pypest · jwhite-usgs · Sep 16, 2020 · Sep 16, 2020 · Sep 16, 2020 · Sep 16, 2020
diff --git a/.nojekyll b/.nojekyll
diff --git a/autotest/pst_from_tests.py b/autotest/pst_from_tests.py
@@ -1202,7 +1202,8 @@ def mf6_freyberg_direct_test():
     #                     index_cols='obsnme', use_cols='obsval', prefix='hds')
 
     df = pd.read_csv(os.path.join(tmp_model_ws, "sfr.csv"), index_col=0)
-    pf.add_observations("sfr.csv", insfile="sfr.csv.ins", index_cols="time", use_cols=list(df.columns.values))
+    pf.add_observations("sfr.csv", insfile="sfr.csv.ins", index_cols="time",
+                        use_cols=["GAGE_1","HEADWATER","TAILWATER"],ofile_sep=",")
     v = pyemu.geostats.ExpVario(contribution=1.0, a=1000)
     gr_gs = pyemu.geostats.GeoStruct(variograms=v,transform="log")
     rch_temporal_gs = pyemu.geostats.GeoStruct(variograms=pyemu.geostats.ExpVario(contribution=1.0, a=60))
@@ -1217,9 +1218,10 @@ def mf6_freyberg_direct_test():
         arr_files = [f for f in os.listdir(tmp_model_ws) if tag in f and f.endswith(".txt")]
         if "rch" in tag:
             for arr_file in arr_files:
+                recharge_files = ["recharge_1.txt","recharge_2.txt","recharge_3.txt"]
                 pf.add_parameters(filenames=arr_file, par_type="grid", par_name_base="rch_gr",
                                   pargp="rch_gr", zone_array=ib, upper_bound=1.0e-3, lower_bound=1.0e-7,
-                                  geostruct=gr_gs,par_style="direct")
+                                  par_style="direct")
 
             for arr_file in arr_files:
                 kper = int(arr_file.split('.')[1].split('_')[-1]) - 1
@@ -1243,7 +1245,7 @@ def mf6_freyberg_direct_test():
         kper = int(list_file.split(".")[1].split('_')[-1]) - 1
         #add spatially constant, but temporally correlated wel flux pars
         pf.add_parameters(filenames=list_file, par_type="constant", par_name_base="twel_mlt_{0}".format(kper),
-                          pargp="twel_mlt".format(kper), index_cols=[0, 1, 2], use_cols=[3],
+                          pargp="twel_mlt_{0}".format(kper), index_cols=[0, 1, 2], use_cols=[3],
                           upper_bound=1.5, lower_bound=0.5, datetime=dts[kper], geostruct=rch_temporal_gs)
 
         # add temporally indep, but spatially correlated wel flux pars
@@ -1266,6 +1268,8 @@ def mf6_freyberg_direct_test():
 
     # build pest
     pst = pf.build_pst('freyberg.pst')
+    cov = pf.build_prior(fmt="non")
+    cov.to_coo("prior.jcb")
     pst.try_parse_name_metadata()
     df = pd.read_csv(os.path.join(tmp_model_ws, "heads.csv"), index_col=0)
     pf.add_observations("heads.csv", insfile="heads.csv.ins", index_cols="time", use_cols=list(df.columns.values),
@@ -1462,5 +1466,5 @@ def mf6_freyberg_varying_idomain():
     #mf6_freyberg_test()
     #mf6_freyberg_shortnames_test()
     # mf6_freyberg_da_test()
-    # mf6_freyberg_direct_test()
-    mf6_freyberg_varying_idomain()
+    mf6_freyberg_direct_test()
+    #mf6_freyberg_varying_idomain()
diff --git a/docs/Makefile b/docs/Makefile
@@ -1,13 +1,12 @@
 # Minimal makefile for Sphinx documentation
 #
 
-# You can set these variables from the command line.
-SPHINXOPTS    =
-SPHINXBUILD   = sphinx-build
-SPHINXPROJ    = pyemu
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
 SOURCEDIR     = .
-#BUILDDIR      = _build
-BUILDDIR      = ../../pyemudoc
+BUILDDIR      = _build
 
 # Put it first so that "make" without argument is like "make help".
 help:
@@ -18,4 +17,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/_autosummary/pyemu.ErrVar.rst b/docs/_autosummary/pyemu.ErrVar.rst
@@ -0,0 +1,6 @@
+pyemu.ErrVar
+============
+
+.. currentmodule:: pyemu
+
+.. autoclass:: ErrVar
diff --git a/docs/_autosummary/pyemu.ParameterEnsemble.rst b/docs/_autosummary/pyemu.ParameterEnsemble.rst
@@ -0,0 +1,6 @@
+pyemu.ParameterEnsemble
+=======================
+
+.. currentmodule:: pyemu
+
+.. autoclass:: ParameterEnsemble
diff --git a/docs/_autosummary/pyemu.Pst.rst b/docs/_autosummary/pyemu.Pst.rst
@@ -0,0 +1,6 @@
+pyemu.Pst
+=========
+
+.. currentmodule:: pyemu
+
+.. autoclass:: Pst
diff --git a/docs/_autosummary/pyemu.Schur.rst b/docs/_autosummary/pyemu.Schur.rst
@@ -0,0 +1,6 @@
+pyemu.Schur
+===========
+
+.. currentmodule:: pyemu
+
+.. autoclass:: Schur
diff --git a/docs/_autosummary/pyemu.rst b/docs/_autosummary/pyemu.rst
@@ -0,0 +1,6 @@
+pyemu
+=====
+
+.. currentmodule:: pyemu
+
+.. automodule:: pyemu
diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
diff --git a/docs/_build/doctrees/index.doctree b/docs/_build/doctrees/index.doctree
diff --git a/docs/_build/doctrees/pst_demo.doctree b/docs/_build/doctrees/pst_demo.doctree
diff --git a/docs/_build/doctrees/source/Monte_carlo.doctree b/docs/_build/doctrees/source/Monte_carlo.doctree
diff --git a/docs/_build/doctrees/source/glossary.doctree b/docs/_build/doctrees/source/glossary.doctree
diff --git a/docs/_build/doctrees/source/introduction.doctree b/docs/_build/doctrees/source/introduction.doctree
diff --git a/docs/_build/doctrees/source/modules.doctree b/docs/_build/doctrees/source/modules.doctree
diff --git a/docs/_build/doctrees/source/oop.doctree b/docs/_build/doctrees/source/oop.doctree
diff --git a/docs/_build/doctrees/source/pst_demo.doctree b/docs/_build/doctrees/source/pst_demo.doctree
diff --git a/docs/_build/doctrees/source/pyemu.doctree b/docs/_build/doctrees/source/pyemu.doctree
diff --git a/docs/_build/doctrees/source/pyemu.mat.doctree b/docs/_build/doctrees/source/pyemu.mat.doctree
diff --git a/docs/_build/doctrees/source/pyemu.pst.doctree b/docs/_build/doctrees/source/pyemu.pst.doctree
diff --git a/docs/_build/doctrees/source/pyemu.utils.doctree b/docs/_build/doctrees/source/pyemu.utils.doctree
diff --git a/docs/_build/html/.buildinfo b/docs/_build/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 456cf1aed9222d9ca0143fcad78d868a
+config: 212d570f185ae4a16a03fde6f4b7681c
 tags: 645f666f9bcd5a90fca523b33c5a78b7
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