ucbds-infra · chrispyles · Jul 30, 2023 · Jul 21, 2023 · Jul 30, 2023 · Jul 30, 2023
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,8 @@
 **v5.1.0 (unreleased):**
 
 * Removed patch that strips cell IDs from notebooks in Otter Assign per [#677](https://github.com/ucbds-infra/otter-grader/issues/677)
+* Added notebook force-save to R notebook assignments per [#474](https://github.com/ucbds-infra/otter-grader/issues/474)
+* Updated default version of `ottr` to v1.4.0
 
 **v5.0.2:**
 

diff --git a/otter/assign/assignment.py b/otter/assign/assignment.py
@@ -244,9 +244,11 @@
         self._logger.debug(f"Initializing with config: {user_config}")
         super().__init__(user_config, **kwargs)
 
-        # convert a boolean to a config object for self.generate if indicated
+        # convert true values masking subkey contains to those containers
         if self.generate is True:
             self.generate = AutograderConfig()
+        if self.export_cell is True:
+            self.export_cell = type(self).ExportCellValue()
 
         if self.variables:
             warnings.warn(
@@ -258,6 +260,8 @@
         ret = super().update(user_config)
         if self.generate is True:
             self.generate = AutograderConfig()
+        if self.export_cell is True:
+            self.export_cell = type(self).ExportCellValue()
         return ret
 
     @property

diff --git a/otter/assign/notebook_transformer.py b/otter/assign/notebook_transformer.py
@@ -109,10 +109,6 @@ def transform_notebook(self, nb) -> "TransformedNotebookContainer":
             transformed_cells += self.cell_factory.create_check_all_cells()
 
         if self.assignment.export_cell:
-            export_cell = self.assignment.export_cell
-            if export_cell is True:
-                export_cell = {}
-
             transformed_cells += self.cell_factory.create_export_cells()
 
         transformed_nb = copy.deepcopy(nb)

diff --git a/otter/assign/r_adapter/cell_factory.py b/otter/assign/r_adapter/cell_factory.py
@@ -29,22 +29,33 @@
         if not self.assignment.export_cell:
             return []
 
+        force_save = not self.assignment.is_rmd and self.assignment.export_cell.force_save
+
         instructions = nbformat.v4.new_markdown_cell()
         instructions.source = "## Submission\n\nMake sure you have run all cells in your " \
             "notebook in order before running the cell below, so that all images/graphs appear " \
-            "in the output. The cell below will generate a zip file for you to submit. **Please " \
-            "save before exporting!**"
+            "in the output. The cell below will generate a zip file for you to submit."
+
+        if not force_save: instructions.source += " **Please save before exporting!**"
 
         if self.assignment.export_cell.instructions:
             instructions.source += '\n\n' + self.assignment.export_cell.instructions
 
-        pdf_arg = ""
+        args = []
         if self.assignment.export_cell.pdf:
-            pdf_arg = ", pdf = TRUE"
+            args.append("pdf = TRUE")
+        if force_save:
+            args.append("force_save = TRUE")
+
+        if args:
+            args = ", " + ", ".join(args)
+        else:
+            args = ""
 
         export = nbformat.v4.new_code_cell()
-        source_lines = ["# Save your notebook first, then run this cell to export your submission."]
-        source_lines.append(f'ottr::export("{self.assignment.notebook_basename}"{pdf_arg})')
+        source_lines = [] if force_save else \
+            ["# Save your notebook first, then run this cell to export your submission."]
+        source_lines.append(f'ottr::export("{self.assignment.notebook_basename}"{args})')
         export.source = "\n".join(source_lines)
 
         lock(instructions)

diff --git a/otter/generate/__init__.py b/otter/generate/__init__.py
@@ -24,7 +24,7 @@
 
 DEFAULT_PYTHON_VERSION = "3.9"
 OTTER_ENV_NAME = "otter-env"
-OTTR_VERSION = "1.2.0"
+OTTR_VERSION = "1.4.0"
 TEMPLATE_DIR = pkg_resources.resource_filename(__name__, "templates")
 GENERAL_TEMPLATE_DIR = os.path.join(TEMPLATE_DIR, "general")
 

diff --git a/test/test_assign/files/r-correct/autograder/r-example.ipynb b/test/test_assign/files/r-correct/autograder/r-example.ipynb
@@ -433,7 +433,7 @@
    "source": [
     "## Submission\n",
     "\n",
-    "Make sure you have run all cells in your notebook in order before running the cell below, so that all images/graphs appear in the output. The cell below will generate a zip file for you to submit. **Please save before exporting!**"
+    "Make sure you have run all cells in your notebook in order before running the cell below, so that all images/graphs appear in the output. The cell below will generate a zip file for you to submit."
    ]
   },
   {
@@ -445,8 +445,7 @@
    },
    "outputs": [],
    "source": [
-    "# Save your notebook first, then run this cell to export your submission.\n",
-    "ottr::export(\"r-example.ipynb\")"
+    "ottr::export(\"r-example.ipynb\", force_save = TRUE)"
    ]
   },
   {

diff --git a/test/test_assign/files/r-correct/student/r-example.ipynb b/test/test_assign/files/r-correct/student/r-example.ipynb
@@ -298,7 +298,7 @@
    "source": [
     "## Submission\n",
     "\n",
-    "Make sure you have run all cells in your notebook in order before running the cell below, so that all images/graphs appear in the output. The cell below will generate a zip file for you to submit. **Please save before exporting!**"
+    "Make sure you have run all cells in your notebook in order before running the cell below, so that all images/graphs appear in the output. The cell below will generate a zip file for you to submit."
    ]
   },
   {
@@ -310,8 +310,7 @@
    },
    "outputs": [],
    "source": [
-    "# Save your notebook first, then run this cell to export your submission.\n",
-    "ottr::export(\"r-example.ipynb\")"
+    "ottr::export(\"r-example.ipynb\", force_save = TRUE)"
    ]
   },
   {

diff --git a/test/test_assign/files/r-example.ipynb b/test/test_assign/files/r-example.ipynb
@@ -11,6 +11,7 @@
     "solutions_pdf: true\n",
     "export_cell:\n",
     "    pdf: false\n",
+    "    force_save: true\n",
     "files:\n",
     "    - data.csv"
    ]

diff --git a/test/test_assign/files/rmd-autograder-correct/setup.sh b/test/test_assign/files/rmd-autograder-correct/setup.sh
@@ -33,4 +33,4 @@ mamba env create -f /autograder/source/environment.yml
 mamba init --all
 
 # install ottr
-mamba run -n otter-env Rscript -e 'install.packages("https://cran.r-project.org/package=ottr&version=1.2.0", dependencies=TRUE, repos=NULL)'
+mamba run -n otter-env Rscript -e 'install.packages("https://cran.r-project.org/package=ottr&version=1.4.0", dependencies=TRUE, repos=NULL)'
diff --git a/test/test_generate/files/autograder-r-correct/setup.sh b/test/test_generate/files/autograder-r-correct/setup.sh
@@ -32,4 +32,4 @@ mamba env create -f /autograder/source/environment.yml
 mamba init --all
 
 # install ottr
-mamba run -n otter-env Rscript -e 'install.packages("https://cran.r-project.org/package=ottr&version=1.2.0", dependencies=TRUE, repos=NULL)'
+mamba run -n otter-env Rscript -e 'install.packages("https://cran.r-project.org/package=ottr&version=1.4.0", dependencies=TRUE, repos=NULL)'
diff --git a/test/test_generate/files/autograder-r-requirements-correct/setup.sh b/test/test_generate/files/autograder-r-requirements-correct/setup.sh
@@ -33,4 +33,4 @@ mamba run -n otter-env Rscript /autograder/source/requirements.r
 mamba init --all
 
 # install ottr
-mamba run -n otter-env Rscript -e 'install.packages("https://cran.r-project.org/package=ottr&version=1.2.0", dependencies=TRUE, repos=NULL)'
+mamba run -n otter-env Rscript -e 'install.packages("https://cran.r-project.org/package=ottr&version=1.4.0", dependencies=TRUE, repos=NULL)'