Re: Setting up a python environment

[zimoun <zimon.toutoune@gmail.com>]

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Hi Roy,

On Mon, 11 May 2020 at 14:49, Roy Lemmon <roy@roylemmon.com> wrote:

> I would like to ask about the general philosophy of setting up a python
> environment under guix.

Well, let me describe my workflow -- and I do not know if it the correct one.

I use 'manifest', 'profile' and "guix environment".  For each project
I am working on, I have dedicated folder containing the code, doc and
other files useful for the very project.  In this folder, I add a
manifest file [1] tracking the tools that the project needs.  From
this manifest, I instantiate a profile in the project folder.  And I
track the channel too to be able to reproduce elsewhere and elsetime.
Time to time, I spawn an environment with the manifest to do some
checks.  Well, basically, the CLI looks like:

   cd /path/to/project
   edit manifest.scm
   guix package -m manifest.scm -p profile
   guix describe -f channels > channels.scm
   git add manifest.scm channels.scm
   git commit -am

   eval $(guix package --search-paths=prefix -p profile)
   ipython

   guix environment -m manifest --ad-hoc python-other-tools

   guix time-machine -C channels.scm -- environment -m manifest.scm


Last, when a package is missing, I use "guix import pypi -r name".  If
the package is correctly packaged on the PyPI side, it is almost done.
;-)
To be concrete, again in the project folder:

   guix import pypi -r astropy > pkgs.scm
   edit pkgs.scm # add define-module etc.
   guix show -L . python-astropy
   edit pkgs.scm # add missing import
   guix show -L . python-astropy # works!

   guix build -L . python-astropy

Well, and then the "hard" packaging job starts. :-)
Find attached 'pkgs.scm' still failing to build but maybe a starting point.


Hope that helps,
simon

[-- Attachment #2: pkgs.scm --]
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(define-module (pkgs)
  #:use-module (guix packages)
  #:use-module (guix download)
  #:use-module (guix build-system python)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (gnu packages python-xyz)
  #:use-module (gnu packages check)
  )

(define-public python-skyfield
  (package
    (name "python-skyfield")
    (version "1.20")
    (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "skyfield" version))
        (sha256
          (base32
            "0lm4j6zdavvw0wgfv5g2rdk77n3dh2b096z44halfcjcf4k4dg2x"))))
    (build-system python-build-system)
    (home-page
      "http://github.com/brandon-rhodes/python-skyfield/")
    (synopsis "Elegant astronomy for Python")
    (description "Elegant astronomy for Python")
    (license license:expat)))

(define-public python-pytest-mpl
  (package
    (name "python-pytest-mpl")
    (version "0.11")
    (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest-mpl" version))
        (sha256
          (base32
            "1km202c1s5kcn52fx0266p06qb34va3warcby594dh6vixxa9i96"))))
    (build-system python-build-system)
    (propagated-inputs
      `(("python-matplotlib" ,python-matplotlib)
        ("python-nose" ,python-nose)
        ("python-pillow" ,python-pillow)
        ("python-pytest" ,python-pytest)))
    (home-page
      "https://github.com/matplotlib/pytest-mpl")
    (synopsis
      "pytest plugin to help with testing figures output from Matplotlib")
    (description
      "pytest plugin to help with testing figures output from Matplotlib")
    (license license:bsd-3)))

(define-public python-pytest-filter-subpackage
  (package
    (name "python-pytest-filter-subpackage")
    (version "0.1.1")
    (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest-filter-subpackage" version))
        (sha256
          (base32
            "1s4s2kd31yc65rfvl4xhy8xx806xhy59kc7668h6b6wq88xgrn5p"))))
    (build-system python-build-system)
    (propagated-inputs
      `(("python-pytest" ,python-pytest)))
    (native-inputs
      `(("python-pytest" ,python-pytest)
        ("python-pytest-cov" ,python-pytest-cov)
        ("python-pytest-doctestplus"
         ,python-pytest-doctestplus)))
    (home-page "https://astropy.org")
    (synopsis
      "Pytest plugin for filtering based on sub-packages")
    (description
      "Pytest plugin for filtering based on sub-packages")
    (license license:bsd-3)))

(define-public python-pytest-arraydiff
  (package
    (name "python-pytest-arraydiff")
    (version "0.3")
    (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest-arraydiff" version))
        (sha256
          (base32
            "05bcvhh2ycxa35znl8b3l9vkcmx7vwm5c3fpakbpw46c7vsn4bfy"))))
    (build-system python-build-system)
    (propagated-inputs
      `(("python-numpy" ,python-numpy)
        ("python-pytest" ,python-pytest)
        ("python-six" ,python-six)))
    (home-page
      "https://github.com/astrofrog/pytest-arraydiff")
    (synopsis
      "pytest plugin to help with comparing array output from tests")
    (description
      "pytest plugin to help with comparing array output from tests")
    (license license:bsd-3)))

(define-public python-pytest-astropy-header
  (package
    (name "python-pytest-astropy-header")
    (version "0.1.2")
    (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest-astropy-header" version))
        (sha256
          (base32
            "1y87agr324p6x5gvhziymxjlw54pyn4gqnd49papbl941djpkp5g"))))
    (build-system python-build-system)
    (propagated-inputs
      `(("python-pytest" ,python-pytest)))
    (native-inputs
      `(("python-astropy" ,python-astropy)
        ("python-codecov" ,python-codecov)
        ("python-coverage" ,python-coverage)
        ("python-numpy" ,python-numpy)
        ("python-pytest" ,python-pytest)
        ("python-pytest-cov" ,python-pytest-cov)))
    (home-page "http://astropy.org")
    (synopsis
      "pytest plugin to add diagnostic information to the header of the test output")
    (description
      "pytest plugin to add diagnostic information to the header of the test output")
    (license #f)))

(define-public python-pytest-openfiles
  (package
    (name "python-pytest-openfiles")
    (version "0.5.0")
    (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest-openfiles" version))
        (sha256
          (base32
            "0n0a7fdc9m86360y96l23fvdmd6rw04bl6h5xqgl9qxfv08jk70p"))))
    (build-system python-build-system)
    (propagated-inputs
      `(("python-psutil" ,python-psutil)
        ("python-pytest" ,python-pytest)))
    (home-page
      "https://github.com/astropy/pytest-openfiles")
    (synopsis
      "Pytest plugin for detecting inadvertent open file handles")
    (description
      "Pytest plugin for detecting inadvertent open file handles")
    (license license:bsd-3)))

(define-public python-pytest-remotedata
  (package
    (name "python-pytest-remotedata")
    (version "0.3.2")
    (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest-remotedata" version))
        (sha256
          (base32
            "1h6g6shib6z07azf12rnsa053470ggbd7hy3bnbw8nf3nza5h372"))))
    (build-system python-build-system)
    (propagated-inputs
      `(("python-pytest" ,python-pytest)
        ("python-six" ,python-six)))
    (home-page "https://astropy.org")
    (synopsis
      "Pytest plugin for controlling remote data access.")
    (description
      "Pytest plugin for controlling remote data access.")
    (license license:bsd-3)))

(define-public python-pytest-doctestplus
  (package
    (name "python-pytest-doctestplus")
    (version "0.6.1")
    (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest-doctestplus" version))
        (sha256
          (base32
            "11f1gjj975aapannwc7xfqc6ijckgqn9w2pbk0n4jn8qljv77jvv"))))
    (build-system python-build-system)
    (propagated-inputs
      `(("python-pip" ,python-pip)
        ("python-pytest" ,python-pytest)))
    (home-page "https://astropy.org")
    (synopsis
      "Pytest plugin with advanced doctest features.")
    (description
      "Pytest plugin with advanced doctest features.")
    (license license:bsd-3)))

(define-public python-pytest-astropy
  (package
    (name "python-pytest-astropy")
    (version "0.8.0")
    (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest-astropy" version))
        (sha256
          (base32
            "18j6z6y2fvykmcs5z0mldhhaxxn6wzpnhlm2ps7m8r5z5kmh1631"))))
    (build-system python-build-system)
    (propagated-inputs
      `(("python-hypothesis" ,python-hypothesis)
        ("python-pytest" ,python-pytest)
        ("python-pytest-arraydiff"
         ,python-pytest-arraydiff)
        ("python-pytest-astropy-header"
         ,python-pytest-astropy-header)
        ("python-pytest-cov" ,python-pytest-cov)
        ("python-pytest-doctestplus"
         ,python-pytest-doctestplus)
        ("python-pytest-filter-subpackage"
         ,python-pytest-filter-subpackage)
        ("python-pytest-openfiles"
         ,python-pytest-openfiles)
        ("python-pytest-remotedata"
         ,python-pytest-remotedata)))
    (home-page
      "https://github.com/astropy/pytest-astropy")
    (synopsis
      "Meta-package containing dependencies for testing")
    (description
      "Meta-package containing dependencies for testing")
    (license license:bsd-3)))

(define-public python-astropy
  (package
    (name "python-astropy")
    (version "4.0.1.post1")
    (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "astropy" version))
        (sha256
          (base32
            "1da4xj793ldck29aajyb514wpz330cml26f3gdp45jj531n4lc2w"))))
    (build-system python-build-system)
    (propagated-inputs
      `(("python-numpy" ,python-numpy)))

    (native-inputs
     `(
       ("python-coverage" ,python-coverage)
          ("python-ipython" ,python-ipython)
          ("python-objgraph" ,python-objgraph)
     ;;     ("python-pytest-astropy" ,python-pytest-astropy)
          ("python-pytest-mpl" ,python-pytest-mpl)
          ("python-pytest-xdist" ,python-pytest-xdist)
          ("python-skyfield" ,python-skyfield)
     ))
    (home-page "http://astropy.org")
    (synopsis
      "Community-developed python astronomy tools")
    (description
      "Community-developed python astronomy tools")
    (license #f)))