Bump onecodex to v0.17.0; remove node, npm packages, and WeasyPrint pins

Bumped `onecodex` to v0.17.0. Removed node, vega npm packages, and WeasyPrint & traitlets pinned fixes.

Due to removing node, the Dockerfile can now be built on ARM machines.

Author: jairideout

.github/workflows/test.yml

@@ -50,7 +50,9 @@ jobs:
 
       - name: Upload Report PDFs
         if: always()
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: example reports
-          path: diff.pdf
+          path: |
+            test/notebooks/diff.pdf
+            test/notebooks/example.pdf

Dockerfile

@@ -38,11 +38,6 @@ RUN apt-get update && apt-get install -yq --no-install-recommends \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/*
 
-# Install Node and vega-cli for server-side image rendering
-RUN curl -sL https://deb.nodesource.com/setup_14.x | bash -
-RUN apt-get -y install nodejs
-RUN npm install -g --unsafe-perm [email protected] [email protected] [email protected]
-
 RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
     locale-gen
 
@@ -62,9 +57,6 @@ ENV LANG en_US.UTF-8
 ENV LANGUAGE en_US.UTF-8
 ENV PATH $HOME/.local/bin:$PATH
 
-# Disable npm package update notifications (DEV-4202)
-ENV NO_UPDATE_NOTIFIER=1
-
 # Create jovyan user with UID=1000 and in the root group
 # See https://github.com/jupyter/docker-stacks/issues/188
 RUN useradd -m -s /bin/bash -N -u $NB_UID -g 0 $NB_USER
@@ -140,12 +132,5 @@ ENV PYTHONPATH "/home/jovyan/.local/lib/python3.9"
 # Provide full access to the Python directory to allow for pip installs
 RUN chown -R $NB_USER:root /usr/local/lib/python3.9
 
-# Fix for transparency issue
-# Pin in onecodex/onecodex once version w/ fix is released
-# https://github.com/Kozea/WeasyPrint/commit/4dfe6079c2d1bd91cccfd9a7d78f8924e2dfabef
-RUN pip install --force-reinstall 'git+https://github.com/Kozea/WeasyPrint.git@4dfe6079c2d1bd91cccfd9a7d78f8924e2dfabef'
-
-RUN pip install --force-reinstall 'git+https://github.com/CourtBouillon/pydyf.git@f340fcc949382e183118b4807491b9f5cab4a89b'
-
 # Switch to unprivileged user, jovyan
 USER $NB_USER

requirements.txt

@@ -8,7 +8,6 @@ nbconvert==6.5.0
 openpyxl==3.0.3
 xlrd==1.2.0
 statsmodels==0.13.2
-onecodex[all,reports]==0.16.0
-traitlets==5.9.0
+onecodex[all,reports]==0.17.0
 taxonomy==0.10.0
 widgetsnbextension

test/notebooks/example_expected.pdf

@@ -61,7 +61,7 @@ def test_render_notebook():
         subprocess.check_output(
             [
                 "diff-pdf",
-                *("--output-diff", "diff.pdf"),
+                *("--output-diff", "test/notebooks/diff.pdf"),
                 "test/notebooks/example.pdf",
                 expected_path,
             ]