singularity: fix build with python3

* Fix python3native inherit added in:
  https://git.yoctoproject.org/cgit/cgit.cgi/meta-virtualization/commit/?id=a1e3f5c92cdee7c4259b7be643bd829ce7c1efa3
  to actually work
* also remove the work arounds for /usr/bin/python being python3
  on the target device
* I haven't tested this in runtime - I don't use it, it was just
  showing that do_configure error in "bitbake world" builds, the
  scripts might need some changes to be really compatible with
  python3, but it was broken already, now it at least builds
* upgrade to new version with
  https://github.com/hpcng/singularity/pull/1762/commits/3c05f06e6a1c490a4b4714bcdf5a0ce2b2498bb5
  would be nice by someone who actually uses this

Signed-off-by: Martin Jansa <Martin.Jansa@gmail.com>
Signed-off-by: Bruce Ashfield <bruce.ashfield@gmail.com>

2 files changed, 151 insertions, 9 deletions

diff --git a/recipes-containers/singularity/singularity/0001-Use-python3.patch b/recipes-containers/singularity/singularity/0001-Use-python3.patch
new file mode 100644
index 00000000..dbfe06e4
--- /dev/null
+++ b/recipes-containers/singularity/singularity/0001-Use-python3.patch
@@ -0,0 +1,148 @@
+From 758c1edc7bf3d2a023954f4fcc9ddf46fd370272 Mon Sep 17 00:00:00 2001
+From: Martin Jansa <Martin.Jansa@gmail.com>
+Date: Thu, 21 May 2020 14:14:56 +0200
+Subject: [PATCH] Use python3
+
+* without /usr/bin/python this just fails to configure with:
+  | checking for python... no
+  | configure: error: Please install python before installing.
+  | WARNING: exit code 1 from a shell command.
+
+Signed-off-by: Martin Jansa <Martin.Jansa@gmail.com>
+---
+ configure.ac                           | 6 +++---
+ etc/configure_transform.py             | 2 +-
+ libexec/python/helpers/json/add.py     | 2 +-
+ libexec/python/helpers/json/delete.py  | 2 +-
+ libexec/python/helpers/json/dump.py    | 2 +-
+ libexec/python/helpers/json/get.py     | 2 +-
+ libexec/python/helpers/json/inspect.py | 2 +-
+ libexec/python/import.py               | 2 +-
+ libexec/python/pull.py                 | 2 +-
+ libexec/python/shub/api.py             | 2 +-
+ libexec/python/size.py                 | 2 +-
+ 11 files changed, 13 insertions(+), 13 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 8ffa5ab32..71a1605b2 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -251,15 +251,15 @@ fi
+ # PYTHON
+ # ---------------------------------------------------------------------
+ 
+-AC_CHECK_PROG(PYTHON_CHECK,python,yes)
++AC_CHECK_PROG(PYTHON_CHECK,python3,yes)
+ if test x"$PYTHON_CHECK" != x"yes" ; then
+-    AC_MSG_ERROR([Please install python before installing.])
++    AC_MSG_ERROR([Please install python3 before installing.])
+ else
+ 
+     PYTHON_MODULES="base64 datetime glob hashlib io itertools json math multiprocessing pickle pwd re shutil signal subprocess stat sys tarfile tempfile time"
+     for PYTHON_MODULE in $PYTHON_MODULES; do
+         AC_MSG_CHECKING([for the $PYTHON_MODULE python module])
+-           python_module_result=`python -c "import $PYTHON_MODULE" 2>&1`
++           python_module_result=`python3 -c "import $PYTHON_MODULE" 2>&1`
+            if test -z "$python_module_result"; then
+                AC_MSG_RESULT([yes])
+            else
+diff --git a/etc/configure_transform.py b/etc/configure_transform.py
+index a1ff5c427..9ec445d21 100755
+--- a/etc/configure_transform.py
++++ b/etc/configure_transform.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ # 
+ # Copyright (c) 2017, SingularityWare, LLC. All rights reserved.
+ #
+diff --git a/libexec/python/helpers/json/add.py b/libexec/python/helpers/json/add.py
+index b24aec75a..22abbbeb9 100644
+--- a/libexec/python/helpers/json/add.py
++++ b/libexec/python/helpers/json/add.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ 
+ '''
+ 
+diff --git a/libexec/python/helpers/json/delete.py b/libexec/python/helpers/json/delete.py
+index 0975e4e60..07e255228 100644
+--- a/libexec/python/helpers/json/delete.py
++++ b/libexec/python/helpers/json/delete.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ 
+ '''
+ 
+diff --git a/libexec/python/helpers/json/dump.py b/libexec/python/helpers/json/dump.py
+index ddba06e4a..37a8edf70 100644
+--- a/libexec/python/helpers/json/dump.py
++++ b/libexec/python/helpers/json/dump.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ 
+ '''
+ 
+diff --git a/libexec/python/helpers/json/get.py b/libexec/python/helpers/json/get.py
+index 355be9040..d1d822aea 100644
+--- a/libexec/python/helpers/json/get.py
++++ b/libexec/python/helpers/json/get.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ 
+ '''
+ 
+diff --git a/libexec/python/helpers/json/inspect.py b/libexec/python/helpers/json/inspect.py
+index 65772a4ef..61c723495 100644
+--- a/libexec/python/helpers/json/inspect.py
++++ b/libexec/python/helpers/json/inspect.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ 
+ '''
+ 
+diff --git a/libexec/python/import.py b/libexec/python/import.py
+index 2ec208417..1c58eda5c 100644
+--- a/libexec/python/import.py
++++ b/libexec/python/import.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ 
+ '''
+ 
+diff --git a/libexec/python/pull.py b/libexec/python/pull.py
+index 1cd705c90..4431023f3 100644
+--- a/libexec/python/pull.py
++++ b/libexec/python/pull.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ 
+ '''
+ 
+diff --git a/libexec/python/shub/api.py b/libexec/python/shub/api.py
+index 850d167e7..3c8313ad5 100644
+--- a/libexec/python/shub/api.py
++++ b/libexec/python/shub/api.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ 
+ '''
+ 
+diff --git a/libexec/python/size.py b/libexec/python/size.py
+index 34331fd27..99581ce52 100644
+--- a/libexec/python/size.py
++++ b/libexec/python/size.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ 
+ '''
+ 
diff --git a/recipes-containers/singularity/singularity_git.bb b/recipes-containers/singularity/singularity_git.bb
index a2653529..103270dd 100644
--- a/recipes-containers/singularity/singularity_git.bb
+++ b/recipes-containers/singularity/singularity_git.bb
@@ -3,9 +3,6 @@
 INSANE_SKIP_${PN} += "dev-so"
 
 RDEPENDS_${PN} += "glibc python3 ca-certificates openssl bash e2fsprogs-mke2fs"
-# Singularity expects to find python3 under the name python, therefore both
-# cannot be installed at the same time.
-RCONFLICTS_${PN} = "python"
 
 LICENSE = "BSD"
 LIC_FILES_CHKSUM = "file://COPYRIGHT.md;md5=be78c34e483dd7d8439358b1e024b294 \
@@ -13,7 +10,9 @@ LIC_FILES_CHKSUM = "file://COPYRIGHT.md;md5=be78c34e483dd7d8439358b1e024b294 \
                     file://LICENSE.md;md5=df4326b473db6424033f1d98a5645e30 \
                     file://debian/copyright;md5=ed267cf386d9b75ab1f27f407e935b10"
 
-SRC_URI = "git://github.com/singularityware/singularity.git;protocol=https"
+SRC_URI = "git://github.com/singularityware/singularity.git;protocol=https \
+    file://0001-Use-python3.patch \
+"
 PV = "2.3.1+git${SRCPV}"
 SRCREV = "e214d4ebf0a1274b1c63b095fd55ae61c7e92947"
 
@@ -23,11 +22,6 @@ inherit python3native autotools-brokensep
 EXTRA_OECONF = "--prefix=/usr/local"
 
 pkg_postinst_${PN}() {
-    # Singularity requires "python" to resolve to "python3" within the commandline.
-    # This creates a symbolic link from python3 to python. A side-effect of this is
-    # that scripts which expect Python 2 may fail to run correctly.
-    ln -sr $D${bindir}/python3 $D${bindir}/python 
-
     # python3 expects CA certificates to be installed in a different place to where
     # they are actually installed. These lines link the two locations.
     rm -r $D${libdir}/ssl/certs