python3.pkgs.rpy2: 2.9.5 -> 3.2.2

There have been significant changes, therefore it doesn't make sense
anymore to maintain the python2 and python3 version in the same file.
We'll be able to drop the python2 version soon, some time after we have
switched sage to python3.

4 files changed, 155 insertions, 34 deletions

diff --git a/pkgs/development/python-modules/rpy2/2.nix b/pkgs/development/python-modules/rpy2/2.nix
new file mode 100644
index 00000000000..aef184d4afc
--- /dev/null
+++ b/pkgs/development/python-modules/rpy2/2.nix
@@ -0,0 +1,108 @@
+{ lib
+, python
+, buildPythonPackage
+, fetchPypi
+, isPyPy
+, isPy27
+, readline
+, R
+, rWrapper
+, rPackages
+, pcre
+, lzma
+, bzip2
+, zlib
+, icu
+, singledispatch
+, six
+, jinja2
+, pytz
+, numpy
+, pytest
+, mock
+, extraRPackages ? []
+}:
+
+buildPythonPackage rec {
+    version = "2.8.6"; # python2 support dropped in 2.9.x
+    pname = "rpy2";
+    disabled = isPyPy;
+    src = fetchPypi {
+      inherit version pname;
+      sha256 = "162zki5c1apgv6qbafi7n66y4hgpgp43xag7q75qb6kv99ri6k80";
+    };
+    buildInputs = [
+      readline
+      R
+      pcre
+      lzma
+      bzip2
+      zlib
+      icu
+    ] ++ (with rPackages; [
+      # packages expected by the test framework
+      ggplot2
+      dplyr
+      RSQLite
+      broom
+      DBI
+      dbplyr
+      hexbin
+      lme4
+      tidyr
+
+      # is in upstream's `requires` although it shouldn't be -- this is easier than patching it away
+      pytest
+    ]) ++ extraRPackages ++ rWrapper.recommendedPackages;
+
+    nativeBuildInputs = [
+      R # needed at setup time to detect R_HOME (alternatively set R_HOME explicitly)
+    ];
+
+    patches = [
+      # R_LIBS_SITE is used by the nix r package to point to the installed R libraries.
+      # This patch sets R_LIBS_SITE when rpy2 is imported.
+      ./r-libs-site.patch
+    ];
+    postPatch = ''
+      substituteInPlace ${ if isPy27 then "rpy/rinterface/__init__.py" else "rpy2/rinterface_lib/embedded.py" } --replace '@NIX_R_LIBS_SITE@' "$R_LIBS_SITE"
+    '';
+
+    doPatchelf = false; # fails because of "missing filename"
+    patchelfPhase = "";
+
+    propagatedBuildInputs = [
+      singledispatch
+      six
+      jinja2
+      pytz
+      numpy
+    ];
+
+    checkInputs = [
+      pytest
+      mock
+    ];
+    # One remaining test failure caused by different unicode encoding.
+    # https://bitbucket.org/rpy2/rpy2/issues/488
+    doCheck = false;
+    checkPhase = ''
+      ${python.interpreter} -m 'rpy2'
+    '';
+
+    # For some reason libreadline.so is not found. Curiously `ldd _rinterface.so | grep readline` shows two readline entries:
+    # libreadline.so.6 => not found
+    # libreadline.so.6 => /nix/store/z2zhmrg6jcrn5iq2779mav0nnq4vm2q6-readline-6.3p08/lib/libreadline.so.6 (0x00007f333ac43000)
+    # There must be a better way to fix this, but I don't know it.
+    postFixup = ''
+      patchelf --add-needed ${readline}/lib/libreadline.so "$out/${python.sitePackages}/rpy2/rinterface/"_rinterface*.so
+    '';
+
+    meta = {
+      homepage = http://rpy.sourceforge.net/rpy2;
+      description = "Python interface to R";
+      license = lib.licenses.gpl2Plus;
+      platforms = lib.platforms.unix;
+      maintainers = with lib.maintainers; [ joelmo ];
+    };
+  }
diff --git a/pkgs/development/python-modules/rpy2/default.nix b/pkgs/development/python-modules/rpy2/default.nix
index 1b4ab4d40db..bc4bc0bcb5b 100644
--- a/pkgs/development/python-modules/rpy2/default.nix
+++ b/pkgs/development/python-modules/rpy2/default.nix
@@ -3,8 +3,6 @@
 , buildPythonPackage
 , fetchPypi
 , isPyPy
-, isPy27
-, readline
 , R
 , rWrapper
 , rPackages
@@ -13,38 +11,38 @@
 , bzip2
 , zlib
 , icu
-, singledispatch
-, six
+, ipython
 , jinja2
 , pytz
+, pandas
 , numpy
+, cffi
+, tzlocal
+, simplegeneric
 , pytest
-, mock
 , extraRPackages ? []
 }:
 
 buildPythonPackage rec {
-    version = if isPy27 then
-      "2.8.6" # python2 support dropped in 2.9.x
-    else
-      "2.9.5";
+    version = "3.2.2";
     pname = "rpy2";
+
     disabled = isPyPy;
     src = fetchPypi {
       inherit version pname;
-      sha256 = if isPy27 then
-        "162zki5c1apgv6qbafi7n66y4hgpgp43xag7q75qb6kv99ri6k80" # 2.8.x
-      else
-        "1nrj8pgyxrwrfdrxzb4j3z1adjwjx1mr8d1n5cmrz4nhlzy8w7xr"; # 2.9.x
+      sha256 = "0b3jpn9x7m2pccriyzgfsdb68qp6nq4ffhvjy1q2ar8wdxvmf5xp";
     };
+
     buildInputs = [
-      readline
       R
       pcre
       lzma
       bzip2
       zlib
       icu
+
+      # is in the upstream `requires` although it shouldn't be -- this is easier than patching it away
+      pytest
     ] ++ (with rPackages; [
       # packages expected by the test framework
       ggplot2
@@ -58,6 +56,10 @@ buildPythonPackage rec {
       tidyr
     ]) ++ extraRPackages ++ rWrapper.recommendedPackages;
 
+    checkPhase = ''
+      pytest
+    '';
+
     nativeBuildInputs = [
       R # needed at setup time to detect R_HOME (alternatively set R_HOME explicitly)
     ];
@@ -65,38 +67,26 @@ buildPythonPackage rec {
     patches = [
       # R_LIBS_SITE is used by the nix r package to point to the installed R libraries.
       # This patch sets R_LIBS_SITE when rpy2 is imported.
-      ./r-libs-site.patch
+      ./rpy2-3.x-r-libs-site.patch
     ];
     postPatch = ''
-      substituteInPlace rpy/rinterface/__init__.py --replace '@NIX_R_LIBS_SITE@' "$R_LIBS_SITE"
+      substituteInPlace 'rpy2/rinterface_lib/embedded.py' --replace '@NIX_R_LIBS_SITE@' "$R_LIBS_SITE"
     '';
 
     propagatedBuildInputs = [
-      singledispatch
-      six
+      ipython
       jinja2
       pytz
+      pandas
       numpy
+      cffi
+      tzlocal
+      simplegeneric
     ];
 
     checkInputs = [
       pytest
-      mock
     ];
-    # One remaining test failure caused by different unicode encoding.
-    # https://bitbucket.org/rpy2/rpy2/issues/488
-    doCheck = false;
-    checkPhase = ''
-      ${python.interpreter} -m 'rpy2.tests'
-    '';
-
-    # For some reason libreadline.so is not found. Curiously `ldd _rinterface.so | grep readline` shows two readline entries:
-    # libreadline.so.6 => not found
-    # libreadline.so.6 => /nix/store/z2zhmrg6jcrn5iq2779mav0nnq4vm2q6-readline-6.3p08/lib/libreadline.so.6 (0x00007f333ac43000)
-    # There must be a better way to fix this, but I don't know it.
-    postFixup = ''
-      patchelf --add-needed ${readline}/lib/libreadline.so "$out/${python.sitePackages}/rpy2/rinterface/"_rinterface*.so
-    '';
 
     meta = {
       homepage = http://rpy.sourceforge.net/rpy2;
diff --git a/pkgs/development/python-modules/rpy2/rpy2-3.x-r-libs-site.patch b/pkgs/development/python-modules/rpy2/rpy2-3.x-r-libs-site.patch
new file mode 100644
index 00000000000..177e4f9a83d
--- /dev/null
+++ b/pkgs/development/python-modules/rpy2/rpy2-3.x-r-libs-site.patch
@@ -0,0 +1,21 @@
+diff --git a/rpy2/rinterface_lib/embedded.py b/rpy2/rinterface_lib/embedded.py
+index cc32b6d..3969ad0 100644
+--- a/rpy2/rinterface_lib/embedded.py
++++ b/rpy2/rinterface_lib/embedded.py
+@@ -113,6 +113,16 @@ def _initr(interactive: bool = True,
+         if isinitialized():
+             return None
+         os.environ['R_HOME'] = openrlib.R_HOME
++
++        # path to libraries
++        existing = os.environ.get('R_LIBS_SITE')
++        if existing is not None:
++            prefix = existing + ':'
++        else:
++            prefix = ''
++        additional = '@NIX_R_LIBS_SITE@'
++        os.environ['R_LIBS_SITE'] = prefix + additional
++
+         options_c = [ffi.new('char[]', o.encode('ASCII')) for o in _options]
+         n_options = len(options_c)
+         n_options_c = ffi.cast('int', n_options)
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 72283056a54..114d2140847 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -5032,7 +5032,9 @@ in {
 
   rpmfluff = callPackage ../development/python-modules/rpmfluff {};
 
-  rpy2 = callPackage ../development/python-modules/rpy2 {};
+  rpy2 = if isPy3k
+    then callPackage ../development/python-modules/rpy2 { }
+    else callPackage ../development/python-modules/rpy2/2.nix { };
 
   rtslib = callPackage ../development/python-modules/rtslib {};