Revert "Preparing release 3.10"

.bandit.yml

@@ -4,4 +4,4 @@
 tests: []
 
 # (optional) list skipped tests here:
-skips: ['B101', 'B403', 'B404', 'B603', 'B607', 'B301', 'B303', 'B311', 'B310', 'B506', 'B321', 'B402', 'B105', 'B602']
+skips: ['B101', 'B403', 'B404', 'B603', 'B607', 'B301', 'B303', 'B311', 'B310', 'B506', 'B321', 'B402']

.github/workflows/build_package.yml

@@ -22,8 +22,8 @@ jobs:
         with:
           python-version: ${{ matrix.python }}
 
-      - name: Upgrade and install pip and wheel
-        run: python -m pip install --upgrade pip wheel
+      - name: Upgrade and install pip
+        run: python -m pip install --upgrade pip
 
       - name: Build sfaira
         run: pip install .

.github/workflows/create_templates.yml

@@ -21,15 +21,13 @@ jobs:
         with:
           python-version: 3.8
 
-      - name: Upgrade and install pip and wheel
-        run: python -m pip install --upgrade pip wheel
+      - name: Upgrade and install pip
+        run: python -m pip install --upgrade pip
 
       - name: Build sfaira
         run: pip install .
 
       - name: Create single_dataset template
         run: |
-          mkdir -p ./d10_1000_j_journal_2022_01_001
-          echo -e "\nEinstein, Albert\n\n10.1000/j.journal.2022.01.001\n1\nX_umap\nURL\nURL2\nHomo sapiens\nY2022\nX\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nindex\n\n" | sfaira create-dataloader
-          sfaira validate-dataloader --doi 10.1000/j.journal.2022.01.001
-          rm -rf ./d10_1000_j_journal_2022_01_001
+          echo -e "\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n" | sfaira create-dataloader
+          rm -rf d10_1000_j_journal_2021_01_001/

.github/workflows/publish_docs.yml

@@ -23,8 +23,8 @@ jobs:
         with:
           python-version: 3.8
 
-      - name: Upgrade and install pip and wheel
-        run: python -m pip install --upgrade pip wheel
+      - name: Install pip
+        run: python -m pip install --upgrade pip
 
       - name: Install doc dependencies
         run: pip install -r docs/requirements.txt

README.rst

@@ -25,19 +25,22 @@
 sfaira - data and model repository for single-cell data
 =======================================================
 
-.. image:: https://github.com/theislab/sfaira/blob/release/resources/images/figure_rtd_intro.png
+.. image:: https://github.com/theislab/sfaira/blob/main/resources/images/concept.png
    :width: 400px
    :align: center
 
 sfaira_ is a model and a data repository in a single python package (`full paper`_).
 We provide an interactive overview of the current state of the zoos on sfaira-portal_.
 
 Its data zoo gives users access to streamlined data loaders that allow reproducible use of published and private data sets for model training and exploration.
-Its model zoo gives user streamlined access to pre-trained models and to common model architectures to ease usage of neural networks in common single-cell analysis workflows.
+Its model zoo gives user streamlined access to pre-trained models and to common model architectures to ease usage of neural networks in common single-cell analysis workflows:
+A model zoo is a software infrastructure that improves user access to pre-trained models which are separately published, such as DCA_ or scArches_:
 Instead of focussing on developing new models, we focus on making models easily accessible to users and distributable by developers.
 sfaira integrates into scanpy_ workflows.
 
 .. _scanpy: https://github.com/theislab/scanpy
 .. _sfaira: https://sfaira.readthedocs.io
 .. _full paper: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02452-6
+.. _DCA: https://github.com/theislab/dca
+.. _scArches: https://github.com/theislab/scarches
 .. _sfaira-portal: https://theislab.github.io/sfaira-portal/