Path: csiph.com!1.us.feeder.erje.net!3.us.feeder.erje.net!2.eu.feeder.erje.net!feeder.erje.net!news.uzoreto.com!aioe.org!bofh.it!news.nic.it!robomod From: PICCA Frederic-Emmanuel Newsgroups: linux.debian.maint.python Subject: Re: dxtbx pytest issue Date: Thu, 01 Sep 2022 15:10:01 +0200 Message-ID: References: X-Mailbox-Line: From debian-python-request@lists.debian.org Thu Sep 1 13:00:39 2022 Old-Return-Path: X-Amavis-Spam-Status: No, score=-0.011 tagged_above=-10000 required=5.3 tests=[BAYES_00=-2, RCVD_IN_MSPIKE_H2=-0.001, THREADTOPIC=2, T_SCC_BODY_TEXT_LINE=-0.01] autolearn=no autolearn_force=no X-Policyd-Weight: using cached result; rate:hard: -5.5 MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 7bit X-Mailer: Zimbra 8.8.15_GA_4272 (ZimbraWebClient - FF91 (Linux)/8.8.15_GA_4257) Thread-Topic: dxtbx pytest issue Thread-Index: FJN0o+S3llYWGI/crGtRPA7V8xVV/g== X-Renater-Ptge-Spamstate: clean X-Renater-Ptge-Spamcause: gggruggvucftvghtrhhoucdtuddrgedvfedrvdekkedgheejucetufdoteggodetrfdotffvucfrrhhofhhilhgvmecutffgpfetvffgtfenuceurghilhhouhhtmecufedttdenucenucfjughrpeffhffvvefkjghfufggtgfgofhtsehtjegttdertdejnecuhfhrohhmpefrkfevveetucfhrhgvuggvrhhitgdqgfhmmhgrnhhuvghluceofhhrvgguvghrihgtqdgvmhhmrghnuhgvlhdrphhitggtrgesshihnhgthhhrohhtrhhonhdqshholhgvihhlrdhfrheqnecuggftrfgrthhtvghrnhepfeejjeffgffhgfejudevvedtteffjeduudffvdffkeetffekhefhtdefhfefueefnecukfhppedutddrvdehgedrvdegtddrudegheenucevlhhushhtvghrufhiiigvpedtnecurfgrrhgrmhepihhnvghtpedutddrvdehgedrvdegtddrudeghedphhgvlhhopeiishhtohhrvgdqsgefqddtuddvrdhprghrthgrghgvrdhrvghnrghtvghrrdhfrhdpmhgrihhlfhhrohhmpefrkfevveetucfhrhgvuggvrhhitgdqgfhmmhgrnhhuvghluceofhhrvgguvghrihgtqdgvmhhmrghnuhgvlhdrphhitggtrgesshihnhgthhhrohhtrhhonhdqshholhgvihhlrdhfrheqpdhnsggprhgtphhtthhopedvpdhrtghpthhtoheptghouggvhhgvlhhpseguvggsihgrnhdrohhrghdprhgtphhtthhopeguvggsihgrnhdqphihthhhohhnsehlihhsthhsrdguvggsihgrnhdrohhrgh X-Mailing-List: archive/latest/20264 List-ID: List-URL: List-Archive: https://lists.debian.org/msgid-search/638662503.3886031.1662036157461.JavaMail.zimbra@synchrotron-soleil.fr Approved: robomod@news.nic.it Lines: 30 Organization: linux.* mail to news gateway Sender: robomod@news.nic.it X-Original-Cc: debian-python X-Original-Date: Thu, 1 Sep 2022 14:42:37 +0200 (CEST) X-Original-Message-ID: <638662503.3886031.1662036157461.JavaMail.zimbra@synchrotron-soleil.fr> X-Original-References: <605521306.3759500.1662031956039.JavaMail.zimbra@synchrotron-soleil.fr> <20220901130312.728e52fd@felix.codehelp> Xref: csiph.com linux.debian.maint.python:14424 For the record, I found it..., the upstream modify the HDF5_PLUGIN_PATH when loading the dxtbx module. they guess that they are using conda and override the path. All this is useless on Debian since the plugin are system installed properly. Cheers Fred # Ensures that HDF5 has the conda_base plugin path configured. # # Ideally this will be properly configured by the conda environment. # However, currently the dials-installer will not install a path-correct # conda_base folder, so it needs to be updated manually. _hdf5_plugin_path = libtbx.env.under_base(os.path.join("lib", "hdf5", "plugin")) # Inject via the environment if h5py not used yet, or else use h5py if "h5py" not in sys.modules: os.environ["HDF5_PLUGIN_PATH"] = ( _hdf5_plugin_path + os.pathsep + os.getenv("HDF5_PLUGIN_PATH", "") ) else: # We've already loaded h5py, so setting the environment variable won't work # We need to use the h5py API to add a plugin path import h5py h5_plugin_paths = [h5py.h5pl.get(i).decode() for i in range(h5py.h5pl.size())] if _hdf5_plugin_path not in h5_plugin_paths: h5py.h5pl.prepend(_hdf5_plugin_path.encode())