Update README.md to emphasize >=python-3.1 is required

[tgac]

Update README.md to emphasize >=python-3.1 is required

[maplesond]

The docs do say that python3 is required, both in the README and the manual. Technically yes python 3.1 is the minimum required version, although I'd be surprised if anyone is still running 3.0 on their system as this about 8 years old. Just out of interest were you running 3.0? If so I'll leave this case open until I've made this clear in the docs.

[mmokrejs]

My default python is 2.7 but I do have also 3.4 and 3.5 installed. Here is what my Gentoo Linux says:

$ eselect python list
Available Python interpreters, in order of preference:
[1] python2.7
[2] python3.5
[3] python3.4 (fallback)
$

And here is the output of configure:

checking for python... /usr/bin/python
checking for python version... 2.7
checking for python platform... linux2
checking for python script directory... ${prefix}/lib64/python2.7/site-packages
checking for python extension module directory... ${exec_prefix}/lib64/python2.7/site-packages
checking for python2.7... (cached) /usr/bin/python
checking for a version of Python >= '2.1.0'... yes
checking for a version of Python >= '3.1'... no
configure: WARNING: this package requires Python >= '3.1'.
If you have it installed, but it isn't the default Python
interpreter in your system path, please pass the PYTHON_VERSION
variable to configure. See ``configure --help'' for reference.

checking for the distutils Python package... yes
checking for Python include path... -I/usr/include/python2.7
checking for Python library path... -L/usr/lib64 -lpython2.7
checking for Python site-packages path... /usr/lib64/python2.7/site-packages

[maplesond]

There is a bug with the pythonversion variable in this release. this means kat expects python3 to be the default on your system. Ive fixed it in the develop branch and this will allow you to keep python2 as default and request a specific version for use with KAT.

[mmokrejs]

Thank you, is this in the HEAD included?

emerge =sci-biology/kat-9999

Verifying ebuild manifests

Emerging (1 of 1) sci-biology/kat-9999::science
Unpacking source...

• Fetching https://github.com/TGAC/KAT.git ...
  git fetch https://github.com/TGAC/KAT.git +HEAD:refs/git-r3/HEAD
  git symbolic-ref refs/git-r3/sci-biology/kat/0/main refs/git-r3/HEAD
• Checking out https://github.com/TGAC/KAT.git to /scratch/var/tmp/portage/sci-biology/kat-9999/work/kat-9999 ...
  git checkout --quiet refs/git-r3/HEAD
  GIT update -->
  repository: https://github.com/TGAC/KAT.git
  at the commit: afc287a
  Source unpacked in /scratch/var/tmp/portage/sci-biology/kat-9999/work
  Preparing source in /scratch/var/tmp/portage/sci-biology/kat-9999/work/kat-9999 ...

checking for python... /usr/bin/python
checking for python version... 2.7
checking for python platform... linux2
checking for python script directory... ${prefix}/lib64/python2.7/site-packages
checking for python extension module directory... ${exec_prefix}/lib64/python2.7/site-packages
checking for python2.7... (cached) /usr/bin/python
checking for a version of Python >= '2.1.0'... yes
checking for a version of Python >= '3.1'... no
configure: WARNING: this package requires Python >= '3.1'.
If you have it installed, but it isn't the default Python
interpreter in your system path, please pass the PYTHON_VERSION
variable to configure. See ``configure --help'' for reference.

checking for the distutils Python package... yes
checking for Python include path... -I/usr/include/python2.7
checking for Python library path... -L/usr/lib64 -lpython2.7
checking for Python site-packages path... /usr/lib64/python2.7/site-packages

[maplesond]

It wont be at the top of master yet as these changes are still development. Hence they are at the top of devel. Im away on holiday starting tomorrow so I dont have time to verify all the changes before then. Ill try to get a proper release out by the end of next week. Hopefully you can work around the issues in the meantime.

[mmokrejs]

OK, I thought I can test the committed patch but take your time.

[maplesond]

The fix should be in the V2.2.0 release. You can select specific python versions when configuring KAT like this:

./configure PYTHON_VERSION=3.4

I'll close the case, but feel free to reopen if there are any outstanding questions.

[mmokrejs]

So I hope I fetched now the 2.2.0 tarball properly:

>>> Downloading 'https://github.com/TGAC/KAT/releases/download/Release-2.2.0/kat-2.2.0.tar.gz'
--2016-11-30 22:18:05--  https://github.com/TGAC/KAT/releases/download/Release-2.2.0/kat-2.2.0.tar.gz
Resolving github.com... 192.30.253.112, 192.30.253.113
Connecting to github.com|192.30.253.112|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://github-cloud.s3.amazonaws.com/releases/13294309/263f1ffc-9d12-11e6-803c-ac6cf6742f1d.gz?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAISTNZFOVBIJMK3TQ%2F20161130%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20161130T211804Z&X-Amz-Expires=300&X-Amz-Signature=11ba4e236eae19cb29647aef7f7cdf2c8863723be20853bd0c996f725d10f8dc&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3Dkat-2.2.0.tar.gz&response-content-type=application%2Foctet-stream [following]
--2016-11-30 22:18:05--  https://github-cloud.s3.amazonaws.com/releases/13294309/263f1ffc-9d12-11e6-803c-ac6cf6742f1d.gz?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAISTNZFOVBIJMK3TQ%2F20161130%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20161130T211804Z&X-Amz-Expires=300&X-Amz-Signature=11ba4e236eae19cb29647aef7f7cdf2c8863723be20853bd0c996f725d10f8dc&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3Dkat-2.2.0.tar.gz&response-content-type=application%2Foctet-stream
Resolving github-cloud.s3.amazonaws.com... 52.216.0.112
Connecting to github-cloud.s3.amazonaws.com|52.216.0.112|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 14253573 (14M) [application/octet-stream]
Saving to: ‘/scratch/usr/portage/distfiles/kat-2.2.0.tar.gz’

When just running ./configure I still get:

checking for python... /usr/bin/python
configure: Found python version: 2.7.12
checking for a version of Python >= '2.1.0'... yes
checking for a version of Python >= '3.1'... no
configure: WARNING: this package requires Python >= '3.1'.
If you have it installed, but it isn't the default Python
interpreter in your system path, please pass the PYTHON_VERSION
variable to configure. See ``configure --help'' for reference.

configure: Ensuring environment variable 'PYTHON_VERSION' set to: 
checking for the distutils Python package... yes

I think the configure should set the PYTHON_VERSION on its own to 2.7 in my case.

The below is rather my Linux-distro-specific but for your info I have the following python versions installed:

# eselect python list
Available Python interpreters, in order of preference:
  [1]   python2.7
  [2]   python3.5
  [3]   python3.4 (fallback)
#

Of course, respecting user's value in PYTHON_VERSION is a good idea. I just wonder whether you could handle more gracefully the cases when users did not specify the python version in advance.

[mmokrejs]

I think to support other python implememtations (jython, pypi etc.) you should not antcipate just version number but whole executable filename. Here I show you prepend "python" in front of "$PYTHON_VERSION" variable:

./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --disable-silent-rules --docdir=/usr/share/doc/kat-2.2.0 --htmldir=/usr/share/doc/kat-2.2.0/html --libdir=/usr/lib64 PYTHON_VERSION=python2_7

...

checking for pythonpython2_7... no
configure: WARNING: Cannot find pythonpython2_7 in your system path
./configure: line 17491: -c: command not found
./configure: line 17494: -c: command not found
./configure: line 17500: -c: command not found
configure: Found python version: 
checking for a version of Python >= '2.1.0'... no
configure: error: in `/scratch/var/tmp/portage/sci-biology/kat-2.2.0/work/kat-2.2.0':
configure: error: 
This version of the AC_PYTHON_DEVEL macro
doesn't work properly with versions of Python before
2.1.0. You may need to re-run configure, setting the
variables PYTHON_CPPFLAGS, PYTHON_LIBS, PYTHON_SITE_PKG,
PYTHON_EXTRA_LIBS and PYTHON_EXTRA_LDFLAGS by hand.
Moreover, to disable this check, set PYTHON_NOVERSIONCHECK
to something else than an empty string.

What you cannot just pick whatever "python" resolves to? You can run "python --version" to see which version it really is.

[maplesond]

Ok, so as I understand it you're requesting two things:

1. If the user does have python3.X installed but this isn't the default implementation then try to automatically detect and use this instead.

2. Modify use of PYTHON_VERSION so it also allows the user to prefix the version number with "python".

If I've understood correctly I'll reopen the case and take a look at these next time I come around to doing more development work on KAT.

[mmokrejs]

If the user does have python3.X installed but this isn't the default implementation then try to automatically detect and use this instead.

Yes. Supposedly "python" points to the preferred implementation. Eventually "python2" or "python3". The below is how Gentoo Linux handles the multiple python installations. NOte the python2 and python3 are symlinks, and are managed by "eselect python" utility.

# ls -latr /usr/bin/python*
-rwxr-xr-x 1 root root   14010 Mar 20  2014 /usr/bin/python-exec-c
-rwxr-xr-x 1 root root    1397 Mar 20  2014 /usr/bin/python-exec
-rwxr-xr-x 1 root root 1001688 Apr 13  2015 /usr/bin/python_ncbi_dbapi_test
-rwxr-xr-x 1 root root    7936 Nov 12 02:02 /usr/bin/python2.7
-rwxr-xr-x 1 root root    1463 Nov 12 02:02 /usr/bin/python2.7-config
-rwxr-xr-x 1 root root    2922 Nov 12 02:04 /usr/bin/python3.5m-config
-rwxr-xr-x 1 root root   12440 Nov 12 02:05 /usr/bin/python3.5m
lrwxrwxrwx 1 root root      17 Nov 12 02:05 /usr/bin/python3.5-config -> python3.5m-config
lrwxrwxrwx 1 root root      10 Nov 12 02:05 /usr/bin/python3.5 -> python3.5m
-rwxr-xr-x 1 root root   12432 Nov 12 02:07 /usr/bin/python3.4m
-rwxr-xr-x 1 root root    2890 Nov 12 02:07 /usr/bin/python3.4m-config
lrwxrwxrwx 1 root root      17 Nov 12 02:07 /usr/bin/python3.4-config -> python3.4m-config
lrwxrwxrwx 1 root root      10 Nov 12 02:07 /usr/bin/python3.4 -> python3.4m
-rwxr-xr-x 1 root root   18136 Nov 14 17:20 /usr/bin/python-exec2c
lrwxrwxrwx 1 root root      31 Nov 14 17:20 /usr/bin/python3-config -> ../lib/python-exec/python-exec2
lrwxrwxrwx 1 root root      13 Nov 14 17:20 /usr/bin/python3 -> python-exec2c
lrwxrwxrwx 1 root root      31 Nov 14 17:20 /usr/bin/python2-config -> ../lib/python-exec/python-exec2
lrwxrwxrwx 1 root root      13 Nov 14 17:20 /usr/bin/python2 -> python-exec2c
lrwxrwxrwx 1 root root      31 Nov 14 17:20 /usr/bin/python-config -> ../lib/python-exec/python-exec2
lrwxrwxrwx 1 root root      13 Nov 14 17:20 /usr/bin/python -> python-exec2c
#

Modify use of PYTHON_VERSION so it also allows the user to prefix the version number with "python".

Not only, so that user can specify any even less common python implementation via this variable: https://wiki.python.org/moin/PythonImplementations
https://www.python.org/download/alternatives