Merge pull request #165 from fonnesbeck/pymc_rename

Rename pymc3 -> pymc

Author: fonnesbeck

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,5 +1,6 @@
 # Thank you for opening a pull request!
 
+
 Please check our [style guide](https://docs.pymc.io/en/latest/contributing/jupyter_style.html), and also make sure that the notebooks you've modified pass the `pre-commit` checks. If, for example, you modified `notebook1.ipynb` and `notebook2.ipynb`, you could do this by running:
 
 ```bash

BCM/CaseStudies/ExtrasensoryPerception.ipynb

@@ -11,7 +11,7 @@
     "import arviz as az\n",
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
-    "import pymc3 as pm\n",
+    "import pymc as pm\n",
     "import scipy as sp\n",
     "\n",
     "from matplotlib import gridspec\n",
@@ -623,7 +623,7 @@
      "output_type": "stream",
      "text": [
       "arviz 0.7.0\n",
-      "pymc3 3.8\n",
+      "pymc 3.8\n",
       "scipy 1.3.1\n",
       "numpy 1.17.3\n",
       "last updated: Mon Apr 27 2020 \n",

BCM/CaseStudies/HeuristicDecisionMaking.ipynb

@@ -9,7 +9,7 @@
     "import arviz as az\n",
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
-    "import pymc3 as pm\n",
+    "import pymc as pm\n",
     "import scipy.io as sio\n",
     "\n",
     "from scipy import stats\n",
@@ -179,7 +179,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/Users/alex_andorra/opt/anaconda3/envs/BCM_pymc3/lib/python3.7/site-packages/pymc3/sampling.py:1585: UserWarning: samples parameter is smaller than nchains times ndraws, some draws and/or chains may not be represented in the returned posterior predictive sample\n",
+      "/Users/alex_andorra/opt/anaconda3/envs/BCM_pymc/lib/python3.7/site-packages/pymc/sampling.py:1585: UserWarning: samples parameter is smaller than nchains times ndraws, some draws and/or chains may not be represented in the returned posterior predictive sample\n",
       "  \"samples parameter is smaller than nchains times ndraws, some draws \"\n"
      ]
     },
@@ -564,7 +564,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/Users/alex_andorra/opt/anaconda3/envs/BCM_pymc3/lib/python3.7/site-packages/ipykernel_launcher.py:8: FutureWarning: arrays to stack must be passed as a \"sequence\" type such as list or tuple. Support for non-sequence iterables such as generators is deprecated as of NumPy 1.16 and will raise an error in the future.\n",
+      "/Users/alex_andorra/opt/anaconda3/envs/BCM_pymc/lib/python3.7/site-packages/ipykernel_launcher.py:8: FutureWarning: arrays to stack must be passed as a \"sequence\" type such as list or tuple. Support for non-sequence iterables such as generators is deprecated as of NumPy 1.16 and will raise an error in the future.\n",
       "  \n"
      ]
     },
@@ -769,7 +769,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/Users/alex_andorra/opt/anaconda3/envs/BCM_pymc3/lib/python3.7/site-packages/pymc3/sampling.py:1585: UserWarning: samples parameter is smaller than nchains times ndraws, some draws and/or chains may not be represented in the returned posterior predictive sample\n",
+      "/Users/alex_andorra/opt/anaconda3/envs/BCM_pymc/lib/python3.7/site-packages/pymc/sampling.py:1585: UserWarning: samples parameter is smaller than nchains times ndraws, some draws and/or chains may not be represented in the returned posterior predictive sample\n",
       "  \"samples parameter is smaller than nchains times ndraws, some draws \"\n"
      ]
     },
@@ -844,7 +844,7 @@
      "text": [
       "numpy 1.18.1\n",
       "arviz 0.7.0\n",
-      "pymc3 3.8\n",
+      "pymc 3.8\n",
       "last updated: Mon Apr 27 2020 \n",
       "\n",
       "CPython 3.7.7\n",
@@ -861,7 +861,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "BCM_pymc3",
+   "display_name": "BCM_pymc",
    "language": "python",
    "name": "bcm_pymc3"
   },

BCM/CaseStudies/MemoryRetention.ipynb

@@ -12,7 +12,7 @@
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
     "import pandas as pd\n",
-    "import pymc3 as pm\n",
+    "import pymc as pm\n",
     "import seaborn as sns\n",
     "import theano\n",
     "\n",
@@ -994,7 +994,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "pymc3   3.8\n",
+      "pymc   3.8\n",
       "pandas  1.0.3\n",
       "arviz   0.7.0\n",
       "seaborn 0.10.0\n",
@@ -1016,7 +1016,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "BCM_pymc3",
+   "display_name": "BCM_pymc",
    "language": "python",
    "name": "bcm_pymc3"
   },

BCM/CaseStudies/MultinomialProcessingTrees.ipynb

@@ -11,7 +11,7 @@
     "import arviz as az\n",
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
-    "import pymc3 as pm\n",
+    "import pymc as pm\n",
     "import scipy.special as sp\n",
     "import theano\n",
     "\n",
@@ -859,7 +859,7 @@
      "output_type": "stream",
      "text": [
       "numpy  1.18.1\n",
-      "pymc3  3.8\n",
+      "pymc  3.8\n",
       "theano 1.0.4\n",
       "arviz  0.7.0\n",
       "last updated: Mon Apr 27 2020 \n",
@@ -878,7 +878,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "BCM_pymc3",
+   "display_name": "BCM_pymc",
    "language": "python",
    "name": "bcm_pymc3"
   },

BCM/CaseStudies/NumberConceptDevelopment.ipynb

@@ -11,7 +11,7 @@
     "import arviz as az\n",
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
-    "import pymc3 as pm\n",
+    "import pymc as pm\n",
     "import scipy.io as sio\n",
     "import theano\n",
     "\n",
@@ -1024,7 +1024,7 @@
      "text": [
       "theano 1.0.4\n",
       "numpy  1.18.1\n",
-      "pymc3  3.8\n",
+      "pymc  3.8\n",
       "arviz  0.7.0\n",
       "last updated: Mon Apr 27 2020 \n",
       "\n",
@@ -1042,7 +1042,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "BCM_pymc3",
+   "display_name": "BCM_pymc",
    "language": "python",
    "name": "bcm_pymc3"
   },

BCM/CaseStudies/PsychophysicalFunctions.ipynb

@@ -10,11 +10,11 @@
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
     "import pandas as pd\n",
-    "import pymc3 as pm\n",
+    "import pymc as pm\n",
     "import theano\n",
     "\n",
     "from matplotlib import gridspec\n",
-    "from pymc3.step_methods.hmc import quadpotential\n",
+    "from pymc.step_methods.hmc import quadpotential\n",
     "from scipy import stats\n",
     "from theano import tensor as tt\n",
     "\n",
@@ -1169,7 +1169,7 @@
       "numpy  1.18.1\n",
       "theano 1.0.4\n",
       "arviz  0.7.0\n",
-      "pymc3  3.8\n",
+      "pymc  3.8\n",
       "pandas 1.0.3\n",
       "last updated: Mon Apr 27 2020 \n",
       "\n",
@@ -1187,7 +1187,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "BCM_pymc3",
+   "display_name": "BCM_pymc",
    "language": "python",
    "name": "bcm_pymc3"
   },

BCM/CaseStudies/SignalDetectionTheory.ipynb

@@ -10,7 +10,7 @@
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
     "import pandas as pd\n",
-    "import pymc3 as pm\n",
+    "import pymc as pm\n",
     "import seaborn as sns\n",
     "\n",
     "from matplotlib.patches import Polygon\n",
@@ -672,7 +672,7 @@
    "metadata": {},
    "source": [
     "### Note from Junpeng Lao\n",
-    "Sampling using HMC (e.g., in STAN and PyMC3), there are better way to diagnose biased inference [[1]](http://mc-stan.org/documentation/case-studies/divergences_and_bias.html), [[2]](http://pymc-devs.github.io/pymc3/notebooks/Diagnosing_biased_Inference_with_Divergences.html)."
+    "Sampling using HMC (e.g., in STAN and PyMC), there are better way to diagnose biased inference [[1]](http://mc-stan.org/documentation/case-studies/divergences_and_bias.html), [[2]](http://pymc-devs.github.io/pymc/notebooks/Diagnosing_biased_Inference_with_Divergences.html)."
    ]
   },
   {
@@ -819,7 +819,7 @@
    "source": [
     "As shown above, there are a lot of divergences in the trace, and the energy plot is very different from the energy_diff. This is a strong indication of bias in the estimation, and better reparameterization is needed.\n",
     "\n",
-    "Moreover, the reparameterization, which works better in BUGS/JAGS using Gibbs sampler, actually perform worse using NUTS. Again, this demonstrates that many of the tricks and intuition we got using BUGS/JAGS might not translate to PyMC3 and STAN."
+    "Moreover, the reparameterization, which works better in BUGS/JAGS using Gibbs sampler, actually perform worse using NUTS. Again, this demonstrates that many of the tricks and intuition we got using BUGS/JAGS might not translate to PyMC and STAN."
    ]
   },
   {
@@ -1061,7 +1061,7 @@
      "output_type": "stream",
      "name": "stdout",
      "text": [
-      "seaborn 0.11.0\npymc3   3.9.2\npandas  1.0.3\narviz   0.10.0\nnumpy   1.18.2\nlast updated: Mon Nov 23 2020 \n\nCPython 3.8.5\nIPython 7.13.0\nwatermark 2.0.2\n"
+      "seaborn 0.11.0\npymc   3.9.2\npandas  1.0.3\narviz   0.10.0\nnumpy   1.18.2\nlast updated: Mon Nov 23 2020 \n\nCPython 3.8.5\nIPython 7.13.0\nwatermark 2.0.2\n"
      ]
     }
    ],

BCM/CaseStudies/TheBARTModelofRiskTaking.ipynb

@@ -10,7 +10,7 @@
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
     "import pandas as pd\n",
-    "import pymc3 as pm\n",
+    "import pymc as pm\n",
     "\n",
     "from scipy import stats\n",
     "from theano import tensor as tt\n",
@@ -463,7 +463,7 @@
      "text": [
       "numpy  1.18.1\n",
       "arviz  0.7.0\n",
-      "pymc3  3.8\n",
+      "pymc  3.8\n",
       "pandas 1.0.3\n",
       "last updated: Tue Apr 28 2020 \n",
       "\n",
@@ -481,7 +481,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "BCM_pymc3",
+   "display_name": "BCM_pymc",
    "language": "python",
    "name": "bcm_pymc3"
   },

BCM/CaseStudies/TheGCMModelofCategorization.ipynb

@@ -10,7 +10,7 @@
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
     "import pandas as pd\n",
-    "import pymc3 as pm\n",
+    "import pymc as pm\n",
     "import scipy.io as sio\n",
     "import seaborn as sns\n",
     "import theano\n",
@@ -201,7 +201,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/Users/alex_andorra/opt/anaconda3/envs/BCM_pymc3/lib/python3.7/site-packages/pymc3/sampling.py:1585: UserWarning: samples parameter is smaller than nchains times ndraws, some draws and/or chains may not be represented in the returned posterior predictive sample\n",
+      "/Users/alex_andorra/opt/anaconda3/envs/BCM_pymc/lib/python3.7/site-packages/pymc/sampling.py:1585: UserWarning: samples parameter is smaller than nchains times ndraws, some draws and/or chains may not be represented in the returned posterior predictive sample\n",
       "  \"samples parameter is smaller than nchains times ndraws, some draws \"\n"
      ]
     },
@@ -696,7 +696,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/Users/alex_andorra/opt/anaconda3/envs/BCM_pymc3/lib/python3.7/site-packages/pymc3/sampling.py:1585: UserWarning: samples parameter is smaller than nchains times ndraws, some draws and/or chains may not be represented in the returned posterior predictive sample\n",
+      "/Users/alex_andorra/opt/anaconda3/envs/BCM_pymc/lib/python3.7/site-packages/pymc/sampling.py:1585: UserWarning: samples parameter is smaller than nchains times ndraws, some draws and/or chains may not be represented in the returned posterior predictive sample\n",
       "  \"samples parameter is smaller than nchains times ndraws, some draws \"\n"
      ]
     },
@@ -778,7 +778,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "pymc3   3.8\n",
+      "pymc   3.8\n",
       "pandas  1.0.3\n",
       "numpy   1.18.1\n",
       "arviz   0.7.0\n",
@@ -800,7 +800,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "BCM_pymc3",
+   "display_name": "BCM_pymc",
    "language": "python",
    "name": "bcm_pymc3"
   },