From 8278f5c3b03c3992078ecc9b768c0606fc2e42a9 Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Mon, 23 May 2022 19:13:10 +0200
Subject: [PATCH 01/11] python39Packages.numba-scipy: update stale
 substituteInPlace

---
 .../python-modules/numba-scipy/default.nix         | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/pkgs/development/python-modules/numba-scipy/default.nix b/pkgs/development/python-modules/numba-scipy/default.nix
index c8f84cbf43f5..525624eb05de 100644
--- a/pkgs/development/python-modules/numba-scipy/default.nix
+++ b/pkgs/development/python-modules/numba-scipy/default.nix
@@ -4,15 +4,19 @@
 , scipy
 , numba
 , pytestCheckHook
+, pythonOlder
 }:
 
 buildPythonPackage rec {
   pname = "numba-scipy";
   version = "0.3.0";
+  format = "setuptools";
+
+  disabled = pythonOlder "3.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "sha256-qJeoWiG1LdtFB9cME1d8xVaC0BXGDJEYjCOEdHvSkmQ=";
+    hash = "sha256-qJeoWiG1LdtFB9cME1d8xVaC0BXGDJEYjCOEdHvSkmQ=";
   };
 
   propagatedBuildInputs = [
@@ -21,14 +25,18 @@ buildPythonPackage rec {
   ];
 
   postPatch = ''
-    substituteInPlace setup.py --replace "scipy>=0.16,<=1.6.2" "scipy>=0.16,<=1.7.3"
+    # https://github.com/numba/numba-scipy/pull/76
+    substituteInPlace setup.py \
+      --replace "scipy>=0.16,<=1.6.2" "scipy>=0.16"
   '';
 
   checkInputs = [
     pytestCheckHook
   ];
 
-  pythonImportsCheck = [ "numba" ];
+  pythonImportsCheck = [
+    "numba_scipy"
+  ];
 
   meta = with lib; {
     description = "Extends Numba to make it aware of SciPy";

From 2e32938d54c380289eb9d19e61d3da793821daa8 Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Mon, 23 May 2022 13:09:45 +0200
Subject: [PATCH 02/11] python310Packages.numba: update disable

---
 .../python-modules/numba/default.nix          | 23 ++++++++++++++-----
 1 file changed, 17 insertions(+), 6 deletions(-)

diff --git a/pkgs/development/python-modules/numba/default.nix b/pkgs/development/python-modules/numba/default.nix
index d656a56e3c17..23921959f596 100644
--- a/pkgs/development/python-modules/numba/default.nix
+++ b/pkgs/development/python-modules/numba/default.nix
@@ -24,11 +24,11 @@ let
 in buildPythonPackage rec {
   version = "0.55.1";
   pname = "numba";
-  disabled = pythonOlder "3.6" || pythonAtLeast "3.10";
+  disabled = pythonOlder "3.6" || pythonAtLeast "3.11";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "sha256-A+kGmiZm0chPk7ANvXFvuP7d6Lssbvr6LwSEKkZELqM=";
+    hash = "sha256-A+kGmiZm0chPk7ANvXFvuP7d6Lssbvr6LwSEKkZELqM=";
   };
 
   postPatch = ''
@@ -42,9 +42,18 @@ in buildPythonPackage rec {
 
   NIX_CFLAGS_COMPILE = lib.optionalString stdenv.isDarwin "-I${lib.getDev libcxx}/include/c++/v1";
 
-  propagatedBuildInputs = [ numpy llvmlite setuptools ] ++ lib.optionals cudaSupport [ cudatoolkit cudatoolkit.lib ];
+  propagatedBuildInputs = [
+    numpy
+    llvmlite
+    setuptools
+  ] ++ lib.optionals cudaSupport [
+    cudatoolkit
+    cudatoolkit.lib
+  ];
 
-  nativeBuildInputs = lib.optional cudaSupport [ addOpenGLRunpath ];
+  nativeBuildInputs = lib.optional cudaSupport [
+    addOpenGLRunpath
+  ];
 
   patches = lib.optionals cudaSupport [
     (substituteAll {
@@ -69,12 +78,14 @@ in buildPythonPackage rec {
   # ImportError: cannot import name '_typeconv'
   doCheck = false;
 
-  pythonImportsCheck = [ "numba" ];
+  pythonImportsCheck = [
+    "numba"
+  ];
 
   meta =  with lib; {
+    description = "Compiling Python code using LLVM";
     homepage = "https://numba.pydata.org/";
     license = licenses.bsd2;
-    description = "Compiling Python code using LLVM";
     maintainers = with maintainers; [ fridh ];
   };
 }

From b7874eee051c6a194935e8b18745a7b9455df419 Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Tue, 24 May 2022 11:44:25 +0200
Subject: [PATCH 03/11] python39Packages.aesara: 2.5.3 -> 2.6.6

---
 .../python-modules/aesara/default.nix         | 54 ++++++++++++-------
 1 file changed, 35 insertions(+), 19 deletions(-)

diff --git a/pkgs/development/python-modules/aesara/default.nix b/pkgs/development/python-modules/aesara/default.nix
index 58a39422a3a3..d34a0fb0770f 100644
--- a/pkgs/development/python-modules/aesara/default.nix
+++ b/pkgs/development/python-modules/aesara/default.nix
@@ -1,30 +1,33 @@
 { lib
 , buildPythonPackage
-, fetchFromGitHub
-, numpy
-, scipy
-, filelock
+, cons
+, cython
 , etuples
+, fetchFromGitHub
+, filelock
 , logical-unification
 , minikanren
-, cons
 , numba
 , numba-scipy
-, libgpuarray
-, sympy
-, cython
+, numpy
 , pytestCheckHook
+, pythonOlder
+, scipy
+, typing-extensions
 }:
 
 buildPythonPackage rec {
   pname = "aesara";
-  version = "2.5.3";
+  version = "2.6.6";
+  format = "setuptools";
+
+  disabled = pythonOlder "3.7";
 
   src = fetchFromGitHub {
     owner = "aesara-devs";
     repo = "aesara";
     rev = "refs/tags/rel-${version}";
-    sha256 = "sha256-20nc70gNdcGjtGxv2WxmYxmswNH8v7yGLkToP2iazjc=";
+    hash = "sha256-ChLMQCXw9EBR0hnNYGdkUbiLF+4oCqOxzsKsnsf22Jk=";
   };
 
   nativeBuildInputs = [
@@ -32,28 +35,41 @@ buildPythonPackage rec {
   ];
 
   propagatedBuildInputs = [
-    numpy
-    scipy
-    filelock
+    cons
     etuples
+    filelock
     logical-unification
     minikanren
-    cons
-    numba
-    numba-scipy
-    libgpuarray
-    sympy
+    numpy
+    scipy
+    typing-extensions
   ];
 
   checkInputs = [
+    numba
+    numba-scipy
     pytestCheckHook
   ];
 
+  postPatch = ''
+    substituteInPlace setup.cfg \
+      --replace "--durations=50" ""
+  '';
+
   preBuild = ''
     export HOME=$(mktemp -d)
   '';
 
-  pythonImportsCheck = [ "aesara" ];
+  pythonImportsCheck = [
+    "aesara"
+  ];
+
+  disabledTestPaths = [
+    # Don't run the most compute-intense tests
+    "tests/scan/"
+    "tests/tensor/"
+    "tests/sandbox/"
+  ];
 
   meta = with lib; {
     description = "Python library to define, optimize, and efficiently evaluate mathematical expressions involving multi-dimensional arrays";

From d69a2ffcea2fec72eb24c8ce202151cb3adfc992 Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Tue, 24 May 2022 12:32:14 +0200
Subject: [PATCH 04/11] python310Packages.persim: disable failing tests on
 Python 3.10

---
 .../python-modules/persim/default.nix         | 25 +++++++++++++++++--
 1 file changed, 23 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/python-modules/persim/default.nix b/pkgs/development/python-modules/persim/default.nix
index 4ac21159d956..4e3717dec07e 100644
--- a/pkgs/development/python-modules/persim/default.nix
+++ b/pkgs/development/python-modules/persim/default.nix
@@ -9,15 +9,20 @@
 , scikit-learn
 , scipy
 , pytestCheckHook
+, pythonAtLeast
+, pythonOlder
 }:
 
 buildPythonPackage rec {
   pname = "persim";
   version = "0.3.1";
+  format = "setuptools";
+
+  disabled = pythonOlder "3.7";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "ef0f0a247adcf6104ecac14117db0b24581710ea8a8d964816805395700b4975";
+    sha256 = "sha256-7w8KJHrc9hBOysFBF9sLJFgXEOqKjZZIFoBTlXALSXU=";
   };
 
   propagatedBuildInputs = [
@@ -41,10 +46,26 @@ buildPythonPackage rec {
     echo "backend: ps" > $HOME/.matplotlib/matplotlibrc
   '';
 
+  pythonImportsCheck = [
+    "persim"
+  ];
+
+  disabledTests = lib.optionals (pythonAtLeast "3.10") [
+    # AttributeError: module 'collections' has no attribute 'Iterable'
+    "test_empyt_diagram_list"
+    "test_empty_diagram_list"
+    "test_fit_diagram"
+    "test_integer_diagrams"
+    "test_lists_of_lists"
+    "test_mixed_pairs"
+    "test_multiple_diagrams"
+    "test_n_pixels"
+  ];
+
   meta = with lib; {
     description = "Distances and representations of persistence diagrams";
     homepage = "https://persim.scikit-tda.org";
     license = licenses.mit;
-    maintainers = [ maintainers.costrouc ];
+    maintainers = with maintainers; [ costrouc ];
   };
 }

From 0fb3b8bddfcb7ddc59693451c7027914035bb730 Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Tue, 24 May 2022 15:40:06 +0200
Subject: [PATCH 05/11] python310Packages.numdifftools: init at 0.9.40

---
 .../python-modules/numdifftools/default.nix   | 51 +++++++++++++++++++
 pkgs/top-level/python-packages.nix            |  2 +
 2 files changed, 53 insertions(+)
 create mode 100644 pkgs/development/python-modules/numdifftools/default.nix

diff --git a/pkgs/development/python-modules/numdifftools/default.nix b/pkgs/development/python-modules/numdifftools/default.nix
new file mode 100644
index 000000000000..bc5914be721c
--- /dev/null
+++ b/pkgs/development/python-modules/numdifftools/default.nix
@@ -0,0 +1,51 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, numpy
+, pytestCheckHook
+, pythonOlder
+, scipy
+}:
+
+buildPythonPackage rec {
+  pname = "numdifftools";
+  version = "0.9.40";
+  format = "setuptools";
+
+  disabled = pythonOlder "3.7";
+
+  src = fetchFromGitHub {
+    owner = "pbrod";
+    repo = pname;
+    rev = "v${version}";
+    hash = "sha256-YLi9cNHcZ/PlhrhvYOMfRTOt4kinQcfxvqInT8/0Qpg=";
+  };
+
+  propagatedBuildInputs = [
+    numpy
+    scipy
+  ];
+
+  # Tests requires algopy and other modules which are optional and/or not available
+  doCheck = false;
+
+  postPatch = ''
+    substituteInPlace setup.py \
+      --replace '"pytest-runner"' ""
+    # Remove optional dependencies
+    substituteInPlace requirements.txt \
+      --replace "algopy>=0.4" "" \
+      --replace "statsmodels>=0.6" ""
+  '';
+
+  pythonImportsCheck = [
+    "numdifftools"
+  ];
+
+  meta = with lib; {
+    description = "Library to solve automatic numerical differentiation problems in one or more variables";
+    homepage = "https://github.com/pbrod/numdifftools";
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ fab ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 3d4ff7c5ebb8..5e8009a838db 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -5862,6 +5862,8 @@ in {
 
   numcodecs = callPackage ../development/python-modules/numcodecs { };
 
+  numdifftools = callPackage ../development/python-modules/numdifftools { };
+
   numericalunits = callPackage ../development/python-modules/numericalunits { };
 
   numexpr = callPackage ../development/python-modules/numexpr { };

From 91824e319240fc6e9a0cc0bcb0bbfaa80aac32fb Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Tue, 24 May 2022 16:19:53 +0200
Subject: [PATCH 06/11] python310Packages.aeppl: init at 0.0.31

---
 .../python-modules/aeppl/default.nix          | 51 +++++++++++++++++++
 pkgs/top-level/python-packages.nix            |  2 +
 2 files changed, 53 insertions(+)
 create mode 100644 pkgs/development/python-modules/aeppl/default.nix

diff --git a/pkgs/development/python-modules/aeppl/default.nix b/pkgs/development/python-modules/aeppl/default.nix
new file mode 100644
index 000000000000..bf7f4b8d02aa
--- /dev/null
+++ b/pkgs/development/python-modules/aeppl/default.nix
@@ -0,0 +1,51 @@
+{ lib
+, aesara
+, buildPythonPackage
+, fetchFromGitHub
+, numdifftools
+, numpy
+, pytestCheckHook
+, pythonOlder
+, scipy
+}:
+
+buildPythonPackage rec {
+  pname = "aeppl";
+  version = "0.0.31";
+  format = "setuptools";
+
+  disabled = pythonOlder "3.7";
+
+  src = fetchFromGitHub {
+    owner = "aesara-devs";
+    repo = pname;
+    rev = "refs/tags/v${version}";
+    hash = "sha256-fbBtjU2skvfDCnRRW+9PIObsEOfKhl15qSLw3TGhl4k=";
+  };
+
+  propagatedBuildInputs = [
+    aesara
+    numpy
+    scipy
+  ];
+
+  checkInputs = [
+    numdifftools
+    pytestCheckHook
+  ];
+
+  preCheck = ''
+    export HOME=$(mktemp -d);
+  '';
+
+  pythonImportsCheck = [
+    "aeppl"
+  ];
+
+  meta = with lib; {
+    description = "Library for an Aesara-based PPL";
+    homepage = "https://github.com/aesara-devs/aeppl";
+    license = licenses.mit;
+    maintainers = with maintainers; [ fab ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 5e8009a838db..d1e09ad6cf48 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -209,6 +209,8 @@ in {
 
   aenum = callPackage ../development/python-modules/aenum { };
 
+  aeppl = callPackage ../development/python-modules/aeppl { };
+
   aesara = callPackage ../development/python-modules/aesara { };
 
   aesedb = callPackage ../development/python-modules/aesedb { };

From 5af41eba18d0c1623836293b4c777910e47bfd0a Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Tue, 24 May 2022 17:52:31 +0200
Subject: [PATCH 07/11] python310Packages.pynndescent: 0.5.6 -> 0.5.7

---
 pkgs/development/python-modules/pynndescent/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/python-modules/pynndescent/default.nix b/pkgs/development/python-modules/pynndescent/default.nix
index 79b914f6122c..8389a7ae9c1f 100644
--- a/pkgs/development/python-modules/pynndescent/default.nix
+++ b/pkgs/development/python-modules/pynndescent/default.nix
@@ -12,14 +12,14 @@
 
 buildPythonPackage rec {
   pname = "pynndescent";
-  version = "0.5.6";
+  version = "0.5.7";
   format = "setuptools";
 
   disabled = pythonOlder "3.6";
 
   src = fetchPypi {
     inherit pname version;
-    hash = "sha256-YfsxiFuqxGnWeTPix8k1tu3rsG7kmOLw+d/JfFnTclw=";
+    hash = "sha256-7LOVJV+janSLWHC0ugMA6g99qLGWSGS47dYld6hN/X0=";
   };
 
   propagatedBuildInputs = [

From 7f38d0a148a5222026929e2b0f79f04ebb3890dd Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Tue, 24 May 2022 18:13:32 +0200
Subject: [PATCH 08/11] python310Packages.datashader: 0.13.0 -> 0.14.0

---
 pkgs/development/python-modules/datashader/default.nix | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/python-modules/datashader/default.nix b/pkgs/development/python-modules/datashader/default.nix
index 243571f248bb..e72d54cde4e3 100644
--- a/pkgs/development/python-modules/datashader/default.nix
+++ b/pkgs/development/python-modules/datashader/default.nix
@@ -15,6 +15,7 @@
 , pyct
 , scipy
 , pytestCheckHook
+, pythonOlder
 , nbsmoke
 , fastparquet
 , nbconvert
@@ -24,12 +25,14 @@
 
 buildPythonPackage rec {
   pname = "datashader";
-  version = "0.13.0";
+  version = "0.14.0";
   format = "setuptools";
 
+  disabled = pythonOlder "3.7";
+
   src = fetchPypi {
     inherit pname version;
-    sha256 = "sha256-6JscHm1QjDmXOLLa83qhAvY/xwvlPM6duQ1lSxnCVV8=";
+    hash = "sha256-VKEDOJV2ITO1gxKLbFQbcem0gEd/fzTIo+QSmZVsMGI=";
   };
 
   propagatedBuildInputs = [

From c18e7de036625a81b8266cf41ed755fb8b4d69d3 Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Tue, 24 May 2022 21:44:44 +0200
Subject: [PATCH 09/11] python39Packages.umap-learn: disable flaky test

---
 .../python-modules/umap-learn/default.nix     | 27 ++++++++++---------
 1 file changed, 15 insertions(+), 12 deletions(-)

diff --git a/pkgs/development/python-modules/umap-learn/default.nix b/pkgs/development/python-modules/umap-learn/default.nix
index 1281d90cdaf5..25016f9b4cc5 100644
--- a/pkgs/development/python-modules/umap-learn/default.nix
+++ b/pkgs/development/python-modules/umap-learn/default.nix
@@ -1,43 +1,45 @@
 { lib
 , buildPythonPackage
 , fetchFromGitHub
-, nose
+, keras
+, numba
 , numpy
+, pynndescent
+, pytestCheckHook
+, pythonOlder
 , scikit-learn
 , scipy
-, numba
-, pynndescent
 , tensorflow
 , tqdm
-, pytestCheckHook
-, keras
 }:
 
 buildPythonPackage rec {
   pname = "umap-learn";
   version = "0.5.3";
+  format = "setuptools";
+
+  disabled = pythonOlder "3.7";
 
   src = fetchFromGitHub {
     owner = "lmcinnes";
     repo = "umap";
     rev = version;
-    sha256 = "sha256-S2+k7Ec4AxsN6d0GUGnU81oLnBgmlZp8OmUFCNaUJYw=";
+    hash = "sha256-S2+k7Ec4AxsN6d0GUGnU81oLnBgmlZp8OmUFCNaUJYw=";
   };
 
   propagatedBuildInputs = [
+    numba
     numpy
+    pynndescent
     scikit-learn
     scipy
-    numba
-    pynndescent
     tqdm
   ];
 
   checkInputs = [
-    nose
-    tensorflow
-    pytestCheckHook
     keras
+    pytestCheckHook
+    tensorflow
   ];
 
   preCheck = ''
@@ -52,6 +54,7 @@ buildPythonPackage rec {
 
     # Flaky test. Fails with AssertionError sometimes.
     "test_sparse_hellinger"
+    "test_densmap_trustworthiness_on_iris_supervised"
 
     # tensorflow maybe incompatible? https://github.com/lmcinnes/umap/issues/821
     "test_save_load"
@@ -61,6 +64,6 @@ buildPythonPackage rec {
     description = "Uniform Manifold Approximation and Projection";
     homepage = "https://github.com/lmcinnes/umap";
     license = licenses.bsd3;
-    maintainers = [ maintainers.costrouc ];
+    maintainers = with maintainers; [ costrouc ];
   };
 }

From cd22937423fc5c97f45677dc8af0895096a3df72 Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Thu, 26 May 2022 23:32:44 +0200
Subject: [PATCH 10/11] python310Packages.arviz: 0.12.0 -> 0.12.1

---
 pkgs/development/python-modules/arviz/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/python-modules/arviz/default.nix b/pkgs/development/python-modules/arviz/default.nix
index 4b5ed5ca687b..8cd1ae1b83da 100644
--- a/pkgs/development/python-modules/arviz/default.nix
+++ b/pkgs/development/python-modules/arviz/default.nix
@@ -31,7 +31,7 @@
 
 buildPythonPackage rec {
   pname = "arviz";
-  version = "0.12.0";
+  version = "0.12.1";
   format = "setuptools";
 
   disabled = pythonOlder "3.7";
@@ -40,7 +40,7 @@ buildPythonPackage rec {
     owner = "arviz-devs";
     repo = pname;
     rev = "v${version}";
-    hash = "sha256-ClARxgfji/CavEy8g5oeYK7pwSZS1yUIZnBiyTbZ/zU=";
+    hash = "sha256-5P6EXXAAS1Q2eNQuj/5JrDg0lPHfA5K4WaYfKaaXm9s=";
   };
 
   propagatedBuildInputs = [

From 9b3553d1c4f685c0654a3b8043814eb458f2faa1 Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Fri, 27 May 2022 00:30:18 +0200
Subject: [PATCH 11/11] python310Packages.numba: 0.55.1 -> 0.55.2

---
 pkgs/development/python-modules/numba/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/python-modules/numba/default.nix b/pkgs/development/python-modules/numba/default.nix
index 23921959f596..a9c152f412f8 100644
--- a/pkgs/development/python-modules/numba/default.nix
+++ b/pkgs/development/python-modules/numba/default.nix
@@ -22,13 +22,13 @@
 let
   inherit (cudaPackages) cudatoolkit;
 in buildPythonPackage rec {
-  version = "0.55.1";
+  version = "0.55.2";
   pname = "numba";
   disabled = pythonOlder "3.6" || pythonAtLeast "3.11";
 
   src = fetchPypi {
     inherit pname version;
-    hash = "sha256-A+kGmiZm0chPk7ANvXFvuP7d6Lssbvr6LwSEKkZELqM=";
+    hash = "sha256-5CjZ4R2bpZKEnMyfegCQA+t9MGEgB+Nlr+dDznEYxvQ=";
   };
 
   postPatch = ''