unpin scipy (#361)

* unpin scipy

* pin numpy in conda

* Update patched version of skbio

Author: grst

.conda/meta.yaml

@@ -29,7 +29,7 @@ requirements:
     - scanpy>=1.6.0
     - pandas>=1.0
     - numpy<1.22
-    - scipy<1.9.0
+    - scipy
     - parasail-python
     - scikit-learn
     - python-levenshtein

.github/workflows/docs.yml

@@ -63,7 +63,7 @@ jobs:
           python -m pip install --upgrade "pip!=22.1"
           # TODO this is to workaround an issue with the skbio dependency
           # This will work in the next release, see https://github.com/biocore/scikit-bio/pull/1813
-          pip install git+https://github.com/grst/scikit-bio.git@a3423e4
+          pip install git+https://github.com/grst/scikit-bio.git@main
           pip install .[doc,test,rpack,dandelion]
       - name: run sphinx
         run: |
@@ -94,10 +94,9 @@ jobs:
         with:
           name: docs
           path: docs/_build/html
-
 # Temporarily disable docs deployment
-# The way the target directory is calculated is broken. It overwrites everything. 
-# 
+# The way the target directory is calculated is broken. It overwrites everything.
+#
 #       - name: Deploy to gh-pages
 #         if: ( matrix.os == 'ubuntu-latest' ) && ( github.event_name != 'pull_request' )
 #         uses: JamesIves/github-pages-deploy-action@releases/v3

.github/workflows/test.yml

@@ -52,7 +52,7 @@ jobs:
           python -m pip install --upgrade "pip!=22.1"
           # TODO this is to workaround an issue with the skbio dependency
           # This will work in the next release, see https://github.com/biocore/scikit-bio/pull/1813
-          pip install git+https://github.com/grst/scikit-bio.git@a3423e4
+          pip install git+https://github.com/grst/scikit-bio.git@main
           pip install .[test,rpack,dandelion]
       - name: Check black formatting
         run: |

pyproject.toml

@@ -29,7 +29,7 @@ dependencies = [
     'scanpy>=1.6.0',
     'pandas>=1.0',
     'numpy>=1.17.0',
-    'scipy<1.9.0',
+    'scipy',
     # parasail 1.2.1 fails to be installd on MacOS
     'parasail != 1.2.1',
     'scikit-learn',