Add python-sparse, Update python-cooler

Done

Details

4 participants

Mădălin Ionel Patrașcu
Maxime Devos
Ricardo Wurmus
zimoun

Owner: unassigned

Submitted by: Mădălin Ionel Patrașcu

Severity: normal

Debbugs page

Mădălin Ionel Patrașcu wrote 4 years ago

(no subject)

Recipients:(address . guix-patches@gnu.org)

Message-ID:76dfa82e-53e2-c4fc-d002-df71f348cdc8@mdc-berlin.de

Mădălin Ionel Patrașcu wrote 4 years ago

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

Recipients:(address . 46955@debbugs.gnu.org)(address . rekado@elephly.net)(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)

Message-ID:20210306005703.25479-1-madalinionel.patrascu@mdc-berlin.de

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

---

gnu/packages/python-xyz.scm | 41 ++++++++++++++++++++++++++++++++++++-

1 file changed, 40 insertions(+), 1 deletion(-)

Toggle diff (61 lines)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@autistici.org>
 ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
 ;;; Copyright © 2019, 2020 Tanguy Le Carrour <tanguy@bioneland.org>
-;;; Copyright © 2019 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2019, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
 ;;; Copyright © 2020 Riku Viitanen <riku.viitanen@protonmail.com>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
 ;;; Copyright © 2020 sirgazil <sirgazil@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

Mădălin Ionel Patrașcu wrote 4 years ago

[PATCH 2/2] gnu: python-cooler: Update to 0.8.10.

Recipients:(address . 46955@debbugs.gnu.org)(address . rekado@elephly.net)(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)

Message-ID:20210306005703.25479-2-madalinionel.patrascu@mdc-berlin.de

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

---

gnu/packages/bioinformatics.scm | 21 ++++++++++++---------

1 file changed, 12 insertions(+), 9 deletions(-)

Toggle diff (54 lines)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

zimoun wrote 4 years ago

control message for bug #46955

Recipients:(address . control@debbugs.gnu.org)

Message-ID:867dlxi6nn.fsf@gmail.com

retitle 46955 Add python-sparse, Update python-cooler

quit

Ricardo Wurmus wrote 4 years ago

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

Recipients:(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)(address . 46955@debbugs.gnu.org)

Message-ID:878s622gc5.fsf@elephly.net

Hi Mădălin,

Toggle quote (2 lines)

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

Thanks for the patch!

Toggle quote (6 lines)

> + (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:

Toggle snippet (25 lines)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

Could you please take a look at this?

Toggle quote (3 lines)

> + ;;https://github.com/pydata/sparse/blob/master/LICENSE

> + (license license:bsd-3)))

No need to include this comment.

Ricardo

Ricardo Wurmus wrote 4 years ago

Re: [PATCH 2/2] gnu: python-cooler: Update to 0.8.10.

Recipients:(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)(address . 46955@debbugs.gnu.org)

Message-ID:875z162ga9.fsf@elephly.net

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

Toggle quote (2 lines)

> * 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

Ricardo Wurmus wrote 4 years ago

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

Recipients:(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)(address . 46955@debbugs.gnu.org)

Message-ID:8735wa2g7t.fsf@elephly.net

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

Toggle quote (1 lines)

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

[…]

Toggle quote (5 lines)

> +(define-public python-sparse

> + (package

> + (name "python-sparse")

> + (version "0.11.2")

“guix lint” tells me:

python-sparse@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

Mădălin Ionel Patrașcu wrote 4 years ago

Re: [ext] bug#46955: Acknowledgement ((no subject))

Recipients:(address . 46955@debbugs.gnu.org)(name . Rekado Wurmus)(address . rekado@elephly.net)

Message-ID:be458c24-9a87-8c38-41d5-74e5378cfa7a@mdc-berlin.de

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

phase `check' succeeded after 1.5 seconds

Toggle snippet (43 lines)

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

> interested parties for their attention; they will reply in due course.

> Your message has been sent to the package maintainer(s):

> guix-patches@gnu.org

> If you wish to submit further information on this problem, please

> send it to 46955@debbugs.gnu.org.

> Please do not send mail to help-debbugs@gnu.org unless you wish

> to report a problem with the Bug-tracking system.

System Administrator

Bioinformatics and Omics Data Science

BIMSB - MDC

Attachment: file

Mădălin Ionel Patrașcu wrote 4 years ago

[PATCH 1/3] gnu: Add python-sparse.

Recipients:(address . 46955@debbugs.gnu.org)(address . rekado@elephly.net)(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)

Message-ID:20210603232503.29253-1-madalinionel.patrascu@mdc-berlin.de

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

---

gnu/packages/python-xyz.scm | 48 ++++++++++++++++++++++++++++++++++++-

1 file changed, 47 insertions(+), 1 deletion(-)

Toggle diff (68 lines)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@autistici.org>
 ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
 ;;; Copyright © 2019, 2020 Tanguy Le Carrour <tanguy@bioneland.org>
-;;; Copyright © 2019 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2019, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
 ;;; Copyright © 2020 Riku Viitanen <riku.viitanen@protonmail.com>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
 ;;; Copyright © 2020 sirgazil <sirgazil@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

Mădălin Ionel Patrașcu wrote 4 years ago

[PATCH 2/3] gnu: Add python-ipytree.

Recipients:(address . 46955@debbugs.gnu.org)(address . rekado@elephly.net)(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)

Message-ID:20210603232503.29253-2-madalinionel.patrascu@mdc-berlin.de

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

---

gnu/packages/python-xyz.scm | 26 ++++++++++++++++++++++++++

1 file changed, 26 insertions(+)

Toggle diff (39 lines)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

Mădălin Ionel Patrașcu wrote 4 years ago

[PATCH 3/3] gnu: python-cooler: Update to 0.8.11.

Recipients:(address . 46955@debbugs.gnu.org)(address . rekado@elephly.net)(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)

Message-ID:20210603232503.29253-3-madalinionel.patrascu@mdc-berlin.de

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

---

gnu/packages/bioinformatics.scm | 39 ++++++++++++++++++++++++++++-----

1 file changed, 33 insertions(+), 6 deletions(-)

Toggle diff (67 lines)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

Maxime Devos wrote 4 years ago

Recipients:(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)(address . 46955@debbugs.gnu.org)(address . rekado@elephly.net)

Message-ID:7c35e0fff0b83ca112cbeda0f6a391536fb2abf8.camel@telenet.be

A comment about a build phase.

Toggle quote (6 lines)

> [...]

> + (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.

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Mădălin Ionel Patrașcu wrote 4 years ago

Recipients:(address . 46955@debbugs.gnu.org)(address . rekado@elephly.net)(name . Maxime Devos)(address . maximedevos@telenet.be)

Message-ID:5ec8d2b3-811a-013b-28db-6e79b6d2b556@mdc-berlin.de

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:

Toggle quote (25 lines)> 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

Mădălin Ionel Patrașcu wrote 4 years ago

[PATCH 1/3] gnu: Add python-sparse.

Recipients:(address . 46955@debbugs.gnu.org)(address . rekado@elephly.net)(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)

Message-ID:20210606000651.28252-1-madalinionel.patrascu@mdc-berlin.de

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

---

gnu/packages/python-xyz.scm | 47 ++++++++++++++++++++++++++++++++++++-

1 file changed, 46 insertions(+), 1 deletion(-)

Toggle diff (67 lines)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@autistici.org>
 ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
 ;;; Copyright © 2019, 2020 Tanguy Le Carrour <tanguy@bioneland.org>
-;;; Copyright © 2019 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2019, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
 ;;; Copyright © 2020 Riku Viitanen <riku.viitanen@protonmail.com>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
 ;;; Copyright © 2020 sirgazil <sirgazil@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

Mădălin Ionel Patrașcu wrote 4 years ago

[PATCH 2/3] gnu: Add python-ipytree.

Recipients:(address . 46955@debbugs.gnu.org)(address . rekado@elephly.net)(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)

Message-ID:20210606000651.28252-2-madalinionel.patrascu@mdc-berlin.de

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

---

gnu/packages/python-xyz.scm | 26 ++++++++++++++++++++++++++

1 file changed, 26 insertions(+)

Toggle diff (39 lines)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

Mădălin Ionel Patrașcu wrote 4 years ago

[PATCH 3/3] gnu: python-cooler: Update to 0.8.11.

Recipients:(address . 46955@debbugs.gnu.org)(address . rekado@elephly.net)(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)

Message-ID:20210606000651.28252-3-madalinionel.patrascu@mdc-berlin.de

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

---

gnu/packages/bioinformatics.scm | 38 +++++++++++++++++++++++++++------

1 file changed, 32 insertions(+), 6 deletions(-)

Toggle diff (66 lines)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

Ricardo Wurmus wrote 4 years ago

Re: [PATCH 2/3] gnu: Add python-ipytree.

Recipients:(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)(address . 46955@debbugs.gnu.org)

Message-ID:87lf7ntstj.fsf@elephly.net

Hi Mădălin,

Toggle quote (2 lines)

> * 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

Ricardo Wurmus wrote 4 years ago

Re: [PATCH 3/3] gnu: python-cooler: Update to 0.8.11.

Recipients:(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)(address . 46955-done@debbugs.gnu.org)

Message-ID:87im2rts7g.fsf@elephly.net

Hi Mădălin,

thanks for the patches!

Toggle quote (3 lines)

> * 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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