gnu: python-py: Update to 1.4.32.

* gnu/packages/python.scm (python-py): Update to 1.4.32.

gnu: python-sphinx-cloud-sptheme: Update to 1.8.0.

* gnu/packages/python.scm (python-sphinx-cloud-sptheme): Update to 1.8.0.

gnu: python-wcwidth: Update to 0.1.7.

* gnu/packages/python.scm (python-wcwidth): Update to 0.1.7.
[source]: Use pypi-uri.

gnu: python-markdown: Update to 2.6.8.

* gnu/packages/python.scm (python-markdown): Update to 2.6.8.

gnu: snakemake: Add runtime dependencies.

* gnu/packages/python.scm (snakemake)[propagated-inputs]: Add python-wrapt and
python-requests.

gnu: Add python-pylint.

* gnu/packages/python.scm (python-pylint, python2-pylint): New variables.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

gnu: Add python2-coverage-test-runner.

* gnu/packages/python.scm (python2-coverage-test-runner): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

gnu: Add python-configparser.

* gnu/packages/python.scm (python-configparser, python2-configparser): New variables.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

gnu: Add python2-backports-functools-lru-cache.

* gnu/packages/python.scm (python2-backports-functools-lru-cache): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

gnu: Add python-isort.

* gnu/packages/python.scm (python-isort, python2-isort): New variables.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

gnu: Add python-astroid.

* gnu/packages/python.scm (python-astroid, python2-astroid): New variables.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>

gnu: snakemake: Update to 3.11.2.

* gnu/packages/python.scm (snakemake): Update to 3.11.2.

gnu: r: Rename to r-minimal.

* gnu/packages/statistics.scm (r): Rename to...
(r-minimal): ...this new variable.
(r-with-recommended-packages): Rename to...
(r): ...this.
* guix/build-system/r.scm (default-r): Reference r-minimal.
* gnu/packages/emacs.scm (emacs-ess)[inputs],
gnu/packages/machine-learning.scm (shogun)[inputs],
gnu/packages/python.scm (python-rpy2)[inputs],
gnu/packages/bioinformatics.scm (ribotaper)[inputs],
(couger)[propagated-inputs],
(roary)[inputs],
(rsem)[inputs],
(rcas-web)[inputs]: Change "r" to "r-minimal".

gnu: r: Do not build recommended packages.

* gnu/packages/statistics.scm (r)[arguments]: Rename phase
"build-recommended-packages-reproducibly" to "build-reproducibly"; add
configure flag "--without-recommended-packages".
* guix/import/cran.scm (default-r-packages): Remove recommended packages.
* gnu/packages/python.scm (python-rpy2)[inputs]: Add r-survival.
* gnu/packages/bioinformatics.scm (r-ape)[propagated-inputs]: Add r-lattice
and r-nlme.
(r-vegan)[propagated-inputs]: Add r-mass.
(r-genefilter)[propagated-inputs]: Add r-survival.
(r-grohmm)[propagated-inputs]: Add r-mass.
(r-bioccheck)[propagated-inputs]: Add r-codetools.
(r-summarizedexperiment)[propagated-inputs]: Add r-matrix.
(r-topgo)[propagated-inputs]: Add r-lattice.
(r-sva)[propagated-inputs]: Add r-mgcv.
(r-raremetals2)[propagated-inputs]: Add r-mass.
(r-vsn)[propagated-inputs]: Add r-lattice.
(r-pcamethods)[propagated-inputs]: Add r-mass.
* gnu/packages/bioinformatics.scm (r-ggplot2)[propagated-inputs]: Add r-mass.
(r-locfit)[propagated-inputs]: Add r-lattice.
(r-coda)[propagated-inputs]: Add r-lattice.
(r-irlba)[propagated-inputs]: Add r-matrix.
(r-glmnet)[propagated-inputs]: Add r-matrix.
(r-e1071)[propagated-inputs]: Add r-class.
(r-spams)[propagated-inputs]: Add r-lattice and r-matrix.
(r-hmisc)[propagated-inputs]: Add r-cluster, r-foreign, r-lattice, r-nnet, and
r-rpart.
(r-zoo)[propagated-inputs]: Add r-lattice.
(r-mixtools)[propagated-inputs]: Add r-boot and r-mass.
(r-flexmix)[propagated-inputs]: Add r-lattice and r-nnet.
(r-prabclus)[propagated-inputs]: Add r-mass.
(r-fpc)[propagated-inputs]: Add r-class, r-cluster, and r-mass.
(r-rcppeigen)[propagated-inputs]: Add r-matrix.
(r-matrixmodels)[propagated-inputs]: Add r-matrix.
(r-lme4)[propagated-inputs]: Add r-mass and r-nlme.
(r-pbkrtest)[propagated-inputs]: Add r-mass and r-matrix.
(r-car)[propagated-inputs]: Add r-mass, r-mgcv, and r-nnet.
(r-tclust)[propagated-inputs]: Add r-cluster.

gnu: python-publicsuffix2: Update to 2.20160818.

* gnu/packages/python.scm (python-publicsuffix2): Update to 2.20160818.

gnu: awscli: Update to 1.11.63.

* gnu/packages/python.scm (awscli): Update to 1.11.63.

gnu: python-botocore: Update to 1.5.26.

* gnu/packages/python.scm (python-botocore): Update to 1.5.26.

gnu: python-ptyprocess: Update to 0.5.1.

* gnu/packages/python.scm (python-ptyprocess): Update to 0.5.1.

gnu: python-waf: Update to 1.9.8.

* gnu/packages/python.scm (python-waf, python2-waf): Update to 1.9.8.
[home-page]: Use https.

gnu: python-parsedatetime: Update to 2.3.

Version 2.1 was apparently time-sensitive and started failing like this:

  ======================================================================
  FAIL: testFloat (tests.TestDelta.test)
  ----------------------------------------------------------------------
  Traceback (most recent call last):
    File "/tmp/guix-build-python2-parsedatetime-2.1.drv-0/parsedatetime-2.1/tests/TestDelta.py", line 64, in testFloat
      self.cal.parse('1.4 months ago', self.source), months=-1.4)
    File "/tmp/guix-build-python2-parsedatetime-2.1.drv-0/parsedatetime-2.1/tests/TestDelta.py", line 37, in assertDelta
      self.assertTrue(diff < 0.05, '%s is not less than 0.05' % diff)
  AssertionError: 0.0666666666667 is not less than 0.05

  ----------------------------------------------------------------------

* gnu/packages/python.scm (python-parsedatetime): Update to 2.3.
[native-inputs]: Add PYTHON-PYTEST and PYTHON-PYTEST-RUNNER.
[propagated-inputs]: New field.