theislab · WeilerP · Oct 14, 2022 · Jul 13, 2021 · Jul 13, 2021 · Jul 14, 2021
diff --git a/.editorconfig b/.editorconfig
@@ -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
diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -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 #
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -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
diff --git a/.gitignore b/.gitignore
@@ -42,3 +42,5 @@ docs/source/scvelo*
 
 # Files generated by unit tests
 .hypothesis/
+.coverage*
+htmlcov/
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -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)

diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
@@ -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.

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -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
diff --git a/docs/source/_key_contributors.rst b/docs/source/_key_contributors.rst
@@ -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
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -148,7 +148,7 @@
 
 
 def setup(app):
-    app.add_stylesheet("custom.css")
+    app.add_css_file("custom.css")
 
 
 # -- Options for other output ------------------------------------------

diff --git a/docs/source/getting_started.rst b/docs/source/getting_started.rst
@@ -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
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -7,6 +7,8 @@ scVelo - RNA velocity generalized through dynamical modeling
    :width: 300px
    :align: left
 
+.. include:: _key_contributors.rst
+
 **scVelo** is a scalable toolkit for RNA velocity analysis in single cells, based on
 `Bergen et al. (Nature Biotech, 2020) <https://doi.org/10.1038/s41587-020-0591-3>`_.
 
@@ -16,7 +18,7 @@ scVelo generalizes the concept of RNA velocity
 by relaxing previously made assumptions with a stochastic and a dynamical model that solves the full
 transcriptional dynamics. It thereby adapts RNA velocity to widely varying specifications such as non-stationary populations.
 
-scVelo is compatible with scanpy_ and hosts efficient implementations of all RNA velocity models.
+scVelo is compatible with Scanpy_ and hosts efficient implementations of all RNA velocity models.
 
 scVelo's key applications
 ^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -104,7 +106,7 @@ For further information visit `scvelo.org <https://scvelo.org>`_.
 .. |travis| image:: https://travis-ci.org/theislab/scvelo.svg?branch=master
    :target: https://travis-ci.org/theislab/scvelo
 
-.. _scanpy: https://scanpy.readthedocs.io
+.. _Scanpy: https://scanpy.readthedocs.io
 
 .. _calendly: https://calendly.com/scvelo
 
@@ -123,4 +125,4 @@ For further information visit `scvelo.org <https://scvelo.org>`_.
 .. |dim| raw:: html
 
    <span class="__dimensions_badge_embed__" data-id="pub.1129830274" data-style="small_rectangle"></span>
-   <script async src="https://badge.dimensions.ai/badge.js" charset="utf-8"></script>
+   <script async src="https://badge.dimensions.ai/badge.js" charset="utf-8"></script>
diff --git a/docs/source/release_notes.rst b/docs/source/release_notes.rst
@@ -4,13 +4,33 @@
 Release Notes
 =============
 
+Version 0.2.5 :small:`Oct 14, 2022`
+-----------------------------------
+
+Changes:
+
+- Catch non-positive parameter values and raise a `ValueError` if necessary (`PR 614 <https://github.com/theislab/scvelo/pull/614>`_).
+- `get_mean_var` uses the same size parameter for mean and variance (`PR 698 <https://github.com/theislab/scvelo/pull/698>`_).
+
+Bugfixes:
+
+- `filter_genes` now works with `adata.layers['unspliced']` being sparse and `adata.layers['spliced']` dense (`PR 537 <https://github.com/theislab/scvelo/pull/537>`_).
+- `show_proportions` actually considers the layer `"ambiguous"` if present (`PR 587 <https://github.com/theislab/scvelo/pull/587>`_).
+- Fix calculation of Pearson's correlation in `csr_vcorrcoef` (`PR 679 <https://github.com/theislab/scvelo/pull/679>`_).
+- Fix `get_mean_var` to work with sparse input and `ignore_zeros=True` (`PR 698 <https://github.com/theislab/scvelo/pull/698>`_).
+- Fix bug in neighbor calculation (`PR 797 <https://github.com/theislab/scvelo/pull/797>`_).
+- Fix `optimization.py::get_weight` to work with numeric, non-integer values (`PR 839 <https://github.com/theislab/scvelo/pull/839>`_).
+- Fix inference with `fit_scaling=False` (`PR 848 <https://github.com/theislab/scvelo/pull/848>`_).
+- Fix saving of velocity embedding stream (`PR 900 <https://github.com/theislab/scvelo/pull/900>`_).
+- Fix Pandas' display precison when passed to `get_df` (`PR 907 <https://github.com/theislab/scvelo/pull/907>`_).
+
 Version 0.2.4 :small:`Aug 26, 2021`
 -----------------------------------
 
 Perspectives:
 
-- Landing page and two notebooks accompanying the perspectives manuscript at MSB. 
-- New datasets: Gastrulation, bone marrow, and PBMCs. 
+- Landing page and two notebooks accompanying the perspectives manuscript at MSB.
+- New datasets: Gastrulation, bone marrow, and PBMCs.
 
 New capabilities:
 
@@ -25,7 +45,7 @@ New capabilities:
 Bugfixes:
 
 - Pinned `sphinx<4.0` and `nbsphinx<0.8.7`.
-- Fix IPython import at CLI. 
+- Fix IPython import at CLI.
 
 
 Version 0.2.3 :small:`Feb 13, 2021`

diff --git a/pytest.ini b/pytest.ini
@@ -1,6 +1,4 @@
 [pytest]
 python_files = test_*.py
-testpaths =
-    tests
-    scvelo
+testpaths = tests/
 xfail_strict = true
diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -2,13 +2,15 @@
 
 -e .
 
-black==20.8b1
+black==22.3.0
 hnswlib
 hypothesis
 flake8==3.8.4
-isort==5.7.0
+isort==5.10.1
 louvain
+magic-impute
 pre-commit>=2.9.0
 pybind11
 pytest>=6.2.2
+pytest-cov
 python-igraph
diff --git a/requirements.txt b/requirements.txt
@@ -14,6 +14,6 @@ umap-learn>=0.3.10    # removed numba warnings (v0.3.10)
 numba>=0.41.0
 numpy>=1.17           # extension/speedup in .nan_to_num, .exp (v1.17)
 scipy>=1.4.1          # introduced PCA sparsity support (v1.4)
-pandas>=0.23          # merging/sorting extensions (v0.23)
+pandas>=0.23, !=1.4.0 # merging/sorting extensions (v0.23)
 scikit-learn>=0.21.2  # bugfix in .utils.sparsefuncs (v0.21.2)
-matplotlib>=3.3.0     # normalize in pie (v3.3.0)
+matplotlib>=3.3.0     # normalize in pie (v3.3.0)
diff --git a/scvelo/__init__.py b/scvelo/__init__.py
@@ -2,7 +2,12 @@
 from anndata import AnnData
 from scanpy import read, read_loom
 
-from scvelo import datasets, logging, pl, pp, settings, tl, utils
+from scvelo import datasets, logging
+from scvelo import plotting as pl
+from scvelo import preprocessing as pp
+from scvelo import settings
+from scvelo import tools as tl
+from scvelo import utils
 from scvelo.core import get_df
 from scvelo.plotting.gridspec import GridSpec
 from scvelo.preprocessing.neighbors import Neighbors
@@ -13,6 +18,10 @@
 from scvelo.tools.velocity import Velocity
 from scvelo.tools.velocity_graph import VelocityGraph
 
+import sys  # isort:skip
+
+sys.modules.update({f"{__name__}.{m}": globals()[m] for m in ["tl", "pp", "pl"]})
+
 try:
     from setuptools_scm import get_version
 

diff --git a/scvelo/core/__init__.py b/scvelo/core/__init__.py
@@ -12,16 +12,18 @@
     set_modality,
     show_proportions,
 )
-from ._arithmetic import clipped_log, invert, prod_sum, sum
+from ._arithmetic import clipped_log, invert, multiply, prod_sum, sum
 from ._linear_models import LinearRegression
 from ._metrics import l2_norm
 from ._models import SplicingDynamics
 from ._parallelize import get_n_jobs, parallelize
+from ._utils import deprecated_arg_names
 
 __all__ = [
     "clean_obs_names",
     "cleanup",
     "clipped_log",
+    "deprecated_arg_names",
     "get_df",
     "get_initial_size",
     "get_modality",
@@ -33,6 +35,7 @@
     "make_dense",
     "make_sparse",
     "merge",
+    "multiply",
     "parallelize",
     "prod_sum",
     "set_initial_size",