Merge pull request #104 from ejolly/dev

0.7.8 Release

Author: ejolly

conda/meta.yaml

@@ -30,7 +30,7 @@ requirements:
     - numpy >=1.16
     - pandas >=1.0,<1.2
     - patsy >=0.5.1
-    - rpy2 
+    - rpy2 >=3.4.5,<3.5.0 
     - scipy >=1.4.0
     - seaborn >=0.10.0
     - r-base

docs/conf.py

@@ -85,11 +85,11 @@
 master_doc = "index"
 
 # General information about the project.
-project = u"pymer4"
+project = "pymer4"
 import time
 
-copyright = u"2017-{}, Eshin Jolly".format(time.strftime("%Y"))
-author = u"Eshin Jolly"
+copyright = "2017-{}, Eshin Jolly".format(time.strftime("%Y"))
+author = "Eshin Jolly"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -247,15 +247,15 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, "pymer4.tex", u"pymer4 Documentation", u"Eshin Jolly", "manual")
+    (master_doc, "pymer4.tex", "pymer4 Documentation", "Eshin Jolly", "manual")
 ]
 
 
 # -- Options for manual page output ---------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [(master_doc, "pymer4", u"pymer4 Documentation", [author], 1)]
+man_pages = [(master_doc, "pymer4", "pymer4 Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output -------------------------------------------
@@ -267,7 +267,7 @@
     (
         master_doc,
         "pymer4",
-        u"pymer4 Documentation",
+        "pymer4 Documentation",
         author,
         "pymer4",
         "One line description of project.",

docs/new.rst

@@ -2,6 +2,12 @@ What's New
 ==========
 Historically :code:`pymer4` versioning was a bit all over the place but has settled down since 0.5.0. This page includes the most notable updates between versions but github is the best place to checkout more details and `releases <https://github.com/ejolly/pymer4/releases/>`_.
 
+0.7.8
+-----
+- Maintenance release that pins :code:`rpy2 >= 3.4.5,< 3.5.1` due to R -> Python dataframe conversion issue on recent :code:`rpy2` versions that causes a `recursion error <https://github.com/rpy2/rpy2/issues/866>`_. 
+- Pending code changes to support :code:`rpy2 >= 3.5.1` are tracked on `this development branch <https://github.com/ejolly/pymer4/tree/dev_rpy2_3.5.1>`_. **Upcoming releases will drop support for** :code:`rpy2 < 3.5.X`
+- Clearer error message when making circular predictions using :code:`Lmer` models
+
 0.7.7
 -----
 - This version is identical to 0.7.6 but supports :code:`R >= 4.1`

pymer4/models/Lmer.py

@@ -951,7 +951,7 @@ def predict(
             required_cols = self.design_matrix.columns[1:]
             if not all([col in data.columns for col in required_cols]):
                 raise ValueError(
-                    "Column names do not match all fixed effects model terms!\nThis may be a false error if some predictors are categorical, in which case you can bypass this check by setting skip_checks=True."
+                    "Column names do not match all fixed effects model terms!\nThis may be a false error if some predictors are categorical, in which case you can bypass this check by setting skip_data_checks=True."
                 )
 
         if use_rfx:

pymer4/stats.py

@@ -429,7 +429,7 @@ def _calc_stats(x, y, val, equal_var):
             vn1 = v1 / n1
             vn2 = v2 / n2
             with np.errstate(divide="ignore", invalid="ignore"):
-                df = (vn1 + vn2) ** 2 / (vn1 ** 2 / (n1 - 1) + vn2 ** 2 / (n2 - 1))
+                df = (vn1 + vn2) ** 2 / (vn1**2 / (n1 - 1) + vn2**2 / (n2 - 1))
             denom = np.sqrt(vn1 + vn2)
         return numerator / denom, df
 
@@ -616,11 +616,11 @@ def rsquared(y, res, has_constant=True):
     """
 
     y_mean = y.mean()
-    rss = np.sum(res ** 2)
+    rss = np.sum(res**2)
     if has_constant:
         tss = np.sum((y - y_mean) ** 2)
     else:
-        tss = np.sum(y ** 2)
+        tss = np.sum(y**2)
     return 1 - (rss / tss)
 
 

pymer4/tests/test_models.py

@@ -156,7 +156,7 @@ def test_gaussian_lmm():
 
     # If the user skips check, but tries to predict with rfx then R will complain so we
     # can check for an exception raised from R rather than pymer
-    with pytest.raises(RRuntimeError):
+    with pytest.raises((RRuntimeError, ValueError)):
         model.predict(X, skip_data_checks=True, use_rfx=True)
 
     # Finally a user can turn off every kind of check in which case we expect circular predictions

pymer4/utils.py

@@ -147,7 +147,7 @@ def _robust_estimator(vals, X, robust_estimator="hc1", n_lags=1, cluster=None):
         weights = 1 - np.arange(n_lags + 1.0) / (n_lags + 1.0)
 
         # First compute lag 0
-        V = np.diag(vals ** 2)
+        V = np.diag(vals**2)
         meat = weights[0] * np.dot(np.dot(X.T, V), X)
 
         # Now loop over additional lags
@@ -161,7 +161,7 @@ def _robust_estimator(vals, X, robust_estimator="hc1", n_lags=1, cluster=None):
 
     else:
         # Otherwise deal with estimators that modify the same essential operation
-        V = np.diag(vals ** 2)
+        V = np.diag(vals**2)
 
         if robust_estimator == "hc0":
             # No modification of residuals
@@ -412,7 +412,7 @@ def _getAplus(mat):
         return Q * xdiag * Q.T
 
     def _getPs(mat, W=None):
-        W05 = np.matrix(W ** 0.5)
+        W05 = np.matrix(W**0.5)
         return W05.I * _getAplus(W05 * mat * W05) * W05.I
 
     def _getPu(mat, W=None):

pymer4/version.py

@@ -1,4 +1,4 @@
 """Specifies current version of pymer4 to be used by setup.py and __init__.py
 """
 
-__version__ = "0.7.8.dev0"
+__version__ = "0.7.8"

requirements.txt

@@ -1,6 +1,6 @@
 pandas >= 1.1.0
 numpy>=1.16.0
-rpy2>=3.4.5
+rpy2>=3.4.5,<3.5.0
 seaborn>=0.10.0
 matplotlib>=3.0
 patsy>=0.5.1