upgrade rpy2 package 2.8.2 -> 3.3.5, upgrade R to 3.6.3, add new dependencies

[videlec]

Main changes:

• https://pypi.org/project/rpy2/, supports python >= 3.6

• cygwin.patch does not apply anymore

• cffi>=1.13.1 is a new dependency, we install latest 1.14.0 (supports python >= 3.2)

• 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

• Testing rpy2/rpy2#670
• ​setup.py: Print CFFI configuration messages only on build rpy2/rpy2#716

Depends on #29851
Depends on #30064
Depends on #30118
Depends on #30067
Depends on #30147
Depends on #29929
Depends on #30149

CC: @mkoeppe @EmmanuelCharpentier @timokau @isuruf @slel @antonio-rojas @embray @dimpase

Component: packages: standard

Author: Vincent Delecroix, Matthias Koeppe

Branch: 54d0f99

Reviewer: Emmanuel Charpentier, Dima Pasechnik

Issue created by migration from https://trac.sagemath.org/ticket/29441

[videlec]

comment:1

The cygwin.patch does not longer apply.

[videlec]

Description changed:

--- 
+++ 
@@ -1,3 +1,3 @@
-The release 3.2.7 is only Python 3 compatible
+The release 3.2.7 is only Python 3 compatible.
 
 tarball: https://files.pythonhosted.org/packages/39/c0/61120f9dae06b4887426d229b68a7a5f0ca1f9cb3986319bb9484819a28d/rpy2-3.2.7.tar.gz

[videlec]

Description changed:

--- 
+++ 
@@ -1,3 +1,11 @@
 The release 3.2.7 is only Python 3 compatible.
 
-tarball: https://files.pythonhosted.org/packages/39/c0/61120f9dae06b4887426d229b68a7a5f0ca1f9cb3986319bb9484819a28d/rpy2-3.2.7.tar.gz
+Main changes:
+- `cygwin.patch` does not apply anymore
+- [https://pypi.org/project/pytest/](https://pypi.org/project/pytest/) is a new dependency (!?)
+- [https://pypi.org/project/cffi/ cffi>=1.13.1](https://pypi.org/project/cffi/ cffi>=1.13.1) is a new dependency
+
+tarballs: 
+- https://files.pythonhosted.org/packages/39/c0/61120f9dae06b4887426d229b68a7a5f0ca1f9cb3986319bb9484819a28d/rpy2-3.2.7.tar.gz
+- https://files.pythonhosted.org/packages/6d/4e/572aed20422dee7fa2bd27995b2a53a32de90c1826e5531c9df6d3ea77ed/pytest-5.4.1.tar.gz
+- https://files.pythonhosted.org/packages/05/54/3324b0c46340c31b909fcec598696aaec7ddc8c18a63f2db352562d3354c/cffi-1.14.0.tar.gz

[videlec]

Description changed:

--- 
+++ 
@@ -4,8 +4,10 @@
 - `cygwin.patch` does not apply anymore
 - [https://pypi.org/project/pytest/](https://pypi.org/project/pytest/) is a new dependency (!?)
 - [https://pypi.org/project/cffi/ cffi>=1.13.1](https://pypi.org/project/cffi/ cffi>=1.13.1) is a new dependency
+- [https://pypi.org/project/pycparser/ pycparser](https://pypi.org/project/pycparser/ pycparser) is a new dependency (required by cffi)
 
 tarballs: 
 - https://files.pythonhosted.org/packages/39/c0/61120f9dae06b4887426d229b68a7a5f0ca1f9cb3986319bb9484819a28d/rpy2-3.2.7.tar.gz
 - https://files.pythonhosted.org/packages/6d/4e/572aed20422dee7fa2bd27995b2a53a32de90c1826e5531c9df6d3ea77ed/pytest-5.4.1.tar.gz
 - https://files.pythonhosted.org/packages/05/54/3324b0c46340c31b909fcec598696aaec7ddc8c18a63f2db352562d3354c/cffi-1.14.0.tar.gz
+- https://files.pythonhosted.org/packages/0f/86/e19659527668d70be91d0369aeaa055b4eb396b0f387a4f92293a20035bd/pycparser-2.20.tar.gz

[videlec]

comment:4

pytest has a lot of dependencies

• attrs
• importlib-metadata
• more-itertools
• pluggy
• py
• zipp
  The easiest might be to patch rpy2 to not depend on pytest. I suspect that only the test suite of rpy2 depends on pytest.

[videlec]

Description changed:

--- 
+++ 
@@ -2,12 +2,15 @@
 
 Main changes:
 - `cygwin.patch` does not apply anymore
+- the `setup.py` script is broken in several ways (!!)
 - [https://pypi.org/project/pytest/](https://pypi.org/project/pytest/) is a new dependency (!?)
 - [https://pypi.org/project/cffi/ cffi>=1.13.1](https://pypi.org/project/cffi/ cffi>=1.13.1) is a new dependency
 - [https://pypi.org/project/pycparser/ pycparser](https://pypi.org/project/pycparser/ pycparser) is a new dependency (required by cffi)
+- [https://pypi.org/project/tzlocal/ tzlocal](https://pypi.org/project/tzlocal/ tzlocal)
 
 tarballs: 
 - https://files.pythonhosted.org/packages/39/c0/61120f9dae06b4887426d229b68a7a5f0ca1f9cb3986319bb9484819a28d/rpy2-3.2.7.tar.gz
 - https://files.pythonhosted.org/packages/6d/4e/572aed20422dee7fa2bd27995b2a53a32de90c1826e5531c9df6d3ea77ed/pytest-5.4.1.tar.gz
 - https://files.pythonhosted.org/packages/05/54/3324b0c46340c31b909fcec598696aaec7ddc8c18a63f2db352562d3354c/cffi-1.14.0.tar.gz
 - https://files.pythonhosted.org/packages/0f/86/e19659527668d70be91d0369aeaa055b4eb396b0f387a4f92293a20035bd/pycparser-2.20.tar.gz
+- https://files.pythonhosted.org/packages/c6/52/5ec375d4efcbe4e31805f3c4b301bdfcff9dcbdb3605d4b79e117a16b38d/tzlocal-2.0.0.tar.gz

[videlec]

comment:6

Good news: tests pass on my machine!

[mkoeppe]

comment:8

See #28998 for pytest

[EmmanuelCharpentier]

comment:9

Replying to @videlec:

pytest has a lot of dependencies

• attrs
• importlib-metadata
• more-itertools
• pluggy
• py
• zipp

Tall order, indeed...

The easiest might be to patch rpy2 to not depend on pytest. I suspect that only the test suite of rpy2 depends on pytest.

My first reaction was: No, no, no, no, no. And no.". A patched version has a very heavy price in terms of maintenance each and every update entails patch checking/upgrading, up to the point the whole mess becomes unmaintainable.

The maintenance price of the added dependencies should be considered, of course, but I suspect that it may be lower than the price of a patch to rpy2.

[EmmanuelCharpentier]

Description changed:

--- 
+++ 
@@ -2,15 +2,12 @@
 
 Main changes:
 - `cygwin.patch` does not apply anymore
-- the `setup.py` script is broken in several ways (!!)
 - [https://pypi.org/project/pytest/](https://pypi.org/project/pytest/) is a new dependency (!?)
 - [https://pypi.org/project/cffi/ cffi>=1.13.1](https://pypi.org/project/cffi/ cffi>=1.13.1) is a new dependency
 - [https://pypi.org/project/pycparser/ pycparser](https://pypi.org/project/pycparser/ pycparser) is a new dependency (required by cffi)
-- [https://pypi.org/project/tzlocal/ tzlocal](https://pypi.org/project/tzlocal/ tzlocal)
 
 tarballs: 
 - https://files.pythonhosted.org/packages/39/c0/61120f9dae06b4887426d229b68a7a5f0ca1f9cb3986319bb9484819a28d/rpy2-3.2.7.tar.gz
 - https://files.pythonhosted.org/packages/6d/4e/572aed20422dee7fa2bd27995b2a53a32de90c1826e5531c9df6d3ea77ed/pytest-5.4.1.tar.gz
 - https://files.pythonhosted.org/packages/05/54/3324b0c46340c31b909fcec598696aaec7ddc8c18a63f2db352562d3354c/cffi-1.14.0.tar.gz
 - https://files.pythonhosted.org/packages/0f/86/e19659527668d70be91d0369aeaa055b4eb396b0f387a4f92293a20035bd/pycparser-2.20.tar.gz
-- https://files.pythonhosted.org/packages/c6/52/5ec375d4efcbe4e31805f3c4b301bdfcff9dcbdb3605d4b79e117a16b38d/tzlocal-2.0.0.tar.gz