GNU bug report logs - #46955
Add python-sparse, Update python-cooler

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Date: Sat, 6 Mar 2021 01:54:41 +0100

Message #8 received at 46955 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <46955 <at> debbugs.gnu.org>
Cc: rekado <at> elephly.net, Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Subject: [PATCH 1/2] gnu: Add python-sparse.
Date: Sat, 6 Mar 2021 01:57:02 +0100

* gnu/packages/python-xyz.scm (python-sparse): New variable.
---
 gnu/packages/python-xyz.scm | 41 ++++++++++++++++++++++++++++++++++++-
 1 file changed, 40 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index fbc9ad688d..b5274c39a9 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -67,7 +67,7 @@
 ;;; Copyright © 2019, 2020 Giacomo Leidi <goodoldpaul <at> autistici.org>
 ;;; Copyright © 2019 Wiktor Żelazny <wzelazny <at> vurv.cz>
 ;;; Copyright © 2019, 2020 Tanguy Le Carrour <tanguy <at> bioneland.org>
-;;; Copyright © 2019 Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de>
+;;; Copyright © 2019, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de>
 ;;; Copyright © 2020 Riku Viitanen <riku.viitanen <at> protonmail.com>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba <at> kadziolka.net>
 ;;; Copyright © 2020 sirgazil <sirgazil <at> zoho.com>
@@ -4719,6 +4719,45 @@ objects.")
 (define-public python2-colormath
   (package-with-python2 python-colormath))
 
+(define-public python-sparse
+  (package
+    (name "python-sparse")
+    (version "0.11.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "sparse" version))
+       (sha256
+        (base32
+         "0kw6ha83gk0dymayrxhh16xxk7aykiyiz3ksxdzj6hhjr3dkap5w"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-numba" ,python-numba)
+       ("python-numpy" ,python-numpy)
+       ("python-scipy" ,python-scipy)))
+    (native-inputs
+     `(("python-dask" ,python-dask)
+       ("python-pytest" ,python-pytest)
+       ("python-pytest-black" ,python-pytest-black)
+       ("python-pytest-cov" ,python-pytest-cov)))
+    (home-page "https://github.com/pydata/sparse/")
+    (synopsis "Library for multi-dimensional sparse arrays")
+    (description
+     "This package implements sparse arrays of arbitrary dimension on top of
+@code{numpy} and @code{scipy.sparse}.  Sparse array is a matrix in which most
+of the elements are zero.  @code{python-sparse} generalizes the
+@code{scipy.sparse.coo_matrix} and @code{scipy.sparse.dok_matrix} layouts, but
+extends beyond just rows and columns to an arbitrary number of dimensions.
+Additionally, this project maintains compatibility with the
+@code{numpy.ndarray} interface rather than the @code{numpy.matrix} interface
+used in @code{scipy.sparse}.  These differences make this project useful in
+certain situations where @code{scipy.sparse} matrices are not well suited, but
+it should not be considered a full replacement.  It lacks layouts that are not
+easily generalized like @dfn{compressed sparse row/column}(CSR/CSC) and
+depends on @code{scipy.sparse} for some computations.")
+    ;;https://github.com/pydata/sparse/blob/master/LICENSE
+    (license license:bsd-3)))
+
 (define-public python-spectra
   (package
     (name "python-spectra")
-- 
2.30.1

Message #11 received at 46955 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <46955 <at> debbugs.gnu.org>
Cc: rekado <at> elephly.net, Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Subject: [PATCH 2/2] gnu: python-cooler: Update to 0.8.10.
Date: Sat, 6 Mar 2021 01:57:03 +0100

* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.8.10/
---
 gnu/packages/bioinformatics.scm | 21 ++++++++++++---------
 1 file changed, 12 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6d21e14360..bc31d50e54 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13636,35 +13636,38 @@ fasta subsequences.")
 (define-public python-cooler
   (package
     (name "python-cooler")
-    (version "0.8.7")
+    (version "0.8.10")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "cooler" version))
        (sha256
         (base32
-         "01g6gqix9ba27sappz6nfyiwabzrlf8i5fn8kwcz8ra356cq9crp"))))
+          "1hi9anwz8b9p9wigzc5hypnwm6a4ikvlv69ixy3ki8939ngb1sj3"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-asciitree" ,python-asciitree)
-       ("python-biopython" ,python-biopython)
        ("python-click" ,python-click)
        ("python-cytoolz" ,python-cytoolz)
-       ("python-dask" ,python-dask)
        ("python-h5py" ,python-h5py)
        ("python-multiprocess" ,python-multiprocess)
        ("python-numpy" ,python-numpy)
        ("python-pandas" ,python-pandas)
        ("python-pyfaidx" ,python-pyfaidx)
        ("python-pypairix" ,python-pypairix)
-       ("python-pysam" ,python-pysam)
        ("python-pyyaml" ,python-pyyaml)
        ("python-scipy" ,python-scipy)
-       ("python-simplejson" ,python-simplejson)))
+       ("python-simplejson" ,python-simplejson)
+       ("python-six" ,python-six)))
     (native-inputs
-     `(("python-mock" ,python-mock)
-       ("python-pytest" ,python-pytest)))
-    (home-page "https://github.com/mirnylab/cooler")
+     `(("python-codecov" ,python-codecov)
+       ("python-dask" ,python-dask)     ;;unittest.runner.TextTestResult
+       ("python-mock" ,python-mock)
+       ("python-pytest" ,python-pytest)
+       ("python-pytest-cov" ,python-pytest-cov)
+       ("python-pytest-flake8" ,python-pytest-flake8)
+       ("python-sparse" ,python-sparse))) ;;unittest.runner.TextTestResult
+    (home-page "https://github.com/open2c/cooler")
     (synopsis "Sparse binary format for genomic interaction matrices")
     (description
      "Cooler is a support library for a sparse, compressed, binary persistent
-- 
2.30.1

Message #16 received at 46955 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Cc: 46955 <at> debbugs.gnu.org
Subject: Re: [PATCH 1/2] gnu: Add python-sparse.
Date: Thu, 01 Apr 2021 17:07:54 +0200

Hi Mădălin,

> * gnu/packages/python-xyz.scm (python-sparse): New variable.

Thanks for the patch!

> +    (native-inputs
> +     `(("python-dask" ,python-dask)
> +       ("python-pytest" ,python-pytest)
> +       ("python-pytest-black" ,python-pytest-black)
> +       ("python-pytest-cov" ,python-pytest-cov)))

In spite of the addition of all these test inputs the test suite is not
run:

--8<---------------cut here---------------start------------->8---
starting phase `check'
running "python setup.py" with command "test" and parameters ()
['numpy', 'scipy>=0.19', 'numba>=0.49']
['numpy', 'scipy>=0.19', 'numba>=0.49']
running test
running egg_info
writing sparse.egg-info/PKG-INFO
writing dependency_links to sparse.egg-info/dependency_links.txt
writing entry points to sparse.egg-info/entry_points.txt
writing requirements to sparse.egg-info/requires.txt
writing top-level names to sparse.egg-info/top_level.txt
reading manifest file 'sparse.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '*.html' under directory 'sparse'
no previously-included directories found matching 'docs/_build'
writing manifest file 'sparse.egg-info/SOURCES.txt'
running build_ext

----------------------------------------------------------------------
Ran 0 tests in 0.000s

OK
phase `check' succeeded after 1.5 seconds
--8<---------------cut here---------------end--------------->8---

Could you please take a look at this?

> +    ;;https://github.com/pydata/sparse/blob/master/LICENSE
> +    (license license:bsd-3)))

No need to include this comment.

-- 
Ricardo

Message #19 received at 46955 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Cc: 46955 <at> debbugs.gnu.org
Subject: Re: [PATCH 2/2] gnu: python-cooler: Update to 0.8.10.
Date: Thu, 01 Apr 2021 17:09:02 +0200

Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de> writes:

> * gnu/packages/bioinformatics.scm (python-cooler): Update to 0.8.10/

There’s a typo (“/” instead of “.”) and the changes to the
propagated-inputs, native-inputs, and home-page fields are not listed.

Could you please add them to the commit message?

Thanks!

-- 
Ricardo

Message #22 received at 46955 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Cc: 46955 <at> debbugs.gnu.org
Subject: Re: [PATCH 1/2] gnu: Add python-sparse.
Date: Thu, 01 Apr 2021 17:10:30 +0200

Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de> writes:

> * gnu/packages/python-xyz.scm (python-sparse): New variable.
[…]
> +(define-public python-sparse
> +  (package
> +    (name "python-sparse")
> +    (version "0.11.2")

“guix lint” tells me:

    python-sparse <at> 0.11.2: can be upgraded to 0.12.0

Is there a reason why you picked 0.11.2?  (Or did I just wait too long
to review your patch…?)

-- 
Ricardo

Message #25 received at 46955 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <46955 <at> debbugs.gnu.org>, Rekado Wurmus <rekado <at> elephly.net>
Subject: Re: [ext] bug#46955: Acknowledgement ((no subject))
Date: Fri, 4 Jun 2021 01:23:54 +0200

[Message part 1 (text/plain, inline)]

Hi guys,


Sorry for the delay!


I read all of Ricardo's comments and I made some changes to these patches.

I will send a new round of patches after this message because after I 
tried to run python tests for the cooler package there was a need for a 
new dependency.

Here are some short answers to Ricardo's comments/questions:

----------------------------------------------------------------------
Ran 0 tests in 0.000s

OK
phase `check' succeeded after 1.5 seconds
--8<---------------cut here---------------end--------------->8---

Could you please take a look at this?

I fixed that! Please check the new patch! Thanks!

“guix lint” tells me:

    python-sparse <at> 0.11.2: can be upgraded to 0.12.0

Is there a reason why you picked 0.11.2?  (Or did I just wait too long
to review your patch…?)

At that time only version 0.11.2 was available.


All the best

     Mădălin!


On 06.03.2021 01:55, GNU bug Tracking System wrote:
> Thank you for filing a new bug report with debbugs.gnu.org.
>
> This is an automatically generated reply to let you know your message
> has been received.
>
> Your message is being forwarded to the package maintainers and other
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-- 
System Administrator
Bioinformatics and Omics Data Science
BIMSB - MDC

[Message part 2 (text/html, inline)]

Message #28 received at 46955 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <46955 <at> debbugs.gnu.org>
Cc: rekado <at> elephly.net, Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Subject: [PATCH 1/3] gnu: Add python-sparse.
Date: Fri, 4 Jun 2021 01:25:01 +0200

* gnu/packages/python-xyz.scm(python-sparse): New variable.
---
 gnu/packages/python-xyz.scm | 48 ++++++++++++++++++++++++++++++++++++-
 1 file changed, 47 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index a5cc04edaf..35ce8d1cbe 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -67,7 +67,7 @@
 ;;; Copyright © 2019, 2020 Giacomo Leidi <goodoldpaul <at> autistici.org>
 ;;; Copyright © 2019 Wiktor Żelazny <wzelazny <at> vurv.cz>
 ;;; Copyright © 2019, 2020 Tanguy Le Carrour <tanguy <at> bioneland.org>
-;;; Copyright © 2019 Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de>
+;;; Copyright © 2019, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de>
 ;;; Copyright © 2020 Riku Viitanen <riku.viitanen <at> protonmail.com>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba <at> kadziolka.net>
 ;;; Copyright © 2020 sirgazil <sirgazil <at> zoho.com>
@@ -5132,6 +5132,52 @@ objects.")
 (define-public python2-colormath
   (package-with-python2 python-colormath))
 
+(define-public python-sparse
+  (package
+    (name "python-sparse")
+    (version "0.12.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "sparse" version))
+       (sha256
+        (base32
+         "05lmzckv69cvxavhdr36k803bgr5dl04cppglid1l880xswc759c"))))
+    (build-system python-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (add-installed-pythonpath inputs outputs)
+             (invoke "pytest" "-vv")
+             #t)))))
+    (propagated-inputs
+     `(("python-numba" ,python-numba)
+       ("python-numpy" ,python-numpy)
+       ("python-scipy" ,python-scipy)))
+    (native-inputs
+     `(("python-dask" ,python-dask)
+       ("python-pytest" ,python-pytest)
+       ("python-pytest-black" ,python-pytest-black)
+       ("python-pytest-cov" ,python-pytest-cov)))
+    (home-page "https://github.com/pydata/sparse/")
+    (synopsis "Library for multi-dimensional sparse arrays")
+    (description
+     "This package implements sparse arrays of arbitrary dimension on top of
+@code{numpy} and @code{scipy.sparse}.  Sparse array is a matrix in which most
+of the elements are zero.  @code{python-sparse} generalizes the
+@code{scipy.sparse.coo_matrix} and @code{scipy.sparse.dok_matrix} layouts, but
+extends beyond just rows and columns to an arbitrary number of dimensions.
+Additionally, this project maintains compatibility with the
+@code{numpy.ndarray} interface rather than the @code{numpy.matrix} interface
+used in @code{scipy.sparse}.  These differences make this project useful in
+certain situations where @code{scipy.sparse} matrices are not well suited, but
+it should not be considered a full replacement.  It lacks layouts that are not
+easily generalized like @dfn{compressed sparse row/column}(CSR/CSC) and
+depends on @code{scipy.sparse} for some computations.")
+    (license license:bsd-3)))
+
 (define-public python-spectra
   (package
     (name "python-spectra")
-- 
2.31.1

Message #31 received at 46955 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <46955 <at> debbugs.gnu.org>
Cc: rekado <at> elephly.net, Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Subject: [PATCH 2/3] gnu: Add python-ipytree.
Date: Fri, 4 Jun 2021 01:25:02 +0200

* gnu/packages/python-xyz.scm (python-ipytree): New variable.
---
 gnu/packages/python-xyz.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 35ce8d1cbe..f416e3a2a8 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -7568,6 +7568,32 @@ away.")
 (define-public python2-ipython-genutils
   (package-with-python2 python-ipython-genutils))
 
+(define-public python-ipytree
+  (package
+    (name "python-ipytree")
+    (version "0.2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "ipytree" version))
+       (sha256
+        (base32
+         "0ss64kxa4la50irf7vy3474f1p924pn4da5gmb02zvhn2x0pra2j"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("python-setuptools" ,python-setuptools)))
+    (propagated-inputs
+     `(("python-ipywidgets" ,python-ipywidgets)
+       ("python-jupyter-packaging" ,python-jupyter-packaging)))
+    (home-page "https://github.com/martinRenou/ipytree")
+    (synopsis "Tree widget using jsTree and Jupyter-widgets")
+    (description
+     "This package provides the possibility to create a tree using
+@code{Jupyter-widgets} protocol and @code{jsTree}.  @code{Jupyter-widgets} is a
+way to create an interactive @dfn{graphical user interface} (GUI) for a Jupyter
+notebook.  @code{JsTree} is a jquery plugin, that provides interactive trees.")
+    (license license:expat)))
+
 (define-public python-ipyparallel
   (package
     (name "python-ipyparallel")
-- 
2.31.1

Message #34 received at 46955 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <46955 <at> debbugs.gnu.org>
Cc: rekado <at> elephly.net, Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Subject: [PATCH 3/3] gnu: python-cooler: Update to 0.8.11.
Date: Fri, 4 Jun 2021 01:25:03 +0200

* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.8.11.
---
 gnu/packages/bioinformatics.scm | 39 ++++++++++++++++++++++++++++-----
 1 file changed, 33 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 94d15cc4c0..55e25ab486 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11591,15 +11591,35 @@ fasta subsequences.")
 (define-public python-cooler
   (package
     (name "python-cooler")
-    (version "0.8.7")
+    (version "0.8.11")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "cooler" version))
        (sha256
         (base32
-         "01g6gqix9ba27sappz6nfyiwabzrlf8i5fn8kwcz8ra356cq9crp"))))
+         "1i96fmpsimj4wrx51rxn8lw2gqxf5a2pvrj5rwdd6ivnm3pmhyrn"))))
     (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-tests
+           (lambda _
+             (substitute* "tests/test_create.py"
+              (("def test_roundtrip")
+                 (string-append "@pytest.mark.skip(reason=\"requires network "
+                                "access to genome.ucsc.edu\")\n"
+                                "def test_roundtrip")))
+             (substitute* "tests/test_util.py"
+              (("def test_fetch_chromsizes")
+                 (string-append "@pytest.mark.skip(reason=\"requires network "
+                                "access to genome.ucsc.edu\")\n"
+                                "def test_fetch_chromsizes")))
+            #t))
+         (replace 'check
+           (lambda _
+             (invoke "python" "-m" "pytest" "-v")
+            #t)))))
     (propagated-inputs
      `(("python-asciitree" ,python-asciitree)
        ("python-biopython" ,python-biopython)
@@ -11615,11 +11635,18 @@ fasta subsequences.")
        ("python-pysam" ,python-pysam)
        ("python-pyyaml" ,python-pyyaml)
        ("python-scipy" ,python-scipy)
-       ("python-simplejson" ,python-simplejson)))
+       ("python-simplejson" ,python-simplejson)
+       ("python-six" ,python-six)
+       ("python-sparse" ,python-sparse)))
     (native-inputs
-     `(("python-mock" ,python-mock)
-       ("python-pytest" ,python-pytest)))
-    (home-page "https://github.com/mirnylab/cooler")
+     `(("python-codecov" ,python-codecov)
+       ("python-ipytree" ,python-ipytree)
+       ("python-mock" ,python-mock)
+       ("python-pytest" ,python-pytest)
+       ("python-pytest-cov" ,python-pytest-cov)
+       ("python-pytest-flake8" ,python-pytest-flake8)))
+    ;;almost all the projects of the Mirnylab are moved under Open2C umbrella
+    (home-page "https://github.com/open2c/cooler")
     (synopsis "Sparse binary format for genomic interaction matrices")
     (description
      "Cooler is a support library for a sparse, compressed, binary persistent
-- 
2.31.1

Message #37 received at 46955 <at> debbugs.gnu.org (full text, mbox):

From: Maxime Devos <maximedevos <at> telenet.be>
To: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>, 46955 <at> debbugs.gnu.org
Cc: rekado <at> elephly.net
Subject: Re: [bug#46955] [PATCH 3/3] gnu: python-cooler: Update to 0.8.11.
Date: Sat, 05 Jun 2021 12:06:01 +0200

[Message part 1 (text/plain, inline)]

A comment about a build phase.

> [...]
> +         (replace 'check
> +           (lambda _
> +             (invoke "python" "-m" "pytest" "-v")
> +            #t)))))

This needs to be something like

+ (replace 'check
+   (lambda* (#:key tests? #:allow-other-keys)
+     (when tests?
+       (invoke "python" "-m" "pytest" "-v"))))

By respecting 'tests?', the --without-tests build transformation can be used.
(Try "guix build python-cooler --without-tests=python-cooler").
This can also be important for cross-compilation (dunno if it applies here
though).

Trailing #t are not required anymore. The warning that results if it is removed
will disappear once core-updates is merged.

Greetings,
Maxime.

[signature.asc (application/pgp-signature, inline)]

Message #40 received at 46955 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <46955 <at> debbugs.gnu.org>
Cc: rekado <at> elephly.net, Maxime Devos <maximedevos <at> telenet.be>
Subject: Re: [ext] Re: [bug#46955] [PATCH 3/3] gnu: python-cooler: Update to
 0.8.11.
Date: Sun, 6 Jun 2021 02:03:33 +0200

Hi Maxime,


Thanks for the explanation, now these things are clear to me!

I applied Maxime's advice and I have made some changes on two patches 
(python-sparse and python-cooler). Because of this reason, I will send 
again the whole series of patches and I will wait for a full review of them.

Thanks, Maxime!

On 05.06.2021 12:06, Maxime Devos wrote:
> A comment about a build phase.
>
>> [...]
>> +         (replace 'check
>> +           (lambda _
>> +             (invoke "python" "-m" "pytest" "-v")
>> +            #t)))))
> This needs to be something like
>
> + (replace 'check
> +   (lambda* (#:key tests? #:allow-other-keys)
> +     (when tests?
> +       (invoke "python" "-m" "pytest" "-v"))))
>
> By respecting 'tests?', the --without-tests build transformation can be used.
> (Try "guix build python-cooler --without-tests=python-cooler").
> This can also be important for cross-compilation (dunno if it applies here
> though).
>
> Trailing #t are not required anymore. The warning that results if it is removed
> will disappear once core-updates is merged.
>
> Greetings,
> Maxime.

-- 
System Administrator
Bioinformatics and Omics Data Science
BIMSB - MDC

Message #43 received at 46955 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <46955 <at> debbugs.gnu.org>
Cc: rekado <at> elephly.net, Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Subject: [PATCH 1/3] gnu: Add python-sparse.
Date: Sun, 6 Jun 2021 02:06:49 +0200

* gnu/packages/python-xyz.scm(python-sparse): New variable.
---
 gnu/packages/python-xyz.scm | 47 ++++++++++++++++++++++++++++++++++++-
 1 file changed, 46 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index b63c2852d5..a4fe31a01f 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -67,7 +67,7 @@
 ;;; Copyright © 2019, 2020 Giacomo Leidi <goodoldpaul <at> autistici.org>
 ;;; Copyright © 2019 Wiktor Żelazny <wzelazny <at> vurv.cz>
 ;;; Copyright © 2019, 2020 Tanguy Le Carrour <tanguy <at> bioneland.org>
-;;; Copyright © 2019 Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de>
+;;; Copyright © 2019, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de>
 ;;; Copyright © 2020 Riku Viitanen <riku.viitanen <at> protonmail.com>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba <at> kadziolka.net>
 ;;; Copyright © 2020 sirgazil <sirgazil <at> zoho.com>
@@ -5147,6 +5147,51 @@ objects.")
 (define-public python2-colormath
   (package-with-python2 python-colormath))
 
+(define-public python-sparse
+  (package
+    (name "python-sparse")
+    (version "0.12.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "sparse" version))
+       (sha256
+        (base32
+         "05lmzckv69cvxavhdr36k803bgr5dl04cppglid1l880xswc759c"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda* (#:key tests? #:allow-other-keys)
+             (when tests?
+               (invoke "python" "-m" "pytest" "-v")))))))
+    (propagated-inputs
+     `(("python-numba" ,python-numba)
+       ("python-numpy" ,python-numpy)
+       ("python-scipy" ,python-scipy)))
+    (native-inputs
+     `(("python-dask" ,python-dask)
+       ("python-pytest" ,python-pytest)
+       ("python-pytest-black" ,python-pytest-black)
+       ("python-pytest-cov" ,python-pytest-cov)))
+    (home-page "https://github.com/pydata/sparse/")
+    (synopsis "Library for multi-dimensional sparse arrays")
+    (description
+     "This package implements sparse arrays of arbitrary dimension on top of
+@code{numpy} and @code{scipy.sparse}.  Sparse array is a matrix in which most
+of the elements are zero.  @code{python-sparse} generalizes the
+@code{scipy.sparse.coo_matrix} and @code{scipy.sparse.dok_matrix} layouts, but
+extends beyond just rows and columns to an arbitrary number of dimensions.
+Additionally, this project maintains compatibility with the
+@code{numpy.ndarray} interface rather than the @code{numpy.matrix} interface
+used in @code{scipy.sparse}.  These differences make this project useful in
+certain situations where @code{scipy.sparse} matrices are not well suited, but
+it should not be considered a full replacement.  It lacks layouts that are not
+easily generalized like @dfn{compressed sparse row/column}(CSR/CSC) and
+depends on @code{scipy.sparse} for some computations.")
+    (license license:bsd-3)))
+
 (define-public python-spectra
   (package
     (name "python-spectra")
-- 
2.31.1

Message #46 received at 46955 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <46955 <at> debbugs.gnu.org>
Cc: rekado <at> elephly.net, Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Subject: [PATCH 2/3] gnu: Add python-ipytree.
Date: Sun, 6 Jun 2021 02:06:50 +0200

* gnu/packages/python-xyz.scm (python-ipytree): New variable.
---
 gnu/packages/python-xyz.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index a4fe31a01f..8ee43b1176 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -7582,6 +7582,32 @@ away.")
 (define-public python2-ipython-genutils
   (package-with-python2 python-ipython-genutils))
 
+(define-public python-ipytree
+  (package
+    (name "python-ipytree")
+    (version "0.2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "ipytree" version))
+       (sha256
+        (base32
+         "0ss64kxa4la50irf7vy3474f1p924pn4da5gmb02zvhn2x0pra2j"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("python-setuptools" ,python-setuptools)))
+    (propagated-inputs
+     `(("python-ipywidgets" ,python-ipywidgets)
+       ("python-jupyter-packaging" ,python-jupyter-packaging)))
+    (home-page "https://github.com/martinRenou/ipytree")
+    (synopsis "Tree widget using jsTree and Jupyter-widgets")
+    (description
+     "This package provides the possibility to create a tree using
+@code{Jupyter-widgets} protocol and @code{jsTree}.  @code{Jupyter-widgets} is a
+way to create an interactive @dfn{graphical user interface} (GUI) for a Jupyter
+notebook.  @code{JsTree} is a jquery plugin, that provides interactive trees.")
+    (license license:expat)))
+
 (define-public python-ipyparallel
   (package
     (name "python-ipyparallel")
-- 
2.31.1

Message #49 received at 46955 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <46955 <at> debbugs.gnu.org>
Cc: rekado <at> elephly.net, Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Subject: [PATCH 3/3] gnu: python-cooler: Update to 0.8.11.
Date: Sun, 6 Jun 2021 02:06:51 +0200

* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.8.11.
---
 gnu/packages/bioinformatics.scm | 38 +++++++++++++++++++++++++++------
 1 file changed, 32 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index dab097381a..988f663ceb 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11717,15 +11717,34 @@ fasta subsequences.")
 (define-public python-cooler
   (package
     (name "python-cooler")
-    (version "0.8.7")
+    (version "0.8.11")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "cooler" version))
        (sha256
         (base32
-         "01g6gqix9ba27sappz6nfyiwabzrlf8i5fn8kwcz8ra356cq9crp"))))
+         "1i96fmpsimj4wrx51rxn8lw2gqxf5a2pvrj5rwdd6ivnm3pmhyrn"))))
     (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-tests
+           (lambda _
+             (substitute* "tests/test_create.py"
+              (("def test_roundtrip")
+                 (string-append "@pytest.mark.skip(reason=\"requires network "
+                                "access to genome.ucsc.edu\")\n"
+                                "def test_roundtrip")))
+             (substitute* "tests/test_util.py"
+              (("def test_fetch_chromsizes")
+                 (string-append "@pytest.mark.skip(reason=\"requires network "
+                                "access to genome.ucsc.edu\")\n"
+                                "def test_fetch_chromsizes")))))
+         (replace 'check
+           (lambda* (#:key tests? #:allow-other-keys)
+             (when tests?
+               (invoke "python" "-m" "pytest" "-v")))))))
     (propagated-inputs
      `(("python-asciitree" ,python-asciitree)
        ("python-biopython" ,python-biopython)
@@ -11741,11 +11760,18 @@ fasta subsequences.")
        ("python-pysam" ,python-pysam)
        ("python-pyyaml" ,python-pyyaml)
        ("python-scipy" ,python-scipy)
-       ("python-simplejson" ,python-simplejson)))
+       ("python-simplejson" ,python-simplejson)
+       ("python-six" ,python-six)
+       ("python-sparse" ,python-sparse)))
     (native-inputs
-     `(("python-mock" ,python-mock)
-       ("python-pytest" ,python-pytest)))
-    (home-page "https://github.com/mirnylab/cooler")
+     `(("python-codecov" ,python-codecov)
+       ("python-ipytree" ,python-ipytree)
+       ("python-mock" ,python-mock)
+       ("python-pytest" ,python-pytest)
+       ("python-pytest-cov" ,python-pytest-cov)
+       ("python-pytest-flake8" ,python-pytest-flake8)))
+    ;;almost all the projects of the Mirnylab are moved under Open2C umbrella
+    (home-page "https://github.com/open2c/cooler")
     (synopsis "Sparse binary format for genomic interaction matrices")
     (description
      "Cooler is a support library for a sparse, compressed, binary persistent
-- 
2.31.1

Message #52 received at 46955 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Cc: 46955 <at> debbugs.gnu.org
Subject: Re: [PATCH 2/3] gnu: Add python-ipytree.
Date: Sun, 06 Jun 2021 08:23:20 +0200

Hi Mădălin,

> * gnu/packages/python-xyz.scm (python-ipytree): New variable.

ipytree contains minified JavaScript that should be built from 
source instead.  We can usually minify JavaScript sources with 
esbuild.

Could you please check if the sources for all minified JavaScript 
are included and then

1. delete all minified JavaScript in a source snippet
2. add a build phase to minify the JavaScript from readable source 
code?

Thanks!

-- 
Ricardo

Message #57 received at 46955-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Cc: 46955-done <at> debbugs.gnu.org
Subject: Re: [PATCH 3/3] gnu: python-cooler: Update to 0.8.11.
Date: Sun, 06 Jun 2021 08:36:35 +0200

Hi Mădălin,

thanks for the patches!

> * gnu/packages/bioinformatics.scm (python-cooler): Update to 
> 0.8.11.

I changed the commit message to mention all changes, including 
those in arguments, propagated-inputs, and native-inputs.

I disabled the one test that needs ipytree and removed ipytree 
from the inputs.

Pushed to the “master” branch with commit d1e7b50dbf (except 
ipytree).

(One more thing: please send updated patches with “git 
format-patch -v2” (or “git send-email -v2”), so that we can 
distinguish different versions of patch series automatically and 
download them in one batch.)

-- 
Ricardo

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