Received: by mail.netbsd.org (Postfix, from userid 605) id 61A7A84E82; Mon, 23 Jul 2018 01:37:57 +0000 (UTC) Received: from localhost (localhost [127.0.0.1]) by mail.netbsd.org (Postfix) with ESMTP id 3464984E47 for ; Mon, 23 Jul 2018 01:37:56 +0000 (UTC) X-Virus-Scanned: amavisd-new at netbsd.org Received: from mail.netbsd.org ([IPv6:::1]) by localhost (mail.netbsd.org [IPv6:::1]) (amavisd-new, port 10025) with ESMTP id ERKNSumm_hfc for ; Mon, 23 Jul 2018 01:37:55 +0000 (UTC) Received: from cvs.NetBSD.org (ivanova.netbsd.org [199.233.217.197]) by mail.netbsd.org (Postfix) with ESMTP id 043A184D6F for ; Mon, 23 Jul 2018 01:37:54 +0000 (UTC) Received: by cvs.NetBSD.org (Postfix, from userid 500) id E6A42FBEC; Mon, 23 Jul 2018 01:37:54 +0000 (UTC) Content-Transfer-Encoding: 7bit Content-Type: multipart/mixed; boundary="_----------=_1532309874264200" MIME-Version: 1.0 Date: Mon, 23 Jul 2018 01:37:54 +0000 From: "Min Sik Kim" Subject: CVS commit: pkgsrc/math/py-pymc3 To: pkgsrc-changes@NetBSD.org Reply-To: minskim@netbsd.org X-Mailer: log_accum Message-Id: <20180723013754.E6A42FBEC@cvs.NetBSD.org> Sender: pkgsrc-changes-owner@NetBSD.org List-Id: pkgsrc-changes.NetBSD.org Precedence: bulk List-Unsubscribe: This is a multi-part message in MIME format. --_----------=_1532309874264200 Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" Module Name: pkgsrc Committed By: minskim Date: Mon Jul 23 01:37:54 UTC 2018 Modified Files: pkgsrc/math/py-pymc3: Makefile PLIST distinfo Log Message: math/py-pymc3: Update to 3.5 New features: - Add documentation section on survival analysis and censored data models - Add check_test_point method to pm.Model - Add Ordered Transformation and OrderedLogistic distribution - Add Chain transformation - Improve error message Mass matrix contains zeros on the diagonal. Some derivatives might always be zero during tuning of pm.sample - Improve error message NaN occurred in optimization. during ADVI - Save and load traces without pickle using pm.save_trace and pm.load_trace - Add Kumaraswamy distribution - Add TruncatedNormal distribution - Rewrite parallel sampling of multiple chains on py3. This resolves long standing issues when transferring large traces to the main process, avoids pickling issues on UNIX, and allows us to show a progress bar for all chains. If parallel sampling is interrupted, we now return partial results. - Add sample_prior_predictive which allows for efficient sampling from the unconditioned model. - SMC: remove experimental warning, allow sampling using sample, reduce autocorrelation from final trace. - Add model_to_graphviz (which uses the optional dependency graphviz) to plot a directed graph of a PyMC3 model using plate notation. - Add beta-ELBO variational inference as in beta-VAE model (Christopher P. Burgess et al. NIPS, 2017) - Add __dir__ to SingleGroupApproximation to improve autocompletion in interactive environments To generate a diff of this commit: cvs rdiff -u -r1.1 -r1.2 pkgsrc/math/py-pymc3/Makefile \ pkgsrc/math/py-pymc3/PLIST pkgsrc/math/py-pymc3/distinfo Please note that diffs are not public domain; they are subject to the copyright notices on the relevant files. --_----------=_1532309874264200 Content-Disposition: inline Content-Length: 4539 Content-Transfer-Encoding: binary Content-Type: text/x-diff; charset=us-ascii Modified files: Index: pkgsrc/math/py-pymc3/Makefile diff -u pkgsrc/math/py-pymc3/Makefile:1.1 pkgsrc/math/py-pymc3/Makefile:1.2 --- pkgsrc/math/py-pymc3/Makefile:1.1 Fri Jul 6 03:46:43 2018 +++ pkgsrc/math/py-pymc3/Makefile Mon Jul 23 01:37:54 2018 @@ -1,6 +1,6 @@ -# $NetBSD: Makefile,v 1.1 2018/07/06 03:46:43 minskim Exp $ +# $NetBSD: Makefile,v 1.2 2018/07/23 01:37:54 minskim Exp $ -DISTNAME= pymc3-3.4.1 +DISTNAME= pymc3-3.5 PKGNAME= ${PYPKGPREFIX}-${DISTNAME} CATEGORIES= math MASTER_SITES= ${MASTER_SITE_PYPI:=p/pymc3/} Index: pkgsrc/math/py-pymc3/PLIST diff -u pkgsrc/math/py-pymc3/PLIST:1.1 pkgsrc/math/py-pymc3/PLIST:1.2 --- pkgsrc/math/py-pymc3/PLIST:1.1 Fri Jul 6 03:46:43 2018 +++ pkgsrc/math/py-pymc3/PLIST Mon Jul 23 01:37:54 2018 @@ -1,4 +1,4 @@ -@comment $NetBSD: PLIST,v 1.1 2018/07/06 03:46:43 minskim Exp $ +@comment $NetBSD: PLIST,v 1.2 2018/07/23 01:37:54 minskim Exp $ ${PYSITELIB}/${EGG_INFODIR}/PKG-INFO ${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt ${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt @@ -94,9 +94,6 @@ ${PYSITELIB}/pymc3/examples/arma_example ${PYSITELIB}/pymc3/examples/baseball.py ${PYSITELIB}/pymc3/examples/baseball.pyc ${PYSITELIB}/pymc3/examples/baseball.pyo -${PYSITELIB}/pymc3/examples/censored_data.py -${PYSITELIB}/pymc3/examples/censored_data.pyc -${PYSITELIB}/pymc3/examples/censored_data.pyo ${PYSITELIB}/pymc3/examples/custom_dists.py ${PYSITELIB}/pymc3/examples/custom_dists.pyc ${PYSITELIB}/pymc3/examples/custom_dists.pyo @@ -148,6 +145,9 @@ ${PYSITELIB}/pymc3/examples/lasso_missin ${PYSITELIB}/pymc3/examples/lightspeed_example.py ${PYSITELIB}/pymc3/examples/lightspeed_example.pyc ${PYSITELIB}/pymc3/examples/lightspeed_example.pyo +${PYSITELIB}/pymc3/examples/rankdata_ordered.py +${PYSITELIB}/pymc3/examples/rankdata_ordered.pyc +${PYSITELIB}/pymc3/examples/rankdata_ordered.pyo ${PYSITELIB}/pymc3/examples/samplers_mvnormal.py ${PYSITELIB}/pymc3/examples/samplers_mvnormal.pyc ${PYSITELIB}/pymc3/examples/samplers_mvnormal.pyo @@ -196,6 +196,12 @@ ${PYSITELIB}/pymc3/memoize.pyo ${PYSITELIB}/pymc3/model.py ${PYSITELIB}/pymc3/model.pyc ${PYSITELIB}/pymc3/model.pyo +${PYSITELIB}/pymc3/model_graph.py +${PYSITELIB}/pymc3/model_graph.pyc +${PYSITELIB}/pymc3/model_graph.pyo +${PYSITELIB}/pymc3/parallel_sampling.py +${PYSITELIB}/pymc3/parallel_sampling.pyc +${PYSITELIB}/pymc3/parallel_sampling.pyo ${PYSITELIB}/pymc3/plots/__init__.py ${PYSITELIB}/pymc3/plots/__init__.pyc ${PYSITELIB}/pymc3/plots/__init__.pyo @@ -364,6 +370,9 @@ ${PYSITELIB}/pymc3/tests/test_model.pyo ${PYSITELIB}/pymc3/tests/test_model_func.py ${PYSITELIB}/pymc3/tests/test_model_func.pyc ${PYSITELIB}/pymc3/tests/test_model_func.pyo +${PYSITELIB}/pymc3/tests/test_model_graph.py +${PYSITELIB}/pymc3/tests/test_model_graph.pyc +${PYSITELIB}/pymc3/tests/test_model_graph.pyo ${PYSITELIB}/pymc3/tests/test_model_helpers.py ${PYSITELIB}/pymc3/tests/test_model_helpers.pyc ${PYSITELIB}/pymc3/tests/test_model_helpers.pyo @@ -379,6 +388,9 @@ ${PYSITELIB}/pymc3/tests/test_models_uti ${PYSITELIB}/pymc3/tests/test_ndarray_backend.py ${PYSITELIB}/pymc3/tests/test_ndarray_backend.pyc ${PYSITELIB}/pymc3/tests/test_ndarray_backend.pyo +${PYSITELIB}/pymc3/tests/test_parallel_sampling.py +${PYSITELIB}/pymc3/tests/test_parallel_sampling.pyc +${PYSITELIB}/pymc3/tests/test_parallel_sampling.pyo ${PYSITELIB}/pymc3/tests/test_pickling.py ${PYSITELIB}/pymc3/tests/test_pickling.pyc ${PYSITELIB}/pymc3/tests/test_pickling.pyo Index: pkgsrc/math/py-pymc3/distinfo diff -u pkgsrc/math/py-pymc3/distinfo:1.1 pkgsrc/math/py-pymc3/distinfo:1.2 --- pkgsrc/math/py-pymc3/distinfo:1.1 Fri Jul 6 03:46:43 2018 +++ pkgsrc/math/py-pymc3/distinfo Mon Jul 23 01:37:54 2018 @@ -1,6 +1,6 @@ -$NetBSD: distinfo,v 1.1 2018/07/06 03:46:43 minskim Exp $ +$NetBSD: distinfo,v 1.2 2018/07/23 01:37:54 minskim Exp $ -SHA1 (pymc3-3.4.1.tar.gz) = 859916e93bf653a15bf0637e63067714d17834ce -RMD160 (pymc3-3.4.1.tar.gz) = 9fed35a862543f2dcaa064efae0b57f7e334427f -SHA512 (pymc3-3.4.1.tar.gz) = 122fdfff3e20489c8fb343d6f42c1ac9c1a45ecb9f416266b514ebb3ed84ca9d070a534e1ceaf9156ffa29ab5ca9bdd949adf5fb81e197acc88383ff0bc5d064 -Size (pymc3-3.4.1.tar.gz) = 47538716 bytes +SHA1 (pymc3-3.5.tar.gz) = d5a699bafd327e455e96fc813915807c1cc86325 +RMD160 (pymc3-3.5.tar.gz) = 8fd3b10bf359a4462e1c7397e69b507e706f94b3 +SHA512 (pymc3-3.5.tar.gz) = 3f0dc51f0088d5262dbd8397a8a328f975718da6c45d4aca29b1e035f583dc0beb1dde7abbea5d459d428699bcb854acaec0680549fd8ba5bb168ca3050e94f6 +Size (pymc3-3.5.tar.gz) = 31996796 bytes --_----------=_1532309874264200--