Merge remote-tracking branch 'upstream/master' into beta

ucbds-infra · Oct 5, 2024 · cb84608 · cb84608
2 parents e03275b + 9eaf5ff
commit cb84608
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diff --git a/.github/workflows/add-issues-to-project.yml b/.github/workflows/add-issues-to-project.yml
diff --git a/.github/workflows/run-docker-tests-beta.yml b/.github/workflows/run-docker-tests-beta.yml
@@ -61,7 +61,7 @@ jobs:
           packages: >-
             poetry
 
-      - uses: mamba-org/setup-micromamba@v1
+      - uses: mamba-org/setup-micromamba@v2
         if: ${{ steps.check-branch.outputs.run == 'true' }}
         with:
           environment-file: environment.yml

diff --git a/.github/workflows/run-docker-tests.yml b/.github/workflows/run-docker-tests.yml
@@ -46,7 +46,7 @@ jobs:
           packages: >-
             poetry
 
-      - uses: mamba-org/setup-micromamba@v1
+      - uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: environment.yml
           init-shell: >-

diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
@@ -40,7 +40,7 @@ jobs:
           packages: >-
             poetry
 
-      - uses: mamba-org/setup-micromamba@v1
+      - uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: environment.yml
           init-shell: >-

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -22,6 +22,14 @@
 * Added ability to monitor grading progress to Otter Grade per [#827](https://github.com/ucbds-infra/otter-grader/issues/827)
 * Added handling of student-created files with the `student_files` configuration in Otter Assign per [#737](https://github.com/ucbds-infra/otter-grader/issues/737)
 
+**v5.7.1:**
+
+* Removed testing code unintentioanlly committed in v5.7.0 per [#849](https://github.com/ucbds-infra/otter-grader/issues/849)
+
+**v5.7.0:**
+
+* Switch grading image from Mambaforge to Miniforge due to the [sunestting of Mambaforge](https://conda-forge.org/news/2024/07/29/sunsetting-mambaforge/) per [#846](https://github.com/ucbds-infra/otter-grader/issues/846)
+
 **v5.6.0:**
 
 * Updated Otter Grade to write grading summary for each notebook per [#814](https://github.com/ucbds-infra/otter-grader/issues/814)

diff --git a/CITATION.cff b/CITATION.cff
@@ -8,10 +8,10 @@ authors:
   -
     name: UC Berkeley Data Science Education Program
 cff-version: "1.1.0"
-date-released: 2024-08-28
+date-released: 2024-10-03
 license: "BSD-3-Clause"
 message: "If you use this software, please cite it as below."
 repository-code: "https://github.com/ucbds-infra/otter-grader"
 title: "Otter-Grader: A Python and R autograding solution"
-version: "5.6.0"
+version: "5.7.1"
 doi: 10.5281/zenodo.5259955
diff --git a/docs/_static/grading-environment-r.yml b/docs/_static/grading-environment-r.yml
@@ -35,5 +35,6 @@ dependencies:
       - dill
       - numpy
       - gspread
-      - otter-grader[grading,plugins]==5.6.0
+      - pypdf
+      - otter-grader[grading,plugins]==5.7.1
       - rpy2
diff --git a/docs/_static/grading-environment.yml b/docs/_static/grading-environment.yml
@@ -23,4 +23,4 @@ dependencies:
       - numpy
       - gspread
       - pypdf
-      - otter-grader[grading,plugins]==5.6.0
+      - otter-grader[grading,plugins]==5.7.1
diff --git a/docs/_static/python_setup.sh b/docs/_static/python_setup.sh
@@ -13,9 +13,9 @@ dpkg -i /tmp/pandoc.deb
 
 # install mamba
 if [ $(uname -p) = "arm" ] || [ $(uname -p) = "aarch64" ] ; \
-    then wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-aarch64.sh \
+    then wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-aarch64.sh \
         -O /autograder/source/mamba_install.sh ; \
-    else wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh \
+    else wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh \
         -O /autograder/source/mamba_install.sh ; \
 fi
 chmod +x /autograder/source/mamba_install.sh

diff --git a/docs/_static/r_setup.sh b/docs/_static/r_setup.sh
@@ -18,9 +18,9 @@ dpkg -i /tmp/pandoc.deb
 
 # install mamba
 if [ $(uname -p) = "arm" ] || [ $(uname -p) = "aarch64" ] ; \
-    then wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-aarch64.sh \
+    then wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-aarch64.sh \
         -O /autograder/source/mamba_install.sh ; \
-    else wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh \
+    else wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh \
         -O /autograder/source/mamba_install.sh ; \
 fi
 chmod +x /autograder/source/mamba_install.sh

diff --git a/docs/_static/tutorial.zip b/docs/_static/tutorial.zip
diff --git a/otter/generate/templates/common/run_autograder b/otter/generate/templates/common/run_autograder
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
-export PATH="/root/mambaforge/bin:$PATH"
-source /root/mambaforge/etc/profile.d/conda.sh
-source /root/mambaforge/etc/profile.d/mamba.sh
+export PATH="/root/miniforge3/bin:$PATH"
+source /root/miniforge3/etc/profile.d/conda.sh
+source /root/miniforge3/etc/profile.d/mamba.sh
 mamba activate {{ otter_env_name }}
 python {{ autograder_dir }}/source/run_otter.py
diff --git a/otter/generate/templates/python/setup.sh b/otter/generate/templates/python/setup.sh
@@ -13,16 +13,16 @@ dpkg -i /tmp/pandoc.deb
 
 # install mamba
 if [ $(uname -p) = "arm" ] || [ $(uname -p) = "aarch64" ] ; \
-    then wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-aarch64.sh \
+    then wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-aarch64.sh \
         -O {{ autograder_dir }}/source/mamba_install.sh ; \
-    else wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh \
+    else wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh \
         -O {{ autograder_dir }}/source/mamba_install.sh ; \
 fi
 chmod +x {{ autograder_dir }}/source/mamba_install.sh
 {{ autograder_dir }}/source/mamba_install.sh -b
-echo "export PATH=/root/mambaforge/bin:\$PATH" >> /root/.bashrc
+echo "export PATH=/root/miniforge3/bin:\$PATH" >> /root/.bashrc
 
-export PATH=/root/mambaforge/bin:$PATH
+export PATH=/root/miniforge3/bin:$PATH
 export TAR="/bin/tar"
 
 # install dependencies with mamba

diff --git a/otter/generate/templates/r/setup.sh b/otter/generate/templates/r/setup.sh
@@ -18,16 +18,16 @@ dpkg -i /tmp/pandoc.deb
 
 # install mamba
 if [ $(uname -p) = "arm" ] || [ $(uname -p) = "aarch64" ] ; \
-    then wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-aarch64.sh \
+    then wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-aarch64.sh \
         -O {{ autograder_dir }}/source/mamba_install.sh ; \
-    else wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh \
+    else wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh \
         -O {{ autograder_dir }}/source/mamba_install.sh ; \
 fi
 chmod +x {{ autograder_dir }}/source/mamba_install.sh
 {{ autograder_dir }}/source/mamba_install.sh -b
-echo "export PATH=/root/mambaforge/bin:\$PATH" >> /root/.bashrc
+echo "export PATH=/root/miniforge3/bin:\$PATH" >> /root/.bashrc
 
-export PATH=/root/mambaforge/bin:$PATH
+export PATH=/root/miniforge3/bin:$PATH
 export TAR="/bin/tar"
 
 # install dependencies with mamba{% if channel_priority_strict %}

diff --git a/otter/run/run_autograder/autograder_config.py b/otter/run/run_autograder/autograder_config.py
@@ -107,7 +107,7 @@ class AutograderConfig(fica.Config):
 
     miniconda_path: str = fica.Key(
         description="the path to the mamba install directory",
-        default="/root/mambaforge",
+        default="/root/miniforge3",
     )
 
     plugins: list[Union[str, dict[str, Any]]] = fica.Key(

diff --git a/otter/version.py b/otter/version.py
@@ -5,7 +5,7 @@
 from textwrap import dedent
 
 
-__version__ = "5.6.0"
+__version__ = "5.7.1"
 
 
 LOGO_WITH_VERSION = rf"""

diff --git a/test/files/partial-dockerfile.txt b/test/files/partial-dockerfile.txt
@@ -1,4 +1,4 @@
-ENV PATH=/root/mambaforge/bin:$PATH
+ENV PATH=/root/miniforge3/bin:$PATH
 ADD __otter-grader /tmp/otter-grader
 RUN mamba run -n otter-env pip install /tmp/otter-grader
 RUN rm -rf /tmp/*
diff --git a/test/test_assign/files/example-autograder-correct/environment.yml b/test/test_assign/files/example-autograder-correct/environment.yml
@@ -6,4 +6,4 @@ dependencies:
   - pip
   - nb_conda_kernels
   - pip:
-      - otter-grader[grading,plugins]==5.6.0
+      - otter-grader[grading,plugins]==5.7.1
diff --git a/test/test_assign/files/example-autograder-correct/run_autograder b/test/test_assign/files/example-autograder-correct/run_autograder
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
-export PATH="/root/mambaforge/bin:$PATH"
-source /root/mambaforge/etc/profile.d/conda.sh
-source /root/mambaforge/etc/profile.d/mamba.sh
+export PATH="/root/miniforge3/bin:$PATH"
+source /root/miniforge3/etc/profile.d/conda.sh
+source /root/miniforge3/etc/profile.d/mamba.sh
 mamba activate otter-env
 python /autograder/source/run_otter.py
diff --git a/test/test_assign/files/example-autograder-correct/setup.sh b/test/test_assign/files/example-autograder-correct/setup.sh
@@ -13,16 +13,16 @@ dpkg -i /tmp/pandoc.deb
 
 # install mamba
 if [ $(uname -p) = "arm" ] || [ $(uname -p) = "aarch64" ] ; \
-    then wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-aarch64.sh \
+    then wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-aarch64.sh \
         -O /autograder/source/mamba_install.sh ; \
-    else wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh \
+    else wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh \
         -O /autograder/source/mamba_install.sh ; \
 fi
 chmod +x /autograder/source/mamba_install.sh
 /autograder/source/mamba_install.sh -b
-echo "export PATH=/root/mambaforge/bin:\$PATH" >> /root/.bashrc
+echo "export PATH=/root/miniforge3/bin:\$PATH" >> /root/.bashrc
 
-export PATH=/root/mambaforge/bin:$PATH
+export PATH=/root/miniforge3/bin:$PATH
 export TAR="/bin/tar"
 
 # install dependencies with mamba

diff --git a/test/test_assign/files/gs-autograder-correct/environment.yml b/test/test_assign/files/gs-autograder-correct/environment.yml
@@ -7,4 +7,4 @@ dependencies:
   - pip
   - nb_conda_kernels
   - pip:
-      - otter-grader[grading,plugins]==5.6.0
+      - otter-grader[grading,plugins]==5.7.1
diff --git a/test/test_assign/files/gs-autograder-correct/run_autograder b/test/test_assign/files/gs-autograder-correct/run_autograder
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
-export PATH="/root/mambaforge/bin:$PATH"
-source /root/mambaforge/etc/profile.d/conda.sh
-source /root/mambaforge/etc/profile.d/mamba.sh
+export PATH="/root/miniforge3/bin:$PATH"
+source /root/miniforge3/etc/profile.d/conda.sh
+source /root/miniforge3/etc/profile.d/mamba.sh
 mamba activate otter-env
 python /autograder/source/run_otter.py
diff --git a/test/test_assign/files/gs-autograder-correct/setup.sh b/test/test_assign/files/gs-autograder-correct/setup.sh
@@ -13,16 +13,16 @@ dpkg -i /tmp/pandoc.deb
 
 # install mamba
 if [ $(uname -p) = "arm" ] || [ $(uname -p) = "aarch64" ] ; \
-    then wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-aarch64.sh \
+    then wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-aarch64.sh \
         -O /autograder/source/mamba_install.sh ; \
-    else wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh \
+    else wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh \
         -O /autograder/source/mamba_install.sh ; \
 fi
 chmod +x /autograder/source/mamba_install.sh
 /autograder/source/mamba_install.sh -b
-echo "export PATH=/root/mambaforge/bin:\$PATH" >> /root/.bashrc
+echo "export PATH=/root/miniforge3/bin:\$PATH" >> /root/.bashrc
 
-export PATH=/root/mambaforge/bin:$PATH
+export PATH=/root/miniforge3/bin:$PATH
 export TAR="/bin/tar"
 
 # install dependencies with mamba

diff --git a/test/test_assign/files/rmd-autograder-correct/environment.yml b/test/test_assign/files/rmd-autograder-correct/environment.yml
@@ -22,4 +22,4 @@ dependencies:
   - r-usethis
   - r-ottr==1.5.0
   - pip:
-      - otter-grader[grading,plugins,r]==5.6.0
+      - otter-grader[grading,plugins,r]==5.7.1
diff --git a/test/test_assign/files/rmd-autograder-correct/run_autograder b/test/test_assign/files/rmd-autograder-correct/run_autograder
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
-export PATH="/root/mambaforge/bin:$PATH"
-source /root/mambaforge/etc/profile.d/conda.sh
-source /root/mambaforge/etc/profile.d/mamba.sh
+export PATH="/root/miniforge3/bin:$PATH"
+source /root/miniforge3/etc/profile.d/conda.sh
+source /root/miniforge3/etc/profile.d/mamba.sh
 mamba activate otter-env
 python /autograder/source/run_otter.py
diff --git a/test/test_assign/files/rmd-autograder-correct/setup.sh b/test/test_assign/files/rmd-autograder-correct/setup.sh
@@ -18,16 +18,16 @@ dpkg -i /tmp/pandoc.deb
 
 # install mamba
 if [ $(uname -p) = "arm" ] || [ $(uname -p) = "aarch64" ] ; \
-    then wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-aarch64.sh \
+    then wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-aarch64.sh \
         -O /autograder/source/mamba_install.sh ; \
-    else wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh \
+    else wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh \
         -O /autograder/source/mamba_install.sh ; \
 fi
 chmod +x /autograder/source/mamba_install.sh
 /autograder/source/mamba_install.sh -b
-echo "export PATH=/root/mambaforge/bin:\$PATH" >> /root/.bashrc
+echo "export PATH=/root/miniforge3/bin:\$PATH" >> /root/.bashrc
 
-export PATH=/root/mambaforge/bin:$PATH
+export PATH=/root/miniforge3/bin:$PATH
 export TAR="/bin/tar"
 
 # install dependencies with mamba

diff --git a/test/test_generate/files/autograder-correct/environment.yml b/test/test_generate/files/autograder-correct/environment.yml
@@ -7,5 +7,5 @@ dependencies:
   - pip
   - nb_conda_kernels
   - pip:
-      - otter-grader[grading,plugins]==5.6.0
+      - otter-grader[grading,plugins]==5.7.1
       - tqdm
diff --git a/test/test_generate/files/autograder-correct/run_autograder b/test/test_generate/files/autograder-correct/run_autograder
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
-export PATH="/root/mambaforge/bin:$PATH"
-source /root/mambaforge/etc/profile.d/conda.sh
-source /root/mambaforge/etc/profile.d/mamba.sh
+export PATH="/root/miniforge3/bin:$PATH"
+source /root/miniforge3/etc/profile.d/conda.sh
+source /root/miniforge3/etc/profile.d/mamba.sh
 mamba activate otter-env
 python /autograder/source/run_otter.py
diff --git a/test/test_generate/files/autograder-correct/setup.sh b/test/test_generate/files/autograder-correct/setup.sh
@@ -13,16 +13,16 @@ dpkg -i /tmp/pandoc.deb
 
 # install mamba
 if [ $(uname -p) = "arm" ] || [ $(uname -p) = "aarch64" ] ; \
-    then wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-aarch64.sh \
+    then wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-aarch64.sh \
         -O /autograder/source/mamba_install.sh ; \
-    else wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh \
+    else wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh \
         -O /autograder/source/mamba_install.sh ; \
 fi
 chmod +x /autograder/source/mamba_install.sh
 /autograder/source/mamba_install.sh -b
-echo "export PATH=/root/mambaforge/bin:\$PATH" >> /root/.bashrc
+echo "export PATH=/root/miniforge3/bin:\$PATH" >> /root/.bashrc
 
-export PATH=/root/mambaforge/bin:$PATH
+export PATH=/root/miniforge3/bin:$PATH
 export TAR="/bin/tar"
 
 # install dependencies with mamba

diff --git a/test/test_generate/files/autograder-custom-env/environment.yml b/test/test_generate/files/autograder-custom-env/environment.yml
@@ -8,5 +8,5 @@ dependencies:
   - nb_conda_kernels
   - pip:
       - statsmodels
-      - otter-grader[grading,plugins]==5.6.0
+      - otter-grader[grading,plugins]==5.7.1
       - tqdm
diff --git a/test/test_generate/files/autograder-custom-env/run_autograder b/test/test_generate/files/autograder-custom-env/run_autograder
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
-export PATH="/root/mambaforge/bin:$PATH"
-source /root/mambaforge/etc/profile.d/conda.sh
-source /root/mambaforge/etc/profile.d/mamba.sh
+export PATH="/root/miniforge3/bin:$PATH"
+source /root/miniforge3/etc/profile.d/conda.sh
+source /root/miniforge3/etc/profile.d/mamba.sh
 mamba activate otter-env
 python /autograder/source/run_otter.py
diff --git a/test/test_generate/files/autograder-custom-env/setup.sh b/test/test_generate/files/autograder-custom-env/setup.sh
@@ -13,16 +13,16 @@ dpkg -i /tmp/pandoc.deb
 
 # install mamba
 if [ $(uname -p) = "arm" ] || [ $(uname -p) = "aarch64" ] ; \
-    then wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-aarch64.sh \
+    then wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-aarch64.sh \
         -O /autograder/source/mamba_install.sh ; \
-    else wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh \
+    else wget -nv https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh \
         -O /autograder/source/mamba_install.sh ; \
 fi
 chmod +x /autograder/source/mamba_install.sh
 /autograder/source/mamba_install.sh -b
-echo "export PATH=/root/mambaforge/bin:\$PATH" >> /root/.bashrc
+echo "export PATH=/root/miniforge3/bin:\$PATH" >> /root/.bashrc
 
-export PATH=/root/mambaforge/bin:$PATH
+export PATH=/root/miniforge3/bin:$PATH
 export TAR="/bin/tar"
 
 # install dependencies with mamba

diff --git a/test/test_generate/files/autograder-r-correct/environment.yml b/test/test_generate/files/autograder-r-correct/environment.yml
@@ -22,4 +22,4 @@ dependencies:
   - r-usethis
   - r-ottr==1.5.0
   - pip:
-      - otter-grader[grading,plugins,r]==5.6.0
+      - otter-grader[grading,plugins,r]==5.7.1
diff --git a/test/test_generate/files/autograder-r-correct/run_autograder b/test/test_generate/files/autograder-r-correct/run_autograder
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
-export PATH="/root/mambaforge/bin:$PATH"
-source /root/mambaforge/etc/profile.d/conda.sh
-source /root/mambaforge/etc/profile.d/mamba.sh
+export PATH="/root/miniforge3/bin:$PATH"
+source /root/miniforge3/etc/profile.d/conda.sh
+source /root/miniforge3/etc/profile.d/mamba.sh
 mamba activate otter-env
 python /autograder/source/run_otter.py
-Original file line number
+Diff line change
@@ Expand Up / @@ -35,5 +35,6 @@ dependencies: @@
           - dill
           - numpy
           - gspread
-          - otter-grader[grading,plugins]==5.6.0
+          - pypdf
+          - otter-grader[grading,plugins]==5.7.1
           - rpy2