[bug#49338] [PATCH 0/8] Repo2docker packages

[bug#49338] [PATCH 0/8] Repo2docker packages

[Hugo Lecomte]

Hi!

Here is a package for repo2docker and one for each of its dependencies that weren't on Guix yet.

WDYT?

Hugo

Hugo Lecomte (8):
  gnu: Add python-escapism.
  gnu: Add python-recommonmark.
  gnu: Add python-pytest-datadir.
  gnu: Add python-pytest-regressions.
  gnu: Add python-jupyter-sphinx.
  gnu: Add python-sphinxcontrib-autoprogram.
  gnu: Add python-pydata-sphinx-theme.
  gnu: Add repo2docker.

 gnu/packages/check.scm      | 57 +++++++++++++++++++++++
 gnu/packages/jupyter.scm    | 73 ++++++++++++++++++++++++++++-
 gnu/packages/python-xyz.scm | 48 +++++++++++++++++++
 gnu/packages/sphinx.scm     | 93 ++++++++++++++++++++++++++++++++++++-
 4 files changed, 269 insertions(+), 2 deletions(-)

-- 
2.31.1

[bug#49338] [PATCH 0/8] Repo2docker packages

[zimoun]

Hi Hugo,

On Fri, 02 Jul 2021 at 16:58, Hugo Lecomte <hugo.lecomte@inria.fr> wrote:

> Here is a package for repo2docker and one for each of its dependencies
> that weren't on Guix yet.

Cool!

> Hugo Lecomte (8):
>   gnu: Add python-escapism.
>   gnu: Add python-recommonmark.
>   gnu: Add python-pytest-datadir.
>   gnu: Add python-pytest-regressions.
>   gnu: Add python-jupyter-sphinx.
>   gnu: Add python-sphinxcontrib-autoprogram.
>   gnu: Add python-pydata-sphinx-theme.
>   gnu: Add repo2docker.

You sent only the cover-letter, I guess, and not all the 8 patches. :-)
Well, I do not find them.

Cheers,
simon

[bug#49338] [PATCH 1/8] gnu: Add python-escapism.

[Hugo Lecomte]

* gnu/packages/python-xyz.scm (python-escapism): New variable.
---
 gnu/packages/python-xyz.scm | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index e655b3b20e..8f3a436e81 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -26042,3 +26042,22 @@ is the cythonized version of @code{fractions.Fraction}.")
      "@code{pathvalidate} is a Python library to sanitize/validate strings
 representing paths or filenames.")
     (license license:expat)))
+
+(define-public python-escapism
+  (package
+    (name "python-escapism")
+    (version "1.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "escapism" version))
+       (sha256
+        (base32
+         "1v74243wifcwhj5zkdiispxc9kb1xvnfzilg8bq308pjnkgnn9bk"))))
+    (build-system python-build-system)
+    (home-page "https://github.com/minrk/escapism")
+    (synopsis "Simple, generic API for escaping strings")
+    (description
+     "Provide a generic API, given a set of safe characters and an escape character,
+to escape safe strings and unescape the result.")
+    (license license:expat)))
-- 
2.31.1

[bug#49338] [PATCH 2/8] gnu: Add python-recommonmark.

[Hugo Lecomte]

* gnu/packages/python-xyz.scm (python-recommonmark): New variable.
---
 gnu/packages/python-xyz.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 8f3a436e81..0796228109 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -26061,3 +26061,32 @@ representing paths or filenames.")
      "Provide a generic API, given a set of safe characters and an escape character,
 to escape safe strings and unescape the result.")
     (license license:expat)))
+
+(define-public python-recommonmark
+  (package
+    (name "python-recommonmark")
+    (version "0.7.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "recommonmark" version))
+       (sha256
+        (base32
+         "0rvdd2ikdr0yg6cx6594fdzn53cmdc0g0i6qsbcdq8i2kxjdpd5x"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-commonmark" ,python-commonmark)
+       ("python-docutils" ,python-docutils)
+       ("python-sphinx" ,python-sphinx)))
+    (arguments
+     '(#:phases (modify-phases %standard-phases
+                  (add-after 'unpack 'delete-test-sphinx
+                    (lambda* (#:key outputs #:allow-other-keys)
+                      (let* ((out (assoc-ref outputs "out")))
+                        (delete-file "tests/test_sphinx.py")))))))
+    (home-page "https://github.com/readthedocs/recommonmark")
+    (synopsis "Docutils-compatibility bridge to CommonMark")
+    (description
+     "A docutils-compatibility bridge to CommonMark, enabling you to write
+CommonMark inside of Docutils & Sphinx projects.")
+    (license license:expat)))
-- 
2.31.1

[bug#49338] [PATCH 3/8] gnu: Add python-pytest-datadir.

[Hugo Lecomte]

* gnu/packages/check.scm (python-pytest-datadir): New variable.
---
 gnu/packages/check.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 658905a7f5..c97e1e721c 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -2924,3 +2924,25 @@ to mark some tests as dependent from other tests.  These tests will then be
 skipped if any of the dependencies did fail or has been skipped.")
     (license license:asl2.0)))
 
+(define-public python-pytest-datadir
+  (package
+    (name "python-pytest-datadir")
+    (version "1.3.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pytest-datadir" version))
+       (sha256
+        (base32
+         "066bg6wlzgq2pqnjp73dfrcmk8951xw3aqcxa3p1axgqimrixbyk"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("python-setuptools-scm" ,python-setuptools-scm)))
+    (propagated-inputs
+     `(("python-pytest" ,python-pytest)
+       ("python-wheel" ,python-wheel)))
+    (home-page "https://github.com/gabrielcnr/pytest-datadir")
+    (synopsis "Pytest plugin for manipulating test data directories and files")
+    (description
+     "Pytest plugin for manipulating test data directories and files")
+    (license license:expat)))
-- 
2.31.1

[bug#49338] [PATCH 4/8] gnu: Add python-pytest-regressions.

[Hugo Lecomte]

* gnu/packages/check.scm (python-pytest-regressions): New variable.
---
 gnu/packages/check.scm | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index c97e1e721c..a6fc88c4eb 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -70,6 +70,7 @@
   #:use-module (gnu packages python-build)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
+  #:use-module (gnu packages python-science)
   #:use-module (gnu packages time)
   #:use-module (gnu packages xml)
   #:use-module (guix utils)
@@ -2946,3 +2947,37 @@ skipped if any of the dependencies did fail or has been skipped.")
     (description
      "Pytest plugin for manipulating test data directories and files")
     (license license:expat)))
+
+(define-public python-pytest-regressions
+  (package
+    (name "python-pytest-regressions")
+    (version "2.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pytest-regressions" version))
+       (sha256
+        (base32
+         "05jpsvv8rj8i4x24fphpnar5dl4s6d6bw6ikjk5d8v96rdviz9qm"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-pytest-datadir" ,python-pytest-datadir)
+       ("python-pyyaml" ,python-pyyaml)))
+    (native-inputs
+     `(("python-matplotlib" ,python-matplotlib)
+       ("python-numpy" ,python-numpy)
+       ("python-pandas" ,python-pandas)
+       ("python-pillow" ,python-pillow)
+       ("python-pre-commit" ,python-pre-commit)
+       ("python-restructuredtext-lint"
+        ,python-restructuredtext-lint)
+       ("python-tox" ,python-tox)
+       ("python-setuptools-scm" ,python-setuptools-scm)
+       ("python-pytest" ,python-pytest)))
+    (home-page "https://github.com/ESSS/pytest-regressions")
+    (synopsis "Easy to use fixtures to write regression tests")
+    (description
+     "This plugin makes it simple to test general data, images, files, and numeric
+tables by saving expected data in a data directory (courtesy of pytest-datadir)
+that can be used to verify that future runs produce the same data.")
+    (license license:expat)))
-- 
2.31.1

[bug#49338] [PATCH 5/8] gnu: Add python-jupyter-sphinx.

[Hugo Lecomte]

* gnu/packages/sphinx.scm (python-jupyter-sphinx): New variable.
---
 gnu/packages/sphinx.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm
index 428a701d87..0ca217e921 100644
--- a/gnu/packages/sphinx.scm
+++ b/gnu/packages/sphinx.scm
@@ -783,3 +783,32 @@ executed during the Sphinx build process.")
     (synopsis "Sphinx cross-reference tool")
     (description "Sphinx objects.inv inspection/manipulation tool.")
     (license license:expat)))
+
+(define-public python-jupyter-sphinx
+  (package
+    (name "python-jupyter-sphinx")
+    (version "0.3.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "jupyter_sphinx" version))
+       (sha256
+        (base32
+         "1wma60787m2451nn4bc4jw7bzqksplplb84wqxm34iaw70499z1p"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-ipython" ,python-ipython)
+       ("python-ipywidgets" ,python-ipywidgets)
+       ("python-nbconvert" ,python-nbconvert)
+       ("python-nbformat" ,python-nbformat)))
+    (native-inputs
+     `(("python-sphinx" ,python-sphinx)))
+    (home-page "https://github.com/jupyter/jupyter-sphinx/")
+    (synopsis "Jupyter Sphinx Extensions")
+    (description
+     "Jupyter-sphinx is a Sphinx extension that executes embedded
+code in a Jupyter kernel, and embeds outputs of that code in the document.  It
+has support for rich output such as images, Latex math and even javascript
+widgets, and it allows to enable thebelab for live code execution with minimal
+effort.")
+    (license license:bsd-3)))
-- 
2.31.1

[bug#49338] [PATCH 6/8] gnu: Add python-sphinxcontrib-autoprogram.

[Hugo Lecomte]

* gnu/packages/sphinx.scm (python-sphinxcontrib-autoprogram): New variable.
---
 gnu/packages/sphinx.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm
index 0ca217e921..14207470c2 100644
--- a/gnu/packages/sphinx.scm
+++ b/gnu/packages/sphinx.scm
@@ -812,3 +812,27 @@ has support for rich output such as images, Latex math and even javascript
 widgets, and it allows to enable thebelab for live code execution with minimal
 effort.")
     (license license:bsd-3)))
+
+(define-public python-sphinxcontrib-autoprogram
+  (package
+    (name "python-sphinxcontrib-autoprogram")
+    (version "0.1.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "sphinxcontrib-autoprogram" version))
+       (sha256
+        (base32
+         "06hzim0d3fd72kf30fyjbbm5n8ibyybic0kf62gm79qp50zjwr5w"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-six" ,python-six)))
+    (native-inputs
+     `(("python-sphinx" ,python-sphinx)))
+    (home-page "https://github.com/sphinx-contrib/autoprogram")
+    (synopsis "Documenting CLI programs")
+    (description
+     "This contrib extension, sphinxcontrib.autoprogram, provides an
+automated way to document CLI programs.  It scans argparse.ArgumentParser object,
+and then expands it into a set of .. program:: and .. option:: directives.")
+    (license license:bsd-2)))
-- 
2.31.1

[bug#49338] [PATCH 7/8] gnu: Add python-pydata-sphinx-theme.

[Hugo Lecomte]

* gnu/packages/sphinx.scm (python-pydata-sphinx-theme): New variable.
---
 gnu/packages/sphinx.scm | 40 +++++++++++++++++++++++++++++++++++++++-
 1 file changed, 39 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm
index 14207470c2..c000cefecc 100644
--- a/gnu/packages/sphinx.scm
+++ b/gnu/packages/sphinx.scm
@@ -48,7 +48,9 @@
   #:use-module (gnu packages python-crypto)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
-  #:use-module (gnu packages time))
+  #:use-module (gnu packages time)
+  #:use-module (gnu packages python-science)
+  #:use-module (gnu packages graph))
 
 (define-public python-sphinx
   (package
@@ -836,3 +838,39 @@ effort.")
 automated way to document CLI programs.  It scans argparse.ArgumentParser object,
 and then expands it into a set of .. program:: and .. option:: directives.")
     (license license:bsd-2)))
+
+(define-public python-pydata-sphinx-theme
+  (package
+    (name "python-pydata-sphinx-theme")
+    (version "0.6.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pydata-sphinx-theme" version))
+       (sha256
+        (base32
+         "055bh3hyh72pafiylvgpsjlk18wm15gg4azc5rjlsww5z475iq1j"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-beautifulsoup4" ,python-beautifulsoup4)))
+    (native-inputs
+     `(("python-beautifulsoup4" ,python-beautifulsoup4)
+       ("python-docutils" ,python-docutils)
+       ("python-jupyter-sphinx" ,python-jupyter-sphinx)
+       ("python-numpy" ,python-numpy)
+       ("python-numpydoc" ,python-numpydoc)
+       ("python-pandas" ,python-pandas)
+       ("python-plotly" ,python-plotly)
+       ("python-pytest" ,python-pytest)
+       ("python-pytest-regressions"
+        ,python-pytest-regressions)
+       ("python-recommonmark" ,python-recommonmark)
+       ("python-sphinx" ,python-sphinx)
+       ("python-xarray" ,python-xarray)
+       ("python-docutils" ,python-docutils)
+       ("python-sphinx" ,python-sphinx)))
+    (home-page "https://github.com/pydata/pydata-sphinx-theme")
+    (synopsis "Bootstrap-based Sphinx theme from the PyData community")
+    (description
+     "Bootstrap-based Sphinx theme from the PyData community")
+    (license license:bsd-3)))
-- 
2.31.1

[bug#49338] [PATCH 8/8] gnu: Add repo2docker.

[Hugo Lecomte]

* gnu/packages/jupyter.scm (repo2docker): New variable.
---
 gnu/packages/jupyter.scm | 73 +++++++++++++++++++++++++++++++++++++++-
 1 file changed, 72 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/jupyter.scm b/gnu/packages/jupyter.scm
index 52869dbeeb..d2d4bf2e20 100644
--- a/gnu/packages/jupyter.scm
+++ b/gnu/packages/jupyter.scm
@@ -33,9 +33,13 @@
   #:use-module (gnu packages python-build)
   #:use-module (gnu packages python-check)
   #:use-module (gnu packages python-xyz)
+  #:use-module (gnu packages python-web)
   #:use-module (gnu packages time)
+  #:use-module (gnu packages xml)
   #:use-module (gnu packages tls)
-  #:use-module (gnu packages xml))
+  #:use-module (gnu packages sphinx)
+  #:use-module (gnu packages serialization)
+  #:use-module (gnu packages docker))
 
 (define-public python-jupyter-protocol
   (package
@@ -310,3 +314,70 @@ are interactive HTML widgets for Jupyter notebooks and the IPython kernel.")
      "This package provides a client library for executing notebooks. Formerly
 nbconvert's @code{ExecutePreprocessor.}")
     (license license:bsd-3)))
+
+(define-public repo2docker
+  (package
+    (name "repo2docker")
+    (version "2021.03.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/jupyterhub/repo2docker/")
+                    (commit "2021.03.0")))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "18w8rgf7fpf79kx36y2c3xi3d52i41z112l3sz719d8kg0bir16m"))))
+    (outputs '("out" "doc"))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases (modify-phases %standard-phases
+                  (add-after 'patch-shebangs 'fix-install-miniforge
+                    (lambda* (#:key outputs #:allow-other-keys)
+                      (let* ((out (assoc-ref outputs "out")))
+                        (substitute* (find-files
+                                      out "^(install-miniforge|install-nix|\
+nix-shell-wrapper|repo2docker-entrypoint)")
+                          (("^#!(.*)/bin/bash")
+                           "#!/bin/bash"))
+                        (substitute* (find-files out "^freeze\\.py$")
+                          (("^#!(.*)/bin/python3")
+                           "#!/bin/python3\n")))))
+                  (add-after 'install 'make-doc
+                    (lambda* (#:key outputs #:allow-other-keys)
+                      (let* ((out (assoc-ref outputs "doc"))
+                             (doc (string-append out "/share/doc/"
+                                                 ,name)))
+                        (setenv "PYTHONPATH"
+                                (string-append (getcwd) ":"
+                                               (getenv "PYTHONPATH")))
+                        (with-directory-excursion "docs"
+                          (invoke  "make" "html")
+                          (copy-recursively "build/html"
+                                            (string-append doc "/html")))))))))
+    (inputs
+     `(("python-traitlets" ,python-traitlets)
+       ("python-toml" ,python-toml)
+       ("python-semver" ,python-semver)
+       ("python-ruamel.yaml" ,python-ruamel.yaml)
+       ("python-requests" ,python-requests)
+       ("python-json-logger" ,python-json-logger)
+       ("python-jinja2" ,python-jinja2)
+       ("python-escapism" ,python-escapism)
+       ("python-docker" ,python-docker)))
+    (native-inputs
+     `(("python-sphinx" ,python-sphinx)
+       ("python-recommonmark" ,python-recommonmark)
+       ("python-sphinxcontrib-autoprogram" ,python-sphinxcontrib-autoprogram)
+       ("python-pydata-sphinx-theme" ,python-pydata-sphinx-theme)))
+    (home-page "https://repo2docker.readthedocs.io/en/latest/index.html#")
+    (synopsis "Generate docker images from repositories")
+    (description
+     "repo2docker fetches a repository (from GitHub, GitLab, Zenodo, Figshare,
+Dataverse installations, a Git repository or a local directory) and builds a
+container image in which the code can be executed.  The image build process is
+based on the configuration files found in the repository. repo2docker can be
+used to explore a repository locally by building and executing the constructed
+image of the repository, or as a means of building images that are pushed to a
+Docker registry.")
+    (license license:bsd-3)))
-- 
2.31.1

bug#49338: [PATCH 0/8] Repo2docker packages

[Ludovic Courtès]

Hi Hugo!  :-)

Hugo Lecomte <hugo.lecomte@inria.fr> skribis:

>   gnu: Add python-escapism.
>   gnu: Add python-recommonmark.
>   gnu: Add python-pytest-datadir.
>   gnu: Add python-pytest-regressions.
>   gnu: Add python-jupyter-sphinx.
>   gnu: Add python-sphinxcontrib-autoprogram.
>   gnu: Add python-pydata-sphinx-theme.
>   gnu: Add repo2docker.

I’ve applied the whole series with minor tweaks to descriptions so they
match our guidelines¹ (for instance writing full sentences, avoiding
acronyms, etc.), and added copyright lines for you.

Thanks!

Ludo’.