Merge pull request #242 from theislab/development

Development
theislab · Sep 13, 2022 · 1059592 · 1059592
2 parents cf96c77 + b617210
commit 1059592
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diff --git a/.cookietemple.yml b/.cookietemple.yml
@@ -15,5 +15,5 @@ full_name: Lukas Heumos
 email: [email protected]
 project_name: spapros
 project_short_description: Fully automated spatial transcriptomics probe selection.
-version: 0.1.0
+version: 0.1.1
 license: MIT
diff --git a/.github/release-drafter.yml b/.github/release-drafter.yml
@@ -1,5 +1,5 @@
-name-template: "0.1.0 🌈" # <<COOKIETEMPLE_FORCE_BUMP>>
-tag-template: 0.1.0 # <<COOKIETEMPLE_FORCE_BUMP>>
+name-template: "0.1.1 🌈" # <<COOKIETEMPLE_FORCE_BUMP>>
+tag-template: 0.1.1 # <<COOKIETEMPLE_FORCE_BUMP>>
 categories:
     - title: "🚀 Features"
       labels:

diff --git a/.github/workflows/build_package.yml b/.github/workflows/build_package.yml
@@ -12,7 +12,7 @@ jobs:
                 python: [3.8, 3.9]
 
         steps:
-            - uses: actions/checkout@v2.4.0
+            - uses: actions/checkout@v3.0.2
               name: Check out source-code repository
 
             - name: Setup Python

diff --git a/.github/workflows/labeler.yml b/.github/workflows/labeler.yml
@@ -11,7 +11,7 @@ jobs:
         runs-on: ubuntu-latest
         steps:
             - name: Check out the repository
-              uses: actions/checkout@v2.4.0
+              uses: actions/checkout@v3.0.2
 
             - name: Run Labeler
               uses: crazy-max/[email protected]

diff --git a/.github/workflows/publish_docs.yml b/.github/workflows/publish_docs.yml
@@ -7,7 +7,7 @@ jobs:
         runs-on: ubuntu-latest
 
         steps:
-            - uses: actions/checkout@v2.4.0
+            - uses: actions/checkout@v3.0.2
               name: Check out source-code repository
 
             - name: Setup Python

diff --git a/.github/workflows/publish_package.yml b/.github/workflows/publish_package.yml
@@ -11,7 +11,7 @@ jobs:
         runs-on: ubuntu-latest
         steps:
             - name: Check out the repository
-              uses: actions/checkout@v2.4.0
+              uses: actions/checkout@v3.0.2
               with:
                   fetch-depth: 2
 

diff --git a/.github/workflows/run_cookietemple_lint.yml b/.github/workflows/run_cookietemple_lint.yml
@@ -7,7 +7,7 @@ jobs:
         runs-on: ubuntu-latest
 
         steps:
-            - uses: actions/checkout@v2.4.0
+            - uses: actions/checkout@v3.0.2
               name: Check out source-code repository
 
             - name: Setup Python

diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
@@ -38,7 +38,7 @@ jobs:
 
         steps:
             - name: Check out the repository
-              uses: actions/checkout@v2.4.0
+              uses: actions/checkout@v3.0.2
 
             - name: Set up Python ${{ matrix.python-version }}
               uses: actions/[email protected]
@@ -78,7 +78,7 @@ jobs:
                   print("::set-output name=result::{}".format(result))
 
             - name: Restore pre-commit cache
-              uses: actions/[email protected].7
+              uses: actions/[email protected].8
               if: matrix.session == 'pre-commit'
               with:
                   path: ~/.cache/pre-commit
@@ -92,14 +92,14 @@ jobs:
 
             - name: Upload coverage data
               if: always() && matrix.session == 'tests'
-              uses: "actions/upload-artifact@v2.3.1"
+              uses: "actions/upload-artifact@v3.1.0"
               with:
                   name: coverage-data
                   path: ".coverage.*"
 
             - name: Upload documentation
               if: matrix.session == 'docs-build'
-              uses: actions/upload-artifact@v2.3.1
+              uses: actions/upload-artifact@v3.1.0
               with:
                   name: docs
                   path: docs/_build
@@ -109,7 +109,7 @@ jobs:
         needs: tests
         steps:
             - name: Check out the repository
-              uses: actions/checkout@v2.4.0
+              uses: actions/checkout@v3.0.2
 
             - name: Set up Python 3.9
               uses: actions/[email protected]
@@ -147,4 +147,4 @@ jobs:
                   nox --force-color --session=coverage -- xml
 
             - name: Upload coverage report
-              uses: codecov/codecov-action@v2.1.0
+              uses: codecov/codecov-action@v3.1.0
diff --git a/.github/workflows/sync_project.yml b/.github/workflows/sync_project.yml
@@ -17,7 +17,7 @@ jobs:
             - name: Install cookietemple
               run: pip install cookietemple
 
-            - uses: actions/checkout@v2.4.0
+            - uses: actions/checkout@v3.0.2
               with:
                   fetch-depth: 0
                   token: "${{ secrets.CT_SYNC_TOKEN }}"

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -5,6 +5,22 @@ Changelog
 This project adheres to `Semantic Versioning <https://semver.org/>`_.
 
 
+0.1.1 (2022-09-13)
+-----------------------
+
+**Added**
+
+* install instructions to docs and readme for a workaround of `issue #234 <https://github.com/theislab/spapros/issues/234>`_
+
+**Fixed**
+
+* `issue #233 <https://github.com/theislab/spapros/issues/233>`_
+
+**Dependencies**
+
+**Deprecated**
+
+
 0.1.0 (2022-08-12)
 -----------------------
 

diff --git a/README.rst b/README.rst
@@ -50,6 +50,15 @@ You can install *spapros* via pip_ from PyPI_:
    $ pip install spapros
 
 
+Note! Currently the pip installation into an environment without `leidenalg` installed can lead to problems when running
+Spapros' knn-based evaluation (see `issue #234 <https://github.com/theislab/spapros/issues/234>`_). To solve this, run
+Spapros in a conda environment and install leidenalg before installing spapros via:
+
+.. code:: console
+
+    $ conda install -c conda-forge leidenalg
+
+
 Usage
 -----
 

diff --git a/cookietemple.cfg b/cookietemple.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.1.0
+current_version = 0.1.1
 
 [bumpversion_files_whitelisted]
 init_file = spapros/__init__.py

diff --git a/docs/conf.py b/docs/conf.py
@@ -102,9 +102,9 @@
 # the built documents.
 #
 # The short X.Y version.
-version = "0.1.0"
+version = "0.1.1"
 # The full version, including alpha/beta/rc tags.
-release = "0.1.0"
+release = "0.1.1"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -22,6 +22,14 @@ you through the process.
 .. _pip: https://pip.pypa.io
 .. _Python installation guide: http://docs.python-guide.org/en/latest/starting/installation/
 
+Note! Currently the pip installation into an environment without `leidenalg` installed can lead to problems when running
+Spapros' knn-based evaluation (see `issue #234 <https://github.com/theislab/spapros/issues/234>`_). To solve this, run
+Spapros in a conda environment and install leidenalg before installing spapros via:
+
+.. code-block:: console
+
+    $ conda install -c conda-forge leidenalg
+
 
 From sources
 ------------