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charset=utf-8 Content-Transfer-Encoding: quoted-printable X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+larch=yhetil.org@gnu.org Sender: guix-patches-bounces+larch=yhetil.org@gnu.org X-Migadu-Country: US X-Migadu-Flow: FLOW_IN ARC-Seal: i=1; s=key1; d=yhetil.org; t=1677781879; a=rsa-sha256; cv=none; b=I03rIHUKmYwG+bViOrf2Tf68nvQ1oYZToUa2+UJPbW3C2e5GTagL99oB2V87B4Ge71T8C9 H8x5ConhoFGddygfndjxBjXZLRxEuvn2n3WKONcXqlMs6zNaBT5tKUi2COhieOzTxA7Qf5 UmESOw9xmR/BlFcDjV8SGmwhQiGEjFJ8d7mXKWkfd+5MnlHlZSkSatmyfto73oqh08U+jq lXChjKcooieUe4m7r5JZEEmXd6kOL6STq2RJDBLjKMbNGr2D9ieEFX+Td5ZWeUxdZReKI9 eH+CuuIrDBvP3q8A01E1RLp5pfTiwWWZdJ1e4qMLzKlW/tH/r9bALRmdAXu6Og== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gnu.org header.s=fencepost-gnu-org header.b=CxIThfza; spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org"; 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dkim=fail ("headers rsa verify failed") header.d=gnu.org header.s=fencepost-gnu-org header.b=CxIThfza; spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org"; dmarc=pass (policy=none) header.from=gnu.org X-TUID: mlzCgf326hJ7 Hi Kyle, kyle skribis: > From: Kyle Andrews > > The intent was to cover the most common cases where R and python using > researchers could rapidly achieve the benefits of reproducibility. That=E2=80=99s a great idea! Overall it looks nice to me. I would suggest reducing the scope a little bit by taking inferiors and the Python 3.6 bit out=E2=80=94these thi= ngs could be discussed in a separate section. Inline comments follow: > +@node Reproducible Research in Practice > +@section Common scientific software environments I=E2=80=99d use the same title for both. > +Many researchers write applied scientific software supported by a Maybe s/researchers/scientists/ to be more inclusive (that would include research software engineers, for instance; I=E2=80=99m one of them, hence t= hat comment. ;-)) > +mixture of more generic tools developed by teams written within the R > +and Python ecosystems and supporting shell utilities. Even researchers s/written within =E2=80=A6 utilities./written in R, Python, and shell./ > +who predominantly stick to using just R or just python often have to use > +both R and python at the same time when collaborating with others. This Make sure to always capitalize =E2=80=9CPython=E2=80=9D (and similarly for = other proper names). > +@example > +(use-modules > + (gnu packages cran) > + (gnu packages statistics)) > + > +(packages->manifest > + (list r r-tidyverse)) > + There=E2=80=99s a missing @end here. For Scheme code, please use @lisp =E2=80=A6 @end lisp instead. That enable syntax highlighting. > +R packages are defined predominantly inside of gnu/packages/cran.scm and > +gnu/packages/statistics.scm files under a guix source repository. Please use @file for file names=E2=80=A6 > +This manifest can be run with the basic guix shell command: =E2=80=A6 and @command{guix shell} here. > +@example > +guix shell --manifest=3Dmanifest.scm --container > +@end example > + > +Please remember at the end to pin your channels so that others in the > +future know how to recover your exact Guix environment. > + > +@example > +guix describe --format=3Dchannels > channels.scm > +@end example > + > +This can be done with Guix time machine: > + > +@example > +guix time-machine --channels=3Dchannels.scm \ > + -- guix shell --manifest=3Dmanifest.scm --container > +@end example Remove =E2=80=98guix=E2=80=99 after the double dash. Here I=E2=80=99d recommend including cross-references to the relevant secti= ons of the manual: =E2=80=9CWriting Manifests=E2=80=9D and =E2=80=9CReplicating= Guix=E2=80=9D. > +If reproducibility becomes an end in itself and not a catlyst towards > +faster discovery, then Guix will be a non-starter for scientists. Their > +goal is to develop useful understanding about particular aspects of the > +world. I don=E2=80=99t fully understand this paragraph. I tend to think that=20 > +Thankfully, three common scenarios cover the vast majority of > +needs. These are: > > +@itemize > +@item > +combining standard package definitions with custom package definitions > +@item > +combining package definitions from the current revision with other revis= ions > +@item > +combining package variants which need a modified build-system > +@end itemize Like Simon, I=E2=80=99d suggest leaving out the second part (inferiors), an= d also avoiding the Python=C2=A03.6 example, both of which make things immediately more complicated. We can keep the rest of the example though, if possible. WDYT? Thanks for your work! Ludo=E2=80=99.