[PATCH 2/2] gnu: multiqc: Update to 0.8.

[PATCH 2/2] gnu: multiqc: Update to 0.8.

[Ra]

[-- Attachment #1: Type: text/plain, Size: 927 bytes --]

[PATCH] gnu: multiqc: Update to 0.8.
is [PATCH 1/2] for this message, sorry for the mistake.
Running multiqc without [PATCH 2/2] systems say that matplotlib requires
nose>=0.11.1, so I added it to the propagated inputs.

---
 gnu/packages/bioinformatics.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioinformatics.scm
b/gnu/packages/bioinformatics.scm
index 43bf701..1167df5 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7863,7 +7863,8 @@ replacement for strverscmp.")
        ("python-pyyaml" ,python-pyyaml)
        ("python-click" ,python-click)
        ("python-matplotlib" ,python-matplotlib)
-       ("python-numpy" ,python-numpy)))
+       ("python-numpy" ,python-numpy)
+       ("python-nose" ,python-nose )))
     (home-page "http://multiqc.info")
     (synopsis "Aggregate bioinformatics analysis reports")
     (description
--
1.9.1

[-- Attachment #2: Type: text/html, Size: 1412 bytes --]

Fwd: Re: [PATCH 2/2] gnu: multiqc: Update to 0.8.

[Ben Woodcroft]

[-- Attachment #1: Type: text/plain, Size: 913 bytes --]

Hi Raoul,

Thanks for the patches.

On 19/12/16 07:36, Ra wrote:
> [PATCH] gnu: multiqc: Update to 0.8.
> is [PATCH 1/2] for this message, sorry for the mistake.
> Running multiqc without [PATCH 2/2] systems say that matplotlib
> requires nose>=0.11.1, so I added it to the propagated inputs.
I notice that 0.9 is out too, so I tried updating to that version. I
also added "python-nose" as a native-input rather than a
propagated-input since it is only used at build time.

However, the tests fail with this error:

FileNotFoundError: [Errno 2] No such file or directory: 'git'

The check phase is still successful so it doesn't stop - this problem is
being fixed by others. I added a patch to ignore the FileNotFoundError,
but then after all that the tests fail. Would you mind investigating
further, perhaps by raising an issue on the multiqc GitHub? My efforts
so far are in the attached patch.

Thanks, ben.


[-- Attachment #2: 0001-gnu-multiqc-Update-to-0.9.patch --]
[-- Type: text/x-patch, Size: 4127 bytes --]

From d1c70ba0a701a31469dcae2b1a0efb624e5409d1 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Fri, 23 Dec 2016 22:13:33 +1000
Subject: [PATCH] gnu: multiqc: Update to 0.9.

* gnu/packages/bioinformatics.scm (multiqc): Update to 0.9.
[origin]: Add patch.
[arguments]: Run tests.
[native-inputs]: Add python-nose, multiqc-test-data.
* gnu/packages/patches/multiqc-fix-git-subprocess-error.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
---
 gnu/local.mk                                       |  1 +
 gnu/packages/bioinformatics.scm                    | 28 ++++++++++++++++++++--
 .../patches/multiqc-fix-git-subprocess-error.patch | 15 ++++++++++++
 3 files changed, 42 insertions(+), 2 deletions(-)
 create mode 100644 gnu/packages/patches/multiqc-fix-git-subprocess-error.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index ee8f1e591..bde8bc235 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -727,6 +727,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/mpc123-initialize-ao.patch		\
   %D%/packages/patches/mplayer2-theora-fix.patch		\
   %D%/packages/patches/module-init-tools-moduledir.patch	\
+  %D%/packages/patches/multiqc-fix-git-subprocess-error.patch	\
   %D%/packages/patches/mumps-build-parallelism.patch		\
   %D%/packages/patches/mupdf-build-with-openjpeg-2.1.patch	\
   %D%/packages/patches/mupen64plus-ui-console-notice.patch	\
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 912941e11..0cbbce1fc 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7853,15 +7853,39 @@ replacement for strverscmp.")
 (define-public multiqc
   (package
     (name "multiqc")
-    (version "0.6")
+    (version "0.9")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "multiqc" version))
        (sha256
         (base32
-         "0avw11h63ldpxy5pizc3wl1wa01ha7q10wb240nggsjz3jaqvyiy"))))
+         "12gs1jw2jrxrij529rnl5kaqxfcqn15yzcsggxkfhdx634ml0cny"))
+       (patches (search-patches "multiqc-fix-git-subprocess-error.patch"))))
     (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let ((data (assoc-ref inputs "multiqc-test-data")))
+               (setenv "PYTHONPATH"
+                       (string-append (getcwd) ":" (getenv "PYTHONPATH")))
+               (with-directory-excursion data
+                 (zero? (system* "python3" "-munittest" "discover")))))))))
+    (native-inputs
+     `(("python-nose" ,python-nose)
+       ("multiqc-test-data"
+        ,(let ((commit "32bf18b4d7c46496ae50bfaf4c94a9df3afd0491"))
+           (origin
+             (method git-fetch)
+             (uri (git-reference
+                   (url "https://github.com/ewels/MultiQC_TestData.git")
+                   (commit commit)))
+             (file-name (string-append "multiqc-test-data" commit "-checkout"))
+             (sha256
+              (base32
+               "079pcr6j2nk0v238qwsslgk480rv82xwsjyy4lf6v48l6zj4llm0")))))))
     (propagated-inputs
      `(("python-jinja2" ,python-jinja2)
        ("python-simplejson" ,python-simplejson)
diff --git a/gnu/packages/patches/multiqc-fix-git-subprocess-error.patch b/gnu/packages/patches/multiqc-fix-git-subprocess-error.patch
new file mode 100644
index 000000000..50807e2b7
--- /dev/null
+++ b/gnu/packages/patches/multiqc-fix-git-subprocess-error.patch
@@ -0,0 +1,15 @@
+Without this patch, the incorrect exception is caught when 'git' is not in PATH.
+
+diff --git a/multiqc/utils/config.py b/multiqc/utils/config.py
+index 01fa554..4a11793 100755
+--- a/multiqc/utils/config.py
++++ b/multiqc/utils/config.py
+@@ -28,7 +28,7 @@ try:
+     git_hash = subprocess.check_output(['git', 'rev-parse', 'HEAD'], stderr=subprocess.STDOUT)
+     git_hash_short = git_hash[:7]
+     version = '{} ({})'.format(version, git_hash_short)
+-except subprocess.CalledProcessError:
++except (subprocess.CalledProcessError, FileNotFoundError):
+     pass
+ os.chdir(cwd)
+ 
-- 
2.11.0

Re: Re: [PATCH 2/2] gnu: multiqc: Update to 0.8.

[Ra]

[-- Attachment #1: Type: text/plain, Size: 1123 bytes --]

Hi Ben,
thanks I will investigate. Does it mean that multiqc is in stand by for now
?

On Fri, Dec 23, 2016 at 2:30 PM Ben Woodcroft <b.woodcroft@uq.edu.au> wrote:

> Hi Raoul,
>
> Thanks for the patches.
>
> On 19/12/16 07:36, Ra wrote:
> > [PATCH] gnu: multiqc: Update to 0.8.
> > is [PATCH 1/2] for this message, sorry for the mistake.
> > Running multiqc without [PATCH 2/2] systems say that matplotlib
> > requires nose>=0.11.1, so I added it to the propagated inputs.
> I notice that 0.9 is out too, so I tried updating to that version. I
> also added "python-nose" as a native-input rather than a
> propagated-input since it is only used at build time.
>
> However, the tests fail with this error:
>
> FileNotFoundError: [Errno 2] No such file or directory: 'git'
>
> The check phase is still successful so it doesn't stop - this problem is
> being fixed by others. I added a patch to ignore the FileNotFoundError,
> but then after all that the tests fail. Would you mind investigating
> further, perhaps by raising an issue on the multiqc GitHub? My efforts
> so far are in the attached patch.
>
> Thanks, ben.
>
>

[-- Attachment #2: Type: text/html, Size: 1943 bytes --]

Re: [PATCH 2/2] gnu: multiqc: Update to 0.8.

[Ben Woodcroft]

Hi Raoul,


On 26/12/16 20:45, Ra wrote:
> Hi Ben,
> thanks I will investigate. Does it mean that multiqc is in stand by 
> for now ?

It would be ideal I think to add tests, and because they are failing it 
would be good to know why. I thought the easiest simply to ask the 
maintainers if they knew why the tests were failing:
https://github.com/ewels/MultiQC/issues/376

I also submitted the exception catching patch here, which we should add 
to our patch if we decide to keep it before pushing our changes.
https://github.com/ewels/MultiQC/pull/377

I figure it makes sense to give them a week or two to respond, and 
reevaluate after that. I presume you have not observed any problems 
using multiqc after this update?
Thanks,
ben

Re: [PATCH 2/2] gnu: multiqc: Update to 0.8.

[Ra]

[-- Attachment #1: Type: text/plain, Size: 1081 bytes --]

Hi Ben,
reading the comments from https://github.com/ewels/MultiQC/issues/376
it seems that in the upcoming release they will solve the problem.
Are we going to wait for the next v. 1.0 or include it now and update later
?

--
Ra

On Mon, Dec 26, 2016 at 1:18 PM Ben Woodcroft <b.woodcroft@uq.edu.au> wrote:

> Hi Raoul,
>
>
> On 26/12/16 20:45, Ra wrote:
> > Hi Ben,
> > thanks I will investigate. Does it mean that multiqc is in stand by
> > for now ?
>
> It would be ideal I think to add tests, and because they are failing it
> would be good to know why. I thought the easiest simply to ask the
> maintainers if they knew why the tests were failing:
> https://github.com/ewels/MultiQC/issues/376
>
> I also submitted the exception catching patch here, which we should add
> to our patch if we decide to keep it before pushing our changes.
> https://github.com/ewels/MultiQC/pull/377
>
> I figure it makes sense to give them a week or two to respond, and
> reevaluate after that. I presume you have not observed any problems
> using multiqc after this update?
> Thanks,
> ben
>

[-- Attachment #2: Type: text/html, Size: 2177 bytes --]

Re: [PATCH 2/2] gnu: multiqc: Update to 0.8.

[Ben Woodcroft]

[-- Attachment #1: Type: text/plain, Size: 1203 bytes --]

Hi Raoul,


On 28/12/16 23:13, Ra wrote:
> Hi Ben,
> reading the comments from https://github.com/ewels/MultiQC/issues/376
> it seems that in the upcoming release they will solve the problem.
> Are we going to wait for the next v. 1.0 or include it now and update 
> later ?

I just pushed an update to 0.9 as 
a29929b32caf9e437d18bdb0cd4d1b22bc096fed. I did not add nose as an input 
because the issue seems to be with matplotlib, not multiqc. 
Specifically, nose is listed in the 'requires.txt' file of matplotlib 
when should only be needed for testing.

So to test the updated package I ran
$ ./pre-inst-env guix environment --ad-hoc multiqc python python-nose 
glibc-locales -C --no-grafts --no-substitutes

[env] # LC_ALL=en_AU.UTF-8 LANG=en_AU.UTF-8 
GUIX_LOCPATH=/gnu/store/hyi7svs0ds79wrcg5l0nr36zzjikqj7i-glibc-locales-2.24/lib/locale/ 
multiqc -h

The use of click with python3 means that we must set locales or it will 
refuse to run. Please do tell if you find any issues with the update - 
I've not used this tool before so I only tested it superficially.
ben

PS. In future would you mind please bottom-posting your emails if 
possible? Around here, we've chosen a side of that debate :)

[-- Attachment #2: Type: text/html, Size: 2060 bytes --]