Merge pull request #284 from theislab/development

Development

.github/workflows/labeler.yml

@@ -14,6 +14,6 @@ jobs:
               uses: actions/checkout@v3.0.2
 
             - name: Run Labeler
-              uses: crazy-max/ghaction-github-labeler@v4.0.0
+              uses: crazy-max/ghaction-github-labeler@v4.1.0
               with:
                   skip-delete: true

.github/workflows/main_master_branch_protection.yml

@@ -20,7 +20,7 @@ jobs:
             # NOTE - this may not work if the PR is coming from a fork, due to limitations in GitHub actions secrets
             - name: Post PR comment
               if: failure()
-              uses: mshick/add-pr-comment@v1
+              uses: mshick/add-pr-comment@v2
               with:
                   message: |
                       Hi @${{ github.event.pull_request.user.login }},
@@ -61,7 +61,7 @@ jobs:
             # NOTE - this may not work if the PR is coming from a fork, due to limitations in GitHub actions secrets
             - name: Post PR comment
               if: failure()
-              uses: mshick/add-pr-comment@v1
+              uses: mshick/add-pr-comment@v2
               with:
                   message: |
                       Hi @${{ github.event.pull_request.user.login }},

.github/workflows/master_branch_protection.yml

@@ -19,7 +19,7 @@ jobs:
             # NOTE - this may not work if the PR is coming from a fork, due to limitations in GitHub actions secrets
             - name: Post PR comment
               if: failure()
-              uses: mshick/add-pr-comment@v1
+              uses: mshick/add-pr-comment@v2
               with:
                   message: |
                       Hi @${{ github.event.pull_request.user.login }},
@@ -60,7 +60,7 @@ jobs:
             # NOTE - this may not work if the PR is coming from a fork, due to limitations in GitHub actions secrets
             - name: Post PR comment
               if: failure()
-              uses: mshick/add-pr-comment@v1
+              uses: mshick/add-pr-comment@v2
               with:
                   message: |
                       Hi @${{ github.event.pull_request.user.login }},

.github/workflows/run_tests.yml

@@ -103,7 +103,7 @@ jobs:
                   print("::set-output name=result::{}".format(result))
 
             - name: Restore pre-commit cache
-              uses: actions/cache@v3.0.8
+              uses: actions/cache@v3.3.1
               if: matrix.session == 'pre-commit'
               with:
                   path: ~/.cache/pre-commit

.readthedocs.yml

@@ -11,8 +11,8 @@ sphinx:
 #mkdocs:
 #  configuration: mkdocs.yml
 
-# Optionally build your docs in additional formats such as PDF and ePub
-formats: all
+# # Optionally build your docs in additional formats such as PDF and ePub
+# formats: all
 
 # Optionally set the version of Python and requirements required to build your docs
 python:

pyproject.toml

@@ -42,11 +42,11 @@ UpSetPlot = "^0.6.0"
 [tool.poetry.dev-dependencies]
 pytest = "^6.2.4"
 coverage = {extras = ["toml"], version = "^6.2"}
-safety = "^1.9.0"
+safety = "^2.3.5"
 mypy = "^0.910"
 typeguard = "^2.13.2"
 xdoctest = {extras = ["colors"], version = "^0.15.5"}
-sphinx = "^4.1.2"
+sphinx = "^5.3.0"
 sphinx-autobuild = "^2021.3.14"
 pre-commit = "^2.13.0"
 flake8 = "^3.9.2"

requirements.txt

@@ -37,7 +37,7 @@ importlib-resources==5.9.0
 ipykernel==5.4.3
 ipython-genutils==0.2.0
 ipython==7.18.1
-ipywidgets==7.7.1
+ipywidgets==8.1.0
 jedi==0.18.1
 jinja2==3.1.2
 joblib==1.1.0
@@ -48,7 +48,7 @@ jupyter-sphinx==0.3.2
 jupyterlab-pygments==0.2.2
 jupyterlab-widgets==1.1.1
 kiwisolver==1.4.4
-leidenalg==0.8.10
+leidenalg==0.10.1
 llvmlite==0.39.0
 lxml==4.9.1
 markupsafe==2.1.1
@@ -93,7 +93,7 @@ python-dateutil==2.8.2
 pytz==2022.1
 pyyaml==5.4.1
 pyzmq==23.2.0
-questionary==1.10.0
+questionary==2.0.0
 requests==2.28.1
 rich==12.5.1
 ruamel.yaml.clib==0.2.6