Merge 24abdda into 447b728

.travis.yml

@@ -1,4 +1,4 @@
-dist: xenial
+dist: jammy
 
 git:
   depth: false
@@ -32,27 +32,29 @@ jobs:
       if: tag IS present
       script:
         - "travis_wait 120 sleep 7200 &"
-        - python setup.py bdist_wheel
         - sudo apt-get install patchelf
+        - python setup.py bdist_wheel
         - auditwheel-symbols --manylinux 2_24 dist/*.whl
         - auditwheel repair dist/*.whl --plat manylinux_2_17_x86_64
         - twine upload -r testpypi --skip-existing /home/travis/build/"$TRAVIS_REPO_SLUG"/wheelhouse/*.whl -u "$TEST_PYPI_USERNAME" -p "$TEST_PYPI_PASSWORD"
     - stage: pypi_deploy
       if: tag IS present
       script:
         - "travis_wait 120 sleep 7200 &"
-        - python setup.py bdist_wheel
         - sudo apt-get install patchelf
+        - python setup.py bdist_wheel
         - auditwheel-symbols --manylinux 2_24 dist/*.whl
         - auditwheel repair dist/*.whl --plat manylinux_2_17_x86_64
         - twine upload --skip-existing /home/travis/build/"$TRAVIS_REPO_SLUG"/wheelhouse/*.whl -u "$PYPI_USERNAME" -p "$PYPI_PASSWORD"
     - stage: docker_deploy
-      if: tag IS present
+      # if: tag IS present
       script:
         - "travis_wait 120 sleep 7200 &"
         - echo "$DOCKER_PASSWORD" | docker login -u "$DOCKER_USERNAME" --password-stdin
-        # Tag the image with a version such as vX.Y.Z,
-        - docker build -t "$TRAVIS_REPO_SLUG":"$TRAVIS_TAG" . 1> out.log
+        # Tag the image with a version such as vX.Y.Z
+        - docker pull "$DOCKER_USERNAME"/ark-analysis:v0.4.3
+        - docker tag "$DOCKER_USERNAME"/ark-analysis:v0.4.3 "$DOCKER_USERNAME"/ark-analysis:v0.4.4
+        # - docker build -t "$TRAVIS_REPO_SLUG":"$TRAVIS_TAG" . 1> out.log
         - docker push --all-tags "$TRAVIS_REPO_SLUG"
 
 after_failure:

Dockerfile

@@ -34,6 +34,9 @@ RUN R -e "library(devtools)"
 RUN R -e "library(doParallel)"
 RUN R -e "library(foreach)"
 
+# Install `rlang` for updated syntax and tidyverse compatibility
+RUN R -e "install.packages('rlang')"
+
 # install arrow from rspm
 RUN R -e "options(BioC_mirror = 'https://packagemanager.rstudio.com/all/__linux__/bullseye/latest', HTTPUserAgent = sprintf(\"R/%s R (%s)\", getRversion(), paste(getRversion(), R.version[\"platform\"], R.version[\"arch\"], R.version[\"os\"])))"
 RUN R -e "install.packages('arrow')"

docs/_rtd/development.md

@@ -196,8 +196,9 @@ next_release_vX.Y.Z
    1. If, in the release notes draft there are PRs that are not categorized, label them appropriately (usually based on the label of their respective Issue).
 2. Make sure that all tests pass for `Ark` on Travis-CI. 
 3. In the `ark-analysis/start_docker.sh` script, change the `VERSION` variable from `vA.B.C` to `vX.Y.Z`
-4. Request a review and merge the `Ark` branch.
-5. Next head to the most recent Drafted Release Notes:
+4. Modify the `.travis.yml` CI configuration script to allow `test_pypi_deploy` to run (comment the line `if: tag IS present`).
+5. Request a review and merge the `Ark` branch.
+6. Next head to the most recent Drafted Release Notes:
    1. Double check that the tag is the appropriate version name.
    2. Publish the Release.
    3. Next the `Ark` will be pushed to PyPI and the Docker Image will be built on Travis CI. 

requirements.txt

@@ -1,17 +1,19 @@
 # NOTE, a new release needs to be made every time a package gets updated.
 cryptography>=3.4.8,<4
 Cython>=0.29.24,<1
-datasets>=2.4.0,<3.0
+datasets>=2.6.1,<3.0
 decorator<5,>=4.3
+dill==0.3.5.1
 feather-format>=0.4.1,<1
 jupyter>=1.0.0,<2
 importlib-metadata>=4.11.4,<5.0
-ipympl==0.9.1
+ipympl>=0.9.2, <1.0.0
 ipython>=8.4.0,<9
 jupyter_contrib_nbextensions>=0.5.1,<1
 jupyterlab>=3.4.3,<4
 jedi>=0.18.1,<0.19
 matplotlib==3.4.3
+multiprocess==0.70.13
 natsort>=8.1.0,<9
 numpy>=1.21.6,<2
 palettable>=3.3.0,<4