Merge pull request #92 from cropsinsilico/minor

Minor bug fixes for the CI and R interface

Author: langmm

.pre-commit-config.yaml

@@ -0,0 +1,12 @@
+-   repo: https://github.com/pycqa/flake8
+    rev: '4.0.1'
+    hooks:
+    -   id: flake8
+-   repo: local
+    hooks:
+    -   id: generate-workflow
+        name: generate-workflow
+        entry: python -c "from yggdrasil.command_line import githook; import sys; sys.exit(githook())"
+        language: system
+        types: [file]
+        files: test\-install\-base\.yml

utils/setup_test_env.py

@@ -783,22 +783,22 @@ def install_deps(method, return_commands=False, verbose=False,
         ]
     if fallback_to_conda:
         cmds.append("%s update --all" % CONDA_CMD)
-    if install_opts['R'] and (not fallback_to_conda) and (not only_python):
-        # TODO: Test split installation where r-base is installed from
-        # conda and the R dependencies are installed from CRAN?
-        if _is_linux:
-            if install_opts['no_sudo']:
-                cmds += [
-                    ("add-apt-repository 'deb https://cloud"
-                     ".r-project.org/bin/linux/ubuntu xenial-cran35/'"),
-                    ("apt-key adv --keyserver keyserver.ubuntu.com "
-                     "--recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9")]
-            else:
-                cmds += [
-                    ("sudo add-apt-repository 'deb https://cloud"
-                     ".r-project.org/bin/linux/ubuntu xenial-cran35/'"),
-                    ("sudo apt-key adv --keyserver keyserver.ubuntu.com "
-                     "--recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9")]
+    # if install_opts['R'] and (not fallback_to_conda) and (not only_python):
+    #     # TODO: Test split installation where r-base is installed from
+    #     # conda and the R dependencies are installed from CRAN?
+    #     if _is_linux:
+    #         if install_opts['no_sudo']:
+    #             cmds += [
+    #                 ("add-apt-repository 'deb https://cloud"
+    #                  ".r-project.org/bin/linux/ubuntu xenial-cran35/'"),
+    #                 ("apt-key adv --keyserver keyserver.ubuntu.com "
+    #                  "--recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9")]
+    #         else:
+    #             cmds += [
+    #                 ("sudo add-apt-repository 'deb https://cloud"
+    #                  ".r-project.org/bin/linux/ubuntu xenial-cran35/'"),
+    #                 ("sudo apt-key adv --keyserver keyserver.ubuntu.com "
+    #                  "--recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9")]
     # if install_opts['zmq'] and (not fallback_to_conda):
     #     cmds.append("echo Installing ZeroMQ...")
     #     if _is_linux:

yggdrasil/languages/R/R/R2python.R

@@ -79,7 +79,7 @@ R2python <- function(robj, not_bytes=FALSE) {
     }
   } else if (is.null(robj)) {
     out <- reticulate::r_to_py(NULL)
-  } else if (is.na(robj)) {
+  } else if ((!is.vector(robj) || (length(robj) == 1)) && is.na(robj)) {
     out <- reticulate::r_to_py(NULL)
   } else {
     # print("Default handling for class:")