From 71cd8a6b1dd049c49fe51de54fe9d88a190b3815 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 15 Jun 2021 10:27:36 +0100 Subject: [PATCH 1/2] Unpin loompy (#99) * Unpin loompy * pin cmake for multicore tsne * Revert "pin cmake for multicore tsne" This reverts commit 29a836c7e2303115d329b8e05a0bc174d28ee978. * Pin cmake in build env * quote pinned cmake * reinstate an unpinned loompy dep, apparently doesn't come from upstream * Pin back from problematic Click * Fix syntax for newest bbknn and pin bbknn to versions with that syntax * Revert "Fix syntax for newest bbknn and pin bbknn to versions with that syntax" This reverts commit 184bd1b4e875259d7ade8d9e2f8fbf5d0f524fef. * Pin back bbknn to last compatible version with current scanpy --- .github/workflows/python-package.yml | 2 +- setup.py | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index d4fe8014..a2fe8c79 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -25,7 +25,7 @@ jobs: - name: Install dependencies run: | - pip install -U setuptools>=40.1 wheel cmake + pip install -U setuptools>=40.1 wheel 'cmake<3.20' pip install . - name: Test with bats diff --git a/setup.py b/setup.py index 8289bdb6..b94c4886 100644 --- a/setup.py +++ b/setup.py @@ -44,12 +44,12 @@ 'scanpy>=1.6.0', 'louvain', 'leidenalg', - 'loompy>=2.0.0,<3.0.0', + 'loompy', 'MulticoreTSNE', - 'Click', + 'Click<8', 'umap-learn<0.4.0', 'harmonypy>=0.0.5', - 'bbknn>=1.3.12', + 'bbknn>=1.3.12,<1.5.0', 'mnnpy>=0.1.9.5' ], ) From 3aedfd00a572ef71e0c6d87b88197917a1e7d813 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 15 Jun 2021 10:33:45 +0100 Subject: [PATCH 2/2] Bump version --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index b94c4886..a5fee6fb 100644 --- a/setup.py +++ b/setup.py @@ -5,7 +5,7 @@ setup( name='scanpy-scripts', - version='0.4.0', + version='0.4.1', author='nh3', author_email='nh3@users.noreply.github.com', description='Scripts for using scanpy from the command line',