Adding requirements-test.txt and remove pymc3 tests (#2169)

* Adding requirements-test.txt

* removing link to pymc3 (as it no longer exists)

* Removing pymc(3) from ci/requirements

* Removing pymc(3) from converter

* removing pymc(3) from tests

* Removing pymc(3) from doc/source/api/data.rst

* black

Co-authored-by: Oriol (ZBook) <oriol.abril.pla@gmail.com>

.azure-pipelines/azure-pipelines-external.yml

@@ -14,15 +14,13 @@ jobs:
         python.version: "3.9"
         pystan.version: "latest"
         cmdstanpy.version: "latest"
-        pymc3.version: "latest"
         emcee.version: "latest"
         name: "External latest"
 
       Python_39_Special_versions:
         python.version: "3.9"
         pystan.version: 2.19.1.1
         cmdstanpy.version: "github"
-        pymc3.version: "github"
         emcee.version: 2
         name: "External special"
 
@@ -74,14 +72,7 @@ jobs:
           python -m pip --no-cache-dir install "emcee<3"
       fi
 
-      if [ "$(pymc3.version)" = "github" ]; then
-           python -m pip --no-cache-dir --log log.txt install git+https://github.com/pymc-devs/pymc3@v3
-           cat log.txt
-      else
-          python -m pip --no-cache-dir install pymc3
-      fi
-
-      grep -Ev '^pystan|^cmdstanpy|^emcee|^pymc3' requirements-external.txt | xargs python -m pip install
+      grep -Ev '^pystan|^cmdstanpy|^emcee' requirements-external.txt | xargs python -m pip install
 
     displayName: 'Install packages'
 

arviz/data/__init__.py

@@ -12,7 +12,6 @@
 from .io_netcdf import from_netcdf, to_netcdf
 from .io_numpyro import from_numpyro
 from .io_pyjags import from_pyjags
-from .io_pymc3 import from_pymc3, from_pymc3_predictions
 from .io_pyro import from_pyro
 from .io_pystan import from_pystan
 from .utils import extract, extract_dataset
@@ -31,8 +30,6 @@
     "convert_to_inference_data",
     "from_beanmachine",
     "from_pyjags",
-    "from_pymc3",
-    "from_pymc3_predictions",
     "from_pystan",
     "from_emcee",
     "from_cmdstan",

arviz/data/converters.py

@@ -9,7 +9,6 @@
 from .io_cmdstanpy import from_cmdstanpy
 from .io_emcee import from_emcee
 from .io_numpyro import from_numpyro
-from .io_pymc3 import from_pymc3
 from .io_pyro import from_pyro
 from .io_pystan import from_pystan
 
@@ -23,14 +22,13 @@ def convert_to_inference_data(obj, *, group="posterior", coords=None, dims=None,
 
     Parameters
     ----------
-    obj : dict, str, np.ndarray, xr.Dataset, pystan fit, pymc3 trace
+    obj : dict, str, np.ndarray, xr.Dataset, pystan fit
         A supported object to convert to InferenceData:
             | InferenceData: returns unchanged
             | str: Attempts to load the cmdstan csv or netcdf dataset from disk
             | pystan fit: Automatically extracts data
             | cmdstanpy fit: Automatically extracts data
             | cmdstan csv-list: Automatically extracts data
-            | pymc3 trace: Automatically extracts data
             | emcee sampler: Automatically extracts data
             | pyro MCMC: Automatically extracts data
             | beanmachine MonteCarloSamples: Automatically extracts data
@@ -89,8 +87,6 @@ def convert_to_inference_data(obj, *, group="posterior", coords=None, dims=None,
             return from_cmdstanpy(**kwargs)
         else:  # pystan or pystan3
             return from_pystan(**kwargs)
-    elif obj.__class__.__name__ == "MultiTrace":  # ugly, but doesn't make PyMC3 a requirement
-        return from_pymc3(trace=kwargs.pop(group), **kwargs)
     elif obj.__class__.__name__ == "EnsembleSampler":  # ugly, but doesn't make emcee a requirement
         return from_emcee(sampler=kwargs.pop(group), **kwargs)
     elif obj.__class__.__name__ == "MonteCarloSamples":
@@ -125,7 +121,6 @@ def convert_to_inference_data(obj, *, group="posterior", coords=None, dims=None,
             "netcdf filename",
             "numpy array",
             "pystan fit",
-            "pymc3 trace",
             "emcee fit",
             "pyro mcmc fit",
             "numpyro mcmc fit",
@@ -152,13 +147,12 @@ def convert_to_dataset(obj, *, group="posterior", coords=None, dims=None):
 
     Parameters
     ----------
-    obj : dict, str, np.ndarray, xr.Dataset, pystan fit, pymc3 trace
+    obj : dict, str, np.ndarray, xr.Dataset, pystan fit
         A supported object to convert to InferenceData:
 
         - InferenceData: returns unchanged
         - str: Attempts to load the netcdf dataset from disk
         - pystan fit: Automatically extracts data
-        - pymc3 trace: Automatically extracts data
         - xarray.Dataset: adds to InferenceData as only group
         - xarray.DataArray: creates an xarray dataset as the only group, gives the
           array an arbitrary name, if name not set