Add more pre-commit checks (#1848)

* exclude docs/data for large files Signed-off-by: zethson <lukas.heumos@posteo.net> * removed pbmc3k data & exclude path Signed-off-by: zethson <lukas.heumos@posteo.net> * add docs data to gitignore Signed-off-by: zethson <lukas.heumos@posteo.net> * add exclude of pre-commit formatting for test data Signed-off-by: zethson <lukas.heumos@posteo.net> * reverted formatting of test files Signed-off-by: zethson <lukas.heumos@posteo.net>
scverse · May 26, 2021 · 4dd8de9 · 4dd8de9
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diff --git a/.flake8 b/.flake8
@@ -34,4 +34,3 @@ exclude =
     build,
     docs/_build,
     dist,
-
diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -1,4 +1,4 @@
-<!-- 
+<!--
 Thanks for opening a PR to scanpy!
 Please be sure to follow the guidelines in our contribution guide (https://scanpy.readthedocs.io/en/latest/dev/index.html) to familiarize yourself with our workflow and speed up review.
 -->
diff --git a/.gitignore b/.gitignore
@@ -7,6 +7,7 @@
 /docs/_build/
 /docs/api/scanpy.*.rst
 /docs/external/scanpy.*.rst
+/docs/data/
 !/docs/api/scanpy.api.rst
 !/docs/api/scanpy.api.AnnData.rst
 !/docs/api/scanpy.plotting.rst

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -12,3 +12,16 @@ repos:
     hooks:
     -   id: autopep8
         args: ["-i"]
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.0.1
+    hooks:
+    -   id: trailing-whitespace
+        exclude: scanpy/tests/_data
+    -   id: end-of-file-fixer
+        exclude: scanpy/tests/_data
+    -   id: check-added-large-files
+    -   id: check-case-conflict
+    -   id: check-toml
+    -   id: check-yaml
+    -   id: check-merge-conflict
+    -   id: detect-private-key
diff --git a/docs/api/scanpy.plotting.rst b/docs/api/scanpy.plotting.rst
@@ -1,23 +1,4 @@
-scanpy.plotting
+scanpy.plotting
 ===============
 
 .. automodule:: scanpy.plotting
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
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-
-
-
diff --git a/docs/dev/ci.rst b/docs/dev/ci.rst
@@ -31,4 +31,4 @@ From here you can view and download the images which were compared, as well as a
 Misc
 ~~~~
 
-:func:`matplotlib.testing.setup` tries to establish a consistent environment for creating plots. Make sure it's active!
+:func:`matplotlib.testing.setup` tries to establish a consistent environment for creating plots. Make sure it's active!
diff --git a/docs/dev/documentation.rst b/docs/dev/documentation.rst
@@ -50,7 +50,7 @@ Plots in docstrings
 
 One of the most useful things you can include in a docstring is examples of how the function should be used.
 These are a great way to demonstrate intended usage and give users a template they can copy and modify.
-We're able to include the plots produced by these snippets in the rendered docs using `matplotlib's plot directive <https://matplotlib.org/devel/plot_directive.html>`__. 
+We're able to include the plots produced by these snippets in the rendered docs using `matplotlib's plot directive <https://matplotlib.org/devel/plot_directive.html>`__.
 For examples of this, see the `Examples` sections of :func:`~scanpy.pl.dotplot` or :func:`~scanpy.pp.calculate_qc_metrics`.
 
 Note that anything in these sections will need to be run when the docs are built, so please keep them computationally light.

diff --git a/docs/dev/getting-set-up.rst b/docs/dev/getting-set-up.rst
@@ -99,7 +99,7 @@ We'll try and get back to you soon!
 Development environments
 ------------------------
 
-It's recommended to do development work in an isolated environment. 
+It's recommended to do development work in an isolated environment.
 There are number of ways to do this, including conda environments, virtual environments, and virtual machines.
 
 We think the easiest is probably conda environments. Simply create a new environment with a supported version of python and make a :ref:`development install <dev-install-instructions>` of `scanpy`.
diff --git a/docs/ecosystem.rst b/docs/ecosystem.rst
@@ -68,16 +68,16 @@ scvi-tools
 
     | scvi-tools hosts deep generative models (DGM) for end-to-end analysis of single-cell
       omics data (e.g., scVI, scANVI, totalVI). It also contains several primitives to build novel DGMs.
-      
+
 
 Adaptive immune receptor repertoire (AIRR)
 ------------------------------------------
 
 * `scirpy <https://github.com/icbi-lab/scirpy>`__ :small:`Medical University of Innsbruck`
-    
-    | scirpy is a scanpy extension to expore single-cell T-cell receptor (TCR) and B-cell receptor (BCR) repertoires. 
-    
-    
+
+    | scirpy is a scanpy extension to expore single-cell T-cell receptor (TCR) and B-cell receptor (BCR) repertoires.
+
+
 Feature selection
 -----------------
 * `triku 🦔 <https://gitlab.com/alexmascension/triku>`__ :small:`Biodonostia Health Research Institute`

diff --git a/docs/release-notes/0.2.1.rst b/docs/release-notes/0.2.1.rst
@@ -6,4 +6,3 @@ trajectory inference, differential expression testing and simulation of gene
 regulatory networks. The implementation efficiently deals with `datasets of more
 than one million cells
 <https://github.com/theislab/scanpy_usage/tree/master/170522_visualizing_one_million_cells>`__. :smaller:`A Wolf, P Angerer`
-
diff --git a/docs/release-notes/0.4.0.rst b/docs/release-notes/0.4.0.rst
@@ -6,4 +6,3 @@
 
 .. _SPRING: https://github.com/AllonKleinLab/SPRING/
 .. _spring tutorial: https://github.com/theislab/scanpy_usage/tree/master/171111_SPRING_export
-
diff --git a/docs/release-notes/1.8.0.rst b/docs/release-notes/1.8.0.rst
@@ -33,7 +33,7 @@
 
 .. rubric:: Documentation
 
-- Clarified docs issues for :func:`~scanpy.pp.neighbors`, 
+- Clarified docs issues for :func:`~scanpy.pp.neighbors`,
   :func:`~scanpy.tl.diffmap`, :func:`~scanpy.pp.calculate_qc_metrics` :pr:`1680` :smaller:`G Palla`
 - Integrated DocSearch_, a find-as-you-type documentation index search. :pr:`1754` :smaller:`P Angerer`
 

diff --git a/docs/release-notes/index.rst b/docs/release-notes/index.rst
@@ -74,4 +74,4 @@ Version 0.2
 Version 0.1
 -----------
 
-.. include:: 0.1.0.rst
+.. include:: 0.1.0.rst
diff --git a/scanpy/datasets/krumsiek11.txt b/scanpy/datasets/krumsiek11.txt
@@ -1,11 +1,11 @@
-# model = /Users/alexwolf/hholtz/01_projects/1512_scanpy/scanpy/scanpy/sim_models/krumsiek11.txt 
+# model = /Users/alexwolf/hholtz/01_projects/1512_scanpy/scanpy/scanpy/sim_models/krumsiek11.txt
 # tmax = 160
 # branching = True
 # nrRealizations = 4
 # noiseObs = 0
 # noiseDyn = 0.001
 # seed = 0
-# it   Gata2   Gata1    Fog1    EKLF    Fli1     SCL   Cebpa    Pu.1    cJun  EgrNab    Gfi1 
+# it   Gata2   Gata1    Fog1    EKLF    Fli1     SCL   Cebpa    Pu.1    cJun  EgrNab    Gfi1
    0  0.8032 -0.0005 -0.0001  0.0003  0.0013  0.0011  0.7997  0.8017  0.0006  0.0009  0.0002
    1  0.7239  0.0016 -0.0003 -0.0010  0.0011  0.0022  0.8195  0.7256  0.0784  0.0077  0.0941
    2  0.6578  0.0013 -0.0010 -0.0027  0.0025  0.0011  0.8358  0.6624  0.1105  0.0239  0.1497

diff --git a/scanpy/sim_models/krumsiek11.txt b/scanpy/sim_models/krumsiek11.txt
@@ -1,14 +1,14 @@
-# See Table 1 in Krumsiek et al. (2011), p. 3 or                             
+# See Table 1 in Krumsiek et al. (2011), p. 3 or
 # Table 1, in Suppl. Mat. of Moignard et al. (2015), p. 28.
 #
-# For each "variable = ", there must be a right hand side: 
-# either an empty string or a python-style logical expression 
-# involving variable names, "or", "and", "(", ")". 
-# The order of equations matters! 
-# 
+# For each "variable = ", there must be a right hand side:
+# either an empty string or a python-style logical expression
+# involving variable names, "or", "and", "(", ")".
+# The order of equations matters!
+#
 # modelType = hill
 # invTimeStep = 0.02
-# 
+#
 # boolean update rules:
 Gata2 = Gata2 and not (Gata1 and Fog1) and not Pu.1
 Gata1 = (Gata1 or Gata2 or Fli1) and not Pu.1
@@ -22,33 +22,33 @@ cJun = Pu.1 and not Gfi1
 EgrNab = (Pu.1 and cJun) and not Gfi1
 Gfi1 = Cebpa and not EgrNab
 # coupling list:
-Gata2      Gata2                 1.0 
-Gata2      Gata1                -0.1 
-Gata2      Fog1                 -1.0 
-Gata2      Pu.1                -1.15 
-Gata1      Gata2                 1.0 
-Gata1      Gata1                 0.1 
-Gata1      Fli1                  1.0 
-Gata1      Pu.1                -1.21 
-Fog1       Gata1                 0.1 
-EKLF       Gata1                 0.2 
-EKLF       Fli1                 -1.0 
-Fli1       Gata1                 0.2 
-Fli1       EKLF                 -1.0 
-SCL        Gata1                 1.0 
-SCL        Pu.1                 -1.0 
-Cebpa      Gata1                -1.0 
-Cebpa      Fog1                 -1.0 
-Cebpa      SCL                  -1.0 
-Cebpa      Cebpa                10.0 
-Pu.1       Gata2                -1.0 
-Pu.1       Gata1                -1.0 
-Pu.1       Cebpa                10.0 
-Pu.1       Pu.1                 10.0 
-cJun       Pu.1                  1.0 
-cJun       Gfi1                 -1.0 
-EgrNab     Pu.1                  1.0 
-EgrNab     cJun                  1.0 
-EgrNab     Gfi1                 -1.3 
-Gfi1       Cebpa                 1.0 
-Gfi1       EgrNab               -5.0 
+Gata2      Gata2                 1.0
+Gata2      Gata1                -0.1
+Gata2      Fog1                 -1.0
+Gata2      Pu.1                -1.15
+Gata1      Gata2                 1.0
+Gata1      Gata1                 0.1
+Gata1      Fli1                  1.0
+Gata1      Pu.1                -1.21
+Fog1       Gata1                 0.1
+EKLF       Gata1                 0.2
+EKLF       Fli1                 -1.0
+Fli1       Gata1                 0.2
+Fli1       EKLF                 -1.0
+SCL        Gata1                 1.0
+SCL        Pu.1                 -1.0
+Cebpa      Gata1                -1.0
+Cebpa      Fog1                 -1.0
+Cebpa      SCL                  -1.0
+Cebpa      Cebpa                10.0
+Pu.1       Gata2                -1.0
+Pu.1       Gata1                -1.0
+Pu.1       Cebpa                10.0
+Pu.1       Pu.1                 10.0
+cJun       Pu.1                  1.0
+cJun       Gfi1                 -1.0
+EgrNab     Pu.1                  1.0
+EgrNab     cJun                  1.0
+EgrNab     Gfi1                 -1.3
+Gfi1       Cebpa                 1.0
+Gfi1       EgrNab               -5.0
diff --git a/scanpy/sim_models/toggleswitch.txt b/scanpy/sim_models/toggleswitch.txt
@@ -1,8 +1,8 @@
-# For each "variable = ", there must be a right hand side: 
-# either an empty string or a python-style logical expression 
-# involving variable names, "or", "and", "(", ")". 
-# The order of equations matters! 
-# 
+# For each "variable = ", there must be a right hand side:
+# either an empty string or a python-style logical expression
+# involving variable names, "or", "and", "(", ")".
+# The order of equations matters!
+#
 # modelType = hill
 # invTimeStep = 0.1
 #
@@ -12,5 +12,5 @@
 # coupling list:
 0          0             1.0
 0          1            -1.0
-1          1             1.0 
-1          0            -1.0 
+1          1             1.0
+1          0            -1.0
-Original file line number
+Diff line change
@@ Expand Up @@
     Misc
     ~~~~
-    :func:`matplotlib.testing.setup` tries to establish a consistent environment for creating plots. Make sure it's active!
+    :func:`matplotlib.testing.setup` tries to establish a consistent environment for creating plots. Make sure it's active!
Original file line number	Diff line number	Diff line change
Expand Up		@@ -6,4 +6,3 @@ trajectory inference, differential expression testing and simulation of gene
		regulatory networks. The implementation efficiently deals with `datasets of more
		than one million cells
		<https://github.com/theislab/scanpy_usage/tree/master/170522_visualizing_one_million_cells>`__. :smaller:`A Wolf, P Angerer`
Original file line number	Diff line number	Diff line change
Expand Up		@@ -6,4 +6,3 @@

		.. _SPRING: https://github.com/AllonKleinLab/SPRING/
		.. _spring tutorial: https://github.com/theislab/scanpy_usage/tree/master/171111_SPRING_export