Trac #29441: upgrade rpy2 package 2.8.2 -> 3.3.5, upgrade R to 3.6.3,…

… add new dependencies

Main changes:
- [[https://pypi.org/project/rpy2/]], supports python >= 3.6
- `cygwin.patch` does not apply anymore
- [[https://pypi.org/project/cffi/|cffi>=1.13.1]] is a new dependency,
we install latest 1.14.0 (supports python >= 3.2)
- [[https://pypi.org/project/pycparser/|pycparser]] is a new dependency
(required by cffi, supports python >= 3.4)
- [[https://pypi.org/project/tzlocal/]] is a new dependency, we install
latest 2.1 (supports python >= 2.7)
- [[https://pypi.org/project/pytz/]] is a new dependency, we update to
latest 2020.1 (supports python >= 2.4)

- add small patches to `setup.py` that
  - disables printing on `stdout` (that perturbs `pip`) - accepted
upstream
  - removes the build dependency on `pytest`
- some more dependencies (pytest, numpy, tzlocal) conditional on
SAGE_CHECK!=no

tarballs: see `checksums.ini` (to download automatically, use
`./configure --enable-download-from-upstream-url`)

Upstream issues and PR
- rpy2/rpy2#670
- ​rpy2/rpy2#716

URL: https://trac.sagemath.org/29441
Reported by: vdelecroix
Ticket author(s): Vincent Delecroix, Matthias Koeppe
Reviewer(s): Emmanuel Charpentier, Dima Pasechnik

build/pkgs/cffi/SPKG.txt

@@ -0,0 +1,15 @@
+= cffi =
+
+== Description ==
+
+development website: https://foss.heptapod.net/pypy/cffi
+documentation website: https://cffi.readthedocs.io/en/latest/
+PyPI page: https://pypi.org/project/cffi/
+
+== License ==
+
+ * MIT
+
+== Upstream Contact ==
+
+ * https://foss.heptapod.net/pypy/cffi

build/pkgs/cffi/checksums.ini

@@ -0,0 +1,5 @@
+tarball=cffi-VERSION.tar.gz
+sha1=2a8f05a7d51d77ef1e641cb359a54e4d8fa019cb
+md5=74845f8d2b7b583dd9a3574f402edf39
+cksum=1594930691
+upstream_url=https://pypi.io/packages/source/c/cffi/cffi-VERSION.tar.gz

build/pkgs/cffi/dependencies

@@ -0,0 +1,5 @@
+$(PYTHON) | $(PYTHON_TOOLCHAIN)
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.

build/pkgs/cffi/package-version.txt

@@ -0,0 +1 @@
+1.14.0

build/pkgs/cffi/spkg-install.in

@@ -0,0 +1 @@
+cd src && sdh_pip_install .

build/pkgs/cffi/type

@@ -0,0 +1 @@
+standard

build/pkgs/pycparser/SPKG.txt

@@ -0,0 +1,15 @@
+= pycparser =
+
+== Description ==
+
+development website: https://github.com/eliben/pycparser
+PyPI page: https://pypi.org/project/pycparser/
+
+== License ==
+
+ * BSD
+
+== Upstream Contact ==
+
+ * https://github.com/eliben/pycparser
+

build/pkgs/pycparser/checksums.ini

@@ -0,0 +1,5 @@
+tarball=pycparser-VERSION.tar.gz
+sha1=0ae93d89b69fab48af3a407a2f8663bcea270c3d
+md5=b8f88de737db8c346ee8d31c07c7a25a
+cksum=3289554032
+upstream_url=https://pypi.io/packages/source/p/pycparser/pycparser-VERSION.tar.gz

build/pkgs/pycparser/dependencies

@@ -0,0 +1,5 @@
+$(PYTHON) | $(PYTHON_TOOLCHAIN)
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.

build/pkgs/pycparser/package-version.txt

@@ -0,0 +1 @@
+2.20

build/pkgs/pycparser/spkg-install.in

@@ -0,0 +1 @@
+cd src && sdh_pip_install .

build/pkgs/pycparser/type

@@ -0,0 +1 @@
+standard

build/pkgs/pytz/checksums.ini

@@ -1,4 +1,5 @@
-tarball=pytz-VERSION.tar.bz2
-sha1=8a01d7f19c8b8b189827e026b76c51be4b537b89
-md5=4b91594c440aa20c76ac92043efa75e1
-cksum=591864951
+tarball=pytz-VERSION.tar.gz
+sha1=60f6db35e92688c4701c16bd3d2b9cbfac1fd604
+md5=0349106ac02f2bfe565dd6d5594e3a15
+cksum=1599443821
+upstream_url=https://pypi.io/packages/source/p/pytz/pytz-VERSION.tar.gz

build/pkgs/pytz/package-version.txt

@@ -1 +1 @@
-2018.7
+2020.1

build/pkgs/r/checksums.ini

@@ -1,4 +1,5 @@
 tarball=R-VERSION.tar.gz
-sha1=8eda2af51d63877fcc6674274b6801af605173c5
-md5=90d23d138cee26d275da14b58296e521
-cksum=1222866983
+sha1=d2383dabc0d6c70f8a0171a0fb1bfdc31ddb5b52
+md5=506c9576ba33e1262ad5b5624db9d96a
+cksum=2403187565
+upstream_url=https://cran.r-project.org/src/base/R-3/R-VERSION.tar.gz

build/pkgs/r/package-version.txt

@@ -1 +1 @@
-3.6.2.p0
+3.6.3

build/pkgs/r/spkg-install.in

@@ -100,6 +100,14 @@ fi
 # See patches/R.sh.patch
 export SAGE_BUILDING_R=yes
 
+R_HOME="$SAGE_LOCAL"/lib/R
+# Set LDFLAGS as it is done in sage-env for $SAGE_LOCAL/lib
+LDFLAGS="-L$R_HOME/lib -Wl,-rpath,$R_HOME/lib $LDFLAGS"
+if [ "$UNAME" = "Linux" ]; then
+ LDFLAGS="-Wl,-rpath-link,$R_HOME/lib $LDFLAGS"
+fi
+export LDFLAGS
+
 config() {
  sdh_configure --enable-R-shlib --with-recommended-packages \
  --with-readline=yes --with-x=$XSUPPORT \

build/pkgs/rpy2/checksums.ini

@@ -1,4 +1,5 @@
 tarball=rpy2-VERSION.tar.gz
-sha1=24f7c538a734618dfcf2343304729c0b1e429717
-md5=729946166b43103db7697e69db8c5c45
-cksum=3858682977
+sha1=af1c7ffe900233ac5add5195f106299bd72fd575
+md5=8a5db07798763b9c6672b5f80451b944
+cksum=828149660
+upstream_url=https://pypi.io/packages/source/r/rpy2/rpy2-VERSION.tar.gz

build/pkgs/rpy2/dependencies

@@ -1,4 +1,4 @@
-$(PYTHON) r six | $(PYTHON_TOOLCHAIN)
+$(PYTHON) r cffi tzlocal pytz | $(PYTHON_TOOLCHAIN) pycparser $(and $(filter-out no,$(SAGE_CHECK_rpy2)), pytest numpy)
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/rpy2/package-version.txt

@@ -1 +1 @@
-2.8.2.p1
+3.3.5

build/pkgs/rpy2/patches/716.patch

@@ -0,0 +1,89 @@
+From 87d0f82e2f4be94893881913018ca9085c0ff8e5 Mon Sep 17 00:00:00 2001
+From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
+Date: Fri, 3 Jul 2020 12:47:41 -0700
+Subject: [PATCH] setup.py: Print CFFI configuration messages only on build
+
+---
+ setup.py | 44 ++++++++++++++++++++++++++------------------
+ 1 file changed, 26 insertions(+), 18 deletions(-)
+
+diff --git a/setup.py b/setup.py
+index e4337838..7fead893 100755
+--- a/setup.py
++++ b/setup.py
+@@ -21,6 +21,7 @@
+ from rpy2 import situation
+
+ from setuptools import setup
++from distutils.command.build import build as du_build
+
+ PACKAGE_NAME = 'rpy2'
+ pack_version = __import__('rpy2').__version__
+@@ -111,7 +112,6 @@ def get_r_c_extension_status():
+
+
+ cffi_mode = situation.get_cffi_mode()
+-print('cffi mode: %s' % cffi_mode)
+ c_extension_status = get_r_c_extension_status()
+ if cffi_mode == situation.CFFI_MODE.ABI:
+ cffi_modules = ['rpy2/_rinterface_cffi_build.py:ffibuilder_abi']
+@@ -135,6 +135,30 @@ def get_r_c_extension_status():
+ # This should never happen.
+ raise ValueError('Invalid value for cffi_mode')
+
++class build(du_build):
++
++ def run(self):
++ print('cffi mode: %s' % cffi_mode)
++
++ du_build.run(self)
++
++ print('---')
++ print(cffi_mode)
++ if cffi_mode in (situation.CFFI_MODE.ABI,
++ situation.CFFI_MODE.BOTH,
++ situation.CFFI_MODE.ANY):
++ print('ABI mode interface built.')
++ if cffi_mode in (situation.CFFI_MODE.API,
++ situation.CFFI_MODE.BOTH):
++ print('API mode interface built.')
++ if cffi_mode == situation.CFFI_MODE.ANY:
++ if c_extension_status == COMPILATION_STATUS.OK:
++ print('API mode interface built.')
++ else:
++ print('API mode interface not built because: %s' % c_extension_status)
++ print('To change the API/ABI build mode, set or modify the environment '
++ 'variable RPY2_CFFI_MODE.')
++
+ LONG_DESCRIPTION = """
+ Python interface to the R language.
+
+@@ -168,6 +192,7 @@ def get_r_c_extension_status():
+ install_requires=requires + ['cffi>=1.10.0'],
+ setup_requires=['cffi>=1.10.0'],
+ cffi_modules=cffi_modules,
++ cmdclass = dict(build=build),
+ package_dir=pack_dir,
+ packages=([PACKAGE_NAME] +
+ ['{pack_name}.{x}'.format(pack_name=PACKAGE_NAME, x=x)
+@@ -193,20 +218,3 @@ def get_r_c_extension_status():
+ package_data={'rpy2': ['rinterface_lib/R_API.h',
+ 'rinterface_lib/R_API_eventloop.h']}
+ )
+-
+- print('---')
+- print(cffi_mode)
+- if cffi_mode in (situation.CFFI_MODE.ABI,
+- situation.CFFI_MODE.BOTH,
+- situation.CFFI_MODE.ANY):
+- print('ABI mode interface built and installed.')
+- if cffi_mode in (situation.CFFI_MODE.API,
+- situation.CFFI_MODE.BOTH):
+- print('API mode interface built and installed.')
+- if cffi_mode == situation.CFFI_MODE.ANY:
+- if c_extension_status == COMPILATION_STATUS.OK:
+- print('API mode interface built and installed.')
+- else:
+- print('API mode interface not build because: %s' % c_extension_status)
+- print('To change the API/ABI build mode, set or modify the environment '
+- 'variable RPY2_CFFI_MODE.')

build/pkgs/rpy2/patches/setup-no-pytest.patch

@@ -0,0 +1,13 @@
+diff --git a/setup.py b/setup.py
+index a9f96f8..7ba69a1 100755
+--- a/setup.py
++++ b/setup.py
+@@ -142,7 +142,7 @@ ipython.
+ if __name__ == '__main__':
+ pack_dir = {PACKAGE_NAME: os.path.join(package_prefix, 'rpy2')}
+
+- requires = ['pytest', 'jinja2', 'pytz', 'tzlocal']
++ requires = ['jinja2', 'pytz', 'tzlocal']
+
+ setup(
+ name=PACKAGE_NAME,

build/pkgs/rpy2/spkg-check.in

@@ -0,0 +1 @@
+pytest

build/pkgs/rpy2/spkg-install.in

@@ -1,9 +1,3 @@
-if [ -z "$SAGE_LOCAL" ]; then
- echo >&2 "SAGE_LOCAL undefined ... exiting"
- echo >&2 "Maybe run 'sage --sh'?"
- exit 1
-fi
-
 set -e
 
 cd src

build/pkgs/tzlocal/SPKG.rst

@@ -0,0 +1,16 @@
+pytz
+====
+
+Description
+-----------
+
+World Timezone Definitions for Python
+
+
+Special Update/Build Instructions
+---------------------------------
+
+The upstream tarball was repackaged after sanitizing the file
+permissions with
+
+$ chmod go-w

build/pkgs/tzlocal/checksums.ini

@@ -0,0 +1,5 @@
+tarball=tzlocal-VERSION.tar.gz
+sha1=7d2d590f68849e6b6371210bd808b40ec5619faf
+md5=c0877603ff9de71cd8ca6ee2b50d2ebd
+cksum=950088034
+upstream_url=https://pypi.io/packages/source/t/tzlocal/tzlocal-VERSION.tar.gz

build/pkgs/tzlocal/dependencies

@@ -0,0 +1,5 @@
+$(PYTHON) | $(PYTHON_TOOLCHAIN)
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.

build/pkgs/tzlocal/package-version.txt

@@ -0,0 +1 @@
+2.1

build/pkgs/tzlocal/spkg-install.in

@@ -0,0 +1 @@
+cd src && sdh_pip_install .

build/pkgs/tzlocal/type

@@ -0,0 +1 @@
+standard