[pkgsrc/trunk]: pkgsrc/math/py-pymc3 math/py-pymc3: Update to 3.5

[minskim <minskim%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/2243c59e049a
branches:  trunk
changeset: 310749:2243c59e049a
user:      minskim <minskim%pkgsrc.org@localhost>
date:      Mon Jul 23 01:37:54 2018 +0000

description:
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

diffstat:

 math/py-pymc3/Makefile |   4 ++--
 math/py-pymc3/PLIST    |  20 ++++++++++++++++----
 math/py-pymc3/distinfo |  10 +++++-----
 3 files changed, 23 insertions(+), 11 deletions(-)

diffs (89 lines):

diff -r e9e12ea3c7b5 -r 2243c59e049a math/py-pymc3/Makefile
--- a/math/py-pymc3/Makefile    Mon Jul 23 01:07:08 2018 +0000
+++ b/math/py-pymc3/Makefile    Mon Jul 23 01:37:54 2018 +0000
@@ -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/}
diff -r e9e12ea3c7b5 -r 2243c59e049a math/py-pymc3/PLIST
--- a/math/py-pymc3/PLIST       Mon Jul 23 01:07:08 2018 +0000
+++ b/math/py-pymc3/PLIST       Mon Jul 23 01:37:54 2018 +0000
@@ -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/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/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/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_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_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
 ${PYSITELIB}/pymc3/tests/test_pickling.pyo
diff -r e9e12ea3c7b5 -r 2243c59e049a math/py-pymc3/distinfo
--- a/math/py-pymc3/distinfo    Mon Jul 23 01:07:08 2018 +0000
+++ b/math/py-pymc3/distinfo    Mon Jul 23 01:37:54 2018 +0000
@@ -1,6 +1,6 @@
-$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