[PATCH 0/2]: Add biom-format.

[PATCH 0/2]: Add biom-format.

[Ben Woodcroft]

Thanks in advance.  I'm not 100% on whether this should just be called 'biom' or 'biom-format'. I figured it'd be more consistent amongst Python 2 & 3 to be 'python-biom-format' and 'python2-biom-format', but I'm open to ideas.

Thanks. ben

[PATCH 1/2] gnu: Add python-pyqi.

[Ben Woodcroft]

* gnu/packages/python.scm (python-pyqi, python2-pyqi): New variables.
---
 gnu/packages/python.scm | 48 ++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 8ae7566..2436a1f 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -8626,6 +8626,54 @@ GnuPG encryption, and more.  It also supports management of Amazon's
 CloudFront content delivery network.")
     (license gpl2+)))
 
+(define-public python-pyqi
+  (package
+    (name "python-pyqi")
+    (version "0.3.2")
+    (source
+     (origin
+       (method url-fetch)
+       ;; Use GitHub as source because PyPI archive does not contain tests.
+       (uri (string-append "https://github.com/biocore/pyqi/archive/"
+                           version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "085gi3xr9q1py2nl96ry9fnb20kba5h1zkxzqrkd5dl3g7xdwvlw"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'remove-version-requirement
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "setup.py"
+               (("if ver not in \\['2.7', '3.3'\\]:")
+                (string-append
+                 "if ver not in ['2.7', '3.3', '"
+                 (string-take (string-take-right
+                               (assoc-ref inputs "python") 5) 3)
+                 "']:")))))
+         (replace 'check
+           (lambda _ (zero? (system* "nosetests")))))))
+    (native-inputs
+     `(("python-nose" ,python-nose)))
+    (home-page "http://bipy.github.io/pyqi")
+    (synopsis "Wrapping commands in multiple interfaces")
+    (description "pyqi is a Python framework designed to support wrapping
+general commands in multiple types of interfaces, including at the command
+line, HTML and API levels. A @dfn{command} is a class that takes some inputs,
+performs some function, and produces some outputs.  An @dfn{interface} is a
+light wrapper around that command that makes it accessible to users.")
+    (license bsd-3)
+    (properties `((python2-variant . ,(delay python2-pyqi))))))
+
+(define-public python2-pyqi
+  (let ((base (package-with-python2 (strip-python2-variant python-pyqi))))
+    (package
+      (inherit base)
+      (native-inputs `(("python2-setuptools" ,python2-setuptools)
+                       ,@(package-native-inputs base))))))
+
 (define-public python-pkgconfig
   (package
     (name "python-pkgconfig")
-- 
2.5.0

Re: [PATCH 1/2] gnu: Add python-pyqi.

[Leo Famulari]

On Sun, Apr 24, 2016 at 10:27:39PM +1000, Ben Woodcroft wrote:
> * gnu/packages/python.scm (python-pyqi, python2-pyqi): New variables.

Thanks for the patches!

> +    (source
> +     (origin
> +       (method url-fetch)
> +       ;; Use GitHub as source because PyPI archive does not contain tests.
> +       (uri (string-append "https://github.com/biocore/pyqi/archive/"
> +                           version ".tar.gz"))

I've had some success asking upstream authors to start releasing their
test suites on PyPi. YMMV. This is not a "blocker".

> +    (arguments
> +     `(#:phases
> +       (modify-phases %standard-phases
> +         (add-before 'build 'remove-version-requirement
> +           (lambda* (#:key inputs #:allow-other-keys)
> +             (substitute* "setup.py"
> +               (("if ver not in \\['2.7', '3.3'\\]:")
> +                (string-append
> +                 "if ver not in ['2.7', '3.3', '"
> +                 (string-take (string-take-right
> +                               (assoc-ref inputs "python") 5) 3)
> +                 "']:")))))

I assume everything works with this change :)

> +    (home-page "http://bipy.github.io/pyqi")

This is what PyPi calls the home page, but I get 404. Did it work for
you, meaning I am experiencing a transient error? Or should we use
something else?

Re: [PATCH 1/2] gnu: Add python-pyqi.

[Ricardo Wurmus]

Leo Famulari <leo@famulari.name> writes:

> On Sun, Apr 24, 2016 at 10:27:39PM +1000, Ben Woodcroft wrote:
>> * gnu/packages/python.scm (python-pyqi, python2-pyqi): New variables.
>
> Thanks for the patches!
>
>> +    (source
>> +     (origin
>> +       (method url-fetch)
>> +       ;; Use GitHub as source because PyPI archive does not contain tests.
>> +       (uri (string-append "https://github.com/biocore/pyqi/archive/"
>> +                           version ".tar.gz"))
>
> I've had some success asking upstream authors to start releasing their
> test suites on PyPi. YMMV. This is not a "blocker".
>
>> +    (arguments
>> +     `(#:phases
>> +       (modify-phases %standard-phases
>> +         (add-before 'build 'remove-version-requirement
>> +           (lambda* (#:key inputs #:allow-other-keys)
>> +             (substitute* "setup.py"
>> +               (("if ver not in \\['2.7', '3.3'\\]:")
>> +                (string-append
>> +                 "if ver not in ['2.7', '3.3', '"
>> +                 (string-take (string-take-right
>> +                               (assoc-ref inputs "python") 5) 3)
>> +                 "']:")))))
>
> I assume everything works with this change :)
>
>> +    (home-page "http://bipy.github.io/pyqi")
>
> This is what PyPi calls the home page, but I get 404. Did it work for
> you, meaning I am experiencing a transient error? Or should we use
> something else?

It’s a 404 for me too.  Maybe change this to

    https://github.com/biocore/pyqi

?

~~ Ricardo

[PATCH 2/2] gnu: Add python-biom-format.

[Ben Woodcroft]

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

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fa67f3b..7207503 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -325,6 +325,46 @@ pybedtools extends BEDTools by offering feature-level manipulations from with
 Python.")
     (license license:gpl2+)))
 
+(define-public python-biom-format
+  (package
+   (name "python-biom-format")
+   (version "2.1.5")
+   (source
+    (origin
+     (method url-fetch)
+     ;; Use GitHub as source because PyPI distribution does not contain
+     ;; test data: https://github.com/biocore/biom-format/issues/693
+     (uri (string-append "https://github.com/biocore/biom-format/archive/"
+                         version ".tar.gz"))
+     (file-name (string-append name "-" version ".tar.gz"))
+     (sha256
+      (base32
+       "1n25w3p1rixbpac8iysmzcja6m4ip5r6sz19l8y6wlwi49hxn278"))))
+   (build-system python-build-system)
+   (propagated-inputs
+    `(("python-numpy" ,python-numpy)
+      ("python-pyqi" ,python-pyqi)
+      ("python-scipy" ,python-scipy)
+      ("python-future" ,python-future)
+      ("python-click" ,python-click)
+      ("python-h5py" ,python-h5py)))
+   (home-page "http://www.biom-format.org")
+   (synopsis "Biological Observation Matrix (BIOM) format utilities")
+   (description
+    "The BIOM file format is designed to be a general-use format for
+representing counts of observations e.g. operational taxonomic units, KEGG
+orthology groups or lipid types, in one or more biological samples
+e.g. microbiome samples, genomes, metagenomes.")
+   (license license:bsd-3)
+   (properties `((python2-variant . ,(delay python2-biom-format))))))
+
+(define-public python2-biom-format
+  (let ((base (package-with-python2 (strip-python2-variant python-biom-format))))
+    (package
+      (inherit base)
+      (native-inputs `(("python2-setuptools" ,python2-setuptools)
+                       ,@(package-native-inputs base))))))
+
 (define-public bioperl-minimal
   (let* ((inputs `(("perl-module-build" ,perl-module-build)
                    ("perl-data-stag" ,perl-data-stag)
-- 
2.5.0

Re: [PATCH 2/2] gnu: Add python-biom-format.

[Leo Famulari]

On Sun, Apr 24, 2016 at 10:27:40PM +1000, Ben Woodcroft wrote:
> * gnu/packages/bioinformatics.scm (python-biom-format,
> python2-biom-format): New variables.

LGTM! I have no opinion no the name; this seems reasonable.

> ---
>  gnu/packages/bioinformatics.scm | 40 ++++++++++++++++++++++++++++++++++++++++
>  1 file changed, 40 insertions(+)
> 
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index fa67f3b..7207503 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -325,6 +325,46 @@ pybedtools extends BEDTools by offering feature-level manipulations from with
>  Python.")
>      (license license:gpl2+)))
>  
> +(define-public python-biom-format
> +  (package
> +   (name "python-biom-format")
> +   (version "2.1.5")
> +   (source
> +    (origin
> +     (method url-fetch)
> +     ;; Use GitHub as source because PyPI distribution does not contain
> +     ;; test data: https://github.com/biocore/biom-format/issues/693
> +     (uri (string-append "https://github.com/biocore/biom-format/archive/"
> +                         version ".tar.gz"))
> +     (file-name (string-append name "-" version ".tar.gz"))
> +     (sha256
> +      (base32
> +       "1n25w3p1rixbpac8iysmzcja6m4ip5r6sz19l8y6wlwi49hxn278"))))
> +   (build-system python-build-system)
> +   (propagated-inputs
> +    `(("python-numpy" ,python-numpy)
> +      ("python-pyqi" ,python-pyqi)
> +      ("python-scipy" ,python-scipy)
> +      ("python-future" ,python-future)
> +      ("python-click" ,python-click)
> +      ("python-h5py" ,python-h5py)))
> +   (home-page "http://www.biom-format.org")
> +   (synopsis "Biological Observation Matrix (BIOM) format utilities")
> +   (description
> +    "The BIOM file format is designed to be a general-use format for
> +representing counts of observations e.g. operational taxonomic units, KEGG
> +orthology groups or lipid types, in one or more biological samples
> +e.g. microbiome samples, genomes, metagenomes.")
> +   (license license:bsd-3)
> +   (properties `((python2-variant . ,(delay python2-biom-format))))))
> +
> +(define-public python2-biom-format
> +  (let ((base (package-with-python2 (strip-python2-variant python-biom-format))))
> +    (package
> +      (inherit base)
> +      (native-inputs `(("python2-setuptools" ,python2-setuptools)
> +                       ,@(package-native-inputs base))))))
> +
>  (define-public bioperl-minimal
>    (let* ((inputs `(("perl-module-build" ,perl-module-build)
>                     ("perl-data-stag" ,perl-data-stag)
> -- 
> 2.5.0
> 
> 

Re: [PATCH 0/2]: Add biom-format.

[Ben Woodcroft]

On 24/04/16 22:27, Ben Woodcroft wrote:
> Thanks in advance.  I'm not 100% on whether this should just be called 'biom' or 'biom-format'. I figured it'd be more consistent amongst Python 2 & 3 to be 'python-biom-format' and 'python2-biom-format', but I'm open to ideas.

Ah, I realise now this will require the python-scikit-bio patch series 
being applied first, sorry.