setup: bump dclab to 0.61.3 (replace rpy2 with wrapper) (close #73, c…

…lose #161)

.github/workflows/check.yml

@@ -35,6 +35,12 @@ jobs:
       uses: r-lib/actions/setup-r@v2
       with:
         r-version: '4.1.2'
+    - name: Install R packages for lme4
+      if: matrix.extras == 'all'
+      shell: bash
+      run: |
+        R --version
+        R -e "install.packages(c('statmod','nloptr','lme4'),repos='http://cran.rstudio.org')"
     - name: Install Python dependencies
       run: |
         # prerequisites

.readthedocs.yml

@@ -8,8 +8,6 @@ build:
   jobs:
     post_checkout:
       - git fetch --unshallow || true
-    pre_install:
-      - RPY2_CFFI_MODE=ABI
 python:
   install:
     - requirements: docs/requirements.txt

CHANGELOG

@@ -1,3 +1,5 @@
+2.18.1
+ - setup: bump dclab to 0.61.3 (replace rpy2 with wrapper) (#73 #161)
 2.18.0
  - BREAKING CHANGE: set default viscosity model for Young's modulus
    computation to "buyukurganci-2022", because it is more accurate

docs/requirements.txt

@@ -2,8 +2,6 @@ dclab>=0.58.2
 h5py
 matplotlib
 numpy
-# Don't forget to set the environment variable RPY2_CFFI_MODE=ABI on rtd!
-rpy2
 pyqt5
 scipy
 sphinx

docs/sec_qg_lme4.rst

@@ -6,25 +6,15 @@ Statistical significance testing (R and lme4)
 Since version 2.5.0, Shape-Out 2 allows you to quantify the statistical
 significance (p-value) when comparing two measurement groups. For this to
 work, you need to have R installed (tested with
-`R 3.6.3 <https://cran.r-project.org/bin/windows/base/old/3.6.3/>`_ ).
+`R 4.1.2 <https://cran.r-project.org>`_ ).
 The analysis uses linear mixed effects models (LMM) as described
 in :cite:`Herbig2018` and yields results identical to those obtained
 with Shape-Out 1.
 
-.. warning::
-    Unfortunately, LMM analysis currently does not work with the .app or
-    .pkg bundle on macOS or the Windows installer. This problem is tracked in
-    `issue #73
-    <https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut2/issues/73>`_ and
-    `issue #161
-    <https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut2/issues/161>`_.
-    If you are using macOS and you would like to use LMM analysis, you have to
-    install Shape-Out 2 as a Python package (see :ref:`sec_installation`).
-
 The LMM analysis is performed using the lme4 R package
 and is based on the :ref:`implementation in dclab <dclab:sec_av_lme4>`
-(please read for more information on the options available) which uses
-`rpy2 <https://github.com/rpy2/rpy2/>`_ to connect to R.
+(please read for more information on the options available) which implements
+a wrapper calling ``Rscript``.
 Here, we make use of the dataset :cite:`FigshareLMM` to illustrate this
 functionality.
 

pyproject.toml

@@ -30,7 +30,7 @@ classifiers = [
 license = {text = "GPL v3"}
 dependencies = [
     "fcswrite>=0.5.1",
-    "dclab[dcor,http]>=0.60.1",
+    "dclab[dcor,http]>=0.61.3",
     "h5py>=2.8.0",
     "numpy>=1.21",  # CVE-2021-33430
     "pyqt5",

shapeout2/gui/compute/comp_lme4_results.py

@@ -38,13 +38,20 @@ def __init__(self, parent, rlme4_results, *args, **kwargs):
 
         # summary text
         summary = []
+        if res["lme4 messages"]:
+            summary += ["lme4 messages"]
+            summary += ["-------------"]
+            summary += str(res["lme4 messages"]).split("\n")
+            summary += "\n"
         summary += ["Model summary"]
         summary += ["-------------"]
         summary += self.parse_r_model_summary(
             str(res["r model summary"]).split("\n"))
+        summary += "\n"
         summary += ["Coefficient table"]
         summary += ["-----------------"]
         summary += str(res["r model coefficients"]).split("\n")
+        summary += "\n"
         summary += ["Anova test"]
         summary += ["----------"]
         summary += str(res["r anova"]).split("\n")

shapeout2/gui/main.py

@@ -7,7 +7,6 @@
 import webbrowser
 
 import dclab
-from dclab.lme4.rlibs import rpy2, MockRPackage
 from dclab.lme4 import rsetup
 import h5py
 import numpy
@@ -126,8 +125,6 @@ def __init__(self, *arguments):
             self.on_action_compute_statistics)
         self.actionComputeSignificance.triggered.connect(
             self.on_action_compute_significance)
-        self.actionComputeSignificance.setVisible(
-            not isinstance(rpy2, MockRPackage))  # only show if rpy2 is there
         # Export menu
         # data
         self.actionExportData.triggered.connect(self.on_action_export_data)
@@ -607,7 +604,7 @@ def on_action_compute_significance(self):
         else:
             QtWidgets.QMessageBox.critical(
                 self, "R not found!",
-                "The R executable was not found by rpy2. Please add it "
+                "The R executable was not found. Please add it "
                 + "to the PATH variable or define it manually in the "
                 + "Shape-Out preferences.")
 
@@ -837,8 +834,6 @@ def on_action_software(self):
                 pg,
                 scipy,
                 ]
-        if not isinstance(rpy2, MockRPackage):
-            libs.append(rpy2)
 
         sw_text = f"Shape-Out {version}\n\n"
         sw_text += f"Python {sys.version}\n\n"

shapeout2/gui/preferences.py

@@ -5,23 +5,16 @@
 import pkg_resources
 import platform
 
-from dclab.lme4.rlibs import (
-    rpy2, MockRPackage, RPY2UnavailableError, RUnavailableError)
 from dclab.rtdc_dataset.fmt_dcor import access_token
 from dclab.lme4 import rsetup
 from PyQt5 import uic, QtCore, QtWidgets
 from PyQt5.QtCore import QStandardPaths
 
+from dclab.lme4.rsetup import RNotFoundError
 from .widgets import show_wait_cursor
 from ..extensions import ExtensionManager, SUPPORTED_FORMATS
 
 
-if isinstance(rpy2, MockRPackage):
-    RPY2_AVAILABLE = not isinstance(rpy2.exception, RPY2UnavailableError)
-else:
-    RPY2_AVAILABLE = True
-
-
 class ExtensionErrorWrapper:
     def __init__(self, ehash):
         self.ehash = ehash
@@ -55,13 +48,13 @@ def __init__(self, parent, *args, **kwargs):
         self.parent = parent
 
         # Get default R path
-        if RPY2_AVAILABLE and rsetup.has_r():
+        if rsetup.has_r():
             rdefault = rsetup.get_r_path()
         else:
             rdefault = ""
 
         # disable R settings
-        self.tab_r.setEnabled(RPY2_AVAILABLE)
+        self.tab_r.setEnabled(rsetup.has_r())
 
         #: configuration keys, corresponding widgets, and defaults
         self.config_pairs = [
@@ -160,7 +153,7 @@ def reload_lme4(self, install=False):
         if pathlib.Path(binary).is_file():
             try:
                 rsetup.set_r_path(binary)
-            except RUnavailableError as exc:
+            except RNotFoundError as exc:
                 QtWidgets.QMessageBox.information(
                     self,
                     "No compatible R version found",

tests/test_gui_compute_lme4.py

@@ -2,12 +2,15 @@
 import pathlib
 import socket
 
+from dclab.lme4 import Rlme4, bootstrapped_median_distributions, rsetup
 from shapeout2.gui.main import ShapeOut2
 from shapeout2 import session
 from shapeout2.gui.compute.comp_lme4 import ComputeSignificance
 import pytest
 
-pytest.importorskip("rpy2")
+
+if not (rsetup.has_r() and rsetup.has_lme4()):
+    pytest.skip(allow_module_level=True)
 
 data_path = pathlib.Path(__file__).parent / "data"
 with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s: