sage, python313Packages.rpy2: unbreak (#441027)

pkgs/by-name/sa/sage/sage-src.nix

@@ -82,6 +82,20 @@ stdenv.mkDerivation rec {
       url = "https://github.com/sagemath/sage/commit/d0cbe9d353722580f98a327694f1a361c9b83ccd.patch?full_index=1";
       hash = "sha256-uV2nttxCKDsNqMf1O+lUmuoiDrx7/CfiS00JBb9kiM8=";
     })
+
+    # https://github.com/sagemath/sage/pull/40156, landed in 10.7.beta5
+    (fetchpatch2 {
+      name = "cython-3.1-update.patch";
+      url = "https://github.com/sagemath/sage/commit/5ea8db28977ec113aec3c4c4b208d1783e3937a7.patch?full_index=1";
+      hash = "sha256-5DPPxMuidPpVHrjK8j0UVZzuwiVy9vQzFd6hBYwNAok=";
+    })
+
+    # https://github.com/sagemath/sage/pull/40175, landed in 10.7.beta8
+    (fetchpatch2 {
+      name = "rpy2-3.6-update.patch";
+      url = "https://github.com/sagemath/sage/commit/db2d8db99d9a7dfa1972d534ecd89e3d2ba5c55b.patch?full_index=1";
+      hash = "sha256-6Bk0uGlKFsiDsgv+ljMC1YnmAT+g+he6aFNkpvw2on0=";
+    })
   ];
 
   patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches;

pkgs/development/python-modules/rpy2-rinterface/default.nix

@@ -0,0 +1,79 @@
+{
+  stdenv,
+  lib,
+  buildPythonPackage,
+  fetchurl,
+  isPyPy,
+  R,
+  rWrapper,
+  xz,
+  bzip2,
+  zlib,
+  zstd,
+  icu,
+  pytestCheckHook,
+  setuptools,
+  cffi,
+}:
+
+buildPythonPackage rec {
+  version = "3.6.3";
+  format = "pyproject";
+  pname = "rpy2-rinterface";
+
+  disabled = isPyPy;
+  src = fetchurl {
+    url = "mirror://pypi/${builtins.substring 0 1 pname}/${pname}/${
+      builtins.replaceStrings [ "-" ] [ "_" ] pname
+    }-${version}.tar.gz";
+    hash = "sha256-R3vC9R0AetG4VnxdS6GvD1mVFobufxBXagbQg03ld28=";
+  };
+
+  patches = [
+    # https://github.com/rpy2/rpy2/pull/1171#issuecomment-3263994962
+    ./restore-initr-simple.patch
+
+    # 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.
+    ./rpy2-3.x-r-libs-site.patch
+  ];
+
+  postPatch = ''
+    substituteInPlace 'src/rpy2/rinterface_lib/embedded.py' --replace '@NIX_R_LIBS_SITE@' "$R_LIBS_SITE"
+  '';
+
+  buildInputs = [
+    xz
+    bzip2
+    zlib
+    zstd
+    icu
+  ]
+  ++ rWrapper.recommendedPackages;
+
+  nativeBuildInputs = [
+    R # needed at setup time to detect R_HOME (alternatively set R_HOME explicitly)
+  ];
+
+  propagatedBuildInputs = [
+    cffi
+    setuptools
+  ];
+
+  nativeCheckInputs = [ pytestCheckHook ];
+
+  # https://github.com/rpy2/rpy2/issues/1111
+  disabledTests = [
+    "test_parse_incomplete_error"
+    "test_parse_error"
+    "test_parse_error_when_evaluting"
+  ];
+
+  meta = {
+    homepage = "https://rpy2.github.io/";
+    description = "Python interface to R";
+    license = lib.licenses.gpl2Plus;
+    platforms = lib.platforms.unix;
+    maintainers = with lib; [ teams.sage ];
+  };
+}

pkgs/development/python-modules/rpy2-rinterface/restore-initr-simple.patch

@@ -0,0 +1,20 @@
+diff --git a/src/rpy2/rinterface/__init__.py b/src/rpy2/rinterface/__init__.py
+index 0ba46083..1f4265aa 100644
+--- a/src/rpy2/rinterface/__init__.py
++++ b/src/rpy2/rinterface/__init__.py
+@@ -1100,6 +1100,15 @@ NA = None
+ NA_Real = None
+ NA_Complex = None
+ 
++def initr_simple() -> typing.Optional[int]:
++    """Initialize R's embedded C library."""
++    with openrlib.rlock:
++        status = embedded._initr()
++        atexit.register(endr, 0)
++        _rinterface._register_external_symbols()
++        _post_initr_setup()
++        return status
++
+ 
+ def initr(
+         interactive: typing.Optional[bool] = None,

pkgs/development/python-modules/rpy2-rinterface/rpy2-3.x-r-libs-site.patch

@@ -0,0 +1,19 @@
+diff --git a/src/rpy2/rinterface_lib/embedded.py b/src/rpy2/rinterface_lib/embedded.py
+index cc9f7da1..10626f13 100644
+--- a/src/rpy2/rinterface_lib/embedded.py b/src/rpy2/rinterface_lib/embedded.py
+@@ -328,6 +328,15 @@ def _initr(
+             _setinitialized()
+             return None
+ 
++        # 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
++
+         # TODO: Setting LD_LIBRARY_PATH after the process has started
+         # is too late. Because of this, the line below does not help
+         # address issues where calling R from the command line is working

pkgs/development/python-modules/rpy2-robjects/default.nix

@@ -0,0 +1,63 @@
+{
+  stdenv,
+  lib,
+  buildPythonPackage,
+  fetchurl,
+  fetchpatch2,
+  isPyPy,
+  R,
+  rpy2-rinterface,
+  ipython,
+  jinja2,
+  numpy,
+  pandas,
+  tzlocal,
+  pytestCheckHook,
+}:
+
+buildPythonPackage rec {
+  version = "3.6.2";
+  format = "pyproject";
+  pname = "rpy2-robjects";
+
+  disabled = isPyPy;
+  src = fetchurl {
+    url = "mirror://pypi/${builtins.substring 0 1 pname}/${pname}/${
+      builtins.replaceStrings [ "-" ] [ "_" ] pname
+    }-${version}.tar.gz";
+    hash = "sha256-rJGvMtXE2iNrBaPNaNr7JM2PWogPAHhim48r8CUFQjs=";
+  };
+
+  patches = [
+    # https://github.com/rpy2/rpy2/pull/1171#issuecomment-3263994962
+    (fetchpatch2 {
+      url = "https://github.com/rpy2/rpy2/commit/524546eef9b8f7f3d61aeb76d7e7fa7beeabd2d2.patch?full_index=1";
+      hash = "sha256-aR44E8wIBlD7UpQKm7B+aMn2p3FQ8dwBwLwkibIpcuM=";
+      relative = "rpy2-robjects";
+      revert = true;
+    })
+  ];
+
+  nativeBuildInputs = [
+    R # needed at setup time to detect R_HOME (alternatively set R_HOME explicitly)
+  ];
+
+  propagatedBuildInputs = [
+    ipython
+    jinja2
+    numpy
+    pandas
+    rpy2-rinterface
+    tzlocal
+  ];
+
+  nativeCheckInputs = [ pytestCheckHook ];
+
+  meta = {
+    homepage = "https://rpy2.github.io/";
+    description = "Python interface to R";
+    license = lib.licenses.gpl2Plus;
+    platforms = lib.platforms.unix;
+    maintainers = with lib.maintainers; [ joelmo ];
+  };
+}

pkgs/development/python-modules/rpy2/default.nix

@@ -4,99 +4,31 @@
   buildPythonPackage,
   fetchPypi,
   isPyPy,
-  R,
-  libdeflate,
-  rWrapper,
-  rPackages,
-  pcre,
-  xz,
-  bzip2,
-  zlib,
-  zstd,
-  icu,
-  ipython,
-  jinja2,
-  pytz,
-  pandas,
-  numpy,
-  cffi,
-  tzlocal,
-  simplegeneric,
+  rpy2-rinterface,
+  rpy2-robjects,
   pytestCheckHook,
-  extraRPackages ? [ ],
 }:
 
 buildPythonPackage rec {
-  version = "3.6.2";
-  format = "setuptools";
+  version = "3.6.3";
+  format = "pyproject";
   pname = "rpy2";
 
   disabled = isPyPy;
   src = fetchPypi {
     inherit version pname;
-    hash = "sha256-F06ld2qR0Ds13VYRiJlg4PVFHp0KvqSr/IwL5qhTd9A=";
+    hash = "sha256-lCYYoSUhljAG0i6IqqTUgakjghwDoXQsmb7uci6w/Fo=";
   };
 
-  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.
-    ./rpy2-3.x-r-libs-site.patch
-  ];
-
-  postPatch = ''
-    substituteInPlace 'rpy2/rinterface_lib/embedded.py' --replace '@NIX_R_LIBS_SITE@' "$R_LIBS_SITE"
-    substituteInPlace 'requirements.txt' --replace 'pytest' ""
-  '';
-
-  buildInputs = [
-    pcre
-    xz
-    bzip2
-    zlib
-    zstd
-    icu
-    libdeflate
-  ]
-  ++ (with rPackages; [
-    # packages expected by the test framework
-    ggplot2
-    dplyr
-    RSQLite
-    broom
-    DBI
-    dbplyr
-    hexbin
-    lazyeval
-    lme4
-    tidyr
-  ])
-  ++ extraRPackages
-  ++ rWrapper.recommendedPackages;
-
-  nativeBuildInputs = [
-    R # needed at setup time to detect R_HOME (alternatively set R_HOME explicitly)
-  ];
-
   propagatedBuildInputs = [
-    ipython
-    jinja2
-    pytz
-    pandas
-    numpy
-    cffi
-    tzlocal
-    simplegeneric
+    rpy2-rinterface
+    rpy2-robjects
   ];
 
-  # https://github.com/rpy2/rpy2/issues/1111
-  disabledTests = [
-    "test_parse_incomplete_error"
-    "test_parse_error"
-    "test_parse_error_when_evaluting"
+  pythonImportsCheck = [
+    "rpy2"
   ];
 
-  nativeCheckInputs = [ pytestCheckHook ];
-
   meta = {
     homepage = "https://rpy2.github.io/";
     description = "Python interface to R";

pkgs/development/python-modules/rpy2/rpy2-3.x-r-libs-site.patch

@@ -1,21 +0,0 @@
-diff --git a/rpy2/rinterface_lib/embedded.py b/rpy2/rinterface_lib/embedded.py
-index ccd3a315..51fb5da4 100644
---- a/rpy2/rinterface_lib/embedded.py
-+++ b/rpy2/rinterface_lib/embedded.py
-@@ -276,6 +276,16 @@ def _initr(
-                  os.environ.get('LD_LIBRARY_PATH', ''))
-                 )
-         )
-+
-+        # 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)

pkgs/top-level/python-packages.nix

@@ -16135,7 +16135,13 @@ self: super: with self; {
 
   rpmfluff = callPackage ../development/python-modules/rpmfluff { };
 
-  rpy2 = callPackage ../development/python-modules/rpy2 { inherit (pkgs) zstd; };
+  rpy2 = callPackage ../development/python-modules/rpy2 { };
+
+  rpy2-rinterface = callPackage ../development/python-modules/rpy2-rinterface {
+    inherit (pkgs) zstd;
+  };
+
+  rpy2-robjects = callPackage ../development/python-modules/rpy2-robjects { };
 
   rpyc = callPackage ../development/python-modules/rpyc { };