theislab
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diff --git a/‎docs/requirements.txt‎
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diff --git a/‎docs/source/getting_started.rst‎
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@@ -0,0 +1,15 @@
+# EditorConfig is awesome: https://EditorConfig.org
+
+# top-most EditorConfig file
+root = true
+
+[*]
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = true
+max_line_length = 88
+
+[*.py]
+indent_size = 4
+indent_style = space
@@ -0,0 +1,19 @@
+## Changes
+<!-- Please remove section if this PR does change an existing feature -->
+
+* ...
+
+## Bug fixes
+<!-- Please give section if this PR does not fix any bugs -->
+
+* ...
+
+## New
+<!-- Please give section if this PR does not implement a new feature -->
+
+* ...
+
+## Related issues
+<!-- Please list related issues. If none exist, open one and reference it here. -->
+
+Closes #
@@ -26,10 +26,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - name: Setup Python 3.7
+      - name: Setup Python 3.8
         uses: actions/setup-python@v2
         with:
-          python-version: 3.7
+          python-version: 3.8
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
@@ -42,19 +42,37 @@ jobs:
   # Run unit tests
   test:
     needs: linting
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
-        python-version: [3.7]
+        os: [ubuntu-latest]
+        python-version: [3.7, 3.8, 3.9]
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: pip install -e '.[dev]'
+      - name: Unit tests
+        timeout-minutes: 60
+        run: python -m pytest --durations=25 --ignore=tests/datasets/test_datasets.py --hypothesis-profile=ci --cov=scvelo -vv
+
+  test-dataset-downloads:
+    needs: test
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Setup Python 3.8
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
       - name: Install dependencies
         run: |
           pip install -e .
           pip install hypothesis pytest pytest-cov
-      - name: Unit tests
-        run: python -m pytest --cov=scvelo
+      - name: Test dataset downloads
+        timeout-minutes: 60
+        run: python -m pytest tests/datasets/test_datasets.py -vv
@@ -42,3 +42,5 @@ docs/source/scvelo*
 
 # Files generated by unit tests
 .hypothesis/
+.coverage*
+htmlcov/
@@ -1,14 +1,14 @@
 repos:
--   repo: https://github.com/ambv/black
-    rev: 20.8b1
+-   repo: https://github.com/psf/black
+    rev: 22.3.0
     hooks:
     - id: black
--   repo: https://gitlab.com/pycqa/flake8
+-   repo: https://github.com/PyCQA/flake8
     rev: 3.8.4
     hooks:
     -   id: flake8
 -   repo: https://github.com/pycqa/isort
-    rev: 5.7.0
+    rev: 5.10.1
     hooks:
     -   id: isort
         name: isort (python)
 
@@ -21,7 +21,15 @@ You can now clone your fork of scVelo and install the development mode
 
     git clone https://github.com/YOUR-USER-NAME/scvelo.git
     cd scvelo
-    git checkout --track origin/develop
+
+
+Unix Systems
+^^^^^^^^^^^^
+
+The installation can be completed with
+
+.. code:: bash
+
     pip install -e '.[dev]'
 
 The last line can, alternatively, be replaced by
@@ -31,16 +39,26 @@ The last line can, alternatively, be replaced by
     pip install -r requirements-dev.txt
 
 
-Finally, to make sure your code follows our code style guideline, install pre-commit:
+Windows
+^^^^^^^
+
+If running Windows, `hsnwlib` needs to be installed via `conda` and the installation with pip slightly adjusted:
 
 .. code:: bash
 
-    pre-commit install
+    conda install -c conda-forge hnswlib
+    pip install -e .[dev]
 
 
 Coding style
 ^^^^^^^^^^^^
 
+Finally, to make sure your code follows our code style guideline, install pre-commit:
+
+.. code:: bash
+
+    pre-commit install
+
 Our code follows `black` and `flake8` coding style. Code formatting (`black`, `isort`) is automated through pre-commit hooks. In addition, we require that
 
 - functions are fully type-annotated.
@@ -69,9 +87,9 @@ The docstrings of scVelo largely follow the `numpy`-style. New docstrings should
 Submitting pull requests
 ^^^^^^^^^^^^^^^^^^^^^^^^
 
-New features and bug fixes are added to the code base through a pull request (PR). To implement a feature or bug fix, create a branch from `develop`. For hotfixes use `master` as base. The existence of bugs suggests insufficient test coverage. As such, bug fixes should, ideally, include a unit test or extend an existing one. Please ensure that
+New features and bug fixes are added to the code base through a pull request (PR). To implement a feature or bug fix, create a branch from `master`. The existence of bugs suggests insufficient test coverage. As such, bug fixes should, ideally, include a unit test or extend an existing one. Please ensure that
 
-- branch names have the prefix `feat/`, `bug/` or `hotfix/`.
+- branch names have the prefix `feat/` or `fix/`.
 - your code follows the project conventions.
 - newly added functions are unit tested.
 - all tests pass locally.
 
@@ -6,8 +6,9 @@ typing_extensions
 importlib_metadata
 sphinx_rtd_theme>=0.3
 sphinx_autodoc_typehints<=1.6
+Jinja2<3.1
 
 # converting notebooks to html
 ipykernel
 sphinx>=1.7,<4.0
-nbsphinx>=0.7,<0.8.7
+nbsphinx>=0.7,<0.8.7
@@ -0,0 +1,7 @@
+.. sidebar:: Key Contributors
+
+    * `Philipp Weiler`_: lead developer since 2021, maintainer
+    * `Volker Bergen`_: lead developer 2018-2021, initial conception
+
+.. _Philipp Weiler: https://twitter.com/PhilippWeiler7
+.. _Volker Bergen: https://twitter.com/volkerbergen
@@ -148,7 +148,7 @@
 
 
 def setup(app):
-    app.add_stylesheet("custom.css")
+    app.add_css_file("custom.css")
 
 
 # -- Options for other output ------------------------------------------
 
@@ -6,7 +6,7 @@ Once you are set, the following tutorials go straight into analysis of RNA veloc
 latent time, driver identification and many more.
 
 First of all, the input data for scVelo are two count matrices of pre-mature (unspliced) and mature (spliced) abundances,
-which can be obtained from standard sequencing protocols, using the `velocyto`_ or `loompy/kallisto`_
+which can be obtained from standard sequencing protocols, using the `velocyto`_ or `kallisto`_
 counting pipeline.
 
 scVelo workflow at a glance
@@ -89,4 +89,4 @@ For every tool module there is a plotting counterpart, which allows you to exami
 
 
 .. _`velocyto`: http://velocyto.org/velocyto.py/tutorial/cli.html
-.. _`loompy/kallisto`: https://linnarssonlab.org/loompy/kallisto/index.html
+.. _`kallisto`: https://www.kallistobus.tools/tutorials/kb_velocity/python/kb_velocity/#generate-rna-velocity-count-matrices