Pipfile refresh for v0.9.0 #148
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Very hacky workaroud to solve dependabot not wanting to upgrade DeepBedMap's dependencies! Best guess is that the PyGMT VCS dependency is the problem (see #137, #139, #140, #142, #143, #144). So, I'm taking it out of the Pipfile and disabling pygmt required tests, have dependabot upgrade the other dependencies, and then restore pygmt into the Pipfile. Had to add xarray explicitly to Pipfile for the meantime. Onwards!
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Manually updating various machine learning/deep learning dependencies in Pipfile. Detailed references to each updated dependencies' release notes and diff commits as follows: - [chainer](https://github.com/chainer/chainer) from 6.0.0b3 to 6.0.0: - [Release notes](https://github.com/chainer/chainer/releases/tag/v6.0.0) - [Commits](chainer/chainer@v6.0.0b3...v6.0.0) - [comet-ml](https://comet.ml/) from 1.0.54 to 1.0.55 - [cupy-cuda100](https://github.com/cupy/cupy) from 6.0.0b3 to 6.0.0: - [Release notes](https://github.com/cupy/cupy/releases/tag/v6.0.0) - [Commits](cupy/cupy@v6.0.0b3...v6.0.0) - [onnx-chainer](https://github.com/chainer/onnx-chainer) from 1.3.3 to 1.4.1: - [Release notes](https://github.com/chainer/onnx-chainer/releases/tag/v1.4.1) - [Commits](chainer/onnx-chainer@v1.3.3...v1.4.1) - [optuna](https://github.com/pfnet/optuna) from 0.8.0 to 0.11.0 - [Release notes](https://github.com/pfnet/optuna/releases/tag/v0.11.0) - [Commits](optuna/optuna@v0.8.0...v0.11.0)
Manually updating various PyData/data science dependencies in Pipfile, references to release notes and diff commits as follows: - [geopandas](https://github.com/geopandas/geopandas) from 0.4.1 to 0.5.0: - [Release notes](https://github.com/geopandas/geopandas/releases/tag/v0.5.0) - [Commits](geopandas/geopandas@v0.4.1...v0.5.0) - [livelossplot](https://github.com/stared/livelossplot) from 0.3.2 to 0.4.1: - [Release notes](https://github.com/stared/livelossplot/releases) - [Commits](stared/livelossplot@v0.3.2...v0.4.1) - [matplotlib](https://github.com/matplotlib/matplotlib) from 3.0.3 to 3.1.0: - [Release notes](https://github.com/matplotlib/matplotlib/releases/tag/v3.1.0) - [Commits](matplotlib/matplotlib@v3.0.3...v3.1.0) - [numpy](https://github.com/numpy/numpy) from 1.16.2 to 1.16.4: - [Release notes](https://github.com/numpy/numpy/releases/tag/v1.16.4) - [Commits](numpy/numpy@v1.16.2...v1.16.4) - [quilt](https://github.com/quiltdata/quilt) from 2.9.14 to 2.9.15: - [Release notes](https://github.com/quiltdata/quilt/releases) - [Commits](quiltdata/quilt@2.9.14...2.9.15) - [scikit-image](https://github.com/scikit-image/scikit-image) from 0.14.2 to 0.15.0: - [Release notes](https://github.com/scikit-image/scikit-image/releases/tag/v0.15.0) - [Commits](scikit-image/scikit-image@v0.14.2...v0.15.0) - [tqdm](https://github.com/tqdm/tqdm) from 4.29.1 to 4.32.1: - [Release notes](https://github.com/tqdm/tqdm/releases/tag/v4.32.1) - [Commits](tqdm/tqdm@v4.29.1...v4.32.1)
Manually updating various development environment dependencies in Pipfile, references to release notes and diff commits as follows: - [jupyterlab](https://github.com/jupyter/jupyterlab) from 0.35.4 to 1.0.0a5: - [Release notes](https://github.com/jupyterlab/jupyterlab/releases/tag/v1.0.0a5) - [Changelog](https://github.com/jupyterlab/jupyterlab/blob/master/docs/source/getting_started/changelog.rst) - [Commits](jupyterlab/jupyterlab@v0.35.4...v1.0.0a5) - [jupytext](https://github.com/mwouts/jupytext) from 1.0.3 to 1.1.4rc1: - [Release notes](https://github.com/mwouts/jupytext/releases/tag/1.1.4-rc1) - [Changelog](https://github.com/mwouts/jupytext/blob/master/HISTORY.rst) - [Commits](mwouts/jupytext@1.0.3...v1.1.4rc1) - [pytest](https://github.com/pytest-dev/pytest) from 4.3.1 to 4.5.0: - [Release notes](https://github.com/pytest-dev/pytest/releases/tag/4.5.0) - [Changelog](https://github.com/pytest-dev/pytest/blob/master/CHANGELOG.rst) - [Commits](pytest-dev/pytest@4.3.1...4.5.0)
weiji14
changed the title
Reinstate pygmt in our Pipfile (bumping it up a few versions) and enable pygmt-related tests once more. Basically reverting ea40d50 now that we've manually updated various dependencies in the Pipfile.
Pinning dask[array] as it was removed in 8d7ea0e as part of the #148 Pipfile refresh. Tracked it down to the scikit-image upgrade from 0.14.2 to 0.15.0 having dask as an optional dependency (see scikit-image/scikit-image#3582). Though we don't actually use dask for skimage, it is needed by xarray.open_mfdataset in the deepbedmap.get_image_and_bounds function... Also revealing in the srgan_train.ipynb file some hidden updates from Chainer/CuPy provided binaries, specifically cudnn from 7402 to 7500 and nccl from 2307 to 2402. Note too that toolz==0.9.0 has been re-added into the Pipfile.lock file
weiji14
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Jun 1, 2019
Closes #148 Pipfile refresh for v0.9.0.
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PyGMT VCS dependency causing problems with dependabot updating Pipfile packages (see #137, #139, #140, #142, #143, #144...). This branch/PR is used to temporarily remove pygmt from the Pipfile so that the other dependencies can be updated properly one-by-one
with dependabot's documented changesmanually!TODO:
pygmtfrom Pipfile and disable pygmt required tests (ea40d50)Have dependabot upgrade various data science dependenciespygmtinto the Pipfile and re-enable pygmt tests (b391724)