Merge pull request #74537 from timokau/rpy2-3.2.2

python3.pkgs.rpy2: 2.9.5 -> 3.2.2

3 files changed, 152 insertions, 33 deletions

diff --git a/pkgs/development/python-modules/rpy2/2.nix b/pkgs/development/python-modules/rpy2/2.nix
new file mode 100644
index 000000000000..aef184d4afc2
--- /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 1b4ab4d40db9..bc4bc0bcb5b8 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 000000000000..177e4f9a83d1
--- /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)