From 2eecf15ad7776f924f8fc01e329d9bd17fbd6bf5 Mon Sep 17 00:00:00 2001
From: Gaetan Lepage <gaetan@glepage.com>
Date: Thu, 2 Jan 2025 11:36:22 +0100
Subject: [PATCH 1/3] python312Packages.deepdish: fix build

---
 .../python-modules/deepdish/default.nix       | 28 ++++++++++++++-----
 1 file changed, 21 insertions(+), 7 deletions(-)

diff --git a/pkgs/development/python-modules/deepdish/default.nix b/pkgs/development/python-modules/deepdish/default.nix
index 04062db872a7..119defd7ea17 100644
--- a/pkgs/development/python-modules/deepdish/default.nix
+++ b/pkgs/development/python-modules/deepdish/default.nix
@@ -1,7 +1,12 @@
 {
   lib,
-  fetchPypi,
   buildPythonPackage,
+  fetchPypi,
+
+  # build-system
+  setuptools,
+
+  # dependencies
   numpy,
   scipy,
   tables,
@@ -10,14 +15,23 @@
 buildPythonPackage rec {
   pname = "deepdish";
   version = "0.3.7";
-  format = "setuptools";
+  pyproject = true;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1wqzwh3y0mjdyba5kfbvlamn561d3afz50zi712c7klkysz3mzva";
+    hash = "sha256-av86vvaTzsNEOPGD8p0aLZhiq6J7uVnU8k1W4AfkH/M=";
   };
 
-  propagatedBuildInputs = [
+  postPatch = ''
+    substituteInPlace deepdish/core.py \
+      --replace-fail "np.ComplexWarning" "np.exceptions.ComplexWarning"
+  '';
+
+  build-system = [
+    setuptools
+  ];
+
+  dependencies = [
     numpy
     scipy
     tables
@@ -32,11 +46,11 @@ buildPythonPackage rec {
   # The tests are broken: `ModuleNotFoundError: No module named 'deepdish.six.conf'`
   doCheck = false;
 
-  meta = with lib; {
+  meta = {
     description = "Flexible HDF5 saving/loading and other data science tools from the University of Chicago";
     mainProgram = "ddls";
     homepage = "https://github.com/uchicago-cs/deepdish";
-    license = licenses.asl20;
-    maintainers = with maintainers; [ ndl ];
+    license = lib.licenses.asl20;
+    maintainers = with lib.maintainers; [ ndl ];
   };
 }

From 41ea9f469098acee3c247bf3860610ee74adefa7 Mon Sep 17 00:00:00 2001
From: Gaetan Lepage <gaetan@glepage.com>
Date: Thu, 2 Jan 2025 11:40:37 +0100
Subject: [PATCH 2/3] python312Packages.pyedflib: init at 0.1.38

---
 .../python-modules/pyedflib/default.nix       | 55 +++++++++++++++++++
 pkgs/top-level/python-packages.nix            |  2 +
 2 files changed, 57 insertions(+)
 create mode 100644 pkgs/development/python-modules/pyedflib/default.nix

diff --git a/pkgs/development/python-modules/pyedflib/default.nix b/pkgs/development/python-modules/pyedflib/default.nix
new file mode 100644
index 000000000000..a83fe89795b0
--- /dev/null
+++ b/pkgs/development/python-modules/pyedflib/default.nix
@@ -0,0 +1,55 @@
+{
+  lib,
+  buildPythonPackage,
+  fetchFromGitHub,
+
+  # build-system
+  cython,
+  numpy,
+  setuptools,
+
+  # tests
+  pytestCheckHook,
+}:
+
+buildPythonPackage rec {
+  pname = "pyedflib";
+  version = "0.1.38";
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "holgern";
+    repo = "pyedflib";
+    tag = "v${version}";
+    hash = "sha256-sj2O5ISAy12u4GdtucLaRfOeSA6o6FJpZWTyiLq5B3U=";
+  };
+
+  build-system = [
+    cython
+    numpy
+    setuptools
+  ];
+
+  pythonImportsCheck = [
+    "pyedflib"
+  ];
+
+  # Otherwise, the module is imported from source and lacks the compiled artifacts
+  # By moving to the pyedflib directory, python imports the installed package instead of the module
+  # from the local files
+  preCheck = ''
+    cd pyedflib
+  '';
+
+  nativeCheckInputs = [
+    pytestCheckHook
+  ];
+
+  meta = {
+    description = "Python library to read/write EDF+/BDF+ files based on EDFlib";
+    homepage = "https://github.com/holgern/pyedflib";
+    changelog = "https://github.com/holgern/pyedflib/releases/tag/v${version}";
+    license = lib.licenses.bsd3;
+    maintainers = with lib.maintainers; [ GaetanLepage ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index c7db18e65452..b5a48837f234 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -11619,6 +11619,8 @@ self: super: with self; {
 
   pyecowitt = callPackage ../development/python-modules/pyecowitt { };
 
+  pyedflib = callPackage ../development/python-modules/pyedflib { };
+
   pyedimax = callPackage ../development/python-modules/pyedimax { };
 
   pyee = callPackage ../development/python-modules/pyee { };

From 6a22aaca7219ede672ab5361b30a3b472223d5fd Mon Sep 17 00:00:00 2001
From: Gaetan Lepage <gaetan@glepage.com>
Date: Sat, 14 Sep 2024 21:06:55 +0200
Subject: [PATCH 3/3] python312Packages.pyseries: init at 1.0.26

---
 .../python-modules/pyseries/default.nix       | 63 +++++++++++++++++++
 pkgs/top-level/python-packages.nix            |  2 +
 2 files changed, 65 insertions(+)
 create mode 100644 pkgs/development/python-modules/pyseries/default.nix

diff --git a/pkgs/development/python-modules/pyseries/default.nix b/pkgs/development/python-modules/pyseries/default.nix
new file mode 100644
index 000000000000..76003eb105af
--- /dev/null
+++ b/pkgs/development/python-modules/pyseries/default.nix
@@ -0,0 +1,63 @@
+{
+  lib,
+  buildPythonPackage,
+  fetchPypi,
+
+  # build-system
+  setuptools,
+
+  # dependencies
+  deepdish,
+  matplotlib,
+  numpy,
+  obspy,
+  pandas,
+  pyedflib,
+  scikit-learn,
+  scipy,
+  seaborn,
+  tabulate,
+}:
+
+buildPythonPackage rec {
+  pname = "pyseries";
+  version = "1.0.26";
+  pyproject = true;
+
+  src = fetchPypi {
+    inherit pname version;
+    hash = "sha256-Cq+DXt0/6Ncae8OO+kaPuTCxouh0cFPHP+T8tGVXxXo=";
+  };
+
+  build-system = [ setuptools ];
+
+  pythonRemoveDeps = [
+    # sklearn is the old name of the scikit-learn package
+    "sklearn"
+  ];
+
+  dependencies = [
+    deepdish
+    matplotlib
+    numpy
+    obspy
+    pandas
+    pyedflib
+    scikit-learn
+    scipy
+    seaborn
+    tabulate
+  ];
+
+  pythonImportsCheck = [ "pyseries" ];
+
+  # no tests in the pypi archive
+  doCheck = false;
+
+  meta = {
+    description = "Package for statistical analysis of time-series data";
+    homepage = "https://pypi.org/project/pyseries/";
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ GaetanLepage ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index b5a48837f234..151fcf870f82 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -10649,6 +10649,8 @@ self: super: with self; {
 
   pysequoia = callPackage ../development/python-modules/pysequoia { };
 
+  pyseries = callPackage ../development/python-modules/pyseries { };
+
   pyschemes = callPackage ../development/python-modules/pyschemes { };
 
   pyschlage = callPackage ../development/python-modules/pyschlage { };