Merge pull request #193990 from swflint/add-lifelines

python310Packages.lifelines: init at 0.27.4

pkgs/development/python-modules/autograd-gamma/default.nix

@@ -0,0 +1,29 @@
+{ lib, buildPythonPackage, fetchFromGitHub, pytestCheckHook, autograd, scipy }:
+
+buildPythonPackage rec {
+  pname = "autograd-gamma";
+  version = "0.4.3";
+
+  src = fetchFromGitHub {
+    owner = "CamDavidsonPilon";
+    repo = "autograd-gamma";
+    rev = "v${version}";
+    sha256 = "0v03gly5k3a1hzb54zpw6409m3riak49qd27hkq2f66ai42ivqz2";
+  };
+
+  propagatedBuildInputs = [
+    autograd
+    scipy
+  ];
+
+  pythonImportsCheck = [ "autograd_gamma" ];
+
+  checkInputs = [ pytestCheckHook ];
+
+  meta = {
+    homepage = "https://github.com/CamDavidsonPilon/autograd-gamma";
+    description = "Autograd compatible approximations to the gamma family of functions";
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ swflint ];
+  };
+}

pkgs/development/python-modules/formulaic/default.nix

@@ -0,0 +1,63 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, pytestCheckHook
+, hatchling
+, hatch-vcs
+, git
+, astor
+, interface-meta
+, numpy
+, pandas
+, scipy
+, sympy
+, wrapt
+, typing-extensions
+}:
+
+buildPythonPackage rec {
+  pname = "formulaic";
+  version = "0.5.2";
+
+  format = "pyproject";
+
+  src = fetchFromGitHub {
+    owner = "matthewwardrop";
+    repo = "formulaic";
+    rev = "v${version}";
+    sha256 = "sha256-sIvHTuUS/nkcDjRgZCoEOY2negIOsarzH0PeXJsavWc=";
+  };
+
+  SETUPTOOLS_SCM_PRETEND_VERSION = version;
+
+  nativeBuildInputs = [
+    hatchling
+    hatch-vcs
+  ];
+
+  propagatedBuildInputs = [
+    astor
+    numpy
+    pandas
+    scipy
+    wrapt
+    typing-extensions
+    interface-meta
+    sympy
+  ];
+
+  pythonImportsCheck = [ "formulaic" ];
+
+  checkInputs = [ pytestCheckHook ];
+
+  disabledTestPaths = [
+    "tests/transforms/test_poly.py"
+  ];
+
+  meta = {
+    homepage = "https://matthewwardrop.github.io/formulaic/";
+    description = "High-performance implementation of Wilkinson formulas for";
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ swflint ];
+  };
+}

pkgs/development/python-modules/interface-meta/0001-fix-version.patch

@@ -0,0 +1,36 @@
+From 581102ae94a7e6dfd3ad3fa5371068189b9e7c44 Mon Sep 17 00:00:00 2001
+From: "Samuel W. Flint" <swflint@flintfam.org>
+Date: Thu, 27 Oct 2022 12:42:07 -0500
+Subject: [PATCH] fix-versions
+
+---
+ interface_meta/_version.py | 2 +-
+ pyproject.toml             | 2 +-
+ 2 files changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/interface_meta/_version.py b/interface_meta/_version.py
+index 3d50665..b3d3818 100644
+--- a/interface_meta/_version.py
++++ b/interface_meta/_version.py
+@@ -1,5 +1,5 @@
+ __author__ = "Matthew Wardrop"
+ __author_email__ = "mpwardrop@gmail.com"
+-__version__ = "0.0.0"
++__version__ = "1.3.0"
+ 
+ __dependencies__ = []
+diff --git a/pyproject.toml b/pyproject.toml
+index 43dab27..e543549 100644
+--- a/pyproject.toml
++++ b/pyproject.toml
+@@ -1,6 +1,6 @@
+ [tool.poetry]
+ name = "interface_meta"
+-version = "0.0.0"
++version = "1.3.0"
+ description = "`interface_meta` provides a convenient way to expose an extensible API with enforced method signatures and consistent documentation."
+ authors = ["Matthew Wardrop <mpwardrop@gmail.com>"]
+ license = "MIT"
+-- 
+2.37.0
+

pkgs/development/python-modules/interface-meta/default.nix

@@ -0,0 +1,38 @@
+{ lib, buildPythonPackage, fetchFromGitHub, pytestCheckHook, poetry-core, poetry-dynamic-versioning }:
+
+buildPythonPackage rec {
+  pname = "interface-meta";
+  version = "1.3.0";
+
+  format = "pyproject";
+
+  src = fetchFromGitHub {
+    owner = "matthewwardrop";
+    repo = "interface_meta";
+    rev = "v${version}";
+    sha256 = "0rzh11wnab33b11391vc2ynf8ncxn22b12wn46lmgkrc5mqza8hd";
+  };
+
+  patches = [
+    ./0001-fix-version.patch
+  ];
+
+  nativeBuildInputs = [
+    poetry-core
+  ];
+
+  propogatedBuildInputs = [
+    poetry-dynamic-versioning
+  ];
+
+  pythonImportsCheck = [ "interface_meta" ];
+
+  checkInputs = [ pytestCheckHook ];
+
+  meta = {
+    homepage = "https://github.com/matthewwardrop/interface_meta";
+    description = "Convenient way to expose an extensible API with enforced method signatures and consistent documentation";
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ swflint ];
+  };
+}

pkgs/development/python-modules/lifelines/default.nix

@@ -0,0 +1,63 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, pytestCheckHook
+, numpy
+, scipy
+, pandas
+, matplotlib
+, autograd
+, autograd-gamma
+, formulaic
+, scikit-learn
+, sybil
+, flaky
+, jinja2
+, dill
+, psutil
+}:
+
+buildPythonPackage rec {
+  pname = "lifelines";
+  version = "0.27.4";
+
+  src = fetchFromGitHub {
+    owner = "CamDavidsonPilon";
+    repo = "lifelines";
+    rev = "v${version}";
+    sha256 = "sha256-KDoXplqkTsk85dmcTBhbj2GDcC4ry+2z5C2QHAnBTw4=";
+  };
+
+  propagatedBuildInputs = [
+    numpy
+    scipy
+    pandas
+    matplotlib
+    autograd
+    autograd-gamma
+    formulaic
+  ];
+
+  pythonImportsCheck = [ "lifelines" ];
+
+  checkInputs = [
+    dill
+    flaky
+    jinja2
+    psutil
+    pytestCheckHook
+    scikit-learn
+    sybil
+  ];
+
+  disabledTestPaths = [
+    "lifelines/tests/test_estimation.py"
+  ];
+
+  meta = {
+    homepage = "https://lifelines.readthedocs.io";
+    description = "Survival analysis in Python";
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ swflint ];
+  };
+}

pkgs/top-level/python-packages.nix

@@ -812,6 +812,8 @@ self: super: with self; {
 
   autograd = callPackage ../development/python-modules/autograd { };
 
+  autograd-gamma = callPackage ../development/python-modules/autograd-gamma { };
+
   autoit-ripper = callPackage ../development/python-modules/autoit-ripper { };
 
   autologging = callPackage ../development/python-modules/autologging { };
@@ -3615,6 +3617,8 @@ self: super: with self; {
 
   FormEncode = callPackage ../development/python-modules/FormEncode { };
 
+  formulaic = callPackage ../development/python-modules/formulaic { };
+
   foundationdb51 = callPackage ../servers/foundationdb/python.nix { foundationdb = pkgs.foundationdb51; };
   foundationdb52 = callPackage ../servers/foundationdb/python.nix { foundationdb = pkgs.foundationdb52; };
   foundationdb60 = callPackage ../servers/foundationdb/python.nix { foundationdb = pkgs.foundationdb60; };
@@ -4710,6 +4714,8 @@ self: super: with self; {
 
   intensity-normalization = callPackage ../development/python-modules/intensity-normalization { };
 
+  interface-meta = callPackage ../development/python-modules/interface-meta { };
+
   internetarchive = callPackage ../development/python-modules/internetarchive { };
 
   interruptingcow = callPackage ../development/python-modules/interruptingcow { };
@@ -5486,6 +5492,8 @@ self: super: with self; {
 
   life360 = callPackage ../development/python-modules/life360 { };
 
+  lifelines = callPackage ../development/python-modules/lifelines { };
+
   lightgbm = callPackage ../development/python-modules/lightgbm { };
 
   lightning-utilities  = callPackage ../development/python-modules/lightning-utilities { };