From 10e1f32e5a3369730c7e59ce17ca70004d8eab42 Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Tue, 16 Nov 2021 16:16:15 +0100
Subject: [PATCH 1/3] python3Packages.cdcs: init at 0.1.5

---
 .../python-modules/cdcs/default.nix           | 44 +++++++++++++++++++
 pkgs/top-level/python-packages.nix            |  2 +
 2 files changed, 46 insertions(+)
 create mode 100644 pkgs/development/python-modules/cdcs/default.nix

diff --git a/pkgs/development/python-modules/cdcs/default.nix b/pkgs/development/python-modules/cdcs/default.nix
new file mode 100644
index 000000000000..9dd8a272395b
--- /dev/null
+++ b/pkgs/development/python-modules/cdcs/default.nix
@@ -0,0 +1,44 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, numpy
+, pandas
+, pytestCheckHook
+, pythonOlder
+, requests
+}:
+
+buildPythonPackage rec {
+  version = "0.1.5";
+  pname = "cdcs";
+  format = "setuptools";
+
+  disabled = pythonOlder "3.6";
+
+  src = fetchFromGitHub {
+    owner = "usnistgov";
+    repo = "pycdcs";
+    rev = "v${version}";
+    sha256 = "0sd0s0mka2bvpxxiz98cjc2h5ncsb7d03af1q3w9w8pmvfsgj7pc";
+  };
+
+  propagatedBuildInputs = [
+    numpy
+    pandas
+    requests
+  ];
+
+  # Project has no tests
+  doCheck = false;
+
+  pythonImportsCheck = [
+    "cdcs"
+  ];
+
+  meta = with lib; {
+    description = "Python client for performing REST calls to configurable data curation system (CDCS) databases";
+    homepage = "https://github.com/usnistgov/pycdcs";
+    license = licenses.mit;
+    maintainers = with maintainers; [ fab ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index c63a35749259..734d1c80281e 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -1409,6 +1409,8 @@ in {
 
   cchardet = callPackage ../development/python-modules/cchardet { };
 
+  cdcs = callPackage ../development/python-modules/cdcs { };
+
   celery = callPackage ../development/python-modules/celery { };
 
   cement = callPackage ../development/python-modules/cement { };

From e6feb74002f5ae542e4a09cf04e04a2f24d8dd89 Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Tue, 16 Nov 2021 17:18:30 +0100
Subject: [PATCH 2/3] python3Packages.potentials: init at 0.3.1

---
 .../python-modules/potentials/default.nix     | 58 +++++++++++++++++++
 pkgs/top-level/python-packages.nix            |  2 +
 2 files changed, 60 insertions(+)
 create mode 100644 pkgs/development/python-modules/potentials/default.nix

diff --git a/pkgs/development/python-modules/potentials/default.nix b/pkgs/development/python-modules/potentials/default.nix
new file mode 100644
index 000000000000..24db19b3c065
--- /dev/null
+++ b/pkgs/development/python-modules/potentials/default.nix
@@ -0,0 +1,58 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, ipywidgets
+, cdcs
+, bibtexparser
+, habanero
+, pandas
+, requests
+, numpy
+, matplotlib
+, unidecode
+, datamodeldict
+, xmltodict
+, pytestCheckHook
+, pythonOlder
+}:
+
+buildPythonPackage rec {
+  version = "0.3.1";
+  pname = "potentials";
+  format = "setuptools";
+
+  disabled = pythonOlder "3.7";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "02l1rav5jdfsb00byxbswyhqdnjljp9y7g4ddn4mivzi7x39qa52";
+  };
+
+  propagatedBuildInputs = [
+    ipywidgets
+    cdcs
+    bibtexparser
+    habanero
+    pandas
+    requests
+    numpy
+    matplotlib
+    unidecode
+    datamodeldict
+    xmltodict
+  ];
+
+  # Project has no tests
+  doCheck = false;
+
+  pythonImportsCheck = [
+    "potentials"
+  ];
+
+  meta = with lib; {
+    description = "Python API database tools for accessing the NIST Interatomic Potentials Repository";
+    homepage = "https://github.com/usnistgov/potentials";
+    license = licenses.mit;
+    maintainers = with maintainers; [ fab ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 734d1c80281e..7c86a8d4bb9f 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -5918,6 +5918,8 @@ in {
 
   pot = callPackage ../development/python-modules/pot { };
 
+  potentials = callPackage ../development/python-modules/potentials { };
+
   potr = callPackage ../development/python-modules/potr { };
 
   power = callPackage ../development/python-modules/power { };

From ad1d0fb77219394407f81a075d4ef789538c2328 Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Tue, 16 Nov 2021 18:01:56 +0100
Subject: [PATCH 3/3] python3Packages.atomman: 1.3.0 -> 1.4.2

---
 .../python-modules/atomman/default.nix        | 47 +++++++++++++++----
 1 file changed, 37 insertions(+), 10 deletions(-)

diff --git a/pkgs/development/python-modules/atomman/default.nix b/pkgs/development/python-modules/atomman/default.nix
index b576504588aa..8e03dbe67af7 100644
--- a/pkgs/development/python-modules/atomman/default.nix
+++ b/pkgs/development/python-modules/atomman/default.nix
@@ -1,39 +1,66 @@
-{ lib, buildPythonPackage, fetchFromGitHub, isPy27
+{ lib
+, buildPythonPackage
 , cython
 , datamodeldict
+, fetchFromGitHub
 , matplotlib
 , numericalunits
 , numpy
 , pandas
+, potentials
 , pytest
+, pythonOlder
 , scipy
 , toolz
 , xmltodict
+, python
 }:
 
 buildPythonPackage rec {
-  version = "1.3.0";
+  version = "1.4.2";
   pname = "atomman";
-  disabled = isPy27;
+  format = "setuptools";
+
+  disabled = pythonOlder "3.6";
 
   src = fetchFromGitHub {
     owner = "usnistgov";
-    repo  = "atomman";
+    repo = "atomman";
     rev = "v${version}";
-    sha256 = "09pfykd96wmw00s3kgabghykjn8b4yjml4ybpi7kwy7ygdmzcx51";
+    sha256 = "sha256-Kq4mDykYf74ylWw2golxc81CYKGokXro64YUsFctLmk=";
   };
 
-  checkInputs = [ pytest ];
-  propagatedBuildInputs = [ xmltodict datamodeldict numpy matplotlib scipy pandas cython numericalunits toolz ];
+  propagatedBuildInputs = [
+    cython
+    datamodeldict
+    matplotlib
+    numericalunits
+    numpy
+    pandas
+    potentials
+    scipy
+    toolz
+    xmltodict
+  ];
+
+  checkInputs = [
+    pytest
+  ];
 
   checkPhase = ''
-    py.test tests -k 'not test_atomic'
+    # pytestCheckHook doesn't work
+    py.test tests -k "not test_rootdir and not test_version \
+      and not test_atomic_mass and not imageflags"
   '';
 
+  pythonImportsCheck = [
+    "atomman"
+  ];
+
   meta = with lib; {
-    homepage = "https://github.com/usnistgov/atomman/";
     description = "Atomistic Manipulation Toolkit";
+    homepage = "https://github.com/usnistgov/atomman/";
     license = licenses.mit;
-    maintainers = [ maintainers.costrouc ];
+    maintainers = with maintainers; [ costrouc ];
   };
 }