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Go back to regular pip #1702
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Go back to regular pip #1702
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This reverts commit f653c3c.
Just checked using this dockerfile, works flawlessly: FROM continuumio/miniconda
RUN conda install python=3.8
RUN pip install flit>=3.1
RUN git clone https://github.com/theislab/scanpy.git
WORKDIR /scanpy
# Go to the mainline-pip branch if it hasn’t been merged into master yet
RUN git checkout mainline-pip || true
RUN FLIT_ROOT_INSTALL=1 flit install -s --dep=develop # Make development install of scanpy
# Make sure the dist-info folder has a plus in its name
RUN SCANPY_VERSION=$(python -c 'from importlib.metadata import version; print(version("scanpy"))') && \
echo $SCANPY_VERSION | grep '+' &&
test -d /opt/conda/lib/python3.8/site-packages/scanpy-$SCANPY_VERSION.dist-info
# Install project that depends on scanpy
RUN pip install scvelo
# Make sure it’s still a dev install
RUN test -L /opt/conda/lib/python3.8/site-packages/scanpy |
ivirshup
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Mar 2, 2021
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More something that should have been caught in previous review, for the Check Build job:
- Flit should be installed with the rest of the dependencies.
- Can some of those tools be removed? For example:
setuptools
.
ivirshup
reviewed
Mar 2, 2021
ivirshup
approved these changes
Mar 2, 2021
Zethson
pushed a commit
that referenced
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Mar 15, 2021
* Go back to regular flit Co-authored-by: Isaac Virshup <[email protected]>
ivirshup
added a commit
that referenced
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Mar 18, 2021
* add flake8 pre-commit Signed-off-by: Zethson <[email protected]> * fix pre-commit Signed-off-by: Zethson <[email protected]> * add E402 to flake8 ignore Signed-off-by: Zethson <[email protected]> * revert neighbors Signed-off-by: Zethson <[email protected]> * fix flake8 Signed-off-by: Zethson <[email protected]> * address review Signed-off-by: Zethson <[email protected]> * fix comment character in .flake8 Signed-off-by: Zethson <[email protected]> * fix test Signed-off-by: Zethson <[email protected]> * black Signed-off-by: Zethson <[email protected]> * review round 2 Signed-off-by: Zethson <[email protected]> * review round 3 Signed-off-by: Zethson <[email protected]> * readded double comments Signed-off-by: Zethson <[email protected]> * Ignoring E262 & reverted comment Signed-off-by: Zethson <[email protected]> * using self for obs_tidy Signed-off-by: Zethson <[email protected]> * Restore setup.py * rm call of black test (#1690) * Fix print_versions for python<3.8 (#1691) * add codecov so we can have a badge to point to (#1693) * Attempt server-side search (#1672) * Fix paga_path (#1047) Fix paga_path Co-authored-by: Isaac Virshup <[email protected]> * Switch to flit This reverts commit d645790 * add setup.py while leaving it ignored * Update install instructions * Circumvent new pip check (see pypa/pip#9628) * Go back to regular pip (#1702) * Go back to regular flit Co-authored-by: Isaac Virshup <[email protected]> * codecov comment (#1704) * Use joblib for parallelism in regress_out (#1695) * Use joblib for parallism in regress_out * release note * fix link in release notes * Add todo for resource test * Add sparsificiation step before sparse-dependent Scrublet calls (#1707) * Add sparsificiation step before sparse-dependent Scrublet calls * Apply sparsification suggestion Co-authored-by: Isaac Virshup <[email protected]> * Fix imports Co-authored-by: Isaac Virshup <[email protected]> * Fix version on Travis (#1713) By default, Travis does `git clone --depth=50` which means the version can’t be detected from the git tag. * `sc.metrics` module (add confusion matrix & Geary's C methods) (#915) * Add `sc.metrics` with `gearys_c` Add a module for computing useful metrics. Started off with Geary's C since I'm using it and finding it useful. I've also got a fairly fast way to calculate it worked out. Unfortunatly my implementation runs into some issues with some global configs set by umap (see lmcinnes/umap#306), so I'm going to see if that can be resolved before changing it. * Add sc.metrics.confusion_matrix * Better tests and output for confusion_matrix * Workaround umap<0.4 and increase numerical stability of gearys_c * Work around lmcinnes/umap#306 by not calling out to kernel function. That code has been kept, but commented out. * Increase numerical stability by casting data to system width. Tests were failing due to instability. * Split up gearys_c tests * Improved unexpected error message * gearys_c working again. Sadly, a bit slower * One option for doc strings * Simplify implementation to use single dispatch * release notes * Fix clipped images in docs (#1717) * Cleanup normalize_total (#1667) * Cleanup normalize_total * Add modification tests and copy kwarg for normalize_total * Test that 'layers' argument is deprecated * Added more mutation checks for normalize_total * release note * Error message * deprecate scvi (#1703) * deprecate scvi * Update .azure-pipelines.yml Co-authored-by: Isaac Virshup <[email protected]> * remove :func: links to scvi in release notes * remove tildes in front of scvi in release notes * Update docs/release-notes/1.5.0.rst Co-authored-by: Michael Jayasuriya <[email protected]> Co-authored-by: Isaac Virshup <[email protected]> * updated ecosystem.rst to add triku (#1722) * Minor addition to contributing docs (#1726) * Preserve category order when groupby is a list (#1735) Preserve category order when groupby is a list * Asymmetrical diverging colormaps and vcenter (#1551) Add vcenter and norm arguments to plotting functions * add flake8 pre-commit Signed-off-by: Zethson <[email protected]> * add E402 to flake8 ignore Signed-off-by: Zethson <[email protected]> * revert neighbors Signed-off-by: Zethson <[email protected]> * address review Signed-off-by: Zethson <[email protected]> * black Signed-off-by: Zethson <[email protected]> * using self for obs_tidy Signed-off-by: Zethson <[email protected]> * rebased Signed-off-by: Zethson <[email protected]> * rebasing Signed-off-by: Zethson <[email protected]> * rebasing Signed-off-by: Zethson <[email protected]> * rebasing Signed-off-by: Zethson <[email protected]> * add flake8 to dev docs Signed-off-by: Zethson <[email protected]> * add autopep8 to pre-commits Signed-off-by: Zethson <[email protected]> * add flake8 ignore docs Signed-off-by: Zethson <[email protected]> * add exception todos Signed-off-by: Zethson <[email protected]> * add ignore directories Signed-off-by: Zethson <[email protected]> * reinstated lambdas Signed-off-by: Zethson <[email protected]> * fix tests Signed-off-by: Zethson <[email protected]> * fix tests Signed-off-by: Zethson <[email protected]> * fix tests Signed-off-by: Zethson <[email protected]> * fix tests Signed-off-by: Zethson <[email protected]> * fix tests Signed-off-by: Zethson <[email protected]> * Add E741 to allowed flake8 violations. Co-authored-by: Isaac Virshup <[email protected]> * Add F811 flake8 ignore for tests Co-authored-by: Isaac Virshup <[email protected]> * Fix mask comparison Co-authored-by: Isaac Virshup <[email protected]> * Fix mask comparison Co-authored-by: Isaac Virshup <[email protected]> * fix flake8 config file Signed-off-by: Zethson <[email protected]> * readded autopep8 Signed-off-by: Zethson <[email protected]> * import Literal Signed-off-by: Zethson <[email protected]> * revert literal import Signed-off-by: Zethson <[email protected]> * fix scatterplot pca import Signed-off-by: Zethson <[email protected]> * false comparison & unused vars Signed-off-by: Zethson <[email protected]> * Add cleaner level determination Co-authored-by: Isaac Virshup <[email protected]> * Fix comment formatting Co-authored-by: Isaac Virshup <[email protected]> * Add smoother dev documentation Co-authored-by: Isaac Virshup <[email protected]> * fix flake8 Signed-off-by: Zethson <[email protected]> * Readd long comment Co-authored-by: Isaac Virshup <[email protected]> * Assuming X as array like Co-authored-by: Isaac Virshup <[email protected]> * fix flake8 Signed-off-by: Zethson <[email protected]> * fix flake8 config Signed-off-by: Zethson <[email protected]> * reverted rank_genes Signed-off-by: Zethson <[email protected]> * fix disp_mean_bin formatting Co-authored-by: Isaac Virshup <[email protected]> * fix formatting Signed-off-by: Zethson <[email protected]> * add final todos Signed-off-by: Zethson <[email protected]> * boolean checks with is Signed-off-by: Zethson <[email protected]> * _dpt formatting Signed-off-by: Zethson <[email protected]> * literal fixes Signed-off-by: Zethson <[email protected]> * links to leafs Signed-off-by: Zethson <[email protected]> * revert paga variable naming Co-authored-by: Philipp A <[email protected]> Co-authored-by: Sergei Rybakov <[email protected]> Co-authored-by: Isaac Virshup <[email protected]> Co-authored-by: Jonathan Manning <[email protected]> Co-authored-by: mjayasur <[email protected]> Co-authored-by: Michael Jayasuriya <[email protected]> Co-authored-by: Alex M. Ascensión <[email protected]> Co-authored-by: Gökçen Eraslan <[email protected]>
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Hahaha and of course after weeks of this bug, everything gets resolved the day I press the merge button. pypa/flit#395 should fix the issues where
pip install scvelo
downgrades aflit install -s
installed scanpy (now thedist-info
dir name contains the correct version)So we can remove the workarounds. No problem,
git blame
won’t be affected much, this almost exclusively deletes lines.