/python-modules/templateflow { }; + tempora = callPackage ../development/python-modules/tempora { }; tenacity = callPackage ../development/python-modules/tenacity { }; From 7a483d6e4f2625b01ed0fd9213401a061a4dbd85 Mon Sep 17 00:00:00 2001 From: Ben Darwin Date: Thu, 2 Nov 2023 13:03:34 -0400 Subject: [PATCH 4/4] python311Packages.niworkflows: init at 1.10.0 --- .../python-modules/niworkflows/default.nix | 101 ++++++++++++++++++ pkgs/top-level/python-packages.nix | 2 + 2 files changed, 103 insertions(+) create mode 100644 pkgs/development/python-modules/niworkflows/default.nix diff --git a/pkgs/development/python-modules/niworkflows/default.nix b/pkgs/development/python-modules/niworkflows/default.nix new file mode 100644 index 000000000000..494a834c937a --- /dev/null +++ b/pkgs/development/python-modules/niworkflows/default.nix @@ -0,0 +1,101 @@ +{ lib +, buildPythonPackage +, fetchFromGitHub +, hatch-vcs +, hatchling +, pytestCheckHook +, attrs +, importlib-resources +, jinja2 +, looseversion +, matplotlib +, nibabel +, nilearn +, nipype +, nitransforms +, numpy +, packaging +, pandas +, pybids +, pyyaml +, scikit-image +, scipy +, seaborn +, svgutils +, templateflow +, traits +, transforms3d +}: + +buildPythonPackage rec { + pname = "niworkflows"; + version = "1.10.0"; + pyproject = true; + + src = fetchFromGitHub { + owner = "nipreps"; + repo = "niworkflows"; + rev = "refs/tags/${version}"; + hash = "sha256-wQPk9imDvomg+NTWk+VeW1TE2QlvMyi1YYVVaznhktU="; + }; + + postPatch = '' + substituteInPlace pyproject.toml --replace '"traits < 6.4"' '"traits"' + ''; + + nativeBuildInputs = [ + hatch-vcs + hatchling + ]; + + propagatedBuildInputs = [ + attrs + importlib-resources + jinja2 + looseversion + matplotlib + nibabel + nilearn + nipype + nitransforms + numpy + packaging + pandas + pybids + pyyaml + scikit-image + scipy + seaborn + svgutils + templateflow + traits + transforms3d + ]; + + env.SETUPTOOLS_SCM_PRETEND_VERSION = version; + + nativeCheckInputs = [ pytestCheckHook ]; + preCheck = ''export HOME=$(mktemp -d)''; + pytestFlagsArray = [ "niworkflows" ]; + # try to download data: + disabledTests = [ + "test_GenerateCifti" + "ROIsPlot" + "ROIsPlot2" + "test_SimpleShowMaskRPT" + "test_cifti_surfaces_plot" + "niworkflows.utils.misc.get_template_specs" + "niworkflows.interfaces.cifti._prepare_cifti" + ]; + disabledTestPaths = [ "niworkflows/tests/test_registration.py" ]; + + pythonImportsCheck = [ "niworkflows" ]; + + meta = with lib; { + description = "Common workflows for MRI (anatomical, functional, diffusion, etc.)"; + homepage = "https://github.com/nipreps/niworkflows"; + changelog = "https://github.com/nipreps/niworkflows/blob/${src.rev}/CHANGES.rst"; + license = licenses.asl20; + maintainers = with maintainers; [ bcdarwin ]; + }; +} diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index d40c4626b625..f1a9bbb95aee 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -8377,6 +8377,8 @@ self: super: with self; { nitransforms = callPackage ../development/python-modules/nitransforms { }; + niworkflows = callPackage ../development/python-modules/niworkflows { }; + nix-kernel = callPackage ../development/python-modules/nix-kernel { inherit (pkgs) nix; };