Merge master into staging-next

5 files changed, 77 insertions, 14 deletions

diff --git a/pkgs/development/python-modules/nipype/default.nix b/pkgs/development/python-modules/nipype/default.nix
index 80ee7691a1a5..2d8eaecf7753 100644
--- a/pkgs/development/python-modules/nipype/default.nix
+++ b/pkgs/development/python-modules/nipype/default.nix
@@ -1,23 +1,19 @@
 { stdenv
 , buildPythonPackage
 , fetchPypi
-, isPy3k
-, isPy38
+, isPy27
 # python dependencies
 , click
-, configparser ? null
 , dateutil
 , etelemetry
 , filelock
 , funcsigs
 , future
-, futures
 , mock
 , networkx
 , nibabel
 , numpy
 , packaging
-, pathlib2
 , prov
 , psutil
 , pybids
@@ -25,6 +21,7 @@
 , pytest
 , pytest_xdist
 , pytest-forked
+, rdflib
 , scipy
 , simplejson
 , traits
@@ -37,10 +34,12 @@
 , bash
 , glibcLocales
 , callPackage
+# causes Python packaging conflict with any package requiring rdflib,
+# so use the unpatched rdflib by default (disables Nipype provenance tracking);
+# see https://github.com/nipy/nipype/issues/2888:
+, useNeurdflib ? false
 }:
 
-assert !isPy3k -> configparser != null;
-
 let
 
  # This is a temporary convenience package for changes waiting to be merged into the primary rdflib repo.
@@ -51,6 +50,7 @@ in
 buildPythonPackage rec {
   pname = "nipype";
   version = "1.5.1";
+  disabled = isPy27;
 
   src = fetchPypi {
     inherit pname version;
@@ -74,7 +74,6 @@ buildPythonPackage rec {
     funcsigs
     future
     networkx
-    neurdflib
     nibabel
     numpy
     packaging
@@ -85,11 +84,7 @@ buildPythonPackage rec {
     simplejson
     traits
     xvfbwrapper
-  ] ++ stdenv.lib.optionals (!isPy3k) [
-    configparser
-    futures
-    pathlib2 # darwin doesn't receive this transitively, but it is in install_requires
-  ];
+  ] ++ [ (if useNeurdflib then neurdflib else rdflib) ];
 
   checkInputs = [
     pybids
diff --git a/pkgs/development/python-modules/pycmarkgfm/default.nix b/pkgs/development/python-modules/pycmarkgfm/default.nix
new file mode 100644
index 000000000000..f1d92a63d401
--- /dev/null
+++ b/pkgs/development/python-modules/pycmarkgfm/default.nix
@@ -0,0 +1,32 @@
+{ lib, buildPythonPackage, fetchPypi, isPy27, cffi, pytest }:
+
+buildPythonPackage rec {
+  pname = "pycmarkgfm";
+  version = "1.0.1";
+  disabled = isPy27;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0wkbbma214f927ikn3cijxsrzkmm5cqz1x4fimrwx9s2wfphj250";
+  };
+
+  propagatedBuildInputs = [ cffi ];
+
+  # I would gladly use pytestCheckHook, but pycmarkgfm relies on a native
+  # extension (cmark.so, built through setup.py), and pytestCheckHook runs
+  # pytest in an environment that does not contain this extension, which fails.
+  # cmarkgfm has virtually the same build setup as this package, and uses the
+  # same trick: pkgs/development/python-modules/cmarkgfm/default.nix
+  checkInputs = [ pytest ];
+  checkPhase = ''
+    pytest
+  '';
+
+  meta = with lib; {
+    homepage = "https://github.com/zopieux/pycmarkgfm";
+    description = "Bindings to GitHub's Flavored Markdown (cmark-gfm), with enhanced support for task lists";
+    platforms = platforms.linux ++ platforms.darwin;
+    license = licenses.gpl3Plus;
+    maintainers = with maintainers; [ zopieux ];
+  };
+}
diff --git a/pkgs/development/python-modules/scikit-fuzzy/default.nix b/pkgs/development/python-modules/scikit-fuzzy/default.nix
new file mode 100644
index 000000000000..7923565c3f4f
--- /dev/null
+++ b/pkgs/development/python-modules/scikit-fuzzy/default.nix
@@ -0,0 +1,34 @@
+{ lib
+, buildPythonPackage
+, isPy27
+, fetchFromGitHub
+, matplotlib
+, networkx
+, nose
+, numpy
+, scipy
+, pytestCheckHook
+}:
+
+buildPythonPackage rec {
+  pname = "scikit-fuzzy";
+  version = "unstable-2020-10-03";
+  disabled = isPy27;
+
+  src = fetchFromGitHub {
+    owner = pname;
+    repo = pname;
+    rev = "eecf303b701e3efacdc9b9066207ef605d4facaa";
+    sha256 = "18dl0017iqwc7446hqgabhibgjwdakhmycpis6zpvvkkv4ip5062";
+  };
+
+  propagatedBuildInputs = [ networkx numpy scipy ];
+  checkInputs = [ matplotlib nose pytestCheckHook ];
+
+  meta = with lib; {
+    homepage = "https://github.com/scikit-fuzzy/scikit-fuzzy";
+    description = "Fuzzy logic toolkit for scientific Python";
+    license = licenses.bsd3;
+    maintainers = [ maintainers.bcdarwin ];
+  };
+}
diff --git a/pkgs/development/python-modules/snowflake-connector-python/default.nix b/pkgs/development/python-modules/snowflake-connector-python/default.nix
index c8f874d4c103..3e958a3076c3 100644
--- a/pkgs/development/python-modules/snowflake-connector-python/default.nix
+++ b/pkgs/development/python-modules/snowflake-connector-python/default.nix
@@ -57,7 +57,7 @@ buildPythonPackage rec {
 
   postPatch = ''
     substituteInPlace setup.py \
-      --replace "'boto3>=1.4.4,<1.15'," "'boto3~=1.15'," \
+      --replace "'boto3>=1.4.4,<1.16'," "'boto3~=1.16'," \
       --replace "'cryptography>=2.5.0,<3.0.0'," "'cryptography'," \
       --replace "'idna<2.10'," "'idna'," \
       --replace "'requests<2.24.0'," "'requests',"
diff --git a/pkgs/development/python-modules/snowflake-sqlalchemy/default.nix b/pkgs/development/python-modules/snowflake-sqlalchemy/default.nix
index 99c5822f3504..bccca3ee6b67 100644
--- a/pkgs/development/python-modules/snowflake-sqlalchemy/default.nix
+++ b/pkgs/development/python-modules/snowflake-sqlalchemy/default.nix
@@ -19,6 +19,8 @@ buildPythonPackage rec {
     snowflake-connector-python
   ];
 
+  # Pypi does not include tests
+  doCheck = false;
   pythonImportsCheck = [ "snowflake.sqlalchemy" ];
 
   meta = with lib; {