Merge pull request #250 from ICB-DCM/develop

Release 0.9.26

.travis.yml

@@ -31,7 +31,7 @@ install:
 # run tests
 
 script:
-- travis_wait 15 python -m pytest --cov=pyabc test/test_*
+- travis_wait 20 python -m pytest --cov=pyabc test/test_*
 - travis_wait 5 xvfb-run -a python -m pytest --cov=pyabc --cov-append test/visualization/test_*
 - if [ "$TRAVIS_PULL_REQUEST" != "false" ]; then travis_wait 15 test/run_notebooks.sh; fi
 

doc/examples/resuming.ipynb

@@ -54,7 +54,7 @@
    "outputs": [],
    "source": [
     "from pyabc import ABCSMC, Distribution, RV\n",
-    "import scipy as sp\n",
+    "import numpy as np\n",
     "from tempfile import gettempdir\n",
     "import os"
    ]
@@ -76,7 +76,7 @@
    "outputs": [],
    "source": [
     "def model(parameter):\n",
-    "    return {\"data\": parameter[\"mean\"] + sp.randn()}\n",
+    "    return {\"data\": parameter[\"mean\"] + np.random.randn()}\n",
     "\n",
     "prior = Distribution(mean=RV(\"uniform\", 0, 5))\n",
     "\n",
@@ -105,14 +105,14 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "INFO:History:Start <ABCSMC(id=44, start_time=2019-11-10 23:36:40.114079, end_time=None)>\n"
+      "INFO:History:Start <ABCSMC(id=1, start_time=2020-01-10 19:58:36.207963, end_time=None)>\n"
      ]
     },
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Run ID: 44\n"
+      "Run ID: 1\n"
      ]
     }
    ],
@@ -143,14 +143,14 @@
      "output_type": "stream",
      "text": [
       "INFO:ABC:Calibration sample before t=0.\n",
-      "INFO:Epsilon:initial epsilon is 1.2912959543955556\n",
-      "INFO:ABC:t: 0, eps: 1.2912959543955556.\n",
-      "INFO:ABC:Acceptance rate: 100 / 224 = 4.4643e-01.\n",
-      "INFO:ABC:t: 1, eps: 0.6651774908568672.\n",
-      "INFO:ABC:Acceptance rate: 100 / 326 = 3.0675e-01.\n",
-      "INFO:ABC:t: 2, eps: 0.33355947653050755.\n",
-      "INFO:ABC:Acceptance rate: 100 / 572 = 1.7483e-01.\n",
-      "INFO:History:Done <ABCSMC(id=44, start_time=2019-11-10 23:36:40.114079, end_time=2019-11-10 23:36:42.568825)>\n"
+      "INFO:Epsilon:initial epsilon is 1.281948779424301\n",
+      "INFO:ABC:t: 0, eps: 1.281948779424301.\n",
+      "INFO:ABC:Acceptance rate: 100 / 193 = 5.1813e-01, ESS=1.0000e+02.\n",
+      "INFO:ABC:t: 1, eps: 0.593462311078578.\n",
+      "INFO:ABC:Acceptance rate: 100 / 338 = 2.9586e-01, ESS=8.2825e+01.\n",
+      "INFO:ABC:t: 2, eps: 0.3285232421992942.\n",
+      "INFO:ABC:Acceptance rate: 100 / 506 = 1.9763e-01, ESS=7.8478e+01.\n",
+      "INFO:History:Done <ABCSMC(id=1, start_time=2020-01-10 19:58:36.207963, end_time=2020-01-10 19:58:41.387478)>\n"
      ]
     }
    ],
@@ -241,7 +241,7 @@
     {
      "data": {
       "text/plain": [
-       "<pyabc.storage.history.History at 0x7fbc67733b70>"
+       "<pyabc.storage.history.History at 0x7fe45e76b9e8>"
       ]
      },
      "execution_count": 7,
@@ -262,16 +262,16 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "INFO:Epsilon:initial epsilon is 0.1529406275096243\n",
-      "INFO:ABC:t: 3, eps: 0.1529406275096243.\n",
-      "INFO:ABC:Acceptance rate: 100 / 1197 = 8.3542e-02.\n",
-      "INFO:History:Done <ABCSMC(id=44, start_time=2019-11-10 23:36:40.114079, end_time=2019-11-10 23:36:44.358045)>\n"
+      "INFO:Epsilon:initial epsilon is 0.19946300333077085\n",
+      "INFO:ABC:t: 3, eps: 0.19946300333077085.\n",
+      "INFO:ABC:Acceptance rate: 100 / 931 = 1.0741e-01, ESS=9.0195e+01.\n",
+      "INFO:History:Done <ABCSMC(id=1, start_time=2020-01-10 19:58:36.207963, end_time=2020-01-10 19:58:48.110429)>\n"
      ]
     },
     {
      "data": {
       "text/plain": [
-       "<pyabc.storage.history.History at 0x7fbc67733b70>"
+       "<pyabc.storage.history.History at 0x7fe45e76b9e8>"
       ]
      },
      "execution_count": 8,

doc/releasenotes.rst

@@ -8,6 +8,20 @@ Release Notes
 ..........
 
 
+0.9.26 (2020-01-24)
+-------------------
+
+* Add optional check whether database is non-existent, to detect typos.
+* Set lower bound in 1-dim KDEs to <= 0 to not wrongly display near-uniform
+  distributions. (both #257)
+* Implement redis password protection for sampler and manage routine (#256).
+* Make samplers available in global namespace (#249).
+* Implement ListTemperature (#248).
+* Allow plotting the relative ESS (#245).
+* Allow resampling of weighted particles (#244).
+* Fix ABCSMC.load with rpy2 (#242).
+
+
 0.9.25 (2020-01-08)
 -------------------