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Tue, 29 Nov 2022 08:39:49 -0500 (EST) From: Konrad Hinsen To: Hugo Buddelmeijer , Thibault Lestang Cc: guix-science Subject: Re: Conda environments and reproducibility In-Reply-To: References: <87pmd7ar8k.fsf@imperial.ac.uk> <87zgcayre2.fsf@imperial.ac.uk> Date: Tue, 29 Nov 2022 14:39:46 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Received-SPF: softfail client-ip=64.147.123.19; envelope-from=konrad.hinsen@cnrs.fr; helo=wout3-smtp.messagingengine.com X-Spam_score_int: -18 X-Spam_score: -1.9 X-Spam_bar: - X-Spam_report: (-1.9 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, RCVD_IN_DNSWL_LOW=-0.7, SPF_HELO_PASS=-0.001, SPF_SOFTFAIL=0.665 autolearn=no autolearn_force=no X-Spam_action: no action X-BeenThere: guix-science@gnu.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-science-bounces+larch=yhetil.org@gnu.org Sender: guix-science-bounces+larch=yhetil.org@gnu.org X-Migadu-Flow: FLOW_IN X-Migadu-Country: US ARC-Message-Signature: i=1; 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aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=messagingengine.com header.s=fm1 header.b="u mOAIXg"; dmarc=none; spf=pass (aspmx1.migadu.com: domain of "guix-science-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-science-bounces+larch=yhetil.org@gnu.org" X-Migadu-Spam-Score: 2.64 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=messagingengine.com header.s=fm1 header.b="u mOAIXg"; dmarc=none; spf=pass (aspmx1.migadu.com: domain of "guix-science-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-science-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: 1B7014E5D X-Spam-Score: 2.64 X-Migadu-Scanner: scn1.migadu.com X-TUID: xs4OE0xb/eA/ Hi Hugo, Buddelmeijer writes: > Hi Konrad, Thibault and others, > > Konrad, is it perhaps possible for you to dig up this broken conda > environment file? Yes: https://gist.github.com/brospars/4671d9013f0d99e1c961482dab533c57 That environment was set up in 2018 on a Linux machine, and then tested under macOS and Windows as well. It broke in early 2019. > First, just like you all, my conclusion is that guix is the answer. The > last two paragraphs by Simon captures it succinctly. However, conda seems > to work fine for most people. It would therefore be instructive to have > concrete 'failure stories' in order to show people that conda is not enou= gh. I have heard many stories of conda failing long-term, i.e. environments not being reproducible after a year or two. Most use cases are probably more short-term. > It doesn't seem common to overwrite conda binaries. Conda takes some (not > enough?) measures to prevent the scenario Konrad describes. In particular, > the filenames include a 'hash' since conda 3 (~2014) [1]: Weird. We worked with official Miniconda downloads from early 2018, and our environment files contain no hashes. > My realization was that improving these hashes is a goose chase and will > ultimately lead to horrific things like "turing-complete yaml files". And > at that point it is clear, at least to me, that guix is the answer. Indeed. Turing-complete Scheme files :-) My conclusion so far is that conda can never attain long-term reproducibility, because it wants to be multi-platform. And that means that it doesn't control the foundations on which it has to build. >From a user's point of view, a big problem with conda is the opacity of the machinery, which in addition changes all the time as you say. With Guix, I can understand how everything is built, and thus understand the potential obstacles to a rebuild many years later. With conda, I don't really know and my understanding is that the build machinery is not even completely public (for Anaconda at least). > One thing that conda (or actualy conda-forge) does well, are their bots. > I'm a maintainer of some conda packages and once a month or so I get a > fully automated pull request to update my package [4], e.g. when the > upstream package is updated, or when a dependency is updated. They even That's nice! > packages, such as compilers. This makes maintaining conda-forge packages a > breeze. Having such bots also within the guix-ecosystem would probably he= lp > attract developers. Indeed. More generally, I think package managers should do a better job in reaching out to upstream maintainers. They are our allies in providing a better UX. Cheers, Konrad --=20 --------------------------------------------------------------------- Konrad Hinsen Centre de Biophysique Mol=C3=A9culaire, CNRS Orl=C3=A9ans Synchrotron Soleil - Division Exp=C3=A9riences Saint Aubin - BP 48 91192 Gif sur Yvette Cedex, France Tel. +33-1 69 35 97 15 E-Mail: konrad DOT hinsen AT cnrs DOT fr http://dirac.cnrs-orleans.fr/~hinsen/ ORCID: https://orcid.org/0000-0003-0330-9428 Twitter: @khinsen ---------------------------------------------------------------------