[PATCH] Add python-scikit-bio.

[PATCH] Add python-scikit-bio.

[Ben Woodcroft]

Thanks in advance for comments.
ben

[PATCH 01/10] gnu: Add python2-pytest-cache.

[Ben Woodcroft]

* gnu/packages/python.scm (python-pytest-cache)[properties]: New field.
(python2-pytest-cache): New variable.
---
 gnu/packages/python.scm | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 0379352..ecd16c5 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -12,7 +12,7 @@
 ;;; Copyright © 2015 Eric Dvorsak <eric@dvorsak.fr>
 ;;; Copyright © 2015, 2016 David Thompson <davet@gnu.org>
 ;;; Copyright © 2015, 2016 Leo Famulari <leo@famulari.name>
-;;; Copyright © 2015 Ben Woodcroft <donttrustben@gmail.com>
+;;; Copyright © 2015, 2016 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2015, 2016 Erik Edrosa <erik.edrosa@gmail.com>
 ;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2015 Kyle Meyer <kyle@kyleam.com>
@@ -6965,7 +6965,17 @@ minimal and fast API targetting the following uses:
     (description "The pytest-cache plugin provides tools to rerun failures from
 the last py.test invocation.")
     (home-page "https://bitbucket.org/hpk42/pytest-cache/")
-    (license license:expat)))
+    (license license:expat)
+    (properties `((python2-variant . ,(delay python2-pytest-cache))))))
+
+(define-public python2-pytest-cache
+  (let ((base (package-with-python2
+                  (strip-python2-variant python-pytest-cache))))
+    (package
+      (inherit base)
+      (native-inputs
+       `(("python2-setuptools" ,python2-setuptools)
+         ,@(package-native-inputs base))))))
 
 (define-public python-pytest-localserver
   (package
-- 
2.5.0

[PATCH 02/10] gnu: Add python-bz2file.

[Ben Woodcroft]

* gnu/packages/python.scm (python-bz2file, python2-bz2file): New
variables.
---
 gnu/packages/python.scm | 40 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index ecd16c5..9c3a9fd 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -8677,6 +8677,46 @@ LDFLAGS and parse the output to build extensions with setup.py.")
 (define-public python2-pkgconfig
   (package-with-python2 python-pkgconfig))
 
+(define-public python-bz2file
+  (package
+    (name "python-bz2file")
+    (version "0.98")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://pypi.python.org/packages/source/b/bz2file/bz2file-"
+             version
+             ".tar.gz"))
+       (sha256
+        (base32
+         "126s53fkpx04f33a829yqqk8fj4png3qwg4m66cvlmhmwc8zihb4"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; python setup.py test does not work as of 0.98
+         ;; but there is only the one test file
+         (replace 'check
+           (lambda _ (zero? (system* "python" "test_bz2file.py")))))))
+    (home-page "https://github.com/nvawda/bz2file")
+    (synopsis "Read and write bzip2-compressed files")
+    (description
+     "Bz2file is a Python library for reading and writing bzip2-compressed
+files.  It contains a drop-in replacement for the file interface in the
+standard library's bz2 module, including features from the latest development
+version of CPython that are not available in older releases.")
+    (license asl2.0)
+    (properties `((python2-variant . ,(delay python2-bz2file))))))
+
+(define-public python2-bz2file
+  (let ((base (package-with-python2
+               (strip-python2-variant python-bz2file))))
+    (package
+      (inherit base)
+      (native-inputs
+       `(("python2-setuptools" ,python2-setuptools))))))
+
 (define-public python-cysignals
   (package
     (name "python-cysignals")
-- 
2.5.0

[PATCH 03/10] gnu: Add python-pytest-pep8.

[Ben Woodcroft]

* gnu/packages/python.scm (python-pytest-pep8, python2-pytest-pep8): New
variables.
---
 gnu/packages/python.scm | 63 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 63 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 9c3a9fd..b5d1005 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -8717,6 +8717,69 @@ version of CPython that are not available in older releases.")
       (native-inputs
        `(("python2-setuptools" ,python2-setuptools))))))
 
+(define-public python-pytest-pep8
+  (package
+    (name "python-pytest-pep8")
+    (version "1.0.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://pypi.python.org/packages/source/p/pytest-pep8/pytest-pep8-"
+             version
+             ".tar.gz"))
+       (sha256
+        (base32
+         "06032agzhw1i9d9qlhfblnl3dw5hcyxhagn7b120zhrszbjzfbh3"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'remove-failing-test
+           ;; Ignore the known test failure.
+           ;; https://bitbucket.org/pytest-dev/pytest-pep8/issues/8/test-failure
+           (lambda _
+             (substitute* "test_pep8.py"
+               (("^def test_ok_verbose") "def dont_run"))
+             #t))
+         (add-after 'install 'post-install-check
+           ;; 'setup.py test' does not run tests
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (setenv "PYTHONPATH"
+                       (string-append
+                        (getenv "PYTHONPATH")
+                        ":"
+                        out
+                        "/lib/python"
+                        (string-take (string-take-right
+                                      (assoc-ref inputs "python") 5) 3)
+                        "/site-packages"))
+               (zero?
+                (system*
+                 (string-append out "/bin/py.test") "test_pep8.py"))))))))
+    (propagated-inputs
+     `(("python-pytest-cache", python-pytest-cache)
+       ("python-pytest" ,python-pytest)
+       ("python-pep8" ,python-pep8)))
+    (home-page "https://bitbucket.org/pytest-dev/pytest-pep8")
+    (synopsis "Pytest plugin to check PEP8 requirements")
+    (description
+     "Pytest-pep8 is a py.test plugin for efficiently checking compliance to
+the PEP8 style guide.  If you type @code{py.test --pep8} every file ending in
+@code{.py} will be discovered and PEP8-checked, starting from the command line
+arguments.")
+    (license license:expat)
+    (properties `((python2-variant . ,(delay python2-pytest-pep8))))))
+
+(define-public python2-pytest-pep8
+  (let ((base (package-with-python2
+               (strip-python2-variant python-pytest-pep8))))
+    (package
+      (inherit base)
+      (native-inputs
+       `(("python2-setuptools" ,python2-setuptools))))))
+
 (define-public python-cysignals
   (package
     (name "python-cysignals")
-- 
2.5.0

[PATCH 04/10] gnu: Add python-pytest-flakes.

[Ben Woodcroft]

* gnu/packages/python.scm (python-pytest-flakes,
python2-pytest-flakes): New variables.
---
 gnu/packages/python.scm | 60 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 60 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index b5d1005..28b1ee0 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -8780,6 +8780,66 @@ arguments.")
       (native-inputs
        `(("python2-setuptools" ,python2-setuptools))))))
 
+(define-public python-pytest-flakes
+  (package
+    (name "python-pytest-flakes")
+    (version "1.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://pypi.python.org/packages/source/p/pytest-flakes/pytest-flakes-"
+             version
+             ".tar.gz"))
+       (sha256
+        (base32
+         "0flag3n33kbhyjrhzmq990rvg4yb8hhhl0i48q9hw0ll89jp28lw"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'post-install-check
+           ;; 'setup.py test' does not run tests
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (setenv "PYTHONPATH"
+                       (string-append
+                        (getenv "PYTHONPATH")
+                        ":"
+                        out
+                        "/lib/python"
+                        (string-take (string-take-right
+                                      (assoc-ref inputs "python") 5) 3)
+                        "/site-packages"))
+               (zero?
+                (system*
+                 "py.test" "test_flakes.py"))))))))
+    (native-inputs
+     `(("python-pytest-pep8" ,python-pytest-pep8)))
+    (propagated-inputs
+     `(("python-pytest-cache" ,python-pytest-cache)
+       ("python-pytest" ,python-pytest)
+       ("python-pyflakes" ,python-pyflakes)))
+    (home-page
+     "https://github.com/fschulze/pytest-flakes")
+    (synopsis "Pytest plugin to check source code with pyflakes")
+    (description
+     "Pytest-pyflakes is a py.test plugin for efficiently checking python source
+with pyflakes.  If you type @code{py.test --flakes} every file ending in
+@code{.py} will be discovered and run through pyflakes, starting from the
+command line arguments.")
+    (license license:expat)
+    (properties `((python2-variant . ,(delay python2-pytest-flakes))))))
+
+(define-public python2-pytest-flakes
+  (let ((base (package-with-python2
+                 (strip-python2-variant python-pytest-flakes))))
+    (package
+      (inherit base)
+      (native-inputs
+       `(,@(package-native-inputs base)
+         ("python2-setuptools" ,python2-setuptools))))))
+
 (define-public python-cysignals
   (package
     (name "python-cysignals")
-- 
2.5.0

[PATCH 05/10] gnu: Add python-future.

[Ben Woodcroft]

* gnu/packages/python.scm (python-future, python2-future): New
variables.
---
 gnu/packages/python.scm | 35 ++++++++++++++++++++++++++++++++++-
 1 file changed, 34 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 28b1ee0..54c3202 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -8833,13 +8833,46 @@ command line arguments.")
 
 (define-public python2-pytest-flakes
   (let ((base (package-with-python2
-                 (strip-python2-variant python-pytest-flakes))))
+               (strip-python2-variant python-pytest-flakes))))
     (package
       (inherit base)
       (native-inputs
        `(,@(package-native-inputs base)
          ("python2-setuptools" ,python2-setuptools))))))
 
+(define-public python-future
+  (package
+    (name "python-future")
+    (version "0.15.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://pypi.python.org/packages/source/f/future/future-"
+             version
+             ".tar.gz"))
+       (sha256
+        (base32
+         "15wvcfzssc68xqnqi1dq4fhd0848hwi9jn42hxyvlqna40zijfrx"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #f)) ; Tests connect to the network
+    (home-page "http://python-future.org")
+    (synopsis "Single-source support for Python 3 and 2")
+    (description
+     "@code{python-future} is the missing compatibility layer between Python 2 and
+Python 3.  It allows you to use a single, clean Python 3.x-compatible codebase
+to support both Python 2 and Python 3 with minimal overhead.")
+    (license license:expat)
+    (properties `((python2-variant . ,(delay python2-future))))))
+
+(define-public python2-future
+  (let ((base (package-with-python2
+               (strip-python2-variant python-future))))
+    (package
+      (inherit base)
+      (native-inputs `(("python2-setuptools" ,python2-setuptools))))))
+
 (define-public python-cysignals
   (package
     (name "python-cysignals")
-- 
2.5.0

[PATCH 06/10] gnu: Add python-cachecontrol.

[Ben Woodcroft]

* gnu/packages/python.scm (python-cachecontrol,
python2-cachecontrol): New variables.
---
 gnu/packages/python.scm | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 54c3202..0fc65fe 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -8873,6 +8873,40 @@ to support both Python 2 and Python 3 with minimal overhead.")
       (inherit base)
       (native-inputs `(("python2-setuptools" ,python2-setuptools))))))
 
+(define-public python-cachecontrol
+  (package
+    (name "python-cachecontrol")
+    (version "0.11.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://pypi.python.org/packages/source/C/CacheControl/CacheControl-"
+             version
+             ".tar.gz"))
+       (sha256
+        (base32
+         "15bn8xll6z15h0zqhfjy1n8dn8p0fcb4m0rhnfanq63z7r2wpprp"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-requests" ,python-requests)
+       ("python-lockfile" ,python-lockfile)))
+    (home-page "https://github.com/ionrock/cachecontrol")
+    (synopsis "httplib2 caching for requests")
+    (description "CacheControl is a port of the caching algorithms in httplib2
+for use with requests session object.  It was written because httplib2's
+better support for caching is often mitigated by its lack of threadsafety.
+The same is true of requests in terms of caching.")
+    (license asl2.0)
+    (properties `((python2-variant . ,(delay python2-cachecontrol))))))
+
+(define-public python2-cachecontrol
+  (let ((base (package-with-python2
+               (strip-python2-variant python-cachecontrol))))
+    (package
+      (inherit base)
+      (native-inputs `(("python2-setuptools" ,python2-setuptools))))))
+
 (define-public python-cysignals
   (package
     (name "python-cysignals")
-- 
2.5.0

[PATCH 07/10] gnu: python-tornado: Use 'python2-variant'.

[Ben Woodcroft]

* gnu/packages/python.scm (python-tornado)[properties]: New field.
(python2-tornado): Build with 'strip-python2-variant'.
---
 gnu/packages/python.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 0fc65fe..f26592e 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -4936,10 +4936,12 @@ originally developed at FriendFeed.  By using non-blocking network I/O,
 Tornado can scale to tens of thousands of open connections, making it ideal
 for long polling, WebSockets, and other applications that require a long-lived
 connection to each user.")
-    (license asl2.0)))
+    (license asl2.0)
+    (properties `((python2-variant . ,(delay python2-tornado))))))
 
 (define-public python2-tornado
-  (let ((tornado (package-with-python2 python-tornado)))
+  (let ((tornado (package-with-python2
+                  (strip-python2-variant python-tornado))))
     (package (inherit tornado)
       (inputs
        `(("python2-backport-ssl-match-hostname"
-- 
2.5.0

[PATCH 08/10] gnu: python-ipython: Use 'python2-variant'.

[Ben Woodcroft]

* gnu/packages/python.scm (python-ipython)[properties]: New field.
(python2-ipython): Use 'strip-python2-variant'.
---
 gnu/packages/python.scm | 26 +++++++++-----------------
 1 file changed, 9 insertions(+), 17 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index f26592e..ea9f47a 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -4359,29 +4359,21 @@ without using the configuration machinery.")
 Powerful interactive shells, a browser-based notebook, support for interactive
 data visualization, embeddable interpreters and tools for parallel
 computing.")
-    (license bsd-3)))
+    (license bsd-3)
+    (properties `((python2-variant . ,(delay python2-ipython))))))
 
 (define-public python2-ipython
-  (let ((ipython (package-with-python2 python-ipython)))
+  (let ((base (package-with-python2
+               (strip-python2-variant python-ipython))))
     (package
-      (inherit ipython)
+      (inherit base)
       ;; FIXME: some tests are failing
-      (arguments
-       `(#:tests? #f ,@(package-arguments ipython)))
-      ;; Make sure we use custom python2-NAME packages.
       ;; FIXME: add pyreadline once available.
-      (propagated-inputs
-       `(("python2-terminado" ,python2-terminado)
-         ,@(alist-delete "python-terminado"
-                         (package-propagated-inputs ipython))))
+      (arguments
+       `(#:tests? #f ,@(package-arguments base)))
       (inputs
-       `(("python2-jsonschema" ,python2-jsonschema)
-         ("python2-mock" ,python2-mock)
-         ("python2-matplotlib" ,python2-matplotlib)
-         ("python2-numpy" ,python2-numpy)
-         ("python2-requests" ,python2-requests)
-         ,@(fold alist-delete (package-inputs ipython)
-                 '("python-jsonschema" "python-matplotlib" "python-numpy" "python-requests")))))))
+       `(("python2-mock" ,python2-mock)
+         ,@(package-inputs base))))))
 
 (define-public python-isodate
   (package
-- 
2.5.0

[PATCH 09/10] gnu: Add python-natsort.

[Ben Woodcroft]

* gnu/packages/python.scm (python-natsort, python2-natsort): New
variables.
---
 gnu/packages/python.scm | 44 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index ea9f47a..7aae6fc 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -8901,6 +8901,50 @@ The same is true of requests in terms of caching.")
       (inherit base)
       (native-inputs `(("python2-setuptools" ,python2-setuptools))))))
 
+(define-public python-natsort
+  (package
+    (name "python-natsort")
+    (version "4.0.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://pypi.python.org/packages/source/n/natsort/natsort-"
+             version
+             ".tar.gz"))
+       (sha256
+        (base32
+         "0f8q66pyczgy1cm3nh8rkh7hgl9h49zx9r06mivg4y5sbzla6sy7"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("python-pytest" ,python-pytest)
+       ("python-pytest-flakes" ,python-pytest-flakes)
+       ("python-pytest-cov" ,python-pytest-cov)
+       ("python-pytest-cache" ,python-pytest-cache)
+       ("python-hypothesis" ,python-hypothesis)
+       ("python-pytest-pep8", python-pytest-pep8)))
+    (home-page "https://github.com/SethMMorton/natsort")
+    (synopsis "Sort lists naturally")
+    (description "When you try to sort a list of strings that contain numbers,
+the normal python sort algorithm sorts lexicographically, so you might not get
+the results that you expect.  @code{natsort} provides a function
+@code{natsorted} that helps sort lists 'naturally', either as real
+numbers (i.e. signed/unsigned floats or ints), or as versions.")
+    (license license:expat)
+    (properties `((python2-variant . ,(delay python2-natsort))))))
+
+(define-public python2-natsort
+  (let ((base (package-with-python2
+               (strip-python2-variant python-natsort))))
+    (package
+      (inherit base)
+      (native-inputs
+       (append (package-native-inputs base)
+               `(("python2-mock" ,python2-mock)
+                 ("python2-pathlib" ,python2-pathlib)
+                 ("python2-enum34" ,python2-enum34)
+                 ("python2-setuptools" ,python2-setuptools)))))))
+
 (define-public python-cysignals
   (package
     (name "python-cysignals")
-- 
2.5.0

[PATCH 10/10] gnu: Add python-scikit-bio.

[Ben Woodcroft]

* gnu/packages/python.scm (python-scikit-bio,
python2-scikit-bio): New variables.
---
 gnu/packages/python.scm | 91 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 91 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 7aae6fc..b359422 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -8945,6 +8945,97 @@ numbers (i.e. signed/unsigned floats or ints), or as versions.")
                  ("python2-enum34" ,python2-enum34)
                  ("python2-setuptools" ,python2-setuptools)))))))
 
+(define-public python-scikit-bio
+  (package
+    (name "python-scikit-bio")
+    (version "0.4.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://pypi.python.org/packages/source/s/scikit-bio/scikit-bio-"
+             version
+             ".tar.gz"))
+       (sha256
+        (base32
+         "06nrcgfz6c3jb2dnaf1wnvx3dyww94p454c4126gvcvfgv6scczy"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; Install procedure installs extraneous binaries.
+         (add-after 'install 'remove-extraneous-files
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin")))
+               (delete-file-recursively bin))
+             #t))
+         ;; `setup.py test' does not run tests, but there are many test
+         ;; failures anyway
+         ;; e.g. https://github.com/biocore/scikit-bio/issues/1308.  Run a
+         ;; simple import test instead.
+         (delete 'check)
+         (add-after 'install 'check-after-install
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((pythonpath
+                    (string-append
+                     (getenv "PYTHONPATH")
+                     ":" (assoc-ref outputs "out")
+                     "/lib/python"
+                     (string-take (string-take-right
+                                   (assoc-ref inputs "python") 5) 3)
+                     "/site-packages")))
+               (setenv "PYTHONPATH" pythonpath)
+               (zero?
+                (with-directory-excursion "ci"
+                  (system*
+                   (string-append
+                    (assoc-ref inputs "python")
+                    "/bin/python")
+                   "-c"
+                   (string-append "import matplotlib; "
+                                  "matplotlib.use(\"Agg\"); "
+                                  "import skbio"))))))))))
+    (native-inputs
+     `(("python-nose" ,python-nose)
+       ("python-pep8" ,python-pep8)
+       ("python-flake8" ,python-flake8)
+       ("python-dateutil" ,python-dateutil-2)))
+    (propagated-inputs
+     `(("python-bz2file" ,python-bz2file)
+       ("python-lockfile" ,python-lockfile)
+       ("python-cachecontrol" ,python-cachecontrol)
+       ("python-contextlib2" ,python-contextlib2)
+       ("python-decorator" ,python-decorator)
+       ("python-future" ,python-future)
+       ("python-ipython" ,python-ipython)
+       ("python-matplotlib" ,python-matplotlib)
+       ("python-natsort" ,python-natsort)
+       ("python-numpy" ,python-numpy)
+       ("python-pandas" ,python-pandas)
+       ("python-scipy" ,python-scipy)
+       ("python-six" ,python-six)))
+    (home-page "http://scikit-bio.org")
+    (synopsis "Resources for bioinformatics")
+    (description
+     "Scikit-bio (canonically pronounced sigh-kit-buy-oh) is a library for
+working with biological data in Python, providing data structures, algorithms
+and educational resources.  It defines python packages for biological
+sequences, alignments, tree, visualisation, diversity calculation and File
+I/O.")
+    (license bsd-3)
+    (properties `((python2-variant . ,(delay python2-scikit-bio))))))
+
+(define-public python2-scikit-bio
+  (let ((base (package-with-python2
+               (strip-python2-variant python-scikit-bio))))
+    (package
+      (inherit base)
+      (native-inputs
+       (append (package-native-inputs base)
+               `(("python2-setuptools" ,python2-setuptools)
+                 ("python2-mock" ,python2-mock)))))))
+
 (define-public python-cysignals
   (package
     (name "python-cysignals")
-- 
2.5.0

Re: [PATCH 10/10] gnu: Add python-scikit-bio.

[Ricardo Wurmus]

Hi Ben,

thanks for your patch.

> * gnu/packages/python.scm (python-scikit-bio,
> python2-scikit-bio): New variables.

I think this should be on one line.  In any case, breaking the line so
soon looks a bit weird.

> ---
>  gnu/packages/python.scm | 91 +++++++++++++++++++++++++++++++++++++++++++++++++
>  1 file changed, 91 insertions(+)
>
> diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
> index 7aae6fc..b359422 100644
> --- a/gnu/packages/python.scm
> +++ b/gnu/packages/python.scm
> @@ -8945,6 +8945,97 @@ numbers (i.e. signed/unsigned floats or ints), or as versions.")
>                   ("python2-enum34" ,python2-enum34)
>                   ("python2-setuptools" ,python2-setuptools)))))))
>  
> +(define-public python-scikit-bio
> +  (package
> +    (name "python-scikit-bio")
> +    (version "0.4.2")
> +    (source
> +     (origin
> +       (method url-fetch)
> +       (uri (string-append
> +             "https://pypi.python.org/packages/source/s/scikit-bio/scikit-bio-"
> +             version
> +             ".tar.gz"))
> +       (sha256
> +        (base32
> +         "06nrcgfz6c3jb2dnaf1wnvx3dyww94p454c4126gvcvfgv6scczy"))))
> +    (build-system python-build-system)
> +    (arguments
> +     `(#:phases
> +       (modify-phases %standard-phases
> +         ;; Install procedure installs extraneous binaries.
> +         (add-after 'install 'remove-extraneous-files
> +           (lambda* (#:key outputs #:allow-other-keys)
> +             (let* ((out (assoc-ref outputs "out"))
> +                    (bin (string-append out "/bin")))
> +               (delete-file-recursively bin))
> +             #t))
> +         ;; `setup.py test' does not run tests, but there are many test
> +         ;; failures anyway

What does it mean that “setup.py test” does not run tests?  Is there
another test target?

> +         ;; e.g. https://github.com/biocore/scikit-bio/issues/1308.  Run a
> +         ;; simple import test instead.
> +         (delete 'check)
> +         (add-after 'install 'check-after-install
> +           (lambda* (#:key inputs outputs #:allow-other-keys)
> +             (let ((pythonpath
> +                    (string-append
> +                     (getenv "PYTHONPATH")
> +                     ":" (assoc-ref outputs "out")
> +                     "/lib/python"
> +                     (string-take (string-take-right
> +                                   (assoc-ref inputs "python") 5) 3)
> +                     "/site-packages")))
> +               (setenv "PYTHONPATH" pythonpath)

I would not use a let here and replace “pythonpath” with the
“(string-append...)” for the new PYTHONPATH.

> +               (zero?
> +                (with-directory-excursion "ci"
> +                  (system*
> +                   (string-append
> +                    (assoc-ref inputs "python")
> +                    "/bin/python")

You can use “python” directly, or “(which "python")”.  The PATH should
include it at this point.

> +                   "-c"
> +                   (string-append "import matplotlib; "
> +                                  "matplotlib.use(\"Agg\"); "
> +                                  "import skbio"))))))))))
> +    (native-inputs
> +     `(("python-nose" ,python-nose)
> +       ("python-pep8" ,python-pep8)
> +       ("python-flake8" ,python-flake8)
> +       ("python-dateutil" ,python-dateutil-2)))
> +    (propagated-inputs
> +     `(("python-bz2file" ,python-bz2file)
> +       ("python-lockfile" ,python-lockfile)
> +       ("python-cachecontrol" ,python-cachecontrol)
> +       ("python-contextlib2" ,python-contextlib2)
> +       ("python-decorator" ,python-decorator)
> +       ("python-future" ,python-future)
> +       ("python-ipython" ,python-ipython)
> +       ("python-matplotlib" ,python-matplotlib)
> +       ("python-natsort" ,python-natsort)
> +       ("python-numpy" ,python-numpy)
> +       ("python-pandas" ,python-pandas)
> +       ("python-scipy" ,python-scipy)
> +       ("python-six" ,python-six)))
> +    (home-page "http://scikit-bio.org")
> +    (synopsis "Resources for bioinformatics")
> +    (description
> +     "Scikit-bio (canonically pronounced sigh-kit-buy-oh) is a library for
> +working with biological data in Python, providing data structures, algorithms
> +and educational resources.  It defines python packages for biological
> +sequences, alignments, tree, visualisation, diversity calculation and File
> +I/O.")

Please capitalise “python” throughout and replace “File” with “file”.
I’d also remove “(canonically pronounced sigh-kit-buy-oh)”.

> +    (license bsd-3)
> +    (properties `((python2-variant . ,(delay python2-scikit-bio))))))
> +
> +(define-public python2-scikit-bio
> +  (let ((base (package-with-python2
> +               (strip-python2-variant python-scikit-bio))))
> +    (package
> +      (inherit base)
> +      (native-inputs
> +       (append (package-native-inputs base)
> +               `(("python2-setuptools" ,python2-setuptools)
> +                 ("python2-mock" ,python2-mock)))))))
> +

Looks good to me.

~~ Ricardo

Re: [PATCH 10/10] gnu: Add python-scikit-bio.

[Ricardo Wurmus]

Ben Woodcroft <donttrustben@gmail.com> writes:

> * gnu/packages/python.scm (python-scikit-bio,
> python2-scikit-bio): New variables.

One more thing: how about placing this in “bioinformatics.scm” instead?
“python.scm” is already so very big because it contains a lot of stuff
that just happens to be written in Python.

~~ Ricardo

Re: [PATCH 09/10] gnu: Add python-natsort.

[Ricardo Wurmus]

Ben Woodcroft <donttrustben@gmail.com> writes:

> * gnu/packages/python.scm (python-natsort, python2-natsort): New
> variables.
> ---
>  gnu/packages/python.scm | 44 ++++++++++++++++++++++++++++++++++++++++++++
>  1 file changed, 44 insertions(+)
>
> diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
> index ea9f47a..7aae6fc 100644
> --- a/gnu/packages/python.scm
> +++ b/gnu/packages/python.scm
> @@ -8901,6 +8901,50 @@ The same is true of requests in terms of caching.")
>        (inherit base)
>        (native-inputs `(("python2-setuptools" ,python2-setuptools))))))
>  
> +(define-public python-natsort
> +  (package
> +    (name "python-natsort")
> +    (version "4.0.4")
> +    (source
> +     (origin
> +       (method url-fetch)
> +       (uri (string-append
> +             "https://pypi.python.org/packages/source/n/natsort/natsort-"
> +             version
> +             ".tar.gz"))

Could you use “(pypi-uri "natsort" version)” instead?

> +       (sha256
> +        (base32
> +         "0f8q66pyczgy1cm3nh8rkh7hgl9h49zx9r06mivg4y5sbzla6sy7"))))
> +    (build-system python-build-system)
> +    (native-inputs
> +     `(("python-pytest" ,python-pytest)
> +       ("python-pytest-flakes" ,python-pytest-flakes)
> +       ("python-pytest-cov" ,python-pytest-cov)
> +       ("python-pytest-cache" ,python-pytest-cache)
> +       ("python-hypothesis" ,python-hypothesis)
> +       ("python-pytest-pep8", python-pytest-pep8)))
> +    (home-page "https://github.com/SethMMorton/natsort")
> +    (synopsis "Sort lists naturally")
> +    (description "When you try to sort a list of strings that contain numbers,
> +the normal python sort algorithm sorts lexicographically, so you might not get
> +the results that you expect.  @code{natsort} provides a function
> +@code{natsorted} that helps sort lists 'naturally', either as real
> +numbers (i.e. signed/unsigned floats or ints), or as versions.")
> +    (license license:expat)
> +    (properties `((python2-variant . ,(delay python2-natsort))))))
> +
> +(define-public python2-natsort
> +  (let ((base (package-with-python2
> +               (strip-python2-variant python-natsort))))
> +    (package
> +      (inherit base)
> +      (native-inputs
> +       (append (package-native-inputs base)
> +               `(("python2-mock" ,python2-mock)
> +                 ("python2-pathlib" ,python2-pathlib)
> +                 ("python2-enum34" ,python2-enum34)
> +                 ("python2-setuptools" ,python2-setuptools)))))))
> +
>  (define-public python-cysignals
>    (package
>      (name "python-cysignals")

The rest looks fine to me.

~~ Ricardo

Re: [PATCH 10/10] gnu: Add python-scikit-bio.

[Ricardo Wurmus]

Ben Woodcroft <donttrustben@gmail.com> writes:

> * gnu/packages/python.scm (python-scikit-bio,
> python2-scikit-bio): New variables.
> ---
>  gnu/packages/python.scm | 91 +++++++++++++++++++++++++++++++++++++++++++++++++
>  1 file changed, 91 insertions(+)
>
> diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
> index 7aae6fc..b359422 100644
> --- a/gnu/packages/python.scm
> +++ b/gnu/packages/python.scm
> @@ -8945,6 +8945,97 @@ numbers (i.e. signed/unsigned floats or ints), or as versions.")
>                   ("python2-enum34" ,python2-enum34)
>                   ("python2-setuptools" ,python2-setuptools)))))))
>  
> +(define-public python-scikit-bio
> +  (package
> +    (name "python-scikit-bio")
> +    (version "0.4.2")
> +    (source
> +     (origin
> +       (method url-fetch)
> +       (uri (string-append
> +             "https://pypi.python.org/packages/source/s/scikit-bio/scikit-bio-"
> +             version
> +             ".tar.gz"))

Here, too: please use “(pypi-uri...)” if possible.

~~ Ricardo

Re: [PATCH 08/10] gnu: python-ipython: Use 'python2-variant'.

[Ricardo Wurmus]

Ben Woodcroft <donttrustben@gmail.com> writes:

> * gnu/packages/python.scm (python-ipython)[properties]: New field.
> (python2-ipython): Use 'strip-python2-variant'.

The commit message should mention the changes to the “inputs” and
“propagated-input” fields because it isn’t obvious whether the list of
inputs actually stays the same.

~~ Ricardo

Re: [PATCH 02/10] gnu: Add python-bz2file.

[Efraim Flashner]

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On Thu, Apr 21, 2016 at 11:21:53PM +1000, Ben Woodcroft wrote:
> * gnu/packages/python.scm (python-bz2file, python2-bz2file): New
> variables.
> ---
>  gnu/packages/python.scm | 40 ++++++++++++++++++++++++++++++++++++++++
>  1 file changed, 40 insertions(+)
> 
> diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
> index ecd16c5..9c3a9fd 100644
> --- a/gnu/packages/python.scm
> +++ b/gnu/packages/python.scm
> @@ -8677,6 +8677,46 @@ LDFLAGS and parse the output to build extensions with setup.py.")
>  (define-public python2-pkgconfig
>    (package-with-python2 python-pkgconfig))
>  
> +(define-public python-bz2file
> +  (package
> +    (name "python-bz2file")
> +    (version "0.98")
> +    (source
> +     (origin
> +       (method url-fetch)
> +       (uri (string-append
> +             "https://pypi.python.org/packages/source/b/bz2file/bz2file-"
> +             version
> +             ".tar.gz"))

(uri (pypi-uri "bz2file" version))

> +       (sha256
> +        (base32
> +         "126s53fkpx04f33a829yqqk8fj4png3qwg4m66cvlmhmwc8zihb4"))))
> +    (build-system python-build-system)
> +    (arguments
> +     `(#:phases
> +       (modify-phases %standard-phases
> +         ;; python setup.py test does not work as of 0.98
> +         ;; but there is only the one test file
> +         (replace 'check
> +           (lambda _ (zero? (system* "python" "test_bz2file.py")))))))
> +    (home-page "https://github.com/nvawda/bz2file")
> +    (synopsis "Read and write bzip2-compressed files")
> +    (description
> +     "Bz2file is a Python library for reading and writing bzip2-compressed
> +files.  It contains a drop-in replacement for the file interface in the
> +standard library's bz2 module, including features from the latest development
> +version of CPython that are not available in older releases.")
> +    (license asl2.0)
> +    (properties `((python2-variant . ,(delay python2-bz2file))))))
> +
> +(define-public python2-bz2file
> +  (let ((base (package-with-python2
> +               (strip-python2-variant python-bz2file))))
> +    (package
> +      (inherit base)
> +      (native-inputs
> +       `(("python2-setuptools" ,python2-setuptools))))))
> +
>  (define-public python-cysignals
>    (package
>      (name "python-cysignals")
> -- 
> 2.5.0
> 

-- 
Efraim Flashner   <efraim@flashner.co.il>   אפרים פלשנר
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Re: [PATCH 02/10] gnu: Add python-bz2file.

[Hartmut Goebel]

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Am 21.04.2016 um 15:21 schrieb Ben Woodcroft:
> +    (arguments
> +     `(#:phases
> +       (modify-phases %standard-phases
> +         ;; python setup.py test does not work as of 0.98
> +         ;; but there is only the one test file
> +         (replace 'check
> +           (lambda _ (zero? (system* "python" "test_bz2file.py")))))))

I wonder if this is actually working. The python-3 package does not
include "python" (except if this was changed the last days).

> +    (description
> +     "Bz2file is a Python library for reading and writing bzip2-compressed
> +files.  It contains a drop-in replacement for the file interface in the

I do not understand "replacement for the file interface". If this like
the "zipfile" module?


-- 
Schönen Gruß
Hartmut Goebel
Dipl.-Informatiker (univ), CISSP, CSSLP, ISO 27001 Lead Implementer
Information Security Management, Security Governance, Secure Software
Development

Goebel Consult, Landshut
http://www.goebel-consult.de

Blog: http://www.goebel-consult.de/blog/feiertagsarbeit-bei-teletrust
Kolumne:
http://www.cissp-gefluester.de/2012-09-steht-ein-manta-fahrer-vor-der-uni


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Re: [PATCH 03/10] gnu: Add python-pytest-pep8.

[Hartmut Goebel]

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Am 21.04.2016 um 15:21 schrieb Ben Woodcroft:
> +         (add-after 'install 'post-install-check
> +           ;; 'setup.py test' does not run tests
> +           (lambda* (#:key inputs outputs #:allow-other-keys)
> +             (let ((out (assoc-ref outputs "out")))
> +               (setenv "PYTHONPATH"
> +                       (string-append
> +                        (getenv "PYTHONPATH")
> +                        ":"
> +                        out
> +                        "/lib/python"
> +                        (string-take (string-take-right
> +                                      (assoc-ref inputs "python") 5) 3)
> +                        "/site-packages"))
> +               (zero?
> +                (system*
> +                 (string-append out "/bin/py.test") "test_pep8.py"))))))))

Have you tried if the tests are run when moving the test-file into a new
subdirectory "tests/"? This would result in much less code.

-- 
Schönen Gruß
Hartmut Goebel
Dipl.-Informatiker (univ), CISSP, CSSLP, ISO 27001 Lead Implementer
Information Security Management, Security Governance, Secure Software
Development

Goebel Consult, Landshut
http://www.goebel-consult.de

Blog: http://www.goebel-consult.de/blog/feiertagsarbeit-bei-teletrust
Kolumne:
http://www.cissp-gefluester.de/2012-09-steht-ein-manta-fahrer-vor-der-uni


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Re: [PATCH 04/10] gnu: Add python-pytest-flakes.

[Hartmut Goebel]

[-- Attachment #1.1: Type: text/plain, Size: 1443 bytes --]

Am 21.04.2016 um 15:21 schrieb Ben Woodcroft:
> +    (arguments
> +     `(#:phases
> +       (modify-phases %standard-phases
> +         (add-after 'install 'post-install-check
> +           ;; 'setup.py test' does not run tests
> +           (lambda* (#:key inputs outputs #:allow-other-keys)
> +             (let ((out (assoc-ref outputs "out")))
> +               (setenv "PYTHONPATH"
> +                       (string-append
> +                        (getenv "PYTHONPATH")
> +                        ":"
> +                        out
> +                        "/lib/python"
> +                        (string-take (string-take-right
> +                                      (assoc-ref inputs "python") 5) 3)
> +                        "/site-packages"))
> +               (zero?
> +                (system*
> +                 "py.test" "test_flakes.py"))))))))

Again: Have you tried if the tests are run when moving the test-file
into a new subdirectory "tests/"? This would result in much less code.

-- 
Schönen Gruß
Hartmut Goebel
Dipl.-Informatiker (univ), CISSP, CSSLP, ISO 27001 Lead Implementer
Information Security Management, Security Governance, Secure Software
Development

Goebel Consult, Landshut
http://www.goebel-consult.de

Blog: http://www.goebel-consult.de/blog/feiertagsarbeit-bei-teletrust
Kolumne:
http://www.cissp-gefluester.de/2012-09-steht-ein-manta-fahrer-vor-der-uni


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[PATCH 2/2] gnu: Add python-scikit-bio.

[Ben Woodcroft]

* gnu/packages/python.scm (python-scikit-bio, python2-scikit-bio):
New variables.
---
 gnu/packages/bioinformatics.scm | 84 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 84 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 899ce1c..fa67f3b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3339,6 +3339,90 @@ optimize the sequencing depth, or to screen multiple libraries to avoid low
 complexity samples.")
     (license license:gpl3+)))
 
+(define-public python-scikit-bio
+  (package
+    (name "python-scikit-bio")
+    (version "0.4.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "scikit-bio" version))
+       (sha256
+        (base32
+         "06nrcgfz6c3jb2dnaf1wnvx3dyww94p454c4126gvcvfgv6scczy"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; Install procedure installs extraneous binaries.
+         (add-after 'install 'remove-extraneous-files
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin")))
+               (delete-file-recursively bin))
+             #t))
+         ;; Tests are intended to be run using 'make test' not 'setup.py
+         ;; test', but there are many test failures anyway
+         ;; e.g. https://github.com/biocore/scikit-bio/issues/1308.  Run a
+         ;; simple import test instead.
+         (delete 'check)
+         (add-after 'install 'check-after-install
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (setenv "PYTHONPATH"
+                     (string-append
+                      (getenv "PYTHONPATH")
+                      ":" (assoc-ref outputs "out")
+                      "/lib/python"
+                      (string-take (string-take-right
+                                    (assoc-ref inputs "python") 5) 3)
+                      "/site-packages"))
+             (zero?
+              (with-directory-excursion "ci"
+                (system*
+                 "python"
+                 "-c"
+                 (string-append "import matplotlib; "
+                                "matplotlib.use(\"Agg\"); "
+                                "import skbio")))))))))
+    (native-inputs
+     `(("python-nose" ,python-nose)
+       ("python-pep8" ,python-pep8)
+       ("python-flake8" ,python-flake8)
+       ("python-dateutil" ,python-dateutil-2)))
+    (propagated-inputs
+     `(("python-bz2file" ,python-bz2file)
+       ("python-lockfile" ,python-lockfile)
+       ("python-cachecontrol" ,python-cachecontrol)
+       ("python-contextlib2" ,python-contextlib2)
+       ("python-decorator" ,python-decorator)
+       ("python-future" ,python-future)
+       ("python-ipython" ,python-ipython)
+       ("python-matplotlib" ,python-matplotlib)
+       ("python-natsort" ,python-natsort)
+       ("python-numpy" ,python-numpy)
+       ("python-pandas" ,python-pandas)
+       ("python-scipy" ,python-scipy)
+       ("python-six" ,python-six)))
+    (home-page "http://scikit-bio.org")
+    (synopsis "Resources for bioinformatics")
+    (description
+     "Scikit-bio is a library for working with biological data in Python,
+providing data structures, algorithms and educational resources.  It defines
+Python packages for biological sequences, alignments, tree, visualisation,
+diversity calculation and file I/O.")
+    (license license:bsd-3)
+    (properties `((python2-variant . ,(delay python2-scikit-bio))))))
+
+(define-public python2-scikit-bio
+  (let ((base (package-with-python2
+               (strip-python2-variant python-scikit-bio))))
+    (package
+      (inherit base)
+      (native-inputs
+       (append (package-native-inputs base)
+               `(("python2-setuptools" ,python2-setuptools)
+                 ("python2-mock" ,python2-mock)))))))
+
 (define-public sra-tools
   (package
     (name "sra-tools")
-- 
2.5.0

[PATCH v2] Add python-scikit-bio.

[Ben Woodcroft]

Apologies, still trying to get used to git send-email; please ignore the 2
patches just sent separate to this iteration.

Thanks,
ben

[PATCH v2 01/10] gnu: Add python2-pytest-cache.

[Ben Woodcroft]

* gnu/packages/python.scm (python-pytest-cache)[properties]: New field.
(python2-pytest-cache): New variable.
---
 gnu/packages/python.scm | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 0379352..ecd16c5 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -12,7 +12,7 @@
 ;;; Copyright © 2015 Eric Dvorsak <eric@dvorsak.fr>
 ;;; Copyright © 2015, 2016 David Thompson <davet@gnu.org>
 ;;; Copyright © 2015, 2016 Leo Famulari <leo@famulari.name>
-;;; Copyright © 2015 Ben Woodcroft <donttrustben@gmail.com>
+;;; Copyright © 2015, 2016 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2015, 2016 Erik Edrosa <erik.edrosa@gmail.com>
 ;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2015 Kyle Meyer <kyle@kyleam.com>
@@ -6965,7 +6965,17 @@ minimal and fast API targetting the following uses:
     (description "The pytest-cache plugin provides tools to rerun failures from
 the last py.test invocation.")
     (home-page "https://bitbucket.org/hpk42/pytest-cache/")
-    (license license:expat)))
+    (license license:expat)
+    (properties `((python2-variant . ,(delay python2-pytest-cache))))))
+
+(define-public python2-pytest-cache
+  (let ((base (package-with-python2
+                  (strip-python2-variant python-pytest-cache))))
+    (package
+      (inherit base)
+      (native-inputs
+       `(("python2-setuptools" ,python2-setuptools)
+         ,@(package-native-inputs base))))))
 
 (define-public python-pytest-localserver
   (package
-- 
2.5.0

[PATCH v2 02/10] gnu: Add python-bz2file.

[Ben Woodcroft]

* gnu/packages/python.scm (python-bz2file, python2-bz2file): New
variables.
---
 gnu/packages/python.scm | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index ecd16c5..c07dae6 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -8677,6 +8677,43 @@ LDFLAGS and parse the output to build extensions with setup.py.")
 (define-public python2-pkgconfig
   (package-with-python2 python-pkgconfig))
 
+(define-public python-bz2file
+  (package
+    (name "python-bz2file")
+    (version "0.98")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "bz2file" version))
+       (sha256
+        (base32
+         "126s53fkpx04f33a829yqqk8fj4png3qwg4m66cvlmhmwc8zihb4"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; python setup.py test does not work as of 0.98
+         ;; but there is only the one test file
+         (replace 'check
+           (lambda _ (zero? (system* "python" "test_bz2file.py")))))))
+    (home-page "https://github.com/nvawda/bz2file")
+    (synopsis "Read and write bzip2-compressed files")
+    (description
+     "Bz2file is a Python library for reading and writing bzip2-compressed
+files.  It contains a drop-in replacement for the I/O interface in the
+standard library's @code{bz2} module, including features from the latest
+development version of CPython that are not available in older releases.")
+    (license asl2.0)
+    (properties `((python2-variant . ,(delay python2-bz2file))))))
+
+(define-public python2-bz2file
+  (let ((base (package-with-python2
+               (strip-python2-variant python-bz2file))))
+    (package
+      (inherit base)
+      (native-inputs
+       `(("python2-setuptools" ,python2-setuptools))))))
+
 (define-public python-cysignals
   (package
     (name "python-cysignals")
-- 
2.5.0

[PATCH v2 03/10] gnu: Add python-pytest-pep8.

[Ben Woodcroft]

* gnu/packages/python.scm (python-pytest-pep8, python2-pytest-pep8): New
variables.
---
 gnu/packages/python.scm | 60 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 60 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index c07dae6..b1a4969 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -8714,6 +8714,66 @@ development version of CPython that are not available in older releases.")
       (native-inputs
        `(("python2-setuptools" ,python2-setuptools))))))
 
+(define-public python-pytest-pep8
+  (package
+    (name "python-pytest-pep8")
+    (version "1.0.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pytest-pep8" version))
+       (sha256
+        (base32
+         "06032agzhw1i9d9qlhfblnl3dw5hcyxhagn7b120zhrszbjzfbh3"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'remove-failing-test
+           ;; Ignore the known test failure.
+           ;; https://bitbucket.org/pytest-dev/pytest-pep8/issues/8/test-failure
+           (lambda _
+             (substitute* "test_pep8.py"
+               (("^def test_ok_verbose") "def dont_run"))
+             #t))
+         (add-after 'install 'post-install-check
+           ;; 'setup.py test' does not run tests
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (setenv "PYTHONPATH"
+                       (string-append
+                        (getenv "PYTHONPATH")
+                        ":"
+                        out
+                        "/lib/python"
+                        (string-take (string-take-right
+                                      (assoc-ref inputs "python") 5) 3)
+                        "/site-packages"))
+               (zero?
+                (system*
+                 (string-append out "/bin/py.test") "test_pep8.py"))))))))
+    (propagated-inputs
+     `(("python-pytest-cache", python-pytest-cache)
+       ("python-pytest" ,python-pytest)
+       ("python-pep8" ,python-pep8)))
+    (home-page "https://bitbucket.org/pytest-dev/pytest-pep8")
+    (synopsis "Pytest plugin to check PEP8 requirements")
+    (description
+     "Pytest-pep8 is a py.test plugin for efficiently checking compliance to
+the PEP8 style guide.  If you type @code{py.test --pep8} every file ending in
+@code{.py} will be discovered and PEP8-checked, starting from the command line
+arguments.")
+    (license license:expat)
+    (properties `((python2-variant . ,(delay python2-pytest-pep8))))))
+
+(define-public python2-pytest-pep8
+  (let ((base (package-with-python2
+               (strip-python2-variant python-pytest-pep8))))
+    (package
+      (inherit base)
+      (native-inputs
+       `(("python2-setuptools" ,python2-setuptools))))))
+
 (define-public python-cysignals
   (package
     (name "python-cysignals")
-- 
2.5.0

[PATCH v2 04/10] gnu: Add python-pytest-flakes.

[Ben Woodcroft]

* gnu/packages/python.scm (python-pytest-flakes,
python2-pytest-flakes): New variables.
---
 gnu/packages/python.scm | 45 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index b1a4969..4175fad 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -8774,6 +8774,51 @@ arguments.")
       (native-inputs
        `(("python2-setuptools" ,python2-setuptools))))))
 
+(define-public python-pytest-flakes
+  (package
+    (name "python-pytest-flakes")
+    (version "1.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pytest-flakes" version))
+       (sha256
+        (base32
+         "0flag3n33kbhyjrhzmq990rvg4yb8hhhl0i48q9hw0ll89jp28lw"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'post-install-check
+           ;; 'setup.py test' does not run tests
+           (lambda _
+             (zero? (system* "py.test" "test_flakes.py")))))))
+    (native-inputs
+     `(("python-pytest-pep8" ,python-pytest-pep8)))
+    (propagated-inputs
+     `(("python-pytest-cache" ,python-pytest-cache)
+       ("python-pytest" ,python-pytest)
+       ("python-pyflakes" ,python-pyflakes)))
+    (home-page
+     "https://github.com/fschulze/pytest-flakes")
+    (synopsis "Pytest plugin to check source code with pyflakes")
+    (description
+     "Pytest-pyflakes is a py.test plugin for efficiently checking python source
+with pyflakes.  If you type @code{py.test --flakes} every file ending in
+@code{.py} will be discovered and run through pyflakes, starting from the
+command line arguments.")
+    (license license:expat)
+    (properties `((python2-variant . ,(delay python2-pytest-flakes))))))
+
+(define-public python2-pytest-flakes
+  (let ((base (package-with-python2
+                 (strip-python2-variant python-pytest-flakes))))
+    (package
+      (inherit base)
+      (native-inputs
+       `(,@(package-native-inputs base)
+         ("python2-setuptools" ,python2-setuptools))))))
+
 (define-public python-cysignals
   (package
     (name "python-cysignals")
-- 
2.5.0

[PATCH v2 05/10] gnu: Add python-future.

[Ben Woodcroft]

* gnu/packages/python.scm (python-future, python2-future): New
variables.
---
 gnu/packages/python.scm | 32 +++++++++++++++++++++++++++++++-
 1 file changed, 31 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 4175fad..28eebf1 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -8812,13 +8812,43 @@ command line arguments.")
 
 (define-public python2-pytest-flakes
   (let ((base (package-with-python2
-                 (strip-python2-variant python-pytest-flakes))))
+               (strip-python2-variant python-pytest-flakes))))
     (package
       (inherit base)
       (native-inputs
        `(,@(package-native-inputs base)
          ("python2-setuptools" ,python2-setuptools))))))
 
+(define-public python-future
+  (package
+    (name "python-future")
+    (version "0.15.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "future" version))
+       (sha256
+        (base32
+         "15wvcfzssc68xqnqi1dq4fhd0848hwi9jn42hxyvlqna40zijfrx"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #f)) ; Tests connect to the network
+    (home-page "http://python-future.org")
+    (synopsis "Single-source support for Python 3 and 2")
+    (description
+     "@code{python-future} is the missing compatibility layer between Python 2 and
+Python 3.  It allows you to use a single, clean Python 3.x-compatible codebase
+to support both Python 2 and Python 3 with minimal overhead.")
+    (license license:expat)
+    (properties `((python2-variant . ,(delay python2-future))))))
+
+(define-public python2-future
+  (let ((base (package-with-python2
+               (strip-python2-variant python-future))))
+    (package
+      (inherit base)
+      (native-inputs `(("python2-setuptools" ,python2-setuptools))))))
+
 (define-public python-cysignals
   (package
     (name "python-cysignals")
-- 
2.5.0

[PATCH v2 06/10] gnu: Add python-cachecontrol.

[Ben Woodcroft]

* gnu/packages/python.scm (python-cachecontrol, python2-cachecontrol):
New variables.
---
 gnu/packages/python.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 28eebf1..ccd4a28 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -8849,6 +8849,37 @@ to support both Python 2 and Python 3 with minimal overhead.")
       (inherit base)
       (native-inputs `(("python2-setuptools" ,python2-setuptools))))))
 
+(define-public python-cachecontrol
+  (package
+    (name "python-cachecontrol")
+    (version "0.11.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "CacheControl" version))
+       (sha256
+        (base32
+         "15bn8xll6z15h0zqhfjy1n8dn8p0fcb4m0rhnfanq63z7r2wpprp"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-requests" ,python-requests)
+       ("python-lockfile" ,python-lockfile)))
+    (home-page "https://github.com/ionrock/cachecontrol")
+    (synopsis "httplib2 caching for requests")
+    (description "CacheControl is a port of the caching algorithms in httplib2
+for use with requests session object.  It was written because httplib2's
+better support for caching is often mitigated by its lack of threadsafety.
+The same is true of requests in terms of caching.")
+    (license asl2.0)
+    (properties `((python2-variant . ,(delay python2-cachecontrol))))))
+
+(define-public python2-cachecontrol
+  (let ((base (package-with-python2
+               (strip-python2-variant python-cachecontrol))))
+    (package
+      (inherit base)
+      (native-inputs `(("python2-setuptools" ,python2-setuptools))))))
+
 (define-public python-cysignals
   (package
     (name "python-cysignals")
-- 
2.5.0

[PATCH v2 07/10] gnu: python-tornado: Use 'python2-variant'.

[Ben Woodcroft]

* gnu/packages/python.scm (python-tornado)[properties]: New field.
(python2-tornado): Build with 'strip-python2-variant'.
---
 gnu/packages/python.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index ccd4a28..ee2cab8 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -4936,10 +4936,12 @@ originally developed at FriendFeed.  By using non-blocking network I/O,
 Tornado can scale to tens of thousands of open connections, making it ideal
 for long polling, WebSockets, and other applications that require a long-lived
 connection to each user.")
-    (license asl2.0)))
+    (license asl2.0)
+    (properties `((python2-variant . ,(delay python2-tornado))))))
 
 (define-public python2-tornado
-  (let ((tornado (package-with-python2 python-tornado)))
+  (let ((tornado (package-with-python2
+                  (strip-python2-variant python-tornado))))
     (package (inherit tornado)
       (inputs
        `(("python2-backport-ssl-match-hostname"
-- 
2.5.0

[PATCH v2 08/10] gnu: python-ipython: Use 'python2-variant'.

[Ben Woodcroft]

* gnu/packages/python.scm (python-ipython)[properties]: New field.
(python2-ipython): Use 'strip-python2-variant'.
[inputs, propagated-inputs]: Do not redefine inherited values.
---
 gnu/packages/python.scm | 26 +++++++++-----------------
 1 file changed, 9 insertions(+), 17 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index ee2cab8..40d28b1 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -4359,29 +4359,21 @@ without using the configuration machinery.")
 Powerful interactive shells, a browser-based notebook, support for interactive
 data visualization, embeddable interpreters and tools for parallel
 computing.")
-    (license bsd-3)))
+    (license bsd-3)
+    (properties `((python2-variant . ,(delay python2-ipython))))))
 
 (define-public python2-ipython
-  (let ((ipython (package-with-python2 python-ipython)))
+  (let ((base (package-with-python2
+               (strip-python2-variant python-ipython))))
     (package
-      (inherit ipython)
+      (inherit base)
       ;; FIXME: some tests are failing
-      (arguments
-       `(#:tests? #f ,@(package-arguments ipython)))
-      ;; Make sure we use custom python2-NAME packages.
       ;; FIXME: add pyreadline once available.
-      (propagated-inputs
-       `(("python2-terminado" ,python2-terminado)
-         ,@(alist-delete "python-terminado"
-                         (package-propagated-inputs ipython))))
+      (arguments
+       `(#:tests? #f ,@(package-arguments base)))
       (inputs
-       `(("python2-jsonschema" ,python2-jsonschema)
-         ("python2-mock" ,python2-mock)
-         ("python2-matplotlib" ,python2-matplotlib)
-         ("python2-numpy" ,python2-numpy)
-         ("python2-requests" ,python2-requests)
-         ,@(fold alist-delete (package-inputs ipython)
-                 '("python-jsonschema" "python-matplotlib" "python-numpy" "python-requests")))))))
+       `(("python2-mock" ,python2-mock)
+         ,@(package-inputs base))))))
 
 (define-public python-isodate
   (package
-- 
2.5.0

[PATCH v2 09/10] gnu: Add python-natsort.

[Ben Woodcroft]

* gnu/packages/python.scm (python-natsort, python2-natsort): New
variables.
---
 gnu/packages/python.scm | 41 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 40d28b1..8ae7566 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -8874,6 +8874,47 @@ The same is true of requests in terms of caching.")
       (inherit base)
       (native-inputs `(("python2-setuptools" ,python2-setuptools))))))
 
+(define-public python-natsort
+  (package
+    (name "python-natsort")
+    (version "4.0.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "natsort" version))
+       (sha256
+        (base32
+         "0f8q66pyczgy1cm3nh8rkh7hgl9h49zx9r06mivg4y5sbzla6sy7"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("python-pytest" ,python-pytest)
+       ("python-pytest-flakes" ,python-pytest-flakes)
+       ("python-pytest-cov" ,python-pytest-cov)
+       ("python-pytest-cache" ,python-pytest-cache)
+       ("python-hypothesis" ,python-hypothesis)
+       ("python-pytest-pep8", python-pytest-pep8)))
+    (home-page "https://github.com/SethMMorton/natsort")
+    (synopsis "Sort lists naturally")
+    (description "When you try to sort a list of strings that contain numbers,
+the normal python sort algorithm sorts lexicographically, so you might not get
+the results that you expect.  @code{natsort} provides a function
+@code{natsorted} that helps sort lists 'naturally', either as real
+numbers (i.e. signed/unsigned floats or ints), or as versions.")
+    (license license:expat)
+    (properties `((python2-variant . ,(delay python2-natsort))))))
+
+(define-public python2-natsort
+  (let ((base (package-with-python2
+               (strip-python2-variant python-natsort))))
+    (package
+      (inherit base)
+      (native-inputs
+       (append (package-native-inputs base)
+               `(("python2-mock" ,python2-mock)
+                 ("python2-pathlib" ,python2-pathlib)
+                 ("python2-enum34" ,python2-enum34)
+                 ("python2-setuptools" ,python2-setuptools)))))))
+
 (define-public python-cysignals
   (package
     (name "python-cysignals")
-- 
2.5.0

[PATCH v2 10/10] gnu: Add python-scikit-bio.

[Ben Woodcroft]

* gnu/packages/python.scm (python-scikit-bio, python2-scikit-bio):
New variables.
---
 gnu/packages/bioinformatics.scm | 84 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 84 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 899ce1c..fa67f3b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3339,6 +3339,90 @@ optimize the sequencing depth, or to screen multiple libraries to avoid low
 complexity samples.")
     (license license:gpl3+)))
 
+(define-public python-scikit-bio
+  (package
+    (name "python-scikit-bio")
+    (version "0.4.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "scikit-bio" version))
+       (sha256
+        (base32
+         "06nrcgfz6c3jb2dnaf1wnvx3dyww94p454c4126gvcvfgv6scczy"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; Install procedure installs extraneous binaries.
+         (add-after 'install 'remove-extraneous-files
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin")))
+               (delete-file-recursively bin))
+             #t))
+         ;; Tests are intended to be run using 'make test' not 'setup.py
+         ;; test', but there are many test failures anyway
+         ;; e.g. https://github.com/biocore/scikit-bio/issues/1308.  Run a
+         ;; simple import test instead.
+         (delete 'check)
+         (add-after 'install 'check-after-install
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (setenv "PYTHONPATH"
+                     (string-append
+                      (getenv "PYTHONPATH")
+                      ":" (assoc-ref outputs "out")
+                      "/lib/python"
+                      (string-take (string-take-right
+                                    (assoc-ref inputs "python") 5) 3)
+                      "/site-packages"))
+             (zero?
+              (with-directory-excursion "ci"
+                (system*
+                 "python"
+                 "-c"
+                 (string-append "import matplotlib; "
+                                "matplotlib.use(\"Agg\"); "
+                                "import skbio")))))))))
+    (native-inputs
+     `(("python-nose" ,python-nose)
+       ("python-pep8" ,python-pep8)
+       ("python-flake8" ,python-flake8)
+       ("python-dateutil" ,python-dateutil-2)))
+    (propagated-inputs
+     `(("python-bz2file" ,python-bz2file)
+       ("python-lockfile" ,python-lockfile)
+       ("python-cachecontrol" ,python-cachecontrol)
+       ("python-contextlib2" ,python-contextlib2)
+       ("python-decorator" ,python-decorator)
+       ("python-future" ,python-future)
+       ("python-ipython" ,python-ipython)
+       ("python-matplotlib" ,python-matplotlib)
+       ("python-natsort" ,python-natsort)
+       ("python-numpy" ,python-numpy)
+       ("python-pandas" ,python-pandas)
+       ("python-scipy" ,python-scipy)
+       ("python-six" ,python-six)))
+    (home-page "http://scikit-bio.org")
+    (synopsis "Resources for bioinformatics")
+    (description
+     "Scikit-bio is a library for working with biological data in Python,
+providing data structures, algorithms and educational resources.  It defines
+Python packages for biological sequences, alignments, tree, visualisation,
+diversity calculation and file I/O.")
+    (license license:bsd-3)
+    (properties `((python2-variant . ,(delay python2-scikit-bio))))))
+
+(define-public python2-scikit-bio
+  (let ((base (package-with-python2
+               (strip-python2-variant python-scikit-bio))))
+    (package
+      (inherit base)
+      (native-inputs
+       (append (package-native-inputs base)
+               `(("python2-setuptools" ,python2-setuptools)
+                 ("python2-mock" ,python2-mock)))))))
+
 (define-public sra-tools
   (package
     (name "sra-tools")
-- 
2.5.0

Re: [PATCH 08/10] gnu: python-ipython: Use 'python2-variant'.

[Ben Woodcroft]

On 22/04/16 01:14, Ricardo Wurmus wrote:
> Ben Woodcroft <donttrustben@gmail.com> writes:
>
>> * gnu/packages/python.scm (python-ipython)[properties]: New field.
>> (python2-ipython): Use 'strip-python2-variant'.
> The commit message should mention the changes to the “inputs” and
> “propagated-input” fields because it isn’t obvious whether the list of
> inputs actually stays the same.

I still struggle with commit messages, does this sound OK as it is in v2?

     gnu: python-ipython: Use 'python2-variant'.

     * gnu/packages/python.scm (python-ipython)[properties]: New field.
     (python2-ipython): Use 'strip-python2-variant'.
     [inputs, propagated-inputs]: Do not redefine inherited values.

Thanks,
ben

Re: [PATCH 08/10] gnu: python-ipython: Use 'python2-variant'.

[Ben Woodcroft]

On 22/04/16 01:14, Ricardo Wurmus wrote:
> Ben Woodcroft <donttrustben@gmail.com> writes:
>
>> * gnu/packages/python.scm (python-ipython)[properties]: New field.
>> (python2-ipython): Use 'strip-python2-variant'.
> The commit message should mention the changes to the “inputs” and
> “propagated-input” fields because it isn’t obvious whether the list of
> inputs actually stays the same.

I still struggle with commit messages, does this sound OK as it is in v2?

     gnu: python-ipython: Use 'python2-variant'.

     * gnu/packages/python.scm (python-ipython)[properties]: New field.
     (python2-ipython): Use 'strip-python2-variant'.
     [inputs, propagated-inputs]: Do not redefine inherited values.

Thanks,
ben

Re: [PATCH 02/10] gnu: Add python-bz2file.

[Ben Woodcroft]

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Hi Hartmut,

Thanks for your comments.

On 22/04/16 04:24, Hartmut Goebel wrote:
> Am 21.04.2016 um 15:21 schrieb Ben Woodcroft:
>> +    (arguments
>> +     `(#:phases
>> +       (modify-phases %standard-phases
>> +         ;; python setup.py test does not work as of 0.98
>> +         ;; but there is only the one test file
>> +         (replace 'check
>> +           (lambda _ (zero? (system* "python" "test_bz2file.py")))))))
>
> I wonder if this is actually working. The python-3 package does not 
> include "python" (except if this was changed the last days).

As I understand, python-wrapper, which provides python as a symlink to 
python3, as a native input. And, it works.

>> +    (description
>> +     "Bz2file is a Python library for reading and writing bzip2-compressed
>> +files.  It contains a drop-in replacement for the file interface in the
>
> I do not understand "replacement for the file interface". If this like 
> the "zipfile" module? 

Better now?

     (description
      "Bz2file is a Python library for reading and writing bzip2-compressed
files.  It contains a drop-in replacement for the I/O interface in the
standard library's @code{bz2} module, including features from the latest
development version of CPython that are not available in older releases.")


ta,
ben

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Re: [PATCH 03/10] gnu: Add python-pytest-pep8.

[Ben Woodcroft]

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On 22/04/16 04:26, Hartmut Goebel wrote:
> Am 21.04.2016 um 15:21 schrieb Ben Woodcroft:
>> +         (add-after 'install 'post-install-check
>> +           ;; 'setup.py test' does not run tests
>> +           (lambda* (#:key inputs outputs #:allow-other-keys)
>> +             (let ((out (assoc-ref outputs "out")))
>> +               (setenv "PYTHONPATH"
>> +                       (string-append
>> +                        (getenv "PYTHONPATH")
>> +                        ":"
>> +                        out
>> +                        "/lib/python"
>> +                        (string-take (string-take-right
>> +                                      (assoc-ref inputs "python") 5) 3)
>> +                        "/site-packages"))
>> +               (zero?
>> +                (system*
>> +                 (string-append out "/bin/py.test") "test_pep8.py"))))))))
>
> Have you tried if the tests are run when moving the test-file into a 
> new subdirectory "tests/"? This would result in much less code.

I'm afraid not. I'm no pythonista, but these tests are written for 
pytest, not in the more vanilla unittest which setup.py expects, I 
think. I tested moving it to tests out as you suggest, to no avail.

Thanks,
ben

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Re: [PATCH v2 03/10] gnu: Add python-pytest-pep8.

[Efraim Flashner]

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On Sun, Apr 24, 2016 at 11:06:17PM +1000, Ben Woodcroft wrote:
> * gnu/packages/python.scm (python-pytest-pep8, python2-pytest-pep8): New
> variables.
> ---
>  gnu/packages/python.scm | 60 +++++++++++++++++++++++++++++++++++++++++++++++++
>  1 file changed, 60 insertions(+)
> 
> diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
> index c07dae6..b1a4969 100644
> --- a/gnu/packages/python.scm
> +++ b/gnu/packages/python.scm
> @@ -8714,6 +8714,66 @@ development version of CPython that are not available in older releases.")
>        (native-inputs
>         `(("python2-setuptools" ,python2-setuptools))))))
>  
> +(define-public python-pytest-pep8
> +  (package
> +    (name "python-pytest-pep8")
> +    (version "1.0.6")
> +    (source
> +     (origin
> +       (method url-fetch)
> +       (uri (pypi-uri "pytest-pep8" version))
> +       (sha256
> +        (base32
> +         "06032agzhw1i9d9qlhfblnl3dw5hcyxhagn7b120zhrszbjzfbh3"))))
> +    (build-system python-build-system)
> +    (arguments
> +     `(#:phases
> +       (modify-phases %standard-phases
> +         (add-before 'build 'remove-failing-test
> +           ;; Ignore the known test failure.
> +           ;; https://bitbucket.org/pytest-dev/pytest-pep8/issues/8/test-failure
> +           (lambda _
> +             (substitute* "test_pep8.py"
> +               (("^def test_ok_verbose") "def dont_run"))
> +             #t))
> +         (add-after 'install 'post-install-check
> +           ;; 'setup.py test' does not run tests
> +           (lambda* (#:key inputs outputs #:allow-other-keys)
> +             (let ((out (assoc-ref outputs "out")))
> +               (setenv "PYTHONPATH"
> +                       (string-append
> +                        (getenv "PYTHONPATH")
> +                        ":"
> +                        out
> +                        "/lib/python"

some of the previous lines should be combined into one line

> +                        (string-take (string-take-right
> +                                      (assoc-ref inputs "python") 5) 3)
> +                        "/site-packages"))
> +               (zero?
> +                (system*
> +                 (string-append out "/bin/py.test") "test_pep8.py"))))))))
> +    (propagated-inputs
> +     `(("python-pytest-cache", python-pytest-cache)
> +       ("python-pytest" ,python-pytest)
> +       ("python-pep8" ,python-pep8)))

Are you sure all of these need to be propagated?

> +    (home-page "https://bitbucket.org/pytest-dev/pytest-pep8")
> +    (synopsis "Pytest plugin to check PEP8 requirements")
> +    (description
> +     "Pytest-pep8 is a py.test plugin for efficiently checking compliance to
> +the PEP8 style guide.  If you type @code{py.test --pep8} every file ending in
> +@code{.py} will be discovered and PEP8-checked, starting from the command line
> +arguments.")
> +    (license license:expat)
> +    (properties `((python2-variant . ,(delay python2-pytest-pep8))))))
> +
> +(define-public python2-pytest-pep8
> +  (let ((base (package-with-python2
> +               (strip-python2-variant python-pytest-pep8))))
> +    (package
> +      (inherit base)
> +      (native-inputs
> +       `(("python2-setuptools" ,python2-setuptools))))))
> +
>  (define-public python-cysignals
>    (package
>      (name "python-cysignals")
> -- 
> 2.5.0
> 
> 

-- 
Efraim Flashner   <efraim@flashner.co.il>   אפרים פלשנר
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Re: [PATCH v2 03/10] gnu: Add python-pytest-pep8.

[Ben Woodcroft]

On 25/04/16 03:04, Efraim Flashner wrote:
> On Sun, Apr 24, 2016 at 11:06:17PM +1000, Ben Woodcroft wrote:
[..]
>> +             (let ((out (assoc-ref outputs "out")))
>> +               (setenv "PYTHONPATH"
>> +                       (string-append
>> +                        (getenv "PYTHONPATH")
>> +                        ":"
>> +                        out
>> +                        "/lib/python"
> some of the previous lines should be combined into one line

I think this is a matter of style, but I've amended it to below, which I 
assume is OK - I have no strong opinions.

+               (setenv
+                "PYTHONPATH"
+                (string-append (getenv "PYTHONPATH")":" out "/lib/python"
+                               (string-take (string-take-right
+                                      (assoc-ref inputs "python") 5) 3)
+                               "/site-packages"))

>
>> +                        (string-take (string-take-right
>> +                                      (assoc-ref inputs "python") 5) 3)
>> +                        "/site-packages"))
>> +               (zero?
>> +                (system*
>> +                 (string-append out "/bin/py.test") "test_pep8.py"))))))))
>> +    (propagated-inputs
>> +     `(("python-pytest-cache", python-pytest-cache)
>> +       ("python-pytest" ,python-pytest)
>> +       ("python-pep8" ,python-pep8)))
> Are you sure all of these need to be propagated?

That's what the install_requires in setup.py is telling me.

Thanks,
ben

Re: [PATCH v2 03/10] gnu: Add python-pytest-pep8.

[Ben Woodcroft]

On 25/04/16 03:04, Efraim Flashner wrote:
> On Sun, Apr 24, 2016 at 11:06:17PM +1000, Ben Woodcroft wrote:
[..]
>> +           ;; 'setup.py test' does not run tests
>> +           (lambda* (#:key inputs outputs #:allow-other-keys)
>> +             (let ((out (assoc-ref outputs "out")))
>> +               (setenv "PYTHONPATH"
>> +                       (string-append
>> +                        (getenv "PYTHONPATH")
>> +                        ":"
>> +                        out
>> +                        "/lib/python"
> some of the previous lines should be combined into one line

I think this is a matter of style, but I've amended it to below, which I 
assume is OK - I have no strong opinions.

+               (setenv
+                "PYTHONPATH"
+                (string-append (getenv "PYTHONPATH")":" out "/lib/python"
+                               (string-take (string-take-right
+                                      (assoc-ref inputs "python") 5) 3)
+                               "/site-packages"))

[..]

>> +    (propagated-inputs
>> +     `(("python-pytest-cache", python-pytest-cache)
>> +       ("python-pytest" ,python-pytest)
>> +       ("python-pep8" ,python-pep8)))
> Are you sure all of these need to be propagated?

That's what the install_requires in setup.py is telling me.

[..]

Thanks,
ben

Re: [PATCH v2 03/10] gnu: Add python-pytest-pep8.

[Ricardo Wurmus]

Ben Woodcroft <donttrustben@gmail.com> writes:

>>> +    (propagated-inputs
>>> +     `(("python-pytest-cache", python-pytest-cache)
>>> +       ("python-pytest" ,python-pytest)
>>> +       ("python-pep8" ,python-pep8)))
>> Are you sure all of these need to be propagated?
>
> That's what the install_requires in setup.py is telling me.

Doesn’t this mean that these packages are only needed at build time?
Could they not be made native-inputs then?

~~ Ricardo

Re: [PATCH v2 03/10] gnu: Add python-pytest-pep8.

[Ben Woodcroft]

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On 25/04/16 18:43, Ricardo Wurmus wrote:
> Ben Woodcroft <donttrustben@gmail.com> writes:
>
>>>> +    (propagated-inputs
>>>> +     `(("python-pytest-cache", python-pytest-cache)
>>>> +       ("python-pytest" ,python-pytest)
>>>> +       ("python-pep8" ,python-pep8)))
>>> Are you sure all of these need to be propagated?
>> That's what the install_requires in setup.py is telling me.
> Doesn’t this mean that these packages are only needed at build time?
> Could they not be made native-inputs then?
|
I don't believe so.

http://pythonhosted.org/setuptools/setuptools.html#new-and-changed-setup-keywords

 >install_requires|
>    A string or list of strings specifying what other  distributions need to be installed when this one is.

ben

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Re: [PATCH v2 03/10] gnu: Add python-pytest-pep8.

[Leo Famulari]

On Mon, Apr 25, 2016 at 10:36:54PM +1000, Ben Woodcroft wrote:
> On 25/04/16 18:43, Ricardo Wurmus wrote:
> >Ben Woodcroft <donttrustben@gmail.com> writes:
> >
> >>>>+    (propagated-inputs
> >>>>+     `(("python-pytest-cache", python-pytest-cache)
> >>>>+       ("python-pytest" ,python-pytest)
> >>>>+       ("python-pep8" ,python-pep8)))
> >>>Are you sure all of these need to be propagated?
> >>That's what the install_requires in setup.py is telling me.
> >Doesn’t this mean that these packages are only needed at build time?
> >Could they not be made native-inputs then?
> |
> I don't believe so.
> 
> http://pythonhosted.org/setuptools/setuptools.html#new-and-changed-setup-keywords
> 
> >install_requires|
> >   A string or list of strings specifying what other  distributions need to be installed when this one is.

This seems like an unusual case, since the package in question appears
to be a build-time tool. So, it would make sense to have things like
python-pytest available during python-pytest-pep8's run-time.

If we have a use case for python-pytest-pep8, it could be worthwhile to
see if it will work without propagating these anyways; I've noticed some
Python packages have a way to link to non-propagated-inputs.

Re: [PATCH v2 01/10] gnu: Add python2-pytest-cache.

[Leo Famulari]

On Sun, Apr 24, 2016 at 11:06:15PM +1000, Ben Woodcroft wrote:
> * gnu/packages/python.scm (python-pytest-cache)[properties]: New field.
> (python2-pytest-cache): New variable.

LGTM!

Re: [PATCH v2 02/10] gnu: Add python-bz2file.

[Leo Famulari]

On Sun, Apr 24, 2016 at 11:06:16PM +1000, Ben Woodcroft wrote:
> * gnu/packages/python.scm (python-bz2file, python2-bz2file): New
> variables.

LGTM!

Re: [PATCH v2 05/10] gnu: Add python-future.

[Leo Famulari]

On Sun, Apr 24, 2016 at 11:06:19PM +1000, Ben Woodcroft wrote:
> * gnu/packages/python.scm (python-future, python2-future): New
> variables.

Thanks!

> +    (arguments
> +     `(#:tests? #f)) ; Tests connect to the network

Is it only a handful of tests? Can we disable those tests?

If not, it's worth an upstream bug report, in my opinion.

One way or another, I don't think this should block packaging if
python-future's seems to work when used by another package.

Re: [PATCH v2 04/10] gnu: Add python-pytest-flakes.

[Leo Famulari]

On Sun, Apr 24, 2016 at 11:06:18PM +1000, Ben Woodcroft wrote:
> * gnu/packages/python.scm (python-pytest-flakes,
> python2-pytest-flakes): New variables.

Thanks!

> +    (arguments
> +     `(#:phases
> +       (modify-phases %standard-phases
> +         (add-after 'install 'post-install-check
> +           ;; 'setup.py test' does not run tests
> +           (lambda _
> +             (zero? (system* "py.test" "test_flakes.py")))))))

Does it work if you replace the check phase? Or does the check phase do
something worthwhile? Or do the tests only work after install? Can you
answer this in the code comment? ;)

> +    (native-inputs
> +     `(("python-pytest-pep8" ,python-pytest-pep8)))
> +    (propagated-inputs
> +     `(("python-pytest-cache" ,python-pytest-cache)
> +       ("python-pytest" ,python-pytest)
> +       ("python-pyflakes" ,python-pyflakes)))

I think this could get messy in practice. If, during the build of some
other package, multiple packages try to propagate pytest, we just have
to hope that whichever pytest passes the conflict resolution mechanism
works as expected.

Can you check if it still works when these are "regular" inputs?

Re: [PATCH v2 06/10] gnu: Add python-cachecontrol.

[Leo Famulari]

On Sun, Apr 24, 2016 at 11:06:20PM +1000, Ben Woodcroft wrote:
> * gnu/packages/python.scm (python-cachecontrol, python2-cachecontrol):
> New variables.

LGTM!

Re: [PATCH v2 07/10] gnu: python-tornado: Use 'python2-variant'.

[Leo Famulari]

On Sun, Apr 24, 2016 at 11:06:21PM +1000, Ben Woodcroft wrote:
> * gnu/packages/python.scm (python-tornado)[properties]: New field.
> (python2-tornado): Build with 'strip-python2-variant'.

Thanks for doing this "housekeeping"!

Re: [PATCH v2 09/10] gnu: Add python-natsort.

[Leo Famulari]

On Sun, Apr 24, 2016 at 11:06:23PM +1000, Ben Woodcroft wrote:
> * gnu/packages/python.scm (python-natsort, python2-natsort): New
> variables.

Thanks!

> +    (synopsis "Sort lists naturally")

How about "Sort lists naturally rather than lexicographically"?

> +(define-public python2-natsort
> +  (let ((base (package-with-python2
> +               (strip-python2-variant python-natsort))))
> +    (package
> +      (inherit base)
> +      (native-inputs
> +       (append (package-native-inputs base)
> +               `(("python2-mock" ,python2-mock)
> +                 ("python2-pathlib" ,python2-pathlib)
> +                 ("python2-enum34" ,python2-enum34)
> +                 ("python2-setuptools" ,python2-setuptools)))))))

Is it possible to use the technique used in 59f151ec54? I think it's
best if all variants of this type are written the same way.

Re: [PATCH v2 10/10] gnu: Add python-scikit-bio.

[Leo Famulari]

On Sun, Apr 24, 2016 at 11:06:24PM +1000, Ben Woodcroft wrote:
> * gnu/packages/python.scm (python-scikit-bio, python2-scikit-bio):
> New variables.

Thanks!

> +    (arguments
> +     `(#:phases
> +       (modify-phases %standard-phases
> +         ;; Install procedure installs extraneous binaries.
> +         (add-after 'install 'remove-extraneous-files
> +           (lambda* (#:key outputs #:allow-other-keys)
> +             (let* ((out (assoc-ref outputs "out"))
> +                    (bin (string-append out "/bin")))
> +               (delete-file-recursively bin))
> +             #t))

That's interesting. How are they extraneous? Would nobody want to use
them?

> +         ;; Tests are intended to be run using 'make test' not 'setup.py
> +         ;; test', but there are many test failures anyway
> +         ;; e.g. https://github.com/biocore/scikit-bio/issues/1308.  Run a
> +         ;; simple import test instead.
> +         (delete 'check)
> +         (add-after 'install 'check-after-install

Are the tests broken, or does scikit-bio simply not work with the
current version of pandas?

More context:
https://github.com/biocore/scikit-bio/pull/1325

> +(define-public python2-scikit-bio
> +  (let ((base (package-with-python2
> +               (strip-python2-variant python-scikit-bio))))
> +    (package
> +      (inherit base)
> +      (native-inputs
> +       (append (package-native-inputs base)
> +               `(("python2-setuptools" ,python2-setuptools)
> +                 ("python2-mock" ,python2-mock)))))))

Same suggestion as for python-natsort.

Re: [PATCH v2 08/10] gnu: python-ipython: Use 'python2-variant'.

[Leo Famulari]

On Sun, Apr 24, 2016 at 11:06:22PM +1000, Ben Woodcroft wrote:
> * gnu/packages/python.scm (python-ipython)[properties]: New field.
> (python2-ipython): Use 'strip-python2-variant'.
> [inputs, propagated-inputs]: Do not redefine inherited values.

Thanks, LGTM!

proper Python inputs (was: gnu: Add python-pytest-pep8.)

[Hartmut Goebel]

Am 25.04.2016 um 20:19 schrieb Leo Famulari:
> This seems like an unusual case, since the package in question appears
> to be a build-time tool. So, it would make sense to have things like
> python-pytest available during python-pytest-pep8's run-time.

> If we have a use case for python-pytest-pep8, it could be worthwhile
> to see if it will work without propagating these anyways; I've noticed
> some Python packages have a way to link to non-propagated-inputs. 

Reading this makes me *totally* confused about how to package Python for
Guix. I think, we should enhance the Guix Python Packaging guide to
clarify thinks for all.

1. Fact: If some Python package lists another package in
"install_requires", then this other Python package is required to run.
In a non Guix-environment, pip would install these other package, too.

2. Until 5 minutes ago I thought, that adding these other packages as
"normal" inputs is enough. But then I found that quite a bunch of
packages are using "propagated-inputs". So I tried to find out, what the
difference is:

  - "normal" inputs get added to PYTHONPATH via the .pth mechanism.

     Example: guix package -i python-execnet puts only
"execnet-1.4.1-py3.4.egg" into site-packages, plus
"python-execnet-1.4.1.pth", which adds the required package via a link
to "/gnu/store/....python-apipkg-1.4/..."

 - "Propagated" inputs are all linked into site-packages

    Example: guix package -i python-zope-interface puts zope-interface
and zope-event into site-packages.

 So this is not much of a difference: In both cases all required inputs
will be available in PYTHONPATH at run-time and can be imported.

3. But anyhow: Trouble is ahead: If some package aaa has a normal input
"zzz@1.2", while package bbb as normal input "zzz@1.1" and package ccc
as propagated input "zzz@1.3", we will end up with this in site-packages:

   - aaa.pth adding path to zzz@1.2
   - bbb.pth adding path to zzz@1.1
   - zzz-1.3.egg

  Which package "zzz" gets imported is somewhat arbitrary [2].

Is this intended? Did I miss something?

IMHO we should clarify his behavior and then bring all existing Python
packages in line and  document it in the manual.


[1]
<https://python-packaging-user-guide.readthedocs.org/en/latest/distributing/?highlight=install_requires#install-requires>

[2] Not exactly, it depends on the lexical order of the filenames, but
this is implementation-dependent and AFAIK not documented.

-- 
Regards
Hartmut Goebel

| Hartmut Goebel          | h.goebel@crazy-compilers.com               |
| www.crazy-compilers.com | compilers which you thought are impossible |

Re: proper Python inputs (was: gnu: Add python-pytest-pep8.)

[Ricardo Wurmus]

Hartmut Goebel <h.goebel@crazy-compilers.com> writes:

> Am 25.04.2016 um 20:19 schrieb Leo Famulari:
>> This seems like an unusual case, since the package in question appears
>> to be a build-time tool. So, it would make sense to have things like
>> python-pytest available during python-pytest-pep8's run-time.
>
>> If we have a use case for python-pytest-pep8, it could be worthwhile
>> to see if it will work without propagating these anyways; I've noticed
>> some Python packages have a way to link to non-propagated-inputs. 
>
> Reading this makes me *totally* confused about how to package Python for
> Guix. I think, we should enhance the Guix Python Packaging guide to
> clarify thinks for all.
>
> 1. Fact: If some Python package lists another package in
> "install_requires", then this other Python package is required to run.
> In a non Guix-environment, pip would install these other package, too.
>
> 2. Until 5 minutes ago I thought, that adding these other packages as
> "normal" inputs is enough. But then I found that quite a bunch of
> packages are using "propagated-inputs". So I tried to find out, what the
> difference is:
>
>   - "normal" inputs get added to PYTHONPATH via the .pth mechanism.
>
>      Example: guix package -i python-execnet puts only
> "execnet-1.4.1-py3.4.egg" into site-packages, plus
> "python-execnet-1.4.1.pth", which adds the required package via a link
> to "/gnu/store/....python-apipkg-1.4/..."
>
>  - "Propagated" inputs are all linked into site-packages
>
>     Example: guix package -i python-zope-interface puts zope-interface
> and zope-event into site-packages.
>
>  So this is not much of a difference: In both cases all required inputs
> will be available in PYTHONPATH at run-time and can be imported.
>
> 3. But anyhow: Trouble is ahead: If some package aaa has a normal input
> "zzz@1.2", while package bbb as normal input "zzz@1.1" and package ccc
> as propagated input "zzz@1.3", we will end up with this in site-packages:
>
>    - aaa.pth adding path to zzz@1.2
>    - bbb.pth adding path to zzz@1.1
>    - zzz-1.3.egg
>
>   Which package "zzz" gets imported is somewhat arbitrary [2].
>
> Is this intended? Did I miss something?

It’s not so easy as “pth” files aren’t necessarily evaluated.  Usually
we propagate inputs that need to be available at runtime.

This often causes problems here at work when people installed
“python2-numpy” a couple of months ago and then install “miso” which
propagates “python2-numpy”.  There are then at least two variants of
numpy in the profile leading to many collisions.

We’ve previously discussed alternatives to propagation:

    http://lists.gnu.org/archive/html/guix-devel/2016-02/msg00810.html

But so far there haven’t been any patch-ready solutions.  I’d really
like to fix this, though, as it’s uncomfortable to have to tell users to
either use manifests (thereby upgrading all of their applications in
their profile before installing something new) or to use separate
profiles for Python stuff.

~~ Ricardo